#bugsigdb

2023-02-21

C. Mirzayi (please do not tag this account) (13:53:24): > @C. Mirzayi (please do not tag this account) has joined the channel

Andres Wokaty (13:53:59): > @Andres Wokaty has joined the channel

Madelyn Carlson (13:53:59): > @Madelyn Carlson has joined the channel

Levi Waldron (13:53:59): > @Levi Waldron has joined the channel

C. Mirzayi (please do not tag this account) (13:54:15): > For our Outreachy submission we needed a channel so here it is!

Madelyn Carlson (13:54:22): > :tada::tada::tada:

Madelyn Carlson (13:54:25): > Thank you!

C. Mirzayi (please do not tag this account) (13:55:24): > I don’t think Fatima has an account on community-bioc so I am adding that as a to-do for her.

Andres Wokaty (13:55:47): > This is great!:slightly_smiling_face:

Andres Wokaty (13:56:48): > Did you submit the project?

C. Mirzayi (please do not tag this account) (13:56:56): > Also thinking about issue tracking and I’m not sure thathttps://github.com/waldronlab/BugSigDB/issuesis the right place as I think about it since that’s about the development of BugSigDB itself. Perhaps we setup BugSigDBcuration or something.

C. Mirzayi (please do not tag this account) (13:56:57): > No

C. Mirzayi (please do not tag this account) (13:57:13): > I’m still reviewing the document.

Madelyn Carlson (13:57:41): > That would be awesome re: BugSigDBcuration

C. Mirzayi (please do not tag this account) (13:58:06): > Have we heard from Fatima recently? Is she still out?

Madelyn Carlson (13:58:38): > I just chatted with her - she’s creating a document with the onboarding readings to link on the application draft

C. Mirzayi (please do not tag this account) (13:58:46): > Ok great.

C. Mirzayi (please do not tag this account) (14:00:48): > https://github.com/waldronlab/BugSigDBcuration/issuesIt exists!

Madelyn Carlson (14:01:07): > thank you very much!!!

C. Mirzayi (please do not tag this account) (14:01:22): > Ok let me continue reading the draft.

Madelyn Carlson (14:01:26): > sounds great

Madelyn Carlson (15:23:30): > thanks so much for reviewing and editing@C. Mirzayi (please do not tag this account). I just went through and resolved edits and responded to comments. I think we’re in a good place to submit the application. After that, our outstanding tasks include: > * @Fatima add link to the onboarding readings google doc on issues draft > * We may not have the Qualtrics survey links ready by the time we post the issues blurb, but I think it’s okay to pause on getting the issues draft published until application is submitted

Fatima Zohra (15:30:28): > @Fatima Zohra has joined the channel

Andres Wokaty (16:01:04): > There’s still time a little time to set up for the contribution period, which begins I believe March 9th.

Fatima Zohra (16:40:03): > @Madelyn Carlson@C. Mirzayi (please do not tag this account)I’m starting the application on outreachy now. Please flag me if you make any new changes on the draft

Madelyn Carlson (16:40:28): > Sounds great, thank you for the heads up !

2023-02-22

Andres Wokaty (11:14:23): > This is just a reminder since I know the outreachy website is sometimes hard to navigate. You can submit the application onhttps://www.outreachy.org/communities/cfp/bioconductor/via ‘Submit a Project Proposal’. After submission, there’s an option for you to invite co-mentors, but co-mentors can also sign up on the same page via ‘select a project to co-mentor’ but only after the proposal has been submitted. - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Madelyn Carlson (11:15:51): > Thank you, Jen!@Fatima Zohralet me know if it would be helpful to have another set of eyes to navigate Outreachy. I have a meeting until 12 and then free between 12-12:30PM my time

Madelyn Carlson (15:31:44): > I know today is when we aimed to submit the application so just checking in to see if there is anything I can help with? Apologies if it’s already submitted & I’m being redundant !

Andres Wokaty (15:38:13): > Let’s aim to have it submitted by tomorrow. Even if you think there are some issues with the application, it can be edited after submission. I just want to make sure that we get this in because I believe we’ll have funding for at least one intern for the project.

Madelyn Carlson (15:39:17): > perfect - sounds great to me. Give me a shout either tonight or tomorrow for anything I can handle/support@Fatima Zohra@C. Mirzayi (please do not tag this account)

2023-02-23

Andres Wokaty (10:30:49): > I’m reviewing the project now. I just want to ask how long has bugsigdb been accepting contributions? and how many regular contributors are there?

Madelyn Carlson (10:33:18): > @C. Mirzayi (please do not tag this account)and@Fatima Zohrawould know better than me but I believe approximately 1 year? (which I’m judging based on the publish date of the articleBugSigDB: accelerating microbiome research through systematic comparison to published microbial signatures) Plz correct me if I’m wrong !

C. Mirzayi (please do not tag this account) (10:34:26): > The project started in 2017.

Madelyn Carlson (10:35:16): > whew thank you, Chloe. Sounds like we can adjust the response to the first application prompt to

Madelyn Carlson (10:35:34): > “The BugSigDB project has accepted publicly submitted contributions since 2017”

Andres Wokaty (10:36:00): > The application has been submitted, but~~~I am not sure if it is complete. ~~~I don’t see any listing of skills or mentorship style.

Andres Wokaty (10:41:48): > @Fatima ZohraI’m going to accept the project; however, it should be updated to list the project skills, your mentorship style, how long bugsigdb has been accepting contributions, and what your contributions have been to bugsigdb. Some of this information is really important to help applicants understand what is needed to be successful and what it will be like to have you as a mentor. You should also provide your username for slack so applicants can reach out to you.

Fatima Zohra (12:23:58) (in thread): > Hi Jen, thank you! Yes I was going to complete the rest of the information today. I’ll ping you as soon as i have everything in.

Fatima Zohra (12:29:28) (in thread): > okay so I’m updating the info on this question “How long has your team been accepting publicly submitted contributions?” to “more than 2 years”.@Andres Wokaty

Fatima Zohra (12:43:42): > @Andres Wokatyfor some reason the form isn’t accepting the 3rd skill. I’ve tried changing the experience levels from “no knowledge required” to “optional” - File (PNG): image.png

Fatima Zohra (13:07:31): > @C. Mirzayi (please do not tag this account)I’ve invited you to sign-up as a mentor. You should be receiving an email from outreachy.

Fatima Zohra (13:11:00) (in thread): > Updated the project skills, communication and mentor details. Please let me know if I missed anything.

C. Mirzayi (please do not tag this account) (13:45:12): > Done.

Andres Wokaty (14:18:00) (in thread): > I think the reason why you can’t submit that is because the skill name is actually a list and you have to select from what’s on the list. There’s nothing like ‘study design’; however, there is ‘research’. I would try to find something similar (although I think such an option doesn’t exist) or I would specify this in the project description, that it’s nice to have knowledge of study design.

Andres Wokaty (14:32:57): > I’ve approved Chloe and the application looks good. Next you can prepare for the contribution period. Let me know if you have questions about that.

2023-02-28

Madelyn Carlson (16:33:50): > hi hi all - I hope that you’re doing well on this snowy, rainy week. I’ve got contribution period on the mind. The tasks in ourOutreachy-BugSigDB app draft docstill accurately capture the next steps needed for the contribution period. Copying that list plus one another task below. Would it be helpful for me to set up time for us to brainstorm and distribute tasks? Let me know. I believe our deadline for setting up everything needed for the contribution period is March 6 (flagging@Andres Wokatyfor confirmation)Contribution Period Tasks > * Post the Draft BugSigDB GitHub Issues that’s on page 6in this doc > * Create 1-2 heavily annotated straightforward articles on microbiome > * Draft mini-curation survey questions > * Develop 5-7 (decide on the #) scavenger hunt prompt for applicants to do on BugSigDB that will be added to Qualtrics

2023-03-02

C. Mirzayi (please do not tag this account) (11:57:42): > I’m not getting notifications on this channel unless you specifically tag me so just FYI on that. I’ve made some changes to the survey and put a preview version here:https://cunysph.az1.qualtrics.com/jfe/preview/previewId/875d1584-c609-4a15-93f8-3f30da482[…]_0cYerh299Ftl49M?Q_CHL=preview&Q_SurveyVersionID=current - Attachment (cunysph.az1.qualtrics.com): Preview - BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

C. Mirzayi (please do not tag this account) (11:58:52): > I have maybe 1-2 hours of time to work on this today. What is the best use of that time? I can create the draft issues but without the article that is being used for the survey I can’t really work on the quiz. I also don’t know the status of the scavenger hunt.@Fatima Zohracan you provide info please?

Madelyn Carlson (12:17:44): > @C. Mirzayi (please do not tag this account)sounds good - will tag. Re: the scavenger hunt, it sounded from the meeting today that Levi might be leaning towards just offering 2 contribution tasks - mini-curation and full curation. Not sure if you heard something different in your check-in with Levi@Fatima Zohra& in terms of key tasks for today, I’d think that the priorities are: > * Deciding whether we’re cutting out the scavenger hunt portion and update the draft issues post accordingly (see link in my previous post) > * Publish the issues post > * Finalize the mini-curation quiz > * Do we want to give Outreachy applicants just 1 article to work from on the mini curation? If we wanted to offer a selection of articles for them to choose from (e.g., 3 articles), we could add a question on the Qualtrics survey to ask which article they used. This would mess up some of the multiple choice questions though.. Could be more simple to keep it to 1 article

Madelyn Carlson (12:18:05): > (FYI this was a dump of priority tasks but they don’t all have to happen today)

Madelyn Carlson (12:25:27): > Love the quiz btw@C. Mirzayi (please do not tag this account)and@Fatima Zohra. A few comments that you can feel free to take or leave: > * On the title page, we could consider adding estimated time to complete (see changes in bold font) “Welcome to BugSigDB! Instructions: Please read carefully. You can return to this quiz at any time from the same browser and your responses will be saved.We estimate this quiz to take 2-3 hours to complete.” > * Re: one of Chloe’s comments, “Ask them to look up EFO for condition and paste the ID” - I really like this idea. > * Do we feel like there needs to be a few more questions? I can’t tell where my gut is landing on that

Fatima Zohra (13:46:42) (in thread): > do you need the annotated version of the article? I’m working that now, but I have the article (https://pubmed.ncbi.nlm.nih.gov/29580894/). > > For the scavenger hunt, not sure if you heard anything different but Levi suggested we put it together in one survey (that would be in the wiki block). and here we basically add questions related to looking up efo ontology terms, finding correct taxonomy IDs from NCBI etc. - Attachment (PubMed): Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder - PubMed > This present findings support the involvement of microbiota alteration in psychiatric diseases and Faecalibacterium may represent a potential novel marker of gut microbiota in ADHD. Future studies are needed to validate these findings and to elucidate the temporal and causal relationships between th …

C. Mirzayi (please do not tag this account) (16:09:06) (in thread): > Ok so this is the source of the quiz? Then I think we need an annotated version of it today if possible.

C. Mirzayi (please do not tag this account) (16:09:36): > Apologies for being incommunicado. Things were busy on my other project. > > I am writing up the issues post now. Fatima has linked an article above and I assume that’s the quiz article so I will try my best to finalize the quiz based on that.

C. Mirzayi (please do not tag this account) (16:15:28) (in thread): > Also this article has a few problems namely: > 1. It is not open access. It is behind a paywall. Making it “freely” accessible to applicants could technically be a copyright issue. > 2. I was able to find a copy of it regardless but I can’t find the supplementary materials anywhere and I think it’s important to get folks used to the idea of there being supplements.

C. Mirzayi (please do not tag this account) (16:16:50) (in thread): > 3. This study has been curated in BugSigDB. A smart applicant could just pull all the info for the quiz from there right? Should we go with something novel so that they can’t just do that.

C. Mirzayi (please do not tag this account) (16:39:41): > Ok given my reservations with the current article, I am going to recommend we use this article instead. It’s open access, not curated in BugSigDB, and has easily accessible supplements which are all important qualities for the task. I am annotating it now. - File (PDF): s41598-023-27436-3.pdf

C. Mirzayi (please do not tag this account) (17:30:47): > Annotated. Updating the survey after dinner to match then generating the github issue post. - File (PDF): s41598-023-27436-3 annotated.pdf

Madelyn Carlson (20:37:17): > Amazing, thank you so much@C. Mirzayi (please do not tag this account)& apologies for the delay in responding - I had a doctors appointment late this afternoon. No rush updating the survey tonight - we can get it done tomorrow. I know I have less experience/skills to offer to this portion of the application/contribution period but I’m happy to add a third pair of hands to any of the changes needed tomorrow.@Fatima Zohraand I are also checking in at 12pm tomorrow. I think she’s going to be working on the quiz in the AM her time. Give me a shout, Chloe, if you want to be added onto that calendar invite. I hope ya’ll have a nice night

C. Mirzayi (please do not tag this account) (22:18:25): > yes please include me.

C. Mirzayi (please do not tag this account) (22:21:18): > Survey has been updated:https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

C. Mirzayi (please do not tag this account) (22:47:59): > Issue postedhttps://github.com/waldronlab/BugSigDBcuration/issues/1 - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Applicants have the option of selecting 1-2 smaller contributions and one optional higher-difficulty-level task.
> Step 1: Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Step 2: Depending on applicants’ capacity, you have the option to complete an additional small contribution task: BugSigDB scavenger hunt. This task provides an opportunity to familiarize yourself with https://bugsigdb.org/Main_Page by performing a series of services such as locating the page listing incomplete signatures, special projects, and leveraging the search function e.g., searching by heart disease and describing the first result. The scavenger hunt is included on the third page of the Qualtrics link shared above. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the Outreachy-BugSigDB GitHub project board and work on a full curation. To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccountand follow the website prompts to complete the curation.

2023-03-03

Fatima Zohra (05:21:48) (in thread): > This is great Chloe! Thank you thank you

Andres Wokaty (09:00:04): > This looks really good and exciting. On the front of the survey, I just wanted to suggest that rather than you telling them to open an issue if they stuck or need help, you might want to consider telling them to ask questions here. Maybe this way they can discuss with each other. I also wanted to suggest that if you have other curators, maybe ask if they’ll join the channel just to answer a question or two or just welcome the applicants during the contribution period just as support. It was really amazing to have@Madelyn Carlsonand others welcoming applicants the last round.

Madelyn Carlson (09:10:12) (in thread): > Amazing!!!!

Madelyn Carlson (09:13:39) (in thread): > @C. Mirzayi (please do not tag this account)Issues post looks amazing. One comment: do we want to delete the section describing the scavenger hunt contribution? Is that one of the final contribution tasks or - based on WL meeting yesterday, are we removing that one and just giving them the mini and full curation tasks for contribution? We could also chat about this in real time during our meeting this afternoon.

Madelyn Carlson (09:15:40): > oops, realizing I sent a double-calendar invite for the check-in at 12. Removing mine. Here is Fatima’s meet link for that time in case it’s useful: (flagging@C. Mirzayi (please do not tag this account))https://us04web.zoom.us/j/72243905046?pwd=c7vdaobTVD4GaScvPndRUpoKui0b0r.1

C. Mirzayi (please do not tag this account) (10:31:45) (in thread): > Ok I can make that change

Andres Wokaty (14:33:26): > @Fatima Zohra@C. Mirzayi (please do not tag this account)One more suggestion: I would recommend that you put the link for applicants to record their contribution tasks in your issue. It should be displayed on the project (to the person who submitted it on Outreachy at least). Applicants must record their contribution to submit their final application to you.

2023-03-06

C. Mirzayi (please do not tag this account) (10:55:00): > Welcome, Outreachy applicants!:tada:My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo:https://github.com/waldronlab/BugSigDBcuration/issues/1Also,between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > * Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > * Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > * Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > * Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > * We are happy to meet with you on a different day or time upon request - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Busayo Ojo (11:31:24): > @Busayo Ojo has joined the channel

Busayo Ojo (11:36:05): > Hi everyone, I’m Busayo Ojo, an outreachy applicant, and I’m very excited to be here to learn and work on this project.

Caroline Shi (11:49:42): > @Caroline Shi has joined the channel

Caroline Shi (11:50:26): > Hi everyone! I’m Caroline, also an Outreachy applicant, and I’m also excited to learn more about BugSigDB

C. Mirzayi (please do not tag this account) (12:04:07): > Welcome Busayo and Caroline!

Riya Sharma (12:17:56): > @Riya Sharma has joined the channel

Riya Sharma (12:21:44): > Hi everyone ! I am Riya , I am also an outreachy applicant ,I am very excited to work on this project and looking forward to learn and explore more about BugSigDB.

irem Kahveci (13:05:18): > @irem Kahveci has joined the channel

irem Kahveci (13:08:25): > Hi everyone! I am İrem Kahveci, I am also an outreachy applicant ,I am very excited to work on this project with you.:blush:

Barakat Dindi (18:05:55): > @Barakat Dindi has joined the channel

Barakat Dindi (18:11:46): > Barakat Dindi here, Hello everyone! I’m a fellow outreachy applicant and glad to be in your midst. I look forward to learn and contribute.:hugging_face:

2023-03-07

Eunice Miriti (02:25:14): > @Eunice Miriti has joined the channel

Eunice Miriti (02:30:04): > Hello team! This is Eunice Miriti here. Pronouns she/her. I am more than pleased to join you. Looking forward to interact and learn more about this project.

Patricia Brianna (02:59:37): > @Patricia Brianna has joined the channel

Patricia Brianna (03:01:32): > hello good people, i am Brianna (Brian), an outreachy applicant and i am a beginner . But willing to learn, grow and make a difference

Sonali Kumari (05:08:02): > @Sonali Kumari has joined the channel

Patricia Brianna (05:22:57): > hello friends, my account is not yet active (i was directed to “request account” in order to contribute). i received an email but the link there in is not directing me to create the account

Patricia Brianna (05:23:19): > any help please

Patricia Brianna (05:30:42): > Jump to:navigation,searchI am shown this message when i click the link sent in my in box”Invalid confirmation code. The code may have expired.” - Attachment (BugSigDB): Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Busayo Ojo (05:36:11): > Hi Patricia, did you request for the code twice?

Patricia Brianna (05:49:09): > i did

Patricia Brianna (05:49:54): > i requested twice but i got a message that my account was pending

Esther (05:50:27): > @Esther has joined the channel

Busayo Ojo (05:52:46): > In your email did you see this message. > “If the account is created, only you will be emailed the password.”?

Esther (05:56:31): > Hello Everyone, > > My name is Esther. > > I chose the Microbiome study curation project and I’m happy to be a part of the team. > Looking forward to having a great experience and also acquiring indepth knowledge.

Patricia Brianna (06:18:47) (in thread): > NO, I got the link to activate my account

Busayo Ojo (06:19:44) (in thread): > Can you send a SS of the mail you received, maybe that could help.

Diana Ofodu (06:42:55): > @Diana Ofodu has joined the channel

Diana Ofodu (06:46:19): > Hello, everyone. I’m Diana Ofodu. I’m a data analyst and optometrist looking forward to contributing to the microbiome study curation project.

Blessing Obafemi (08:14:13): > @Blessing Obafemi has joined the channel

Blessing Obafemi (08:21:22): > Hello, everyone. My name is Blessing Obafemi. I am an outreachy applicant. I am excited to be here

C. Mirzayi (please do not tag this account) (09:32:35): > Good morning everyone. Nice to meet you all.

C. Mirzayi (please do not tag this account) (09:33:45) (in thread): > Hi Patricia, > > I’m not sure what went wrong. I am going to check in with Professor Waldron in 30 minutes and I’ll see if he can troubleshoot what went wrong with setting up your account and see if we can get it resolved.

Fatima Zohra (09:36:51): > Welcome everyone!

C. Mirzayi (please do not tag this account) (10:09:21): > @Patricia BriannaI spoke with Levi and he says your account should be active now. Let me know if you have any trouble accessing it.

Ufuoma Ejite (10:45:53): > @Ufuoma Ejite has joined the channel

Ufuoma Ejite (10:54:44): > Hello everyone! I’m Ufuoma:blush:

Maryam Gbemisola (11:00:04): > @Maryam Gbemisola has joined the channel

Petrah (11:04:52): > @Petrah has joined the channel

Evan Chinny (11:14:20): > @Evan Chinny has joined the channel

Janani Ravi (11:15:15): > @Janani Ravi has joined the channel

Ludwig Geistlinger (11:15:54): > @Ludwig Geistlinger has joined the channel

Evan Chinny (11:17:09): > Hi Everyone!

Sreeyusha Vajinapally (11:36:49): > @Sreeyusha Vajinapally has joined the channel

Busayo Ojo (11:44:18): > Hi@C. Mirzayi (please do not tag this account)plz I’m trying to curate a study. when I click on add a study, it says “You do not have permission to edit this page”

Shravani Nag (11:50:29): > @Shravani Nag has joined the channel

C. Mirzayi (please do not tag this account) (11:58:18) (in thread): > Can you confirm for me that you are logged in by clicking on the person icon on the top right? It will show your name if you’re logged in. - File (PNG): image.png

KritikaVerma (12:11:36): > @KritikaVerma has joined the channel

Busayo Ojo (12:13:15) (in thread): > Ahh, yes I wasn’t logged in. It’s working fine now. > Thank you!

KritikaVerma (12:14:02): > Hi @everyone. > I am Kritika Verma. I am currently studying B Tech with IT and Mathematical Innovation as majors and Computational Biology as minor. I am an applicant in the May cohort for Outreachy. I look forward to learning from all of you. > Thank you

C. Mirzayi (please do not tag this account) (12:16:35) (in thread): > You’re welcome!

Sweta Kumari (12:19:10): > @Sweta Kumari has joined the channel

Maria Doyle (12:38:50): > @Maria Doyle has joined the channel

Ameerah Kabir (13:56:33): > @Ameerah Kabir has joined the channel

Ameerah Kabir (14:01:55): > Hiiiiii, I am Ameerah Kabir, a python developer, technical writer and journalist, and a machine learning and AI engineer. Really forward to this, microbiome is one of the reasons I am studying AI, can’t wait to contribute. Thank youu.

C. Mirzayi (please do not tag this account) (14:21:10): > Welcome all who joined. Happy to have you with us.

Fatima Zohra (14:39:27): > Everyone who requested an account in Bugsigdb should be receiving an email with a temporary password. Please make sure to check your spam folder if you can’t find it in your inbox. Thanks for joining!

Sweta Kumari (14:41:18): > Hello Everyone, this is Sweta Kumari from IIT Patna pursuing BTech and an outreachy applicant, i really find Microbiome Study Curation project very interesting and i want to learn more while doing this project. Looking forward to gain more knowledge and experience.

Monalika Patnaik (15:07:47): > @Monalika Patnaik has joined the channel

Ibizugbe Merit (15:22:22): > @Ibizugbe Merit has joined the channel

Ibizugbe Merit (16:53:59): > Hi@C. Mirzayi (please do not tag this account)pleaseI’mtrying to create an account on bugsigdb

C. Mirzayi (please do not tag this account) (16:57:59) (in thread): > Hi. Did you fill out the request an account page? Located here:https://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Ameerah Kabir (17:22:15): > Hi@C. Mirzayi (please do not tag this account)I have a question relating to the PDF file, should I ask it here or privately?

C. Mirzayi (please do not tag this account) (17:22:51): > You can ask here. Others might have the same question.

Ameerah Kabir (17:25:54): > A few more minutes of staring and it clicked, sorry:sweat_smile:.

C. Mirzayi (please do not tag this account) (17:32:34): > Ok I might consider figure 2 as not necessary for our purposes and look further down at the other figures. They will often have multiple figures showing the same or similar analyses in different forms.

C. Mirzayi (please do not tag this account) (17:34:11): > (And to give a bigger hint: I highlighted captions of figures that have relevant information for our purposes)

Ameerah Kabir (17:37:16): > Thank you so very much

2023-03-08

Kelvin Joseph (00:33:26): > @Kelvin Joseph has joined the channel

Busayo Ojo (01:26:26) (in thread): > So does it mean we don’t have to use all of the figure images as signatures? Is it to be at our discretion, or are there like other criterias that must be met before making a figure a signature?

Atrayee Samanta (02:18:50): > @Atrayee Samanta has joined the channel

Atrayee Samanta (02:24:03): > Hello everyone! I am Atrayee Samanta, an outreachy applicant, and I’m looking forward to learn, explore, as well as contribute to BugSigDB!

irem Kahveci (02:56:46): > Hello@C. Mirzayi (please do not tag this account). When will our BugSigDB requests be approved?

Vivian Ginikachukwu Ikeh (04:41:36): > @Vivian Ginikachukwu Ikeh has joined the channel

Vivian Ginikachukwu Ikeh (04:55:11): > Hello everyone, I am Vivian Ikeh an applicant for the May cohort, looking forward to learning and contributing.

Levi Waldron (06:51:58) (in thread): > A signature should correspond results of an analysis that identified differentially abundant between two conditions (group 0 and group 1) as described in an Experiment, so if the figure is the primary way those results are reported, then you would use it to create the signature. Sometimes results from the same “Experiment” are reported in multiple places (in text, in a figure, in a table), in which case you should decide what the best place to find complete reporting of the signature from that experiment is. In summary - the most important thing to decide is what are the “Experiments” that were performed (here Experiment refers to the groups that were contrasted and the methods that were used), then decide where to get the results from that Experiment. In some uncommon instances there may be multiple very similar Experiments contrasting the same two groups of participants, differing only in some of the methods used, in which case it is appropriate to select one representative Experiment so as not to enter highly redundant signatures for the same contrast. Does that make sense? It’s a good question, sorry I don’t have a simpler answer!

Levi Waldron (06:53:51) (in thread): > They should all be approved now - I’ve been approving them as soon as I see them, but sometimes it’s up to 8-10 hours after the request depending on time of day.

Levi Waldron (06:54:18) (in thread): > Welcome!

Levi Waldron (06:56:54) (in thread): > Welcome! Interesting note - one of the frequently asked questions about BugSigDB is whether AI could replace the work of curators. I think we are still a long ways away from being able to do that even with the most modern text mining, but it’s something to think about as you see what’s involved!

Levi Waldron (06:57:31) (in thread): > Welcome!

Levi Waldron (06:57:52) (in thread): > Welcome!

Levi Waldron (06:58:15) (in thread): > Welcome!

Levi Waldron (06:58:25) (in thread): > Welcome!

Levi Waldron (07:17:00) (in thread): > @Busayo Ojoyour account should be active nowhttps://bugsigdb.org/User:Boosayo - Attachment (BugSigDB): User:Boosayo

Busayo Ojo (07:20:09) (in thread): > Thank you for the response, I’ll go through the material again and hopefully this should help.

Busayo Ojo (07:22:05) (in thread): > Do you mean@Patricia Brianna? > My account has been active and I’ve been able to access it since Monday. Thanks!

Levi Waldron (07:33:52) (in thread): > Ah I misunderstood - and@Patricia Brianna’s account is active as well - Attachment (BugSigDB): User:Brian

Levi Waldron (07:35:33) (in thread): > Welcome@Patricia Brianna- your account should be active, let us know if you still have any problems accessing it.

Levi Waldron (07:35:53) (in thread): > Welcome!

Levi Waldron (07:36:00) (in thread): > Welcome!

Levi Waldron (07:36:16) (in thread): > Welcome!

Levi Waldron (07:36:23) (in thread): > Welcome!

Levi Waldron (07:36:43) (in thread): > Welcome!

Levi Waldron (07:42:40) (in thread): > Welcome!

Levi Waldron (07:42:54) (in thread): > Welcome!

Vivian Ginikachukwu Ikeh (07:43:34) (in thread): > Thank you@Levi Waldron

Levi Waldron (07:44:34) (in thread): > Thank you too for your interest!

irem Kahveci (07:47:22) (in thread): > Thank you for your help:blush:

Levi Waldron (07:47:53) (in thread): > You’re welcome, thank you for your interest!

Vivian Ginikachukwu Ikeh (07:49:18) (in thread): > The pleasure is mine. I hope to make an outstanding impression

Sweta Kumari (08:16:11) (in thread): > Thank you Sir

Moritz E. Beber (08:43:47): > @Moritz E. Beber has joined the channel

Atrayee Samanta (08:50:55) (in thread): > Thank you!

C. Mirzayi (please do not tag this account) (09:14:49) (in thread): > Thanks Levi!

Namusisi Sharon (09:56:44): > @Namusisi Sharon has joined the channel

C. Mirzayi (please do not tag this account) (10:14:36): > Welcome everyone and good morning/afternoon/evening to you wherever you are! > > I just wanted to point out that we have our curation meeting and office hours tomorrow morning at 10 AM EST (3 PM GMT). Please join us at:https://us02web.zoom.us/j/2737200499

Desire Oluwarotimi (10:31:11): > @Desire Oluwarotimi has joined the channel

Desire Oluwarotimi (10:32:56): > Hello everyone, I’m Desire, an Outreachy applicant and I’m looking forward to contributing positively to the community.

Busayo Ojo (12:01:57) (in thread): > Hi Desire, Welcome

irem Kahveci (14:34:39): > Hello! I want to add the NCBI source of ataskincluded in the “match unknown names to NCBI taxonomy” task. The site gives a warning that “You do not have permission to edit this page”. What path can I follow? - Attachment (BugSigDB): Study 658/Experiment 1/Signature 1

Ibizugbe Merit (14:44:11) (in thread): > Thanks:pray:Account created successfully

C. Mirzayi (please do not tag this account) (14:45:33) (in thread): > Hi Irem what NCBI taxonomy are you trying to match here? Can you link me to the taxon on the NCBI taxonomy browser?

Ameerah Kabir (14:49:02) (in thread): > I would love to attend, a reminder before it starts would be appreciated, my timing is different.

irem Kahveci (14:51:17) (in thread): > In thislink - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Fortune Nnamdi (15:02:00): > @Fortune Nnamdi has joined the channel

Patricia Brianna (15:21:35) (in thread): > thanks, account is up and running

Busayo Ojo (15:38:00): > Hi@C. Mirzayi (please do not tag this account)yesterday, I was working on study 186, when I set it to auto and added the Doi number(http://dx.doi.org/10.1136/gutjnl-2021-325021) it populated all the required fields, that is the journal, authors, year and abstract. I don’t know what’s wrong now, but all the populated fields are not showing. Only the Doi number. Should I enter it manually?

C. Mirzayi (please do not tag this account) (16:00:12) (in thread): > I think it’s based on PMID. I just added that and the paper seems to have correctly populated.

Busayo Ojo (16:03:37) (in thread): > Yes, it’s back to normal now. > Thank you!

Desire Oluwarotimi (16:43:55) (in thread): > Thank you Busayo.

OLADIRAN OLUWASHOLA (18:08:01): > @OLADIRAN OLUWASHOLA has joined the channel

Reece (23:43:23): > @Reece has joined the channel

2023-03-09

Tsoure (00:01:00): > @Tsoure has joined the channel

sophy (00:03:45): > @sophy has joined the channel

sophy (00:27:47): > Hi, I am sophy. Happy to join the microbiome project.

Ameerah Kabir (00:53:22): > Hi@C. Mirzayi (please do not tag this account)I curated a study, link :https://bugsigdb.org/Study_340, I would love a review on it. - Attachment (BugSigDB): Study 340

OLADIRAN OLUWASHOLA (02:11:37): > Good morning everyone, i’ve been waiting for the zoom meeting to start for over 10 minutes but hasn’t. Hope I’m correct with the time conversion?

irem Kahveci (02:21:06) (in thread): > Good morning! I think you wrong convert your time conversion.There are 8 more hours to the meeting according to my own time zone.

Busayo Ojo (02:22:52) (in thread): > It’s starting 4pm Nigerian time

OLADIRAN OLUWASHOLA (02:23:21) (in thread): > Oh, thank you.

Shallie (03:22:19): > @Shallie has joined the channel

K Nodia (04:23:03): > @K Nodia has joined the channel

K Nodia (04:27:04): > Hello Everyone , i m K Nodia Happy to join this community , and Hoping to contribute to my Best and learn from you all

anshika bhatt (04:46:49): > @anshika bhatt has joined the channel

Fortune Nnamdi (05:05:46) (in thread): > You’re welcome:relaxed:

Fortune Nnamdi (05:07:45) (in thread): > You’re welcome, Sophy

Ameerah Kabir (05:18:12) (in thread): > You are welcome@K Nodia:blush:

Chioma Grace (06:30:34): > @Chioma Grace has joined the channel

Chioma Grace (06:58:05): > Hello everyone, I am Chioma an applicant for outreachy Internship, I look forward to learning and contributing positively to Microbiome Study Curation Project. Thank you

Fatima Zohra (07:00:01): > Hello all, just a reminder we have our curation team meeting and office hour today at 10 AM EST (3 PM GMT). You are welcome to join at:https://us02web.zoom.us/j/2737200499

Bazgha Razi (08:36:05): > @Bazgha Razi has joined the channel

Aditi Singh (09:14:10): > @Aditi Singh has joined the channel

C. Mirzayi (please do not tag this account) (09:35:18): > Thanks for the reminder Fatima. Hopefully see some of you in 25 minutes!

Rukky (09:57:11): > @Rukky has joined the channel

Shallie (10:07:40): > @Shallie has left the channel

Riya Sharma (10:19:57): > @Riya Sharma has left the channel

Aiysha shahid (10:55:03): > @Aiysha shahid has joined the channel

Patricia Brianna (11:04:15): > hello everyone

Patricia Brianna (11:14:13) (in thread): > hello

Patricia Brianna (11:19:29) (in thread): > is it okay for me to start with this “Category talk:Pages with missing NCBI ID”

Patricia Brianna (11:19:58) (in thread): > hello

Patricia Brianna (11:20:33) (in thread): > is it okay if i start with this “Category talk:Pages with missing NCBI ID”

Patricia Brianna (11:24:17) (in thread): > thanks please, the account is up and running

Patricia Brianna (11:24:36): > hello everyone

Aiysha shahid (11:25:18) (in thread): > hello,

Patricia Brianna (11:28:17) (in thread): > have you attended the meeting

Busayo Ojo (11:30:58) (in thread): > Yes! The meeting ended about 40 mins ago

Patricia Brianna (11:32:20) (in thread): > my connection wasnt good

Patricia Brianna (11:32:35) (in thread): > i really missed

Busayo Ojo (11:32:54) (in thread): > So sorry

Busayo Ojo (11:33:58) (in thread): > We had our introductions, and someone presented a curation they worked on.

Busayo Ojo (11:36:29) (in thread): > Then, Chloe and Fatima said they’ll try to make more articles available for we to work on, (for the optional second contribution). Also, we can also look for articles we would like to curate and send it to them, so they approve and can assign us to it.

Busayo Ojo (11:37:00) (in thread): > Those are the major things we spoke about.

Patricia Brianna (11:39:07) (in thread): > thank mr. Ojo

Patricia Brianna (11:39:24) (in thread): > i highly appreciate

Busayo Ojo (11:40:25) (in thread): > You’re welcome:hugging_face:I’m Busayo (she)

Busayo Ojo (11:40:48) (in thread): > @EstherThis is the thread

Patricia Brianna (11:40:52) (in thread): > i am currently on this “Category talk:Pages with missing NCBI ID” any advice

Patricia Brianna (11:41:14) (in thread): > as in anyone else on it too

Busayo Ojo (11:41:24) (in thread): > On github?

Esther (11:41:50) (in thread): > @Busayo Ojothank you

Patricia Brianna (11:41:56) (in thread): > https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID

Patricia Brianna (11:42:11) (in thread): > website

Busayo Ojo (11:44:28) (in thread): > I think you need to check Github for available articles to work on first, then ask to be assigned. Have you done that?

Patricia Brianna (11:44:38) (in thread): > are the contributions restricted only to github, or

Busayo Ojo (11:45:56) (in thread): > Not really

Busayo Ojo (11:46:00) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/1 - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Busayo Ojo (11:46:24) (in thread): > Have you gone through this link?

khadijah (12:10:41): > @khadijah has joined the channel

Ameerah Kabir (13:02:33): > Hi@C. Mirzayi (please do not tag this account)can I record my contribution if it is still in review?

C. Mirzayi (please do not tag this account) (13:32:17) (in thread): > Yes.

Patricia Brianna (15:58:00) (in thread): > yeah, i have read and taken the survey

Patricia Brianna (15:58:15) (in thread): > thanks alot

Patricia Brianna (16:01:38): > task recorded, should i wait for results or i go ahead with the contribution

C. Mirzayi (please do not tag this account) (16:44:16) (in thread): > You can move forward with the optional task if you like.

C. Mirzayi (please do not tag this account) (17:31:19): > Hi all I am going to be out tomorrow but I wanted to thank you all for your interest in the project so far and you have all been exceptionally dedicated. I’m very impressed! > > Please continue to post questions here and Fatima and I will get to them ASAP.

Aguobi Amara (23:00:02): > @Aguobi Amara has joined the channel

Aguobi Amara (23:03:33): > Hello everyone > I am Aguobi Amara, nice to be here. > I am excited to know and learn more about Bugsigdb

Aguobi Amara (23:04:43): > Hello everyone I just joined. After the introduction please how to I get started with my first contribution, I am a little bit confused.

Andres Wokaty (23:17:22) (in thread): > Hi, I would look athttps://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839. - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Aguobi Amara (23:44:23) (in thread): > Thank you@Andres Wokaty

2023-03-10

Levi Waldron (01:54:55) (in thread): > Welcome,Aguobi!

Fatima Zohra (06:43:30) (in thread): > Hi@Patricia Briannathank you for your interest. You’ll be able to work on that section after the contribution period ends. For now, as part of the contribution period here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo:https://github.com/waldronlab/BugSigDBcuration/issues/1 - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Levi Waldron (07:14:21) (in thread): > Welcome, Chioma!

Chioma Grace (07:50:09) (in thread): > Thank you Levi

Chioma Nnadi (09:04:58): > @Chioma Nnadi has joined the channel

Chioma Nnadi (09:06:17): > Hello everyone I just joined. After the introduction, please tell me how to get started with my first contribution. I am a little bit confused. > I look forward to giving value, building a great network, and learning from the community.

Andres Wokaty (09:11:45) (in thread): > I recommend reading Chloe’s posthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839, which has a lot of good information to get started. I believe Chloe is out today, but maybe@Fatima Zohraor others can give guidance if you get stuck. - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Chioma Nnadi (09:12:39) (in thread): > Thank you so much

Aguobi Amara (09:44:05) (in thread): > Welcome dear, after the introduction please head on to readChloe’spost.

Barakat Dindi (09:44:26): > Pls I’m confused, after the submission of our primary task how do we get the Url to record on our outreachy application.

Aguobi Amara (09:45:44): > Hello everyone

Fatima Zohra (09:45:50) (in thread): > Thank you@Andres Wokaty.@Chioma Graceplease reach out if you have further questions.

Andres Wokaty (09:46:14) (in thread): > It’s listed on the issue

Aguobi Amara (09:46:34) (in thread): > You have to go through the outreachy website I guess

Andres Wokaty (09:46:35) (in thread): > https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Barakat Dindi (09:50:02) (in thread): > @Andres Wokatyand@Aguobi AmaraOkay thank you , would do that

Aiysha shahid (09:50:41) (in thread): > hello

Fatima Zohra (09:51:27) (in thread): > If its difficult to find please use this link to record your contributions in Outreachy athttps://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Barakat Dindi (09:51:55) (in thread): > Okay Thank you@Fatima Zohra

Aguobi Amara (09:53:41) (in thread): > Thank you so much:blush:

Aguobi Amara (09:53:57) (in thread): > @Levi Waldron

Aguobi Amara (10:50:39): > Has anyone made a contribution? I really need help as everything seems so overwhelming to me

Aguobi Amara (10:51:06): > I have created an account on bugsigdb

Aguobi Amara (10:51:34): > I am currently watching the video tutorials

Busayo Ojo (10:57:17) (in thread): > So sorry you feel that way, the videos you’re watching now might help a lot. > If its still unclear after that, feel free to ask any question you might have.

Aguobi Amara (10:58:09) (in thread): > Ok thank you so much

Fatima Zohra (11:09:53) (in thread): > Hi@Aguobi Amaraplease follow this link for instructions on how to get to your first contribution. feel free to reach out to me if you have specific questions.

Aguobi Amara (11:11:15) (in thread): > Thank you:pray:I appreciate

Chioma Nnadi (11:28:58) (in thread): > @Aguobi AmaraThank you so much:hugging_face:

Roseline (13:21:35): > @Roseline has joined the channel

Ibizugbe Merit (16:15:13): > Hi@C. Mirzayi (please do not tag this account)please how do I get my contribution to be reviewed?And how do I get the link to my contribution?

Aguobi Amara (16:53:46) (in thread): > Hello@Ibizugbe Meritkindly check this link to read up@C. Mirzayi (please do not tag this account)pinned message on how to make your first contributionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839 - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Ibizugbe Merit (16:57:26) (in thread): > Thanks alot@Aguobi Amara

Aguobi Amara (16:59:27) (in thread): > You are welcome > If you need any help kindly send a message across.I’llbe willing to help

Ibizugbe Merit (17:05:59) (in thread): > Noted.

Aguobi Amara (18:05:50): > Please can someone clear my confusion > When I click on the curation form it takes me to another Topic. - File (JPEG): IMG_0181

Aguobi Amara (18:08:10): > The topic we are to create a mini curation is it on Human micro biome or on Breast cancer patient

Aguobi Amara (18:08:34): > Idon’tunderstand this part - File (JPEG): IMG_0182

Andres Wokaty (20:34:50) (in thread): > All of these studies should be microbiome studies. From the title, the study is on the gut bacteria (microbiome) of patients who have breast cancer.

Aguobi Amara (23:57:45) (in thread): > Oh thank you

2023-03-11

Chioma Grace (01:07:57) (in thread): > Thank you so much @Jennifer Wokaty

Atrayee Samanta (03:47:42): > Hello, I had finished my first task and had requested a bugsigdb account more than 12 hours ago, but I haven’t received the account or any confirmation email. Can someone please help me out? Do I have to follow some more steps (other than requesting account at the website) too?

Busayo Ojo (04:49:36) (in thread): > Have you checked your spam/junk

Atrayee Samanta (05:29:27) (in thread): > Yes I did check those folders, but I did not find anything :(

Busayo Ojo (05:38:03) (in thread): > So sorry, maybe you should reach out to one of the mentors.

Atrayee Samanta (05:44:17) (in thread): > yes, I’ll do that

Atrayee Samanta (05:46:03) (in thread): > @C. Mirzayi (please do not tag this account)@Fatima Zohra@Levi Waldroncould you please help me out?

Levi Waldron (05:51:48) (in thread): > What username did you request?

Levi Waldron (05:53:40) (in thread): > It looks like you have two active accounts. Try logging in with Google?https://bugsigdb.org/User:Atrayeehttps://bugsigdb.org/User:Atrayees - Attachment (BugSigDB): User:Atrayee - Attachment (BugSigDB): User:Atrayees

Atrayee Samanta (06:07:16) (in thread): > @Levi WaldronYes, logging in with my google account finally worked, thanks a lot!

Levi Waldron (06:08:30) (in thread): > You’rewelcome!Let me know which accountyou’renot using,andI’lldeactivate it.

Atrayee Samanta (06:09:28) (in thread): > I’m not using the one with the username as ‘Atrayee’, thanks once again!

Hannah Honda (06:51:57): > @Hannah Honda has joined the channel

Levi Waldron (07:17:53) (in thread): > @Ameerah Kabirdid you intentionally refer to the study “Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn’s Disease” which has been in the database for a couple years?

Ameerah Kabir (07:39:49) (in thread): > oh no, I made Research on NCIB and choosed it, wasn’t aware it was. > > Ameerah Kabir

Chioma Nnadi (07:53:22): > Hi everyone, > I sincerely appreciate the help you provided yesterday in helping me navigate the project and the community. I do appreciate you very much. > Moreover, I pledge to ask questions as soon as I’ve finished reading and watching the videos if I come across any and also to provide help to others. Indeed yesterday’s help made me feel at home. > Shout out to the great mentors here;@Fatima Zohra@C. Mirzayi (please do not tag this account)and to others providing help to Newbies like me

Levi Waldron (07:53:45) (in thread): > What’s your bugsigdb user name? I was trying to see what you edited butcouldn’tfind your username.

Ameerah Kabir (07:58:13) (in thread): > Cyberian. I thought we would pick a study and curate it, read the instructions clearly and I have picked out a study issue on GitHub

Levi Waldron (07:59:52) (in thread): > Where did you curate? Idon’tsee your edits onhttps://bugsigdb.org/Study_340.It’strue this study still needs curation because the existing experiments clearly belong to a different study. - Attachment (BugSigDB): Study 340

Ameerah Kabir (08:00:12) (in thread): > This is really new to me, I apologise for my mistake, I would ask a lot of questions, while working on it.

Ameerah Kabir (08:03:28) (in thread): > Okay I will work on it

Levi Waldron (08:04:44) (in thread): > Idon’tyet understand what your mistake was:slightly_smiling_face:

Ameerah Kabir (08:12:50) (in thread): > What I did was, imputing the DOI and d PMID and the rest of the information popped up, I thought it was completed

Prudence Levison (08:37:13): > @Prudence Levison has joined the channel

Levi Waldron (08:40:12) (in thread): > You did that from New Study starting point,not from bugsigdb.org/Study_340?

Cindy Apiyo (10:56:57): > @Cindy Apiyo has joined the channel

Cindy Apiyo (11:04:24): > Hello everyone > My name is Cindy Apiyo. I just joined the group chat and I’m looking foward to adding value and learning as well here on#bugsigdb

Levi Waldron (12:24:40) (in thread): > And I’m confused becausehttps://github.com/waldronlab/BugSigDBcuration/issues/18that you signed up for refers to a different publication (Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy) - Attachment: #18 Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy > Condition: Leukemia
> URL: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7592783/

Emmanuel Taiwo devbird007 (12:29:18): > @Emmanuel Taiwo devbird007 has joined the channel

Ameerah Kabir (12:41:30) (in thread): > Yes I did it from new study.

Ameerah Kabir (12:42:19) (in thread): > Oh no, I just commented on the GitHub issue today, I am aware it is different:sweat_smile:

Esther (13:55:58) (in thread): > Hello Cindy, > > Kindly clicked on the pinned message to get started.

Cindy Apiyo (14:08:40) (in thread): > Thankyou for the update

Patricia Brianna (16:05:17) (in thread): > thanks for your support

Patricia Brianna (16:05:33) (in thread): > i personally appreciate

Patricia Brianna (16:13:09): > hello everyone

Patricia Brianna (16:13:17): > are we fine

Patricia Brianna (16:26:19): > i have been assigned an issue on github, so how do i make contributions to my issue please,

Patricia Brianna (16:26:37): > any help please

Andres Wokaty (16:34:37) (in thread): > Can you share the link to your issue?

Patricia Brianna (16:44:58) (in thread): > Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel diseaseassignedoutreachy may23paper to curatesecond contribution

Patricia Brianna (16:46:08) (in thread): > i was thinking of going to create a study on the website

Andres Wokaty (16:46:37) (in thread): > I believe this is for the ‘optional stretch task’ athttps://github.com/waldronlab/BugSigDBcuration/issues/1. - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Andres Wokaty (16:47:12) (in thread): > Yes, I believe that’s right. You should make an account and then try to fill out the study.

Patricia Brianna (16:48:35) (in thread): > true it is an optional task, does it mean i have made my first contribution already, if yes how do i record it

Patricia Brianna (16:50:17) (in thread): > arent we supposed to do optional tasks, if no, where do we go after the first task being recorded

Andres Wokaty (16:51:39) (in thread): > did you already do the quiz?

Patricia Brianna (16:53:22) (in thread): > yeah, i did it

Andres Wokaty (16:53:45) (in thread): > If you did the quiz, you can record your contribution through the link at the bottom of the issue under Contributions.

Patricia Brianna (16:53:48) (in thread): > are we supposed to get results for the quiz

Patricia Brianna (16:54:16) (in thread): > thakns a;ot

Andres Wokaty (16:54:19) (in thread): > Oh, I am not sure about that. I would ask the mentors for this project.

Patricia Brianna (16:55:07) (in thread): > alright thanks alot

Patricia Brianna (16:55:32) (in thread): > lemme do this extra and then record my contributions

ezinne (19:17:16): > @ezinne has joined the channel

ezinne (19:18:08): > Hello, i’m Ezinne an outreachy applicant, i am super excited to be here and i look forward to contributing to this project

Aguobi Amara (20:48:57) (in thread): > Hello Ezinne welcome to this bugsigdb, feel free to ask questions

Aguobi Amara (20:51:06) (in thread): > Hello Cindy, welcome to bugsigdb

Hannah Honda (21:56:32): > Hi all, I finished my first task and requested a bugsigdb account to get started on the second task. I was wondering roughly how long the wait time is for the account request to be approved?

Aguobi Amara (22:04:18) (in thread): > Itdoesn’treally take much time, I got my account approved in a short time

Barakat Dindi (23:04:08): > Hi@Fatima Zohra@C. Mirzayi (please do not tag this account)I am trying to curate a study but After filling my DOI the informations aren’t populating. > > Here’s the linkhttp://dx.doi.org/https://doi.org/10.3920/BM2019.0039

2023-03-12

Chioma Grace (00:24:46) (in thread): > Please what is the first task…..

Hannah Honda (01:14:06) (in thread): > @Aguobi AmaraThanks, i’ll keep checking.@Chioma Grace

Hannah Honda (01:15:38) (in thread): > @Chioma Gracehttps://github.com/waldronlab/BugSigDBcuration/issues/1has the instructions — its under Contribution task. The link is too a qualtrics survey form that is like a mini curation task? - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Busayo Ojo (01:55:27) (in thread): > Try adding the PMID: 32073296

Busayo Ojo (01:55:35) (in thread): > That should work

Ibizugbe Merit (03:30:51) (in thread): > Hello@Barakat Dindimake sure to click complete after filling each information for a particular section(experiment or signature )

Barakat Dindi (03:40:28) (in thread): > @Ibizugbe MeritI did that. > > I would try what Busayo suggests.@Ibizugbe Meritand@Busayo OjoThank you both.

Barakat Dindi (04:11:27) (in thread): > @Busayo OjoIt worked. > > Thank you.

Busayo Ojo (04:34:46) (in thread): > You welcome!

Fatima Zohra (06:57:47) (in thread): > Hi@Patricia Briannayou’ll be getting a copy of your survey responses in your email by tomorrow. You can use that record your contribution in outreachy.

ezinne (07:24:37): > please after the first contribution where can i submit it?

Fatima Zohra (08:41:50): > Hi all,due to the weekendI’munable to address all your requests right away. Thank you for being patient. Newarticles for the second contribution will be added on GitHub bytomorrow. Those who didn’t get a chance to claim any yet please keep an eye out. Thanks all for your contributions:raised_hands:

Levi Waldron (09:13:06) (in thread): > Welcome, Cindy!

Levi Waldron (09:13:17) (in thread): > Welcomne, Chioma!

Ibizugbe Merit (10:25:31): > Hi,@C. Mirzayi (please do not tag this account)I curated a study,I would love a review on it and also please help me check my progress:pray:Link:https://bugsigdb.org/Study_747 - Attachment (BugSigDB): Study 747

Levi Waldron (11:10:34): > <!channel>whenyou’reready for your study to be reviewed,please update the GitHub issue with the link to bugsigdb-you can also post a note here, but your Issue will be the place for organized communication.

Maryam Gbemisola (11:14:02) (in thread): > I didn’t do the first Contribution. Can I still do it or I will just join the second contribution

Levi Waldron (11:34:09): > I’ve added a bunch more second studies tohttps://github.com/waldronlab/BugSigDBcuration/issues, there should be enough for everyone now!

Busayo Ojo (11:39:03) (in thread): > You have to do the first contribution

Aiysha shahid (11:39:32) (in thread): > hlo, for the first contribution you have to give a quiz and if u want to record your contribution you can do it by here:https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Maryam Gbemisola (11:41:53) (in thread): > How do I get started please?

Busayo Ojo (11:47:37) (in thread): > Take a look at this first, if you have more questions feel free to ask.https://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839 - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Ibizugbe Merit (11:54:00) (in thread): > Please@Levi WaldronI’mnot really clear about what you mean by ‘update the GiftHub issue with the link to bugsigdb’.Can you help me with a clearer explanation:pray:

Atrayee Samanta (11:59:40) (in thread): > @Ibizugbe MeritI think you’ll have to link the study (that you have done in a bigsigdb page) of the paper you have been assigned in the comment section of the issue in github

Aguobi Amara (12:21:04) (in thread): > Thank you

Aguobi Amara (12:40:59) (in thread): > It means after you are done:white_check_mark:with the study on bugsigdb, copy the link and send to GitHub so that they can review it.

Ibizugbe Merit (12:59:41) (in thread): > I think I get it clearly now thanks@Atrayee Samantaand@Aguobi Amara

Atrayee Samanta (13:10:19) (in thread): > No problem!

Aguobi Amara (13:42:16) (in thread): > Your welcome

Patricia Brianna (14:25:32) (in thread): > thanks a lot

Patricia Brianna (14:29:32) (in thread): > this has helped me too

Patricia Brianna (14:29:44) (in thread): > thanks alot please

Patricia Brianna (14:39:26) (in thread): > is it possible to do more than one second study

Chioma Grace (15:13:37) (in thread): > Thank you@Hannah Honda. > I have completed the first task.

Aguobi Amara (15:48:32) (in thread): > Your welcome

Ibizugbe Merit (16:46:59) (in thread): > Thank you:pray:

Ibizugbe Merit (17:04:31) (in thread): > Thanks for the question,as I would also love to know

Chioma Nnadi (17:30:45) (in thread): > Thank you@Levi Waldron

Levi Waldron (17:39:43) (in thread): > Thatis ok with me! although you should finish one paper before signing up for the next.

Levi Waldron (17:41:45) (in thread): > Thank you for your help with explaining@Aguobi Amaraand@Atrayee Samanta!

Patricia Brianna (17:49:15) (in thread): > thanks@Levi Waldron

Patricia Brianna (17:52:12) (in thread): > hello@Fatima Zohrathe copy for the survey hs not reached me yet. So i cant record my contribution so far,…

Ibizugbe Merit (17:57:30) (in thread): > Good.Thanks@Levi Waldron

Chioma Nnadi (17:59:04): > Hello@Andres WokatyTrust you are well. Just to confirm, after the quiz, I can go ahead to request to claim an article for the optional task by posting a response to the issue with my name right? or Is there something else that should be done?

Andres Wokaty (18:02:06) (in thread): > Yes. You may have to wait for it to be assigned to you as it is still the weekend.

Andres Wokaty (18:03:12) (in thread): > Please be patient. It is still the weekend in some places.

Chioma Nnadi (18:15:58) (in thread): > Sure I will wait. Thank you so much:hugging_face:

Desire Oluwarotimi (23:05:40): > Hello@Levi Waldron, I tried to create a BugSigDB account so I can commence curation but I’m yet to receive an email with regards to that effect.

Aguobi Amara (23:05:56) (in thread): > Your welcome@Levi Waldron

Aguobi Amara (23:07:42) (in thread): > Hello desire, just wait and keep checking your email,you’lldefinitely receive an email, maybe they are away at the moment

2023-03-13

Aguobi Amara (00:36:21): > Please those that have recorded their contribution on outreachy, how do I get my URL - File (PNG): IMG_0200

Ibizugbe Merit (01:52:18) (in thread): > Welcome@ezinnewe’reglad to have you join us:hugging_face:

Ibizugbe Merit (02:03:27) (in thread): > Hi@Aguobi AmaraI think you can do that by going to your bugsigdb account,and copying the link to your contribution to record on outreachy…..Though this is what I think,butlet’swait for the mentors to give us a helping handing so we can be clear on it. - File (JPEG): IMG_9586

Barakat Dindi (02:44:03): > @Aguobi Amarayou can use the url that directed you to the task or this below.https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Harrydas Ombati (02:45:11): > @Harrydas Ombati has joined the channel

Aguobi Amara (02:46:43) (in thread): > Thank you so much@Barakat Dindithis is super helpful

Aguobi Amara (02:47:30) (in thread): > Thank you@Ibizugbe Merit

Ibizugbe Merit (03:05:38) (in thread): > How about for the optional task?@Barakat Dindi

Ibizugbe Merit (03:06:05) (in thread): > You’rewelcome

Barakat Dindi (03:07:44) (in thread): > @Ibizugbe MeritI think the Url of the paper curated on BugSigDb

Barakat Dindi (03:08:09) (in thread): > @Aguobi Amarayou are welcome.

Ibizugbe Merit (03:09:09) (in thread): > @Barakat DindiOk.Thanks a lot

Barakat Dindi (03:09:43) (in thread): > @Ibizugbe Merityou’re welcome

Barakat Dindi (03:16:50): > Pls what’s the maximum number of signature one can add? > > Should every signature be dual comprising increase and decrease or some can show only increase? > > > I’m also finding it difficult to interpret the LeFSe pie chart, any help please?

Fatima Zohra (03:20:37) (in thread): > @Aguobi Amarafor the first contribution, your URL would be the mini survey URL. For the second contribution, use the link for the entire study. For examplehttps://bugsigdb.org/Study_747 - Attachment (BugSigDB): Study 747

Aguobi Amara (03:22:30) (in thread): > Ok thank you:pray:

Harrydas Ombati (03:23:29) (in thread): > Hi guys,am new here….how does one create a BugSigdb account

Aguobi Amara (03:23:34) (in thread): > Please@Fatima Zohrais this the correct link to the mini surveyhttps://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M

Busayo Ojo (03:24:02) (in thread): > Levi gave an explanation on how to go about signatures, I’ll tag you to it.

Barakat Dindi (03:24:51) (in thread): > Okay@Busayo Ojo

Busayo Ojo (03:25:10) (in thread): > @Barakat DindiThis is it!

Fatima Zohra (03:25:29) (in thread): > Thank you@Levi Waldron

Barakat Dindi (03:26:17) (in thread): > @Busayo OjoThanks a lot.

Fatima Zohra (03:26:20) (in thread): > Thanks Busayo!

Fatima Zohra (03:28:45) (in thread): > Yes

Aguobi Amara (03:29:26) (in thread): > Ok thank you

Fatima Zohra (03:35:22) (in thread): > @Patricia Briannacould you please confirm your email address again?

Fatima Zohra (03:37:53) (in thread): > Thank you Busayo!

Ibizugbe Merit (03:49:16) (in thread): > Hi@Harrydas OmbatiI recommend you read Chloe’s posthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839. Or open the pinned message on the#bugsigdbchannel to get started - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Harrydas Ombati (03:50:23) (in thread): > Thank you for your insights

Ibizugbe Merit (03:52:43) (in thread): > I’mglad I could help

Levi Waldron (03:53:45) (in thread): > Welcome,@ezinne!

Levi Waldron (03:57:50) (in thread): > Responding to another question from@Barakat Dindibut putting it here to organize in the same thread.Someexperiments can have only a signature ofincrease, or some might not have any significant increases or decreases! But it is still worth recording the experiment to record the negative result and any alpha diversity comparisons they made.

Barakat Dindi (03:59:44) (in thread): > @Levi WaldronThank you, it gives me more direction.

Suwaibat Suleiman (04:00:59): > @Suwaibat Suleiman has joined the channel

Levi Waldron (04:10:06) (in thread): > @Desire Oluwarotimiyour account was already active (https://bugsigdb.org/Special:ListUsers) - would you try logging in with google? - Attachment (BugSigDB): Special:ListUsers

Busayo Ojo (04:23:14) (in thread): > @EstherHere you go

Esther (04:24:39) (in thread): > @Busayo Ojothank you

Atrayee Samanta (04:28:41) (in thread): > Hey@Busayo Ojocould you please tag me too? I’m having trouble with signatures too

Busayo Ojo (04:30:15) (in thread): > @Atrayee SamantaHere

Busayo Ojo (04:31:41) (in thread): > @Fatima ZohraPlz can we pin Levi’s response to the channel. It seems a lot of people might need it.

Atrayee Samanta (04:32:17) (in thread): > Thanks@Busayo Ojo!

khadijah (04:35:41): > hi@Fatima Zohrai have dropped a link to my study under the issue assigned to me for a review.

Chioma Nnadi (04:41:32): > Hello everyone, > As we all work towards the goal of being on this channel, I’d like to encourage us to take as much time as we can to eat, rest, and stay positive. It will undoubtedly get better. > Cheers to a new week:clinking_glasses:.

Levi Waldron (05:28:56): > <!channel>I noticed that there has mistakenly been at least one study assigned as a “second contribution” that already existed in bugsigdb. (https://github.com/waldronlab/BugSigDBcuration/issues/15). bugsigdb will prevent the creation of a new study with the same PubMed IDSifthey have the same study design, but if you enter a different study design, or enter the PMID differently or use manual entry of study information, it will allow creation of a new study. That was intended for the rare instance that results from two different study designs are reported in the same publication, but in this case, it is a duplication of efforts (although in this case@Kelvin Josephcorrectly identified the study design as case-control while the original curator and reviewer both got it wrong!) If you are going to start on a “second contribution”, would you please double-check that this study doesn’t already exist in bugsigdb before creating a new study? And@ftzohra22/@C. Mirzayi (please do not tag this account), please double/triple-check that any new studies you assign are not already in the database - let’s discuss offline how to resolve this duplicated data. - Attachment: #15 Alterations in Oral Microbiota in HIV Are Related to Decreased Pulmonary Function > Condition: HIV
> URL: https://pubmed.ncbi.nlm.nih.gov/31682463/

Aguobi Amara (05:37:18) (in thread): > Alright, I will check that mine is not already existing

Atrayee Samanta (05:49:30) (in thread): > @Levi WaldronI just wanted to clarify- this means that if it has been mentioned that a particular result is just highly abundant in a particular group of participants and significantly less abundant in the other group of participants (but not necessarilydifferentiallyabundant), it is worth creating a signature based on this experiment, right?

Desire Oluwarotimi (06:18:02) (in thread): > I did try logging in with google as you suggested on GitHub but it says the credentials are not associated with any user.

Patricia Brianna (06:19:57) (in thread): > briannapatricia7@gmail.com, thanks a lot

Levi Waldron (06:36:22) (in thread): > Try the “Forgot your password?” link from the login page, because your account is active and we can’t reset your password ourselves. If all else fails we’ll delete your account and you can go through the setup process again with hopefully better results.

Kelvin Joseph (06:37:18): > Okay so can I add it as my contribution to the Outreachy page? As I got it correctly

Levi Waldron (06:37:40) (in thread): > My only guess is that you may have used a different email address to register…I just wrote on your Talk page so you should receive an email at the address associated with your account.

Levi Waldron (06:38:34) (in thread): > Yes you can@Kelvin Joseph

Levi Waldron (06:45:55) (in thread): > I’m not quite sure what you mean, because to me, “significantly less abundant” means the same thing as “differentially abundant” and merits creating a signature. However, “Highly abundant in a particular group” does not mean it is differentially abundant or significantly less abundant in another group, so would not merit creating a signature.

Kelvin Joseph (06:46:54) (in thread): > How can I offer more contribution to your projects

Chioma Nnadi (06:52:50): > Hello > I just requested for my BugSigDB account but I have not received any mail yet.

Atrayee Samanta (07:00:23) (in thread): > Yes, I understand it now, thank you so much! I had framed it unclearly- but after I went through the doi properly the terms and experiment results became clearer to me

Desire Oluwarotimi (07:04:19) (in thread): > I tried reseting my password but there no response to that effect in my mail.

Desire Oluwarotimi (07:05:26) (in thread): > And I don’t think I used another mail. The mail I used isrotimidesire@gmail.com

Desire Oluwarotimi (07:06:04) (in thread): > You can help confirm this please. Thank You.

Desire Oluwarotimi (07:06:39) (in thread): > Or maybe deleting the existing account so I can start all over is the way forward.

Levi Waldron (07:12:09) (in thread): > @Desire Oluwarotimiplease go ahead and create a new account with this email address.

Levi Waldron (07:12:30) (in thread): > (with a different user name)

Chioma Nnadi (07:16:22) (in thread): > I found this already in my Spam section of my mail. Thanks

Desire Oluwarotimi (07:23:05) (in thread): > I have done just that using a different username “Deacme”.

Desire Oluwarotimi (07:23:41) (in thread): > I’m hoping I get a confirmation mail this time around. Thank you@Levi Waldron

Levi Waldron (07:26:18) (in thread): > Your new account is approved.

Desire Oluwarotimi (07:28:08) (in thread): > I got the mail now and I have access as a registered user. Thank you so much@Levi Waldron

Parul Chaddha (08:56:48): > @Parul Chaddha has joined the channel

Barakat Dindi (08:58:28) (in thread): > @Busayo Ojopls where did you get the PMID no on the article, I have been perusing calmly through out the paper but I seem not to find it, Although I’m done with curating but for future sake. Thank you.

Fatima Zohra (08:59:46) (in thread): > @Barakat Dindiplease search for the title of the paper onhttps://pubmed.ncbi.nlm.nih.gov/and grab the PMID from there. Let me know ifyou’restill stuck - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 35 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Fatima Zohra (09:31:17) (in thread): > @Kelvin Josephas we discussed on the team meeting you can search for your own microbiome articles at this point. Please send it to me or Chloe for confirmation before you curate it on bugsigdb.

Barakat Dindi (09:40:34) (in thread): > @Fatima ZohraGot it! > > Thank you. > > it worked, I found it.

Levi Waldron (09:50:45) (in thread): > @Kelvin JosephI thinks it’s also OK to choose your next paper from the unassigned GitHub issues (https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+-label%3Aassigned+) - we should be able to keep a steady supply of studies available there!

Fatima Zohra (09:52:43) (in thread): > Thanks Levi. Kelvin already claimed one of the new papers, I’ll assign it to them

C. Mirzayi (please do not tag this account) (09:55:49): > Good morning everyone. How is everyone today? Please let me know if you have any questions.

Levi Waldron (10:37:54): > Quick announcement - if something isn’t right when you enter a new study inbugsigdb.orgfor your second contribution, please edit that study until you get it right rather than creating another new study to try again. Note that you must enter a PMID in order for the study information to auto-complete.

Chioma Grace (11:31:14) (in thread): > Hello Levi, please how should we edit the study because if I input the PMID, the page will not save rather this Note: Most of the Study information is automatically included based on the PMID was stated.

C. Mirzayi (please do not tag this account) (12:06:00) (in thread): > @Chioma Gracehttps://bugsigdb.org/Study_753It looks like you’ve already added the PMID for this study. Why do you need to edit the PMID? - Attachment (BugSigDB): Study 753

Chioma Grace (12:09:39) (in thread): > Thank you@C. Mirzayi (please do not tag this account),@Fatima Zohrahave help me solve the problem I was facing. That’s why I was able to input the PMID.

C. Mirzayi (please do not tag this account) (12:09:52) (in thread): > Gotcha.

Suwaibat Suleiman (13:36:07) (in thread): > I’ve been dealing with this! Thank you so much@Chioma Nnadi!

Esther (13:45:49): > hello, > > Is it possible for a study not to have alpha diversity?

Levi Waldron (13:51:24) (in thread): > Yes, sometimes alpha diversity is not investigated at all.It does also go by different names, like richness, Shannon Diversity,or others in the Experiment form.

Esther (13:51:48) (in thread): > Oh ok. > thank you

Fatima Zohra (14:31:20) (in thread): > Patricia please use this link as your contribution URL to record your contribution. You will not need a copy of your survey to record your contribution. Add this link to the contribution URL field.https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Kelvin Joseph (14:37:44) (in thread): > Thanks a lot@Levi Waldronand@Fatima Zohrafor the concern let me get started

Patricia Brianna (15:22:53): > hello friends from all corners of the earh, what next after recording my contribution

Patricia Brianna (15:23:36): > i feel excited each day that passes to contribute in this life changing projects.

Patricia Brianna (15:24:40) (in thread): > thanks a lot

Patricia Brianna (15:25:33) (in thread): > i really appreciate your selfless service. So after, what next please, > > On Tue, 14 Mar 2023 at 00:28, Patricia Brianna <briannapatricia7@gmail.com> wrote: > > thanks a lot

Patricia Brianna (15:26:10) (in thread): > can i go ahead and do the second tasks > > On Tue, 14 Mar 2023 at 00:29, Patricia Brianna <briannapatricia7@gmail.com> wrote: > > i really appreciate your selfless service. So after, what next please, > > > > On Tue, 14 Mar 2023 at 00:28, Patricia Brianna <briannapatricia7@gmail.com> wrote: > > thanks a lot

Patricia Brianna (15:59:00): > @Fatima Zohra,@C. Mirzayi (please do not tag this account)can i proceed and apply to bioconductor since i have recorded my contributio

Patricia Brianna (15:59:26): > or i first record some more contributions

Patricia Brianna (15:59:40): > thanks once again

Ameerah Kabir (16:13:18): > Hi@C. Mirzayi (please do not tag this account)@Levi Waldronif I am curating a study and there is only one group in the study, which group should I put it in? Thought about putting it in group zero but it doesn’t have group description and group one doesn’t have group size option

C. Mirzayi (please do not tag this account) (16:51:17) (in thread): > If this is about “Gut microbiota profiles of treatment-naïve adult acute myeloid leukemia patients with neutropenic fever during intensive chemotherapy” It looks like this study is comparing pre-treatment vs. post-treatment in which case the group 0 is the pre-treatment and group 1 is the post-treatment.

C. Mirzayi (please do not tag this account) (16:51:28) (in thread): > I believe so yes.

Ameerah Kabir (17:05:19) (in thread): > Alright, I would go through it again, thank youuu.

Desire Oluwarotimi (17:13:39): > Hi Chloe, Regarding my assigned article, there’s only one group case which is colorectal cancer after which is about four different case studies from both BMI and physical activity. How do I go about the group 1 and 0 please??

C. Mirzayi (please do not tag this account) (17:18:07) (in thread): > This is a complicated one. Looking at the paper you’re going to need several experiments, one for each contrast so: > (Group 1) vs. (Group 0) > Inactive vs. active > Overweight vs. normal weight > Obese vs. normal weight > Normal weight inactive vs. normal weight active > etc.

C. Mirzayi (please do not tag this account) (17:20:05) (in thread): > This is not uncommon in these studies where they have more than one group 1 and/or group 0. We have to enter these as separate experiments.

Desire Oluwarotimi (17:22:38) (in thread): > That definitely gave me some clarity. I’d give it a shot and get back to you if I get stuck.

Anushka Sharma (17:47:45): > @Anushka Sharma has joined the channel

Anushka Sharma (17:53:48): > Hello everyone I am Anushka sharma an outreachy applicant from India . I am happy to be a part of this community and looking forward to have a new learning experience. Also I would like to know how to begin with this project as I already requested for the account but haven’t recieved the mail yet .kindly guide how to begin the project. > Thank you

C. Mirzayi (please do not tag this account) (20:26:23) (in thread): > Hi Anushka. See the instructions here:https://github.com/waldronlab/BugSigDBcuration/issues/1 - Attachment: #1 Microbiome Study Curation - Outreachy Applicant Instructions > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_0cYerh299Ftl49M. > > Please submit a fully completed mini-curation via the form above before continuing. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Patricia Brianna (22:03:06) (in thread): > @C. Mirzayi (please do not tag this account), so about applying, what do I feel in “Outreachy internship project timeline:”

Patricia Brianna (22:56:59) (in thread): > hello friends

Patricia Brianna (22:57:25) (in thread): > “You verified the time commitments listed on your initial application are correct.****You have not provided answers to community-specific questions. Please double check with your mentor and coordinator if you need to provide additional information.****You are not applying to Google Summer of Code.****Timeline of tasks for the internship period:”

Patricia Brianna (22:59:39) (in thread): > You verified the time commitments listed on your initial application are correct.You have not provided answers to community-specific questions. Please double check with your mentor and coordinator if you need to provide additional information.You are not applying to Google Summer of Code.Timeline of tasks for the internship period: kindly @C. Mirzayi (please do not tag this account)@Fatima Zohra, i request for your help here, how do i go through the above

Patricia Brianna (23:04:36): > https://bugsigdb.org/Special:FormEdit/Experiment/Study_739/Experiment_1?reload=1&returnto=Study_739please any advice here. thanks - Attachment (BugSigDB): Special:FormEdit/Experiment/Study 739/Experiment 1

2023-03-14

Hannah Honda (02:00:38) (in thread): > Thank you so much@Barakat Dindi

Harrydas Ombati (02:18:33): > Hi@C. Mirzayi (please do not tag this account)I did request for a BugSigdb account yesterday, I haven’t however received the logins, specifically, the password to my supposed account. Could you please help?

Busayo Ojo (02:21:19) (in thread): > Plz check your spam folder to start of

Harrydas Ombati (02:23:06) (in thread): > I did check, clicked on the link then was “told” the request had been sent….@Ojo

Harrydas Ombati (02:25:20) (in thread): > I however haven’t received the password

Harrydas Ombati (02:43:59): > Hello guys, after the completion of task 1 what link should we put in our contribution phase and how do you know whether your task was accepted? In other words what do I fill below? - File (JPEG): Screenshot_2023-03-14-09-40-45-470_com.android.chrome.jpg

Esther (03:32:03) (in thread): > Hello good morning, > > Please,do you mind giving a simple definition of what group 1 and group 0 is in the article?

Busayo Ojo (04:03:32) (in thread): > @Levi Waldronwill help look into it

Busayo Ojo (04:05:48) (in thread): > Paste the link to the survey that you filled as your contribution URL,

Harrydas Ombati (04:15:37) (in thread): > I already killed the tab…does it mean I’ll have to redo it again? Because a new link will have an empty or a non-filled survey or it doesn’t matter??

Harrydas Ombati (04:16:26) (in thread): > Thank you , I really appreciate:blush:

Levi Waldron (04:17:16) (in thread): > Created just now!

Harrydas Ombati (04:18:55) (in thread): > Thank you , seen it @lwaldron

Levi Waldron (04:21:23) (in thread): > You’re welcome!

Levi Waldron (04:25:11) (in thread): > @Estherin general, “group 0” is the reference or control group - this is the “normal” group against which whatever is being studied is being compared to. If you’re studying cancer, the control group would be people without cancer, if you’re studying obesity it could be people of normal weight, if you’re studying the effect of antibiotics it could be people who have not received antibiotics. “group 1” is the study group, the group that represents something different that you want to study, like people with cancer, obesity, or receiving antibiotics. Does that help?

Fatima Zohra (04:25:32) (in thread): > We’ll review your study. Thank you

Esther (04:25:59) (in thread): > Yes it does. > > Thank you

Busayo Ojo (04:29:08) (in thread): > It doesn’t matter

Harrydas Ombati (04:30:36) (in thread): > Okay thank you, you my friend is a saviour

Fatima Zohra (04:31:04) (in thread): > Thank you@Busayo Ojo

Chioma Nnadi (05:10:07): > https://bugsigdb.org/Study_530please any advice here. Thanks@Fatima Zohra - Attachment (BugSigDB): Study 530

Fatima Zohra (05:12:44) (in thread): > Are you done curating this?

Chioma Nnadi (05:13:21) (in thread): > yes.

Fatima Zohra (05:13:33) (in thread): > Okay we’ll review thanks

Ibizugbe Merit (05:31:47): > https://bugsigdb.org/Study_747please I need a review on this…Corrections and assistance will be much appreciated:pray:@Fatima Zohra - Attachment (BugSigDB): Study 747

Fatima Zohra (05:37:21) (in thread): > Hi@Ibizugbe Meritthank you for completing your curation. Please be patient. We will review your paper as soon as possible and get back to you.

Ibizugbe Merit (05:40:09) (in thread): > Thank you so much@Fatima ZohraCan I pick another issue to work on while I wait?

Levi Waldron (05:43:10) (in thread): > I made a note on the Discussion page, did you receive an email about that discussion?

Barakat Dindi (06:13:24): > https://bugsigdb.org/Study_745Here’s my curation. Kindly help review too. Thank you. - Attachment (BugSigDB): Study 745

Chioma Nnadi (06:23:11) (in thread): > I didn’t

Busayo Ojo (06:29:42) (in thread): > Hi, I don’t think it’s compulsory to send your article for review here, as long as you have informed them on GitHub that your article is ready for review they have seen it and will review it in time. So the group is not just filled with links.

Ameerah Kabir (06:36:52) (in thread): > Hi, sorry for the late reply. > > Okay, in medical  Research studies, they are different types, let’s use an observational study as an example. > > The current study I am curating is an observational study, they were study patients before and after they undergo chemotherapy. > > Now my group 0 is the before chemotherapy and my group 1 is after chemotherapy. > > In some cases they would have two set of people, healthy and people with the condition they are studying, read the abstract, they would give an insight of how the study went. > > Wishing you all the best…

Esther (06:45:54) (in thread): > @Ameerah Kabirthank you

Barakat Dindi (07:16:39) (in thread): > Okay I thought@Levi Waldronmentioned after submitting on Github, we can also post a note here.

Busayo Ojo (07:21:13) (in thread): > That’s fine then, I didn’t know he said so.

Levi Waldron (07:22:32) (in thread): > Just know that posting here probably won’t affect when your contribution gets reviewed, we’ll work our way through the issues on GitHub as soon as we can.

Barakat Dindi (07:24:01) (in thread): > Okay. > > Thank you@Levi Waldron

Barakat Dindi (07:24:58) (in thread): > @Busayo OjoYes he did.

Kelvin Joseph (07:48:29) (in thread): > Finished my curationhttps://github.com/waldronlab/BugSigDBcuration/issues/27and is waiting reviews thanks - Attachment: #27 The subgingival microbiome of clinically healthy current and never smokers > https://pubmed.ncbi.nlm.nih.gov/25012901/

Mugdha Pendse (08:00:11): > @Mugdha Pendse has joined the channel

Emile-Daisy (08:09:12): > @Emile-Daisy has joined the channel

Emile-Daisy (08:10:08): > Hello everyone I am Emile Daisy an applicant from Cameroon. Please where do i begin

Chioma Nnadi (08:26:38) (in thread): > Hi@Emile-DaisyYou are welcome

Emile-Daisy (08:27:00) (in thread): > thank you choima

Emile-Daisy (08:27:20) (in thread): > are tasks being assigned or where can I begin

Chioma Nnadi (08:27:47) (in thread): > You can go ahead to check@C. Mirzayi (please do not tag this account)pinned message in this channel. - File (PNG): image.png

Emile-Daisy (08:29:55) (in thread): > thank you@Chioma Nnadilet me go through it

Chioma Nnadi (08:30:41) (in thread): > You are welcome

Ibizugbe Merit (08:35:25) (in thread): > Welcome @Emile-Daisy

Chioma Grace (08:44:52) (in thread): > Welcome@Emile-DaisyCheck out what@Chioma Nnadiposted and ask any question if not clear.

Emile-Daisy (08:46:34) (in thread): > Okay thank you very much@Chioma Grace

Emile-Daisy (08:46:57) (in thread): > Thank you@Ibizugbe Merit

C. Mirzayi (please do not tag this account) (08:59:54) (in thread): > Welcome! Please post any questions on this channel. I look forward to seeing your contributions!

C. Mirzayi (please do not tag this account) (09:01:58) (in thread): > Hi@Patricia Briannalet me check on this and get back to you.

C. Mirzayi (please do not tag this account) (09:08:28) (in thread): > Can you give a bit more detail–can you not access the community-specific questions?

Emile-Daisy (09:20:39) (in thread): > thank you@C. Mirzayi (please do not tag this account)

Levi Waldron (09:24:18): > Sorry for the late notice, but for anyone interested, the monthly Microbiome Virtual International Forum that colleagues and I organize just started 20 minutes ago - great place to attend a microbiome mini-conference for free:https://hopin.com/events/microbiome-vif-n-17-42e1ef53-2805-4a5a-8fa3-c34c794da5ff - Attachment (hopin.com): Microbiome-VIF n.17 - Mar 14 | Hopin > Get tickets to Microbiome-VIF n.17, taking place 03/14/2023 to 03/16/2023. Hopin is your source for engaging events and experiences.

Elisheba Asiimwe Joanita (10:00:31): > @Elisheba Asiimwe Joanita has joined the channel

Levi Waldron (10:16:04): > Hi everyone - we are behind on reviewing second contributions, so I have a request: if you have done second contribution, please wait until it is reviewed before starting on a third contribution. Otherwise, we are worried about having you move ahead too far before getting feedback, which could result in repeating the same mistakes. Instead, I would recommend a couple other things if you have more time you’d like to spend on bugsigdb: > 1. review your own contribution again on anything you’re unsure of, keeping in mind that accuracy is the primary concern and the most important aspect we will be assessing.Some common mistakes are: a) incorrect study design. For example, if participants are selected for an observational study based on the outcome or exposure of interest, then this is a case-control study. If they are selected without regard to the outcome or exposure and then the outcome/exposure are simply identified, then this may be a “cross-sectional observational, not case-control”. Case-control is much more common. b) Entering forConditionsomething that is shared by all participants, rather than what was contrasted between group 1 and group 0. Or, entering forConditionorBody sitean ontology term that is too specific, not specific enough, or entering multiple terms when a single term would be more precise and correct. c) Entering invalid taxa when these could have been mapped to valid terms in the NCBI taxonomy. If your microbial names are showing in orange then check again whether it is possible to match them tohttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi. Not all taxa can be mapped, so if you cannot find a valid match then leave it as-is. Seehttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_IDfor some challenges that have and haven’t been solved in the wiki, and a long video of me trying to solve scientific nomenclature problems. d) basic errors like reversing the “increased” and “decreased” abundance in group 1 signatures, putting the control group as group 1, entering taxa that weren’t identified as significantly different, or not entering taxa that were identified as significantly different. > 2. You could look at athttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_IDto see if there are any taxonomic issues you think you can solve (very challenging!) or at the corresponding page (https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID). I would rather that for now you not yet make corrections in the wiki, but resolving scientific nomenclature would be a very interesting discussion to have here. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID - Attachment (BugSigDB): Category:Pages with missing NCBI ID

Suwaibat Suleiman (11:21:50) (in thread): > How about a study involving two groups conducted on a longitudinal design? Does this make it a time series study or a case-control study? Both groups are different, it’s almost as if the factor that differentiates them is a confounding factor? > (I may not be wording this correctly, I’d appreciate corrections on this)

Levi Waldron (11:22:38) (in thread): > Great question. What is the contrast between group 0 and group 1?

Suwaibat Suleiman (11:23:12) (in thread): > Body mass index

Levi Waldron (11:23:38) (in thread): > But is the contrast a later time vs an earlier time, or is it a contrast between different people at a specific point in time?

Suwaibat Suleiman (11:25:24) (in thread): > It’s a contrast between different people at a specific point in time > Although the study is conducted at different times > A study on exercise’s effects on the gut microbiome between two groups of different BMI’s

Suwaibat Suleiman (11:27:38) (in thread): > Here, it is said that “the study was conducted on a longitudinal design lasting 14weeks”

Levi Waldron (11:31:28) (in thread): > It sounds like a tricky one, but if the contrast is really between different people at a specific point in time, then the relevant contrast is case-control rather than time series/longitudinal. Also if it is high BMI vs low BMI but participants were not selected on the basis of BMI, that might be cross-sectional observational but not case-control.

Suwaibat Suleiman (11:34:49) (in thread): > Ohhhh this makes so much sense > Thank you so much!

Eunice Miriti (12:00:36): > https://bugsigdb.org/Study_540I have a question on lab analysis for this issue. When curating there is WMS and 16S analysis and on this study they conducted a MWAS instead. How do I go about that. - Attachment (BugSigDB): Study 540

Eunice Miriti (12:00:48): > https://bugsigdb.org/Study_540I have a question on lab analysis for this issue. When curating there is WMS and 16S analysis and on this study they conducted a MWAS instead. How do I go about that.

Suwaibat Suleiman (12:28:37) (in thread): > Hello, is this under sequencing types? > Because if it is, (perhaps the mentors will clarify on this) MWAS doesn’t seem to be a sequencing type

Fatima Zohra (12:39:30) (in thread): > WMS (whole metagenome shotgun sequencing) and 16S are the two types of sequencing. MWAS is not a type of sequencing. They do mention what type of sequencing they used. The methods section will have this information.

Eunice Miriti (12:40:49) (in thread): > Thank you for the clarification.

C. Mirzayi (please do not tag this account) (13:22:48) (in thread): > Yeah MWAS is not a sequencing type. It’s a riff on “GWAS” which is an analytic technique. Looking at the supplementary methods for this paper, I think the type of sequencing used should be fairly evident. I would read through that carefully–specifically the paragraph after “Sample collection and DNA extraction.”

Blessing Obafemi (15:20:49) (in thread): > @C. Mirzayi (please do not tag this account)Hi Chloe, I had a similar issue. I have been able to identify group 1 and 0 from BMI and gut diversity but there are no increased or decreased abundances stated. Do I still need to add a signature? If yes, can you give tips on how to go about it?

C. Mirzayi (please do not tag this account) (15:21:23) (in thread): > @Blessing ObafemiCan you link me to the paper so I can investigate?

Blessing Obafemi (15:21:40) (in thread): > Okay

Blessing Obafemi (15:21:55) (in thread): > https://bugsigdb.org/Study_677 - Attachment (BugSigDB): Study 677

C. Mirzayi (please do not tag this account) (15:23:35) (in thread): > Oh it’s there. Hint: I would look for the words “different abundance… between the two groups”:slightly_smiling_face:

Blessing Obafemi (15:24:24) (in thread): > Oh! Thanks. I will do that

Esther (15:53:27) (in thread): > Is it possible to have different signature for Group 1 and group 0 > > For example, > > In an experiment 1 ,I could have signature that shows differentially abundant increase or decrease for group 1 > > And experiment 2,I have a signature that shows differentially abundant increase or decrease for group 0

Levi Waldron (15:57:44) (in thread): > No - signatures must represent differential abundance between group 1 and group 0. Without twogroups there’sno “differential”. While it is of interest biologically sometimes just to describe what microbes are present in participants (ie the first human microbiome project), if you are studying any disease, condition,or exposure,it only makes sense scientifically to compare to a control group.

Esther (15:58:58) (in thread): > Oh ok > > Thanks.

Levi Waldron (16:00:58) (in thread): > By the way@Ameerah Kabir- comparing before to after chemotherapy counts as a longitudinal study.

Esther (16:21:43) (in thread): > Is it possible for a study not to have NCBI just diagram or link that shows that there’s a differential increase or decrease:face_with_peeking_eye:

Ameerah Kabir (16:33:16) (in thread): > Thank youu > > Ameerah Kabir

Patricia Brianna (17:06:32) (in thread): > ooh, i actually can access the questions

Patricia Brianna (17:06:48) (in thread): > lemme send the link

Patricia Brianna (17:11:58) (in thread): > thanks a lot

Desire Oluwarotimi (17:54:50): > Hi@C. Mirzayi (please do not tag this account)my article didn’t specify the alpha diversity for overweight vs normal weight patients. Is it okay to make use of the alpha diversity of obese vs normal weight patients or to leave it blank?

C. Mirzayi (please do not tag this account) (18:03:04) (in thread): > Do not repeat it for something that wasn’t done. Leave it blank.

Desire Oluwarotimi (18:03:50) (in thread): > Okay. Thanks

Esther (18:12:02): > Hi@C. Mirzayi (please do not tag this account)Is it possible for an article to not have taxa that show a significant abundant increase or decrease? but just a diagram that shows a significant increase or decrease

C. Mirzayi (please do not tag this account) (18:12:31) (in thread): > Can you link the article please?

Esther (18:37:00) (in thread): > do you mean the entire link to the study or just the link to the diagram that shows differential abundance?@C. Mirzayi (please do not tag this account)

Esther (18:39:41) (in thread): > ijerph-15-02479.pdf

Esther (19:06:16) (in thread): > https://www.frontiersin.org/articles/10.3389/fcimb.2022.886872/full#f2

C. Mirzayi (please do not tag this account) (19:34:39) (in thread): > There are taxa that are differentially abundant. Consider the figure captions carefully.

Levi Waldron (23:49:31) (in thread): > @Estherit’sbest to keep “threads” on a single topic and post a new question in the main channel.Yes most studies do not list NCBI IDs and just show names of differentially abundant taxa in a figure, table, or the text.

2023-03-15

Cindy Apiyo (02:56:43): > Hi@C. Mirzayi (please do not tag this account)I completed my mini-curation how do I get my contribution url in order for me to submit it?

Busayo Ojo (03:08:49) (in thread): > Hi, use the same URL you used to take the survey.

Cindy Apiyo (03:13:43) (in thread): > I thought so as well but it taking me back to an undone survey!! Is that okay?

Busayo Ojo (03:14:51) (in thread): > Yes, it’s OK!

Cindy Apiyo (03:16:26) (in thread): > Thank you@Busayo Ojo

Esther (03:45:16) (in thread): > Ok. > > Thank you.

Esther (03:45:55) (in thread): > Ok

Patricia Brianna (04:31:51): > anyone that has submitted the application in here? how did you deal with this part of “Description of this contribution for review by the Outreachy coordinators and organizers during intern selection. If you used advanced tools to create this contribution, mention them here.”

Patricia Brianna (04:32:08): > some help

Patricia Brianna (04:32:53): > otherwise personally i learn something new in here every single day that passes

Patricia Brianna (08:38:43): > @Fatima Zohra, kindly requesting for your say on thishttps://bugsigdb.org/Study_739 - Attachment (BugSigDB): Study 739

Patricia Brianna (08:39:18): > @C. Mirzayi (please do not tag this account), how good is this curationhttps://bugsigdb.org/Study_751 - Attachment (BugSigDB): Study 751

Patricia Brianna (08:39:38): > always willing to learn

Fatima Zohra (08:41:07) (in thread): > I’llreview Patricia. Thanks

Rishi Singh (08:46:16): > @Rishi Singh has joined the channel

Suwaibat Suleiman (09:49:00) (in thread): > Oh for the first contribution, I gave a small description of the mini-curation we were asked to do. The topic of the paper and what we were asked to do. > If anyone else has an answer, that would be awesome!

Suwaibat Suleiman (09:50:46): > Hello, about the data transformation techniques, I need a little more clarification:sweat_smile:

Fatima Zohra (09:51:33): > Goodmorning all, we are working on reviewing all the completed curations. As Levi mentioned yesterday please wait until your second contributions are reviewed before starting new papers. If there are any questions feel free to ask. Thank you. (https://community-bioc.slack.com/archives/C04RATV9VCY/p1678803364578459). - Attachment: Attachment > Hi everyone - we are behind on reviewing second contributions, so I have a request: if you have done second contribution, please wait until it is reviewed before starting on a third contribution. Otherwise, we are worried about having you move ahead too far before getting feedback, which could result in repeating the same mistakes. Instead, I would recommend a couple other things if you have more time you’d like to spend on bugsigdb: > 1. review your own contribution again on anything you’re unsure of, keeping in mind that accuracy is the primary concern and the most important aspect we will be assessing. Some common mistakes are: a) incorrect study design. For example, if participants are selected for an observational study based on the outcome or exposure of interest, then this is a case-control study. If they are selected without regard to the outcome or exposure and then the outcome/exposure are simply identified, then this may be a “cross-sectional observational, not case-control”. Case-control is much more common. b) Entering for Condition something that is shared by all participants, rather than what was contrasted between group 1 and group 0. Or, entering for Condition or Body site an ontology term that is too specific, not specific enough, or entering multiple terms when a single term would be more precise and correct. c) Entering invalid taxa when these could have been mapped to valid terms in the NCBI taxonomy. If your microbial names are showing in orange then check again whether it is possible to match them to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi . Not all taxa can be mapped, so if you cannot find a valid match then leave it as-is. See https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID for some challenges that have and haven’t been solved in the wiki, and a long video of me trying to solve scientific nomenclature problems. d) basic errors like reversing the “increased” and “decreased” abundance in group 1 signatures, putting the control group as group 1, entering taxa that weren’t identified as significantly different, or not entering taxa that were identified as significantly different. > 2. You could look at at https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID to see if there are any taxonomic issues you think you can solve (very challenging!) or at the corresponding page (https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID). I would rather that for now you not yet make corrections in the wiki, but resolving scientific nomenclature would be a very interesting discussion to have here.

Suwaibat Suleiman (10:08:26): > @Fatima ZohraIs it possible for a paper to have a non-unique PMID? Whenever I save the PMID of the paper I’m curating, that section gets flagged as “must be unique”

Fatima Zohra (10:08:58) (in thread): > may I know the title of the paper?

Suwaibat Suleiman (10:20:49) (in thread): > Exercise Alters Gut Microbiota Composition and Function in Lean and Obese Humans

Fatima Zohra (10:44:41) (in thread): > This paper is already in the database. Would you please be able to claim another article ?

Suwaibat Suleiman (10:53:23) (in thread): > Oh okay. Can the study I created be deleted?https://bugsigdb.org/Study_633 - Attachment (BugSigDB): Study 633

Grace Wangui (10:56:07): > @Grace Wangui has joined the channel

Fatima Zohra (11:05:49) (in thread): > Yes we are taking care of it no worries. Thank you for sending along the link

Suwaibat Suleiman (11:45:28) (in thread): > Okay:)

Eunice Miriti (12:09:41): > Hello. I have a question, my microbial names are showing in orange after adding the signatures, How do I check possibility of matching them to the NCBI? Also when curating, how do I add the second set of decreasing signatures when the microbial names are not listed on the tables in the study article as well as the supplementary information?

Eunice Miriti (12:09:57): > https://github.com/waldronlab/BugSigDBcuration/issues/50 - Attachment: #50 Metagenome-wide association study of gut microbiome revealed novel aetiology of rheumatoid arthritis in the Japanese population > Initiated at https://bugsigdb.org/Study_540. Note - there are no guarantees that information already entered here (such as study design) is correct, so please proceed as you would for a new study with no information pre-entered.

Suwaibat Suleiman (12:16:29) (in thread): > Hello, for the first question, did you input the names by typing the first letter then looking through the list that pops up?

Eunice Miriti (12:17:35) (in thread): > Yes, that is what I did.

Suwaibat Suleiman (12:35:29) (in thread): > Oh then I guess I don’t have an answer > Perhaps the mentors will help out

Levi Waldron (13:13:04) (in thread): > You should also search for names onhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi, and enter the integer ID if you can find it there. I’ve made some tips on this athttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID

Eunice Miriti (13:59:43) (in thread): > Thank you.

idubor itohan (18:41:02): > @idubor itohan has joined the channel

Patricia Brianna (21:28:59) (in thread): > thanks a lot, can i record a contribution that is under review

2023-03-16

Atrayee Samanta (05:29:00): > hello@Levi Waldron, I was going through the taxonomic issues in the pages with missing NCBI IDs, and I believe I was able to solve one (from this page:https://bugsigdb.org/Study_279/Experiment_2/Signature_1); the study (https://bugsigdb.org/Study_279) has a doi, and the sources to the experiment signature (the text, tables s2, s3 and figure 6) all show that the required NCBI is of ‘candida’, whose taxonomy is available in the NCBI (the NCBI mentioned in the study is ’g__candida’, which is not present in the source). > > Also I haven’t made any edits to the study, it would be great if you could tell me if I am correct! - Attachment (BugSigDB): Study 279/Experiment 2/Signature 1 - Attachment (BugSigDB): Study 279

Levi Waldron (05:31:12) (in thread): > What numeric NCBI ID do you think it is?

Atrayee Samanta (05:32:32) (in thread): > I think it should be 5475

Levi Waldron (05:33:30) (in thread): > Nice work, I think you’re right!:100:would you go ahead and make the edit?

Atrayee Samanta (05:34:01) (in thread): > Yes sure! I’ll make the edit now

Levi Waldron (05:39:00) (in thread): > This actually points to another probable error in this curation - the abstract of the study says “Illumina MiSeq 16S rRNA gene (V4) and internal transcribed spacer 2 (ITS2) sequencing were used” but eukaryotes do not have a 16S rRNA gene - it would have been the ITS sequencing, not the 16S sequencing, that identified the eukaryotes reported in this study.

Levi Waldron (05:45:34) (in thread): > I’ve just added ITS / ITS2 to the list of allowed values for “sequencing type”. If you’d like to correct more of the fungal genera on this page, and the sequencing type, please go ahead!

Atrayee Samanta (05:51:35) (in thread): > Yes, thank you, I’m trying to correct other fungal genera too! Also, how I should identify that a probable error was the sequencing type? Should the error in the fungus indicate that I should look for other issues (like sequencing type in this case) in the curation?

Levi Waldron (05:56:41) (in thread): > I only knew that was a probably error because I knew that sequencing of the 16s rRNA genecan’tdetect fungi, whose homologous gene is called 18S. The 18S gene is sometimes used to identify fungi, but conversely,sequencing the 18S gene or these internal transcribed spacerswon’tidentify prokaryotes.

Atrayee Samanta (05:58:18) (in thread): > Oh, thank you, I find this very interesting!

Levi Waldron (05:58:44) (in thread): > Me too!

Levi Waldron (06:27:55) (in thread): > Dear@Suwaibat Suleiman- I’m sorry you spent your time working on a publication already in the database, but your effort wasn’t wasted! By comparing your entries withhttps://bugsigdb.org/Study_534I identified a couple errors in the original curation: their Experiment 2 incorrectly referred to figure 2d instead of 2e, and had three genera in one signature instead of two each in signatures of increase and decrease as you correctly had. I also saw a couple errors in your curation that I’ll point out to help with your next and “official” second contribution: > 1. the body site where microbiota were sampled was Feces, not Feces and Blood (Blood was used for other purposes, not measuring the microbiota reported), > 2. you should have created a second experiment for the 3rd and 4th signatures (like study 534 did) since they were collected under different conditions (once immediately after the exercise program, the other after a 6-week washout). > 3. you correctly listed the antibiotics exclusion criteria, but then should not list antibiotics again under “Matched on” or “Confounders controlled for” unless antibiotics exposure was used again in some way in the analysis beyond this general exclusion criteria. You are correct to list “sedentary lifestyle” as something participants were matched on, but we usually use “Matched on” to refer to things that have variability within cases and controls but that variability is matched, as opposed to inclusion criteria that apply to everyone in the study. For example, if the varying degrees of sedentary behavior allowed within the exclusion criteria were balanced between the lean and obese participants. > 4. finally, “body mass index” is not a confounder controlled for: body mass index is the exposure of interest, not a confounder - that is getting into some real Epidemiology! > I am going to delete Study 633 now, but for anyone interested,hereis the original study, and it will still be possible to view the earlier state of these pages in the wiki history.

Patricia Brianna (07:14:29): > hello friends should we wait till the review is done to make more curations

Patricia Brianna (07:16:54): > @Levi Waldron, any say on thishttps://bugsigdb.org/Study_739 - Attachment (BugSigDB): Study 739

Patricia Brianna (07:17:20): > and this toohttps://bugsigdb.org/Study_751 - Attachment (BugSigDB): Study 751

Patricia Brianna (07:17:45): > what is and not right, thanks

Levi Waldron (07:19:00): > I did a quick unofficial review of that study becauseit’snot being scored, but for all “official” second contributions we have a little longer team review process to go through.

Busayo Ojo (07:31:12) (in thread): > Yes plz, you can check the pinned message from Levi for more information.

C. Mirzayi (please do not tag this account) (08:56:50): > Hi everyone our team meeting and office hours will be at 10 AM EDT today (in 1 hour).

khadijah (10:04:44) (in thread): > Link please

Busayo Ojo (10:05:29) (in thread): > https://us02web.zoom.us/j/2737200499

C. Mirzayi (please do not tag this account) (10:10:49): > https://us02web.zoom.us/j/2737200499link to our meeting + office hours (happening now!)

Aguobi Amara (10:44:00) (in thread): > Thank you > It was nice joining the meeting

Aguobi Amara (10:44:49) (in thread): > Alright

Crestable Ayesiga (12:09:23): > @Crestable Ayesiga has joined the channel

Crestable Ayesiga (12:32:15): > Hello@C. Mirzayi (please do not tag this account),@Fatima Zohraand every one here, my name is Crestable Ayesiga. I am an outreachy applicant interested in the Microbiome curation study project. I would like to know if I still have time to start my contribution and please some guidance on what steps to follow in doing this. I am glad to be here. Thank you very much.

Aiysha shahid (12:36:39) (in thread): > hlo, welcome crestable yes u still have time to do the contribution if are willing to do.For the first contribution you can read the pinned comment by@C. Mirzayi (please do not tag this account)she has given the whole information and guidance for the contribution. If u need anykind of help you can post it here mentors and other contributor’s would love to help u out.

Ibizugbe Merit (12:42:56) (in thread): > Welcome@Crestable Ayesiga:hugging_face:

Aiysha shahid (12:45:49) (in thread): > if u are unable to find that pinned msg u can check it on github:https://github.com/waldronlab/BugSigDBcuration/issues/1#issue-1607892490

Crestable Ayesiga (12:53:46) (in thread): > Oh thank you very much@Aiysha shahidand@Ibizugbe Merit

Ibizugbe Merit (12:58:51) (in thread): > You’rewelcome@Crestable Ayesiga - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Suwaibat Suleiman (14:38:13) (in thread): > @Levi WaldronI’m so glad you pointed these out! Thank you so much! I will definitely keep this in mind for my forthcoming contributions. Thank you!

Queen Anthony (16:44:03): > @Queen Anthony has joined the channel

Queen Anthony (17:00:01): > Hello@C. Mirzayi (please do not tag this account),@Fatima Zohraand everyone, I’m Queen Anthony an applicant of outreachy from Nigeria. I am happy to be part of this community and I would love to contribute to the Microbiome curation study project. I don’t know if I have missed alot already, please I would appreciate any tip on how to get started. Thank you

Ibizugbe Merit (17:00:27) (in thread): > You’rewelcome@Queen Anthony

Beekaz (17:06:54): > @Beekaz has joined the channel

Ibizugbe Merit (17:12:42) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839 - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Queen Anthony (17:13:49) (in thread): > Thanks alot I really appreciate

Ibizugbe Merit (17:14:35) (in thread): > You’rewelcome…I’mglad I could help.

Beekaz (17:16:16): > Hello@C. Mirzayi (please do not tag this account),@Fatima Zohraand Everyone, I’m Beekaz an Outreachy applicant, and I’m looking forward to learn, explore, as well as contribute to BugSigDB and I wish to participate in the MIcrobiome study curation project. I hope its not too late to get started here.

Ibizugbe Merit (17:28:48) (in thread): > Hi@Beekaz,you’rewelcome here…It’s actually not too late to get work done..You should go through@C. Mirzayi (please do not tag this account)pinned message on the#bugsigdbchannel to get started right away

C. Mirzayi (please do not tag this account) (19:25:38) (in thread): > Not too late at all. Welcome!

C. Mirzayi (please do not tag this account) (19:25:52) (in thread): > Welcome!

Natalie Ohaneje (20:00:20): > @Natalie Ohaneje has joined the channel

Natalie Ohaneje (20:05:26): > Hi everyone! I am Natalie, an outreachy applicant and I am excited to work on this project and looking forward to learn and explore more about BugSigDB.

Esther (20:25:09): > Hello, > > Is it compulsory to add 2 or more experiment to the study? > Or I could add more signatures to experiment 1 instead of creating more experiments?

2023-03-17

Ibizugbe Merit (01:43:14) (in thread): > Welcome@Natalie Ohaneje

Aguobi Amara (03:34:37) (in thread): > Welcome@Natalie Ohaneje

Suwaibat Suleiman (03:43:00) (in thread): > I don’t think it’s compulsory. It depends on the study. Experiments are dependent on the conditions they’re done under

Suwaibat Suleiman (03:43:24) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1678962475789159?thread_ts=1678889306.099349&cid=C04RATV9VCY - Attachment: Attachment > Dear @Suwaibat Suleiman - I’m sorry you spent your time working on a publication already in the database, but your effort wasn’t wasted! By comparing your entries with https://bugsigdb.org/Study_534 I identified a couple errors in the original curation: their Experiment 2 incorrectly referred to figure 2d instead of 2e, and had three genera in one signature instead of two each in signatures of increase and decrease as you correctly had. I also saw a couple errors in your curation that I’ll point out to help with your next and “official” second contribution: > 1. the body site where microbiota were sampled was Feces, not Feces and Blood (Blood was used for other purposes, not measuring the microbiota reported), > 2. you should have created a second experiment for the 3rd and 4th signatures (like study 534 did) since they were collected under different conditions (once immediately after the exercise program, the other after a 6-week washout). > 3. you correctly listed the antibiotics exclusion criteria, but then should not list antibiotics again under “Matched on” or “Confounders controlled for” unless antibiotics exposure was used again in some way in the analysis beyond this general exclusion criteria. You are correct to list “sedentary lifestyle” as something participants were matched on, but we usually use “Matched on” to refer to things that have variability within cases and controls but that variability is matched, as opposed to inclusion criteria that apply to everyone in the study. For example, if the varying degrees of sedentary behavior allowed within the exclusion criteria were balanced between the lean and obese participants. > 4. finally, “body mass index” is not a confounder controlled for: body mass index is the exposure of interest, not a confounder - that is getting into some real Epidemiology! > I am going to delete Study 633 now, but for anyone interested, here is the original study, and it will still be possible to view the earlier state of these pages in the wiki history.

Esther (03:56:16) (in thread): > Thank you@Suwaibat Suleiman

Suwaibat Suleiman (04:04:43) (in thread): > Happy to help:)

Cindy Apiyo (04:45:32): > @Levi Waldron@C. Mirzayi (please do not tag this account)I applied for BugSigDB account days ago but I am yet to receive a mail with the details of my password. Kindly assist

Ibizugbe Merit (05:04:23) (in thread): > Hello@Cindy Apiyotry checking your spam folder just incase

Cindy Apiyo (05:05:02) (in thread): > I checked.. it’s not there

Ibizugbe Merit (05:11:03) (in thread): > Okay..let’swait for our mentors to clarify then

Levi Waldron (06:56:50) (in thread): > Dear Cindy, apologies for the delay, I just approved your account. Welcome!

Levi Waldron (07:00:04) (in thread): > You are welcome@Suwaibat Suleiman! And thank you for going on to share your knowledge with others.

Levi Waldron (07:00:42) (in thread): > Welcome,@Natalie Ohaneje!

Cindy Apiyo (07:17:16) (in thread): > Thankyou@Levi WaldronI appreciate

Patricia Brianna (10:00:20) (in thread): > thanks

Suwaibat Suleiman (10:29:02) (in thread): > :D glad to be of help!

Natalie Ohaneje (11:13:30) (in thread): > thank you all

Aiysha shahid (13:20:20): > hlo@Levi Waldroni have applied for an bugsigd account a few days ago but i didn’t receive an email i have checked my spam folder but it’s empty.Kindly help. Thank you.

Levi Waldron (14:24:46) (in thread): > Hmm, all new accounts have been approved- do you see the username you requested under Help - ListUsers? Have you tried logging in with Google?https://bugsigdb.org/Special:ListUsers - Attachment (BugSigDB): Special:ListUsers

Aiysha shahid (15:04:54) (in thread): > yes, i have tried logging through but it showing this message: The supplied credentials are not associated with any user on this wiki. YES,the username is present in this list. Should i use the forgot password option?

Levi Waldron (16:46:07) (in thread): > Yes, and if you tell me which username I can post onit’suser page so the system sends an email to the associated address. It sounds like it has a different email address associated with it.

Levi Waldron (16:48:11) (in thread): > You should have just received an email about the note I just left on your talk pagehttps://bugsigdb.org/User_talk:Aiysha_shahid - Attachment (BugSigDB): User talk:Aiysha shahid

2023-03-18

Hannah Honda (02:37:16): > Hi@C. Mirzayi (please do not tag this account),@Fatima Zohra,@Levi Waldron— I’m having some trouble logging my curation for #12 on Predominance of Escherichia-Shigella in TBM patients. > The main goal of the study seems to be to observe and test hypothesis mechanisms of gut dysbiosis in TBM patients which possibly lead to higher concentrations of plasma TNF-a that affect BBB permeability. But logging the curation is confusing me because there seems to be two portions to the study — the human participants and then the mice experiments.

Hannah Honda (02:50:43) (in thread): > Sorry, this is a big long. The first half of the paper looks at stool samples for gut diversity in 3 groups (Healthy controls, PTB, and TBM groups) - I don’t know how to log 3 groups (or add Group 2) and then follows that up with a plasma analysis for a different sample size [the stool samples were from 31 ppl ;9 HC, 13 PTB, 9 TBM], but the plasma samples were 10 HC, 10 PTB, and 14 TBM - they don’t specify if they were the same participants.

Aiysha shahid (02:57:46) (in thread): > sorry but i didn’t receive any email regarding could please delete this account, so that i can request a new account with another email.id.

Hannah Honda (02:58:09) (in thread): > The study observes higher levels of TNF-a in TBM patients, and the second half of the paper looks whether this is observable in mice — they orally administer e coli in mice to observe increase of escherichia-shigella in gut of mice, then proceed to inject m. tuberculosis in the mice to see if there there was a increase in BBB permeability

Hannah Honda (02:59:17) (in thread): > I guess my question is how do I log a curation for this study, since there seems to be multiple mini-studies of sorts within the one study? — sorry for the long posts. Any insight would be greatly appreciated.

Aiysha shahid (03:15:00) (in thread): > HI@Hannah Hondaas you said there are 3 groups you can add 2exp for stool samples in first you can HC and PTB and for the signature u check the abudance of increasead increase and decreased. And for 2exp you can HC and TBM and you can repeat the above processs and so on. And according to me, the result comparison must be given in the research paper. Hope this helps!! and if i am wrong sorry in advance the mentors will surely reply..

Hannah Honda (03:18:35) (in thread): > @Aiysha shahid, thank you for the advice. I will try that with the stools and see if I can do that for the blood and then the mice. I guess I was worried that it would all be really cluttered with so many variables

Chioma Grace (03:20:29) (in thread): > Hello Hannah, looking at the title of the study which is focused on TBM patients and if group 2 can’t be created…..I think the main focus will be between healthy control and TBM patients. > And possibly create another experiment for HC and PTB…..as the case may be. > This is my thought. Though we can wait for the mentors to advise better.

Aiysha shahid (03:21:51) (in thread): > Yeah i can understand. No worries, Good luck:heart:

Hannah Honda (03:36:12) (in thread): > Hi@Aiysha shahid,@Chioma Gracethank you for the responses! I was looking at the past posts on this community, and I think I have some direction. Taking yalls advice, I think I’ll split up the study into different experiments — 2 for HC+PTB, HC+TBM:heart:Not too sure about the second portion using mice — The oral administration of CEC can be logged I think since it affects gut microbiome in mice, but I guess I’m still confused with the last one about m.tuberculosis injection to observe BBB permeability - it looks at the pathway for TBM patients from their gut microbiome to inflammation in the brain, but I’m not sure whether that should be logged or not

Atrayee Samanta (04:44:44) (in thread): > I think what you should consider most is if the microbes have differentially increased/decreased in the group 1 species (here is is the mice). If so, then you should include that in your experiment signature!

Ameerah Kabir (08:11:28): > Hi everyone, I hope, we are doing great?

Aiysha shahid (08:36:00) (in thread): > hlooooo:raised_hands:

Kelvin Joseph (08:54:11): > Hello mentors@Levi Waldron@C. Mirzayi (please do not tag this account)@Fatima Zohraand the bugsigdb community at large hope for the Outreachy applicants curations are going on well still patiently waiting for the reviews

Ibizugbe Merit (09:04:03) (in thread): > Hello:blush:

Atrayee Samanta (09:12:54) (in thread): > helloo:relaxed:

Beekaz (09:55:18) (in thread): > thanks alot

Levi Waldron (10:01:59): > You are all doing great!It’sbeen such an amazing responsewe’vehad to reorganize ourselves and make more time, butwe’llbe posting a lot of reviews in the coming week.

Levi Waldron (10:17:15) (in thread): > Really tricky one! (https://github.com/waldronlab/BugSigDBCuration/issues/12) I would say just curate the human part of the study, and make a note on your GitHub issue that this is what you did, because the mouse part would require a different study because the study design is different. - Attachment: #12 Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis > Condition: Meningitis
> URL: https://journals.asm.org/doi/10.1128/spectrum.01926-22

Aiysha shahid (10:58:18) (in thread): > hi@Levi Waldronsorry to disturb, i have requeted another account with another email.id could please check it. Thank you.

Levi Waldron (12:17:55) (in thread): > Approved, and blocked your original account to avoid confusion. Hopefully you got the confirmation email?

Suhana (12:25:46): > @Suhana has joined the channel

Suhana (12:26:55): > hello@C. Mirzayi (please do not tag this account)and@Fatima ZohraI joined slack now. I want to start contributing

Busayo Ojo (12:28:43) (in thread): > Welcome Suhana, kindly go through this link. It contains all the information you will need.https://community-bioc.slack.com/archives/C04RATV9VCY/p1678118100244839 - Attachment: Attachment > Welcome, Outreachy applicants! :tada: My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Fatima on the BugSigDB project for some time and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on out Github repo: https://github.com/waldronlab/BugSigDBcuration/issues/1 > > Also, between now and Monday, April 3, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participant or observe these meetings as well as ask questions. These meetings are scheduled for: > • Thursday March 9, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 16, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 23, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • Thursday March 30, 10-11 AM ET (https://us02web.zoom.us/j/2737200499) > • We are happy to meet with you on a different day or time upon request

Aiysha shahid (13:05:39) (in thread): > nope i still didn’t get any confirmation email i have checked my spam folder and also tried logging through my google account still failed to login.

Aiysha shahid (13:13:54) (in thread): > what should i do. kindly guide@Levi Waldron

Levi Waldron (14:09:34) (in thread): > Your user name is “Aiysha shahid” and your email isaiyhashahid79@gmail.com, and your account is activated - perhaps try the lost password option?

Ibizugbe Merit (14:52:38) (in thread): > You’rewelcome@Suhana:hugging_face:

Aiysha shahid (15:04:33) (in thread): > hi could please check and block my pervious 2 id’s as i request an new id from a newly generate email id. hopefully this woud works for me.:smiling_face_with_tear:And sorry for troubling you so much.

Levi Waldron (16:09:27) (in thread): > This time I tried something different-created your account with Google, so you can only login using the Google button.Will you try that?

Patricia Brianna (16:30:37) (in thread): > can we make edits during this period

Aguobi Amara (19:03:05) (in thread): > Wow nice to hear

Aguobi Amara (19:03:38) (in thread): > Welcome@Suhana

Aguobi Amara (19:04:16) (in thread): > Hello:wave:

Atrayee Samanta (23:03:36) (in thread): > Welcome@Suhana!

2023-03-19

Aiysha shahid (02:27:10) (in thread): > Thanks at last it’s done:heart::raised_hands:

Atrayee Samanta (03:33:03): > hello@Levi Waldron, I was going through another taxonomic issue (on this page:https://bugsigdb.org/Study_268/Experiment_1/Signature_1) and the microbe with the missing NCBI id as according to the source (Figure 4) wasLeptotrichia amnionii, and I found a species on the NCBI taxonomy browser calledSneathia vaginalis(Taxonomy ID: 187101), whose heterotypic synonym isLeptotrichia amnionii; could this be useful information? - Attachment (BugSigDB): Study 268/Experiment 1/Signature 1 - File (PNG): image.png - File (PNG): image.png

Levi Waldron (06:19:04) (in thread): > Yes, you solved it!:star2:will you go ahead and make the edit?

Atrayee Samanta (06:26:17) (in thread): > Yes, sure I’m doing it right now!

Levi Waldron (07:42:13) (in thread): > You could also search for the same name in the wiki to see if it can be corrected anywhere else…

Levi Waldron (07:43:06) (in thread): > Hooray!:tada:

Levi Waldron (07:44:22) (in thread): > @Patricia Briannayou can make edits to your own contributions all you want, but for other parts of the wiki my request right now is that you post here first.

Aiysha shahid (07:46:50): > Hello@Levi WaldronI was going through this studyhttps://bugsigdb.org/Study_701in this the taxonomy id where missing according to the source( Fig 4 and 5) shows the abundance of microbe in CD and NON IBD ’’As shown in Fig.5a and supplementary Table 1, comparison of the microbial changes between CD patients and non-IBD controls showed a significant increase in the abundance of 15 genera and a significant decrease in 40 genera in CD patients. These included an increase in the abundance of the generaEscherichia,Ruminococcus(R. gnavus),Cetobacterium,ActinobacillusandEnterococcus” i have found the above microbe taxonomy id on NCBI browser. And also think there will be intotal 3exp 1st is listed and rest 2exp will be UC and NON IBD && UC and CD. So, could you check that if I am correct.! - Attachment (BugSigDB): Study 701 - Attachment (SpringerLink): Analysis of endoscopic brush samples identified mucosa-associated dysbiosis in inflammatory bowel disease > Journal of Gastroenterology - The mucosa-associated gut microbiota directly modulates epithelial and mucosal function. In this study, we investigated the mucosa-associated microbial community in…

Atrayee Samanta (08:07:23) (in thread): > Oh yes, I will definitely do that

Reece11 (12:48:07): > @Reece11 has joined the channel

Aiysha shahid (13:04:08): > Hllo@Levi Waldroni was going through missing NCBI id page(https://bugsigdb.org/Study_186) in this study according to the curator (FIG 2) has abundance of microbe but the microbe list on research paper and on the curated study are different (“Twenty bacteria (p<0.05, FC>1.5) were altered significantly in cigarette smoke-exposed mice (figure 2C). Among these,E. lentaandStaphylococcus capitiswere enriched while gut-beneficial bacteria includingLactobacillus reuteri,Parabacteroides distasonisandBacteroides doreiwere depleted with cigarette smoke exposure.”). Should i proceed further and edit the page? Kindly guide. - Attachment (BugSigDB): Study 186

Patricia Brianna (14:14:38) (in thread): > ok, thanks@Levi Waldron

Levi Waldron (15:15:41) (in thread): > Great find,@Aiysha shahid

Levi Waldron (15:18:43) (in thread): > 1. yes there are a number of missing items from Figure 5 (I wouldn’t use Figure 4 at all). Supplemental tables 1-3 have many more microbes I guess because they haven’t applied an LDA effect size cutoff, but I would stick to Figure 5 because the tables would be a lot more to enter and many probably false positives (although neither choice would be wrong here). > 2. Yes you are right there are 3 total experiments!

Levi Waldron (15:18:55) (in thread): > Please go ahead and make these changes if you’d like!

Levi Waldron (15:20:09) (in thread): > (and also mark it as complete if you do)

Levi Waldron (15:21:46) (in thread): > Perhaps hold off on this one, it is an Outreachy applicant:slightly_smiling_face:

2023-03-20

khadijah (02:21:54): > Hello@Fatima Zohrawhen do we get reviews from our previous task

Fatima Zohra (02:29:29) (in thread): > Hi we are working our best to get contributions reviewed in order of review requests. You’ll be getting feedback by the end of this week/next week. Thank you for being patient.

Aiysha shahid (02:39:49) (in thread): > okay thank you:raised_hands:

Aiysha shahid (02:40:20) (in thread): > yup i was thinking the same. Thanks for the guidance.

Harrydas Ombati (03:40:16): > Hello@Fatima Zohracould you please help review thishttps://bugsigdb.org/Study_732 - Attachment (BugSigDB): Study 732

Suwaibat Suleiman (04:20:58): > Hello@Levi Waldron@Fatima Zohrathe study I’m working on,https://bugsigdb.org/Study_633“Fecal metabolomic signatures in colorectal adenoma patients are associated with gut microbiota and early events of colorectal cancer pathogenesis”, provides a supplementary table which includes arcsine square root transformed data but the differential abundance does not seem clear to me; although, the study references another paper “moreover for each sample characterised herein, a paired gut microbiome profile was available as part of a data set that was reported previously…” which has clearer differential abundance data but the current study’s sample size is a subset of the previous study’s. Can you pleasee clarify me on how to report the microbial signatures?? - Attachment (BugSigDB): Study 633

Suwaibat Suleiman (04:35:18) (in thread): > I began using the differential abundance data in the previous study for the first signature

Levi Waldron (04:43:22) (in thread): > I think you are right, I don’t see any reporting of differential taxonomic abundance in this paper - sorry for my mistake in assigning it! The correct thing to do would be to create a new bugsigdb study for that previous publication, then we can move your existing work on experiments and signatures to that study.

Levi Waldron (04:43:52) (in thread): > (and update the github issue to point to the correct publication and bugsigdb study)

Levi Waldron (04:45:20) (in thread): > But the parent study seems to be already in the database,https://bugsigdb.org/Study_646 - Attachment (BugSigDB): Study 646

Suwaibat Suleiman (05:00:17) (in thread): > Ohhh I understand > Did you look at the supplementary table? It was meant to be Table S2 not S1:sweat_smile:

Levi Waldron (05:11:53) (in thread): > Yes, like you said it provides taxonomic relative abundance data but not results of differential abundance analysis

Suwaibat Suleiman (05:13:32) (in thread): > Okay thank you!

Levi Waldron (05:15:21) (in thread): > Perhaps you could take a look at study 646 for any discrepancies with what you did, as a review of that entry. I just changed the study design in 646 that was incorrectly entered as “cross-sectional observational, not case-control” to “case-control”

Suwaibat Suleiman (05:17:50) (in thread): > Okay I will. Thank you so much!

Levi Waldron (05:20:16) (in thread): > I see that 646 got the condition right (ademona is correct, not colorectal cancer) but got the statistical test wrong (should be LEfSe, not linear regression)…

Levi Waldron (05:23:59) (in thread): > (actually maybe it is linear regression - the Figure 2 looks exactly like LEfSe output, but their methods say linear regression. I suspect they actually used LEfSe to produce Figure 2, but we have to go with what they state were the methods:sweat_smile:)

Suwaibat Suleiman (05:29:05) (in thread): > I wonder they’d do that:sweat_smile:

Suwaibat Suleiman (05:40:29) (in thread): > It also looks like multiple testing was done, can I go ahead and add that?

Levi Waldron (05:41:02) (in thread): > Do you mean correction for multiple hypothesis testing?

Suwaibat Suleiman (05:41:13) (in thread): > Yes:sweat_smile:

Levi Waldron (05:41:25) (in thread): > Yes, go ahead

Suwaibat Suleiman (05:41:42) (in thread): > Okay

Aiysha shahid (07:36:12) (in thread): > hlo@Levi Waldroni found one more thing that in first experiment the sample size of CD patient is 26 in research paper “Patients and sample collectionTwenty-six patients with CD, 43 patients with UC and 14 non-IBD participants were enrolled.” but in the curation it’s 23 can you check and tell me should i edit that?

Levi Waldron (08:00:39) (in thread): > You’re right about sample size, and I also noticed a couple more errors: the study design is incorrect (should be case-control), and the Condition is incorrect (should only be the single ontology term that corresponds to group 1 in the contrast being made in that experiment; in Experiment 1 that is Crohn’s Disease)

Aiysha shahid (09:29:13) (in thread): > Yh i also notice “The result was further analyzed statistically using Welch’sttest .Benjamini–Hochberg-correctedPvalues (<0.05) were used to determine the statistical significance between the groups” does this mean’s it’s a MHT correct value? because according to in our first contribution to identify MHT if there was Benjamini–Hochberg in research paper it’s means it’s a MHT. I m correct?

C. Mirzayi (please do not tag this account) (09:34:28): > Good morning everyone. I hope you are all having a nice start to your week. We are working to review your contributions and get you feedback this week. Thanks everyone who has contributed so far.

Levi Waldron (10:05:25) (in thread): > Yes, Benjamini-Hochberg is a method to control false discovery rate in multiple hypothesis testing.

Kelvin Joseph (11:15:19) (in thread): > Great can’t wait to work on the projects. Also our final applications are due on 1st april so will it be possible to add the contributions before then. > Can I help in reviewing the works of the applicants?

C. Mirzayi (please do not tag this account) (11:20:30) (in thread): > You should be able to add your contributions now. You can note that you completed the curation form as well as a link to the github issue for the 2nd curation you completed (if applicable). We have documentation of what you’ve completed as well.

Kelvin Joseph (11:21:14) (in thread): > Thanks a lot for the good work

Aiysha shahid (13:38:23) (in thread): > “One-dimensional statistical analysis included Student’s t-test and multiple analysis of variation” Does this also means there is a MHT is the research?

Levi Waldron (14:16:37) (in thread): > That sentencedoesn’tprovide any clue abou whether a MHT correction was applied or not. Note that nearly ALL microbiome differential abundance analysis involves multiple hypothesis testing, but this field is about whether pvalues were correct for multiple hypothesis testing or not.

Patricia Brianna (16:52:52): > thanks@C. Mirzayi (please do not tag this account)and the team, can we still curate in this period ?

sophy (22:31:05) (in thread): > @C. Mirzayi (please do not tag this account)I have included the missing signatures forhttps://bugsigdb.org/Study_738as mentioned. Please, let me know if there are further changes to make. Thanks for the review. - Attachment (BugSigDB): Study 738

2023-03-21

Aguobi Amara (02:03:42) (in thread): > Thank you so much

Aiysha shahid (03:14:50) (in thread): > Ok thank you, if in a research paper there are 3statical analysis “t test for alpha diversity and Using LEfSe software, a nonparametric factorial Kruskal Wallis (KW) sum-rank test was conducted to identify species with distinct abundance differences” then we have to mentioned all 3 or only Lefse because LDA score is given.

Aiysha shahid (03:39:29) (in thread): > I have a doubt according to the research paper “The microbial changes in UC patients compared to non-IBD controls were characterized by a significant increase in eight genera and a significant decrease in 42 genera (Fig. 5b; supplementary Table 2). These included an increase in the abundance of the genera Blautia, Veillonella, Bifidobacterium, Citrobacter and Lactobacillus, and a decrease of the genera Prevotella, Coprococcus, Pseudomonas, and Alistipes.” but if are comapring UC WITH IBD. We have show the abundance of microbe in IBD, which is Pseudomonas, and Alistipes etc. Because in 1st exp we compare IBD WITH CD. SO in 2nd exp we will UC with IBD. AND in 3rd CD WITH UC. KINDLY GUIDE IF I AM CORRECT SHOULD I MAKE A CURATION IN THE STUDY.?

Levi Waldron (03:43:12) (in thread): > To answer the first question above,you would only enter the statistical method used to generate the taxonomic signature you entered. They say they used t test for diversity,not microbes. And the mention of kw test is just explaining LEfSe

Levi Waldron (03:44:56) (in thread): > AndI’mconfused by your second question because CD and UC are two subtypes of IBD

Levi Waldron (03:45:40) (in thread): > Did you confuse IBD with non-IBD?

Levi Waldron (03:46:30) (in thread): > Hi Patricia,I gave some tips above about things you can still do while waiting for your review

Aiysha shahid (04:03:09) (in thread): > Yes, in the research paper it’s given 3exp 1st CD and non IBD, 2nd UC and non IBD and 3rd UC and CD so we have to all the 3exp na?

Levi Waldron (04:05:01) (in thread): > yes those are the 3 experiments.

Levi Waldron (04:14:07) (in thread): > In particular you can review other unreviewed studies in the database and talk about any potential issues you find here - there are a lot of unreviewed studies andit’sa high priority to review them all.

Aiysha shahid (04:44:56) (in thread): > So, for 2nd exp group 0 UC and group1 will be non IBD?

Suhana (06:12:58): > @Suhana has left the channel

Fatima Zohra (06:54:00) (in thread): > @Aiysha shahidThank you for completing this paper I started. For the comparison groups and total number of experiments, we need to make sure they match the figure(s) we are curating. So for the second experiment, since you are curating figure 5B, the contrast would be UC vs. Control. By control they are talking about Non-IBD controls (mentioned in the result section)

Aiysha shahid (08:53:50) (in thread): > Thank you for your feedback, so if we keep NON IBD in group1 what will be the condition and definition?

Kelvin Joseph (09:09:36) (in thread): > Hello for me to review other works do I have to wait till I’m assigned the task or??

Fatima Zohra (09:09:44) (in thread): > Non-IBD is the control/unexposed group and controls should always be group 0. The case here is UC.

Aiysha shahid (09:12:45) (in thread): > okay thank you, i will be edit it.:heart::raised_hands:

Queen Anthony (10:44:05): > Please mentors@Levi Waldron@C. Mirzayi (please do not tag this account)I commented on the issue #48. I want to work on it. Please assign me

Aiysha shahid (12:43:45): > Hello,@Levi WaldronI was going through this studyhttps://bugsigdb.org/Study_712in this the taxonomy id was missing according to the source( Text, Fig 3) but in the research paper there is no Fig 3 and according to research paper* “(Figure 1D and Supplementary Table 1, available on the Arthritis & Rheumatology web site at http://onlinelibrary.wiley.com/doi/10.1002/art.40485/abstract). Certain species were significantly more abundant in patients with RA, including those belonging to the genera Actinomyces , Cryptobacterium (OR 36), Dialister (OR 4), Desulfovibrio (O, Fretibacterium (ORS 9-12), Leptotrichia (ORs 7-26), Prevotella (ORS 0.04-6), Selenomonas (ORS 0-7), Treponema (ORs 0–7), and Veillonellaceae [G1] (ORS 0-6).*In contrast, several species belonging to the genera Aggregatibacter, Gemella, Granulicatella, Haemophilus, Neisseria, and Streptococci not only demonstrated lower abundances but were also less frequently detected in RA.” So could please check if i am correct! - Attachment (BugSigDB): Study 712

Aiysha shahid (13:09:41) (in thread): > https://bugsigdb.org/Study_701. I have edited it. Kindly review it and give your valuable feedback. Thank you!!! - Attachment (BugSigDB): Study 701

Levi Waldron (16:33:26) (in thread): > I haven’t had a chance to read the full paper, but the set up of your experiments looks great! What does matching on maternal age mean? Did they really do that in the study?

2023-03-22

Rukky (02:46:10): > Hello@C. Mirzayi (please do not tag this account)@Fatima Zohrai recently commented on issue #48 as the others have already been assigned to other people. Please I’ll like to work on this. I’ll appreciate it if this is assigned to me. I look forward to your reply. > Thank you.

Aguobi Amara (03:25:23): > Hello everyone > I hope you all are doing great

Aiysha shahid (03:28:49) (in thread): > hlooo

Kelvin Joseph (05:51:39): > Who has started filling their Outreachy final applications?

Patricia Brianna (07:45:42): > @Kelvin Josephany qns

Patricia Brianna (07:45:52): > hello good people

Patricia Brianna (07:46:31): > cant wait for@C. Mirzayi (please do not tag this account),@Fatima Zohraand@Levi Waldronto announce the review results

Patricia Brianna (07:47:01): > meanwhile, can we continue with the curations please

Patricia Brianna (07:47:09): > thanks a lot

Atrayee Samanta (10:26:52): > Hello@Levi Waldron@C. Mirzayi (please do not tag this account)@Fatima ZohraI was going through this study (https://bugsigdb.org/Study_264) and the abundance of the species in the signatures seem to be wrong- according to the LDA score given in the source, the signature curated as “increased abundance” is actually the ones that have a decreased abundance and vice versa, if I am not wrong? - Attachment (BugSigDB): Study 264 - File (PNG): image.png

C. Mirzayi (please do not tag this account) (11:09:05) (in thread): > Good question. If you look at the figure legend, the text in the article, and the very top of the figure, it appears that this was curated correctly. > > I agree that this is very confusing and difficult to determine from just the figure itself. It took me multiple passes reading through the results to understand why they had chosen to present it this way. One of the challenges of this work is the confusing way people choose to present results! - File (PNG): image.png

Atrayee Samanta (11:47:54) (in thread): > Oh yes I went through the results and got your point! Thanks a lot :))

Aiysha shahid (12:18:43): > Hello,@C. Mirzayi (please do not tag this account)I was going through this studyhttps://bugsigdb.org/Study_640in this curation, signature was missing and according to the research paper (Figure 3) show the abundance of the microbe. So, could you please check if i am correct! - Attachment (BugSigDB): Study 640

Esther (12:21:49): > @Fatima Zohra@Levi WaldronPlease could you assist me with this. > > The text and diagram shows an increase and decrease but they don’t belong to the taxa group. - File (PNG): screenshot_28.png - File (JPEG): Screenshot_20230322-084709.jpg

Esther (12:22:20): > @Fatima Zohra@Levi WaldronPlease could you assist me with this. > > The text and diagram shows an increase and decrease but they don’t belong to the taxa group. - File (PNG): screenshot_28.png - File (JPEG): Screenshot_20230322-084709.jpg

Kelvin Joseph (13:37:40) (in thread): > as I was applying for my final application I saw this “Some communities or projects may want you to answer additional questions. Please check with your mentor and community coordinator to see if you need to provide any additional information after you save your final application.” > help me out

Kelvin Joseph (13:38:12) (in thread): > also, “Please work with your mentor to provide a timeline of the work you plan to accomplish on the project and what tasks you will finish at each step. Make sure take into account any time commitments you have during the Outreachy internship round. If you are still working on your contributions and need more time, you can leave this blank and edit your application later. >”

Kelvin Joseph (13:39:45): > hello@C. Mirzayi (please do not tag this account)as I was applying for my final application I saw this “Some communities or projects may want you to answer additional questions. Please check with your mentor and community coordinator to see if you need to provide any additional information after you save your final application.” > help me out

Kelvin Joseph (13:39:59): > also, “Please work with your mentor to provide a timeline of the work you plan to accomplish on the project and what tasks you will finish at each step. Make sure take into account any time commitments you have during the Outreachy internship round. If you are still working on your contributions and need more time, you can leave this blank and edit your application later. >”

Fatima Zohra (14:20:32) (in thread): > This is not a figure to curate as this has nothing to do with differential abundance of bacteria

Esther (14:21:15) (in thread): > Oh nice > > Thank you

C. Mirzayi (please do not tag this account) (15:45:13): > Hi everyone I am working to answer your questions but I just wanted to mention that we have a meeting tomorrow at 10 AM EDT athttps://us02web.zoom.us/j/2737200499You can convert it to your time zone here:https://www.timeanddate.com/worldclock/converter.html?iso=20230323T140000&p1=179

C. Mirzayi (please do not tag this account) (15:46:06) (in thread): > Hi Kelvin as long as you completed the quiz as well as any curations we have what we need to assess your application as a candidate. You are welcome to log your completion of the survey and the curation as contributions on Outreachy as well.

C. Mirzayi (please do not tag this account) (15:46:35) (in thread): > This is examining metabolomic pathways not microbiome. We do not curate this.

C. Mirzayi (please do not tag this account) (15:46:44) (in thread): > There may be a microbiome component in the paper.

Esther (15:47:08) (in thread): > Oh ok > > Thanks Chloe

C. Mirzayi (please do not tag this account) (15:47:40) (in thread): > This is part of the challenge of this work–there’s a lot of extraneous information to sift through!

Esther (15:48:41) (in thread): > Lolz true > > But thanks to the mentors guiding us through

C. Mirzayi (please do not tag this account) (15:48:54) (in thread): > You’re right this is is incomplete. Feel free to open up an issue onhttps://github.com/waldronlab/BugSigDBcurationand I can assign it to you if you wish to complete it.

Aiysha shahid (15:51:23) (in thread): > ok sure, i will do that. Thank you!

Patricia Brianna (17:46:56): > hello friends

Patricia Brianna (17:48:04) (in thread): > thanks@C. Mirzayi (please do not tag this account)

Patricia Brianna (17:48:15) (in thread): > well answered

Patricia Brianna (17:49:11) (in thread): > can we wait to curate for now till review is done …?

Ibizugbe Merit (17:55:13) (in thread): > Hi:blush:

Patricia Brianna (17:59:46) (in thread): > thanks@Levi Waldronfor that, was so nice

2023-03-23

Suwaibat Suleiman (02:28:30): > Hello@C. Mirzayi (please do not tag this account)@Levi WaldronDoes “gid” equal gastrointestinal disease? I added a missing ncbi Id and discovered there were some inconsistencies in a study curation although I’m not sure I’m correcthttps://bugsigdb.org/Study_751. Also, what are the numbers after “gid” for? - Attachment (BugSigDB): Study 751 - File (WebP): 40168_2018_448_Fig3_HTML.webp

Ameerah Kabir (04:23:57): > Hi@Levi Waldronand@C. Mirzayi (please do not tag this account), if I am working on a study and in the study Research papers, they are no key words included, do I have to find the key words?

Aiysha shahid (07:39:20): > hi@Levi Waldron@Fatima Zohra@C. Mirzayi (please do not tag this account)in my research paper there is a microbe name is given “Proteobacteria” which i not listed in NCBI but I have got microbe on NCBI TAXNOMY whose name isPseudomonadota whosehomotypic synonym and NCBI blast name is proteobacteria and also there is an microbe name which name is given “Ruminococcaceae” which is also not listed on NCBI TAXONOMY but there is another microbe on NCBI name ”Oscillospiraceae” whose heterotypic synonym is”Ruminococcaceae” .So could please tell me should I use them and edit the signature’s?

Suwaibat Suleiman (07:55:16) (in thread): > Hello@Ameerah Kabirmaybe we could tackle this together, what do you mean by “key words”?

Chioma Grace (08:53:56) (in thread): > Hello@Aiysha shahid, in my understanding of this project, you are not meant to edit any signature. Rather if there is anything wrong with the signatures, you pen down a detailed discussion of it and a possible suggestion as part of your contribution.

C. Mirzayi (please do not tag this account) (09:19:23): > Good morning everyone. We have our weekly meeting and office hours at 10 AM EDT (in 40 minutes) athttps://us02web.zoom.us/j/2737200499

C. Mirzayi (please do not tag this account) (09:20:03) (in thread): > Yeah not really sure what you mean here. Can you explain a bit more?

Suwaibat Suleiman (09:24:44) (in thread): > Oh no I found out it was another applicant’s curation. My bad:woman-facepalming:

C. Mirzayi (please do not tag this account) (09:29:22) (in thread): > For reference I assume gid means “genus ID” it was their way of identifying unique genera.

Aiysha shahid (09:37:33) (in thread): > But few days ago,https://community-bioc.slack.com/archives/C04RATV9VCY/p1679211183084869, faced the same problem so lwadron she can use heterotypic synonym but i am not sure that should about should i use homotypic synomym or not:smiling_face_with_tear: - Attachment: Attachment > hello @Levi Waldron , I was going through another taxonomic issue (on this page: https://bugsigdb.org/Study_268/Experiment_1/Signature_1 ) and the microbe with the missing NCBI id as according to the source (Figure 4) was Leptotrichia amnionii, and I found a species on the NCBI taxonomy browser called Sneathia vaginalis (Taxonomy ID: 187101), whose heterotypic synonym is Leptotrichia amnionii; could this be useful information?

Suwaibat Suleiman (09:40:10) (in thread): > Oh okay. Thank you. > Do I go ahead with adding the edits?

C. Mirzayi (please do not tag this account) (09:46:25) (in thread): > Yeah this curation looks incomplete so feel free to edit.

Chioma Grace (09:46:53) (in thread): > @Aiysha shahid, I think you can but it have to form a detailed part of your discussion when contributing. We are to rectify any issue we encounter and back up with a meaningful explanation. You can state you used the homotypic synonym which is what is available in the taxonomy.

Aiysha shahid (09:48:50) (in thread): > Okay, thank you:heart::raised_hands:

C. Mirzayi (please do not tag this account) (09:48:53) (in thread): > Chioma is right–find the best synonym and use it.

Suwaibat Suleiman (09:50:34) (in thread): > Okay

Ameerah Kabir (10:02:39) (in thread): > Okay… > > The study I am working on, don’t have keywords, it is usually at the top of the paper, words that are mentioned a lot in the study. I am wondering if I have to read the paper and create a list of keywords, or there’s no need?

Ameerah Kabir (10:05:50) (in thread): > phew:sweat_smile:I have been trying to put it into words for days, i am so sorry for confusing you. > the last paper i worked on had keywords, like a list of words that are mentioned a lot in the study, and the current one doesn’t, I am confused if I am to find them and include them while curating a study > > Ameerah Kabir

Suwaibat Suleiman (10:09:28) (in thread): > Oh do you have access to thebugsigdb.orgplatform?

Levi Waldron (10:21:06) (in thread): > Some journals require authors to provide keywords to make their papers more searchable, but not all journals do. They’re not part of what we manually enter inbugsigdb.org.

Levi Waldron (10:26:27) (in thread): > @Kelvin Josephyou can review other studies not assigned to you, just ask any questions you have here before editing the database.

Kelvin Joseph (10:27:27) (in thread): > Thanks for the information

Beekaz (11:12:57) (in thread): > Thanks for the opportunity @Chloe Mirzayi … Am logged in already.. but guess the meeting is yet to start

Busayo Ojo (11:19:55) (in thread): > Hi, the meeting is over

Beekaz (11:23:38) (in thread): > Soooo sad… It’s was actually 3pm and I miscalculated it as 4pm in my time zone

Beekaz (11:24:26) (in thread): > How was it@Busayo Ojo

Busayo Ojo (11:32:55) (in thread): > Sorry about that@BeekazThe meeting was good. > They spoke about how to properly identify the study design in the article you’re curating. And in regards to outreachy, reviews are still currently ongoing.

Beekaz (11:33:57) (in thread): > I missed alottttttt:sob:

Busayo Ojo (11:37:10) (in thread): > Try and set a reminder, that might help :) . The meeting is still same time next week.

Queen Anthony (13:05:04): > Please mentors@Levi Waldron@Fatima Zohra@C. Mirzayi (please do not tag this account)please I commented on issue 13 since and I have not gotten any reply. > Please assign me to it:pray:

Trishna Patel (13:59:49): > @Trishna Patel has joined the channel

C. Mirzayi (please do not tag this account) (14:12:00) (in thread): > Assigned.

C. Mirzayi (please do not tag this account) (15:23:37): > The recording from the last part of today’s meeting and office hours. I apologize for not recording the full thing. - File (MPEG 4 Video): video1192941539.mp4

C. Mirzayi (please do not tag this account) (16:44:01): > Hi everyone just want to emphasize that there are two common mistakes we’re seeing in curations: > 1. Not checking for supplemental tables and figures with additional differential abundance results to curate > 2. Combining all results into a single experiment. Many studies have multiple experiments with their own sets of differential abundance results. Different experiments are often needed when they have results for different conditions, body sites, or statistical tests. Please ensure you are not entering results for different experiments into the same experiment.

C. Mirzayi (please do not tag this account) (16:44:22): > Please feel free to ask questions on here if you are unsure about how to curate something. We are here to help.

Ufuoma Ejite (16:56:17) (in thread): > Thank you for the review@C. Mirzayi (please do not tag this account)

Ufuoma Ejite (17:00:08): > Hello@C. Mirzayi (please do not tag this account)Please, I want to be sure about something. Regarding theantibiotic exclusion, I filled in “4 weeks”, however, you made a correction of “1 month”. > Just to be sure, is 4 weeks the same as 1 month, when we are making our curations?

Beekaz (17:05:46) (in thread): > Thank you

C. Mirzayi (please do not tag this account) (17:14:51): > If I scored it incorrectly can you link me to the issue and I will fix the score?

Ufuoma Ejite (17:17:00) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/33Thank you - Attachment: #33 Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis > https://pubmed.ncbi.nlm.nih.gov/28750650/

Busayo Ojo (17:58:02) (in thread): > @C. Mirzayi (please do not tag this account)my assigned study has been reviewed, my reviewer mentioned that I did not enter all the required bacterias from the Image in Fig 2c. And truly there are still a lot of bacterias in fig 2c, but I do not know what criteria to use in picking the right ones, previously I only picked the bacterias mentioned in the article which says: > “E. lenta and Staphylococcus capitis were enriched while gut- beneficial bacteria including Lactobacillus reuteri, Parabacteroides distasonis and Bacteroides dorei were depleted with cigarette smoke exposure” > I was already working on updating it, but i do not want to just go ahead and curate the wrong thing, so if you could plz explain. > > The link to issue:https://github.com/waldronlab/BugSigDBcuration/issues/7 - Attachment: #7 Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites > Condition: Cigarette smoke
> URL: https://gut.bmj.com/content/gutjnl/71/12/2439.full.pdf

2023-03-24

Atrayee Samanta (07:28:20): > Hello mentors, I had been assigned a second contribution and the complete DOI wasn’t available for free, so I had curated my study based on what was available in the NCBI link given itself, is that alright? I was a bit anxious because most of the time the DOI contains tables and images that are crucial to the curation

Levi Waldron (08:41:46) (in thread): > Give sci-hub.now.sh a try -thereare a few options for getting full text but this is the easiest

Levi Waldron (08:43:31) (in thread): > You are right that full text is essential!

Atrayee Samanta (09:17:59) (in thread): > Yes, I got the full text, thanks a lot!

Atrayee Samanta (11:14:11): > If I cannot find a particular species mentioned anywhere even after googling it, should I still add it to the signature? Or should I leave it out?

Chioma Grace (12:40:28) (in thread): > https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi.@Levi Waldronshared this link for us to check and confirm the authenticity of any Microbiome. It will be helpful. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Busayo Ojo (13:02:20): > @C. Mirzayi (please do not tag this account)Please my assigned study has been reviewed, my reviewer mentioned that I did not enter all the required bacterias from the Image in Fig 2c. And truly there are still a lot of bacterias in fig 2c, but I do not really understand the criteria for choosing the right bacterias. > Previously I only picked the bacterias mentioned in the article which says: > “E. lenta and Staphylococcus capitis were enriched while gut- beneficial bacteria including Lactobacillus reuteri, Parabacteroides distasonis and Bacteroides dorei were depleted with cigarette smoke exposure” > I was already working on updating it, but i do not want to just go ahead and curate the wrong thing, so if you could plz explain. > > The link to issue:https://github.com/waldronlab/BugSigDBcuration/issues/7 - Attachment: #7 Cigarette smoke promotes colorectal cancer through modulation of gut microbiota and related metabolites > Condition: Cigarette smoke
> URL: https://gut.bmj.com/content/gutjnl/71/12/2439.full.pdf

Levi Waldron (14:18:50) (in thread): > Ihaven’tlooked at this paper, butit’scommon that a figure or table shows all microbes identified by the statistical test, and the text only highlights a few of them that the authors though were most interesting.

C. Mirzayi (please do not tag this account) (14:37:17) (in thread): > Fixed.

Ameerah Kabir (15:51:40): > Hi@Levi Waldronand@C. Mirzayi (please do not tag this account)if three groups are mentioned in the study, how do I go about recording it?

Levi Waldron (15:58:12) (in thread): > You’dlook for anywhere they reported the results for contrasting two of those groups.

Levi Waldron (15:59:13) (in thread): > And if youcan’tfind the NCBI ID, enter the name as-is and it will appear in orange.

Levi Waldron (16:00:22) (in thread): > We’renot looking for abundance of the microbes,we’relooking for relative abundance between two conditions

Aiysha shahid (16:02:36) (in thread): > Yup, sorry for missing that.:smiling_face_with_tear:

Levi Waldron (18:07:38) (in thread): > Don’tworry@Aiysha shahidit was still helpful!

Ufuoma Ejite (18:32:42): > Hello@C. Mirzayi (please do not tag this account)I’ve worked on the outstanding issues in this study:https://github.com/waldronlab/BugSigDBcuration/issues/33Thank you:blush: - Attachment: #33 Quantitative metagenomics reveals unique gut microbiome biomarkers in ankylosing spondylitis > https://pubmed.ncbi.nlm.nih.gov/28750650/

Atrayee Samanta (22:16:04) (in thread): > yes okay

2023-03-25

Suwaibat Suleiman (04:48:14): > Hello@C. Mirzayi (please do not tag this account)@Levi WaldronI ended up completing this curation. Could you please review this study?https://bugsigdb.org/Study_751. It would be great to know how well I’ve done and if there are any mistakes - Attachment (BugSigDB): Study 751

Suwaibat Suleiman (06:52:54): > I was wondering about the timeline we were meant to fill in, in our final application. Do we send in the template to you@C. Mirzayi (please do not tag this account)and@Levi Waldron

Lydia Edogiawerie (09:26:51): > @Lydia Edogiawerie has joined the channel

Patricia Brianna (16:19:13): > hello everyone, wanted to thank the reviewing team for the work done and let us improve on our weaknesses. THANKS@C. Mirzayi (please do not tag this account),@Busayo Ojo,@Levi Waldronand everyone in here. I got my results and going to improve too.

Patricia Brianna (16:31:48) (in thread): > thanks a lot, mine is a question, does the score we got have some implication.

Patricia Brianna (16:32:20) (in thread): > as in is there a pass mark sort of stuff

Patricia Brianna (16:39:32) (in thread): > thanks for this

Ufuoma Ejite (17:27:03): > Hello@C. Mirzayi (please do not tag this account)@Levi WaldronPlease, I accidentally marked this study as “reviewed”:pensive:https://bugsigdb.org/Study_725 - Attachment (BugSigDB): Study 725

sophy (19:41:19): > @Levi Waldron@C. Mirzayi (please do not tag this account)@Fatima ZohraI am trying to make corrections on study 708https://bugsigdb.org/Study_708based on review comments. The study mentioned Weighted Unifrac as the test used to distinguish microbial signatures between study groups no LefSe analysis. It seems Weighted Unifrac is not accepted for statistical test when making corrections. Please, what do you recommend? - Attachment (BugSigDB): Study 708

Kelvin Joseph (21:32:43) (in thread): > Had a question on this too

2023-03-26

Suwaibat Suleiman (02:30:56) (in thread): > Hello:wave:definitely not a mentor but > Weighted unifrac isn’t a statistical test, it’s used to calculate Beta-diversity, from what I’ve learnt so far > Perhaps you can look into the section that reads statistical analyses in the paper. I’m not sure of the exact answer, maybe you’d have a clue.

Suwaibat Suleiman (02:35:15) (in thread): > Yeahh > During the Wednesday meeting, the mentors asked if someone could send in the template so they’d provide us with something we could all use. I was wondering if someone already did that.

Chioma Nnadi (04:26:40) (in thread): > I agree with@Suwaibat Suleiman

sophy (07:55:34): > Thanks for your response. I know Weighted Unifrac Distance is not a statistical test but that’s what the paper mentioned. The paper is not clear on the statistical tests used for differential analysis of relative abundances of the different study groups.

sophy (08:01:30): - File (PNG): image.png

Emmanuel Adamolekun (09:09:16): > @Emmanuel Adamolekun has joined the channel

Desire Oluwarotimi (09:58:38): > @C. Mirzayi (please do not tag this account)@Levi WaldronUsing the supplementary tables as mentioned in the review ofhttps://bugsigdb.org/Study_444, how do I differentiate between the increased and decreased abundances for each of the case studies? - Attachment (BugSigDB): Study 444

Desire Oluwarotimi (10:01:44): > In the review,@C. Mirzayi (please do not tag this account)also requested for a further contrast in patients condition beyond colorectal cancer, Can I make use of the condition of group 1 patients to further differentiate?

Chioma Nnadi (10:49:14): > Hello@C. Mirzayi (please do not tag this account)this is the only part that shows the group 1 description for the various groups > > Is it right if I say for example > Group 1: current smokers > Group 1 description: Current smokers comprised 36.6% of the 1616 participants who smoked at the time of the experiment. - File (PNG): css.png

Patricia Brianna (14:41:35): > hello friends, i went to edit my curation as advised in the review report i got. but found someone had done some edits already and curated them, is it allowed

Patricia Brianna (14:45:34): > @Busayo Ojowhat do you say on the above issue

Patricia Brianna (14:50:24): > hello once again, where can i fill the variable region on this experiment,

Patricia Brianna (14:50:50): > cause the review indicated it was missing

Patricia Brianna (15:08:04): > hello@C. Mirzayi (please do not tag this account)any say on the above issues please,

Ufuoma Ejite (15:32:24): > Hello@C. Mirzayi (please do not tag this account)@Levi WaldronFor the study I’m curating, the condition isatopic dermatitis. However, there is no option for that exact condition. What I can see are: recalcitrant atopic dermatitis, dermatitis, contact dermatitis, etc > What should I curate as the condition? Dermatitis?

Ufuoma Ejite (15:48:37): > UpdateI just discovered that atopic dermatitis is also known as “eczema” based on this link gotten from the article:https://www.omim.org/entry/603165@C. Mirzayi (please do not tag this account)@Levi Waldronshould I fill in the condition as “eczema”? > Here’s the study:https://pubmed.ncbi.nlm.nih.gov/27562258/ - Attachment (omim.org): Entry - %603165 - DERMATITIS, ATOPIC - OMIM > 603165 - DERMATITIS, ATOPIC >
> - ATOD;; > ECZEMA, ATOPIC >
>
> - DERMATITIS, ATOPIC, 1, INCLUDED; ATOD1, INCLUDED - Attachment (PubMed): Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare - PubMed > Whole metagenome analysis has the potential to reveal functional triggers of skin diseases, but issues of cost, robustness and sampling efficacy have limited its application. Here, we have established an alternative, clinically practical and robust metagenomic analysis protocol and applied it to 80 …

Patricia Brianna (22:41:41): > hello everyone, how did we finalize with this issue of “Timeline of tasks for the internship period:”. any updates please

Patricia Brianna (22:50:32): > hello@Levi Waldron,@C. Mirzayi (please do not tag this account)and@Fatima Zohra, i kindly request the review on thishttps://bugsigdb.org/Study_739 - Attachment (BugSigDB): Study 739

Patricia Brianna (22:52:36): > how many signatures am i supposed to have on the curation and what determines it?

Patricia Brianna (22:53:34): > and experiments too, how many are they supposed to be, and what determines it?

Patricia Brianna (22:53:44): > thanks

2023-03-27

Suwaibat Suleiman (01:49:32) (in thread): > I agree that it isn’t clear. Perhaps the mentors would know what to do here

Blessing Obafemi (03:28:51) (in thread): > @Patricia BriannaI think what determines the number of signatures is the number of significantly different relative abundances between the group 0 and 1 in an experiment. > > You can have several experiments, just check for where the groups were differentiated based on the relative abundances. The experiments could differ based on a timeline, body site used, the groups experimented on. > > I hope this helps

Chioma Nnadi (03:40:21) (in thread): > yes, this is it. I have 3 experiments in my article because it states three different groups.

Evan Chinny (03:44:25): > https://github.com/waldronlab/BugSigDBcuration/issues/42. Good day. I finished working on this issue few days ago and it haven’t been reviewed. - Attachment: #42 Gut microbiota: impacts on gastrointestinal cancer immunotherapy > Initiated at https://bugsigdb.org/Study_659. Note - there are no guarantees that information already entered here (such as study design) is correct, so please proceed as you would for a new study with no information pre-entered.

Kelvin Joseph (04:05:33): > Hello@Levi Waldronand@C. Mirzayi (please do not tag this account)did a review on this curation and you can help checkhttps://bugsigdb.org/Study_461 - Attachment (BugSigDB): Study 461

Busayo Ojo (06:47:07) (in thread): > As long as the corrections your reviewer assigned to you is still undone, then plz try and still update your curation

C. Mirzayi (please do not tag this account) (14:55:58) (in thread): > If you haven’t already, please update the issue onhttps://github.com/waldronlab/BugSigDBcuration

C. Mirzayi (please do not tag this account) (14:56:16) (in thread): > We’ll have some info on the timeline later this week.

C. Mirzayi (please do not tag this account) (14:56:51) (in thread): > Looks like someone helped you out with it.

C. Mirzayi (please do not tag this account) (14:57:13) (in thread): > Yes beta diversity is not curated which weighted unifrac is. Great answer Suwaibat.

C. Mirzayi (please do not tag this account) (14:57:40) (in thread): > Reviewing now.

C. Mirzayi (please do not tag this account) (14:58:34) (in thread): > Almost certainly Mann-Whitney U

Kelvin Joseph (15:00:53) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Suwaibat Suleiman (15:38:29) (in thread): > Thank you@C. Mirzayi (please do not tag this account)I’m glad I could help!

C. Mirzayi (please do not tag this account) (15:44:36) (in thread): > Can you open up an issue on github (and maybe write a quick summary of the changes you made)? That would be very helpful. Thanks!

C. Mirzayi (please do not tag this account) (15:45:08) (in thread): > Marked it as needs review. We will get back to you soon.

sophy (16:52:20) (in thread): > Mann-Whitney was mentioned in the study. I will go with that. Thanks.

C. Mirzayi (please do not tag this account) (17:13:25) (in thread): > I’d use eczema. We already have studies in BugSigDB curated with eczema as the condition.

C. Mirzayi (please do not tag this account) (17:16:12): > Regarding timeline: We will have an update for you on what to submit for this section later this week. The project is based on curation of published research and therefore there is no real ending to the project–the expectation is that you are curating several articles over the course of the internship but the amount of effort involved in each curation can vary widely so it’s difficult to say “Curate X number of articles by this date.” > > Still our plan is to have some guidance on what you can put in this section. Just know that other parts of your application such as the quality of your contributions, your participation as an applicant, etc. will probably be considered much more important than what you put in the timeline when we assess applicants.

C. Mirzayi (please do not tag this account) (17:17:12) (in thread): > Just to add generally speaking each experiment will have 2 signatures: (1) taxa that were increased in cases relative to controls and (2) taxa that were decreased in cases relative to controls.

C. Mirzayi (please do not tag this account) (17:20:02): > Regarding other curators updating your curation: We’re aware that other curators are making updates and reviewing and editing existing contributions. This is a feature of the collaborative environment–we can all review, edit, and check each other’s work. All changes made to your curation are saved as well as your original curation (visible in the History tab). We will review your work as you completed it of course.

Ufuoma Ejite (17:20:02) (in thread): > Okay, thank you very much@C. Mirzayi (please do not tag this account)

C. Mirzayi (please do not tag this account) (17:25:15): > Regarding pending reviews: We are working diligently to get you all feedback this week. We recognize that the contribution window is almost over (Ends Monday April 3rd and 4 PM UTC). We are taking into consideration the fact that some people may not have as much time to revise your contributions as others. > > We appreciate your patience as we continue to review. We have been overwhelmed by the amount of interest we’ve had and the productivity of all of you. You are all truly amazing and, once we have to make a decision, it is going to be incredibly difficult, but we will ensure that you are all considered fairly!

Ufuoma Ejite (18:08:28): > Thank you for the updates@C. Mirzayi (please do not tag this account):blush:

Aguobi Amara (19:48:26) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Chioma Nnadi (23:09:27) (in thread): > Thank you so much for this@C. Mirzayi (please do not tag this account). Kudos to the entire team:hugging_face:

2023-03-28

Ibizugbe Merit (02:11:54) (in thread): > Thanks for your guidance so far@C. Mirzayi (please do not tag this account)and the entire team

Aguobi Amara (02:37:11): > Hello everyone

Blessing Obafemi (05:37:35) (in thread): > Thank you for the updates

Chioma Nnadi (06:06:38) (in thread): > Hi Amaka > Hope you’re good

Ibizugbe Merit (06:14:11) (in thread): > Hi there

Chioma Grace (06:37:20) (in thread): > Thank you for this insights@C. Mirzayi (please do not tag this account)

Atrayee Samanta (09:30:15) (in thread): > Thank you so much

Chioma Nnadi (09:30:50): > hello@C. Mirzayi (please do not tag this account),@Levi Waldron,@Fatima ZohraI kindly request the review on thishttps://bugsigdb.org/Study_530Thanks. - Attachment (BugSigDB): Study 530

Rukky (09:50:06) (in thread): > Hi there

Atrayee Samanta (10:17:43): > If oral rinse samples are used in a particular experiment, can I use the body site as ‘mouth’?

Chioma Nnadi (10:35:56) (in thread): > Yes, I had same in my article

Atrayee Samanta (10:46:59) (in thread): > Oh alright, thanks <33

Aguobi Amara (10:54:00) (in thread): > Yes I am@Chioma Nnadi

Aguobi Amara (10:54:36) (in thread): > How are you guys@Rukkyand@Ibizugbe Merit

Ibizugbe Merit (10:58:49) (in thread): > I’mfine:hugging_face:How are you doing?

Kelvin Joseph (12:05:15) (in thread): > Okay

Levi Waldron (12:55:03) (in thread): > Yea, although I believe there is a “saliva” EFO term? That would be ideal.

Patricia Brianna (14:00:12) (in thread): > thanks a loot for this

Patricia Brianna (14:01:14) (in thread): > thanks Busayo

C. Mirzayi (please do not tag this account) (14:37:39) (in thread): > I agree with Levi. Saliva.http://purl.obolibrary.org/obo/UBERON_0001836

Patricia Brianna (14:38:12): > hello friends

Patricia Brianna (14:38:49): > so how did we conclude with the issue of the timeline for the application

Patricia Brianna (14:43:16): > it required consulting from mentors, anything so far

Ufuoma Ejite (14:58:39) (in thread): > @C. Mirzayi (please do not tag this account)mentioned this::point_down:****“Regarding timeline: We will have an update for you on what to submit for this section later this week. The project is based on curation of published research and therefore there is no real ending to the project–the expectation is that you are curating several articles over the course of the internship but the amount of effort involved in each curation can vary widely so it’s difficult to say”Curate X number of articles by this date.”*******Still, our plan is to have some guidance on what you can put in this section. Just know that other parts of your application such as the quality of your contributions, your participation as an applicant, etc. will probably be considered much more important than what you put in the timeline when we assess applicants.”***Based on the above information, we’d be having the timeline within the week

Chioma Grace (15:45:41) (in thread): > Yes saliva is ideal….I had saliva and tongue as body sites in my curation.

Rukky (16:12:15) (in thread): > Yo, I’m good:blush:

2023-03-29

Evan Chinny (02:06:12): > Good day. I worked on “Gut microbiota :impact on gastrointestinal cancer” before. But i got a review on github that there is no signatures for the study and was asked to look for another unassigned ones. Please can this be assigned to me. Have already asked on github but haven’t gotten a response@C. Mirzayi (please do not tag this account)@Levi Waldronhttps://github.com/waldronlab/BugSigDBcuration/issues/47

Atrayee Samanta (04:06:48) (in thread): > Thank you@Levi Waldron@C. Mirzayi (please do not tag this account)@Chioma Grace!

Aiysha shahid (08:15:45): > @Chioma Nnadihello in your curation i have correct the taxon id of******Atopobium********** **********parvulum and i have also created a talk/ discussion page for that u can check that so ,please kindly don’t delete the changes. It’s only increasing the issues on the missing NCBI ID page. If u want you check it on NCBI TAXONOMY BROWSER.******

Chioma Nnadi (08:17:51) (in thread): > Duly noted. Thanks

C. Mirzayi (please do not tag this account) (14:01:38) (in thread): > Assigned to you.

Desire Oluwarotimi (14:39:44): > Hi@C. Mirzayi (please do not tag this account)I’ve been trying to study the supplementary tables in my article to curate for the increased and decreased abundances for days now but I can’t seem to catch in on a difference. Could you help please??https://bugsigdb.org/Study_444 - Attachment (BugSigDB): Study 444

C. Mirzayi (please do not tag this account) (14:51:00) (in thread): > Looking at supplementary table 2, increased in cases relative to controls would have a positive log2 fold change. Decreased in cases relative to controls would have a negative log2 fold change. > > They do a lot of comparisons which would each need their own experiment. Each experiment would then have two signatures: increased and decreased.

C. Mirzayi (please do not tag this account) (14:51:29) (in thread): > Supplementary table 3 is also curatable

C. Mirzayi (please do not tag this account) (14:54:56): > Hi everyone if you have made changes as a result of a review please indicate as such on the Github issue and do not tag us here or send us direct messages telling us. We use the Github issues as a reference when reviewing.

C. Mirzayi (please do not tag this account) (14:58:58): > Also thanks to Levi we have 6 new papers to curate available as issues 56 through 61. Preference will be given to those who have not had a chance to curate a paper yet. Please do not claim any of these papers if you are still making updates or working on another curation for now.

C. Mirzayi (please do not tag this account) (15:04:59): > And while I am giving updates: we will be meeting at 10 AM EDT tomorrow for our final meeting + office hours as part of the applicant window. Most of the hour will be devoted to your questions so please come with questionsHere is a time zone calculator to convert to your local time zonehttps://www.timeanddate.com/worldclock/converter.html?iso=20230330T140000&p1=179

Ufuoma Ejite (15:27:41) (in thread): > Noted. Thank you:blush:

Harrydas Ombati (16:19:07) (in thread): > Noted

Harrydas Ombati (16:21:17) (in thread): > Thank you….shall be there

Ufuoma Ejite (16:35:26): > Just curious…:thinking_face:Please,@C. Mirzayi (please do not tag this account)@Levi Waldronwhat does theNS label in some of the GitHub issues mean? > Thank you:blush:

Busayo Ojo (16:37:49) (in thread): > I believe it means Not scored.

Ufuoma Ejite (16:43:54) (in thread): > Oh!:grin:That makes a lot of sense now

C. Mirzayi (please do not tag this account) (16:46:53) (in thread): > This is correct.

Chioma Nnadi (17:03:01) (in thread): > Noted

C. Mirzayi (please do not tag this account) (17:06:08): > Application Timeline Guidelines:Thank you for your patience as we developed guidelines for the timeline section of your applications. To remind you, the internship begins on Monday, May 29th and runs until Friday, August 25th and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > * Fixing curation issues. As presented on this page:https://bugsigdb.org/Help:Contents#TODO_for_reviewers, there are many missing NCBI taxonomies that can be investigated, incomplete studies, and other issues. > * The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > * Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > * Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > Our hope is that our intern can spend a lot of their time working on curation issues (bullet point number one) so I would recommend emphasizing that in your timeline.Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Eunice Miriti (18:08:58) (in thread): > Noted with thanks.

Ufuoma Ejite (19:12:39) (in thread): > Noted. Thank you@C. Mirzayi (please do not tag this account):blush:

2023-03-30

Atrayee Samanta (01:01:02) (in thread): > Thank you for the information:relaxed:

Chioma Grace (06:00:39) (in thread): > Thank you so much@C. Mirzayi (please do not tag this account). You have been a wonderful mentor.

Chioma Grace (06:05:13) (in thread): > Thanks for the reminder.

Ibizugbe Merit (08:24:57) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Kelvin Joseph (08:53:45): > Hello BugSigDB team hope you’re doing well. Thanks for the timeline and would like to thank all the mentors@C. Mirzayi (please do not tag this account)@Fatima Zohra@Levi Waldronfor the great work in letting us feel welcomed to the community and appreciated for the little contributions we were able to make given the short window.

C. Mirzayi (please do not tag this account) (09:23:34): > Hi everyone, our meeting and office hours will be in about 35 minutes athttps://us02web.zoom.us/j/2737200499. I hope to see you there!

C. Mirzayi (please do not tag this account) (09:23:55) (in thread): > Thank you! We really appreciate all your hard work during the contribution period.

sophy (10:28:48): > Is the meeting over? I can’t join.

Madelyn Carlson (10:29:30) (in thread): > Hi there, we’re still in the meeting. Are you stuck in the waiting room?

sophy (10:29:50): > yes please

Kelvin Joseph (10:32:13) (in thread): > It has been like this for minutes - File (JPEG): Screenshot_20230330-173001_Zoom.jpg

Chioma Nnadi (10:57:54): > Hello everyone, > Attached to this message is the file I presented on the call > Thanks - File (PDF): Microbiome Study Curation - Outreachy Applicants.pdf

Esther (11:17:26): > Hello@C. Mirzayi (please do not tag this account)Trust you are doing great. > > Please do you mind sharing the recordings of the meeting

Ufuoma Ejite (11:20:56) (in thread): > So beautiful!:blush:

Busayo Ojo (11:23:53): > Hi@C. Mirzayi (please do not tag this account)so I’m curating the bacteria’s, and I get this message on these 2 bacteria’s: > “The taxon (492670) is a potential contaminant”. > Does this mean anything? - File (PNG): image.png

C. Mirzayi (please do not tag this account) (11:25:51) (in thread): > It means that these bacteria could be potentially a contaminant, but don’t worry about it. They are common and you don’t need to do anything about them.

C. Mirzayi (please do not tag this account) (11:26:08) (in thread): > I will have it posted by the end of the day.

Esther (11:27:52) (in thread): > Thank you

Aguobi Amara (11:28:41) (in thread): > Thank you

Busayo Ojo (11:40:27) (in thread): > Thank you!

Chioma Grace (11:41:05) (in thread): > Thank you for the meeting@C. Mirzayi (please do not tag this account)It’s was insightful, detailed and encouraging. > Kind Regards.

Busayo Ojo (13:04:24): > Hi everyone, if you’re not sure how to go about creating your project timeline, this is a template that can help.https://docs.google.com/document/d/13n3E84n1y10itBiEesg6d9jENFoot_zKUhI3ELGxeWw/edit?usp=sharingPlz try not to edit the template and only make a copy. - File (Google Docs): Internship project timeline

Chioma Nnadi (13:09:28) (in thread): > Thanks

Ibizugbe Merit (17:50:42) (in thread): > Thank you@Busayo Ojo:hugging_face:

2023-03-31

Aguobi Amara (02:33:15) (in thread): > Thank you

Saksham Gupta (06:33:49): > @Saksham Gupta has joined the channel

Eunice Miriti (08:07:42) (in thread): > Thank you

Blessing Obafemi (09:28:56) (in thread): > Thank you@Busayo Ojo

C. Mirzayi (please do not tag this account) (10:40:26): > Apologies for the delay in posting. Here is yesterday’s meeting recording. - File (MPEG 4 Video): video1460015103.mp4

Atrayee Samanta (11:44:50): > if one of the factors of ‘matched on’ is alcohol consumption, can we enter it as ‘alcohol drinking’?

C. Mirzayi (please do not tag this account) (11:49:39) (in thread): > That sounds good to me.

Atrayee Samanta (11:54:13) (in thread): > alright, thanks!

Rukky (18:49:55) (in thread): > Thank youu

2023-04-01

Harrydas Ombati (02:07:21) (in thread): > Thank you. You are a life saver

Aiysha shahid (06:37:58): > if in a study buccal swab samples were collected so body site can be Internal cheek pouch?

Esther (08:29:44): > @Fatima Zohra@Levi WaldronIf set of questionnaires were used to determine participants enrolment for the study, > > Can it the questionnaires be used as a Matched factor?

Levi Waldron (08:33:00) (in thread): > Idon’tthink so. Inclusion and exclusion criteria that determine eligibility for the study are not the same as a matching factor, which is something that is balanced between cases and controls, for example matching for comparable ages or similar balance of sex. For anything,it would have to be more specific than “questionnaire”.

Levi Waldron (08:34:47) (in thread): > Sounds right, I assume internal cheek pouch is one of the autocomplete options?

Esther (08:41:57) (in thread): > Thank you@Levi WaldronDoes this statement shows age as a Matched factor? > Because I have read the study over and over again and this is the only statement that shows a matched factor between the case and controls. - File (JPEG): Screenshot_20230401-133733_1.jpg

Levi Waldron (08:43:21) (in thread): > Yes it shows age and gender (or more accurately sex) as matching factors

Esther (08:44:02) (in thread): > Thank you so much.

Aiysha shahid (08:52:47) (in thread): > Yes..

Levi Waldron (08:53:10) (in thread): > Perfect

Aiysha shahid (08:53:44) (in thread): > :smile:

Aiysha shahid (10:59:56): > hello,@Levi Waldronin this curationhttps://bugsigdb.org/Study_554can’t we simplify all the microbe at phylum, class, genus etc in 1signature. I mean we can create a signature1 : the gut microbe increased in PD patients at phylum,class, genus, species etc. and same for the decreased one, instead of creating 10signatures for each level. Also, they 2Statistical test1st is t test which is shown in Fig 2 and 2nd is LEfSe analysis at Fig 3.More importantly, we identified several taxa that showed significant difference in abundance between PD patients and healthy controls using ******t**********-test and LEfSe analysis( according to the research paper). SO, it means we will created only 2 experiment. The curator has created 4exp 2are from supplementary paper ( ANOVA AND Wilcoxon rank-sum test). But I think so, ANOVA shouldn’t be included because it only ****analysis to assess the impact of gender and PD on gut microbiota taxa identified by LDA scores>4 in LEfSe analysis. Could please check if I am correct!. And should make edit. SORRY IF I WENT WRONG SOMEWHERE.:smiling_face_with_tear: - Attachment (BugSigDB): Study 554

Levi Waldron (11:10:47) (in thread): > I think you are right on all counts@Aiysha shahid! But rather than create two experiments for what will be similar results for the same contrast by two slightly different statistical tests done for sensitivity analysis, I would just choose one (what did they report as their “primary” analysis?) and ignore the other. You are right that the different taxonomic levels should be combined in a single signature, and that ANOVA results shouldn’t be included because it’s not a contrast between two groups.

Levi Waldron (11:12:31) (in thread): > This study needs a lot of cleanup!

Levi Waldron (11:16:08) (in thread): > Based on the methods section “Differential Abundance Analysis of Gut Microbiota Between PD Patients and Controls” it looks like LEfSe is presented as the primary analysis and t-test as a sensitivity analysis, so I would recommend only recording the LEfSe results: > > Linear discriminant analysis (LDA) effect size (LEfSe) analysis (Segata et al., 2011) was conducted using the LEfSe software, and the threshold for LDA score was set at 4. Permutation tests were conducted between groups at various classification levels (phylum, class, order, family, genus, and species) by using the R software, andP-values were obtained. TheP-values were modified toq-values (White et al., 2009) by using the Benjamini and Hochberg false discovery rate method. Differences between groups were also analyzed using thet-test and Wilcoxon rank-sum test in R software.

Atrayee Samanta (12:33:23): > The sequencing platform seems wrong here because shotgun metagenomics sequencing is a sequencing type, but I had a doubt: is it possible to have both 16S as well as metagenomic sequencing both in the same experiment? Or should they be present in separate experiments? (The paper mentions both sequencing types) > > [The curation link ishttps://bugsigdb.org/Study_634] - Attachment (BugSigDB): Study 634 - File (JPEG): Screenshot_20230401-215306_Chrome.jpg

Aiysha shahid (17:05:34) (in thread): > yup, so can you please the delete the experiments so I can add a new experiment:smiling_face_with_tear:

sophy (18:22:29) (in thread): > Hi Atrayee, metagenomics sequencing is not a sequencing platform but a sequencing method like 16S. Unlike 16S in which a particular region of the bacteria genome is targeted for sequencing, metagenomics means the whole bacteria genome was sequenced. Sequencing platform means the machine/company used to generate the sequencing data e.g. Illumina Miseq. I hope this helps.

Levi Waldron (19:53:24) (in thread): > Sometimes papers do use both 16S and WMS, but any given signature would be produced by one or the other, so you could either curate the more important method that they use to present the major results, or if you curate both, they would be separate experiments. This whole Study 634 should not really have been created, since it is a review paper and not a meta-analysis. It is more informative to curate the original publications than a review paper, since reviews usually pick and choose which results they summarize. There are also many curation errors here and I am tempted just to delete this study, although that should be accompanied by putting the reviewed studies on our TODO list!

Levi Waldron (20:05:46) (in thread): > @Aiysha shahidI just gave you elevated permissions as a reviewer:slightly_smiling_face:- are you able to delete those experiments & signatures now?

Levi Waldron (20:07:39) (in thread): > @Atrayee SamantaI’ve also given you reviewer permissions - thanks for all your reviewing work!

Atrayee Samanta (23:05:21) (in thread): > Thanks a lot for the clarification! And the thing about this being a review paper was what I was thinking about too! And does reviewed study means just curating what is there in the paper, or am I getting it wrong?:sweat_smile:Because if the curation is to be completed before putting it on the TODO list I would love to do it

Atrayee Samanta (23:06:35) (in thread): > Yes, thank you@Levi Waldron!

Atrayee Samanta (23:07:27) (in thread): > Thank you@sophy!

2023-04-02

Aguobi Amara (02:35:27): > Hello:wave:everyone, I hope we are making progress:blush:

Aiysha shahid (03:17:04) (in thread): > Hello@Levi Waldronthank you, but I am still not able to delete any of the experiment’s nor the signatures. Permission error is coming, only Administrators can delete it!:smiling_face_with_tear:

Levi Waldron (07:47:44) (in thread): > This particular study 634 should just be deleted becauseit’snot presenting original analysis, but I created a GitHub issue just to note that the original research articles cited within should be added to the wiki:blush:ifyou’dlike to curate any of those, just create a new GitHub issue for it and go ahead!

Aiysha shahid (08:11:10) (in thread): > Hello,@Levi Waldroncan you simply delete the whole study instead of deleting experiments and signatures,as this would more time taking:smiling_face_with_tear:. I would simply create a github issue and work on this curation

Atrayee Samanta (08:52:58) (in thread): > Thank you@Levi WaldronI’ll do just that!

Levi Waldron (10:14:56) (in thread): > Actually deleting a study doesn’t delete the experiments and signatures contained within, instead they end up on a list of orphaned experiments or orphaned signatures athttps://bugsigdb.org/Help:Cleanup. So I deleted everything but Experiment 1 and Signatures 1-2, and marked those Incomplete, so you can take edit those and create new experiments or signatures as needed. Thanks@Aiysha shahid! - Attachment (BugSigDB): Help:Cleanup

Levi Waldron (10:15:59) (in thread): > I’ll try to find out which permissions are needed to delete pages, but that probably won’t come up very often.

Aiysha shahid (10:17:55) (in thread): > okay thank you@Levi Waldron!

Patricia Brianna (12:28:43): > yeah

Patricia Brianna (12:28:46): > we are

Patricia Brianna (12:28:49): > thanks

Levi Waldron (20:30:25): > <!channel>as far as I know, all first “second contributions” have received at least their first review by now. Please let us know if we’ve missed yours!

2023-04-03

Busayo Ojo (02:26:11) (in thread): > I curated an article I found online a while ago, after getting permission from Fatima. Should i go ahead and Open a new issue for it?

Hannah Honda (03:50:40) (in thread): > Thank you, this is so helpful!

Evan Chinny (04:18:51) (in thread): > https://bugsigdb.org/Study_710. Hi sir, i curated this study but haven’t received any review - Attachment (BugSigDB): Study 710

Atrayee Samanta (05:34:00) (in thread): > Hi@Levi Waldron@C. Mirzayi (please do not tag this account)@Fatima ZohraI had opened an issue on github but then realized that the curation of that paper already exists on bugsigdb; I’m so sorry for the confusion > > I have already closed that issue on github

Fatima Zohra (06:16:35) (in thread): > @Busayo Ojoplease link the paper for me again.I’llopen it as an issue for you and assign

Fatima Zohra (06:52:09) (in thread): > @Evan Chinnyunder review

Busayo Ojo (08:41:22) (in thread): > Hi@Fatima Zohrathis is a link to the paper.https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01472-7 - Attachment (BioMed Central): Altered infective competence of the human gut microbiome in COVID-19 - Microbiome > Background Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group. Results We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls. Conclusions Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract

C. Mirzayi (please do not tag this account) (09:33:01) (in thread): > No worries.

Aiysha shahid (09:51:22): > Hello,@Levi Waldronin this studyhttps://bugsigdb.org/Study_607I think so, experiment 2 and 3 are irrelvant because in exp 2 everything is same, only difference is that the curator has added signatures that could have been added in exp 1. And in exp3 the curator has given the source as fig 4,which is only the analysis of a particular microbe in male and female. SORRY IF I WENT WRONG IN THIS:smiling_face_with_tear: - Attachment (BugSigDB): Study 607

Atrayee Samanta (10:24:16): > It seems to me that Study 741 (https://bugsigdb.org/Study_741) and Study 744 (https://bugsigdb.org/Study_744) are duplicate- both of them have the same DOI. - Attachment (BugSigDB): Study 741 - Attachment (BugSigDB): Study 744

Busayo Ojo (10:32:46): > Hi everyone today is the last day for submitting your Outreachy contributions, if you’ve not already done so, pls do so now. > All the best:hugging_face:

Suwaibat Suleiman (11:47:03) (in thread): > I think I see what’s going on here > Experiment 1 contains statistically significant species, whereas experiment 2 contains statistically significant genera > Genera are of a higher classification than species > Paraphrased: “We curate all statistically significant results” > I was advised by the mentors in a review > As for exp. 3, I’m not quite sure, yes it seems to be statistically significant but there’s an extra microbe there that might fit into another experiment, I’m not quite sure > No problem, I believe, with having one microbe and/or signature

Suwaibat Suleiman (11:49:36): > Good luck everyone!:saluting_face:I’m happy to have been a part of this! > Again, open science is so cool, goodluck to us all!!:partying_face:

Aiysha shahid (12:05:04) (in thread): > Thank you@Suwaibat SuleimanBut, instead of creating a whole new exp we could have simply mentioned that abundant in genera and species. And for the 3rd exp, i am also not sure about it.

Suwaibat Suleiman (13:21:08) (in thread): > That’s actually a great idea:thinking_face:. > My best guess is if the study says so, then so be it but the mentors might tackle this differently.

Levi Waldron (14:13:19) (in thread): > Thank you for spotting these@Atrayee Samanta- I deleted both since no further work had been done on them, and it’s better to start with adding just a PMID.

Ibizugbe Merit (14:44:20): > Thank you everyone for your continuous support during this contribution period, good luck to us all:tada:

Levi Waldron (21:31:43) (in thread): > Good find! It is fine to mix different taxonomic ranks in a single signature, and it’s incorrect to create a new experiment when both experiments are the same. However if the contrast is different (such as performing the contrast in males only or females only), then that is a separate experiment.

2023-04-04

Aiysha shahid (05:34:09) (in thread): > Hnn, so can u please delete the exp2 and it’s signature’s as I have edited and merge the signature’s in exp1.

Fatima Zohra (07:02:28): > Hi all, thank you very much for all your contribution. For those editing studies please double check to make sure you’re not editing an outreachy applicant’s contribution on bugsigdb. We appreciate your efforts!

Kelvin Joseph (07:23:04): > I appreciate the teamwork effort that the Bugsigdb community put to place to ensure that every applicant was granted a chance to contribute to the open software community

Aguobi Amara (08:58:02): > Thank you everyone > Goodluck to everyone

Suwaibat Suleiman (09:53:29): > Can we continue curating and reviewing?

khadijah (10:04:50): > Hi@Fatima Zohraare you still revising some of the curation that was previously reviewed..

Fatima Zohra (10:09:20) (in thread): > yes we are going over the second set of review after corrections

khadijah (10:12:07) (in thread): > Alright I tagged you under my GitHub issue. > Would be expecting your review. > Thanks

Cindy Apiyo (11:47:34): > It been the best journey for me > I wish all the best for us all as well > A big thanks to our mentors as well@Levi Waldron@C. Mirzayi (please do not tag this account)@Fatima Zohrayou have been amazing despite the pressure

Cindy Apiyo (11:47:49) (in thread): > Yes

Cindy Apiyo (11:48:13) (in thread): > Good luck:blush:

C. Mirzayi (please do not tag this account) (11:55:09): > Thank you all for your hard work. We were blown away by all of you and we have a truly tough choice ahead of us.

Aiysha shahid (12:51:48): > Hello@Levi Waldroncould please delete exp2 in this studyhttps://bugsigdb.org/Study_681it’s same as exp1, only difference it that, the curator didn’t add any signature in exp1. - Attachment (BugSigDB): Study 681

Suwaibat Suleiman (14:36:04) (in thread): > Alright. Thank you@Cindy Apiyo

2023-04-05

Patricia Brianna (05:19:07): > hello everyone

Patricia Brianna (05:19:19): > how are you doing

Aiysha shahid (05:55:20) (in thread): > Hellooo

Levi Waldron (12:23:58) (in thread): > Sorry for the delay! What about Experiment 3?

Levi Waldron (12:24:07) (in thread): > I just deleted Experiment 2.

C. Mirzayi (please do not tag this account) (14:29:03): > Good afternoon everyone. I just wanted to mention that we have a team meeting tomorrow at 10 AM EDT. You are all welcome to join if you’re interested in continuing to work with the BugSigDB project.https://us02web.zoom.us/j/2737200499Please note that participation in this meeting will not be used as part of our evaluation process for applicants.

Aiysha shahid (15:15:30) (in thread): > Thank you! exp3 and 4 are ok exp3 : Old (≥ 65 yrs) vs. young, exp4: Current smoking vs. not smoking

Kelvin Joseph (15:59:20) (in thread): > Noted@C. Mirzayi (please do not tag this account)I will be there

2023-04-06

Arda Keles (07:07:37): > @Arda Keles has joined the channel

Aiysha shahid (07:32:25): > Hello@Levi Waldronin this studyhttps://bugsigdb.org/Study_579we can use fig9&10 to show the relative abundance between two groups. - Attachment (BugSigDB): Study 579

Levi Waldron (10:26:34) (in thread): > Yes you are right! I’m changing the status of Experiment 1 to “incomplete” to reflect that these signatures are still missing.

Aiysha shahid (10:31:04) (in thread): > OK, THANK YOU!

Levi Waldron (10:42:35): > I’ve had a few questions from Outreachy applicants about how they can continue participating. First of all, thank you, we would love to continue working with you. Here are some ways that you can participate: > 1. Fix issues found on the “TODO for reviewers” section of the Help page (https://bugsigdb.org/Help:Contents#TODO_for_reviewers) represent highest-priority issues for fixing in the wiki. It is my hope to clear the huge backlog of issues here so that we only have to keep up on new issues that arise. There is a variety of issues here, and you could work on any of them. When you have any doubts, please post here to confirm your proposed edits, but you are free to make corrections that you are confident in. > 2. Being available to curate studies that are requested athttps://github.com/BugSigDBCuration/issues > 3. Testing different functionality of the wiki, reporting any problems with wiki functionality that you find > 4. You could choose a field of study that is of interest to you, do a literature review on that topic, and add studies to the wiki until it contains all relevant publications in that field of study. You could then perform analyses in that field of study following examples fromhttps://waldronlab.io/bugSigSimple/or improving / updating / extending those analyses. These analyses are much more challenging and should be preceded by gaining good familiarity with microbiome research, but can be suitable for undergraduate or master’s level research projects. > 5. participating in our weekly group meetings. These are currently Thursdays at 10am New York time, but could be rescheduled for availability of people in different time if there is need. - Attachment (BugSigDB): Help:Contents - Attachment (waldronlab.io): Simple exploratory analysis of curated microbe signatures > bugSigSimple provides simple exploratory analysis of curated microbe signatures from bugsigdb.org.

Levi Waldron (10:43:47) (in thread): > By the way, that repo is titled “Simple” exploratory analysis because the repo aims to make those analyses more simple, not because the analyses themselves are that “simple”:slightly_smiling_face:

Atrayee Samanta (23:27:07): > I do not see any DOI mentioned in the PMID mentioned in this study (https://bugsigdb.org/Study_657), does it indicate that the original paper isn’t available anymore? - Attachment (BugSigDB): Study 657 - File (PNG): image.png

2023-04-07

Chioma Grace (01:32:23) (in thread): > Hi Waldron, thank you for the update. I am available to curate studies. Please assign paper #60 to me. I have indicated interest here:https://github.com/BugSigDBCuration/issues. > Thank you.

Kelvin Joseph (03:50:26) (in thread): > You can use the pmid then wait for it to generate the rest

Atrayee Samanta (05:34:22) (in thread): > The PMID was already there in the existing study, but there was no DOI generated

Fatima Zohra (05:57:00) (in thread): > Not sure about the DOI but looks like this article doesn’t contain any signatures. Thanks for bringing it up.

Aiysha shahid (08:29:33): > Hello@Levi Waldroncould you please delete exp3 from this studyhttps://bugsigdb.org/Study_579, it was by mistake:smiling_face_with_tear: - Attachment (BugSigDB): Study 579

C. Mirzayi (please do not tag this account) (09:26:43) (in thread): > Deleted.

Aiysha shahid (10:36:31) (in thread): > Thank you!:hugging_face::heart:

Aiysha shahid (12:38:37): > hello, this study should be deletedhttps://bugsigdb.org/Study_746as theURI mentioned in this study which shows that the study is on**** “****Altered Gut Microbiome in Patients With Dermatomyositis” and it’s DOI is 10.1002/acr2.11436. And this studyhttps://bugsigdb.org/Study_747has the same DOI. SAME IS WITH STUDY 742https://bugsigdb.org/Study_742AND STUDY 743https://bugsigdb.org/Study_743IT’S ORIGINAL STUDY IS 745https://bugsigdb.org/Study_745 - Attachment (BugSigDB): Study 746 - Attachment (BugSigDB): Study 747 - Attachment (BugSigDB): Study 742 - Attachment (BugSigDB): Study 743 - Attachment (BugSigDB): Study 745

Ibizugbe Merit (12:58:32) (in thread): > https://bugsigdb.org/Study_746https://bugsigdb.org/Study_742Thanks for pointing this out@Aiysha shahidplease these should be deleted,as they were entered wrongly

2023-04-11

Levi Waldron (01:27:30) (in thread): > Done,thank you@Aiysha shahid!

Levi Waldron (01:32:26) (in thread): > I consider the DOI optional if there is a PMID. But there are a few instances of a study not in pubmed that can only be linked to by doi or uri. I imagine that any study having a pmid also has a doi, and the doi is supposed to last forever regardless of whether the paper is available or not.

Atrayee Samanta (12:18:40) (in thread): > oh I see, thanks for clarifying!

2023-04-12

Chioma Grace (07:37:48): > Hello@Levi WaldronIssue #60 was published in the Journal of Periodontology and I have not been able to download the full article for proper curation. > It stated I should pay some amount of money to access it. Please help me out with it. > Thank you

Levi Waldron (12:25:53) (in thread): > I just attached the PDF to the issue (from sci-hub:sweat_smile:) - File (PDF): PMID-28844190.pdf

Chioma Grace (12:31:47) (in thread): > Thank you so much Sir. > I appreciate this

Levi Waldron (12:31:58) (in thread): > Thank YOU!

Aiysha shahid (16:30:02): > hello this study should be deletedhttps://bugsigdb.org/Study_737the DOI mentioned in this study which shows that the study is on “Structural and Functional Dysbiosis of Fecal Microbiota in Chinese Patients With Alzheimer’s Disease” and original curation of this study is thishttps://bugsigdb.org/Study_736. SAME IS WITH THE STUDY 724https://bugsigdb.org/Study_724IT’S ORIGINAL STUDY IShttps://bugsigdb.org/Study_729. SAME IS WITH THE STUDY 668https://bugsigdb.org/Study_668IT’S ORIGINAL STUDY IShttps://bugsigdb.org/Study_662 - Attachment (BugSigDB): Study 737 - Attachment (BugSigDB): Study 736 - Attachment (BugSigDB): Study 724 - Attachment (BugSigDB): Study 729

2023-04-13

Chioma Grace (05:12:10): > @Levi WaldronGreetings, > Please OTU (Operational Units) alpha Diversity was used in study #60, but I didn’t see it in the list of Alpha Diversity during curation in BugsigDB. Please is there any other similar term in the list for OTU. Thanks.

Atrayee Samanta (09:09:41): > In a particular case-control study, it has been mentioned that the experiment is divided into three groups- current smokers, former smokers and never smokers, and that the total number of subjects for all 3 cases is 316. But it has not been mentioned how many subjects belong to a particular group, how should I curate this? Should I just not curate the number of sunjects in the respective groups?

C. Mirzayi (please do not tag this account) (09:19:56) (in thread): > If it’s number of unique OTUs that would be equivalent to richness.

C. Mirzayi (please do not tag this account) (09:20:51) (in thread): > If they don’t report it, they don’t report it unfortunately. If you have a link, I can take a second look at it just to be sure.

C. Mirzayi (please do not tag this account) (09:21:32): > Good morning everyone. I just wanted to mention that we have a team meeting today at 10 AM EDT (in 40 minutes). You are all welcome to join if you’re interested in continuing to work with the BugSigDB project.https://us02web.zoom.us/j/2737200499Please note that participation in this meeting will not be used as part of our evaluation process for applicants.

Chioma Grace (09:21:42) (in thread): > Okay > Thank you@C. Mirzayi (please do not tag this account)

C. Mirzayi (please do not tag this account) (09:22:24) (in thread): > Thanks! All have been deleted.

Chioma Grace (09:26:43): > Please how can I assess a table that is not in the PDF of a paper. I have searched online and only the PDF is available. > Example > The supplementary table 3 of paper #60 which is not in the PDF, I need to curate signatures significant in Marginal Bone Loss during healing. > Thank you.

Atrayee Samanta (09:40:17) (in thread): > Yes, this is the link:https://www.frontiersin.org/articles/10.3389/fcimb.2021.658203/full, thanks a lot! - Attachment (Frontiers): Association Between Oral Microbiota and Cigarette Smoking in the Chinese Population > The oral microbiota has been observed to be influenced by cigarette smoking and linked to several human diseases. However, research on the effect of cigarette smoking on the oral microbiota has not been systematically conducted in the Chinese population. We profiled the oral microbiota of 316 healthy subjects in the Chinese population by 16S rRNA gene sequencing. The alpha diversity of oral microbiota was different between never smokers and smokers (P = 0.002). Several bacterial taxa were first reported to be associated with cigarette smoking by LEfSe analysis, including Moryella (q = 1.56E-04), Bulleidia (q = 1.65E-06), and Moraxella (q = 3.52E-02) at the genus level and Rothia dentocariosa (q = 1.55E-02), Prevotella melaninogenica (q = 8.48E-08), Prevotella pallens (q = 4.13E-03), Bulleidia moorei (q = 1.79E-06), Rothia aeria (q = 3.83E-06), Actinobacillus parahaemolyticus (q = 2.28E-04), and Haemophilus parainfluenzae (q = 4.82E-02) at the species level. Two nitrite-producing bacteria that can increase the acidity of the oral cavity, Actinomyces and Veillonella, were also enriched in smokers with FDR-adjusted q-values of 3.62E-06 and 1.10E-06, respectively. Notably, we observed that two acid production-related pathways, amino acid-related enzymes (q = 6.19E-05) and amino sugar and nucleotide sugar metabolism (q = 2.63E-06), were increased in smokers by PICRUSt analysis. Finally, the co-occurrence analysis demonstrated that smoker-enriched bacteria were significantly pos…

C. Mirzayi (please do not tag this account) (10:03:32) (in thread): > Can you link me to the article? I can investigate.

Chioma Grace (10:06:43) (in thread): > Okay - File (PDF): PMID-28844190.pdf

Chioma Grace (10:12:24) (in thread): > https://pubmed.ncbi.nlm.nih.gov/28844190/ - Attachment (PubMed): Smoking May Lead to Marginal Bone Loss Around Non-Submerged Implants During Bone Healing by Altering Salivary Microbiome: A Prospective Study - PubMed > Smoking shapes the salivary microbiome in states of clinical health, and further may influence MBL during bone healing by creating high at-risk-for-harm communities. Understanding of the distinctly divergent oral microbiome in smokers and non-smokers is a base for personalized therapeutics for this …

Kelvin Joseph (13:33:06): > @C. Mirzayi (please do not tag this account)and@Levi Waldronis it possible to only have a single signature in a curation or?

C. Mirzayi (please do not tag this account) (14:32:57) (in thread): > You should be able to calculate the group sizes from this table I believe? - File (PNG): image.png

C. Mirzayi (please do not tag this account) (15:46:46) (in thread): > Yeah I suppose it’s possible if there’s a single experiment/contrast and all observed differential abundances were in a single direction.

C. Mirzayi (please do not tag this account) (15:50:09) (in thread): > Unfortunately the supplement is behind a paywall and I am unable to find a way to access it.

Chioma Grace (15:59:18) (in thread): > Thank you for your efforts@C. Mirzayi (please do not tag this account). I appreciate.

2023-04-15

Kelvin Joseph (01:16:18) (in thread): > Thanks a lot will mark my curation for review since I was looking for the reduced signature but couldn’t find any

Kelvin Joseph (02:29:48) (in thread): > @C. Mirzayi (please do not tag this account)tried adding an extra signature to the curationhttps://bugsigdb.org/Study_635and it is not reflecting have tried severally hope they won’t all reflect later - Attachment (BugSigDB): Study 635

Atrayee Samanta (05:23:09) (in thread): > Oh yes, I’ll be able to calculate it. Thanks a lot!

Atrayee Samanta (06:03:48) (in thread): > I’m facing a similar issue, I added 2 signatures to Experiment 1 but it isn’t reflecting in the curation (https://bugsigdb.org/Study_660). - Attachment (BugSigDB): Study 660

2023-04-16

Chioma Grace (08:35:11): > Hello@Levi Waldron, greetings. > Please in paper #60, one of the tables on MBL (marginal bone loss) to be curated is not in the PDF file of this paper. Rather it is in a site that have to be paid for. So experiment 2 (MBL) have no signature because of that. > > I have been able to curate two experiments and four signatures. > I mistakenly duplicated Experiment 2, please kindly delete before review. > Thank you.

Aiysha shahid (16:31:30): > hello@Levi Waldronin this studyhttps://bugsigdb.org/Study_528there will be 3experiments and we can use figure3 to curate their signature’s? - Attachment (BugSigDB): Study 528

2023-04-17

Aiysha shahid (05:35:10): > hello this studies,https://bugsigdb.org/Study_664,https://bugsigdb.org/Study_723should be deleted as study 664 AND 668, doesn’t contain information like DOI, PMID etc. AND STUDY 723, the DOI mentioned is not working. - Attachment (BugSigDB): Study 664 - Attachment (BugSigDB): Study 723

C. Mirzayi (please do not tag this account) (09:01:15) (in thread): > Deleted 664 for being empty and 723 turned out to be a duplicate when I figured out the correct DOI. Thank you.

C. Mirzayi (please do not tag this account) (09:05:20) (in thread): > Three experiments curated from the S1 dataset, though it looks like they have no significant results.

C. Mirzayi (please do not tag this account) (09:07:52) (in thread): > That is unfortunate. I also do not have access to this supplement.

Chioma Grace (11:10:01) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Aiysha shahid (14:42:45) (in thread): > So,should i create the 3exp or leave it..?

Aiysha shahid (14:43:22) (in thread): > Welcome:hugging_face::heart:

2023-04-18

Levi Waldron (08:40:55) (in thread): > I’ll check this - supplemental tables are usually available without paying, but if not I can check the CUNY library, and if it’s not there request it through interlibrary loan.@Chioma Gracewhat is the supplement that you need so I can request it?

Levi Waldron (08:43:06) (in thread): > @Kelvin Joseph@Atrayee Samantado you mean you created signatures that are not appearing on these studies? That sounds like a serious problem. Would you report this as an issue athttps://github.com/waldronlab/bugsigdb/issues?

Levi Waldron (08:44:35) (in thread): > Is this the supplement you were referring to? I can check through the CCNY library and request an interlibrary loan, if you haven’t already@C. Mirzayi (please do not tag this account)?

Atrayee Samanta (08:52:04) (in thread): > Yes, that was what I meant. I’ll definitely open the issue! Should I add the ‘bug’ tag to the issue?

Levi Waldron (08:53:00) (in thread): > Thank you! Yes, if it will allow you to.

Chioma Grace (08:54:32) (in thread): > Thank you@Levi WaldronThe table is (supplementary Table 3 in online Journal of Periodontology) which contains the signatures implicated in MBL (marginal bone loss). Below is the PDF of the paper. - File (PDF): PMID-28844190.pdf

Atrayee Samanta (09:02:10) (in thread): > Thank you, I have added the issue #175@Levi Waldron

Kelvin Joseph (10:07:18): > Hello bugsigdb team hope you are all doing well.

Kelvin Joseph (10:08:57) (in thread): > Hello@Levi Waldronthe issue was sorted and now the site is doing okay thanks

Atrayee Samanta (11:07:54) (in thread): > Hi I’m good, hope you’re alright too : D

C. Mirzayi (please do not tag this account) (11:09:44) (in thread): > @Levi WaldronIt’s not available at CUNY libraries but I can make an ILL request.

C. Mirzayi (please do not tag this account) (11:21:23) (in thread): > I couldn’t figure out how to specify an ILL request for a supplement so I wrote an email to the CCNY library to see what they advise.

C. Mirzayi (please do not tag this account) (11:22:55) (in thread): > You can create them and then leave them empty I suppose to make it clear that they did the tests–they just had no significant results.

Aiysha shahid (11:31:30) (in thread): > ok thank you:hugging_face:

Ibizugbe Merit (14:12:52) (in thread): > I’mdoing great over here…Hopeyou’redoing alright too?:blush:

Aiysha shahid (14:47:36): > hlo,@C. Mirzayi (please do not tag this account)in this studyhttps://bugsigdb.org/Study_575the curator has combine all these 3 in group 1 IAP (27), postnatal antibiotics (24), and IAP and postnatal antibiotics (22). Is that ok? I think so there will 3exp. - Attachment (BugSigDB): Study 575

Levi Waldron (16:21:37): > <!channel>this Thursday from 09:00 - 12:00 NYC time is this month’s Microbiome International Forum (Atlantic edition - the Pacific edition is today 9pm NYC time). It’s free and I am one of the organizers. If you are interested in expanding your knowledge of current microbiome research, and meeting other microbiome researchers, you should attend - Attachment (microbiome-vif.org): Home > WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM! DECEMBER 8th 2021 MICROBIOME Microbiome Virtual International Conference (MVIF)

Aiysha shahid (16:27:48): > hlo, this studyhttps://bugsigdb.org/Study_668should be deleted as this a duplicate ofhttps://bugsigdb.org/Study_540 - Attachment (BugSigDB): Study 668 - Attachment (BugSigDB): Study 540

Chioma Grace (16:32:16) (in thread): > Thank you@Levi Waldronand@C. Mirzayi (please do not tag this account). > I appreciate your efforts. You are wonderful mentors.

Chioma Grace (16:41:52) (in thread): > @Fatima Zohrareplied that “the supplmental table reporting species association with MBL is not exactly a differential abundance result. Those are results showing correlation which we don’t need to curate”. > > I think this solves the issue. Thank you.

Levi Waldron (16:43:04) (in thread): > Good - I was just looking into it, and had access to the PDF through CUNY, but the online version doesn’t have supplementary tables!

Levi Waldron (16:45:27) (in thread): > Done, thank you@Aiysha shahid!

2023-04-19

Aiysha shahid (06:04:59) (in thread): > welcome:hugging_face::heart:

Aiysha shahid (06:45:37): > hlo, in this studyhttps://bugsigdb.org/Study_560exp 2,3,4 should be deleted as they are similar/duplicate of exp 1. - Attachment (BugSigDB): Study 560

C. Mirzayi (please do not tag this account) (09:44:29) (in thread): > I spoke with a CCNY librarian and made an ILL request for the supplemental materials.

C. Mirzayi (please do not tag this account) (09:50:09) (in thread): > You’re right. Deleted.

Aiysha shahid (11:05:31) (in thread): > :hugging_face:

Aiysha shahid (11:10:55) (in thread): > Thank you@C. Mirzayi (please do not tag this account),but exp 4 is still there…

C. Mirzayi (please do not tag this account) (11:13:00) (in thread): > Whoops. Nice catch.

C. Mirzayi (please do not tag this account) (12:35:55) (in thread): > I also had a friend at another institution check and they were unable to access the supplement despite having access to the Wiley version. I am going to write to the journal.

Levi Waldron (12:37:26) (in thread): > Same here, CUNY has access but I think the journal just forgot to post the supplemental materials…

C. Mirzayi (please do not tag this account) (12:43:23) (in thread): > I wrote an email to the editorial office.

2023-04-20

C. Mirzayi (please do not tag this account) (07:57:27): > Please note: We will be having our BugSigDB meeting onFriday at 10 AM EDT so that we can attend MVIF today. Please consider attending MVIF if you’re interested in learning more about studying the microbiome. It’s online and free - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Ufuoma Ejite (15:09:32): > Hi everyone > I’m having an issue here. I’ve been trying to work on this study:https://bugsigdb.org/Study_728For the updates I’m making, it is not reflecting on the site. > I mean, I try to add signatures, and it doesn’t show that it’s been added - Attachment (BugSigDB): Study 728

C. Mirzayi (please do not tag this account) (16:47:50) (in thread): > The editorial office got back to me. They thought I was an author on the paper (despite me stating multiple times that I am just a reader) and directed me to another contact for authors of articles that have been accepted. I am reaching out to that person. > > The ILL librarians were unable to find the supplements either.

Levi Waldron (16:48:57) (in thread): > Wow,doesn’tinspire confidence in this journal!

Chioma Grace (16:56:33) (in thread): > Wow, what a hurdle. Sorry for the stress. > Thank you@C. Mirzayi (please do not tag this account)and@Levi Waldron.

C. Mirzayi (please do not tag this account) (16:57:17) (in thread): > At this point I have to take this to its end. I can’t just leave this hanging now. I am so curious of how much more effort it’s going to take.

Levi Waldron (16:58:06) (in thread): > An email to authors might be illuminating for them!

Chioma Grace (17:02:41) (in thread): > May be try refreshing the page. > Again, you can click on the entry just after the topic of the paper…….this worked for me > I had similar challenge. > I hope this helps.

C. Mirzayi (please do not tag this account) (17:03:25) (in thread): > Sent them an email.

Kelvin Joseph (19:16:03) (in thread): > Hello please don’t try with many attempts as they will later reflect and you might end up with 5 to 6 duplicated signatures for a single experiment you can just be patient and wait for the site to reboot

2023-04-21

Atrayee Samanta (05:57:45) (in thread): > I agree with Kelvin, and if the problem persists let the mentors know

C. Mirzayi (please do not tag this account) (09:28:02) (in thread): > The corresponding author wrote back that they submitted the supplements to the journal. He is following up with the journal.

Levi Waldron (09:41:20) (in thread): > That’swild that they no longer have a copy.

2023-04-23

Ufuoma Ejite (21:12:32): > Hello@C. Mirzayi (please do not tag this account)@Levi WaldronI’m still having this issue

2023-04-24

Levi Waldron (08:20:46) (in thread): > Sorry for the late reply Chioma! Would you file an issue atGitHub.com/waldronlab/bugsigdb/issuesto report the problem? Make a note of which experiments you added a signature to, and how many signatures you see there and how many more it should show.The wiki developer will see a report there right away.

Levi Waldron (08:21:55) (in thread): > Sorry Ufuoma! See the above thread, it would be great if you will report the issue on our issue tracker.

Ufuoma Ejite (17:10:15) (in thread): > Thank you@Levi WaldronI have done that already

2023-04-26

Patricia Brianna (05:25:51): > hello friends

Patricia Brianna (05:26:07): > it has been a while

Patricia Brianna (05:27:12): > what could be the best advice if i want to continue contributing

Patricia Brianna (05:27:34): > where is the best starting point

Patricia Brianna (05:27:40): > thanks

Ibizugbe Merit (06:58:33) (in thread): > I’ve had a few questions from Outreachy applicants about how they can continue participating. First of all, thank you, we would love to continue working with you. Here are some ways that you can participate: > 1. Fix issues found on the “TODO for reviewers” section of the Help page (https://bugsigdb.org/Help:Contents#TODO_for_reviewers) represent highest-priority issues for fixing in the wiki. It is my hope to clear the huge backlog of issues here so that we only have to keep up on new issues that arise. There is a variety of issues here, and you could work on any of them. When you have any doubts, please post here to confirm your proposed edits, but you are free to make corrections that you are confident in. > 2. Being available to curate studies that are requested athttps://github.com/BugSigDBCuration/issues > 3. Testing different functionality of the wiki, reporting any problems with wiki functionality that you find > 4. You could choose a field of study that is of interest to you, do a literature review on that topic, and add studies to the wiki until it contains all relevant publications in that field of study. You could then perform analyses in that field of study following examples fromhttps://waldronlab.io/bugSigSimple/or improving / updating / extending those analyses. These analyses are much more challenging and should be preceded by gaining good familiarity with microbiome research, but can be suitable for undergraduate or master’s level research projects. > 5. participating in our weekly group meetings. These are currently Thursdays at 10am New York time, but could be rescheduled for availability of people in different time if there is need. - Attachment (BugSigDB): Help:Contents - Attachment (waldronlab.io): Simple exploratory analysis of curated microbe signatures > bugSigSimple provides simple exploratory analysis of curated microbe signatures from bugsigdb.org.

Ibizugbe Merit (07:00:01) (in thread): > This was dropped on the bugsigdb channel by @lwaldron

C. Mirzayi (please do not tag this account) (17:33:03) (in thread): > Thanks for helping Ibizugbe!

C. Mirzayi (please do not tag this account) (17:33:47): > Good afternoon everyone. I just wanted to mention that we have a team meeting tomorrow at 10 AM EDT. You are all welcome to join if you’re interested in continuing to work with the BugSigDB project.https://us02web.zoom.us/j/2737200499

Ibizugbe Merit (19:53:20) (in thread): > Noted.

2023-05-01

Kelvin Joseph (10:43:45): > Hello#bugsigdbteam hope your week is coming along well

Kelvin Joseph (10:45:17) (in thread): > Hello@Ufuoma Ejitedid the issue get sorted or it’s still not adding signatures and new experiments

2023-05-02

Ufuoma Ejite (16:37:51) (in thread): > Hello@Kelvin JosephThe issue hasn’t been sorted yet

2023-05-03

Levi Waldron (09:36:57) (in thread): > Can you respond tohttps://github.com/waldronlab/BugSigDB/issues/179with exactly what you’re not seeing, and any other instances where something is missing? We need examples of where this is happening to troubleshoot and fix it everywhere. - Attachment: #179 Edits made are not reflecting for Study_728 > I’ve been trying to work on this study: https://bugsigdb.org/Study_728
> For the updates I’m making, it is not reflecting on the site.
> I mean, I try to add signatures, and it doesn’t show that it’s been added.
> Also, I made some edits to the Experiments, but it doesn’t show that an update has been made.

Levi Waldron (09:52:02) (in thread): > The problem can be that different users see something different when looking at the same study, and the problem doesn’t occur on every study:laughing:

Levi Waldron (09:55:03): > Hi everyone!

Levi Waldron (09:56:32): > There is a new request for a curation, from a PhD student in my lab Haoyan Zhong:https://github.com/waldronlab/BugSigDBcuration/issues/66 - Attachment: #66 Comparison of the respiratory microbiome in healthy nonsmokers and smokers > Morris A, Beck JM, Schloss PD, Campbell TB, Crothers K, Curtis JL, Flores SC, Fontenot AP, Ghedin E, Huang L, Jablonski K, Kleerup E, Lynch SV, Sodergren E, Twigg H, Young VB, Bassis CM, Venkataraman A, Schmidt TM, Weinstock GM; Lung HIV Microbiome Project. Comparison of the respiratory microbiome in healthy nonsmokers and smokers. Am J Respir Crit Care Med. 2013 May 15;187(10):1067-75. doi: 10.1164/rccm.201210-1913OC. PMID: 23491408; PMCID: PMC3734620.

2023-05-04

Fatima Zohra (07:46:30) (in thread): > Yes it was listed as an unassigned issue..Atrayee requested to work on this so I assigned it to her. Just want to clarify, since Haoyan opened the issue are they working on it then? In that caseI’llexplain to Atrayee that this is already taken

sophy (13:02:12): > @sophy has left the channel

Busayo Ojo (14:00:28): > Congratulations@Atrayee Samanta:partying_face:

Atrayee Samanta (14:05:26) (in thread): > Thank you so much Busayo < 3

Kelvin Joseph (14:35:09) (in thread): > Congrats@Atrayee Samanta

Sonali Kumari (14:47:07) (in thread): > Congratulations@Atrayee Samanta:partying_face:

Chioma Grace (16:23:53): > Congratulations@Atrayee Samanta

Atrayee Samanta (21:45:20) (in thread): > Thank you so much@Kelvin Joseph@Sonali Kumari!

Atrayee Samanta (21:46:12) (in thread): > Thanks a lot@Chioma Grace!

2023-05-05

C. Mirzayi (please do not tag this account) (15:38:25): > I just want to extend a thank you to everyone who contributed. It was not an easy choice and we wished we could have picked several of you. You’re all diligent and talented and I wish you all the best in your future endeavors. I know I’ve said it before but Levi, Fatima, and the rest of the BugSigDB team were all blown away by your efforts. > > If you’re interested in continuing to help out with BugSigDB, please let us know.

2023-05-06

Ibizugbe Merit (12:10:30): > Congratulations@Atrayee Samanta:kissing_heart:

Atrayee Samanta (12:20:39) (in thread): > Thank you so much!

2023-05-07

Kelvin Joseph (03:59:57) (in thread): > Am interested

2023-05-08

irem Kahveci (04:13:53) (in thread): > I am interested too

2023-05-10

Aiysha shahid (01:10:10) (in thread): > Me:raised_hands:

Suwaibat Suleiman (11:42:05) (in thread): > Pretty late to the party! > Congratulations@Atrayee Samanta!

2023-05-17

Samuel Gamboa (09:28:34): > @Samuel Gamboa has joined the channel

2023-05-31

Atrayee Samanta (00:57:50): > I am unable to access this article with the DOIhttp://dx.doi.org/https://doi.org/10.3920/BM2019.0039via sci-hub, is there any other way/website to access it?

C. Mirzayi (please do not tag this account) (13:18:40): > Hi everyone, we will be having our meeting tomorrow at 10 AM EDT at this Zoom link:https://us02web.zoom.us/j/2737200499. We currently do not have anyone signed up to present so it may be a short meeting.

2023-06-01

Atrayee Samanta (03:19:37): > The body site mentioned in this experiment (https://www.sciencedirect.com/science/article/pii/S2211124721012195) is ‘duodenal aspirates’, but this is not available in the bugsigdb study. Should I use the body site as ‘Duodenum’ for the curation? - Attachment (sciencedirect.com): Age and the aging process significantly alter the small bowel microbiome > Gut microbial diversity decreases with aging, but existing studies have used stool samples, which do not represent the entire gut. We analyzed the duo…

C. Mirzayi (please do not tag this account) (09:28:57) (in thread): > Yep that works.

Levi Waldron (13:11:23): > I noticed that we have 33 “orphaned” signatures and 1 orphaned experiment, seehttps://bugsigdb.org/Help:Cleanup. This happens when an administrator deletes a study or experiment without deleting the experiments and signatures contained within. These are a priority to delete, because if not, they will become “adopted” by the next study and experiment created with the same study number, creating a mismatch of signature or experiment to an unrelated study.@C. Mirzayi (please do not tag this account)@Atrayee Samantawould you take a look and delete the orphaned experiments and signatures? - Attachment (BugSigDB): Help:Cleanup

C. Mirzayi (please do not tag this account) (15:29:44) (in thread): > I’ll start deleting these this afternoon.

2023-06-02

Atrayee Samanta (01:42:07) (in thread): > Yes, I’ll work on it soon too.

Atrayee Samanta (02:41:13): > I had a doubt, if we use different LDA/p-values for different species in abundance testing, does that count as MHT correction? I came across it in this article:https://molecularbrain.biomedcentral.com/articles/10.1186/s13041-023-01014-0#Sec2(curated at study 730) - Attachment (BioMed Central): The gut microbiota and metabolite profiles are altered in patients with spinal cord injury - Molecular Brain > Background Metabolites secreted by the gut microbiota may play an essential role in microbiota–gut–central nervous system crosstalk. In this study, we explored the changes occurring in the gut microbiota and their metabolites in patients with spinal cord injury (SCI) and analyzed the correlations among them. Methods The structure and composition of the gut microbiota derived from fecal samples collected from patients with SCI (n = 11) and matched control individuals (n = 10) were evaluated using 16S rRNA gene sequencing. Additionally, an untargeted metabolomics approach was used to compare the serum metabolite profiles of both groups. Meanwhile, the association among serum metabolites, the gut microbiota, and clinical parameters (including injury duration and neurological grade) was also analyzed. Finally, metabolites with the potential for use in the treatment of SCI were identified based on the differential metabolite abundance analysis. Results The composition of the gut microbiota was different between patients with SCI and healthy controls. At the genus level, compared with the control group, the abundance of UBA1819, Anaerostignum, Eggerthella, and Enterococcus was significantly increased in the SCI group, whereas that of Faecalibacterium, Blautia, Escherichia–Shigella, Agathobacter, Collinsella, Dorea, Ruminococcus, Fusicatenibacter, and Eubacterium was decreased. Forty-one named metabolites displayed significant differential abundance between SCI patients and healthy controls, including 18 that were upregulated and 23 that were downregulated. Correlation analysis further indicated that the variation in gut microbiota abundance was associated with changes in serum metabolite levels, suggesting that gut dysbiosis is an important cause of metabolic disorders in SCI. Finally, gut dysbiosis and serum metabolite dysregulation was found to be associated with injury duration and severity of motor dysfunction after SCI. Conclusions We present a comprehensive landscape of the gut microbiota and metabolite profiles in patients with SCI and provide evidence that their interaction plays a role in the pathogenesis of SCI. Furthermore, our findings suggested that uridine, hypoxanthine, PC(18:2/0:0), and kojic acid may be important therapeutic targets for the treatment of this condition. - File (PNG): image.png

C. Mirzayi (please do not tag this account) (13:54:55) (in thread): > Generally no unless they say something like “Bonferroni-adjusted p-values” or “FDR-adjusted p-values” but LDA scores are usually from LeFSe analysis and that does not correct for MHT so it’s very rare to see a LeFSe study that does.

C. Mirzayi (please do not tag this account) (13:56:00) (in thread): > Also you can really only adjust p-values for MHT. I am not sure how one would adjust an LDA score for MHT.

C. Mirzayi (please do not tag this account) (14:16:08): > All orphaned signatures and experiments have been deleted.

2023-06-04

Atrayee Samanta (23:22:47) (in thread): > Oh thank you!

2023-06-05

Levi Waldron (10:25:43) (in thread): > Great!

2023-06-06

Aiysha shahid (10:52:31): > https://bugsigdb.org/Study_593this study should be deleted as this is the duplication ofhttps://bugsigdb.org/Study_594. - Attachment (BugSigDB): Study 593 - Attachment (BugSigDB): Study 594

C. Mirzayi (please do not tag this account) (12:19:42) (in thread): > Deleted. Thank you!

Aiysha shahid (13:08:03): > https://bugsigdb.org/Study_636can you please delete signature 3 in this study.. and can i use condition as smokingbehaviorbecause tobacco smoking is not available. - Attachment (BugSigDB): Study 636

Aiysha shahid (15:24:14): > https://bugsigdb.org/Study_466andhttps://bugsigdb.org/Study_549should be deleted as it is a duplicate ofhttps://bugsigdb.org/Study_543 - Attachment (BugSigDB): Study 466 - Attachment (BugSigDB): Study 549 - Attachment (BugSigDB): Study 543

Levi Waldron (16:20:28) (in thread): > Thank you@Aiysha shahid! I’ve just given you rights to delete pages, so you can go ahead with these. Just make sure first delete signatures, then experiments, then the study, to avoid having “orphaned” pages.

Levi Waldron (16:20:47) (in thread): > Yes “smoking behavior” sounds correct, and you can now delete the signature.

2023-06-07

Atrayee Samanta (02:32:23): > For this particular paper (https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-014-0250-2) there exist multiple body sites, should I curate them as ‘Mouth’ and ‘Buccal Mucosa’? - Attachment (BioMed Central): Alcohol and tobacco consumption affects bacterial richness in oral cavity mucosa biofilms - BMC Microbiology > Background Today there are more than 2 billion alcohol users and about 1.3 billion tobacco users worldwide. The chronic and heavy use of these two substances is at the heart of numerous diseases and may wreak havoc on the human oral microbiome. This study delves into the changes that alcohol and tobacco may cause on biofilms of the human oral microbiome. To do so, we used swabs to sample the oral biofilm of 22 subjects; including 9 control-individuals with no or very low consumption of alcohol and no consumption of tobacco, 7 who were chronic and heavy users of both substances and 6 active smokers that reported no significant alcohol consumption. DNA was extracted from swabs and the V1 region of the 16S rRNA gene was PCR amplified and sequenced using the Ion Torrent PGM platform, generating 3.7 million high quality reads. DNA sequences were clustered and OTUs were assigned using the ARB SILVA database and Qiime. Results We found no differences in species diversity and evenness among the groups. However, we found a significant decrease in species richness in only smokers and in smokers/drinkers when compared to controls. We found that Neisseria abundance was significantly decreased in both groups when compared to controls. Smokers had significant increases in Prevotella and Capnocytophaga and reductions in Granulicatella, Staphylococcus, Peptostreptococcus and Gemella when compared to the two other groups. Controls showed higher abundance of Aggregibacter, whilst smokers/drinkers had lower abundances of Fusobacteria. Samples from only smokers clustered closer together than to controls and smokers/drinkers, and also had a significant reduction in inter-group dissimilarity distances, indicating a more homogenous group than controls. Conclusions Our results indicate that the continued use of tobacco or alcohol plus tobacco significantly reduces bacterial richness, which apparently leads to a reduction in inter-group variability, turning the respective biofilms into a more homogenous microenvironment in terms of bacterial community composition, with possible consequences for human oral diseases. - File (PNG): image.png

Levi Waldron (04:42:49) (in thread): > Since the different different mouth mucosal sites were all pooled together for measurement, I would just use “mouth mucosa” (http://purl.obolibrary.org/obo/UBERON_0003729)

Atrayee Samanta (05:39:25) (in thread): > Alright, thanks a lot!

Levi Waldron (05:41:32) (in thread): > Thank you! Posting the screenshot of the relevant methods made it easy to help.

Aiysha shahid (06:03:49) (in thread): > okay thank you:hugging_face:

C. Mirzayi (please do not tag this account) (09:06:28): > Hi everyone we will be having our weekly team meeting at 10 AM EDT tomorrow. Danya and Atrayee will be presenting.https://us02web.zoom.us/j/2737200499

C. Mirzayi (please do not tag this account) (10:28:26): > @Andre NanaWelcome

Andre Nana (10:28:27): > @Andre Nana has joined the channel

Andre Nana (10:29:00) (in thread): > Thank you Chloe.

2023-06-08

Sehyun Oh (09:42:56): > @Sehyun Oh has joined the channel

C. Mirzayi (please do not tag this account) (11:37:22): > @Jacquelyn Shevinwelcome

Jacquelyn Shevin (11:37:28): > @Jacquelyn Shevin has joined the channel

C. Mirzayi (please do not tag this account) (13:09:39): > @Levi WaldronDocumentation already existed for the taxon-level quality control alerts but I made some updates to the Potential contaminants and body site-typical help items:https://bugsigdb.org/Help:Quality_control#Taxon-level_alerts. I also added the symbols to the headers so it’s easier to know which one is which at a glance. > > I just tagged Ludwig to ask how the not host-associated list was derived as that’s the one that I couldn’t find any definitive information on where it was coming from exactly.

2023-06-09

C. Mirzayi (please do not tag this account) (10:14:12): > This article it a tough one:https://www.sciencedirect.com/science/article/pii/S1075996422001457 > * Data availability statement says no data was used for the analysis. > * RCT that was registered but trial was registered retrospectively (It’s notwrong to do this but it’s a bit of a warning sign). > * Claims to have used chi-squared test for all analyses which doesn’t really make sense to me unless they were categorizing taxa into increased vs. decreased for analysis. > * Results are super unclear with sentences like: “Among bacterial classes no significant change in OTUs was observed in before and after intervention samples in the treatment group. In the post-intervention sample, there was a drop in class Clostridia in the treatment group, and an increase in the placebo group.” > > * It’s almost entirely unclear which results were statistically significant and which were not. > Thanks to@Atrayee Samantafor bringing this to my attention. - Attachment (sciencedirect.com): Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease > To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients.Patients were randomly allocated t…

2023-06-12

C. Mirzayi (please do not tag this account) (12:32:49): > I made this quick diagram to explain confounding to Atrayee today and figured I’d post it here in case it’s useful for anyone. For a longer explanation of what confounding is and how we can account for it, you can also check out my Epidemiology for Bioinformaticians workshop (https://chloemirzayi.com/epiforbioworkshop2022/articles/EpiForBioWorkshop.html). Several recordings of this workshop are also on Youtube. - Attachment (chloemirzayi.com): Epidemiology for Bioinformaticians > epiforbioworkshop2022 - File (PNG): image.png

2023-06-14

Atrayee Samanta (00:06:41): > The statistical test used to curate this experiment (link to the article:https://www.cell.com/cell-host-microbe/fulltext/S1931-3128(14)00063-8?_returnURL=ht[…]vier.com%2Fretrieve%2Fpii%2FS1931312814000638%3Fshowall%3Dtrue) is mentioned as ‘MaAsLin’, but that is not available on bugsigdb as a test, should I leave it blank? - File (PNG): image.png

C. Mirzayi (please do not tag this account) (00:08:58) (in thread): > MaAsLin is a linear model so use “linear regression”

Atrayee Samanta (00:14:48) (in thread): > Alright, thanks!

C. Mirzayi (please do not tag this account) (15:34:26): > Hi everyone we will be having our weekly team meeting at 10 AM EDT tomorrow. Atrayee will be presenting and we will be talking about Jacquelyn’s capstone project.https://us02web.zoom.us/j/2737200499

2023-06-15

Jacquelyn Shevin (08:51:28): > Is it possible to record the second half of our team meeting this week? That way myself and others can go back and review.

C. Mirzayi (please do not tag this account) (09:43:09) (in thread): > Sure. You just need to remind me when it starts because I will forget.

Jacquelyn Shevin (09:53:12) (in thread): > Sounds good.

C. Mirzayi (please do not tag this account) (11:05:44): > @Jacquelyn ShevinI think 2887205 and the others are greengenes identifiers

C. Mirzayi (please do not tag this account) (11:10:12) (in thread): > Yes they are. I downloaded greengenes 13.8 and it is present.

Jacquelyn Shevin (11:11:43) (in thread): > Thanks, Chloe! That makes sense.

C. Mirzayi (please do not tag this account) (12:00:05): > Recording of how to download and process individual-level data through the Nephele pipeline. Please let me know if you have any questions. - File (MPEG 4 Video): video1152022303.mp4

Jacquelyn Shevin (12:07:42) (in thread): > Thanks, Chloe. I downloaded it.

Jacquelyn Shevin (16:44:48): > Hi@C. Mirzayi (please do not tag this account), after I download “ena-file-download-20230615-2042.sh” how do I start the downloading of all the files there are links for in document.

C. Mirzayi (please do not tag this account) (16:45:43) (in thread): > Windows, Mac, or Linux?

Jacquelyn Shevin (16:47:57) (in thread): > Windows

C. Mirzayi (please do not tag this account) (16:51:07) (in thread): > https://gitforwindows.org/Install Git which includes Git Bash which can run .sh files. - Attachment (gitforwindows.org): Git for Windows > We bring the awesome Git VCS to Windows

Jacquelyn Shevin (17:08:18) (in thread): > When I try to open it with Git Bash, I get ‘command not found’.

2023-06-16

Jacquelyn Shevin (12:12:02) (in thread): - File (PNG): GITBASHSNIP.png

2023-06-19

Levi Waldron (07:40:04) (in thread): > Looks like you need to install wget too:sweat_smile:running command line programs on windows can be an adventure. Microsoft’s Bing Chat sent me here (can’t believe I’m now trying Bing instead of Google, but it actually gave a full set of instructions in addition to the link to Stack Overflow!):path - wget command not found in git bash - Stack Overflow. I personally would use Docker to run a real Linux environment within Windows, but that has its own tricks, in particular the need to share a volume with your native file system to be able to save files persistently. - Attachment (Stack Overflow): wget command not found in git bash > I’ve already tried pip install wget in my cmd, which reads > >pip install wget > Requirement already satisfied: wget in c:...-32-packages (3.2) > > however when I t…

Levi Waldron (07:40:54) (in thread): > BTW@Jacquelyn Shevinwe can give you an account on the lab server or on AnVIL if this is holding you up.

2023-06-20

Atrayee Samanta (00:26:41): > I’m reviewing a particular curation (Study 636), and I see the alpha diversity curated as “unchanged” when the alpha diversity had a slight increase/decrease in the article (link to the article is:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9151971/). Should slight differences be treated as ‘unchanged’? Or should I curate them as increased/decreased no matter how small the difference is? (In the bugsigdb screenshot, the Group 1 is E- Electronic cigarette smokers.) - Attachment (PubMed Central (PMC)): Effect of electronic cigarette and tobacco smoking on the human saliva microbial community > Increasing evidence demonstrated the oral microbial community profile characteristics affected by conventional cigarettes smoking, but few studies focus on oral microbiome in response to electronic cigarettes (E-cigarettes). This study aimed to investigate … - File (PNG): image.png - File (PNG): image.png

Levi Waldron (11:36:47): > @C. Mirzayi (please do not tag this account), do you have the clustering figure that identified those two papers with an identical paper and signature?

Levi Waldron (11:38:26) (in thread): > The pairs with one or more “” are identified as statistically significantly different - if p < 0.05 is the threshold, then any number of is enough to be included. If there are no asterisks, then record it as unchanged.

Levi Waldron (11:39:18) (in thread): > For example in panel A, “QS” and “NS” are decreased compared to “S”, but no other contrasts are significant.

Jacquelyn Shevin (11:50:55) (in thread): > @Levi WaldronI attempted to get wget running on Windows and found it too difficult to get running. If I could get access to a Linux server that would probably help me on my path. Thanks!

C. Mirzayi (please do not tag this account) (14:30:07) (in thread): > Just to put it directly though Levi pretty much said the same thing: as with taxa, we only record statistically significant differences in alpha diversity. The magnitude of the difference (i.e. whether it is slight/moderate/extreme) is not important as you can find statistically significant results with even small differences or have non significant results with even large differences (depending on your power to detect differences which is primarily a function of sample size).

C. Mirzayi (please do not tag this account) (14:30:41) (in thread): > I don’t. Frans made it. I can reach out to her and see if she still has it.

C. Mirzayi (please do not tag this account) (14:47:10) (in thread): > Excuse me. It was Sharmila.

C. Mirzayi (please do not tag this account) (15:23:32) (in thread): > From Sharmilla. Study 667, with PMID: 32925716, is the one with duplicated figures from study 688 (PMID: 29097493). - File (PNG): image.png

C. Mirzayi (please do not tag this account) (15:30:21) (in thread): > The figures from the papers. Lefthand one is the original and right is the one that reproduces it. - File (PNG): image.png - File (PNG): image.png

Levi Waldron (15:49:43) (in thread): > Thank you Chloe!!!

Atrayee Samanta (23:06:47) (in thread): > Thank you so much@Levi Waldron@C. Mirzayi (please do not tag this account)that makes sense

2023-06-21

Atrayee Samanta (00:53:53): > This study (https://bugsigdb.org/Study_750) is about Profiling the salivary microbiome and there are several experiments with case and control groups as male/female, people with dentures/no dentures, etc. Can the experiments comparing groups such as the one with dentures/no dentures have the condition as ‘dentures’? What do I enter as the condition where the case and control groups are male/female? (I did not find any condition that was similar to ‘profiling the salivary microbiome’) - Attachment (BugSigDB): Study 750

C. Mirzayi (please do not tag this account) (11:47:10) (in thread): > The condition is always what they are contrasting on in a given experiment. Profiling the salivary microbiome is not a condition; it is the methodology. For the dentures vs. no dentures you would use: dentures which is an efo term (https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0010078). For male vs female pick male or female to be group 1 and use the correct efo term (for example here is the efo term for male:https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0000384).

Atrayee Samanta (12:27:22) (in thread): > Yes got it, thanks a lot!

Andre Nana (13:17:40): > I came across this study and was thinking that I can be added to BugSigDB. It is a case control study on the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis versus Healthy Individuals, published in 2021.https://pubmed.ncbi.nlm.nih.gov/33935458/ - Attachment (PubMed): Analysis of the Conjunctival Microbiome in Patients with Atopic Keratoconjunctivitis and Healthy Individuals - PubMed > The results indicated that the diversity and composition of the microbiome differs between patients with AKC and HCs.

C. Mirzayi (please do not tag this account) (15:32:31) (in thread): > Yep this looks curatable.

C. Mirzayi (please do not tag this account) (16:46:16): > Hi everyone we will be having our weekly team meeting at 10 AM EDT tomorrow. Atrayee will be presenting and we can take a look at bugSigSimple together.https://us02web.zoom.us/j/2737200499

2023-06-22

Andre Nana (09:40:50): > In this studyhttps://bugsigdb.org/Study_549, they recruited 27 patients and 37 healthy controls (HCs), but several of the study participants were excluded at some point during the quality control. Therefore, the actual experiment was conducted on 20 patients and 10 HCs. I reported these 20 patients (Group 1) and 10 controls (Group 0). Would appreciate a feedback. - Attachment (BugSigDB): Study 549

C. Mirzayi (please do not tag this account) (14:56:20) (in thread): > Awesome job Andre! This was a truly excellent first curation. I made a few small changes: > * They evaluated species richness and found no differences. This was the “Jackknife” analysis they referred to so it wasn’t clear that it was a richness test. > * You could also curate table 1 as part of the signatures. A single phylum (Parcubacteria_OD1) was decreased in cases. This taxon took some digging to figure out but I found it on NCBI’s taxonomy browser:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1794811&lvl=3&p=h[…]&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock > I have made these changes and marked the paper as reviewed. Excellent first curation! - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Andre Nana (16:11:16) (in thread): > Thanks Chloe. I was hesitating for Table 1, as it is at a higher taxonomic rank (phylum), but I can add it for sure. Will do that once I get home.

2023-06-23

Jacquelyn Shevin (12:41:32) (in thread): > @Levi WaldronWill access to supermicro allow me to run Linux? I am still working on formatting the longitudinal data.

Levi Waldron (12:42:47) (in thread): > Yes.@Andres Wokatyare you able to create the account today? If not I can do it.

Jacquelyn Shevin (12:45:24) (in thread): > Jennifer set me up with an account already. I was just making sure this was the correct account. Thanks so much.

Levi Waldron (12:45:53) (in thread): > Ah ok! Yes it is a Linux machine.

Levi Waldron (12:47:36) (in thread): > Nice work@Andre Nana!

Andre Nana (13:16:27) (in thread): > Thank you for the feedback, Professor.

2023-06-26

Atrayee Samanta (02:09:07): > Is this screenshot curatable? I was a bit confused since there’s no statistical significance mentioned; they’re just comparing the relative abundances in the samples. - File (PNG): image.png - File (PDF): alanee2018.pdf

Fatima Zohra (02:46:49) (in thread): > Not figure 4. but table 1 looks like it’s curatable. They are reporting significant differences in urinary samples in table 1.

Atrayee Samanta (09:20:04) (in thread): > Thank you! And I had curated table 1 too, I was just wondering about figure 4

Fatima Zohra (19:47:16) (in thread): > Right and you are correct since figure 4 is only comparing relative abundances with no report of statistical significance we are nor curating this figure

2023-06-27

Atrayee Samanta (09:31:20): > If I am understanding the figure 1H of this paper(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8748098/) correctly, it should be curated in three experiments: > 1. groups 0 and 1 as control vs constipation > 2. groups 0 and 1 as control vs non-constipation > 3. groups 0 and 1 as constipation vs non-constipation > is that right? > (The study has been curated athttps://bugsigdb.org/Study_741) - Attachment (PubMed Central (PMC)): An analysis of the characteristics of the intestinal flora in patients with Parkinson’s disease complicated with constipation > Parkinson’s disease (PD) is a degenerative disease of the central nervous system (CNS) and is common among the middle-aged and elderly populations. Increasing evidence shows that the gut microbiota may trigger PD through the “gut-microbiota-brain” … - Attachment (BugSigDB): Study 741 - File (PNG): image.png

C. Mirzayi (please do not tag this account) (10:47:34) (in thread): > The default for LEfSe is one against all I believe so I would curate this as: > 1. Non-constipation PD (group 1) vs. constipation PD AND controls (group 0) > > 1. Curate blue bars as increased > > 1. Constipation PD (group 1) vs. non-constipation PD AND controls (group 0) > > 1. Curate red bars as increased > > 1. Non-constipation AND constipation PD vs. controls (group 0) > > 1. Curate green bars asdecreased

Atrayee Samanta (10:53:00) (in thread): > Alright, understood, thanks!

2023-06-28

C. Mirzayi (please do not tag this account) (12:51:28): > Hi everyone we will be having our weekly team meeting at 10 AM EDT tomorrow. Jackie will be presenting her Parkinson’s Disease BugSigDB analysis. There is still room on the schedule if anyone would like to also present.https://us02web.zoom.us/j/2737200499

Andre Nana (13:34:08): > Hi Chloe, I started curating another paper on conjunctival microbiome in Trachoma. I will add more experiment this evening. I will present tomorrow for feedback.https://bugsigdb.org/Study_563/Experiment_1 - Attachment (BugSigDB): Study 563/Experiment 1

C. Mirzayi (please do not tag this account) (15:42:13) (in thread): > Awesome please put yourself on the schedule here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EST - Attachment (BugSigDB): PresentationSignup

Andre Nana (15:58:03) (in thread): > Done! Thank you.

2023-06-29

Atrayee Samanta (09:16:25): > For this studyhttps://bugsigdb.org/Study_749, I cannot find the DOI from the PMID, but the given DOI is wrong - Attachment (BugSigDB): Study 749

Atrayee Samanta (09:17:47): > (I can’t find the article via sci-hub using the PMID either)

C. Mirzayi (please do not tag this account) (11:07:28) (in thread): > Looks like it should be 32717152 but that’s already curated. Deleting this one.

2023-06-30

USLACKBOT (09:19:58): > WaldronLabhas joined this channel by invitation fromcommunity-bioc.

2023-07-03

Atrayee Samanta (06:51:07): > The caption says that the different letters- a, b and c indicate the statistical significance. Does this mean that two values belonging to different columns are statistically significant to each other only if both of them are marked by the same letter (say, if both are marked with an ‘a’)? - File (PNG): image.png

Levi Waldron (15:25:55) (in thread): > As I read it, those with the same letter across a row are NOT significantly different from each other. If they don’t share the same letter then they’re different. That seems to comport with differences in the means too.

2023-07-04

Atrayee Samanta (08:05:22) (in thread): > Okay, got it. Thanks a lot@Levi Waldron!

2023-07-05

C. Mirzayi (please do not tag this account) (09:28:15) (in thread): > This is a common way of reporting results from an ANOVA with post-hoc pairwise comparisons called compact letter display or CLDhttps://en.wikipedia.org/wiki/Compact_letter_display. - Attachment: Compact letter display > Compact Letter Display (CLD) is a statistical method to clarify the output of multiple hypothesis testing when using the ANOVA and Tukey’s range tests. CLD can also be applied following the Duncan’s new multiple range test (which is similar to Tukey’s range test). CLD facilitates the identification of variables, or factors, that have statistically different means (or averages) vs. the ones that do not have statistically different means (or averages). > The basic technique of compact letter display is to label variables by one or more letters, so that variables are statistically indistinguishable if and only if they share at least one letter. The problem of doing so, using as few distinct letters as possible can be represented combinatorially as the problem of computing an edge clique cover of a graph representing pairs of indistinguishable variables.As well as marking distinguishability in this way, CLD also ranks variables, or factors, by their respective mean (or average) in descending order. The CLD methodology can be applied to tabular data (spreadsheet, data frame) or visual data (box plot and bar chart).

Atrayee Samanta (12:32:28) (in thread): > Ohh, that helps a lot, thank you!

2023-07-06

UBNSEMS3S (09:02:39): > Hi everyone we will be having our weekly team meeting at 10 AM EDT today. Jackie and Atrayee will be presenting.https://us02web.zoom.us/j/2737200499

UBNSEMS3S (10:39:51): > Requested recording of me presenting on analyzing BSDB. - File (MPEG 4 Video): video1764587779.mp4

Andre Nana (10:44:07) (in thread): > Thank you Chloe.

U03L1PX3D52 (11:04:08): > Hi everyone, I was wondering what people do when curating an article and the author has OTU numbers along with the taxon name. Does this affect the curation at all? - File (PNG): OTUSNIP2070623.png - File (PNG): OUTSNIP1070623.png

2023-07-07

U1LCB8WEA (10:00:59) (in thread): > Do you know what those OTU IDs mean and whetherthey’rethe same across studies? I could just answer butit’sa good learning opportunity to read a bit about it.

2023-07-09

U03L1PX3D52 (17:32:37) (in thread): > OTU IDs represent a taxonomic unit of a bacteria species or genus identified by a cluster of similar sequence variants of the 16S rDNA marker. So my understanding is that it is part of the raw data that is used when analyzing 16S data. This leads me to believe OTU IDs should not influence the curation as they have already been accounted for in the signatures.

2023-07-10

UBNSEMS3S (12:57:22): > Since I am going to be out of town Thursday. July 13th through Thursday, July 20th, I wanted to check to see if people would potentially want to meet on 7/12 and 7/21 instead for weekly team meetings?

2023-07-11

U1LCB8WEA (11:47:21) (in thread): > Operational Taxonomic Units are generated byde novoclustering of reads based on sequence similarity at an arbitrary degree of similarity like 97.5% shared sequences. Each cluster is then mapped to the bacterial taxonomy, usually at the genus level. So OTU IDs aren’t part of the raw data, but the actual numbers refer only to the clustering specifically in that dataset, and are unrelated to OTU IDs in another dataset - the only thing that can be compared to another dataset is the genus, class, family, or order that they’ve named, so you shouldn’t record the OTU number.

UBNSEMS3S (16:35:48): > Hi everyone we will be having our weekly team meeting at 10 AM EDT tomorrow (Wednesday). No one has signed up to present yet.https://us02web.zoom.us/j/2737200499

2023-07-18

Atrayee Samanta (04:59:01): > This figure (Figure 8 of the paper) displays the only the p-values, but nothing other than that. How do I record the increase/decrease in the signatures? (Link to the paper:https://link.springer.com/article/10.1007/s00277-019-03599-w) - Attachment (SpringerLink): The oral microbiome of patients undergoing treatment for severe aplastic anemia: a pilot study > Annals of Hematology - The microbiome, an intriguing component of the human body, composed of trillions of microorganisms, has prompted scientific exploration to identify and understand its… - File: image.png

U1LCB8WEA (08:37:50) (in thread): > The only species that they provide direction of differential abundance for, and on quick scan the only ones they discuss in the text, areHaemophilus parainfluenzae,Rothia mucilaginosa, andPrevotella histicola. Youcouldconsider thesupplemental tabletaxa that are “Not in HMP but present in…” as signatures, but I’m doubtful it’s worthwhile given the lack of taxonomic specificity in that table and the challenges of comparing across studies.

Atrayee Samanta (23:50:37) (in thread): > Yes got it, thank you!

2023-07-21

UBNSEMS3S (09:33:21): > Hi everyone we will be having our weekly team meeting at 10 AM EDT today. Atrayee has signed up to present.https://us02web.zoom.us/j/2737200499

2023-07-26

UBNSEMS3S (15:21:19): > Hi everyone we will be having our weekly team meeting at 10 AM EDT tomorrow (Thursday). Jackie and Andre have signed up to present.https://us02web.zoom.us/j/2737200499

Andre Nana (15:30:38) (in thread): > Thanks Chloe. I just signed up to present this article as well. It is an interesting paper but there are some issues that I would like to discuss.https://www.frontiersin.org/articles/10.3389/fmicb.2015.00020/full - Attachment (Frontiers): Microbiota disbiosis is associated with colorectal cancer > The dysbiosis of the human intestinal microbiota is linked to sporadic colorectal carcinoma (CRC). The present study was designed to investigate the gut microbiota distribution features in CRC patients. We performed pyrosequencing based analysis of the 16S rRNA gene V3 region to investigate microbiota of the cancerous tissue and adjacent non-cancerous normal tissue in proximal and distal CRC samples. The results revealed that the microbial structures of the CRC patients and healthy individuals differed significantly. Firmicutes and Fusobacteria were over-represented whereas Proteobacteria was under-represented in CRC patients. In addition, Lactococcus and Fusobacterium exhibited a relatively higher abundance while Pseudomonas and Escherichia-Shigella was reduced in cancerous tissues compared to adjacent non-cancerous tissues. Meanwhile, the overall microbial structures of proximal and distal colon cancerous tissues were similar; but certain potential pro-oncogenic pathogens were different. These results suggested that the mucosa-associated microbiota is dynamically associated with CRC, which may provide evidences for microbiota-associated diagnostic, prognostic, preventive, and therapeutic strategies for CRC.

UBNSEMS3S (15:34:26) (in thread): > Awesome! Looking forward to your presentation.

2023-07-27

U03L1PX3D52 (12:28:53): > Hello, I am working on removing 5 signatures from my data to improve the quality of my heatmap. I am not quite sure how to go about this, I tried the select(-) function but I don’t think that was correct. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + select(-"723 1/2", -"741 3/1", -"723 5/2", -"716 3/2", -"724 3/1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > Error in `select()`: > ! Can't subset columns that don't exist. > ✖ Column `723 1/2` doesn't exist. > Backtrace: > 1. ... %>% mutate(Condition = tolower(Condition)) > 5. dplyr:::select.data.frame(., -"723 1/2", -"741 3/1", -"723 5/2", -"716 3/2", -"724 3/1") >

UBNSEMS3S (13:35:14) (in thread): > usefilterinstead of select

UBNSEMS3S (13:35:30) (in thread): > selectselects columns,filterselects rows.

U03L1PX3D52 (13:42:43) (in thread): > Thanks. I have a new error message. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(-"723 1/2", -"741 3/1", -"723 5/2", -"716 3/2", -"724 3/1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > Error in `filter()`: > ℹ In argument: `-"723 1/2"`. > Caused by error in `-"723 1/2"`: > ! invalid argument to unary operator > Backtrace: > 1. ... %>% mutate(Condition = tolower(Condition)) > 5. dplyr:::filter.data.frame(., -"723 1/2", -"741 3/1", -"723 5/2", -"716 3/2", -"724 3/1") > 6. dplyr:::filter_rows(.data, dots, by) > 7. dplyr:::filter_eval(...) > 9. mask$eval_all_filter(dots, env_filter) > 10. dplyr (local) eval() >

UBNSEMS3S (13:47:09) (in thread): > You need to specify what column you’re filtering on see an example here:https://www.statology.org/dplyr-filter-not-in/ - Attachment (Statology): dplyr: How to Use a “not in” Filter - Statology > This tutorial explains how to use a “not in” filter in dplyr, including several examples.

U03L1PX3D52 (14:15:40) (in thread): > I tried it out just removing one of the signatures and got this error message. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(-!Study %in% c('Study 723') & !Experiment %in% c('Experiment 1') & !Signature page name %in% c('Signature 2')) %>% > Error: unexpected symbol in: > " dplyr::filter(`Condition` == "Parkinson's disease") %>% > filter(-!Study %in% c('Study 723') & !Experiment %in% c('Experiment 1') & !Signature page" >

U03L1PX3D52 (14:51:55) (in thread): > I tried to filter just for the signatures I want to remove and the code worked. But then I get an error on the next step. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(!Study %in% c('Study 723') & !Experiment %in% c('Experiment 1') & !`Signature page name` %in% c('Signature 2')) %>% > + filter(!Study %in% c('Study 741') & !Experiment %in% c('Experiment 3') & !`Signature page name` %in% c('Signature 1')) %>% > + filter(!Study %in% c('Study 723') & !Experiment %in% c('Experiment 5') & !`Signature page name` %in% c('Signature 2')) %>% > + filter(!Study %in% c('Study 716') & !Experiment %in% c('Experiment 3') & !`Signature page name` %in% c('Signature 2')) %>% > + filter(!Study %in% c('Study 724') & !Experiment %in% c('Experiment 3') & !`Signature page name` %in% c('Signature 1')) %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.sub[,"Condition"]) > > parkinson's disease > 35 > > allsige <- bugsigdbr::getSignatures(dat.subc , tax.id.type = "taxname") > Error in names(sigs) <- paste(snames$id, snames$titles, sep = "_") : > 'names' attribute [1] must be the same length as the vector [0] >

UBNSEMS3S (14:58:55) (in thread): > It should look likefilter (!Study %in% c('Study 716', 'Study 723', ETC.))

U03L1PX3D52 (15:06:25) (in thread): > OK my code looks better but I am getting the same error message. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(-!Study %in% c('Study 723', 'Study 741', 'Study 723', 'Study 716', 'Study 724') & !Experiment %in% c('Experiment 1', 'Experiment 3', 'Experiment 5', 'Experiment 3', 'Experiment 3') & !`Signature page name` %in% c('Signature 2', 'Signature 1', 'Signature 2', 'Signature 2', 'Signature 1')) %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.sub[,"Condition"]) > > parkinson's disease > 35 > > allsige <- bugsigdbr::getSignatures(dat.subc , tax.id.type = "taxname") > Error in names(sigs) <- paste(snames$id, snames$titles, sep = "_") : > 'names' attribute [1] must be the same length as the vector [0] >

UBNSEMS3S (15:12:38) (in thread): > Can you show me what’s indat.subc?

U03L1PX3D52 (15:32:31) (in thread): - File (PNG): snipofcleaneddata072723.png

2023-07-28

UBNSEMS3S (09:29:02) (in thread): > So it’s empty. That’s the issue.

UBNSEMS3S (09:29:06) (in thread): > Something is wrong with the filter.

U03L1PX3D52 (12:49:27) (in thread): > The issue only started when I added this line of code: > filter(-!Study %in% c(‘Study 723’, ‘Study 741’, ‘Study 723’, ‘Study 716’, ‘Study 724’) & !Experiment %in% c(‘Experiment 1’, ‘Experiment 3’, ‘Experiment 5’, ‘Experiment 3’, ‘Experiment 3’) & !‘Signature page name’ %in% c(‘Signature 2’, ‘Signature 1’, ‘Signature 2’, ‘Signature 2’, ‘Signature 1’)) %>%

U03L1PX3D52 (13:56:28) (in thread): > I am trying to filter out 5 signatures but filtering out everything instead, I think.

U03L1PX3D52 (14:19:07) (in thread): > I seperated the code to look at each signature I wanted removed. I think they are filtering out more than just the 1 I am hoping for. It looks like this line of code is removing 21 signatures on it’s own. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + # filter(-!Study %in% c('Study 723', 'Study 741', 'Study 723', 'Study 716', 'Study 724') & !Experiment %in% c('Experiment 1', 'Experiment 3', 'Experiment 5', 'Experiment 3', 'Experiment 3') & !'Signature page name' %in% c('Signature 2', 'Signature 1', 'Signature 2', 'Signature 2', 'Signature 1')) %>% > + filter(-!Study %in% c('Study 723') & !Experiment %in% c('Experiment 1') & !'Signature page name' %in% c('Signature 2')) %>% > + # filter(-!Study %in% c('Study 741') & !Experiment %in% c('Experiment 3') & !'Signature page name' %in% c('Signature 1')) %>% > + # filter(-!Study %in% c('Study 723') & !Experiment %in% c('Experiment 5') & !'Signature page name' %in% c('Signature 2')) %>% > + # filter(-!Study %in% c('Study 716') & !Experiment %in% c('Experiment 3') & !'Signature page name' %in% c('Signature 2')) %>% > + # filter(-!Study %in% c('Study 724') & !Experiment %in% c('Experiment 3') & !'Signature page name' %in% c('Signature 1')) %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.subc[,"Condition"]) > > parkinson's disease > 14 >

2023-07-31

UBNSEMS3S (09:46:09) (in thread): > Ok I think I see what’s wrong. When you do a filter like& !Experiment %in% c('Experiment 1', 'Experiment 3', 'Experiment 5', 'Experiment 3', 'Experiment 3')You are saying to excludeevery Experiment 1, Experiment 3, etc. The code doesn’t take into account the study filters as that is part of a separate statement separated by an AND operator. > > The way I would do it is define a unique identifier for each study-experiment-signature combination and then filter out the unwanted ones based on that identifier. Something like: > > dat.subc$id <- paste(dat.subc$Study, dat.subc$Experiment, dat.subc$`Signature page name`, sep="-") > dat.subc %>% filter(id != "Study 263-Experiment 1-Signature 2") %>% filter(id != "Study 283-Experiment 2-Signature 3") etc. > > You could probably do it all in a single filtering step using!id %in%but I like separating it out for two reasons: 1. I find it much easier to read when it’s separated out like this and 2. it’s easier to modify.

U03L1PX3D52 (14:22:00) (in thread): > > > dat.subc$id <- paste(dat.subc$Study, dat.subc$Experiment, dat.subc$`Signature page name`, sep="-") > > dat.subc %>% #filter(id != "Study 723-Experiment 1-Signature 2") %>% #filter(id != "Study 741-Experiment 3-Signature 1") %>% > + #filter(id != "Study 723-Experiment 5-Signature 2") %>% > + #filter(id != "Study 716-Experiment 3-Signature 2") %>% > + #filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.subc[,"Condition"]) > > parkinson's disease > 14 > > When I run the code this way, it only selects for 14 signatures whether or not I filter out the 5 experiments. > > > dat.subc$id <- paste(dat.subc$Study, dat.subc$Experiment, dat.subc$`Signature page name`, sep="-") > > dat.subc %>% filter(id != "Study 723-Experiment 1-Signature 2") %>% filter(id != "Study 741-Experiment 3-Signature 1") %>% > + filter(id != "Study 723-Experiment 5-Signature 2") %>% > + filter(id != "Study 716-Experiment 3-Signature 2") %>% > + filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.subc[,"Condition"]) > > parkinson's disease > 14 >

UBNSEMS3S (14:28:58) (in thread): > Because you didn’t save the results of your filtering to any object.

U03L1PX3D52 (15:44:25) (in thread): > OK I think I saved the filters to an object but now it is filtering out all but 11 signatures which is new but still wrong (it should be 31 total). > > > dat.subc$id <- paste(dat.subc$Study, dat.subc$Experiment, dat.subc$`Signature page name`, sep="-") > > dat.subc <- dat.subc %>% #filter(id != "Study 723-Experiment 1-Signature 2") %>% > + filter(id != "Study 741-Experiment 3-Signature 1") %>% > + filter(id != "Study 723-Experiment 5-Signature 2") %>% > + filter(id != "Study 716-Experiment 3-Signature 2") %>% > + filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.subc[,"Condition"]) > > parkinson's disease > 11 >

UBNSEMS3S (15:46:36) (in thread): > Recreate the dat.subc object from scratch as it was likely overwritten by one of your previous filters. In general I like to save filtered objects to new variable names to prevent this sort of issue.

U03L1PX3D52 (15:56:43) (in thread): > I realized it could also be because I am missing the line of code selecting for Parkinson’s articles curated by me. This gets a whole new error message. > > > dat.subc$id <- paste(dat.subc$Study, dat.subc$Experiment, dat.subc$`Signature page name`, sep="-") > > dat.subc <- dat.subc %>% subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(id != "Study 723-Experiment 1-Signature 2") %>% > + filter(id != "Study 741-Experiment 3-Signature 1") %>% > + filter(id != "Study 723-Experiment 5-Signature 2") %>% > + filter(id != "Study 716-Experiment 3-Signature 2") %>% > + filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > Error in dat.subc %>% subsetByCurator(dat, "Jacquelynshevin") %>% dplyr::filter(Condition == : > could not find function "%>%" > > suppressPackageStartupMessages({ > + library(bugSigSimple) > + library(bugsigdbr) > + library(BugSigDBStats) > + library(tidyverse) > + library(stringr) > + library(kableExtra) > + library(dplyr) > + library(ComplexHeatmap) > + }) > > dat.subc$id <- paste(dat.subc$Study, dat.subc$Experiment, dat.subc$`Signature page name`, sep="-") > > dat.subc <- dat.subc %>% subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(id != "Study 723-Experiment 1-Signature 2") %>% > + filter(id != "Study 741-Experiment 3-Signature 1") %>% > + filter(id != "Study 723-Experiment 5-Signature 2") %>% > + filter(id != "Study 716-Experiment 3-Signature 2") %>% > + filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > Error in `filter()`: > ℹ In argument: ``%in%`(...)`. > Caused by error: > ! object 'Jacquelynshevin' not found > Backtrace: > 1. ... %>% mutate(Condition = tolower(Condition)) > 19. Jacquelynshevin %in% `<df[,50]>` >

U03L1PX3D52 (15:58:11) (in thread): > I tried renaming but got this error message. > > > dat.sube$id <- paste(dat.sube$Study, dat.sube$Experiment, dat.sube$`Signature page name`, sep="-") > Error: object 'dat.sube' not found >

UBNSEMS3S (16:14:24) (in thread): > You need to create an object called dat.sube first. If you’re working with dat as the initial BSDB export then a simpledat.sube <- datwill suffice.

U03L1PX3D52 (16:22:59) (in thread): > OK that worked. Thank you! I am still coming up with issues related to adding this line of code. “subsetByCurator(dat,”Jacquelynshevin”) %>% > dplyr::filter(Condition == “Parkinson’s disease”) %>%” but if I do not include it, the table pulls up articles not curated by me.

U03L1PX3D52 (16:25:48) (in thread): > Whether I try “subsetByCurator(dat,…” or “subsetByCurator(dat.sube,…” I get the same error message. > > Error in `filter()`: > ℹ In argument: ``%in%`(...)`. > Caused by error: > ! object 'Jacquelynshevin' not found > Backtrace: > 1. ... %>% mutate(Condition = tolower(Condition)) > 19. Jacquelynshevin %in% `<df[,50]>` >

UBNSEMS3S (17:04:51) (in thread): > Put your name in quotation marks

U03L1PX3D52 (17:16:09) (in thread): > I tried. It is still giving me the same error whether I do “Jacquelynshevin” or ‘Jacquelynshevin’ > > > dat.sube <- dat > > dat.sube$id <- paste(dat.sube$Study, dat.sube$Experiment, dat.sube$`Signature page name`, sep="-") > > dat.sube <- dat.sube %>% subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(id != "Study 723-Experiment 1-Signature 2") %>% > + filter(id != "Study 741-Experiment 3-Signature 1") %>% > + filter(id != "Study 723-Experiment 5-Signature 2") %>% > + filter(id != "Study 716-Experiment 3-Signature 2") %>% > + filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > Error in `filter()`: > ℹ In argument: ``%in%`(...)`. > Caused by error: > ! object 'Jacquelynshevin' not found > Backtrace: > 1. ... %>% mutate(Condition = tolower(Condition)) > 19. Jacquelynshevin %in% `<df[,50]>` >

UBNSEMS3S (17:22:32) (in thread): > Ah it’s because you are using two different objectsdatanddat.sube. Try: > > subsetByCurator(dat.sube, "Jacquelynshevin") %>% > dplyr::filter(`Condition` == "Parkinson's disease") %>% > filter(id != "Study 723-Experiment 1-Signature 2") %>% > filter(id != "Study 741-Experiment 3-Signature 1") %>% > filter(id != "Study 723-Experiment 5-Signature 2") %>% > filter(id != "Study 716-Experiment 3-Signature 2") %>% > filter(id != "Study 724-Experiment 3-Signature 1") %>% > mutate(`Body site` = tolower(`Body site`)) %>% > mutate(`Condition` = tolower(`Condition`)) >

U03L1PX3D52 (17:31:40) (in thread): > I tried that too. The error changed slightly. > > > dat.sube <- dat > > dat.sube$id <- paste(dat.sube$Study, dat.sube$Experiment, dat.sube$`Signature page name`, sep="-") > > dat.sube <- dat.sube %>% subsetByCurator(dat.sube, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(id != "Study 723-Experiment 1-Signature 2") %>% > + filter(id != "Study 741-Experiment 3-Signature 1") %>% > + filter(id != "Study 723-Experiment 5-Signature 2") %>% > + filter(id != "Study 716-Experiment 3-Signature 2") %>% > + filter(id != "Study 724-Experiment 3-Signature 1") %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > Error in `filter()`: > ℹ In argument: ``%in%`(...)`. > Caused by error: > ! object 'Jacquelynshevin' not found > Backtrace: > 1. ... %>% mutate(Condition = tolower(Condition)) > 19. Jacquelynshevin %in% `<df[,51]>` >

U03L1PX3D52 (17:32:03) (in thread): > It’s <df[,51]> instead of <df[,50]>

UBNSEMS3S (17:40:46) (in thread): > Because you can’t have that first bit

UBNSEMS3S (17:40:56) (in thread): > Remove the dat.sube %>% from the beginning

U03L1PX3D52 (18:07:06) (in thread): > Thank you, Chloe! That worked perfectly.

2023-08-01

U03L1PX3D52 (15:07:36): > Hello everyone, I am working on editing the labels of the rows and columns of a heatmap. To set up the commands for having each row and column display just the study/experiment/signature values without any additional text, would I start with something like: > top_annotation = HeatmapAnnotation(df = data.frame(name = colnames(jmate)…. > right_annotation = rowAnnotation(df = data.frame(name = rownames(jmate)), > Is that on the right track? > > > sigcorse <- cor(t(cmate)) > > siglengthse <- sapply(sigse, length) > > hae <- HeatmapAnnotation(`Signature Length` = anno_barplot(siglengthse)) > > hre <- rowAnnotation(`Signature Length` = anno_barplot(siglengthse)) > > hme <- Heatmap( > + sigcorse, > + top_annotation = hae, left_annotation = hre, > + row_names_max_width = unit(.05, "cm"), > + column_names_max_height = unit(.1, "cm"), > + # row_labels = sub(".+:", "", rownames(sigcors)), ##removing study just to make signature names legible > + column_labels = sub(".+:", "", colnames(sigcorse)) > + ) > > hme >

U03L1PX3D52 (15:09:47) (in thread): > Basically, I am having trouble reading the heatmap to actually see where the final possible signature needing to be removed is depicted on the heatmap.

2023-08-09

Andre Nana (11:01:48): > I curated this newly published article on oral cancer. Would appreciate a feedback (needs review).Thank you.https://bugsigdb.org/Study_657 - Attachment (BugSigDB): Study 657

UBNSEMS3S (11:17:23) (in thread): > Hi Andre, why don’t you present this curation at tomorrow’s meeting?

Andre Nana (11:18:16) (in thread): > Sure. I will do that.

UBNSEMS3S (14:07:29): > Hi everyone. We will be meeting tomorrow (Thursday) at 10 AM EDT. Andre is signed up to present.https://us02web.zoom.us/j/2737200499

2023-08-10

Atrayee Samanta (00:12:19): > Hi I’m a bit late, but I signed up to present too!

Andre Nana (10:54:26): > In this article that I curated, the authors analyzed the microbiome composition in oral cancer versus healthy controls and went further to include the smoking status, using the Global Test (globaltest package, version 5.44.0) in R. I wonder if the results are curatable. I provided the article, the supplementary file on Global Test, and the result file as well. Thank you. - File (Word Document): 40168_2023_1613_MOESM2_ESM.docx - File (Excel Spreadsheet): 40168_2023_1613_MOESM3_ESM.xlsx - File (PDF): Salivary microbiome profiles of oral cancer patients analyzed before and after treatment.pdf

2023-08-11

U1LCB8WEA (02:18:12): > I don’t think the Global Test they’re describing was used to test association between individual taxa and the outcome , so itwouldn’tproduce a signature to record. Or did you find something?edgeR on the other hand would produce signatures.

Andre Nana (12:06:05): > I see. Indeed, they generated a heatmap with EdgeR (Figure A2.1 in the additional Doc. file) showing the impact of covariates on the salivary microbiome. It would have been nice to curate the impact of dentition, but the quality of the image doesn’t allow me to accurately associate all zOTUs to their specific values (colors). I think, I will stick to the key results in the main paper. Thank you.

U1LCB8WEA (12:13:59): > Sounds good!

2023-08-17

UBNSEMS3S (09:30:26): > Hi everyone. We will be meeting today (Thursday) at 10 AM EDT. Andre and Atrayee are signed up to present.https://us02web.zoom.us/j/2737200499

2023-08-18

UBNSEMS3S (11:30:25): > <@U02CNMR4YEA>

UBNSEMS3S (11:30:44): > Let us know if you can see this

U02CNMR4YEA (21:20:06): > Yes, sorry I am just seeing it now. Thank you!

2023-08-21

UBNSEMS3S (09:49:26): > Great!

2023-08-23

UBNSEMS3S (16:48:58): > Hi everyone. We will be meeting tomorrow (Thursday) at 10 AM EDT. Mary is signed up to present.https://us02web.zoom.us/j/2737200499

U02CNMR4YEA (23:09:01): > Hi Everyone! Since I am just re-engaging with BugSigDB material, I am hoping you might all be willing to help me with the “Statistical Analysis” and “Alpha Diversity” portions for the paper I am curating PMID 37586456. Thanks in advance:grinning:

2023-08-24

UBNSEMS3S (09:08:35): > Looking forward to it Mary! As a note, I may have to be on mute for most of the meeting unfortunately. They are doing work in my apartment today and there is a lot of banging. I will be sure to give plenty of feedback and comments when I can though. Sorry for the inconvenience.

2023-08-26

USLACKBOT (19:48:53): > This message was deleted.

2023-08-27

U1LCB8WEA (08:34:41) (in thread): > Mysterious…

U01MW62UDQR (12:29:11) (in thread): > I’m sorry. I somehow pocket slacked that text and an image.

2023-08-30

UBNSEMS3S (16:51:56): > Hi everyone. We will be meeting tomorrow (Thursday) at 10 AM EDT. Currently no one is signed up to present but we can still convene to see if there are any questions or topics for discussion.https://us02web.zoom.us/j/2737200499

Andre Nana (20:06:45): > Hi Chloe, sorry for the late notice. I will be presenting this article that I curatedhttps://bugsigdb.org/Study_758. > Also, there are 3 experiments instead of 4 (number 2 and number 4 are the same). I decided to include the phylum data and wanted to make the reading easy by aligning baseline controls vs patients experiments first. But after duplicating experiment 2 to push it to the last position, I cannot delete the repeated number 2 position as I am not an administrator of the Website. We can discuss this during the lab meeting. Thanks - Attachment (BugSigDB): Study 758 - File (PDF): xu2014.pdf

2023-08-31

UBNSEMS3S (10:33:12): > Metastats:https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1000352LEfSe:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218848/pdf/gb-2011-12-6-r60.pdf - Attachment (journals.plos.org): Statistical Methods for Detecting Differentially Abundant Features in Clinical Metagenomic Samples > Author Summary The emerging field of metagenomics aims to understand the structure and function of microbial communities solely through DNA analysis. Current metagenomics studies comparing communities resemble large-scale clinical trials with multiple subjects from two general populations (e.g. sick and healthy). To improve analyses of this type of experimental data, we developed a statistical methodology for detecting differentially abundant features between microbial communities, that is, features that are enriched or depleted in one population versus another. We show our methods are applicable to various metagenomic data ranging from taxonomic information to functional annotations. We also provide an assessment of taxonomic differences in gut microbiota between lean and obese humans, as well as differences between the functional capacities of mature and infant gut microbiomes, and those of microbial and viral metagenomes. Our methods are the first to statistically address differential abundance in comparative metagenomics studies with multiple subjects, and we hope will give researchers a more complete picture of how exactly two environments differ.

2023-09-04

U02CNMR4YEA (17:46:15): > I hope everyone is having a great weekend! I am noticing that when I begin to enter a taxon in bugsigdb, it never provides options from which to choose. The name I enter is allowed but then is flagged. When I look the taxon up and use the number, it is not flagged. Any ideas? (As an aside, I think I remember when I was curating papers previously (before this semester) I would begin to enter a taxon and as soon as it recognized the first letters, options would appear from which to choose.) Thanks for any assistance and have a great afternoon!

2023-09-05

UBNSEMS3S (09:24:34) (in thread): > Yeah it should be appearing when you start to type it in. Let me look and make sure it’s working on my end.

Atrayee Samanta (10:44:39) (in thread): > I think it’s been several weeks since I faced this, I just thought it was a redesign of BugSigdb. It’s been accepting only taxonomic ids for me for a pretty long time too

UBNSEMS3S (11:39:10) (in thread): > Yeah I can confirm it’s not working right. I am going to make a bug report on bugsigdb’s github. I encourage you to point these things out as soon as they occur as always because it’s often a bug and not a feature removal.

2023-09-06

U1LCB8WEA (05:16:25) (in thread): > Thank you for reporting this bug<@U02CNMR4YEA>! Curators are our most important testers, so do make sure to let us know if something is not working as you expected. And thank you for making the formal bug report<@UBNSEMS3S>(https://github.com/waldronlab/BugSigDB/issues/188) - Attachment: #188 Taxon name autocomplete not working > When I type in a taxon ID, BugSigDB autocomplete works; however, it no longer works with taxon name like it used to. Some examples of it not suggesting anything for common taxa: > > image
> image
> image

2023-09-07

UBNSEMS3S (09:19:15): > Hi everyone. We will be meeting today (Thursday) at 10 AM EDT. Mary and Jackie are signed up to present.https://us02web.zoom.us/j/2737200499

UBNSEMS3S (10:09:14): > https://github.com/waldronlab/BugSigDB/issues

U03L1PX3D52 (11:02:24): > In case anyone wants to look over my Capstone Proposal draft: - File (Word Document): Capstone Research Paper Proposal Worksheet_Shevin (1).docx

Andre Nana (11:21:09) (in thread): > I see that you already have a figure in your proposal showing the molecular mechanism ( point 16).

Andre Nana (11:21:45) (in thread): > So, my suggestion is no longer relevant.

U03L1PX3D52 (11:34:09) (in thread): > That’s the DAG. The image you sent could be good for presenting.

2023-09-08

U1LCB8WEA (10:19:01) (in thread): > This looks good<@U03L1PX3D52>! It should be good enough for a Capstone proposal, but a bit of feedback: > * the DAG isn’t acyclic, and dopaminergic medication isn’t a confounder according to the direction of the arrows > * “using RStudio to analyze curated metagenomic data from published articles” is too generic to be part of how you are addressing a gap in the literature. The sentence that you are performing meta-analysis gets you started on the right track. > * your answer to “What is the relevance of your question” is good in that it shows engagement with the literature. but eventually for your Introduction you would want to synthesize/connect these summaries more, and make clear the specific relevance of your research question aboutPrevotellaceae > * For the specific hypothesis, it is specifically* ****relative abundance*ofPrevotellaceae** > * For the “what variables” question, state how the variables are measured by the studies

2023-09-09

U02CNMR4YEA (11:23:25): > Happy Saturday! I began entering a study and it seems that they only reported relative abundances with no statistical analyses. Can I request confirmation and, if I am correct, also request removal of the study? The study is PMID 32717380. Thank you and I apologize for the inconvenience. Have a great day everyone!

U02CNMR4YEA (14:48:20): > Do we include studies of microbiota in subgroups of “healthy” individuals? For example, I found a paper that analyzed the difference in ocular surface microbiome of young vs older participants and male vs female differences. Thank you!

U1LCB8WEA (14:50:37): > Absolutely!Age and sex-associated microbiomes are interesting.

U02CNMR4YEA (15:59:31) (in thread): > Awesome! Thank you.

2023-09-10

U02CNMR4YEA (18:20:22) (in thread): > Good afternoon! Hopefully, everyone is having a good weekend. What would we put for the “Condition” when curating a study that only looks at subgroups in the healthy state?

2023-09-12

U1LCB8WEA (09:41:09) (in thread): > What subgroups are they comparing?

U03L1PX3D52 (16:33:00): > I was able to get this code running before but now I get an error: > > > suppressPackageStartupMessages({ > + library(bugSigSimple) > + library(bugsigdbr) > + library(BugSigDBStats) > + library(tidyverse) > + library(stringr) > + library(kableExtra) > + library(dplyr) > + library(ComplexHeatmap) > + }) > Error in value[[3L]](cond) : > Package 'bugsigdbr' version 1.7.4 cannot be unloaded: > Error in unloadNamespace(package) : namespace 'bugsigdbr' is imported by 'bugSigSimple' so cannot be unloaded > > >

Ludwig Geistlinger (19:25:02): > 5 years in the making. 3000 microbial signatures from 750 studies, and counting. > BugSigDB is out in Nature Biotechnology - Attachment (Nature): BugSigDB captures patterns of differential abundance across a broad range of host-associated microbial signatures > Nature Biotechnology - A database of microbial signatures is used for systematic comparison of differential abundance patterns.

Ludwig Geistlinger (19:25:31): > Huge thanks to all curators! It is your hard work and the scrutiny that you apply to every single paper that makes BugSigDB possible and that makes it a valuable resource for the interpretation of microbiome studies going forward.

U02CNMR4YEA (20:26:16) (in thread): > Sex and age

U02CNMR4YEA (20:26:44) (in thread): > Male/female and “young”/“old”

2023-09-13

U1LCB8WEA (08:50:25): > Also there is a “Research Briefing” summarizing the work in one page for a broader aucience, in Nature:https://rdcu.be/dlVRl

UBNSEMS3S (09:34:42) (in thread): > Amazing!

UBNSEMS3S (09:35:03) (in thread): > We can take a look during the meeting tomorrow.

U03L1PX3D52 (13:37:10) (in thread): > I got it working! I think it was the path file location.

U03L1PX3D52 (13:44:58) (in thread): > I have a new error we can look at tomorrow. somehow this is returning 0 observations now. > > > dat.subc <- subsetByCurator(dat, "Jacquelynshevin") %>% > + dplyr::filter(`Condition` == "Parkinson's disease") %>% > + filter(-!Study %in% c('Study 723', 'Study 741', 'Study 723', 'Study 716', 'Study 724') & !Experiment %in% c('Experiment 1', 'Experiment 3', 'Experiment 5', 'Experiment 3', 'Experiment 3') & !`Signature page name` %in% c('Signature 2', 'Signature 1', 'Signature 2', 'Signature 2', 'Signature 1')) %>% > + mutate(`Body site` = tolower(`Body site`)) %>% > + mutate(`Condition` = tolower(`Condition`)) > > table(dat.sub[,"Condition"]) > > parkinson's disease > 35 > > allsige <- bugsigdbr::getSignatures(dat.subc , tax.id.type = "taxname") > Error in names(sigs) <- paste(snames$id, snames$titles, sep = "_") : > 'names' attribute [1] must be the same length as the vector [0] >

U1LCB8WEA (13:52:18) (in thread): > Use the closest terms from the Experimental Factor Ontology for condition, for whichever is their comparison group. For example, they have Male and Female sex:https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FPATO_0001894&lang=en&viewMode=All&siblings=false

U1LCB8WEA (14:09:01) (in thread): > For age, you can use “age at assessment”https://www.ebi.ac.uk/ols/ontologies/efo/terms?iri=http%3A%2F%2Fwww.ebi.ac.uk%2Fefo%2FEFO_0008007&lang=en&viewMode=All&siblings=false

U1LCB8WEA (14:09:30) (in thread): > Then just describe the group 0 and group 1

2023-09-14

U1LCB8WEA (02:19:37): > Has anyone noticed thebugsigdb.orgfrom page loading slower, at least whenyou’relogged in? If so, when did you notice it start?

irem Kahveci (04:17:15) (in thread): > I am not someone who works on the project, but since I learned about the project during the outreachy period, I currently log in to the site at least 3 times a week to benefit from my uni projects. I noticed that it has been loading slower since Saturday last week.

Levi Waldron (04:20:44) (in thread): > Thank you@irem Kahveci! Let me know any time you see anything thatdoesn’tseem right:pray:

Levi Waldron (04:21:44) (in thread): > Do you mean since Saturday 9 September?

irem Kahveci (04:22:09) (in thread): > yes

UBNSEMS3S (09:34:58): > Hi everyone. We will be meeting today (Thursday) at 10 AM EDT.https://us02web.zoom.us/j/2737200499Apologies for the late notice as I wasn’t sure if I would be feeling well enough to attend.

U02CNMR4YEA (17:24:09): > I am sorry I missed the meeting.I thought weweren’tmeeting because you were at a conference this week:pensive:. I should have checked.Hope everyone is having a great day!

U02CNMR4YEA (17:25:43) (in thread): > I was on Sat and Sun (9th and 10th) anddidn’tnotice it as particularly slow.

2023-09-15

UBNSEMS3S (09:31:17) (in thread): > No worries. There wasn’t going to be one but then I got COVID and didn’t go to the conference.

U02CNMR4YEA (12:31:22) (in thread): > Oh no!I’mso sorry:disappointed:.

2023-09-18

U02CNMR4YEA (22:43:53): > Hi All! When more than one sample is taken from on individual, should the sample sizes reflect the number of samples taken from each group or should it be the number of individuals in each group? (I think I remember an FAQ document or website maybe? I don’t want to keep asking questions here that have been answered elsewhere as I’m sure it gets annoying to keep providing the same responses over and over:disappointed:so if such a resource exists, please remind me where it is). Thank you in advance!

2023-09-19

Levi Waldron (09:19:11): > Sorry for the late post, but Microbiome Virtual International Forum n. 21 Atlantic-first is live NOW! Pacific replay will be in ~36 hours.https://hopin.com/events/microbiome-vif-n-21 - Attachment (hopin.com): Microbiome-VIF n.21 - Sep 19 | RingCentral Events > MVIF.21 September event: bite-sized microbiome meeting

Levi Waldron (09:21:16) (in thread): > Good question that I don’t have a good general answer to… if they are comparing individuals and using a mixed model or averaging to combine repeated measures, then I’d say it would be individual. If they’re doing time series analysis and comparing times, then I’d say it would be time points.

UBNSEMS3S (12:21:59) (in thread): > Yeah I agree with Levi. Sample size should represent what are the fundamental units of study. As always, this can be dependent on the analysis so I would think carefully about what’s being analyzed and what the study authors are imagining as the unit of analysis. Of course, this is not always easy to determine given the limitations of what exists in the publication. If there’s any ambiguity, feel free to bring to one of our meetings so we can consider it.

2023-09-20

UBNSEMS3S (19:56:27): > Hi everyone. We will be meeting tomorrow (Thursday) at 10 AM EDT. Currently no one is signed up to present (you can sign up here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EST).https://us02web.zoom.us/j/2737200499

2023-09-22

UBNSEMS3S (14:02:15): > https://doodle.com/meeting/participate/id/eVQ8rMvd~~~~ Doodle poll for the workathon as discussed. I tried to do a mix of morning, afternoon, and evening times.~~~~Nevermind had a time zone issue. New doodle poll soon. - Attachment (doodle.com): Doodle > Doodle is the simplest way to schedule meetings with clients, colleagues, or friends. Find the best time for one-to-ones and team meetings with our user-friendly calendar tool. Get started today!

2023-09-24

U02CNMR4YEA (13:13:41): > Happy Sunday Everyone! I have a signature that lists a family name and then, separately, the same family name “other”. (see below) Do they both get included and, if so, how? Thank you in advance:blush:. - File (PNG): image.png - File (PNG): image.png

U02CNMR4YEA (13:31:14) (in thread): > I have gone in and marked by availability. Unfortunately, I am traveling this week for work and have much less availability than usual. Also, I noted you had some times that looked very early so I’m not sure the am/pm is denoted as you intended?

U02CNMR4YEA (14:04:33): > Hi all! What does it mean when an article cannot be found in PubMed? Are we not able to curate? This is the article I am not seeing in PubMedhttps://www.mdpi.com/1422-0067/24/18/14091 - Attachment (MDPI): The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease > Although dry eye disease (DED) is one of the most common ocular surface diseases worldwide, its pathogenesis is incompletely understood, and treatment options are limited. There is growing evidence that complex interactions between the ocular surface microbiome (OSM) and tear fluid constituents, potentially leading to inflammatory processes, are associated with ocular surface diseases such as DED. In this study, we aimed to find unique compositional and functional features of the OSM associated with human and microbial tear proteins in patients with DED. Applying whole-metagenome shotgun sequencing of forty lid and conjunctival swabs, we identified 229 taxa, with Actinobacteria and Proteobacteria being the most abundant phyla and Propionibacterium acnes the dominating species in the cohort. When DED patients were compared to controls, the species Corynebacterium tuberculostearicum was more abundant in conjunctival samples, whereas the family Propionibacteriaceae was more abundant in lid samples. Functional analysis showed that genes of L-lysine biosynthesis, tetrapyrrole biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis, and the super pathway of L-threonine biosynthesis were enriched in conjunctival samples of controls. The relative abundances of Acinetobacter johnsonii correlated with seven human tear proteins, including mucin-16. The three most abundant microbial tear proteins were the chaperone protein DnaK, the arsenical resistance protein ArsH, and helicase. Compositional and functional features of the OSM and the tear proteome are altered in patients with DED. Ultimately, this may help to design novel interventional therapeutics to target DED.

Levi Waldron (14:08:13) (in thread): > Some MDPI journals are on a list of “predatory” journals that you can Google - ifit’son that list thenit’slikely not meaningfully peer reviewed.Journals not indexed in pubmed deserve extra caution butthey’renot necessarily ruled out.

Levi Waldron (14:18:29) (in thread): > The first one has a _ cut off at the end, making me think some thing is missing in that name. The second one you could use something likehttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=82569&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock? - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Levi Waldron (14:19:12) (in thread): > The first would just be the family of you take it at face value and assumethere’sno cut-off printing error.

U02CNMR4YEA (14:20:50) (in thread): > Thank you! I did put the first one in at face value and will do as you suggest and enter the other as the unclassified.:blush:

Levi Waldron (14:21:25) (in thread): > Great - leave notes on the Discussion page and maybe the taxon review page, then do your best and move on with such vague information:sweat_smile:

2023-09-25

UBNSEMS3S (10:38:56) (in thread): > Oh yeah it looks like something got messed up with the time zones. I meant to have some evening times. Let me delete and try again.

2023-09-26

UBNSEMS3S (10:06:38): > The taxon name autocompletes should be working now. Please let me know if it isn’t.

2023-09-27

UBNSEMS3S (17:25:37): > Hi everyone. We will be meeting tomorrow (Thursday) at 10 AM EDT. Currently no one is signed up to present (you can sign up here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EST).https://us02web.zoom.us/j/2737200499 - Attachment (BugSigDB): PresentationSignup

Andre Nana (19:38:09) (in thread): > Thanks. Just signed to present this study from PlosOnehttps://bugsigdb.org/Study_765 - Attachment (BugSigDB): Study 765

2023-09-30

U02CNMR4YEA (17:48:06) (in thread): > There is now a PubMed ID 37762390:blush:

U02CNMR4YEA (17:51:32): > I am curating PubMed ID 37762390 and am not finding anything regarding the alpha diversity:thinking_face:https://www.mdpi.com/1422-0067/24/18/14091 - Attachment (MDPI): The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease > Although dry eye disease (DED) is one of the most common ocular surface diseases worldwide, its pathogenesis is incompletely understood, and treatment options are limited. There is growing evidence that complex interactions between the ocular surface microbiome (OSM) and tear fluid constituents, potentially leading to inflammatory processes, are associated with ocular surface diseases such as DED. In this study, we aimed to find unique compositional and functional features of the OSM associated with human and microbial tear proteins in patients with DED. Applying whole-metagenome shotgun sequencing of forty lid and conjunctival swabs, we identified 229 taxa, with Actinobacteria and Proteobacteria being the most abundant phyla and Propionibacterium acnes the dominating species in the cohort. When DED patients were compared to controls, the species Corynebacterium tuberculostearicum was more abundant in conjunctival samples, whereas the family Propionibacteriaceae was more abundant in lid samples. Functional analysis showed that genes of L-lysine biosynthesis, tetrapyrrole biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis, and the super pathway of L-threonine biosynthesis were enriched in conjunctival samples of controls. The relative abundances of Acinetobacter johnsonii correlated with seven human tear proteins, including mucin-16. The three most abundant microbial tear proteins were the chaperone protein DnaK, the arsenical resistance protein ArsH, and helicase. Compositional and functional features of the OSM and the tear proteome are altered in patients with DED. Ultimately, this may help to design novel interventional therapeutics to target DED.

U1LCB8WEA (17:57:37) (in thread): > I think they just didn’t study diversity!

U02CNMR4YEA (17:58:35) (in thread): > Okay- good to know you didn’t see it either:slightly_smiling_face:.So it’s still okay to curate the relative abundance results?

U02CNMR4YEA (18:01:34) (in thread): - File (PNG): image.png

U1LCB8WEA (20:35:19) (in thread): > Of course!

2023-10-02

UBNSEMS3S (09:45:16): > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started:https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > Contribution Task > > Review article on the human microbiome that is heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) and complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing. > > (Optional) Stretch Task: As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation.
> To claim an article for curation, post a response to the issue with your name and we will mark it as claimed.
> To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

myles (12:38:08): > Recently completed a research assistant position, aiding the PI in a bioinformatics project, including carrying out data analytics . Hopefully I make meaningful contributions here. This is just the kind of project I’d love to be part of. > > PS my name is Myles. Hope to see the mentors and everyone else on Thursday! > > Good day to you all:grin:

UBNSEMS3S (12:38:27) (in thread): > Awesome! Welcome Myles!

myles (12:38:52) (in thread): > Thank you Chloe! Great to be here:grin:

Chinwendu Enyinna (13:29:36): > Hello everyone, I’m Chinwendu, a Software developer with a background in Applied Biochemistry. > > I was looking for an open-source project that intersected with life sciences, and I was excited to have discovered the Bioconductor repository on GitHub over the weekend. > > Fortunately, I got accepted as an Outreachy intern applicant today and found Bioconductor as one of the listed projects:grinning:! > > I am excited about this opportunity, and ready to making a significant contributions. I look forward to meeting other contributors and mentors during our first office hours.

Peace Sandy (13:43:26): > Hello Everyone , My name is Peace Sandy ,I’ma Technical Writer , Software Developer and a Recent graduate of Microbiology,This project resonates with my field of interest and I can not wait to start contributing and applying every thingI’velearnt for a couple of years now.I’msuper excited to be in this community and to contribute. > > I look forward to connecting with everybody and helping out as well. > > Looking forward to meeting the mentors and follow contributors.

Peace Sandy (13:44:41) (in thread): > Welcome@myles

UBNSEMS3S (13:58:55) (in thread): > Welcome Chinwendu!

UBNSEMS3S (13:59:04) (in thread): > Welcome Peace!

Peace Sandy (13:59:39) (in thread): > Thank you so much:tada:

Faizah Salami (14:00:39): > Hi everyone. My name is Faizah Salami from Nigeria. I am Physiology graduate with a strong research background, and a Software Quality Assurance Engineer. I am excited to contribute to the Microbiome Study Curation project, and I look forward to working with other applicants on the project.

UBNSEMS3S (14:02:06) (in thread): > Welcome Faizah!

Faizah Salami (14:03:24) (in thread): > Thank you Chloe

Aleru Divine (14:05:17): > Hi everyone, I’m Aleru Divine Chinwendu and I’m from Nigeria. I am a software developer, technical writer, and a recent Biochemistry graduate. > > I am absolutely thrilled to be part of this community as this project aligns seamlessly with my field of interest and I am ready to make meaningful contributions. > > I’m looking forward to connecting with everyone from the mentors to the contributors. > > Cheers

Aleru Divine (14:06:10) (in thread): > Hey:sweat_smile:we bear the same name, sort of.

UBNSEMS3S (14:16:55) (in thread): > Welcome Aleru!

Aleru Divine (14:18:13) (in thread): > Thanks Chloe!

Desire Oluwarotimi (14:38:57): > Hello everyone, I’m Desire Oluwarotimi from Lagos, Nigeria. I’m a software developer and Radiographer. > > I’m elated to be a part of this community and ready to be valuable with facilitating reproducible analysis of data from biological assays. > > Let’s get to work.

UBNSEMS3S (14:57:31) (in thread): > Welcome Desire!

Onalo Deborah (15:14:50): > Hi everyone, hope you’re having a great day. I’m Deborah, from Nigeria. A product designer, researcher and with a strong background in pharmaceutical science and pharmaceutical microbiology.I am super excited to be here and to contribute to the Microbiome Study Curation project as an outreachy intern as I had an interest in contributing to a life science open source project.I’m looking forward to making significant contributions to the project and working with mentors and other applicants.Let’s connect:https://www.instagram.com/designwithdebbs

Chinwendu Enyinna (15:16:50) (in thread): > Thank you, Chloe:grinning:

Chinwendu Enyinna (15:18:06) (in thread): > Oh, really? Nice to meet you!@Aleru Divine:grin:

Desire Oluwarotimi (15:18:32) (in thread): > Thank you Chloe!

UBNSEMS3S (15:40:23) (in thread): > Welcome Deborah!

Onalo Deborah (15:51:33) (in thread): > Thank you so much Chloe!

Joan C. Chukwuemeka (16:18:41): > Hello Everyone:wave:My name is Joan Chukwuemeka, you can call me Joan:grinning:I’m a Data Analyst with a strong passion for Health Data Analytics. My background in Medical Parasitology, where I applied medical statistics during my graduate research, fueled my interest in bioinformatics. > > I’m absolutely thrilled to be part of the Bioconductor community and to dive into the Microbiome Study Curation project. It’s an exciting opportunity to combine my analytical & Literature review skills with my love for the biological sciences.:seedling:I’m eager to collaborate with other interns and mentors to make meaningful contributions to this important project while also honing my skills for future career growth. > > I look forward to connecting with mentors and fellow contributors to learn, grow, and make positive impact together. Let’s embark on this journey of discovery and innovation:slightly_smiling_face:

UBNSEMS3S (16:46:52) (in thread): > Welcome Joan!

Joan C. Chukwuemeka (16:52:05) (in thread): > Thanks Chloe:relaxed:

UBNSEMS3S (17:25:34): > Welcome to all the Outreachy applicants who joined us this afternoon. I’m about to sign off for the day. Looking forward to seeing your contributions soon.

Peace Sandy (17:59:54) (in thread): > Welcome:wave:

Peace Sandy (18:00:17) (in thread): > Okay:clap:

Joan C. Chukwuemeka (18:01:06): > Alright:slightly_smiling_face:

Faizah Salami (18:11:53) (in thread): > Thank you Chloe

Onalo Deborah (18:15:04): > Hello everyone. After making the first contribution, what URL are we supposed to fill while reporting that contribution? Or do we wait till we’re done with the second contribution before we start reporting the contributions on outreachy?<@UBNSEMS3S>@C. Mirzayi (please do not tag this account)

2023-10-03

Chinwendu Enyinna (00:37:36) (in thread): > Thank you Chloe

Chinwendu Enyinna (00:49:30) (in thread): > Although I am not 100% sure about this but I think we need to enter the URL of the GitHub repository and probably a link to the document that contains the contribution.

Komuhangi Tumuhairwe (01:06:52): > Hello everyone, my name is Komuhangi Tumuhairwe. I’m a software engineer by education but a very willing and enthusiastic fellow by nature. I appreciate technology and better decision making aided by studies and data(s). I come in as an Outreachy intern who is looking forward to being part of the Microbiome Study Curation project and can’t wait to collaborate with you all. I hope you are all doing okay.

Sinmi Adesanya (02:52:57): > Hi everyone, > > I’m Sinmi Adesanya, and my background is in research. I am eager to contribute to this project because I am passionate about Bioconductor’s values and mission. I’m excited about the possibility to join this project as an Outreachy intern and passionate about contributing to life science open-source projects! > > I’m looking forward to making meaningful contributions to the microbiome study curation project and collaborating with mentors and fellow interns.

Peace Sandy (02:55:28) (in thread): > I think we will have daily meetings where things will be explained, but before that you can read the contribution guidelines on the Outreachy page

Peace Sandy (02:55:43) (in thread): > Welcome:wave:

Grace Ogundaini (03:04:17): > Hello everyone. My name is Grace Ogundaini. I am a data analyst with a background in Microbiology and Public Health. I am very excited about joining this program through Outreachy as it aligns with my career prospects. My passion lies in using my knowledge in the health and technology sector to drive better health outcomes.

Faizah Salami (03:12:58) (in thread): > Welcome Sinmi:+1:

Faizah Salami (03:13:12) (in thread): > Welcome Grace

Onalo Deborah (03:13:27) (in thread): > The first contribution doesn’t really have a link on its own that can be submitted for the Microbiome study curation. Hence my question<@UBNSEMS3S><@UBNSEMS3S>

Sinmi Adesanya (03:20:50) (in thread): > Thank you, Faizah.

Sinmi Adesanya (03:21:21) (in thread): > Welcome Grace:wave:

Peace Sandy (03:44:45) (in thread): > Welcome Grace

Peace Sandy (03:45:02) (in thread): > Welcome Sinmi

Joan C. Chukwuemeka (03:59:35) (in thread): > Hi everyone:blush::blush:

Joan C. Chukwuemeka (04:02:32) (in thread): > @Onalo DeborahThere is an information on the GitHub Issues page (https://github.com/waldronlab/BugSigDBcuration/issues/94) with a form link: > > Link to curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEuPlease submit a fully completed mini-curation via the form above before continuing to the second contribution task. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Onalo Deborah (04:03:41) (in thread): > Thanks Jane. On submitting the form, there’s no link to input or show I have completed this task. Do I just go ahead and fill the url of this form?<@UBNSEMS3S>

Joan C. Chukwuemeka (04:04:09) (in thread): > Hope this helps.:slightly_smiling_face:I believe@C. Mirzayi (please do not tag this account)will respond once she is available.

Onalo Deborah (04:04:16) (in thread): > That is why I’m asking if I should do the second first or just input the link to this form.

Joan C. Chukwuemeka (04:07:12) (in thread): > okay, do you mean link to submit to Outreachy as a record for your first contribution?

Onalo Deborah (04:09:10) (in thread): > Yes@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:18:51) (in thread): > Alright. I don’t think you’ll need to do a second contribution before submitting a first contribution, since the second contribution is optional > > Pending when@C. Mirzayi (please do not tag this account)is available, there’s a likely way to check if you submission link will go to your response and not the blank form

Joan C. Chukwuemeka (04:19:09) (in thread): > do you use a chrome browser?

Joan C. Chukwuemeka (04:22:42) (in thread): > @Onalo Deborahdo you use a chrome browser?

Onalo Deborah (04:23:02) (in thread): > Yes I do

Onalo Deborah (04:23:40) (in thread): > Please share with me@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:23:48) (in thread): > yea

Joan C. Chukwuemeka (04:27:00) (in thread): > @Onalo DeborahIf you click the Avatar portion of the chrome tab, there is “other profile” section, where you have “guest”. select the guest to open a new guest chrome window

Joan C. Chukwuemeka (04:28:03) (in thread): > @Onalo Deborahcopy the link at your response page and paste in the new guest window

Joan C. Chukwuemeka (04:29:24) (in thread): > @Onalo DeborahThat will give you a view of what another browser user will see when the link is accessed

Onalo Deborah (04:30:03) (in thread): > Okay, thank you very much. I already closed the tab but I’d try to get it again

Joan C. Chukwuemeka (04:30:32) (in thread): > Alright:thumbsup:

Aleru Divine (04:32:24) (in thread): > Thanks Chloe!:partying_face:

Peace Sandy (04:48:31) (in thread): > Welcome Joan, would like to be your friend:sweat_smile:

Joan C. Chukwuemeka (04:56:33) (in thread): > Nice to have you here@Grace Ogundaini

Joan C. Chukwuemeka (05:02:03) (in thread): > Good to have you here@Sinmi Adesanya

Grace Ogundaini (05:02:13) (in thread): > Thank you everyone:blush:

Joan C. Chukwuemeka (05:03:03) (in thread): > Nice to meet you here@Komuhangi Tumuhairwewelcome:blush:

Joan C. Chukwuemeka (05:15:44) (in thread): > @Onalo DeborahHow did it go?

Sinmi Adesanya (05:19:14) (in thread): > Thank you Peace and Joan! Nice to meet you both.

Onalo Deborah (05:39:25) (in thread): - File (JPEG): Image from iOS

Joan C. Chukwuemeka (05:41:23) (in thread): > @Onalo Deborahoh.. wow…the blank page before response is recorded.:thinking_face:

Onalo Deborah (05:41:51) (in thread): > Is yours different? I didn’t get a blank page

Onalo Deborah (05:46:51) (in thread): - File (PNG): Image from iOS

Joan C. Chukwuemeka (05:47:42) (in thread): > @Onalo Deborah..by blank page I meant, it’s not showing your responses that you filled. > > If I get any other solution, I’d revert back here. In the meantime, Let’s hold on for@C. Mirzayi (please do not tag this account).

Onalo Deborah (05:48:11) (in thread): > It’s not. Did yours show the responses you filled?

Joan C. Chukwuemeka (05:49:01) (in thread): > Not yet

Onalo Deborah (05:50:17) (in thread): > Thanks a lot for your help. I appreciate it!

Joan C. Chukwuemeka (05:50:56) (in thread): > you’re welcome:blush:

Komuhangi Tumuhairwe (07:35:46) (in thread): > Thank you Joan C. I’m glad to be here

Komuhangi Tumuhairwe (07:49:09) (in thread): > Thank you Sandy:blush:

Joan C. Chukwuemeka (07:49:26) (in thread): > Oh@Peace Sandyjust seeing this:slightly_smiling_face:. Thanks…I’m delighted to have the opportunity to make your acquaintance

UBNSEMS3S (09:08:35) (in thread): > Good question. Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application.

UBNSEMS3S (09:08:47) (in thread): > Welcome!

UBNSEMS3S (09:08:58) (in thread): > Welcome Sinmi!

UBNSEMS3S (09:09:08) (in thread): > Welcome!

Joan C. Chukwuemeka (09:12:00) (in thread): > Thanks for the Clarification<@UBNSEMS3S>

Chinwendu Enyinna (09:19:25) (in thread): > Thank you Chloe.

Grace Ogundaini (09:28:46) (in thread): > Thank you!

Komuhangi Tumuhairwe (09:38:14) (in thread): > Thank you Chloe:blush:, it is an honor

U1LCB8WEA (09:39:07) (in thread): > Welcome Myles!

U1LCB8WEA (09:39:37) (in thread): > Welcome Chinwendu, glad to have you here!

U1LCB8WEA (09:39:50) (in thread): > Welcome Peace, great to have you here!

U1LCB8WEA (09:40:07) (in thread): > Welcome Faizah, glad to have you!

U1LCB8WEA (09:40:28) (in thread): > Welcome Aleru, happy to have you here!

U1LCB8WEA (09:40:49) (in thread): > Welcome Desire, thanks for your interest in the project!

U1LCB8WEA (09:41:03) (in thread): > Welcome Onalo, great to see you here!

Komuhangi Tumuhairwe (09:41:59): > Even though my name is Komuhangi Tumuhairwe, kom or komu or tumu can do… life can be simpler this way.:slightly_smiling_face:Thank you for the warm welcome

U1LCB8WEA (09:42:36) (in thread): > Welcome, Joan, I’m glad you’re here!

Chinwendu Enyinna (09:44:52) (in thread): > Thank you, Levi.

U1LCB8WEA (09:46:09) (in thread): > I just approved the first account requests from Sandy, Ojotuleonalo, and huhu…<@UBNSEMS3S>and@Svetlana Ugarcina Perovicyou can approve these too, under the bottom left-hand side toolbox “Confirm account requests”https://bugsigdb.org/Special:ConfirmAccounts - Attachment (BugSigDB): Special:ConfirmAccounts

U1LCB8WEA (09:50:09) (in thread): > (tools - “Special pages” then “Confirm account requests” )

Peace Sandy (09:51:35) (in thread): > Thank you so much@Levi Waldron

Joan C. Chukwuemeka (09:52:40) (in thread): > Thanks<@U1LCB8WEA>. Grateful for the opportunity

Chioma Onyido (09:59:06): > Hi all, I’m Chioma Blessing, an outreachy applicant. I’m an Academic researcher with a special interest in Cancer and Malaria research. Delving into literature review and health research has been a thrilling adventure throughout my career, imagine my excitement when I came across the Microbiome project!:sweat_smile:I eagerly anticipate contributing and connecting with mentors and fellow interns. > My linkedIn is:https://www.linkedin.com/in/chioma-onyido/

UBNSEMS3S (10:01:44) (in thread): > Welcome Chioma!

UBNSEMS3S (10:02:42): > Good morning everyone. I was sending some messages while on the train this morning but I am now at the CUNY SPH campus. It’s warm and sunny here in New York today. Hope you’re all doing well and having beautiful weather. Please feel free to post any questions and we will get to them ASAP!

UBNSEMS3S (10:03:45) (in thread): > Thanks for the heads up Levi. I will keep my eyes on this page.

Chioma Onyido (10:34:01) (in thread): > Thank you!:slightly_smiling_face:

Sinmi Adesanya (10:35:55) (in thread): > Thank you,<@UBNSEMS3S>!

Onalo Deborah (11:01:27) (in thread): > Thank you so much<@UBNSEMS3S>and<@U1LCB8WEA>

Desire Oluwarotimi (11:07:03): > @C. Mirzayi (please do not tag this account)Regarding the citation aspect of my curation, the details aren’t autocompleting after providing the DOI. Do I have to manually input the details? > > If yes, how do I get access to those details? > > Thank you.

Desire Oluwarotimi (11:13:01) (in thread): > Thank you Levi!

Levi Waldron (11:14:12) (in thread): > Welcome, Komuhangi, glad you’re here!

Levi Waldron (11:15:06) (in thread): > Welcome Sinmi, thanks for expressing your passion! Looking forward to your contributions.

Levi Waldron (11:15:49) (in thread): > Welcome Grace, it’s great to have a microbiologist amongst us, thanks for your interest!

Levi Waldron (11:16:19) (in thread): > Got it, welcome Kom!

Levi Waldron (11:17:30) (in thread): > Thanks for sharing your excitement Chioma, it’s infectious!

Levi Waldron (11:18:47) (in thread): > Autocomplete only works for PMIDs. If the paper is PMID-indexed (which should be the case unless it is a pre-print) you should provide that and not any other citation information (not even DOI or URI). If it is a pre-print, you have to enter other citation information manually.

Desire Oluwarotimi (11:27:02) (in thread): > Thank you Levi! > That’s clarified.

Chioma Onyido (11:53:38) (in thread): > Thank you Levi.:grin:

Peace Sandy (11:54:57) (in thread): > Okay Chloe > Thank You:pray:

Peace Sandy (11:55:16) (in thread): > Welcome Chioma

Peace Sandy (11:56:58) (in thread): > Thank You@Levi Waldron:confetti_ball:

Chinwendu Enyinna (12:01:01) (in thread): > Oh yeah, Chloe. Currently working on my first contribution. I hope you are doing well too. Thank you.

Ugoo-Okonkwo Stella Ozioma (12:31:02): > Hello everyone, > > My name is Stella Ugoo-Okonkwo from Nigeria, am an outreachy applicant and I have a background in microbiology. I am looking forward to contributing to this project and learning more from you all. I also hope to use my skills such as Html, Css and JavaScript where necessary to add value to this project.

UBNSEMS3S (12:33:24) (in thread): > Hi Stella! Nice to meet you!

Ugoo-Okonkwo Stella Ozioma (12:35:03) (in thread): > Thank you Chloe, nice to meet you too

Chidimma Blessing Onuora (12:36:09): > Good evening everyone. I’m Chidimma. Happy to be here as an aspiring Outreachy intern. I look forward to contributing to this project with my knowledge as a Biochemist and Tech enthusiast.

Chidimma Blessing Onuora (12:36:36) (in thread): > Nice to have you here

Ugoo-Okonkwo Stella Ozioma (12:37:36) (in thread): > Thank you Chidinma

Ugoo-Okonkwo Stella Ozioma (12:38:20) (in thread): > Welcome Chidimma, nice to meet you

Peace Sandy (12:55:25) (in thread): > Welcome:hugging_face:

U1LCB8WEA (13:26:43) (in thread): > You’rewelcome!

Aleru Divine (13:30:17) (in thread): > Welcome Chidinma:grinning:

Peace Sandy (13:33:20): > Is anyone finding difficult navigating to the first contribution?I’mwilling to help. > If you have questions feel free to reach out

Desire Oluwarotimi (13:39:23) (in thread): > Thank you for your generosity Peace. > > I’d also love to assist anyone in case any help is needed.

Desire Oluwarotimi (13:40:44): > @Levi Waldron@C. Mirzayi (please do not tag this account)Is it possible at all that a study has nothing to do with antibiotics exclusion?

UBNSEMS3S (13:41:02) (in thread): > Yes if they don’t mention it, it’s possible there was no antibiotics exclusion.

UBNSEMS3S (13:41:14) (in thread): > Welcome!

Desire Oluwarotimi (13:41:32) (in thread): > Alright. > Thank you Chloe!

Aminat Odedeyi (14:12:36): > Hi everyone. I’m Aminat, an Outreachy Applicant and I’m very excited to be here. Looking forward to connecting, learning and contributing to the community.

C. Mirzayi (please do not tag this account) (14:13:00) (in thread): > Hi Aminat! Welcome!

Aminat Odedeyi (14:15:34) (in thread): > Hi Chloe, thank you for the warm welcome and nice to meet you

Peace Sandy (14:16:40) (in thread): > Welcome Amina !

Karen254. Kingecha (14:19:44): > Hey everyone, I am Karen, an Outreachy Applicant, I am very excited to connect with you all.

C. Mirzayi (please do not tag this account) (14:19:59) (in thread): > Welcome Karen!

Chioma Onyido (14:26:08) (in thread): > You’rewelcome, Karen.

Chioma Onyido (14:29:50) (in thread): > Thank you, Peace.:grin:

Ugoo-Okonkwo Stella Ozioma (14:55:34) (in thread): > Welcome Karen:partying_face:

Ugoo-Okonkwo Stella Ozioma (14:56:12) (in thread): > Welcome Aminat

Aminat Odedeyi (15:20:50) (in thread): > Thank you@Peace Sandy@Ugoo-Okonkwo Stella Oziomanice to meet you too

Peace Sandy (15:42:21) (in thread): > Welcome Karen

Komuhangi Tumuhairwe (16:50:47) (in thread): > Thank you Chloe, I hope you are well too

Odigiri Great Alume (18:13:28): > Hi everyone, my name is GREAT ODIGIRI, I am a biologist. I’m excited to be a part of this community to connect and collaborate with everyon. I look forward to contributing my “2 cents”.:pray:

Odigiri Great Alume (18:33:01): > It’s a bit confusing. Please I’d be grateful if anyone can help explain to me how I can proceed from here onward. > > Thanks

U1LCB8WEA (18:35:29) (in thread): > I’mpinning this kind message to help keep it prominent.It looks like@Odigiri Great Alumecould use your help:blush:

U1LCB8WEA (18:36:44) (in thread): > Welcome Great, we’re happy you’re here!

U1LCB8WEA (18:37:34) (in thread): > Welcome Aminat,we’regladyou’rehere!

U1LCB8WEA (18:38:10) (in thread): > Welcome Karen, looking forward to working with you!

Aleru Divine (19:28:21) (in thread): > Hi Great, I understand how you feel. Go through this carefully. Hope this helps.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Onalo Deborah (20:20:36) (in thread): > Hi Great, adding to the comment above, your first task is a mini curation. Once you’re done, you have to record your contribution in the outreachy website. If you follow the message above, it will help you out!

Onalo Deborah (20:21:23) (in thread): > Well done Peace

Onalo Deborah (20:22:56) (in thread): > Thank you Chloe. Hope you’re having a great day

Aleru Divine (21:39:22) (in thread): > Hey Peace! I need help. I thought i understood how to make my first contribution but i don’t think i do. Can you help me please? So this mini curation, is it just the form? Like the survey we filled? > > What I mean is, is the survey the first contribution?

2023-10-04

Odigiri Great Alume (02:28:30) (in thread): > Thank you so much sir. Going through the responses now.:pray:

Odigiri Great Alume (02:30:21) (in thread): > Thank you Deborah. Going through the link now.:pray:

Chinwendu Enyinna (02:47:22): > Hi everyone, how’s your contribution going. For anyone who doesn’t know the next steps after completing the survey, which is the mini curation task, here’s an answer from<@UBNSEMS3S>. I hope this helps.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696338515723009?thread_ts=1696284904.239279&cid=C04RATV9VCY - Attachment: Attachment > Good question. Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application.

Chioma Onyido (02:49:44): > Hi<@UBNSEMS3S>@Levi WaldronCompliments of the day and I hope you’re well. TMy first curation has been a bit challenging but thanks to your videos and tips on here, I’ve been able to make headsway. I Appreciate your guidance so far.:sweat_smile:Question: Do we have to wait for our curation to be reviewed before we proceed to filling in the survey?

Chioma Onyido (02:55:34) (in thread): > This is helpful Chinwendu, thank you.

Peace Sandy (02:58:35) (in thread): > Hi@Aleru DivineI’min your DM

Peace Sandy (03:00:08) (in thread): > Welcome Great ! > How is your contribution going

Peace Sandy (03:00:47) (in thread): > Hi@Odigiri Great Alumehave you been able to figure it out.

Onalo Deborah (03:08:54) (in thread): > No we don’t. Isn’t the survey the first task? Or how did you go about yours?

Onalo Deborah (03:10:15) (in thread): > Yes@Aleru Divineit is just the form. The survey is the first contribution

Aleru Divine (03:12:04) (in thread): > Hi Chioma, the survey is the first contribution.

Aleru Divine (03:12:54) (in thread): > Thanks@Peace Sandy@Onalo DeborahI was pretty confused last night.

Chioma Onyido (03:15:04) (in thread): > No wonder, it was looking so alien on my end.:weary:Thank you so much!:pray:

Chinwendu Enyinna (03:16:40) (in thread): > Glad I could help

Peace Sandy (03:16:48) (in thread): > You are welcome,always feel free to reach out

Onalo Deborah (03:17:00) (in thread): > You’re welcome. If you need any other help or clarification, I’m here to help

Odigiri Great Alume (03:18:05) (in thread): > I’m currently reading and watching the videos on the guide. I’d reach out if and when I get stuck. Thanks Peace.

Peace Sandy (03:19:57) (in thread): > Okay

Aleru Divine (03:20:22) (in thread): > Thank you<@U1LCB8WEA>

Chioma Onyido (03:24:00) (in thread): > Already made a whole curation on the annotated pdf.:sweat_smile:Apologies for the mixup Chloe and Levi.:pray:Thank you Deborah and Divine.:pray:

Svetlana Ugarcina Perovic (03:49:54): > Hello dear outreachy contributors, I’m Svetlana (https://www.linkedin.com/in/svetlana-ugarcina-perovic/), a microbiome scientist and mentor for the Microbiome Study Curation project. Together with<@UBNSEMS3S>@Levi WaldronI’m available for your questions. Mostly during 7-10 am UTC when Levi and Chloe are still sleeping:slightly_smiling_face:

Svetlana Ugarcina Perovic (03:51:06) (in thread): > Correct: the survey is the first contribution.

Svetlana Ugarcina Perovic (03:52:22) (in thread): > @Peace Sandy:bouquet:thanks for all your clarifications!

Maryam Gbemisola (03:53:55) (in thread): > Thank you@Svetlana Ugarcina Perovic. I will send a DM soon

Joan C. Chukwuemeka (04:04:15) (in thread): > Alright:blush:…. Thanks@Svetlana Ugarcina Perovic

Peace Sandy (04:15:55) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:hugging_face:

Peace Sandy (04:16:41) (in thread): > My pleasure@Svetlana Ugarcina Perovic

Chioma Onyido (04:20:40) (in thread): > Great! Thank you,@Svetlana Ugarcina Perovic

Chinwendu Enyinna (04:21:00) (in thread): > Thank you@Svetlana Ugarcina Perovic

Peace Sandy (04:32:28): > @Svetlana Ugarcina Perovic@Levi Waldron@C. Mirzayi (please do not tag this account)After completing the first contribution,should we go ahead and record it on Outreachy website.

Svetlana Ugarcina Perovic (04:36:41) (in thread): > Here is<@UBNSEMS3S>’s helpful answer:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696338515723009?thread_ts=1696284904.239279&cid=C04RATV9VCY - Attachment: Attachment > Good question. Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application.

Peace Sandy (04:42:27) (in thread): > Okay > Thank you so much@Svetlana Ugarcina Perovic

edilawit (04:54:42) (in thread): > Thank you so much

Chiagoziem David (04:59:27): > Hello everyone , I am Chiagoziem David. > > I am so excited to be here.

Peace Sandy (05:08:57) (in thread): > Welcome

Aleru Divine (05:09:01) (in thread): > Hi David, great to have you.

Chinwendu Enyinna (05:21:51) (in thread): > Welcome, David!

Chiagoziem David (05:32:54) (in thread): > Thanks… > > Ppss: it seems I am the only male here:slightly_smiling_face::dotted_line_face:

Maryam Gbemisola (05:37:05) (in thread): > Welcome Chigozie

Aleru Divine (05:38:58): > Hi@Svetlana Ugarcina Perovichow do I know if my first contribution is accepted or merged?

Svetlana Ugarcina Perovic (05:42:22) (in thread): > Once you complete the survey we will have a record of it. Don’t worry!

Aleru Divine (05:45:14) (in thread): > Okay, we are required to fill the date the contribution was accepted or merged.How do we go about that?

Chioma Onyido (05:45:14) (in thread): > For clarity,@Svetlana Ugarcina PerovicWe were asked to fill in the date for “accepted or merged” on the Outreachy contribution page, do you advise we leave it blank?

Peace Sandy (05:45:29) (in thread): > So what date do we enter as when the contribution was accepted or merged@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:49:35) (in thread): > OK, I see. Let’s confirm this with<@UBNSEMS3S>Thank you for your patience! @Aleru Divine@Chioma Onyido@Peace Sandy

Peace Sandy (05:50:14) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Aleru Divine (05:50:26) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Komuhangi Tumuhairwe (05:54:51): > Hi everyone, I hope you are all doing okay.

Chioma Onyido (06:00:07) (in thread): > Hi Kom,I’mdoing fine. Just waiting for first contribution to be approved by our mentors so that I can be assigned an article for the second contribution. > Wby?How’s yours going?

Joan C. Chukwuemeka (06:11:10) (in thread): > Thanks:+1:Svetlana

Peace Sandy (06:36:36) (in thread): > Hi Kom,:wave:Trust you are well

Chinwendu Enyinna (06:59:37) (in thread): > Hello Kom, thanks for checking up! Hope you’re doing okay as well.

Desire Oluwarotimi (07:08:04): > Good day@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicI’m not sure how to come up with the value of significance threshold. Please help.

Nwajei Edgar (07:32:14) (in thread): > Thanks for this, much appreciated

Ajoke Yusuf (07:32:32) (in thread): > Thank you@Svetlana Ugarcina Perovic. I will be in your DM when I’ve further questions if I have done my research and didn’t get an explicit way for getting things done

Chloe (07:56:30): > hello everyone, Am Chloe Nabachwa an outreachy applicate and am really exicited to contribute to the community. Am ready to learn all i dont know and share what i know:slightly_smiling_face:

Chinwendu Enyinna (07:58:19) (in thread): > Hi Chloe:wave:, welcome to the community!

Chinwendu Enyinna (07:59:51) (in thread): > You can check this out if you’re yet to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Chioma Onyido (07:59:58) (in thread): > Hi Chloe. Good to have you here.:grinning:

Iram Jamshed (08:10:52): > Hello everyone. I am an Outreachy applicant, very excited and enthusiast to contribute in this project. I have done my Bachelors and Masters in Biotechnology. I have also worked as a Research Fellow in All India Institute for Medical Sciences(AIIMS), New Delhi, India. I believe my background and passion for research completely aligns with the project requirements. I’m thrilled to join this community and look forward to engaging in insightful discussions and potential contributions.:blush:

Fortune Nnamdi (08:12:16) (in thread): > Thanks@Svetlana Ugarcina PerovicI’llbe sending a message soon:blush:

Fortune Nnamdi (08:16:01): > Hi everyone! > > I’m Fortune Nnamdi.I’man Outreachy applicant.I’mhappy to be here!

Nwajei Edgar (08:23:58) (in thread): > Welcome:innocent:

Chioma Onyido (08:25:06) (in thread): > Welcome Fortune! Good to have you here. > > You can look through the pinned messages by the mentors on how to go about your first contribution.

Wangui Thuo (08:25:08): > Hey everyone, > My name’s Wangui, an Outreachy applicant, researcher and Data Scientist. > Excited to be here and I can’t wait to engage and learn with y’all.

Nwajei Edgar (08:25:49) (in thread): > Welcome Wangui, check the pinned message to get started.:innocent:

Chioma Onyido (08:25:52) (in thread): > Welcome Wangui! Good to have you here. > > You can look through the pinned messages on how to go about your first contribution.

Wangui Thuo (08:27:10) (in thread): > Thank you@Chioma Onyidoand@Nwajei Edgar. > Lemme check it out

Chinwendu Enyinna (08:27:34) (in thread): > Hello Wangui, welcome to the community!

Nwajei Edgar (08:27:54) (in thread): > You welcome. If you have any issues, ask here so others can help you

Chinwendu Enyinna (08:27:58) (in thread): > Hi Fortune, welcome to the community

Wangui Thuo (08:28:32) (in thread): > Thank you for the warm welcome@Chinwendu Enyinna

Nwajei Edgar (08:30:10) (in thread): > WelcomeJamshed, check the pinned message to get started.:innocent:

Nwajei Edgar (08:30:50) (in thread): > What’sthe issue?

Peace Sandy (08:36:02) (in thread): > Welcome:pray:

Peace Sandy (08:36:15) (in thread): > Welcome!

Peace Sandy (08:36:36) (in thread): > Hi Fortune > Welcome

Peace Sandy (08:36:56) (in thread): > Welcome@Wangui Thuo

Komuhangi Tumuhairwe (08:44:23) (in thread): > I’m having a field day trying to make my first contribution. Other than that I should be fine, thank you.

U1LCB8WEA (08:47:53) (in thread): > Welcome,@Svetlana Ugarcina Perovic, it’s great to have you! Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion.

Iram Jamshed (08:56:34) (in thread): > Thank you for your responses!

Sinmi Adesanya (08:56:55) (in thread): > Thank you, Levi! It has been quite interesting so far.

Sinmi Adesanya (08:57:42) (in thread): > Pleasure to meet you Svetlana!

Chiagoziem David (08:58:28) (in thread): > Hy fortune, welcome

Chiagoziem David (08:58:53) (in thread): > Welcome

Chiagoziem David (08:59:35) (in thread): > Welcome chloe

U1LCB8WEA (09:00:02) (in thread): > This is the threshold they used to determine what to include in the signature. p < 0.05 is the most common significance threshold, but sometimes p < 0.01 or other values are used. The question about whether multiple hypothesis testing correction was applied is also related to this threshold.

Chiagoziem David (09:00:22) (in thread): > Thanks:+1:

U1LCB8WEA (09:00:23) (in thread): > Welcome,@Chinwendu Enyinna! It’s great to have you here.

Nwajei Edgar (09:00:33) (in thread): > Thank you:innocent::innocent:.@Desire Oluwarotimicheck this out

Esther Afuape (09:09:25): > Hello everyone,My name is Esther.I’ma recent graduate of microbiology and I partook in bioinformatics and phage genomics as part of my course work in school.We annotated phages using different bioinformatics tools. I look forward to working on this project alongside you all.

Nwajei Edgar (09:09:41) (in thread): > Hello friend welcome

Nwajei Edgar (09:09:46) (in thread): > Check this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Esther Afuape (09:10:17) (in thread): > Thank you

Nwajei Edgar (09:10:49) (in thread): > If you need any help, ask so others can help:innocent::innocent::innocent:

Peace Sandy (09:11:11) (in thread): > Welcome !

UBNSEMS3S (09:18:35) (in thread): > Fill in the date you submitted the completed mini-curation (the first contribution).

Peace Sandy (09:19:28) (in thread): > Thank you so much for your clarification@C. Mirzayi (please do not tag this account)

Chioma Onyido (09:19:33) (in thread): > This is helpful. Thank you, Chloe.:pray:

Peace Sandy (09:19:46) (in thread): > @Chinwendu Enyinnahere is a reply

U1LCB8WEA (09:21:54) (in thread): > Welcome@Iram Jamshedit’s great to have you!

U1LCB8WEA (09:22:36) (in thread): > Welcome,@Fortune Nnamdiit’s great to have you here!

U1LCB8WEA (09:23:00) (in thread): > Welcome,@Wangui Thuo, glad to have you here!

U1LCB8WEA (09:23:25) (in thread): > Welcome,@Esther Afuapeglad to have you here!

Olajumoke Adeoyo (09:27:06): > Hi everyone. I’m Adeoyo Olajumoke, a passionate physiotherapy graduate and a devoted Health tech enthusiast. I am thrilled to introduce myself as an individual keen on continuous growth, learning, and exploring new opportunities. It is my pleasure to express my genuine interest in this project, a groundbreaking initiative that delves into the intricate world of the human microbiome.

Aleru Divine (09:27:26) (in thread): > Thanks you so much<@UBNSEMS3S>

U1LCB8WEA (09:27:32) (in thread): > Welcome,@Olajumoke Adeoyo, glad you’re here!

Peace Sandy (09:27:58) (in thread): > Welcome !:hugging_face:

Nwajei Edgar (09:28:37) (in thread): > Welcome friend:innocent::innocent:

Chioma Onyido (09:29:01) (in thread): > Hi Olajumoke, Health tech enthusiast here too!:wave:Welcome to the community.

Esther Afuape (09:32:17) (in thread): > Thank you!

Peace Sandy (09:39:09) (in thread): > Ouuu…I’ma microbiologist too

Ugoo-Okonkwo Stella Ozioma (09:50:56) (in thread): > Nice to meet you too

Iram Jamshed (09:55:49) (in thread): > Thank you so much for your warm welcome!@Levi Waldron:blush:

Onalo Deborah (10:09:13) (in thread): > Nice to meet you@Svetlana Ugarcina Perovic

Onalo Deborah (10:09:42) (in thread): > Yes you should

Onalo Deborah (10:10:09) (in thread): > Lol no.@Desire Oluwarotimiis male too

Onalo Deborah (10:15:18) (in thread): > Welcome@Olajumoke Adeoyo:wave:

Chinwendu Enyinna (10:19:34) (in thread): > Thanks for the tag@Peace Sandy

Chinwendu Enyinna (10:22:43) (in thread): > Welcome Esther

Chinwendu Enyinna (10:23:45) (in thread): > Welcome, Olajumoke! Great to have you here.

Greatman Ugorji (10:24:23): > Hello everyone. I’m Greatman Ugorji, an Outreachy applicant. A technical writer and front-end developer. I’m looking forward to contributing and networking with you all:blush:

Nwajei Edgar (10:32:24) (in thread): > Welcome Greatman, nice to have you here…:innocent::innocent:You can start here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Greatman Ugorji (10:34:09) (in thread): > Thank you. Hope to get along with you all:blush::blush:

Joan C. Chukwuemeka (10:34:14) (in thread): > :relaxed:Thanks a lot<@UBNSEMS3S>

Nwajei Edgar (10:35:22) (in thread): > Anytime:innocent:

Desire Oluwarotimi (10:38:59) (in thread): > Thank you Levi.

Desire Oluwarotimi (10:39:06) (in thread): > Thank you too Edgar.

Peace Sandy (10:50:49) (in thread): > Welcome

Nwajei Edgar (10:54:22): > I have a question. After getting account approval, how do I contribute?

Nwajei Edgar (10:54:49) (in thread): > For the second Contribution task..

Chinwendu Enyinna (10:59:07) (in thread): > You can claim an article here:https://github.com/waldronlab/BugSigDBcuration/issues

Chinwendu Enyinna (10:59:39) (in thread): > Here’s an additional guide fromhttps://github.com/waldronlab/BugSigDBcuration/issues/94Second Contribution Task (Optional) > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged“paper to curate”and work on a full curation. > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. - Attachment (BugSigDB): Special:RequestAccount - Attachment: #94 Welcome Outreachy Applicants!

Nwajei Edgar (11:00:04) (in thread): > Thanks

Chinwendu Enyinna (11:00:22) (in thread): > You’re welcome

Sabastine Iroka (11:01:22): > Hello everyone > I’m Sabastine Iroka, a content writer with background in biochemistry and passionate about research. > Thrilled to be here, to contribute and network with you guys. > > I’ve just gone through the study materials and completed the first task. > Can’t wait for it to be reviewed so I can keep contributing.

Peace Sandy (11:03:53) (in thread): > Welcome@Sabastine IrokaGlad to have you here

Nwajei Edgar (11:04:45) (in thread): > Asked to curate one…. Thank you:hugging_face::hugging_face:

Sabastine Iroka (11:04:59) (in thread): > Thanks@Peace SandyHoping to learn from y’all.

Peace Sandy (11:05:23) (in thread): > Sure ! > Feel free to ask any questions

Chinwendu Enyinna (11:05:47) (in thread): > Hello Sabastine, welcome to the community!

Sabastine Iroka (11:06:42) (in thread): > Hi@Chinwendu Enyinna, thanks! > Already learning from some of your answers.

Chinwendu Enyinna (11:13:24): > Hey everyone, if you’re facing any issues navigating your first contribution, do not hesitate to reach out.

Chiagoziem David (11:16:25) (in thread): > Oh:sweat_smile:

U1LCB8WEA (11:19:14) (in thread): > Welcome,@Greatman Ugorji! We’re glad to have you here.

Shakira Ndagire (11:19:46): > Hello Everyone, > I am Shakira Ndagire, an Outreachy applicant from Uganda. Looking forward to contributing on the Bugsigdb project and working with you all.

Nwajei Edgar (11:20:11) (in thread): > Welcome friend:hugging_face::hugging_face:

U1LCB8WEA (11:20:14) (in thread): > Welcome@Shakira Ndagire! Good to have you onboard.

Shakira Ndagire (11:22:03) (in thread): > Thank you peace for the guidance

Shakira Ndagire (11:23:06) (in thread): > Thank you@Nwajei Edgarand<@U1LCB8WEA>

Chinwendu Enyinna (11:24:33) (in thread): > Hi Shakira, welcome to the community. Feel free to reach out if you face any issues while navigating your first contribution.

Sabastine Iroka (11:33:00) (in thread): > Welcome@Shakira NdagireGlad to have you here

Greatman Ugorji (11:36:21) (in thread): > Thank you@Peace Sandyand<@U1LCB8WEA>

Peace Sandy (11:46:20) (in thread): > Welcome@Shakira Ndagire

Shakira Ndagire (11:49:50) (in thread): > Thank you for the warm welcome.@Peace Sandy@Sabastine Irokaand@Chinwendu Enyinna. Will definitely reach out for help.

Peace Sandy (11:52:05) (in thread): > You are welcome,always feel free to reach out

UBNSEMS3S (12:00:29): > Good morning everyone, > > I just wanted to clarify that youdo notneed to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here:https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article.

Nwajei Edgar (12:01:04) (in thread): > Thanks Chole

Nwajei Edgar (12:01:30) (in thread): > Already asked for an article to curate

Peace Sandy (12:01:47) (in thread): > Thank you so much Chloe

UBNSEMS3S (12:01:52) (in thread): > I just assigned it to you@Nwajei Edgar

Nwajei Edgar (12:02:09) (in thread): > Thank you:hugging_face::hugging_face:

Joan C. Chukwuemeka (12:02:25): > Hello everyone, Trust our day has been great

UBNSEMS3S (12:03:44): > I think I’ve caught up with everyone who has requested assignment for their second contribution but if I missed you please let me know.

Peace Sandy (12:04:08) (in thread): > Seen mine ! > Thank you so much:relaxed:

Peace Sandy (12:04:23) (in thread): > Hi Joan , how have you been ?

Iram Jamshed (12:04:29) (in thread): > Sure!

Joan C. Chukwuemeka (12:06:53): > The article for the initial contribution is an interesting read.:slightly_smiling_face:As a discussion point, Is there a specific reason or reasons why antibiotic exclusion criteria for the cases differs from that of the Healthy Controls?:thinking_face:

Chinwendu Enyinna (12:07:01) (in thread): > Thank you Chloe:hugging_face:. I’ve seen mine.

Iram Jamshed (12:07:43) (in thread): > Thank you so much for your clarification.<@UBNSEMS3S>

UBNSEMS3S (12:08:49) (in thread): > I’ll turn it around and ask if you have any thoughts about why a study might do that.

Peace Sandy (12:09:06) (in thread): > Yes they is a need > Antibiotics can affect the outcome of the results

Peace Sandy (12:10:11) (in thread): > You are welcome

Joan C. Chukwuemeka (12:11:15) (in thread): > I’m doing great@Peace Sandy

Aleru Divine (12:15:40) (in thread): > Thank you so much<@UBNSEMS3S>

Karen254. Kingecha (12:16:45) (in thread): > <@UBNSEMS3S>Thanks, that was very helpful

Karen254. Kingecha (12:17:55) (in thread): > Where are you getting the contribution url ? I am kinda confused

Peace Sandy (12:18:26): > Hi Everyone:wave:Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here:https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion.@C. Mirzayi (please do not tag this account)@Levi Waldronand@Svetlana Ugarcina Perovicare our mentors > > If you just joined you can get started here:point_down:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Peace Sandy (12:19:16) (in thread): > Oh…okay

Peace Sandy (12:19:28) (in thread): > So what is the reason ?

Joan C. Chukwuemeka (12:19:49) (in thread): > @Peace SandyYes… however,I was pointing at the difference in criteria applied between the 2 groups. one group is current use, another is 4 weeks

Nwajei Edgar (12:20:19): > Insightful and well curated.. nice work Peace:hugging_face::hugging_face::hugging_face:

Peace Sandy (12:20:45) (in thread): > You are welcome!

UBNSEMS3S (12:22:12) (in thread): > @Karen254. KingechaYou can just use this URL to document your contribution on outreachy:https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu. We will know which survey response is yours. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

UBNSEMS3S (12:23:03) (in thread): > Thank you for compiling these! I will add these to the FAQ here:https://github.com/waldronlab/BugSigDBcuration/issues/96as well. - Attachment: #96 Outreachy Frequently Asked Questions > Hi Outreachy applicants! > > We wanted to share some answers to some frequently asked questions we received during our last contribution period. > > I asked a question on Slack but haven’t received an answer yet. Are you ignoring me? > > We are not ignoring you. We do our best to answer questions as soon as possible. Please note that I am on American Eastern Daylight time and Svetlana is on Central European Summer Time so we may not be quick to answer questions outside normal business hours in these time zones. > > Can I make more than one second contribution? > > We ask that you only claim one article for your second contribution initially. You should focus on making that curation as perfect as possible as it will be used when we assess your performance during the contribution period. We strongly encourage you aim for quality over quantity. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, here is some ways you can help out with BugSigDB: > > • Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the Github issue for that curation > • Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > • See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > I submitted my second contribution for grading. Why hasn’t it been graded yet? > > Grading takes us some time. We aim to have your contribution graded within a week. Thank you for patience! > > I have a question not covered here. > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Peace Sandy (12:24:11) (in thread): > You are welcome:hugging_face:

Karen254. Kingecha (12:25:29) (in thread): > Thank you

Chinwendu Enyinna (12:26:05) (in thread): > Well done Peace for compiling this:hugging_face:

Shakira Ndagire (12:27:23) (in thread): > This is really insightful. Thank you Peace

Peace Sandy (12:29:35) (in thread): > Thank You@Chinwendu Enyinna:hugging_face:

Peace Sandy (12:29:51) (in thread): > Thank You@Shakira Ndagire:hugging_face:

Joan C. Chukwuemeka (12:33:08) (in thread): > <@UBNSEMS3S>:blush:.okay > > From my research, I found that due to the significant impact of antibiotics on the composition and diversity of the gut microbiome, such studies that are focused on the microbiome may have stricter antibiotic exclusion criteria for the healthy controls. > > Reason: To minimize potential confounding effects of antibiotic exposure on the microbiome > > Hoping to gain more insight into that from<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>and fellow contributors here:blush:

UBNSEMS3S (12:39:18) (in thread): > But why would you have stricter criteria for the controls compared to the cases? Our goal in health research is for cases and controls to be as similar as possible so that we can compare them so it seems odd to have different criteria for cases compared to controls.

Peace Sandy (12:41:02) (in thread): > Same concerns

Joan C. Chukwuemeka (12:41:05) (in thread): > <@UBNSEMS3S>Secondly, during Study curation, are both criteria included? or the focus is the criteria for the cases?

Joan C. Chukwuemeka (12:47:45) (in thread): > <@UBNSEMS3S>Is it okay, if I paste an excerpt of the part that led to the question for context?

Aleru Divine (13:07:31) (in thread): > Thank you Peace! This was very thoughtful:clap:

Peace Sandy (13:19:29) (in thread): > You are welcome@Aleru Divine:hugging_face:

Chioma Onyido (13:25:38) (in thread): > I’veseen mine. Thank you Chloe.

Chioma Onyido (13:36:14) (in thread): > Co-asking:sweat_smile:@C. Mirzayi (please do not tag this account)I noticed the difference in the HC and BC groups.

Onalo Deborah (14:17:44) (in thread): > @Nwajei Edgaris also male:sweat_smile:

Nwajei Edgar (14:18:15) (in thread): > :joy::joy::joy:

Tolulope Ogunleye (14:20:19): > Hello, my name is Tolulope Ogunleye. I am excited to join this project. It will be my first time contributing to open source but I’m sure I’ll be fine with the right amount of focus, resilience and support from this community . > I look forward to having a great time learning and contributing to the best of my ability ! > I studied microbiology in my undergrad after which I worked as a laboratory scientist/researcher before delving into product management and scrum mastery and I think this project is a great fit for me.I am thrilled to be joining as an outreachy applicant!

Onalo Deborah (14:23:04) (in thread): > Welcome Tolulope:wave:. Great to have you here.

Chioma Onyido (14:27:25) (in thread): > Welcome Tolulope, some of us here are also first timers:blush:butit’sbeen warm in here, thanks to the mentors and fellow interns. > Hopefully, making your first contributionwon’tb so challenging with all the tips available. > You can go through the pinned msgs and/or the brief FAQs with their respective answers posted by@Peace Sandy.

Peace Sandy (14:29:41) (in thread): > Welcome:wave:

UBNSEMS3S (14:34:38) (in thread): > Welcome Tolulope!

UBNSEMS3S (14:36:32) (in thread): > Well the curation is limited to multiple choice. If you pick an option that applies to either group, it will be counted as a correct answer. > > It’s an important lesson to note though that articles can be ambiguous or information that varies in a way that makes it difficult to curate. Hence the importance of asking questions, talking with peers, and then making an informed decision.

Chinwendu Enyinna (14:50:55) (in thread): > Hi Tolulope, welcome to the community!

Iram Jamshed (15:39:39) (in thread): > Breast cancer patients, particularly those undergoing treatment, are more likely to have recently used antibiotics due to compromised immune systems (because they had chemotherapy). Excluding them while on antibiotics helps to prevent any microbiota disturbances. Healthy controls, who are believed to have stable baselines, face a lengthier exclusion period to adjust for any previous antibiotic effects. This guarantees that detected microbiota differences are most likely due to health state rather than recent treatment. I hope it might one of reasons for difference in exclusion timeline.<@UBNSEMS3S>

Onyewuchi Esther Chikamso (15:47:24) (in thread): > Thank you@Peace Sandyfor this

Peace Sandy (15:48:02) (in thread): > You are welcome@Onyewuchi Esther Chikamso

Tolulope Ogunleye (15:53:25) (in thread): > Thank you all:blush:

UBNSEMS3S (16:05:02): > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday). Mary has signed up to present.https://us02web.zoom.us/j/2737200499

Nwajei Edgar (16:05:49) (in thread): > Noted….

Joan C. Chukwuemeka (16:07:43) (in thread): > Okay….:thinking_face:@Iram JamshedI think that could be a possibility… Thanks for sharing your perspective:slightly_smiling_face:

Chioma Onyido (16:10:06) (in thread): > Different criteria also To avoid the possibility of bias in the study.. hmmm.. This makes a lot of sense@Iram Jamshed,:+1:

UBNSEMS3S (16:18:09) (in thread): > That’s an excellent answer@Iram Jamshed.

Peace Sandy (16:18:45) (in thread): > Thank you so much

Chioma Onyido (16:20:26) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Chloe (16:28:10) (in thread): > Thanks

Chinwendu Enyinna (16:30:23) (in thread): > Thank you Chloe. Looking forward to it!

U1LCB8WEA (16:46:14) (in thread): > Thank you,@Peace Sandy!

Esther Afuape (16:46:54) (in thread): > Thank you

U1LCB8WEA (16:47:37) (in thread): > Thank you for joining us,@Tolulope Ogunleye- microbiology is a very useful background to have for this project!

Esther Afuape (16:48:28) (in thread): > Thank you!This will clear a lot of confusion

Peace Sandy (16:49:06) (in thread): > You are welcome@Esther Afuape:hugging_face:

Peace Sandy (16:49:30) (in thread): > Always my pleasure@Levi Waldron

U1LCB8WEA (16:59:16) (in thread): > I meant, welcome@Chloe!

Joan C. Chukwuemeka (17:05:13) (in thread): > Okay… Thanks<@UBNSEMS3S>

edilawit (17:06:59) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Onalo Deborah (17:40:25) (in thread): > Looking forward to it!

Tolulope Ogunleye (17:47:38) (in thread): > Noted….Can’t wait !

Shakira Ndagire (19:27:03) (in thread): > Looking forward to it

Fortune Nnamdi (19:38:12) (in thread): > Thank you,everyone for the warm welcome:hugging_face:

Wangui Thuo (23:18:46) (in thread): > <@U1LCB8WEA>Thank you for the warm welcome

2023-10-05

Sabastine Iroka (00:32:49) (in thread): > Looking forward to it

Iram Jamshed (00:45:23) (in thread): > Looking forward to it! Thanks<@UBNSEMS3S>

Iram Jamshed (00:47:04) (in thread): > I’m glad that it was helpful!:blush:<@UBNSEMS3S>@Joan C. Chukwuemeka@Chioma Onyido

Sabastine Iroka (01:23:18) (in thread): > Thanks for this Compilation@Peace SandyPreviously, I was waiting for my first contribution to be approved, but now I can go ahead and curate more papers.

Chioma Onyido (01:44:25): > Hi@Svetlana Ugarcina PerovicGood morning.:blush:I’mcurrently on the study curation part and for the article I was assigned to, I noticed they had different antibiotics selection criteria for case and control. We had an interesting discussion earlier with@C. Mirzayi (please do not tag this account)on possible reasons why this is so, however myquestionis: Do we report for both case and control during curation or only the case?

Iram Jamshed (02:10:56): > Hi, I think I can answer this. In the same discussion thread that you mentioned<@UBNSEMS3S>has mentioned “Well the curation is limited to multiple choice. If you pick an option that applies to either group, it will be counted as a correct answer”. So yeah, it is your choice to pick whichever you wish both will be correct only. Hope it helps.

Chioma Onyido (02:13:01) (in thread): > Hi Iram, thanks for your response. I saw this but I assumed she was only referring to the mini-curation, which is the first contribution.

Iram Jamshed (02:22:21) (in thread): > Yeah okay, you can confirm from her. In my opinion it will apply to this as well.:blush:

Thara Ehizogie (03:42:45) (in thread): > Hello Chiwendu, i am having an issue with the part where i need to search for the disease of interest on the EBI link.

Aleru Divine (03:45:16) (in thread): > Looking forward to it

Onyewuchi Esther Chikamso (03:45:35) (in thread): > Looking forward to it

Thara Ehizogie (03:45:39): > Hello Guys, please can someone explain the part of searching for a disease of interest on the EBI site. It is in contribution 1 andI don’treally understand it

Nwajei Edgar (03:47:08) (in thread): > Copy the name of the disease and paste in the search option

Iram Jamshed (03:50:31) (in thread): > You have to find the disease that is specifically studied in the article and search the same on EBI. From there, you have to pick the EFO or MONDO of the best matched result.

Nwajei Edgar (03:51:42) (in thread): > @Thara Ehizogie

Tolulope Ogunleye (03:52:52) (in thread): > I’m so in love with the project already, it feels like my thesis all over again!

Chinwendu Enyinna (03:56:35) (in thread): > Hi@Thara EhizogieOn the EBI page, you need to enter the disease of interest in the search box. This will display a number of options similar to the disease of interest you searched for. You then have to click on any that is closely related to the disease of interest(tip: you can compare the study topics). This takes you to the detail page for that disease, then you can copy the EOI number which should look like this format:EFO_0000186

Iram Jamshed (03:58:09) (in thread): > @Nwajei EdgarHi, I just had submitted an account request. But when opening the link in the mail for confirmation it is saying” Invalid confirmation code. The code may have expired”. What could be the reason?

Nwajei Edgar (04:01:48) (in thread): > Did you use the link for account request from the GitHub page?

Iram Jamshed (04:02:47): > <@UBNSEMS3S>I am facing issues whenever I visithttps://www.ebi.ac.uk/ols/ontologies/efo. It says Something went wrong! Use the issue tracker or the support mail below to report any bugs or give feedback. > * Issue Tracker > * ols-support@ebi.ac.uk > Cause unknown (no exception details available).

Iram Jamshed (04:03:39) (in thread): > No, from this community chats.

Nwajei Edgar (04:04:02) (in thread): > Can you share a screenshot ?

Nwajei Edgar (04:06:28) (in thread): > This is the link to request for an accounthttps://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Sabastine Iroka (04:08:52): > Hi@C. Mirzayi (please do not tag this account),<@U1LCB8WEA>How long does it take to get a confirmation email after requesting for an account? > > I requested some hours ago, but yet to get one.

Chioma Onyido (04:09:59) (in thread): > Hi Iram, try:https://www.ebi.ac.uk/efoand use the search bar to input disease of interest. - Attachment (ebi.ac.uk): The Experimental Factor Ontology < EMBL-EBI > The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets. We also add terms for external users when requested. If you are new to ontologies, there is a short introduction on the subject available and a blog post by James Malone on what ontologies are for.

Tolulope Ogunleye (04:10:51): > I’ve completed the first task and signified interest to work on a paper by responding under the issue with my name as instructed but my user request account has not been approved…. I want to start making my second contribution right away, any idea on what to do before my user account is approved ?

Nwajei Edgar (04:11:16) (in thread): > Be patient it will be approved

Sabastine Iroka (04:11:35) (in thread): > Hi@Tolulope OgunleyeI guess you should wait until it’s approved. > I’m waiting for that too:slightly_smiling_face:

Nwajei Edgar (04:11:53) (in thread): > It will be approved, just be patient:hugging_face::hugging_face:

Tolulope Ogunleye (04:12:25) (in thread): > Alright…Thank you

Sabastine Iroka (04:12:46) (in thread): > Thanks:smiley:

Nwajei Edgar (04:13:45) (in thread): > Anytime:innocent::innocent:

Tolulope Ogunleye (04:23:30) (in thread): > Hi Sebastian,you can check your spam folder , I just found mine there.

Tolulope Ogunleye (04:25:37) (in thread): > I just checked my spam folder and the confirmation email is there:blush:

Tolulope Ogunleye (04:28:38): > If you’ve requested a user account and it’s taking time to get a confirmation mail, you can check your spam/junk or promotions folder…that was where I found mine after waiting for hours.

Nwajei Edgar (04:29:07) (in thread): > Great:innocent:

Iram Jamshed (04:47:26) (in thread): > I am able to search on this website but after getting search results, I’m not able to open the results.

Sabastine Iroka (04:53:23) (in thread): > Thanks@Tolulope OgunleyeFound mine some minutes ago and headed here to tell you too:joy:

Chioma Onyido (05:08:45) (in thread): > I just tried it too and I encountered the same error you previously mentioned. I think it could be technical issues or problems with the server.

Iram Jamshed (05:10:31): > I got the mail for verification but my mail was not verified. It says code expired.

Tolulope Ogunleye (05:12:32) (in thread): > You can try to log in with your username and temporary password supplied in the 2nd mail instead

Iram Jamshed (05:13:24) (in thread): > I have not recieved any password.

Joan C. Chukwuemeka (05:16:03): > Hello Everyone, > Please while requesting for account are all the fields on the page required to be filled?

Kabirat Adeniyi (05:17:00) (in thread): > The ones that are not required to be filled are tagged (optional)

Joan C. Chukwuemeka (05:18:19) (in thread): > Okay….

Peace Sandy (05:18:37) (in thread): > Yes they are

Joan C. Chukwuemeka (05:18:52) (in thread): > Thanks@Kabirat Adeniyi

Joan C. Chukwuemeka (05:19:49) (in thread): > :thinking_face:… Including the cv upload aspect@Peace Sandy

Nwajei Edgar (05:20:13): > Question: When creating a study, how do I go about the citation using PMDI, DOI or URI

Peace Sandy (05:20:47): > Hey Everyone:wave:Let’s not forget our weekly team meeting and Outreachy Office hour. > For Nigeriansit’s3:00pm local timehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696449902004719 - Attachment: Attachment > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday). Mary has signed up to present. https://us02web.zoom.us/j/2737200499

Peace Sandy (05:21:09) (in thread): > No, I think that can be added later

Sinmi Adesanya (05:22:39): > Hello everyone, I trust you’re all well.

Sinmi Adesanya (05:22:57) (in thread): > A huddle started

Sinmi Adesanya (05:24:06): > Apolgies regarding that. Thank you,@Peace Sandyfor the reminder!

Iram Jamshed (05:24:23) (in thread): > Yeah. Maybe.

Sabastine Iroka (05:36:29) (in thread): > Hi@Tolulope Ogunleyehow long did you wait before getting the temporary password

Tolulope Ogunleye (05:42:12) (in thread): > It took about 2 hours from the time I got the confirmation email to get the temporary password

Nwajei Edgar (05:48:39) (in thread): > @Chioma Onyidothanks for your help:hugging_face::hugging_face:

Chioma Onyido (05:53:09) (in thread): > You’rewelcome Edgar.:clap:Posting it here for anyone with similar concerns:It’sadvisable to use the PMID*, during curation. > > if youdon’tfind the PMID in your article, you can look it up on Pubmed (a database for scientific and biomedical literature maintained by the NLM and NIH), the PMID will be there ifit’sin their db.

Chioma Onyido (05:55:49) (in thread): > Thanks for the reminder, Peace. > For EAT, 5:00pm local time.

Iram Jamshed (05:56:26) (in thread): > Okay. I will wait.

Ayowale Ojo (05:59:00) (in thread): > Experiencing something similar.

Iram Jamshed (06:02:36) (in thread): > <@UBNSEMS3S>Could you please help us with this issue.

Svetlana Ugarcina Perovic (06:03:00) (in thread): > @Chioma Onyidocorrect, thanks for clarification!During curation use PMID.You can instead enter a DOI or URL to identify the source: note those other identifiers are only needed if there is not a PMID, otherwise PMID alone is enough. > > cc@Nwajei Edgar

Svetlana Ugarcina Perovic (06:06:58) (in thread): > In my opinion both should be reported. Let’s ask<@UBNSEMS3S>and confirm it, since she is more familiar with db curation options. Thanks for your patience!

Svetlana Ugarcina Perovic (06:09:14) (in thread): > Yes, sometimes the resources can be slow or stuck, due to e.g. a lot of us searching for info :)

Svetlana Ugarcina Perovic (06:09:43) (in thread): > Thanks for your patience!:tulip:

Svetlana Ugarcina Perovic (06:10:32) (in thread): > Thanks for your patience!:tulip:

Iram Jamshed (06:10:56) (in thread): > Hi@Svetlana Ugarcina Perovic, Thank you for your response. Im facing some issue when requesting for account creation. Can you please help.

Nwajei Edgar (06:11:18) (in thread): > Thank you:hugging_face::hugging_face:

Svetlana Ugarcina Perovic (06:12:10) (in thread): > Please be patient:slightly_smiling_face:and check your spam folder.

Svetlana Ugarcina Perovic (06:12:57) (in thread): > See you soon! :)

Svetlana Ugarcina Perovic (06:13:27) (in thread): > For me it will be also afternoon:teapot:

Iram Jamshed (06:13:31) (in thread): > Yeah, I have checked. Actually I could not access the link for verifying my email. It says it is expired. Will I still receive the password?

Chioma Onyido (06:16:31) (in thread): > Looking forward to it!@Svetlana Ugarcina Perovic

Chioma Onyido (06:17:25) (in thread): > Thank you.:raised_hands:

Svetlana Ugarcina Perovic (06:18:24) (in thread): > Hi@Iram Jamshedtry again to open an account from scratch and let me know how it goes.

Svetlana Ugarcina Perovic (06:29:50) (in thread): > SOLVED:slightly_smiling_face:with opening again the account with other email address.

Iram Jamshed (06:30:45) (in thread): > We did it.:blush::+1:

Svetlana Ugarcina Perovic (06:31:15) (in thread): > Actually you did it@Iram JamshedGood job!

Iram Jamshed (06:33:12) (in thread): > Thanks.:blush:Others facing the issue can try with new email id and new username.

Chioma Onyido (06:33:21): > Hi everyone,:grinning:I hope we’re doing great and making progress with our tasks. > > I’ve been going through the recent chats (questions) on the channel and with the approval of@Svetlana Ugarcina Perovic, I created a document to make it easier to collate questions (on the project and contributions) for the mentors in preparation for our meeting today. > > Please feel free to add your questions. > Here’s the link:https://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/edit?usp=sharing

Nwajei Edgar (06:33:58): > Awesome work Chioma , this will be helpful

Peace Sandy (06:40:03) (in thread): > Can’twait to see you@Svetlana Ugarcina Perovic

Peace Sandy (06:40:18) (in thread): > Awesome

Chioma Onyido (06:40:21) (in thread): > Indeed it is. Encountered some challenges while on my second contribution andI’mstuck, I can only imagine how many others with similar concerns, already added 2 questions:sweat_smile:

Sabastine Iroka (06:41:48) (in thread): > I’ve tried opening with a new email address and username. > Now waiting for the temporary password:crossed_fingers:

Peace Sandy (06:42:29) (in thread): > Thank You

Peace Sandy (06:44:13): > I highly recommend watching the YouTube Videos, if possible the whole playlist,take time to go through the onboarding materials,most concepts and howtos where thoroughly explained.

Esther Afuape (06:44:49) (in thread): > I think both should be reported. A curation is supposed to show every important information that might account for the changes observed during the study.

Iram Jamshed (06:45:39) (in thread): > But in that form we had the option to select only one.

Esther Afuape (06:46:02) (in thread): > Thank you

Joan C. Chukwuemeka (06:46:16): > Good morning@Svetlana Ugarcina PerovicTrust the day is going great. > > I’m waiting for account request approval and assigning of a claimed article on the GitHub Issues > > Thanks.

Chioma Onyido (06:47:48) (in thread): > @Svetlana Ugarcina Perovicmy thoughts too. I reported both.

Esther Afuape (06:48:13) (in thread): > Check your junk/spam folder while you wait.It’spossible your approval went there.

Chioma Onyido (06:48:21) (in thread): > @Esther Afuapetrue!

Chioma Onyido (06:49:38) (in thread): > @Iram Jamshedyes, I thinkit’sbecause it’s multiple choice, just as@C. Mirzayi (please do not tag this account)explained.

Kabirat Adeniyi (06:49:51): > Good morning. Im trying log in with busigdb but its not allpwing me. Ive requested a password change and it just said it will be snt to my mail. Ive checked spam and promotions and there no mail there

Iram Jamshed (06:50:33) (in thread): > So how did u report both the options.

Svetlana Ugarcina Perovic (06:50:52) (in thread): > A good question@Iram Jamshed

Peace Sandy (06:51:05) (in thread): > Have you requested for an account ?

Peace Sandy (06:51:43) (in thread): > You are welcome@Chioma Onyido:hugging_face:

Joan C. Chukwuemeka (06:51:59) (in thread): > Yea…I get, but It’s yet to come:slightly_smiling_face:….I just made the request few minutes ago, so was just calling the attention. > > Last mail was to confirm my email, which I have done.

Iram Jamshed (06:52:54) (in thread): > @Svetlana Ugarcina Perovic@Chioma OnyidoActually I was also trying to select both but it didn’t allow.

Onyewuchi Esther Chikamso (06:57:43) (in thread): > What would I do next after my confirmation email has been received?

Chioma Onyido (07:00:01) (in thread): > Something along the lines of e.g. > Prostate cancer: 2 weeks > healthy controls: 4 weeks:sweat_smile:not sure about this, but I guess we’ll have to wait for@C. Mirzayi (please do not tag this account)’s response

Onyewuchi Esther Chikamso (07:01:12) (in thread): > I’m currently experiencing this issue. Thank you for putting this out@Iram Jamshed, I’d patiently wait for my temporary password

Chioma Onyido (07:01:34) (in thread): > @Iram JamshedI think there’s a mixup. For the survey, I only reported one. > I’m referring to our second contribution here.

Iram Jamshed (07:01:36) (in thread): > Okay. Actually I was talking about mini curation one.

Esther Afuape (07:02:03) (in thread): > Alright

Iram Jamshed (07:02:07) (in thread): > Yeah, got it!:smiley:@Chioma Onyido

Chioma Onyido (07:02:46) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696484665818399 - Attachment: Attachment > Hi @Svetlana Ugarcina Perovic Good morning. :blush: > > I’m currently on the study curation part and for the article I was assigned to, I noticed they had different antibiotics selection criteria for case and control. We had an interesting discussion earlier with @C. Mirzayi (please do not tag this account) on possible reasons why this is so, however my question is: Do we report for both case and control during curation or only the case?

Onyewuchi Esther Chikamso (07:03:40) (in thread): > @Iram JamshedDoes this mean I’d have to request an account again?

Onyewuchi Esther Chikamso (07:04:06) (in thread): > My code expired too

Iram Jamshed (07:04:13) (in thread): > Yes with new id and username.

Kabirat Adeniyi (07:09:38) (in thread): > yes

Onyewuchi Esther Chikamso (07:13:16) (in thread): > I’m experiencing the same thing with the second email:disappointed:

Iram Jamshed (07:19:28) (in thread): > expired code?

Chinwendu Enyinna (07:25:43) (in thread): > Good one! This will help.

Chinwendu Enyinna (07:27:05) (in thread): > Maybe you should give it some time then check your mail again.

Bonheur (07:31:45): > Good morning everyone, I am happy to be here with you guys, it’s a pleasure!!

Peace Sandy (07:36:21) (in thread): > Welcome!

Chioma Onyido (07:36:59) (in thread): > Yes please.

Kabirat Adeniyi (07:45:13) (in thread): > thanks

Onyewuchi Esther Chikamso (07:49:27) (in thread): > Welcome!:hugging_face:

Nwajei Edgar (07:49:51) (in thread): > Ask for an article to curate using the GitHub link…..https://github.com/waldronlab/BugSigDBcuration/issues. > > Search for an article not assigned and indicate you want it assigned to you via a comment.

Chinwendu Enyinna (07:49:51) (in thread): > Hi Bonheur, good to have you here!

Onyewuchi Esther Chikamso (07:50:37) (in thread): > Yes. Expired code

Onyewuchi Esther Chikamso (07:52:03) (in thread): > Start by visiting the GitHub link.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Esther Afuape (07:53:27): > Hello everyone > As part of the task in contribution 1,I’mtrying to search for a differentially abundant bacteria from the study on NCBI but it keeps saying “no result found in the taxonomy database for complete name”

Chinwendu Enyinna (08:00:25) (in thread): > I’d suggest you double-check the spelling of the bacteria you’re trying to search for. Or search for another differentially abundant bacteria listed in the article.

Peace Sandy (08:05:26) (in thread): > Copy and paste directly

Nwajei Edgar (08:06:20): > When I’m done with an articlefor contribution 2, what’s next?

Esther Afuape (08:16:58) (in thread): > Thank you.I’vebeen able to sort it

U1LCB8WEA (08:18:40) (in thread): > You can claim another article if you wish-keep in mind though that accuracy of your contributions is very important,so you may want to spend extra time confirming the accuracy of your responses. (This is a general statement, not based on the creation you’ve already done.)

Nwajei Edgar (08:19:08) (in thread): > Thanks for feedback…

Nwajei Edgar (08:19:33) (in thread): > Can I as well add it as a contribution on Outreachy?

Chioma Onyido (08:20:22) (in thread): > Hi Edgar, I think the mentors advised to wait for the office hour before submitting second contributions, to ensure accuracy and that we don’t make mistakes.

U1LCB8WEA (08:20:58) (in thread): > That is a good idea - accuracy is important

Nwajei Edgar (08:21:36) (in thread): > Noted….

Spyke Lionel (08:27:14): > Hello, Nice to be here. Can someone please provide me with a guide on how to get started with the contribution? Thanks

Chinwendu Enyinna (08:28:42) (in thread): > Welcome Lionel. You can start by going through this.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Chinwendu Enyinna (08:30:01) (in thread): > Also, we’d be having our office hours todayhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696449902004719 - Attachment: Attachment > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday). Mary has signed up to present. https://us02web.zoom.us/j/2737200499

Spyke Lionel (08:36:47) (in thread): > Thanks very much@Chinwendu Enyinna. I will go through

Joan C. Chukwuemeka (08:40:03) (in thread): > Account has been created. Thanks<@U1LCB8WEA>:slightly_smiling_face:Now, awaiting my claimed article to be assigned.

U1LCB8WEA (08:41:46) (in thread): > You’rewelcome!I’mcurious, does it give you the option of login using Google instead of the random password sent?

Joan C. Chukwuemeka (08:43:27) (in thread): > Yes it does

U1LCB8WEA (08:44:20) (in thread): > Nice! I also have the option of approval using Google, but I think if I do that no email is sent.

Peace Sandy (08:45:34): > @Levi Waldronis it possible for a study not to have groups 0 and 1, ifit’sa cross observational study? If yes, how do I fill the group section in the Experiment section

U1LCB8WEA (08:47:49) (in thread): > If they did any kind of comparison there are two groups - there almost always are. Only if they report presence or prevalence of taxa without any kind of comparison would there not be two groups.

Peace Sandy (08:48:41) (in thread): > Okay,thanks for the clarifications

Joan C. Chukwuemeka (08:49:36) (in thread): > Okay.. Good to know > > Just tried it out, but got this response, “The supplied credentials are not associated with any user on this wiki.”:grinning:I guess this is because the approval type was for password not google.

Iram Jamshed (09:33:10) (in thread): > @Levi WaldronCould you please assign me the requested paper?

Iram Jamshed (09:34:20) (in thread): > Did u try again?

Kabirat Adeniyi (09:50:28): > please can anyone assist me on the page with the step by step guide on how to perform the first and second tasks?

Peace Sandy (09:50:45) (in thread): > Okay,Sure

Nwajei Edgar (09:51:25) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Peace Sandy (09:51:32) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation|https://www.outreachy.org/outreachy-may-2023-internship-cohort/communities/bioconductor/#microbiome-study-curation.

Peace Sandy (09:51:40) (in thread): > This is the issue link

Kabirat Adeniyi (09:52:10) (in thread): > thank you very much

Kabirat Adeniyi (09:55:13) (in thread): > once we have the paper to curate, and we have the special account, what doe we do next?

Nwajei Edgar (09:55:48) (in thread): > Comment under the article to have it assigned to you

Kabirat Adeniyi (09:56:20) (in thread): > its already been assigned?

Kabirat Adeniyi (09:56:27) (in thread): > what next

Nwajei Edgar (09:56:58) (in thread): > If assigned, check the GitHub link on how to document a signature in BugSigDB

Nwajei Edgar (09:57:58) (in thread): > Watch the attached video

Chioma Onyido (09:58:20) (in thread): > Also, try as much as possible to watch the videos, the materials are all in the github link shared above.

Chinwendu Enyinna (09:59:22) (in thread): > I’d advise you go through the video links listed above to see how to curate a study

Tolulope Ogunleye (10:00:03): > This is a gentle reminder aboutour weekly team meeting and Outreachy Office hour.For Nigerians it’s 3:00pm local timehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696449902004719 - Attachment: Attachment > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday). Mary has signed up to present. https://us02web.zoom.us/j/2737200499

Esther Afuape (10:00:37): > Concerning account creation: When you request for an account, check your spam/ junk folder for the email to confirm your account and another email containing your temporary password. If the confirmation email says the code has expired, go ahead and attempt to login with the temporary password provided. > If you do not receive an email with your temporary password,request for an account with a different email and username.

Chinwendu Enyinna (10:00:55): > Hello everyone, just a reminder it’s time for our meetinghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696449902004719

Kabirat Adeniyi (10:01:32) (in thread): > ive watched the videos, I have a grip on it now

Iram Jamshed (10:03:15): > Hello everyone, meeting has started. Kindly join.

Chiagoziem David (10:32:14): > Where’s the meeting link

Joan C. Chukwuemeka (10:32:52): > https://us02web.zoom.us/j/2737200499@Chiagoziem David

Chiagoziem David (10:34:21): > Thanks

Onalo Deborah (10:52:04): > Hello<@UBNSEMS3S>, I dropped off for a bit, please can you accept me back in

Svetlana Ugarcina Perovic (11:02:37): > Thank you ALL for the great discussion today! Is it ok for you if I post our meeting photo on Twitter (https://twitter.com/svetlana_up)? - Attachment (X (formerly Twitter)): Svetlana U. Perović (@svetlana_up) / X > • microbiome scientist • global communication @microbiomeVIF ✎ https://t.co/2GrC1VcaWY… - File (PNG): outreachy_oct2023.png

Shakira Ndagire (11:02:37) (in thread): > the meeting has ended

Esther Afuape (11:03:01): > Thank you all for your insightful questions and responses.It’sreally exciting to be doing this alongside you:hugging_face:

Esther Afuape (11:03:25) (in thread): > That’d be great!

Nwajei Edgar (11:04:06) (in thread): > Thank you for the discussion. Learnt a lot:innocent::innocent:

Grace Ogundaini (11:06:53) (in thread): > Yes!

Peace Sandy (11:06:53) (in thread): > Yes Sure

Aleru Divine (11:07:17) (in thread): > Thank you so much@Svetlana Ugarcina PerovicIt is absolutely fine by me.

Chinwendu Enyinna (11:07:54) (in thread): > Its’s fine

Desire Oluwarotimi (11:09:47): > @C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina PerovicIn a situation where the statistical analysis provides multiple tests, how do you get to pick the exact one to fill in for curation as the statistical test?

Iram Jamshed (11:22:25) (in thread): > Yes, definitely!

Chioma Onyido (11:27:56) (in thread): > Yes please. Thank you.

Aishat Adebayo (11:36:42) (in thread): > Thanks this is helpful

Onyewuchi Esther Chikamso (11:45:50) (in thread): > Yup. I got the password not long ago. Thank you so much > What should I do next?

Olajumoke Adeoyo (12:12:07): > Hi<@UBNSEMS3S>. I mistakenly submitted my survey for the first contribution task without completing it. Is it possible for me to retake it?

Chioma Onyido (13:23:23): > Hi everyone.@Levi Waldronhas added answers to the questions in the document. Thank you very much Levi. > Please do well to go through it if you need some clarity. > > Again, here’s the link:https://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/edit

Chioma Onyido (13:25:17): > Also please I have a question@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina PerovicIf differential microbes appeared in both increased and decreased, Is it okay to document both?

UBNSEMS3S (13:39:00) (in thread): > Yes you can retake it, if you accidentally submitted it without completing it.

UBNSEMS3S (13:40:41) (in thread): > You want to select the one that is the statistical test used for differential abundance analysis. Sometimes identifying which test was used for this specific analysis can be difficult but I would thoroughly review the Data Analysis/Statistical Analysis section of the Methods.

UBNSEMS3S (13:41:29) (in thread): > Yes you can document them in both. This can happen due to limitations in the methods for detecting and labeling different bacterial taxa.

UBNSEMS3S (13:42:35) (in thread): > @Nwajei EdgarYou can add a link to the second contribution as a contribution on Outreachy and any subsequent contributions can similarly be added.

Nwajei Edgar (13:43:26) (in thread): > Thank you so much

UBNSEMS3S (13:43:44): > I can confirm that Levi and I have responded to all pending account creation requests. Please let me know if you’re still waiting on an account.

Iram Jamshed (14:02:53) (in thread): > Hi<@UBNSEMS3S>. When I was doing my 1st task EBI website was not working, like after giving the query the results came however I couldn’t open them. Although I did my level best to answer the best matched result but I believe I would want to check result details as well if they are opening at sometime. So can I also update my results? If yes, how can I do that?

Iram Jamshed (14:07:11) (in thread): > @Chloe Mirzayi Thanks my account was created. Could you please assign me the article. I have requested it.:innocent:

Iram Jamshed (14:09:34) (in thread): > Assigned. Thank you<@UBNSEMS3S>

UBNSEMS3S (14:16:30) (in thread): > Hi Iram, I looked through your first contribution and I don’t think it’s necessary for you to redo it. You can proceed to the 2nd contribution.

Peace Sandy (14:16:33): > @Levi WaldronThis is a gentle reminder to share the recording

UBNSEMS3S (14:17:07): > I have the recording and will be posting it momentarily. It’s been a busy day.

UBNSEMS3S (14:18:56): > Here’s the recording of today’s office hours. - File (MPEG 4 Video): video1456188298.mp4

Iram Jamshed (14:19:20) (in thread): > Thank you for your humble response!:smiley:

Chioma Onyido (14:24:08) (in thread): > Got it! Thank you Chloe,:blush:

Spyke Lionel (14:27:46) (in thread): > Please I just requested for an account creation. Waiting for your response<@UBNSEMS3S>. Thanks

UBNSEMS3S (14:28:44) (in thread): > @Spyke LionelApproved.

Mildred Anashie (14:29:08): > Hello everyone, my name is Mildred AnashieI am an Outreachy applicantandI’ma microbiologist,very excited tojoin this community andcontributetothis project. Although I have no idea on how to go forward from here.:pray::blush:

Nwajei Edgar (14:29:41) (in thread): > Welcome Mildred:hugging_face::hugging_face:Checkhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Joan C. Chukwuemeka (14:30:14) (in thread): > Welcome@Mildred Anashie

Mildred Anashie (14:31:16) (in thread): > Thankyou

Joan C. Chukwuemeka (14:32:59) (in thread): > Follow this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation.

Spyke Lionel (14:34:06) (in thread): > Thanks much<@UBNSEMS3S>. Will I receive another mail with the password? Or How do I login please?

Chioma Onyido (14:35:01) (in thread): > Hi<@UBNSEMS3S>:pray:

UBNSEMS3S (14:35:28) (in thread): > I believe you should receive another email with a temporary password. Be sure to check your spam folder.

UBNSEMS3S (14:35:54) (in thread): > This is a good question. I would use the criteria used for the cases.

UBNSEMS3S (14:36:08) (in thread): > Welcome!

Iram Jamshed (14:36:28) (in thread): > Welcome@Mildred Anashie:blush:If you face any issue through the process feel free to reach out. You can check the pinned messages for more clarification!

Chioma Onyido (14:37:00) (in thread): > Got it! Thank you.:blush:

Iram Jamshed (14:40:40) (in thread): > You can start your second contribution! Get your article assigned.:blush:

Spyke Lionel (14:45:08) (in thread): > Thanks! Logged in.

Spyke Lionel (14:55:29) (in thread): > Please another thing. Is there a guide on how to go about the contributions. I have been assigned an issue on GitHub already. Kindly waiting

UBNSEMS3S (15:04:28) (in thread): > Please see the videos linked under Prep Work here:https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation.

Odigiri Great Alume (15:18:46) (in thread): > Welcome here Mildred

Peace Sandy (15:21:01) (in thread): > Welcome Mildred

Chika Nwachukwu (15:29:52): > Hello everyone, > I am Chika Nwachukwu, an outreachy applicant. I am a material engineer and data analyst. I am so glad to be here in your midst. I am very eager to contribute.

Desire Oluwarotimi (15:34:15) (in thread): > Thank you Chloe!

Sinmi Adesanya (15:40:34) (in thread): > Thank you so much to the team. This was super helpful to watch!

Chloe (15:40:57) (in thread): > hello i still have a pending account creation

Sinmi Adesanya (15:42:01) (in thread): > Amazing. Thanks Chioma!

Peace Sandy (15:49:35) (in thread): > Hi Chika:wave:Welcome

Peace Sandy (15:50:18) (in thread): > Get started here

Peace Sandy (15:50:22) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Nana Fidausi Mohammed (16:00:04): > Hello, Good evening. I’m Nana Fidausi Mohammed, an Outreachy applicant. I am a product designer and its nice to meet you all

Iram Jamshed (16:22:26) (in thread): > Hi welcome! Happy Contributing:blush:

Iram Jamshed (16:23:53) (in thread): > This will help you getting started.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation.

Iram Jamshed (16:24:36) (in thread): > Welcome!

Esther Afuape (16:26:16) (in thread): > Welcome Mildred

Khadija (16:37:48): > Hey everyone, this is Khadija from Pakistan and I’ll be contributing towards this project for outreachy intership.

Onyewuchi Esther Chikamso (17:19:42) (in thread): > Hi Khadija. Welcome!!!

Onyewuchi Esther Chikamso (17:20:20) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696537433962939?thread_ts=1696536004.212529&cid=C04RATV9VCY - Attachment: Attachment > This will help you getting started. https://github.com/waldronlab/BugSigDBcuration/issues/94

Peace Sandy (17:27:15) (in thread): > Welcome

Spyke Lionel (20:01:07) (in thread): > Thanks<@UBNSEMS3S>I will look into that ASAP

2023-10-06

Olajumoke Adeoyo (00:04:08) (in thread): > Thank you chloe

Spyke Lionel (00:05:38): > Hello everyone,<@UBNSEMS3S>I have completed my first and second contribution task. How can I go about recording this on Outreachy platform? I attended the last meeting but I didn’t quite understand. Please I will like to get some guide on how to go about this. Thanks

Ayowale Ojo (00:30:59) (in thread): > Go to the project list, click the project you want to record contribution to. You should see a green box that says record contribution and apply to this project, click on it, you should be good form here. Check the screenshot I attached - File (JPEG): 1696566411943.jpg

Ayowale Ojo (00:32:48) (in thread): > Have you seen this alsohttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Spyke Lionel (00:41:38) (in thread): > Thanks much

Chioma Onyido (02:13:00) (in thread): > Hi@Spyke Lionel, to record yoursecond contribution on Outreachy, use the link to your study curation on BugSigDB, > Example: https://bugsigdb.org/Study_xxx

Chioma Onyido (02:22:47) (in thread): > Let’sconfirm with the mentors:pray:

Onalo Deborah (02:32:02) (in thread): > Yes

Kabirat Adeniyi (02:34:39): > Good morning, everyone. Your contribution would be appreciated. In my article, there are two differential abundance analyses conducted on three kinds of groups (pre-T2D, T2D, and healthy controls). The comparisons of one abundance analysis were conducted mainly on pre-T2D vs. healthy and T2D vs. healthy. The second comparison for the second differential analysis had no major difference for T2D vs. healthy, while there was a difference for pre-T2D vs. healthy. So I decided to conduct two different experiments for the first differential analysis. Also, there were results, but no explicit Alpha diversity was mentioned. So two questions: > 1. Do I have to self-deduce the alpha diversity? > 2. Do I have to conduct more than two experiments for the second differential abundance analysis? > Thank you very much - File (PNG): image.png

Chinwendu Enyinna (02:35:05) (in thread): > Yea, I think@Chioma Onyidosuggestion is right. Since it’s similar to how we recorded the first contribution.

Chioma Onyido (02:57:07) (in thread): > Hi@Kabirat Adeniyi, for the first question, do you mean that you see results of the Alpha diversity but method wasn’t mentioned? Hmmm if this is so, I think that you should go through it again, if there are results then the estimator should be stated.:thinking_face:Another way is to try searching your pdf with some of the alpha diversity estimators like “Chao1”, “Shannon”, “ACE”, “Jackknife”, etc. > > If you have tried that and it still brings out nothing. I don’t think you should just deduce, your study probably didn’t use alpha diversity.

Sinmi Adesanya (03:00:06): > Hello everyone and good morning from here. > > I’m currently working on my second contribution and have a quick question: Is it acceptable if my study information does not have a PMID number? I found the DOI for my article and tried to generate the information automatically, but it didn’t work. I resorted to imputing the information manually and could not find the PMID even after checking the NIH site. I’m considering leaving that section blank without the PMID number and I would like to know if that is fine. > > Any guidance would be appreciated. Thank you!@Svetlana Ugarcina Perovic@Levi Waldron<@UBNSEMS3S>

Chioma Onyido (03:00:49) (in thread): > For reference, kindly refer to the answer provided by@Levi Waldronto question 1 in this document:https://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/edit?usp=sharingSorry I don’t have definite answers to your second question, hopefully@Svetlana Ugarcina Perovicwould be available soon to provide more clarity.:pray:

Kabirat Adeniyi (03:02:08) (in thread): > thanks for the feedback.

Nwajei Edgar (03:02:23) (in thread): > Here’ssomething that might helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696500180883949?thread_ts=1696497613.399709&channel=C04RATV9VCY&message_ts=1696500180.883949 - Attachment: Attachment > @Chioma Onyido correct, thanks for clarification! > > During curation use PMID. > You can instead enter a DOI or URL to identify the source: note those other identifiers are only needed if there is not a PMID, otherwise PMID alone is enough. > > cc @Nwajei Edgar

Kabirat Adeniyi (03:04:58) (in thread): > What I did was, I looked for the article on PubMed central and copied the PMID. It worked after that

Chioma Onyido (03:04:58) (in thread): > You’rewelcome. Also you can check the answer toquestion 4in the word document, someone asked a question similar to yours about having more than one group 1 and Levi answered.

Sinmi Adesanya (03:06:21) (in thread): > Thank you both!

Kabirat Adeniyi (03:06:34) (in thread): > Thats why I’m doing separate experiments. The question is, Is doing more than two allowed for the same article?

Peace Sandy (03:07:14) (in thread): > You can look up your PMID number on Pubmed this is preferred to DOI when curating

Peace Sandy (03:08:08) (in thread): > Then I think you should do separate experiments

Sinmi Adesanya (03:08:18) (in thread): > Thanks Peace. I have now seen it.

Chioma Onyido (03:08:22) (in thread): > While going through some of the completed curations, I saw some with up to four experiments for one article, so Idon’tthinkit’slimited to 2. > WhatI’mnot sure of is the criteria/ terms for choosing more than 2.

Peace Sandy (03:08:33) (in thread): > I’lladvise you watch the office hour video

Peace Sandy (03:08:59) (in thread): > You are welcome:pray:

Kabirat Adeniyi (03:09:03) (in thread): > i was there, the question was not just asked

Chioma Onyido (03:11:12) (in thread): > @Peace SandyAnd report the differential taxa for each right? Making it 3 experiments. I have the same thoughts too. But I’m not certain.:eyes:

Peace Sandy (03:12:22) (in thread): > Yes, what I do is to go through other curated papers,you’llfind a study similar to that and take an idea from what they did

Peace Sandy (03:12:34) (in thread): > Let’sconfirm from the mentors

Chinwendu Enyinna (03:41:00) (in thread): > @Peace SandyI use the same approach too:grinning:. Pick ideas from other curated paper.

Peace Sandy (03:41:36) (in thread): > You are on point@Chinwendu Enyinna:hugging_face:

Odigiri Great Alume (04:44:50): > Hello@C. Mirzayi (please do not tag this account), I started my second contribution already, however, I have been stuck with requesting a bugsigbd account since yesterday. > A confirmation email has been sent, which I followed the link and it confirms that the account has been confirmed. But I still haven’t been emailed my password hence I’m still unable to log into the account. > > Please I need help

Nwajei Edgar (04:45:25) (in thread): > Check your spam

Odigiri Great Alume (04:46:05) (in thread): > I have been checking my spam and refreshing but still nothing

Nwajei Edgar (04:49:35) (in thread): > <@UBNSEMS3S>your help is needed here

Nwajei Edgar (04:49:52) (in thread): > Just be patient it will get sorted out:innocent::innocent:

Chioma Onyido (04:53:11) (in thread): > @C. Mirzayi (please do not tag this account)would probably still asleep by now.:sweat_smile:We’re like 5 hours ahead. > Hopefully,@Svetlana Ugarcina Perovicwould be here soon.

Chioma Onyido (05:00:54) (in thread): > Hi@Odigiri Great Alume, I just tried something now, > Try searching your username here,http://bugsigdb.org/Special:ListUsersIt takes you to a page with “User list” as the header, enter the username you used for registration, scroll down, you’d see your username directly below the “show” icon. > > Let me know if this works. - Attachment (BugSigDB): Special:ListUsers

Odigiri Great Alume (05:01:41) (in thread): > It worked. But here’s what I got. - File (JPEG): Screenshot_20231006-095650.jpg

Odigiri Great Alume (05:02:17) (in thread): > It’s still saying I don’t have permission to edit the page…..

Chioma Onyido (05:02:53) (in thread): > Hmm Okay I guess you’d have to wait for the mentors. It has to be verified:sweat_smile:

Odigiri Great Alume (05:03:39) (in thread): > Thank you so much Chioma. > Getting stuck is heartbreaking:cry:

Iram Jamshed (05:04:09) (in thread): > Don’t be heartbroken, you will get it soon!

Chioma Onyido (05:04:35) (in thread): > Sorry about that.You’redoing great.:hugging_face:Be patient,they’llbe here soon.

Odigiri Great Alume (05:04:40) (in thread): > Thanks alot guys

Odigiri Great Alume (05:04:43) (in thread): > I’m grateful

Chloe (05:26:44) (in thread): > A huddle started

Svetlana Ugarcina Perovic (05:58:01) (in thread): > Hi all, with the platform issue we have to wait<@UBNSEMS3S><@U1LCB8WEA>THANKS for your patient!

Svetlana Ugarcina Perovic (06:00:36) (in thread): > https://twitter.com/svetlana_up/status/1710231302580871555You are ALL doing great! Keep up the good work and HAPPY FRIDAY!

Chioma Onyido (06:01:46) (in thread): > Thank you@Svetlana Ugarcina Perovic, needed the boost and Happy Friday!:smile:

Iram Jamshed (06:03:37) (in thread): > Happy contributing, Happy Friday!:grin:

Svetlana Ugarcina Perovic (06:03:53) (in thread): > I see you are doing great:slightly_smiling_face:and yes you can curate more than 2 experiments if there are done in the study for differential analysis.

Chinwendu Enyinna (06:04:18) (in thread): > Thank you@Svetlana Ugarcina Perovicand happy Friday to you too:grinning:

Svetlana Ugarcina Perovic (06:04:54) (in thread): > This is sooo awesome, such a supportive environment: you are finding solutions to your challenges together!

Kabirat Adeniyi (06:05:34) (in thread): > thank you for clarifying that. Also Im looking through other curated works to see how it was done

Peace Sandy (06:09:05): > @Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi WaldronIn a case where the comparison is between the Total time breastfeeding group and breastfeeding bouts group. Should these be used as my groups, if yes how do I get the sample size. Because the total sample size is 46 gotten from both mother and infants respectively but what is being compared is the breastfeeding pattern and infant caregiving ecology. Most of the figures are comparing total time breastfeeding and breastfeeding bouts, should that be used as the group. > > Should my group be the same as my description in the signature part

Esther Afuape (06:23:47): > Helloeveryone@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicI’ve been stuck and confused about a lot of things in the paper I chose for curation.I took no notice of the note attached to the paperandwas aboutto begin curationwhen Inoticed to my utter dismay that the paper is a meta analysis and I have no working knowledge of that!I’d like to work on a regular paper for my first curation. May I be allowed to change the paper to curate? I apologize for any inconvenience this might cause.

Hodan Abdirisak (06:41:53): > I am new comer still I am not start to finish first contribution also it is the firts time to contribute public open source

Hodan Abdirisak (06:42:10): > Hope it we fine and smoothly work

Chinwendu Enyinna (06:45:29) (in thread): > Sure it will:hugging_face:. Give it your shot and feel free to reach out for help

Chioma Obioha (06:45:56): > Hello everyone, I just joined. Please could someone bring me up to speed on where to start. Cheers

Onyewuchi Esther Chikamso (06:48:08) (in thread): > Hi Chioma, welcome

Onyewuchi Esther Chikamso (06:48:12) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 24 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communications regarding specific tasks should be done on the Slack BioC channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation.

Onyewuchi Esther Chikamso (06:48:27) (in thread): > You can start by going through this

Odigiri Great Alume (06:57:41) (in thread): > Thank you

Hodan Abdirisak (07:14:19) (in thread): > @Chioma ObiohaWelcome to the community

Hodan Abdirisak (07:16:15) (in thread): > Cheers:pray:

Odigiri Great Alume (07:33:31) (in thread): > Welcome to the community. > Focus on the prep work and watch all the videos. > Read through the articles > Then download the annotated pdf. > Read it and focus on the annotated portions (open it with a pdf reader so you can view the comments) > Then go to the survey form and answer the questions. > You will also need to open a GitHub acct as you will need your username while filling the survey. > > > I hope this is detailed and it helps

UBNSEMS3S (09:22:27) (in thread): > I’ve approved all pending account creation requests so you should be good to go@Odigiri Great Alumebut let me know if that’s not the case.

UBNSEMS3S (09:23:28) (in thread): > Yes that’s fine. I’ll remove you from the assignment of that paper. You can choose another.

UBNSEMS3S (09:30:55) (in thread): > This is a good question. Let me review the paper.

Peace Sandy (09:31:26) (in thread): > Okay

UBNSEMS3S (09:35:44) (in thread): > The unit of study in this paper is what’s called adyad–this includes the mother and the infant. Therefore the sample size should be recorded in dyads. > > There were two main contrasts: total time breasfeeding as well as breastfeeding bouts. They divided each of these contrasts into three groups. I won’t give all the answers away but you should be able to find the group sizes in the paper. > > And please note that taking a look at the results you should expect to have at least 4 experiments.

UBNSEMS3S (09:36:14) (in thread): > Welcome Chika!

UBNSEMS3S (09:36:21) (in thread): > Welcome Nana!

UBNSEMS3S (09:36:29) (in thread): > Welcome Khadija!

UBNSEMS3S (09:36:55) (in thread): > Chioma has it right. Record your second contribution using the link to the bugsigdb study page.

UBNSEMS3S (09:37:44) (in thread): > Welcome Hodan! Feel free to ask any questions you have.

UBNSEMS3S (09:37:53) (in thread): > Welcome Chioma!

Peace Sandy (10:23:42) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Peace Sandy (10:25:02) (in thread): > How do I record a sample size in dyads@C. Mirzayi (please do not tag this account)

UBNSEMS3S (10:26:38) (in thread): > Just say the number. For instance if there were 10 mother-infant pairs in the low total time breastfeeding group that would be recorded as a group size of 10.

Tolulope Ogunleye (10:55:09): > @Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)please what would you advice in a situation where someone also commented on a paper I had previously showed interest in by commenting and currently working on buthasn’tbeen assigned ?

Joan C. Chukwuemeka (10:55:34): > Hello everyone:wave:Trust we’re all good > > Please I have some questions: > The study I’m curating is about using shotgun metagenomic sequencing to compare the vaginal microbiota of women at high risk of preterm birth (n = 35) vs. a low-risk control group (n = 14). > > 1.) The condition being studied is Preterm birth (PTB), while filling it in the autocomplete showed “spontaneous Preterm birth”, as a result I used the “find a term” option to checked on the EFO site, and it showed “premature birth”. I hope I’m correct to use “premature birth”, which is also available on BugSigDB autocomplete and not “spontaneous Preterm birth”? > > 2.) Its a Prospective cohort study, that sought to compare the vaginal microbiota of women at high risk of preterm birth (n = 35) vs. a low-risk control group (n = 14). However, the Analysis section had 2 sub groups under each main group, that is, At risk group had risk_PTB and risk_FTB, while the control group had non-risk PTB & non-risk FTB, > Where: > risk_PTB = preterm birth refers to those women who delivered prior to 37 weeks’ gestation. > risk_FTB = refers to those women with risk factors for preterm birth but who delivered full term. > > non-risk PTB = refers to low-risk women who delivered prior to 37 weeks’ gestation. > non-risk FTB = refers to low-risk women who delivered at term. > > In the experiment grouping, should > group 0 be non-risk PTB = refers to low-risk women who delivered prior to 37 weeks’ gestation.? & > group 1 be risk_PTB = preterm birth refers to those women who delivered prior to 37 weeks’ gestation.?:thinking_face:And its a Prospective cohort study not case-control study?<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Tolulope Ogunleye (10:59:49) (in thread): > Hi Everyone:wave:Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > 1. how do i record my contribution in the outreachy website? > AnswerOnce you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application.2. Do I need to wait for first contribution to approved or reviewed before I start the second contributionAnswerYou do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here:https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article.3. How do I know if my first contribution is accepted or merged?AnswerOnce you complete the survey we will have a record of it. Don’t worry!4. Should I always send a DM to mentorsAnswerEveryone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion.@C. Mirzayi (please do not tag this account)@Levi Waldronand@Svetlana Ugarcina Perovicare our mentorsIf you just joined you can get started here:point_down:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Tolulope Ogunleye (11:01:19) (in thread): > @Hodan Abdirisakplease go through this message curated by@Peace Sandy. > You’ll find it helpful.

Hodan Abdirisak (11:10:39) (in thread): > Thanks dear mentor@C. Mirzayi (please do not tag this account)and@Tolulope Ogunleyefor your info.

Odigiri Great Alume (11:25:10): > Based on your description, it indeed appears to be a prospective cohort study since you are following two groups of women (high-risk and low-risk) over time to compare the incidence of premature birth and the vaginal microbiota. In your experiment grouping: > > Group 0 can be “non-risk PTB” and represents low-risk women who delivered prior to 37 weeks’ gestation. > Group 1 can be “risk_PTB” and represents women at high risk who delivered prior to 37 weeks’ gestation.

Odigiri Great Alume (11:25:17): > I hope this helps.

Mildred Anashie (11:25:19) (in thread): > Hi@Hodan AbdirisakI’mnew too and currently working on my first contribution…Let me know if I can be of help, At least I havesomethings figured out due to help from@Odigiri Great Alume

Joan C. Chukwuemeka (11:28:00): > In a prospective cohort study, participants are enrolled before the outcome of interest occurs and then followed over time to see who develops the outcome. > > Here, the researchers are interested in comparing the vaginal microbiota of women who develop preterm birth to the vaginal microbiota of women who do not develop preterm birth.@Odigiri Great AlumeThen, this conclusion is right,:point_right:? The other two subgroups, risk_FTB and non-risk FTB, are not relevant to the study’s primary objective. even though they may be included in the analysis as additional subgroups, but they would not be the main focus of the study.

Hodan Abdirisak (11:28:27) (in thread): > Thanks for your help

Odigiri Great Alume (11:33:18): > I’m not sure I understand what you mean. However, > I agree that is a cohort study since you don’t know the OUTCOME yet. It’s after following the groups you can determine the incidence of PRB and the vaginal microbiata.

Odigiri Great Alume (11:42:04) (in thread): > Alright I will check now ma’am > Thank you

Mildred Anashie (11:42:43): > Hello everyone…I just finished my first contribution,what’snext please:pray:Do I need to record immediately?And how can I do that

Hodan Abdirisak (11:49:44) (in thread): > @Mildred AnashieCongratulations to step up next stage

Odigiri Great Alume (11:51:30) (in thread): > @C. Mirzayi (please do not tag this account)Thank you a lot. I have been able to log into the account with with user #OdigiriGreat. However I thought it was my email that was messing up at first so I used my other email to request another account with user #GreatDaniel and #GreatOdigiri. Please could you delete these and leave #OdigiriGreat. > > > #OdigiriGreat is the account I have chosen. > > Please:pleading_face:I’m really sorry for the inconveniences. > > Thank you again.

Joan C. Chukwuemeka (11:53:12): > Is there a way to perform a search on BugSigDB based on the study design type?:thinking_face:yet to see a sample of curated study that was prospective cohort,,, hoping to get a guide….would keep searching:grinning:, that’s part of research

Odigiri Great Alume (11:57:51) (in thread): > https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation/contributions/add/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Odigiri Great Alume (11:58:06) (in thread): > Follow this link to record your contribution

Odigiri Great Alume (11:59:58) (in thread): > You only need to say that you carried a mini curation after studying an annotated pdf by completing the survey. > Then include the link to the survey or GitHub link where the information about the first and second contribution is described

Odigiri Great Alume (12:00:13) (in thread): > I hope this helps.

Esther Afuape (12:05:17) (in thread): > Thank you so much.I’vecommented my name for another paper.

UBNSEMS3S (12:05:46) (in thread): > 1. The goal is to pick the most accurate ontology term for the condition. It sounds to me like that is what you did when you searched the EFO and found a more fitting term. > 2. It is common that studies will do subgroup analyses and therefore have more than one experiment. If that’s the case, you will need to add more than one experiment so that you can curate each pair of contrasts.

Joan C. Chukwuemeka (12:07:04) (in thread): > Okay, Thanks<@UBNSEMS3S>

UBNSEMS3S (12:07:23) (in thread): > It’s not perfect but just searching for prospective cohort seems to turn up a bunch of studies:https://bugsigdb.org/w/index.php?search=+prospective+cohort&title=Special%3ASearch&profile=advanced&fulltext=1&ns0=1&ns102=1&ns108=1 - Attachment (BugSigDB): Special:Search

UBNSEMS3S (12:08:23) (in thread): > Hi Tolulope I see what happened. I was just about to assign that to you. I will ask the other person to stop.

Tolulope Ogunleye (12:09:21) (in thread): > Alright,thanks

Joan C. Chukwuemeka (12:09:33) (in thread): > I’ve been using random page option though, just saw one some seconds ago. > > I just did the search and saw the bunch of studies:smiley:… It’s fine…I’d go through some, hopefully I’d get clues on how to carry on with mine

Chioma Obioha (12:15:42) (in thread): > @Onyewuchi Esther Chikamso@Hodan Abdirisak@Odigiri Great Alume@C. Mirzayi (please do not tag this account)This really helps. Thanks guys

UBNSEMS3S (12:22:02): > I know we’re running low on papers to assign for second contributions. I’m going to try to get 5-10 more posted this afternoon.

Mildred Anashie (12:23:29) (in thread): > Thank you so much@Odigiri Great Alume

Odigiri Great Alume (12:23:53) (in thread): > My pleasure

Hodan Abdirisak (12:25:12): > I have completed my first contribution now I am gonna make second contribution

Hodan Abdirisak (12:28:36): > It is recording the first contribution needed?

Hodan Abdirisak (12:29:43): > @C. Mirzayi (please do not tag this account)

Chioma Onyido (12:33:48) (in thread): > @Hodan Abdirisakyou can paste either the survey link or GitHub issue link with a description.Here’s the link:https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation/contributions/add/

Chioma Onyido (12:34:36) (in thread): > And yes please it is necessary.

Hodan Abdirisak (12:34:47) (in thread): > Thanks

Mildred Anashie (12:37:25) (in thread): > congratulations and well done

Mildred Anashie (12:38:17) (in thread): > From my understanding, it is necessary

Hodan Abdirisak (12:40:37) (in thread): > @thanks for help

UBNSEMS3S (12:44:12) (in thread): > Yes just document on Outreachy that you completed it and you can just link to the survey if needed.

UBNSEMS3S (12:44:42): > I have added 11 more papers to curate. I tried to pick from several different topics. I will try to add 5-10 more this weekend as well.

Hodan Abdirisak (12:45:30): > Is that start time and emerge time same date or not - File (JPEG): IMG_20231006_194128.jpg

Grace Ogundaini (12:46:19) (in thread): > Hello. I’ve completed the mini-curation and recorded it. I’m trying to fill the final application, what do I fill in the Outreachy internship project timeline please?

UBNSEMS3S (12:46:20) (in thread): > You can enter the same date.

Mildred Anashie (12:47:10) (in thread): > Yes…I think it is, if you started and finished the same date

Hodan Abdirisak (12:47:53): > What about the description which points should be must to mention

Mildred Anashie (12:49:54) (in thread): > This is what I recorded for mine….I carried out a mini curation after studying an annotated pdf and completed the survey.

Grace Ogundaini (12:50:32): > Hello all. I just completed my first contribution, I’ve recorded it and I’m trying to submit my final application. My questions > 1. I plan to do a second curation, should I submit my final application after the second curation? > 2. What do I fill in place of the Outreachy internship project timeline in my final application?

Peace Sandy (12:58:30) (in thread): > Wow…Thank You

Hodan Abdirisak (12:58:42): > I recorded the first contribution and next page is like this

Chioma Onyido (13:03:31) (in thread): > I think you should finish your second curation first before submitting your final application. > > After your second curation is graded by the mentors, I thinkthey’dgive us more information on the project timeline and every other thing we need to know.

Hodan Abdirisak (13:03:47): > Should I go to the next step to create final application or do second contribution

Chioma Onyido (13:04:35) (in thread): > Hi@Hodan Abdirisak, I think you should go ahead to do your second contribution before creating final application.

Onyewuchi Esther Chikamso (13:06:19) (in thread): > But you would record your first contribution right?

Hodan Abdirisak (13:07:43) (in thread): > Yes,@Onyewuchi Esther ChikamsoI write description, dat, enter the URL and save

Grace Ogundaini (13:35:21) (in thread): > Thank you!

Odigiri Great Alume (13:36:04) (in thread): > Apt:100:

Hodan Abdirisak (14:23:43): > I created an account and waiting to confirmation

Chinwendu Enyinna (14:40:30) (in thread): > Well done@Hodan Abdirisak:clap:

UBNSEMS3S (15:36:09) (in thread): > Approved.

Hodan Abdirisak (15:44:41) (in thread): > Dear mentor, I did not get the email

UBNSEMS3S (17:38:17): > Our first week is drawing to a close. Thank you all so much for your contributions so far. I just wanted to give you all a heads up that Monday is a holiday here in NYC so I will not be working my normal hours; however, I plan to check in and answer questions for a bit Monday morning.

Peace Sandy (18:59:00) (in thread): > Okay,Chloe

2023-10-07

Hodan Abdirisak (00:04:25) (in thread): > Noted@C. Mirzayi (please do not tag this account)

Hodan Abdirisak (00:05:41): > @C. Mirzayi (please do not tag this account)how I know that my account is approved bc I did not get email:incoming_envelope:

U01MW62UDQR (00:32:11) (in thread): > I saw that Chloe did mention that your account was approved. If you haven’t seen the email, I recommend checking your spam. When my account was created, the subject was ‘Account creation for A Comprehensive Database of Microbial Signatures’.

Hodan Abdirisak (00:54:04) (in thread): > Thanks to remember me that I forget the spam

Hodan Abdirisak (00:57:48) (in thread): > @C. Mirzayi (please do not tag this account)sorry, I forget to check my spam in email i get the email but unfortunately says your code expired

Hodan Abdirisak (00:58:19) (in thread): - File (JPEG): Screenshot_2023-10-07-07-53-48-965_com.android.chrome.jpg

Hodan Abdirisak (00:59:01) (in thread): > I get but invalid:pleading_face:

Chinwendu Enyinna (02:29:33) (in thread): > Alright

Karen254. Kingecha (03:42:19) (in thread): > Noted@C. Mirzayi (please do not tag this account)

Karen254. Kingecha (03:46:29) (in thread): > @Hodan AbdirisakI’m not in a position to answer that but when@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldroncome online they’ll be able to answer you.

Sinmi Adesanya (04:49:57) (in thread): > Noted Chloe. Thanks for the heads up!

Peace Sandy (05:29:37) (in thread): > You would surely get a mail

Hodan Abdirisak (05:34:46) (in thread): > I get in spam I checked but the code invalid

Esther Afuape (09:47:19) (in thread): > Thank you

Mildred Anashie (09:58:17) (in thread): > Noted > > Thank you

Peace Sandy (10:43:39): > Hey Everyone:wave:Please who has used the EFO Site yet

Joan C. Chukwuemeka (10:45:28): > Hello@Peace Sandyhow are you doing? > I used the site yesterday

Peace Sandy (10:45:53) (in thread): > Okay

Hodan Abdirisak (10:49:01) (in thread): > For me not

Joan C. Chukwuemeka (10:49:38) (in thread): > Which link did you use to access it?@Peace Sandy

Peace Sandy (10:51:20) (in thread): > I just typed EFO on Google

Peace Sandy (10:51:44) (in thread): > Is they another link@Joan C. Chukwuemeka

Joan C. Chukwuemeka (10:52:34) (in thread): > The EFO site helps one to pick the most accurate ontology term for condition, body site, etc.

Peace Sandy (10:52:53) (in thread): > Yes,I’maware

Peace Sandy (10:53:09) (in thread): > What do we enter on the search bar

Peace Sandy (10:53:43) (in thread): > What prompt will you enter to get the body site

Peace Sandy (10:53:52) (in thread): > Okay

Peace Sandy (10:56:49) (in thread): > @Esther Afuapeyou will find the messages here helpful

Esther Afuape (10:57:10) (in thread): > Thank you so much, Peace

Peace Sandy (11:01:12) (in thread): > You are welcome@Esther Afuape

Peace Sandy (11:01:35) (in thread): > Also, how were you able to use the site to extract data

Joan C. Chukwuemeka (11:02:43) (in thread): > The body site is usually stated in the study, but sometimes may not show up in BugSigDB autocomplete, so the search term will be the “body site as stated in the study”

Joan C. Chukwuemeka (11:04:24) (in thread): > Here is the site linkhttps://www.ebi.ac.uk/efo/ - Attachment (ebi.ac.uk): The Experimental Factor Ontology < EMBL-EBI > The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets. We also add terms for external users when requested. If you are new to ontologies, there is a short introduction on the subject available and a blog post by James Malone on what ontologies are for.

Peace Sandy (11:10:29) (in thread): > Did you use it get data for your study

Joan C. Chukwuemeka (11:10:41) (in thread): > @Peace Sandylet me share a brief media on how to do so, just noticed the site has been updated to a new one

Peace Sandy (11:13:48) (in thread): > Okay

Peace Sandy (11:13:56) (in thread): > Thank you so much@Joan C. Chukwuemeka

Esther Afuape (11:29:19) (in thread): > Please share it with me also@Joan C. Chukwuemeka

Peace Sandy (11:30:19) (in thread): > She hasn’t shared it yet

Peace Sandy (11:30:55) (in thread): > You can just share it here so everyone can benefit@Joan C. Chukwuemeka

Joan C. Chukwuemeka (11:37:02) (in thread): > yea… sure

Joan C. Chukwuemeka (11:47:58) (in thread): > An example: The condition being studied is Preterm birth (PTB), while filling it in the autocomplete showed “spontaneous Preterm birth”, as a result I used the****“find a term”****option to checked on the EFO site. > > When you click the “find a term” it brings a page with another site link. click the new link and input your search term, So here I inputted the preterm birth, different results are shown. Using the filter side bar, type in EFO, it showed “premature birth” as the closest EFO ontology term. Going back to my BugSigDB page. the****” “premature birth” ****available:blush:Alternatively, instead of clicking the****“find a term” ****option, you can open the link in a new tab and search - File (MPEG 4 Video): EFO navigation.mp4

Joan C. Chukwuemeka (11:57:27) (in thread): > @Peace SandyDoes this answer the question?

Peace Sandy (12:29:48) (in thread): > Yes, Thank you so much@Joan C. Chukwuemeka

Joan C. Chukwuemeka (12:31:38) (in thread): > Alright@Peace Sandyglad it did

Joan C. Chukwuemeka (12:32:02): > @Hodan Abdirisakhello

Hodan Abdirisak (12:36:15) (in thread): > Can I contribute the second contribution without confirming my account

Joan C. Chukwuemeka (12:42:27) (in thread): > @Hodan AbdirisakYou will need your account set up before you can create study and start inputting your curation in the BugSigDB site<@UBNSEMS3S>@Svetlana Ugarcina Perovicand<@U1LCB8WEA>will help sort that out for you, once they are available

Joan C. Chukwuemeka (12:43:32) (in thread): > the site requires login

Hodan Abdirisak (12:57:46) (in thread): > Thanks@Joan C. Chukwuemekafor your response@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicI am looking forward to hearing from you

Shakira Ndagire (13:31:21) (in thread): > Noted thanks@C. Mirzayi (please do not tag this account)

Greatman Ugorji (15:58:43): > Hello<@UBNSEMS3S>, I’ve been assigned my first article and I’ve completed the curation. Can I ask to be assigned another paper?

U1LCB8WEA (22:20:17) (in thread): > If you aren’t able to use the password, there is a password reset button, or try “Login with Google” ?

U1LCB8WEA (22:21:10) (in thread): > Welcome@Mildred Anashie, thank you everyone for helping!

U1LCB8WEA (22:21:27) (in thread): > We’re glad you’re here too!

U1LCB8WEA (22:21:59) (in thread): > Welcome, Nana! Thank you Iram for your help :)

U1LCB8WEA (22:22:35) (in thread): > Welcome, Khadija, and thank you Onyewuchi for your help!

U1LCB8WEA (22:26:10) (in thread): > I agree, it’s wonderful!

U1LCB8WEA (22:38:53) (in thread): > Sorry for the trouble@Odigiri Great Alume! Accounts can’t be deleted once they’re created, but I’ve blocked GreatDaniel and GreatOdigiri for security, and left OdigiriGreat.

U1LCB8WEA (22:41:07) (in thread): > Welcome,@Hodan Abdirisak, and thanks everyone for your help!

U1LCB8WEA (22:45:00) (in thread): > One other very minor point, I would avoid using acronyms like “PTB” in group names, because when these signatures come up in high-throughput enrichment analysis, analysts won’t immediately have the context to know what it means.

U1LCB8WEA (22:54:41) (in thread): > This video is a great demonstration@Joan C. Chukwuemekathat I want to save for others! I have a question about “spontaneous preterm birth” vs “premature birth”. In the study, were some premature births induced? If not, they would all been spontaneous even though the condition was not listed as such. Sometimes since authors are not looking at the ontology, they actually don’t choose the most appropriate terminology for the condition they are studying :)

2023-10-08

Odigiri Great Alume (02:12:52) (in thread): > Thank you so much@Levi Waldron.

Hodan Abdirisak (04:09:59): > Hello,@C. Mirzayi (please do not tag this account), now my account is confirmed:+1:so could you assign me an issue please!!

Karen254. Kingecha (06:31:43) (in thread): > Hello@Greatman Ugorjihttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696508320242999?thread_ts=1696507580.471419&cid=C04RATV9VCYYes you can claim another article if you wish - Attachment: Attachment > You can claim another article if you wish - keep in mind though that accuracy of your contributions is very important, so you may want to spend extra time confirming the accuracy of your responses. (This is a general statement, not based on the creation you’ve already done.)

Chloe (07:12:58): > how do you know the study design of a given study?

Peace Sandy (07:24:22) (in thread): > Comment on any paper you want to claim it, it would be assigned to you

Greatman Ugorji (07:40:49) (in thread): > Thank you for the clarity.

Chioma Onyido (07:54:36) (in thread): > Hi@ChloeSometimes it is stated explicitly in the abstract section of the paper, if youdon’tsee it there, you can also search for the study design in “Methods” section. Or ctrl + F to search for it in the paper.

Joan C. Chukwuemeka (08:06:01) (in thread): > Oh…:thinking_face:That’s right….Thanks a lot<@U1LCB8WEA>

Joan C. Chukwuemeka (08:07:56) (in thread): > Good day<@U1LCB8WEA>… Thanks for the clarity. There was no induced premature birth in the study, the additional note was that None of the women had preterm premature rupture of membranes.

Hodan Abdirisak (08:55:52) (in thread): > @ChloeLook at upper part of the paper where mostly study design mentioned

Hodan Abdirisak (08:56:54) (in thread): - File (PNG): Screenshot 2023-10-08 011103.png

Hodan Abdirisak (08:57:03) (in thread): > @Peace SandyI commented

Grace Ogundaini (09:53:23): > Hello all. Is it possible to include more than one study design in an article? Especially if it has multiple experiments of different kinds?

Chloe (10:03:30) (in thread): > thnxs@Chioma Onyido@Hodan Abdirisak

Chinwendu Enyinna (10:04:37) (in thread): > Hi, I don’t think the study design is dependent on the number of experiments in the paper.

Chinwendu Enyinna (10:07:12) (in thread): > Also, looking at the previously curated papers, I haven’t come across any with more than one study design.

Mildred Anashie (10:37:29) (in thread): > Hello@C. Mirzayi (please do not tag this account)I got a link after requesting for my account and I followed the link but it says invalid > > What do I do?

Paulina Boadiwaa Mensah (11:22:49): > <@UBNSEMS3S>@Svetlana Ugarcina PerovicCould I be assigned a paper for my second contribution please? I commented my name on one but I’m yet to be assigned.

Grace Ogundaini (11:23:46) (in thread): > Thanks!

Peace Sandy (11:25:42) (in thread): > I think most papers have one study design

Hodan Abdirisak (11:33:25) (in thread): > almost it is one

Nwajei Edgar (11:39:44) (in thread): > Just be patient:innocent::innocent:

Hodan Abdirisak (11:47:47) (in thread): > Have you got temporary password

Hodan Abdirisak (11:47:49) (in thread): > Also

Mildred Anashie (11:51:56) (in thread): > YesIt’sall sorted out now:thumbsup:

Mildred Anashie (11:52:08) (in thread): > Thank you@Hodan Abdirisak

Hodan Abdirisak (11:53:19) (in thread): > You welcome@Mildred Anashie

Hodan Abdirisak (11:53:56) (in thread): > I am waiting also

Hodan Abdirisak (12:38:43): > Hello,@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)I am going to do my second contribution could you assign me please, I commented issue #110

Joan C. Chukwuemeka (12:46:33): > Hello@Hodan Abdirisak, how do you do today? > I believe you will get it assigned once either<@UBNSEMS3S>or@Svetlana Ugarcina Perovicis available. > > I’ll suggest you read through the article and familiarize yourself with the aspects of it that will need to be curated. > Alternatively, you can log in to your BugSigDB account, click on “Random page” to get curated records( especially the ones marked “Reviewed”, read the article from the doi link provided and check how it was curated on BugSigDB > > These will help you once commence yours.

Hodan Abdirisak (12:51:32): > Thanks@Joan C. Chukwuemekayour information guide me to go forward to do the curation:pray:

UBNSEMS3S (12:55:23): > Hi everyone, I think I’m caught up on assignments. Did I miss anyone? Please note that it is the weekend so we might be a bit slower to respond as a result.

UBNSEMS3S (12:55:48) (in thread): > Most papers have one study design if you think there is a case where there’s more than one study design, please share it and we can take a look.

Joan C. Chukwuemeka (12:56:42): > See this too@Hodan Abdirisak - File (MPEG 4 Video): Random page.mp4

Hodan Abdirisak (12:58:33): > @C. Mirzayi (please do not tag this account)I am waiting to assign me and articles to curate, I commented #110

Hodan Abdirisak (12:59:23) (in thread): > @Chloe Mirzayi I am waiting to assign me and articles to curate, I commented #110

Grace Ogundaini (12:59:35): > Is it possible to edit the mini-curation form after submitting it?

Hodan Abdirisak (13:00:11) (in thread): > Thanks for your help

Joan C. Chukwuemeka (13:02:04): > @Grace Ogundainifor the first contribution?

Grace Ogundaini (13:02:23) (in thread): > Yes

Joan C. Chukwuemeka (13:04:29) (in thread): > I’m not sure you can, however,<@UBNSEMS3S>is in a better position to let you know if you can or not.

Hodan Abdirisak (13:06:42) (in thread): > My be@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)more suitable for us to answer

UBNSEMS3S (13:11:08) (in thread): > No we don’t allow editing it. Sorry. I took a glimpse at your mini-curation form and I think you did fine. I’d focus on doing a really thorough second curation.

UBNSEMS3S (13:13:23) (in thread): > Hi Hodan, I don’t see any comments on 110 but I can assign it to you if you comment on it real quick.

Grace Ogundaini (13:15:07) (in thread): > Thank you!@C. Mirzayi (please do not tag this account)

Hodan Abdirisak (13:15:19) (in thread): - File (PNG): Screenshot 2023-10-08 101424.png

Hodan Abdirisak (13:15:53) (in thread): > Is there@C. Mirzayi (please do not tag this account)I take screenshots

Chioma Onyido (13:18:25) (in thread): > These are really helpful videos Joan:smiley:Thank you.

UBNSEMS3S (13:20:24) (in thread): > I think perhaps you have some sort of privacy setting active or something because I can’t see your comments at all but it is assigned to you and you can start curating.

Hodan Abdirisak (13:21:57) (in thread): > I don’t know the problem but I will try to solve it later thanks@C. Mirzayi (please do not tag this account)to assign

Joan C. Chukwuemeka (13:24:09) (in thread): > You’re welcome@Hodan Abdirisak@Chioma OnyidoGlad to help:relaxed:

Peace Sandy (13:31:13) (in thread): > @Hodan Abdirisakprobablyit’syour privacy settings

Hodan Abdirisak (13:37:27) (in thread): > @Peace Sandycan you help me to solve please!

Peace Sandy (13:37:50) (in thread): > Sure

Peace Sandy (13:38:02) (in thread): > Check your settings on GitHub

Peace Sandy (13:40:42) (in thread): > Navigate to your repository > Click on the settings tab at the right end of the menu bar > Scroll down to the “Danger Zone” section > Look for the “change repository visibility” option > Choose public

UBNSEMS3S (13:41:52) (in thread): > That shouldn’t make a difference for the BugSigDBcuration repo which is already public.

Chioma Onyido (13:42:07): > Hello@C. Mirzayi (please do not tag this account)@Levi Waldron, I think I was able to solvehttps://bugsigdb.org/Study_750/Experiment_2/Signature_1while going over pages with missing NCIB IDs- taxonomic issues.https://bugsigdb.org/Study_750has a missing NCBI ID Saccharibacteria TM7 whose taxonomy is showing as orange. > To do this, I confirmed from Wikipedia its synonym, “Candidate division, TM7” which is available on NCBI taxonomy as “Candidatus Saccharibacteria” with the ID 95818. > > Could you confirm if this is correct please? - Attachment (BugSigDB): Study 750/Experiment 2/Signature 1

Mildred Anashie (13:49:03): > Hello everyoneI’mhaving difficulty picking an article for my second contribution > > Do I pick any article? > Also, can I pick an article that has “Needs review”? > Can anyone help?

Chioma Onyido (13:52:47) (in thread): > Hi Mildred, articles with the “needs review” tag are already curated articles awaiting reviews from Mentors.:sweat_smile:Articles you should focus on are those with “second contribution”, “outreachy oct2023” “paper to curate”.:+1:

Chioma Onyido (13:54:23) (in thread): > I would also avoid those with “Assigned” tags.

Mildred Anashie (13:54:53) (in thread): > Thankyou@Chioma Onyido

Chioma Onyido (13:55:47) (in thread): > You’rewelcome.

Hodan Abdirisak (13:57:21) (in thread): - File (MPEG 4 Video): Your Profile - Google Chrome 2023-10-08 10-45-23.mp4

Hodan Abdirisak (13:58:20) (in thread): > That is My general settings

Hodan Abdirisak (13:58:25) (in thread): > In GitHub

Hodan Abdirisak (13:59:28) (in thread): > https://community-bioc.slack.com/files/U05UTDTUHMH/F06087HQZEE/random_page.mp4This video from@Joan C. Chukwuemekamy help you - File (MPEG 4 Video): Random page.mp4

Joan C. Chukwuemeka (14:07:48): > @Mildred AnashieHere’s a link to articles to pick from:https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22Like@Chioma Onyidopointed out select from ones not having “assigned” tag > Once you decide, comment on the issue with your name and request for it.

Chiagoziem David (14:43:23): > Hello guys

Chiagoziem David (14:44:36): > How are we doing and coping, hope we are all making progress, I think we should host a huddle where we could find a way to assist ourselves, this is for the outreachy applicant

Chiagoziem David (14:45:04): > 8 pm tomorrow would do, unless we have other suggestions

Joan C. Chukwuemeka (15:06:36): > @Peace Sandyfor alpha diversity, not sure about derivation from mean. It’s usually stated in the study as increased, decreased , or no change (e..g Shannon, Simpsons, etc)…

Peace Sandy (15:06:56) (in thread): > This was not what I meant

Peace Sandy (15:07:17) (in thread): > I understand the alpha diversity part,I’llpost my questions shortly

Joan C. Chukwuemeka (15:07:37) (in thread): > Alright:+1:

Peace Sandy (15:13:22): > In a case where I have high, low and meduim - where the meduim is the reference group, so I compare the meduim with both high and low respectively

Chinwendu Enyinna (15:16:59) (in thread): > Thanks for the clarification,<@UBNSEMS3S>. Similar to the above question, is it also possible to have more than one body site reported in a study? Assuming your paper indicates more than one place where microbial samples were extracted from, for example, feces and saliva. In this case, would I have to report both as the body sites.

Chioma Onyido (15:40:53) (in thread): > Hi Peace. From my understanding, the group 0 is usually for lower dose, that is for cases where the taxa ofdifferent doseswere compared. > From your example, if medium vs low, I believe low (which is the lower dose) should be group 0 and medium group 1. > Let’s confirm with the mentors:sweat_smile:

Joan C. Chukwuemeka (16:04:24) (in thread): > From the office hour, group 0 is the control/reference group, group 1 is the case group, which has the disease/condition of interest.. > > Now the curation aims at Identifying differential microbial signatures of the group 1( increased & decreased abundance), if the study analysed low vs medium & high vs low, then you likely will have to record 2 experiments. > > Each experiment will have the microbial signatures for its group 1 curated accordingly. In this case for low, then for high. > > That’s my thoughts on it…:hugging_face:<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>I believe, can clarify further:pray:

Joan C. Chukwuemeka (16:17:40): > Hi@Chiagoziem David, That’s a nice suggestion… However, we have people on different timezones here, which should be factored in…. > > Secondly, I think the advice of the mentors where we post questions here on slack is better so that one can easily refer back to it, if one encounters similar challenge. Perhaps if the huddle can be recorded too and made available, that could work. > > That’s my opinion though:slightly_smiling_face::raised_hands:

Peace Sandy (16:18:23) (in thread): > Thank you so much@Joan C. Chukwuemeka

Peace Sandy (16:18:33) (in thread): > Thank you so much@Chioma Onyido

Peace Sandy (16:25:22) (in thread): > @Chioma Onyido

Chiagoziem David (16:41:49): > @Joan C. Chukwuemekathat’s very true… okay then.

Peace Sandy (17:14:51): > I think we should be responding to questions directly under it, like replying in a thread, it helps us trace the questions in incase someone is trying to get the same information

Chiagoziem David (18:33:24): > Hello<@UBNSEMS3S>, please if an experiment is conducted and then it now makes use of a control group, would it be right to pick both laboratory experiments and case control in the study design field?

Chiagoziem David (18:33:30): > Thanks

Peace Sandy (18:40:22): > In the paper I’m curating, we have two contrast, Total time breastfeeding and breastfeeding bout. Each of these contrasts where divided into three groups, low , meduim and high for each contrast. The meduim is the reference group. And I’m supposed to do 4 experiments. Should I compare low to meduim of total time breastfeeding as part of the experiment or low breastfeeding bouts to low total time breastfeeding@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldron

Chiagoziem David (18:58:35): > My next question is along this line too<@UBNSEMS3S>@Svetlana Ugarcina Perovic, how do we curate a paper where there are two groups and then one is further divided into three groups, one of the three groups is then made a control group, does this automatically negate the initial separation into two groups

Clarissa Abidog (21:13:02): > Hello Everyone! My name is Clarissa and I am from the US. I’m looking forward to contributing to the project and learning from each other throughout this process!

Nana (22:44:52): > Hello Friends, I am chinelsy from Nigeria. I just joined and I look forward to contributing to this project

U1LCB8WEA (23:45:57) (in thread): > @Joan C. Chukwuemekasummarizes the discussion well. Usually the authors will identify a control/reference group, and increased or decreased abundance is reported relative to that reference group. In some comparative studies it is arbitrary which is the reference group (such as a comparison of males against females, and maybe in this case you bring up), in such cases it’s best just follow the lead of the paper.

U1LCB8WEA (23:46:52) (in thread): > Welcome,@Clarissa Abidog!

U1LCB8WEA (23:47:13) (in thread): > Welcome,@Nana!

U1LCB8WEA (23:50:30) (in thread): > This question should be determined by what contrasts are reported in the paper…I’m not sure I understand the question, but each experiment will define a distinct contrast between two groups, where differential microbial abundance or differential alpha diversity was tested. You wouldn’t include a signature of a comparison that is somehow distinct from the experiment it is under.

U1LCB8WEA (23:51:48) (in thread): > What ultimately matters is: what (sub)groups did they calculate differential abundance or differential alpha diversity between? That’s a decision that was made by the original authors so you shouldn’t have to decide.

U1LCB8WEA (23:54:09) (in thread): > I don’t understand - almost all studies, including experiments and observational studies, should have a control group. In the very unusual paper where there are actually two different study designs, we have a workaround, but I would want to be sure because there is almost always only a single study design.

Nana (23:58:44) (in thread): > Thank you. Filled out my Request account form, and they said an email would be sent to me. Did not receive such an email. I have also requested an issue on github.

2023-10-09

Chioma Onyido (00:33:56) (in thread): > Okay. This is clearer now.Thatmeans Medium is the reference group in@Peace Sandy’s study.

Hodan Abdirisak (01:10:02) (in thread): > Welcome@Clarissa Abidog

Hodan Abdirisak (01:12:08) (in thread): > Welcome@Nanaafter when you send the request check your emails inbox if it is not present there, check your spam then open the link to confirm your account

Hodan Abdirisak (01:20:52) (in thread): > @Peace Sandy@Chioma Onyido@Joan C. Chukwuemeka<@U1LCB8WEA>I get important notes from your discussion thank you

Hodan Abdirisak (01:24:07) (in thread): > @Chiagoziem DavidMay be to write the question in here is the best way that we can help each other because of time variation

Karen254. Kingecha (01:25:06) (in thread): > Welcome@Clarissa Abidog

Karen254. Kingecha (01:26:13) (in thread): > Welcome@Nanayou can check out the email on your spam

Chioma Onyido (01:40:54) (in thread): > Me too@Hodan Abdirisak:hugging_face:

Chiagoziem David (02:07:52) (in thread): > Okay, I understand now… although my question is that experiments were conducted on two groups , one of the groups Futher divided to include a control group

Chiagoziem David (02:09:02) (in thread): > Wow…. this is very helpful, streamlines a lot of things.. thank you very much

Chiagoziem David (02:10:10) (in thread): > Welcome@Nana, let me know where I can be of help

Peace Sandy (02:21:36) (in thread): > Welcome

Peace Sandy (02:21:59) (in thread): > Welcome@Clarissa Abidog

Peace Sandy (02:22:54) (in thread): > Okay,Thank you for the clarification@Levi Waldron

Mildred Anashie (02:25:21) (in thread): > Welcome@Clarissa Abidog

Mildred Anashie (02:26:28) (in thread): > Welcome@Nana

Mildred Anashie (02:46:59) (in thread): > @Komuhangi Tumuhairweplease follow this link and got through Prep work, watch the videos and we can take it up from there if you still need clarityhttps://github.com/waldronlab/BugSigDBcuration/issues/94#issue-1921928547

Mildred Anashie (02:49:51): > Hello@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicI commented on issue #97 for my second contribution, could you please assign it to me > Thank you:pray:

Karen254. Kingecha (03:08:56): > Hello, I accidentally cancelled my study in the bugsigdb account but I saved, where can I find it?

Chiagoziem David (03:10:36): > Hello<@UBNSEMS3S>@Svetlana Ugarcina Perovicplease in the paper I am curating, it gives the effect of a hormone on a condition induced by another condition , which should be the condition we take in the condition field

Chiagoziem David (03:12:08): > @Karen254. KingechaIs this for your first contribution or second

Karen254. Kingecha (03:13:13): > I Figured it out. Thank you.@Chiagoziem DavidIts my second contribution

Chiagoziem David (03:14:25): > Alright@Karen254. Kingecha

Nana (03:54:55) (in thread): > @Hodan Abdirisakthanks It is in my spam. I just confirmed it. But I have already filled out the survey which was the first task. Will confirming my email later affect it? As i just did.

Nana (03:55:25) (in thread): > Thank you all for the warm welcome. I really appreciate it.

Nana (03:56:14) (in thread): > @Chiagoziem Davidno problem. I will sha disturb you. Lol

Hodan Abdirisak (03:56:18) (in thread): > @Nanano problems the first contribution no need of account you can do without account

Nana (03:57:22) (in thread): > @Hodan Abdirisakok..thanks

Hodan Abdirisak (03:57:30) (in thread): > You deserve the help:pray:

Hodan Abdirisak (03:57:41) (in thread): > Thanks too

Peace Sandy (04:00:14): > @Nanaget started herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Nana (04:07:35): > @Peace SandyI have requested for an issue to be assigned to me on the Github already. waiting to be assigned

Nana (04:20:59): > please<!here>the survey I filled when I copied the link and pasted it on my browser, it shows a new form that has not been filled is that what it is supposed to look like, is that what I should paste on the outreachy contribution website as my first contribution?

Onyewuchi Esther Chikamso (04:22:16) (in thread): > Did you save the form you filled?

Karen254. Kingecha (04:22:24): > yes@Nana

Nana (04:23:13): > Thanks@Karen254. Kingecha

Nana (04:23:50) (in thread): > I clicked on submit

Nwajei Edgar (04:26:35) (in thread): > Good morning, are you done with the first contribution?

Nana (04:28:35) (in thread): > The one that is objective in nature if so yes. I answered all and then submitted it. I was taken to that session after filling out for request account

Hodan Abdirisak (04:34:27) (in thread): > After when you finish your first contribution form it show s you this alert massage I think you see it - File (JPEG): IMG-20231006-WA0006.jpg

Hodan Abdirisak (04:36:09) (in thread): > Congratulations:tada:@Nanagreat job

Nana (04:38:09) (in thread): > @Hodan Abdirisakyes i saw that and i made a screenshot of it

Nana (04:38:44) (in thread): > my question is what should i paste on the outreachy website as my first curated

Hodan Abdirisak (04:38:49) (in thread): > Okey, you have done:+1:

Joan C. Chukwuemeka (04:40:46) (in thread): > Hello@NanaWelcome to the group.. Here’s where the question was answered previouslyhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696338515723009?thread_ts=1696284904.239279&cid=C04RATV9VCY - Attachment: Attachment > Good question. Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application.

Hodan Abdirisak (04:41:36) (in thread): > https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation/contributions/add/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Joan C. Chukwuemeka (04:42:23) (in thread): > So, it’s okay to paste the survey link when you record the contribution on Outreachy

Hodan Abdirisak (04:43:02) (in thread): > Follow the link put:date:date project description and form link or github issue link

Nana (04:44:15) (in thread): > @Hodan Abdirisakmy form link looks empty like how it was before i started filling it.

Joan C. Chukwuemeka (04:45:56) (in thread): > @Nanado check my previous response

Hodan Abdirisak (04:49:56) (in thread): > All ready recorded!! I think you can’t check so go forward to fill this form and add the contribution also after when you save don’t go the final application stop there!!!

Hodan Abdirisak (04:50:37) (in thread): > @NanaI think I have answered your question

Nana (04:56:44) (in thread): > @Joan C. Chukwuemekai just did

Nana (04:58:03) (in thread): > @Joan C. Chukwuemekastill confused can i jump on a huddle with you

Joan C. Chukwuemeka (04:58:09) (in thread): > Alright:+1:. Trust you’re clarified?

Nana (04:58:21) (in thread): > nope

Joan C. Chukwuemeka (04:59:03) (in thread): > In which aspect, are you confused?

Hodan Abdirisak (05:00:28) (in thread): > @Nanayou can huddle with feel free

Nana (05:01:10) (in thread): > The first form i filled already said your response has been recorded . when i paste that link on my another broswer so i can paste it on outreachy Contribution URL: it is blank..a new form altogther thats my confusion

Joan C. Chukwuemeka (05:02:55) (in thread): > The mentors<@UBNSEMS3S>@Svetlana Ugarcina Perovichave our records of the survey. So, although the link maybe a new form after you paste it as you rightly said, If/when required they can forward it to Outreachy organisers. > > Remember the first section has your details. So they’ll know the response that is for each person..

Joan C. Chukwuemeka (05:04:43) (in thread): > @Nanado you understand now?

Nwajei Edgar (05:17:47) (in thread): > Just paste the link,don’tworry about anything like@Joan C. Chukwuemekasaid, the mentors have our records:innocent::innocent:

Hodan Abdirisak (05:23:50): > @Nanahttps://youtu.be/yfpnwxefLFc?si=04QiR00f0KyZdgN8follow this link to watch more about how add study in waldron lab - Attachment (YouTube): Adding a study to bugsigdb.org

Nana (05:30:22) (in thread): > @Joan C. Chukwuemekayes i do

Nana (05:30:44) (in thread): > @Hodan Abdirisakthanks for your time i really appreciate

Hodan Abdirisak (05:32:20) (in thread): > @Nanathanks too:pray:

Peace Sandy (05:38:42) (in thread): > Hi@Nanaglad I could help

Peace Sandy (05:39:12) (in thread): > @C. Mirzayi (please do not tag this account)will assign it when she is available

Nana (05:39:55) (in thread): > @Peace Sandyok

Karen254. Kingecha (05:44:43) (in thread): > @NanaYou can just use this URL to document your contribution on outreachy:https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu. the mentors will know which survey response is yours even though its blank - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Tolulope Ogunleye (05:53:05): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicI noticed most of the studies have no PMID, is there a reason why?Also is there an alternative way to find the PMID?

Fortune Nnamdi (05:54:00) (in thread): > You’rewelcome,Clarissa:blush:

Nana (05:54:44) (in thread): > Already did thanks

Peace Sandy (05:55:11) (in thread): > To get your PMID , search your article on PubMed

Chioma Onyido (05:59:54) (in thread): > In line with what@Peace Sandystated,Here’sthe link:http://pubmed.ncbi.nlm.nih.gov

Chioma Onyido (06:00:44) (in thread): > Also, this response from@Svetlana Ugarcina Perovicmight help:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696500180883949?thread_ts=1696497613.399709&channel=C04RATV9VCY&message_ts=1696500180.883949 - Attachment: Attachment > @Chioma Onyido correct, thanks for clarification! > > During curation use PMID. > You can instead enter a DOI or URL to identify the source: note those other identifiers are only needed if there is not a PMID, otherwise PMID alone is enough. > > cc @Nwajei Edgar

Tolulope Ogunleye (06:07:27) (in thread): > Alright,thank you@Chioma Onyido@Peace Sandy

Chioma Onyido (06:17:28) (in thread): > Awaiting your comments…@Levi Waldron:eyes::palms_up_together:

Fortune Nnamdi (06:23:24): > Hello everyone, I hope we’re all doing fine? > > I have a question for those of us, who haven’t really gotten a hang of everything going on. > > I was scrolling by and I saw someone had explained how to choose a contribution but I suddenly can’t find it anymore because of the number of messages we have here:sweat_smile:So, I’d like to plead with whoever sent this earlier to do so again:pray:Some of us joined late (some early too, maybe) but we’re still confused.

Nwajei Edgar (06:24:28) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Fortune Nnamdi (06:24:53) (in thread): > Alright I think I just found a hint. If I have more questions,I’llstill ask. Thank you:blush: - File (PNG): IMG_5383

Fortune Nnamdi (06:25:43) (in thread): > Thank you@Nwajei Edgar

Tolulope Ogunleye (06:55:15) (in thread): > I would like to clarify if the URL is for the pubmed site or the original link

Chioma Onyido (06:58:21) (in thread): > This url is for the pubmed site:http://pubmed.ncbi.nlm.nih.govSoyou’reto copy and paste the title of your article orit’sdoi to the search bar on the pubmed page.You’dsee the PMID just beside or under the article when you hit search - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Tolulope Ogunleye (07:03:46) (in thread): > I mean the url field under citation, right after the DOI field

Chioma Onyido (07:14:16) (in thread): > Once you fill in the PMID, under “form data”, click on “complete” and save, every other thing autofills.

Tolulope Ogunleye (07:17:07) (in thread): > Thanks for the clarification

Svetlana Ugarcina Perovic (07:20:40): > Good morning,ALL paper requests assigned. Happy Monday! > CC<@UBNSEMS3S><@U1LCB8WEA>

Hodan Abdirisak (07:26:44) (in thread): > @Fortune Nnamdiread all:pushpin:pinned massage

Israel Anguiano (07:28:50): > hello, I’m new here. I’ve just finished the first assignement hope it’s not too late to ask for a second contribution

Nwajei Edgar (07:29:15) (in thread): > No it’s not:innocent::innocent:

Svetlana Ugarcina Perovic (07:35:44) (in thread): > If I missed someone please let me know. > > Also, I’ll be adding new papers for 2nd contribution this afternoon.

Israel Anguiano (07:36:23) (in thread): > thanks!

Israel Anguiano (07:36:47) (in thread): > great:smile:

Mildred Anashie (07:40:04) (in thread): > Thankyou

Peace Sandy (07:41:01) (in thread): > Good Morning@Svetlana Ugarcina Perovic

Peace Sandy (07:41:21) (in thread): > You are not late

Peace Sandy (07:41:35) (in thread): > You can start making your first contribution

Israel Anguiano (07:42:49) (in thread): > already submited:+1:

Hodan Abdirisak (07:43:26) (in thread): > Thanks:pray:@Svetlana Ugarcina Perovic

Tolulope Ogunleye (07:44:32): > Please I noticed the body site used as an example in the tutorial video is a sample type (feces ) rather than than body site( gut), do I go ahead using the pattern?@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic - File (PNG): IMG_6967

Israel Anguiano (07:44:52) (in thread): > Nice to meet you all, by the way!

Svetlana Ugarcina Perovic (07:55:26) (in thread): > Both are correct.

Tolulope Ogunleye (07:56:21) (in thread): > Alright, thanks

Hodan Abdirisak (08:03:39) (in thread): > Welcome@Israel Anguianoyou are not late

Esther Afuape (08:26:45): > Hello Everyone. I’m working on a paper that did a comparison of the infant gut microbiome before versus after the start of Covid-19 pandemic. Since there is no disease being studied in this case, what do I fill in as the condition while creating an experiment?@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Nana (08:46:07) (in thread): > Thank you

Nana (09:05:18) (in thread): > @Svetlana Ugarcina Perovicgood afternoon, I can’t sign in to my account even though I have been assigned an issue. I requested an account yesterday confirmed my email today but a password has not been sent to my email?

Svetlana Ugarcina Perovic (09:09:07) (in thread): > @Nanatry “Login with Google”

Nana (09:13:31) (in thread): > I did I was sent back to put my username and password.

Nana (09:14:08) (in thread): > Even though the email I used during my registration was associated with my Google account

Nana (09:20:26) (in thread): > @Svetlana Ugarcina PerovicThanks I have been logged in.

U1LCB8WEA (09:51:25) (in thread): > Ijust caught up with approving new account requests,including yours@Nana

U1LCB8WEA (09:54:35) (in thread): > There is a condition something like “health study participant” that you could use.

Nana (09:56:23) (in thread): > @Levi WaldronI was able to login. Thanks

U1LCB8WEA (09:58:45) (in thread): > But unless they sampled directly from the intestine,such as from a colonoscopy,if they used expelled waste it is a feces sample.

U1LCB8WEA (10:00:24) (in thread): > We can always infer that feces came from the colon, but when using an ontology you should strive to use the most literally precise term available.

U1LCB8WEA (10:06:08) (in thread): > It sounds like the condition is the hormone treatment.My question is always:what are they comparing to produce the taxonomic differential abundance signatures?

U1LCB8WEA (10:07:32) (in thread): > Anything you saved still exists,you might have to search to find the URL in the wiki though if youdon’tknow the study number

Chiagoziem David (10:07:46) (in thread): > Hmmmm, that would act as the condition sir?

Esther Afuape (10:11:29) (in thread): > Thank you

Chiagoziem David (10:12:02) (in thread): > Because from the video tutorial about how to add a study, the example condition used there was graves ophthalmopathy, which in itself cannot be compared to produce taxonomic signatures as it is an effect and not a microbiome

Mildred Anashie (10:22:49): > Hello everyone. Two groups were involved in the article I’m curating, a randomised placebo controlled study was used for the first group and a prospective observational study was used for the second group. I’m confused on what study design was actually used, should I record both?:thinking_face:@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Peace Sandy (10:25:13) (in thread): > I’llusually advise you read about the different study designs first, then go ahead to read your article you will get a better view

Peace Sandy (10:25:43) (in thread): > It’susually one study design, might not have all the answers

Peace Sandy (10:26:05) (in thread): > I’msure@C. Mirzayi (please do not tag this account)and@Svetlana Ugarcina Perovicwill have a better response

U1LCB8WEA (10:28:00) (in thread): > in that example the experiment contrasts individuals with the condition against controls who do not have the condition.

U1LCB8WEA (10:29:53) (in thread): > Ie, it identified differential taxonomic abundance by comparing individuals with graves ophthalmopathy to individuals without

Chiagoziem David (10:31:54) (in thread): > Oh, okay… > > Thank you very much sir for the response, let me read through again… > > I just hope I don’t become a nuisance with my questions(either here or on the channel)

Chiagoziem David (10:32:20) (in thread): > But I think the channel is better, for reusability

UBNSEMS3S (10:33:33) (in thread): > Amazing work!

Chiagoziem David (10:33:41) (in thread): > Yeah, it’s usually one study design

U1LCB8WEA (10:33:43) (in thread): > Most likely only one of these designs was used for the contrast that produced the signatures. For example, if some subjects from a prospective cohort study were randomized to placebo or treatment to assess the effect of a treatment on the microbiome , then this is a randomized experiment. That’s because the contrast was based on an experiment, where is the cohort was only used for recruiting participants.

Chiagoziem David (10:33:48) (in thread): > Unless in some special cases

Mildred Anashie (10:34:42) (in thread): > Thank you@Peace Sandy…I’llread the article again while I wait for their response

UBNSEMS3S (10:35:05) (in thread): > If they have multiple comparison groups–say between a case group and a control group and then they do another comparison between a severe case group and a less severe case group–then those would be curated as multiple experiments.

Chiagoziem David (10:37:02) (in thread): > Okay<@UBNSEMS3S>thanks for the response

UBNSEMS3S (10:45:20) (in thread): > Yeah what Levi said is the most accurate response but let’s phrase this as a question: > > What study design was used to analyze the differential abundance results? Were the samples randomly assigned a case or control? Doesn’t sound like it to me. Were they all part of the same cohort? Doesn’t sound like it to me. Were they selected as cases and controls? That sounds more similar. But I haven’t read the study so this is up to you to decide.

Tolulope Ogunleye (10:47:38) (in thread): > Thank you

Mildred Anashie (10:47:53) (in thread): > Thank you<@U1LCB8WEA>and<@UBNSEMS3S>I’vegot more clarification on this:pray:

UBNSEMS3S (10:57:16) (in thread): > @Chinwendu EnyinnaCorrect. Some studies with do oral + gut, for instance. Those would be entered as separate experiments.

Chiagoziem David (10:58:22): > Please, if the sample size of the groups from which we are getting our taxonomic differential signatures aren’t given , what do we fill as our group sample size… > > > The only sample size given in the paper, was just the size of the group from which feces was extracted from , this is different from the two groups behind studied for differences in signatures

Joan C. Chukwuemeka (11:09:42): > Hello all, > please how can one decipher if a data transformation was applied or not to microbial abundance measurements prior to differential abundance testing?<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic

Hodan Abdirisak (11:11:57) (in thread): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic<@U1LCB8WEA>are more suitable to answer this than us

Onyewuchi Esther Chikamso (11:12:11) (in thread): > I think you should check the study’s methods, examine data distribution for changes or review preprocessing steps

Joan C. Chukwuemeka (11:21:51): > @Onyewuchi Esther ChikamsoThis is not clear:thinking_face:Here is an image with options of data transformation type to choose from, if any - File (PNG): image.png

Onyewuchi Esther Chikamso (11:23:34) (in thread): > I mean you should check the methodology carefully. Most times, data transformation methods are done before analysis

U1LCB8WEA (11:23:58) (in thread): > Unless they say otherwise, usually it will be raw counts or relative abundances. Sometimes you have to infer from the statistical methods, for example, a glm, DESeq2, or edgeR, require raw counts. LEfSe requires relative abundance input.

U1LCB8WEA (11:24:21) (in thread): > Also t-test,

U1LCB8WEA (11:24:34) (in thread): > and Wilcoxon test would require relative abundance.

Joan C. Chukwuemeka (11:26:59) (in thread): > Alright, thanks<@U1LCB8WEA>much clarified.

Chioma Onyido (11:42:12) (in thread): > Awesome:sunglasses:May I have your permission to edit this?

Chiagoziem David (12:11:06): > If there were no antibiotics exclusion , should we just say there was none

Chiagoziem David (12:11:59): > And can someone please throw more light on the “matched on” and “confounders controlled for” fields

Joan C. Chukwuemeka (12:23:02) (in thread): > @Chiagoziem DavidMatched on refers to factors on which subjects have been matched on in a case-control study. Its usually done to make both control group and case group as similar as possible. e,g sex, age, race, etc

Chioma Onyido (12:23:08) (in thread): > Matched on is used when they select controls and cases and match them on some characteristics such as age, gender, race etc.Use ctrl + F and search for the word “match” in your paper,

Chioma Onyido (12:24:24) (in thread): > Also I recommend you Read throughbugsigdb.org/Curation_Policy#Matched_OnTo get more clarity on matched on and confounders controlled for. - Attachment (BugSigDB): Curation Policy

Chiagoziem David (12:31:17) (in thread): > Thanks, although chatgpt came in handy for me:sweat_smile::sweat_smile:

Chioma Onyido (12:32:42) (in thread): > @Chiagoziem DavidJust remembered that I asked a similar question during the office hour, because matched on wasn’t explicitly stated in the paper I selected and to avoid assumptions, I tried to clarify with the mentors. > > Chloe said to leave it blank, in cases where matched on wasn’t stated in the article. > > For more of@C. Mirzayi (please do not tag this account)’s response,it’shere at**** 35:09**:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696529936787429 - Attachment: Attachment > Here’s the recording of today’s office hours.

Chiagoziem David (12:33:55) (in thread): > Great, by the way you are very resourceful:sweat_smile::sweat_smile::sweat_smile:

Chioma Onyido (12:41:22) (in thread): > Thank you:sweat_smile:

Peace Sandy (12:59:57): > Can I have an experiment without a contrast, just one Group ?@Levi Waldron@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)

Hodan Abdirisak (13:03:27): > After when I downloaded the PDF in assigned issue what is the next, can I coppy the DOI: link and go to add study?

Chioma Onyido (13:04:58) (in thread): > Copy the**** PMID ****and go to add study.

Chiagoziem David (13:10:14) (in thread): > Chioma has said well:sweat_smile:

Nana (13:13:35) (in thread): > I just learnt from what@Levi Waldronanswered on how to go about my own

Esther Afuape (13:19:30) (in thread): > If youcan’tfind the PMID in the article, search for the article on Pubmed.

Chiagoziem David (13:21:45): > Hey<@UBNSEMS3S>, if the alpha diversity shows no changes in the several indices but checking the degree of similarity (using the beta-diversity) shows some variations, should we fill the alpha diversity fields for the individual indices as unchanged? > > Thanks for your swift response

Chiagoziem David (13:22:50) (in thread): > :sweat_smile::sweat_smile::sweat_smile::sweat_smile:, I was trying to get that bit of information for her too, really came in handy for me, as the DOI alone wasn’t causing the fields to auto populate

Nana (13:28:03): > Hello all, based on my article how do I pick my study design, group 0, group 1, and condition too. I need clarification

Joan C. Chukwuemeka (13:28:19): > In terms of taxonomic analysis, Hers’s an instance of the study record: > The only species thatsignificantly differed between full-term and preterm groupswere Lactobacillus crispatus, Lactobacillus gasseri, and Bifidobacterium breve, with a higher respective mean relative abundance infull-term groups. > > Please does the above statement translate to decreased abundance in preterm group?<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic

Hodan Abdirisak (13:28:20) (in thread): - File (PNG): Screenshot 2023-10-09 102746.png

Hodan Abdirisak (13:28:48) (in thread): > No PMID present only DOI

Hodan Abdirisak (13:30:27) (in thread): > @Esther Afuapewhere is pubmed

Paulina Boadiwaa Mensah (13:31:48) (in thread): > Not necessarily. What we can derive from the excerpt is that full-term groups had higher abundance…it does not mean that the “normal”/“original” levels in pre-term groups have decreased.

Paulina Boadiwaa Mensah (13:32:50) (in thread): > Group 0 is for Control participants (those without the condition being tested for.) Group 1 is for those with the condition…I.e. the Case group

Esther Afuape (13:33:19) (in thread): > I’lladvise you check your article to see if the study design was mentioned.If itwasn’tmentioned,you’llhave to google the different study designs if articles and deduce the type your article is.Also, watch the YouTube videos on adding a study to bugSigDB,it’sin the list of materialsyou’remeant to study before curating.You’llbe able to tell which is group 0 (usually the healthy group) and group 1( those with the condition).

Chiagoziem David (13:33:20) (in thread): > https://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Chiagoziem David (13:33:26) (in thread): > There you go

Hodan Abdirisak (13:33:59) (in thread): > I my understanding Group 0 means healthy control groun while group 1 is un healthy

Hodan Abdirisak (13:37:46) (in thread): > Then I enter what?

Hodan Abdirisak (13:38:28) (in thread): > In a search bar

Peace Sandy (13:48:09) (in thread): > Enter your article title

Peace Sandy (13:48:29) (in thread): > @Hodan Abdirisaktype Pubmed on Google

Hodan Abdirisak (13:52:51) (in thread): > Thanks:+1:@Chioma Onyido@Esther Afuape@Chiagoziem David@Peace Sandy

Esther Afuape (13:58:29): > Can covariates be filled in for confounders controlled for?@Levi Waldron

Grace Ogundaini (13:59:04): > Does increased abundance of a taxon in Group 0 mean a decreased abundance in Group 1 and vice versa?

Nana (14:01:47) (in thread): > Thank you all, your answers where helpful

Peace Sandy (14:03:49) (in thread): > You are welcome

U1LCB8WEA (14:45:48) (in thread): > Yes those are equivalent statements,sort of like saying “daytime is warmer than nighttime” is another way of saying “nighttime is cooler than daytime”

U1LCB8WEA (14:50:35) (in thread): > Differential abundance is a comparison of one condition to another, so I thinkyou’rejust restating the same thing in a different way like in my day/night example below. So I would say yes @Paulina Boadiwaa MensahI’minterested in why you saw differently?

Chiagoziem David (15:02:00) (in thread): > I have gotten the answer to this, you should fill in unchanged,

Chinwendu Enyinna (15:10:06) (in thread): > Alright. Thank you for the clarification<@UBNSEMS3S>

Hodan Abdirisak (15:10:35): - File (PNG): Screenshot 2023-10-09 120923.png

Hodan Abdirisak (15:11:36): > Am I right to pick as laboratory experiments study design of this study

Grace Ogundaini (15:14:54) (in thread): > Thank you for the clarification

Paulina Boadiwaa Mensah (15:31:07) (in thread): > <@U1LCB8WEA>Oh right! The “relative” makes me get it.@Joan C. ChukwuemekaI hope it makes sense now.<@U1LCB8WEA>is there a scenario where say, the numbers of a specific gut microbe in a group A are at their normal levels but then in a group B they are increased because of probiotic use or an intervention. In that case would it be right to say that species in group A has decreased relative abundance, but not decreased abundance in general? Can a distinction be made?

U1LCB8WEA (15:36:56) (in thread): > The thing is there is no such thing as “normal” except in comparison to a control group…

U1LCB8WEA (15:38:09) (in thread): > So you are actually describing two separate “experiments” here: group A vs control, and group B vs control.

U1LCB8WEA (15:45:17) (in thread): > And I put “experiments “ in quotes because bugsigdb has a specific meaning of the word - we might have been clearer to call them “contrasts” because it refers to a contrast or comparison between two groups.

U1LCB8WEA (15:46:53) (in thread): > I think there are only a couple examples of that in bugsigdb, likehttps://bugsigdb.org/Study_608 - Attachment (BugSigDB): Study 608

U1LCB8WEA (15:47:47) (in thread): > This is a report of prevalence of species in a group of participants, without any comparison to anything.

U1LCB8WEA (15:48:18) (in thread): > Thanks everyone!

U1LCB8WEA (15:49:28) (in thread): > Yes, if no significant difference in alpha diversity was found then it is unchanged.Beta diversity is another thing that wedon’trecord.

U1LCB8WEA (15:51:11) (in thread): > If they were covariates in a multi variable model but not the main exposure or outcome of interest,they you can call it a confounded controlled for.

U1LCB8WEA (15:53:31) (in thread): > That’snot enough information there to say. To be a laboratory experiment,assignment to treatment or control must be randomly assigned by the researchers.

U1LCB8WEA (15:54:37) (in thread): > OhI’mcurious,what did Chatgpt say?

Odigiri Great Alume (16:02:06): > Good evening@C. Mirzayi (please do not tag this account)Please How do I go about recording taxa with numbers e.g fucobacterium.03. > Mine appears as orange. But I don’t know what it means. > > Please I need clarifications.

Chioma Onyido (16:06:04) (in thread): > I found that researchers add numbers as labels to the names, to distinguish a certain variant or maybe subtypes of that microorganism. > > I know that when it appears as orange in Busigdb, it goes under the taxonomic issues page as missing signatures. > What I’m not sure of and really curious about too is how to present this on BugSigDB without it highlighting as orange.:thinking_face:

Chiagoziem David (16:07:40) (in thread): > Different answers for each query, but the underlying Idea is the same, which is( I guess:sweat_smile:) : marching is finding covariates that could influence the microbiome composition in your samples or the samples you’re comparing against . > > You could throw more light sir

Esther Afuape (16:08:13) (in thread): > You mean if the covariates do not directly affect the outcome of interest,they can be used as confounders controlled for?

Chiagoziem David (16:08:30) (in thread): > Thank you very much<@U1LCB8WEA>

Odigiri Great Alume (16:20:33) (in thread): > Randomized control trials (RCTs) I guess

Odigiri Great Alume (16:22:06) (in thread): > @Levi Waldronplease:pleading_face:we need your help here

U1LCB8WEA (16:22:59) (in thread): > At one point I recorded a long video of doing detective work trying to resolve taxonomic nomenclature:sweat_smile:seehttps://bugsigdb.org/Category:Pages_with_missing_NCBI_ID - Attachment (BugSigDB): Category:Pages with missing NCBI ID

U1LCB8WEA (16:23:42) (in thread): > Also,treatment must be assigned randomly by the researchers.

U1LCB8WEA (16:26:59) (in thread): > In this case@Chioma Onyidois probably right, it is probably an unidentified species of theFusobacteriumgenus. But they might provide some additional context as to how they used the numeric labels.

Chioma Onyido (16:28:58) (in thread): > Ohh This is one really detailed video which gave me clue to one of the issue I was able to solve. I’ve been looking for this video, Thank you:clap:I have it bookmarked already:smiley:

Joan C. Chukwuemeka (16:42:15) (in thread): > Alright, Thanks a lot<@U1LCB8WEA>

Peace Sandy (17:34:35) (in thread): > Thank You@Levi Waldron

Paulina Boadiwaa Mensah (19:14:11) (in thread): > Thank you for throwing more light on this.<@U1LCB8WEA>

Desire Oluwarotimi (19:16:14) (in thread): > That video by Levi is really a great resource. I’m currently going through it.

Chiagoziem David (22:08:39): > Hello, please could anyone throw some light on the source and description fields on the create signature page….<@UBNSEMS3S>

Chiagoziem David (22:23:19): > Also, in an article where several tests were carried out to check the effect of different substances on the life form, and hence the abundance of different microbes, should we fill this as different experiments, or should our concern just be on cases where alpha diversity was mentioned?

Hodan Abdirisak (22:51:51) (in thread): > Thanks<@U1LCB8WEA>for your clarification:pray:

Hodan Abdirisak (22:52:15) (in thread): > Thanks@Odigiri Great Alume

Hodan Abdirisak (22:59:06) (in thread): > Thanks<@U1LCB8WEA>this video is really help full

Hodan Abdirisak (23:05:38) (in thread): > @Chiagoziem DavidAlso I am looking to get this clarification:pray:

Chiagoziem David (23:44:36) (in thread): > Okay…

Chioma Onyido (23:47:41) (in thread): > Hi@Chiagoziem David, The source refers to the table/ figure in your selected paper presenting the differential abundance taxa, > > While the description field is where you input a short text describing the groups that were compared. > For more context, See the highlights in the attached screenshot below: - File (JPEG): IMG_4882

Chiagoziem David (23:48:44) (in thread): > 2 hours:sweat_smile::sweat_smile::sob::sob::sweat_smile::sweat_smile:

Chiagoziem David (23:50:45) (in thread): > So If I have different tests having different differential abundance, Id relate that as a new experiment and just focus on the particular test the differential abundance is happening on yeah?

Chiagoziem David (23:51:53) (in thread): > And what of a case where you have not two but three three groups, control groups included

2023-10-10

Chioma Onyido (01:00:59) (in thread): > Hmmm Not sure I get your first question.:sweat_smile:But for the second, it’s good to check the groups that were contrasted, again by checking the figures, tables and also the paper to see if the control or reference groups were explicitly stated. > > Here’s a link to@Levi Waldron‘s response to a similar question.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696823430705139?thread_ts=1696804822.000619&channel=C04RATV9VCY&message_ts=1696823430.705139 - Attachment: Attachment > This question should be determined by what contrasts are reported in the paper… I’m not sure I understand the question, but each experiment will define a distinct contrast between two groups, where differential microbial abundance or differential alpha diversity was tested. You wouldn’t include a signature of a comparison that is somehow distinct from the experiment it is under.

Chinwendu Enyinna (01:07:34) (in thread): > Really helpful video! Thank you for sharing<@U1LCB8WEA>

Paulina Boadiwaa Mensah (01:22:46) (in thread): > @Chiagoziem Davidyes, you’d create a new wexperiment for each of the different “tests” and add the signatures noted under that test. For example if three different case-control tests were done in your study, you’d create three different experiments and record the microbial signatures specific for each of the three experiments under the same study.

Paulina Boadiwaa Mensah (01:24:07) (in thread): > @Chiagoziem Davidyes, you’d create a new wexperiment for each of the different “tests” and add the signatures noted under that test. For example if three different case-control tests were done in your study, you’d create three different experiments and record the microbial signatures specific for each of the three experiments under the same study.

Paulina Boadiwaa Mensah (01:27:05) (in thread): > You would still record the different experiments even if no alpha diversity was mentioned for them.

Clarissa Abidog (02:15:40): > I know I’m decently late to the game, but I finally got the chance to sit down with the onboarding materials and complete the First Contribution this evening. This task makes me miss my grad program and I’m looking forward to more papers being posted to curate! > > Happy curating everyone!

claudia isabel reyes moreno (02:22:29): > Hello everyone, I am Claudia Reyes from Colombia Latin America. It’s a pleasure to be with you all. I am a Data and Machine learning Engineer, the first Latin American mentee of Kaggle and nowadays I am a mentor and leader of the South America region of the Kaggle BIPOC program whose goal is to democratize Data Science and ML in the most vulnerable communities around the world. In this great adventure, I am finishing my first assignment and hope to soon be able to apply for my second contribution. I thank all of you for your contributions, which have been of great help in the development of my contributions. The power of science and technology lies in the solidarity and brotherhood of the communities that drive them and their capacity to transform lives. I encourage all of you who have just arrived or are in the process of implementing your first contribution, all of your contributions are valuable to the projects and communities they impact.:muscle:

Karen254. Kingecha (02:33:14) (in thread): > @Chiagoziem Daviddid you get an answer?

Hodan Abdirisak (02:38:04) (in thread): > @Clarissa Abidogcongratulations to complete the first contribution > wishing you the best

Chiagoziem David (02:42:51) (in thread): > Welcome@claudia isabel reyes moreno, don’t hesitate to mention if you reach any roadblock

Chiagoziem David (02:45:16) (in thread): > Okay, in the individual tests , there are three groups, are we to compare the control group and the two other groups as different experiments also? That would be a whole lot of experiments

Chiagoziem David (02:46:50) (in thread): > Alright guys, thanks for the responses

Nwajei Edgar (02:51:18) (in thread): > Welcome to the community Claudia:partying_face::partying_face:

Hodan Abdirisak (02:58:04) (in thread): > Welcome@claudia isabel reyes moreno

Esther Afuape (03:28:52) (in thread): > @Levi Waldron

Nana (04:12:51) (in thread): > Welcome@claudia isabel reyes moreno

Hodan Abdirisak (04:14:51): > Hello@Nana

Nana (04:14:56): > Yes

Hodan Abdirisak (04:15:45): > https://pubmed.ncbi.nlm.nih.gov/find PMID in this website - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Spyke Lionel (04:16:27) (in thread): > congratulations. Wish you more luck ahead

Hodan Abdirisak (04:19:32): > Coppy your article title and paste as I did by the help of@Chiagoziem Davidand@Peace Sandy

Nana (04:24:53): > @Hodan AbdirisakOh! I have seen the previous reply

Svetlana Ugarcina Perovic (04:27:08) (in thread): > Yes, “health study participation”

Mildred Anashie (04:27:44) (in thread): > Welcome@claudia isabel reyes moreno

Svetlana Ugarcina Perovic (04:38:31): > Good morning:teapot:ALL paper requests assigned. Enjoy your curation andcontinue discussing it with your colleagues, you’re doing GREAT! > CC<@UBNSEMS3S><@U1LCB8WEA>

Nwajei Edgar (04:39:21) (in thread): > Good morning Svetlana:innocent::innocent:

Hodan Abdirisak (04:49:23) (in thread): > Good morning:sunrise_over_mountains:@Svetlana Ugarcina Perovic

Israel Anguiano (04:57:06) (in thread): > Good morning and thank you. Have a great day!

Israel Anguiano (04:58:09) (in thread): > btw I’ve just submited my request for bugsig account

Sinmi Adesanya (04:59:30) (in thread): > Good morning@Svetlana Ugarcina Perovic

Hodan Abdirisak (05:08:25): - File (PNG): Screenshot 2023-10-10 020754.png

Hodan Abdirisak (05:09:46): > I am at first step of adding study, can I press Needs review or jump to add experiment

Svetlana Ugarcina Perovic (05:12:55) (in thread): > continue adding the experiment(s)

Hodan Abdirisak (05:13:52) (in thread): > Thanks@Svetlana Ugarcina Perovic

Odigiri Great Alume (05:19:00) (in thread): > Add experiment pls

Chioma Onyido (05:21:08) (in thread): > I think what@Levi Waldronwas say is that: let’s startfromthe basicsSo you know covariates are additional variables that are not your main variables of interest (exposure and outcome) but may influence on the relationship between them.So in research/ statistics, as a way to make the results more accurate and robust, including covariates is a way of accountingfor/controlling their confounding effects.So now@Levi Waldronis saying that if you’re sure that they are actually covariates, (and not the main exposure or outcome), then you can call it confounders controlled for.

Esther Afuape (05:25:45) (in thread): > Good morning. Thank you for the encouragement

Esther Afuape (05:26:08) (in thread): > Thank you, Chioma

Hodan Abdirisak (05:41:52): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01516-ythe location is not mention this study, also there is confusion of host species it is mice or human - Attachment (BioMed Central): Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem - Microbiome > Background Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal load increases in the gastrointestinal tract following antibiotic treatment, but better characterization is clearly needed of how antibiotics directly or indirectly affect the mycobiota and thus the entire microbiota. Design We used samples from humans (infant cohort) and mice (conventional and human microbiota-associated mice) to study the consequences of antibiotic treatment (amoxicillin-clavulanic acid) on the intestinal microbiota. Bacterial and fungal communities were subjected to qPCR or 16S and ITS2 amplicon-based sequencing for microbiota analysis. In vitro assays further characterized bacterial-fungal interactions, with mixed cultures between specific bacteria and fungi. Results Amoxicillin-clavulanic acid treatment triggered a decrease in the total fungal population in mouse feces, while other antibiotics had opposite effects on the fungal load. This decrease is accompanied by a total remodelling of the fungal population with the enrichment in Aspergillus, Cladosporium, and Valsa genera. In the presence of amoxicillin-clavulanic acid, microbiota analysis showed a remodeling of bacterial microbiota with an increase in specific bacteria belonging to the Enterobacteriaceae. Using in vitro assays, we isolated different Enterobacteriaceae species and explored their effect on different fungal strains. We showed that Enterobacter hormaechei was able to reduce the fungal population in vitro and in vivo through yet unknown mechanisms. Conclusions Bacteria and fungi have strong interactions within the microbiota; hence, the perturbation initiated by an antibiotic treatment targeting the bacterial community can have complex consequences and can induce opposite alterations of the mycobiota. Interestingly, amoxicillin-clavulanic acid treatment has a deleterious effect on the fungal community, which may have been partially due to the overgrowth of specific bacterial strains with inhibiting or competing effects on fungi. This study provides new insights into the interactions between fungi and bacteria of the intestinal microbiota and might offer new strategies to modulate gut microbiota equilibrium. Video Abstract

Hodan Abdirisak (05:46:00) (in thread): > @Svetlana Ugarcina PerovicI need help

Svetlana Ugarcina Perovic (05:55:39) (in thread): > What is the main goal of this study? What the researchers did to study their research question?@Hodan Abdirisak

Nana (05:57:19): > @Levi Waldron@Svetlana Ugarcina Perovicplease can i have a study that does not include group 0 . where group 0 will be “NA” No comparison with the diseased one. only unhealthy were mentioned

Svetlana Ugarcina Perovic (05:58:50) (in thread): > There should be a comparison group. Unless they did something very specific.<@U1LCB8WEA>already talked about it above. Please find that thread.

Mildred Anashie (06:01:22) (in thread): > Good Morning@Svetlana Ugarcina Perovicand Thank you

Fortune Nnamdi (06:05:07) (in thread): > Hey@Chiagoziem Davidwere you able to find the answer to your question? > > Because I think that although a 30-day antibiotics exclusion is used generally in some studies, we should just say there was no exclusion since it wasn’t indicated.

Chiagoziem David (06:09:11) (in thread): > Nah, in this study it was even stated that they were subjected to antibiotics:sweat_smile:

Fortune Nnamdi (06:23:18) (in thread): > Then I guess you should just indicate that there was no antibiotics exclusion. > > But surely our mentors and colleagues might have a better suggestion/answer.

Hodan Abdirisak (06:26:18) (in thread): > the main goal is to investigate the consequences of antibiotic treatment, specifically amoxicillin-clavulanic acid, on the intestinal microbiota.

Svetlana Ugarcina Perovic (06:29:39) (in thread): > how they did that investigation?

Chioma Onyido (06:38:09): > Hi@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldron > 1. Does negative log2 fold change automatically mean thatthere’sa decreased abundance and positive for increased? > 2. Also, what if under that figure, it was reported thatthere’sreduced abundance in microbial taxa for group 1 (for example) and somewhere else in the article, it was still reported thatthere’san increased abundance in that same microbial taxa for the same group 1. > How do I navigate this?

Mildred Anashie (06:42:32) (in thread): > From my understanding every study has a who, what and where…I scanned through the paper and your study seems to be in vivo…. No idea if there’s an exemption for such studies…..As for the host species, samples were collected from humans (infants) and transferred to mice, I don’t know if this helps to give you an idea

Hodan Abdirisak (06:44:36) (in thread): > By quantitative polymerase chain reaction

Hodan Abdirisak (06:45:10) (in thread): > @Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:47:12) (in thread): > Antibiotics were administered tomicedaily in order to answer the main study questions.

Hodan Abdirisak (06:49:23) (in thread): - File (PNG): Screenshot 2023-10-10 034818.png

Hodan Abdirisak (06:51:22) (in thread): - File (PNG): Screenshot 2023-10-10 035042.png

Hodan Abdirisak (06:51:40) (in thread): > Yes daily in 10 days

Chioma Onyido (06:52:24) (in thread): > It says in the article that “Negative log fold change estimates correspond to reduced abundance of each OTU in the Healthy controls (left plots) and CD samples (right plots)”. > > For example, Akkermansia which is under the negative log2fold for UC vs CD group (right plot) and was still mentioned somewhere in the article as differentially abundant (second screenshot). > > I’m confused as to where to fix the taxa, whether increase or decrease. - File (JPEG): IMG_4890 - File (JPEG): IMG_4891

Svetlana Ugarcina Perovic (06:54:43) (in thread): > My point is that this study was done on mice model, right?

Hodan Abdirisak (06:57:03) (in thread): > Yes

Svetlana Ugarcina Perovic (06:59:00) (in thread): > ok, so we have answer to your question

Svetlana Ugarcina Perovic (06:59:12) (in thread): > as for location, see for example herehttps://bugsigdb.org/Study_516 - Attachment (BugSigDB): Study 516

Svetlana Ugarcina Perovic (06:59:36) (in thread): > What’s their mice location?:mouse:

Svetlana Ugarcina Perovic (07:00:44) (in thread): > … the lab location

Hodan Abdirisak (07:03:42) (in thread): > What about the location of the study

Hodan Abdirisak (07:05:54) (in thread): > Lab location is not mentioned

Svetlana Ugarcina Perovic (07:06:37) (in thread): > Yes, it is. In the authors’ affiliation.

Nana (07:09:59) (in thread): > Ok..thanks

Hodan Abdirisak (07:13:36) (in thread): > Mice model means mus musculus - File (JPEG): IMG_20231010_141313.jpg

Hodan Abdirisak (07:15:26): - File (PNG): Screenshot 2023-10-10 041458.png

Hodan Abdirisak (07:16:25) (in thread): > Also in authors affiliatation some them are in France while others are in Finland

Hodan Abdirisak (07:17:18) (in thread): > Can I mention both

Onyewuchi Esther Chikamso (07:17:24): > @Svetlana Ugarcina Perovic@Levi WaldronIn my research paper, no specific location was mentioned. But the research was carried out in a laboratory setting. What do I do? > Link to the research paper;https://doi.org/10.1007/s11427-019-9540-

Svetlana Ugarcina Perovic (07:20:53) (in thread): > You can see in the section**** Contributions:****MS and MLR designed the study and analyzed and interpreted the data. > MS is the first author, MLR is the last author. Usually the first and last author’s affiliation is the one where the lab work was done.

Nana (07:22:55): > @Levi Waldron@Svetlana Ugarcina Perovicplease I have a lot figures in my work, how do I know the exactly one to pick as signature for my experiment 1

Hodan Abdirisak (07:23:19) (in thread): > @Svetlana Ugarcina Perovicthanks for your clarification

Hodan Abdirisak (07:25:03) (in thread): > Look in authors’s affiliation find location of the first and last authors take that location as@Svetlana Ugarcina Perovichelped me to get that

Onyewuchi Esther Chikamso (07:36:27) (in thread): > Thank you

Nana (07:37:53) (in thread): > @Peace Sandyafter going through that article did you still have only one group

Esther Afuape (07:40:45) (in thread): > The signature depends on what your experiment one is contrasting.It’sthe result of the groups that the experiment is comparing to eachother. Each experiment compares 2 things and has a result.

Fortune Nnamdi (07:44:32): > Hey people! > > I hope we’re all doing good? > > I just requested for a “paper to curate” > This is task 2 (second contribution task). > > Should I go ahead to create a bugsigdb account while waiting for the paper to be assigned?

Chiagoziem David (07:48:09) (in thread): > Yes you should

Spyke Lionel (07:48:35) (in thread): > Hello,@Fortune Nnamdi, if this paper/issue is not yet assigned to someone, you can comment with your name and start working on it. It will definitely be assigned to you.

Fortune Nnamdi (07:50:44) (in thread): > Okay,thanks guys!

Nana (07:56:52) (in thread): > Yes go ahead and request an account. Then do what@Spyke Lionelsaid

Nana (07:57:24) (in thread): > @Esther Afuapethanks

Hodan Abdirisak (07:57:41) (in thread): > Yeah, go ahead

Svetlana Ugarcina Perovic (08:10:22) (in thread): > Thank you ALL for your great directing of your colleague(s)!

Nana (08:17:19) (in thread): > @Svetlana Ugarcina Perovicyou are welcome sir

Odigiri Great Alume (08:20:39) (in thread): > The experiment can also contrast two things to one . For instance the study I’m working on contrasted Active smokers and former smokers to Never smokers

Odigiri Great Alume (08:26:35) (in thread): > Okay send link to your study

Odigiri Great Alume (08:26:44) (in thread): > I mean your article

Nana (08:29:09) (in thread): > @Odigiri Great Alumedo you have a figure that explains that in your article

Nana (08:31:33): > @Levi Waldron@Svetlana Ugarcina Perovicmy location of subjects is in Africa. However there’s no African rather than Central African Republic and South Africa that pops out that I can choose from, in this type of suitation what do I do. For I can’t even type

Peace Sandy (08:44:06) (in thread): > Look for the location where the participants used for the experiment were taken from

Nana (08:47:48) (in thread): > @Peace Sandy: Recently, in sub-Saharan Africa (Zimbabwe [2, 3], Malawi [4], South Africa [5, 6]), a novel HCLD phenotype, obliterative bronchiolitis, was detected at high prevalence (>30%) among older children and adolescents living with HIV [3].

Nana (08:49:03) (in thread): > you see why i am looking for Africa for the study only used samples from Zimbabwe and Malawi and not even from SA

Nana (08:50:05) (in thread): > please there’s one conversation i tag you can you answer that one too

Peace Sandy (08:54:20) (in thread): > Okay,let me check

Peace Sandy (08:55:37) (in thread): > Nope,I have more than one group, I was considering adding another experiment thatdoesn’thave a group, that was why I asked

Nana (08:57:51) (in thread): > ok

Odigiri Great Alume (08:59:53) (in thread): > Yes. I do. It was a table

Aleru Divine (08:59:58) (in thread): > Hi guys, it’s possible that are no antibiotics exclusions and you can just indicate that there was none. Check this thread for a reply from@C. Mirzayi (please do not tag this account).https://community-bioc.slack.com/archives/C04RATV9VCY/p1696354844767099 - Attachment: Attachment > @Levi Waldron @C. Mirzayi (please do not tag this account) > > Is it possible at all that a study has nothing to do with antibiotics exclusion?

Nana (09:01:54) (in thread): > ok

Aleru Divine (09:02:09) (in thread): > Thank you@Svetlana Ugarcina Perovic

Grace Ogundaini (09:19:08): > Hello. I just recorded my second contribution, just to be sure this means I’ve submitted right?

Peace Sandy (09:21:39) (in thread): > Is it on the outreachy website

Hodan Abdirisak (09:27:30) (in thread): > Look authors location the first and last one location is where study takes place

Hodan Abdirisak (09:28:42) (in thread): > Do mean you did final application?

Nana (09:34:40) (in thread): > @Hodan AbdirisakSo authors location is same as subject location

Hodan Abdirisak (09:43:06) (in thread): > Yeah

Hodan Abdirisak (09:43:38) (in thread): > First one and last one must be same location

Nana (09:45:57) (in thread): > Please can you throw more light on this first one and last one?

Hodan Abdirisak (09:50:11) (in thread): - File (PNG): Screenshot 2023-10-10 041458.png

Hodan Abdirisak (09:50:30) (in thread): > Can you see that part authors affiliation

Nana (09:55:36) (in thread): > Is not so in my own

Nana (09:56:09) (in thread): > I saw authors and affliction but the first and last are not same

Hodan Abdirisak (09:57:33) (in thread): > Then@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)may give you father help

Nana (09:58:21) (in thread): > Ok..thanks

Grace Ogundaini (10:05:16) (in thread): > Yes I recorded my contribution on the Outreachy site. Ihaven’tclicked submit yet becauseI don’thave the project timeline yet. My question is if the mentors can see my contribution after I recorded it even without pressing submit?

Nana (10:05:28): > @Levi Waldron@Svetlana Ugarcina Perovic(this question is a blocker for me) my location of subjects is in Africa. However there’s no African rather than Central African Republic and South Africa that pops out that I can choose from, in this type of suitation what do I do. For I can’t even type

Hodan Abdirisak (10:09:05) (in thread): > @Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)are more suitable to answer than me.

Mildred Anashie (10:19:41): > Hi everyone > > How do you identify the condition in your article > > Also, saliva samples were collected for the experiment in my article, Can I use saliva for body site or mouth?:confused:

Chiagoziem David (10:36:32) (in thread): > I think you should use saliva.

Chiagoziem David (10:38:16) (in thread): > Thank you@Svetlana Ugarcina Perovic

Chiagoziem David (10:39:20) (in thread): > Welcome@Hodan Abdirisak

Chiagoziem David (10:39:49) (in thread): > Thanks@Aleru Divine

Mildred Anashie (10:44:50) (in thread): > Okay > > Thank you:pray:

Chloe (10:47:40): > how can i identify a condition in the article please

Nwajei Edgar (10:48:47) (in thread): > Check the abstract, should be stated there

Grace Ogundaini (10:50:13) (in thread): > The condition is the disease affecting the case group e.g cancer, diabetes

Iram Jamshed (11:05:14) (in thread): > Article must be containing specific diseases/definitions for certain conditions studied in the research. For example, prevalent diabetes, cancer etc

Chloe (11:07:12) (in thread): > hmmm…… i think am figuring it now..

Mildred Anashie (11:07:51): > Hi@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)says “Thirty-five participants co-enrolled in two AIDS Clinical Trials Group (ACTG) studies, A5272 and A5280, with 70 paired saliva samples and complete data sets were assessed”. does this mean the sample size for each group is 35 since it mentions co-enrollment and paired samples?. 2) The groups were given names as A5272 and A5280 without any mention of healthy control or cases/treatment groups. Should I input these assigned names instead?

Chloe (11:08:25) (in thread): > so Dysbiosis is a condition…

Iram Jamshed (11:19:22) (in thread): > Saliva is fine!

Clarissa Abidog (11:22:01) (in thread): > The condition is the disease being studied like Huntington’s, diabetes, or cancer. Hope this helps!

Joan C. Chukwuemeka (12:09:32) (in thread): > Hello@Nana, have you sorted this? > > If not, the author’s location may not always be the same as the subjects location. have you checked the methods section of the article?

UBNSEMS3S (12:11:14) (in thread): > Good question. Log fold change is a measure of effect size. A negative log fold change generally indicates a decrease in cases relative to controls and a positive log fold change generally indicates an increase in cases relative to controls.

UBNSEMS3S (12:12:00) (in thread): > Your second question is unclear to me. Are they just repeating the same finding twice? It should still be curated only once unless it’s a new experiment or something changed.

UBNSEMS3S (12:12:21) (in thread): > Leave it blank if the sample size is unclear.

Chioma Onyido (12:14:09) (in thread): > I find this log fold change discussion interesting because I was confused for a while!:face_holding_back_tears:Thank you for the clarification.

Chioma Onyido (12:18:18) (in thread): > For my second question, I was trying to say that Akermansia according to figure 4 was indicated as a negative log fold change which means a decrease for CD group but in the second screenshot, they stated “significant differential Akkermansia abundance in CD vs UC”. > > I feel these 2 things are different contrasting each other and it’s confusing?:thinking_face:

Hodan Abdirisak (12:27:21): > i ma working of this studyhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01516-yso there is som confusion for me - Attachment (BioMed Central): Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem - Microbiome > Background Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal load increases in the gastrointestinal tract following antibiotic treatment, but better characterization is clearly needed of how antibiotics directly or indirectly affect the mycobiota and thus the entire microbiota. Design We used samples from humans (infant cohort) and mice (conventional and human microbiota-associated mice) to study the consequences of antibiotic treatment (amoxicillin-clavulanic acid) on the intestinal microbiota. Bacterial and fungal communities were subjected to qPCR or 16S and ITS2 amplicon-based sequencing for microbiota analysis. In vitro assays further characterized bacterial-fungal interactions, with mixed cultures between specific bacteria and fungi. Results Amoxicillin-clavulanic acid treatment triggered a decrease in the total fungal population in mouse feces, while other antibiotics had opposite effects on the fungal load. This decrease is accompanied by a total remodelling of the fungal population with the enrichment in Aspergillus, Cladosporium, and Valsa genera. In the presence of amoxicillin-clavulanic acid, microbiota analysis showed a remodeling of bacterial microbiota with an increase in specific bacteria belonging to the Enterobacteriaceae. Using in vitro assays, we isolated different Enterobacteriaceae species and explored their effect on different fungal strains. We showed that Enterobacter hormaechei was able to reduce the fungal population in vitro and in vivo through yet unknown mechanisms. Conclusions Bacteria and fungi have strong interactions within the microbiota; hence, the perturbation initiated by an antibiotic treatment targeting the bacterial community can have complex consequences and can induce opposite alterations of the mycobiota. Interestingly, amoxicillin-clavulanic acid treatment has a deleterious effect on the fungal community, which may have been partially due to the overgrowth of specific bacterial strains with inhibiting or competing effects on fungi. This study provides new insights into the interactions between fungi and bacteria of the intestinal microbiota and might offer new strategies to modulate gut microbiota equilibrium. Video Abstract

Chioma Onyido (12:28:05) (in thread): > They repeated the same results twice and they were contradicting each other. My question is I’m not sure where this falls, increase or decrease.

Hodan Abdirisak (12:29:13): > 1. there were 2 sequencing type 16S and ITS2 which one i pick? 2. how many experiment could i add

Hodan Abdirisak (12:31:30) (in thread): > Is about type of sample so saliva would be best to select

UBNSEMS3S (12:32:46) (in thread): > The second screenshot does not indicate direction right? I don’t think it’s a contradiction. I would curate Akkermansia as decreased.

UBNSEMS3S (12:33:36) (in thread): > Oh jeeze that’s very difficult to understand. Let me take a closer look at the paper.

Chioma Onyido (12:35:14) (in thread): > Much clearer now. Thank you so much:blush:

UBNSEMS3S (12:36:26) (in thread): > It was 35 participants total. As for how many were in the case (group 1) and control (group 0) that is more complicated. I recommend closely reading the paper for experiments 1 and 2 to determine the sample size for each. It is stated but it may take some searching in the results.

UBNSEMS3S (12:37:49) (in thread): > I would enter 16S for the bacterial sequencing and ITS for the fungal sequencing and therefore have these as separate experiments.

UBNSEMS3S (12:38:27) (in thread): > Dysbiosis is not generally the condition of interest. Dysbiosis indicates that the microbiome in a given body site is disrupted or altered.

UBNSEMS3S (12:38:59) (in thread): > They recruited participants from all of Africa? Not a specific country? That is very unusual. Can you link me to the paper please?

UBNSEMS3S (12:39:30) (in thread): > @Grace OgundainiPlease be sure to comment on the Github issue for the paper so that we know it’s ready to review.

UBNSEMS3S (12:40:21) (in thread): > The author affiliations are not a good indicator of where the study was actually conducted. You can find my name on studies done in Turkey, for instance.

UBNSEMS3S (12:40:58) (in thread): > I think the source of the confusion here@Nanais that you’re pulling those country names from the Introduction where they are mentioning previous studies. We want the location where the present study was conducted. This should be mentioned in the Methods section.

UBNSEMS3S (12:41:42) (in thread): > Yeah we want to curate differential abundance results so many tables and figures will be irrelevant. On the other hand, many papers will do multiple analyses so these can be entered as separate experiments.

UBNSEMS3S (12:42:22): > I think I’m caught up on all the questions but please let me know if I missed any. I’m very sorry if you did but you all are very active! It’s impressive how much conversation is happening!

Grace Ogundaini (12:45:07) (in thread): > @C. Mirzayi (please do not tag this account)okay I will

UBNSEMS3S (12:45:08) (in thread): > I think you should be able to edit it. Let me know if that’s not the case.

Chioma Onyido (12:45:46) (in thread): > Yes I have been able to edit it.:pray:

UBNSEMS3S (12:45:56) (in thread): > Awesome. Glad to hear it.

Esther Afuape (12:50:03): > My paper has a supplementary information file that has the differential abundance of group 1 without controlling for covariates. This differential abundance was not included in the main result in the paper, only in the supplementary information file. > Should I create a new signature for this or it isn’t consequential since it isn’t in the main result?@C. Mirzayi (please do not tag this account)

Iram Jamshed (12:56:51): > In my paper there are two groups. One is the main study group. It consists of a random population sample of 13,437 individuals aged 25–74 years from six geographic regions in Finland. These individuals were invited to participate in the FINRISK 2002 study from 6 different regions of Finland. Another group is used for external validation. It is a case–control study of patients with atrial fibrillation (AF) and matched controls. The cases are patients with AF who were specifically collected for the examination of the gut microbiome between October 2019 and March 2020 at the University Clinic Hamburg-Eppendorf, Germany.. My question is what should I label as group 1 and group 2(It further has case and control group) ? And since two locations are used. Which one should I consider?<@UBNSEMS3S>

Nana (13:00:07) (in thread): > <@UBNSEMS3S>https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01460-x - Attachment (BioMed Central): Sputum bacterial load and bacterial composition correlate with lung function and are altered by long-term azithromycin treatment in children with HIV-associated chronic lung disease - Microbiome

UBNSEMS3S (13:03:24) (in thread): > Look carefully at the Methods > Study design section. The locations are listed there and you should be able to add multiple countries in your curation.

UBNSEMS3S (13:04:07) (in thread): > I would include it as a new experiment.

Mildred Anashie (13:04:43) (in thread): > I have searched through the paper and there was no mention of sample size for each of the groups asides the 35 participants earlier mentioned

Chioma Onyido (13:04:45) (in thread): > Sometimes the same findings are usually presented in multiple figures/ tables, it is your choice to pick the best representation of signatures. In a case where the figures/tables report different results (I.e. differential abundant taxa), my guess is to curate as another experiment:eyes:

Esther Afuape (13:04:52) (in thread): > Is there a way to remove a signature?I’munable to delete asI’mnot an administrator

UBNSEMS3S (13:04:58) (in thread): > The group with AF would be the case group. You should be able to add both countries as the location.

UBNSEMS3S (13:05:15) (in thread): > Send me a link to the signature and I can delete it.

Chioma Onyido (13:06:14): > Hi@C. Mirzayi (please do not tag this account)@Levi Waldron, while solving another taxonomic issue,https://bugsigdb.org/Study_509/Experiment_2/Signature_2, I confimed that the missing taxa, Escherichia shigella and uncultured Phyllobacteiaceae are available in NCBI taxonomy as1940338and 257462 respectively. > > Also I found that Escherichia shigella is rightly supposed to be in the “increased abundance” group, not decreased according to Table 2 of the paper.

UBNSEMS3S (13:06:35) (in thread): > It’s not explicitly stated but I think you can figure it out. Think about what was group 0 and group 1 for each experiment then look closely at where you might find information describing those groups. For instance, if they contrasted on a certain disease status–perhaps earlier on in the paper they break down how many people had that status.

UBNSEMS3S (13:06:56) (in thread): > Nice catch!

Hodan Abdirisak (13:07:35) (in thread): > So, it Two experiment in all study

Nana (13:08:05) (in thread): > @ all thanks

Esther Afuape (13:08:11) (in thread): > https://bugsigdb.org/Special:FormEdit/Signature/Study_800/Experiment_1/Signature_2?reload=1&returnto=Study%20800 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 800/Experiment 1/Signature 2

Iram Jamshed (13:08:51) (in thread): > So group 1 would be the random population from Finland and group 2 would be external validation group having AF, right?<@UBNSEMS3S>

Esther Afuape (13:09:52) (in thread): > There’sno table or figure representing the result in question though. I guess the source will be “supplementary information”?

Desire Oluwarotimi (13:09:58): > @C. Mirzayi (please do not tag this account)@Levi WaldronDo you think it possible to record two conditions for a study? Both conditions seem somewhat related anyways. > Say “body weight” and “body fat percentage”.

Chioma Onyido (13:10:16) (in thread): - File (PNG): IMG_4907

Chioma Onyido (13:10:54) (in thread): > Yes.:+1:

Esther Afuape (13:11:54) (in thread): > How did you realizeit’ssupposed to be increased and not decreased as in the paper?

Mildred Anashie (13:12:20) (in thread): > Okay…I’ll read through again but I actually read through the paper and what was stated was the descriptive characteristics of the cohorts being studied

Chioma Onyido (13:14:03) (in thread): > In the screenshot I shared, Escherichia shigella has higher meanvalues in smoking compared to non-smoking.

Mildred Anashie (13:14:38) (in thread): > For the group names and assigning to group 0 and group 1, it was stated that the study is limited by a lack of HIV-negative controls. And “As all participants are HIV-infected, our study evaluates the effect of both HIV control and ART on the salivary microbiome”.I’m still confused

Mildred Anashie (13:15:50) (in thread): > Thank you everyone for your help:pray:I figured that out

Chioma Onyido (13:18:16) (in thread): > Since this is confirmed, I will edit this shortly<@UBNSEMS3S>I hopethat’sokay.:blush:

Fortune Nnamdi (13:36:19) (in thread): > I’ll like to know the answer to this too.

Fortune Nnamdi (13:38:56) (in thread): > But I do think that it’s quite possible. Since body weight and body fat are very much related. > > In fact, body weight consists of a person’s total weight including bones, muscles and of course body fat

U1LCB8WEA (13:40:35) (in thread): > My question is always “which groups were compared to produce the signatures you will be entering under that experiment?”

UBNSEMS3S (13:51:31) (in thread): > Yes. These would be entered as separate experiments.

UBNSEMS3S (13:51:37) (in thread): > It’s possible for a study to have several conditions.

Esther Afuape (13:58:57) (in thread): > Okay, that makes sense. > So you simply searched for the taxa in NCBI?

Joan C. Chukwuemeka (14:02:06): > In terms of statistical test, the one to be curated, is it the one for the abundance comparison or alpha diversity? > > Below is findings from the study:Student’s t-test was used to compare the relative abundance of the ten most abundant species between the two delivery outcome groups [Full term birth (FTB) and Preterm Birth (PTB)].Wilcoxon’s test was used to compare the alpha diversity of the vaginal microbiome between the Full term birth (FTB) and Preterm Birth (PTB) groups, as well as between the non_risk_FTB (low-risk women who delivered at term) and risk_FTB (women with risk factors for preterm birth but who delivered full term) groups.PERMANOVA was used to compare the beta diversity of the vaginal microbiome between the FTB and PTB groups, as well as between the non_risk_FTB and risk_FTB groups.

UBNSEMS3S (14:05:29) (in thread): > It’s the one for differential abundance comparison.

Joan C. Chukwuemeka (14:11:34) (in thread): > Okay thanks

Esther Afuape (14:17:13) (in thread): > In my study, the statistical tests mentioned were only for alpha diversity:thinking_face:. It says “we conducted a series of t-tests and chi-square tests to compare the pre-pandemic and pandemic groups on demographic and environmental characteristics”. > For differential abundance,it only says “to examine differential abundance, we used microbiome multivariable associations with linear models v2 R package v1.7.3 with default model type, transformation, and normalization parameters”. > > GuessI’llbe recording chi-test and t-tests as the statistical tests even though they were under alpha diversity?@C. Mirzayi (please do not tag this account)

Peace Sandy (14:23:20) (in thread): > @Esther Afuapecheck the one for differential abundance

Kabirat Adeniyi (14:30:35): > Can a table be a basis for extracting the differentially abundant microbiota signatures? In the study I’m doing, increased abundance are noted in the table but not the figures used. eg - File (PNG): image.png

UBNSEMS3S (14:30:53) (in thread): > @Esther AfuapeA linear model is a type of statistical model. Linear regression.

UBNSEMS3S (14:31:33) (in thread): > Well let’s start at the beginning. Please share your definitions for group 0 and group 1 for each experiment.

UBNSEMS3S (14:32:25) (in thread): > Deleted.

UBNSEMS3S (14:33:20) (in thread): > Yes. It can be: a table, a figure, a supplemental table or figure, or in the text of the paper.

Esther Afuape (14:33:24) (in thread): > Oh! Thank you!

Kabirat Adeniyi (14:34:32) (in thread): > thank you very much

Chiagoziem David (14:35:33) (in thread): > Alright<@UBNSEMS3S>, thanks for the response

Joan C. Chukwuemeka (14:38:40): > In the study, > The researchers employed shotgun metagenomic sequencing (WMS) to compare the vaginal microbiota of**** women at high risk of preterm birth (n = 35) ****vs.a low-risk control group (n = 14).From the above, It seems that the groups will be:Group 0 - a low-risk control group (n = 14)Group 1 - high risk of preterm birth (n = 35)However, Of the 49 women with samples in the second trimester, 8 delivered preterm (before 37 weeks) and 41 delivered at full term (after 37 weeks). The researchers then divided the women into four groups: > 1. Risk factors for PTB and delivered preterm (risk_PTB) > 2. Risk factors for PTB but delivered at full term (risk_FTB) > 3. No risk factors for PTB and delivered at full term (no-risk_FTB) > 4. No risk factors for PTB but delivered preterm (no-risk_PTB) > Thus,2 groups from low-risk control group (n = 14)No risk factors for PTB and delivered at full term (no-risk_FTB)(n = 13) > No risk factors for PTB but delivered preterm (no-risk_PTB) (n = 1)And 2 groups from high risk of preterm birth (n = 35)Risk factors for PTB and delivered preterm (risk_PTB ) (n = 7) > Risk factors for PTB but delivered at full term (risk_FTB) (n = 28)******“And we are to use groups which were compared to produce the signatures in the study to curate for experiment section”******In the study, so far the comparison I see was done for the delivery outcomes which is:Full term birth (FTB) (n=41) - [combination of (no-risk_FTB)(n = 13) & (risk_FTB) (n = 28)]Preterm Birth (PTB)] (n=8) - [combination of (no-risk_PTB) (n = 1) & (risk_PTB ) (n = 7)]And in some instance:the non_risk_FTB (low-risk women who delivered at term) )(n = 13)and risk_FTB (women with risk factors for preterm birth but who delivered full term) groups. (n = 28)Hence, I’m thinking that instead of:Group 0 - a low-risk control group (n = 14)Group 1 - high risk of preterm birth (n = 35)My experiments are likely going to be:Experiment 1 - for the delivery outcomes:Group 0 - Full term birth (FTB) (n=41)Group 1 - Preterm Birth (PTB)] (n=8)Experiment 2Group 0 - Non_risk_ Full term birth (FTB) (n = 13)Group 1 - Risk_FTB Full term birth (FTB) (n = 28)would like to check in, if I’m on the right track with the experiment categorization:thinking_face:?<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic(edited)

Kabirat Adeniyi (14:42:04): > Also is it possible not to see the microbe mentioned in the study in the NCBI taxon identifier

Mildred Anashie (14:43:42) (in thread): > Do you mean what I understand by group 0 and group 1?

UBNSEMS3S (14:50:17) (in thread): > It’s possible some taxa do not appear in the NCBI taxonomy. Please post them and perhaps others may have some ideas on how to identify them.

UBNSEMS3S (14:50:36) (in thread): > What are the cases and controls in this study?

Kabirat Adeniyi (14:52:06) (in thread): > oh thank you, the microbe I’m trying to identify isBacteroides coprocola

Chloe (14:53:26) (in thread): > now how do i identify the condition..? what do i have to base on to

Iram Jamshed (14:56:34) (in thread): > @Levi WaldronThat’s a good point. I’ll keep that in mind!

UBNSEMS3S (15:00:21) (in thread): > What is the article about?

U1LCB8WEA (15:01:10) (in thread): > The answer is given by what comparisons differential abundance is reported for, which can only be found in the paper. One request - in the “group 0” and “group 1” names, avoid acronyms like “FTP” and “PTB” and just write the full group names out.

U1LCB8WEA (15:02:26) (in thread): > So this sounds conclusive: “In the study, so far the comparison I see was done for the delivery outcomes which is:” that your Experiment 1 is correct.

U1LCB8WEA (15:03:14) (in thread): > And if differential abundance or alpha diversity are reported for “And in some instance:” then your experiment 2 is also correct.

Joan C. Chukwuemeka (15:06:57) (in thread): > okay. thanks a lot<@U1LCB8WEA>The article requires a lot of “in-between the lines” read.:slightly_smiling_face:

Chioma Onyido (15:07:51) (in thread): > Yes@Esther Afuapeand ifit’snot there, I search for it in uniprot.

Esther Afuape (15:08:20) (in thread): > That’svery insightful.Thank you!

Mildred Anashie (15:19:15) (in thread): > I’d say Participants in the group administered with the ART are the cases while those given the placebo are the control since the study was done to know the influence immune status has on the oral microbiome of HIV infected persons after ART > > On the contrast, I think it was baseline and after 24 weeks of administering the therapy (Could this be pre and post treatment)? > Am I confusing myself?:woman-facepalming:

Nana (15:21:01) (in thread): > Ok..thanks

Esther Afuape (15:52:05) (in thread): > @Kabirat Adeniyihttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696957574364819 - Attachment: Attachment > Hi @C. Mirzayi (please do not tag this account) @Levi Waldron, while solving another taxonomic issue, https://bugsigdb.org/Study_509/ Experiment_2/Signature_2, I confimed that the missing taxa, Escherichia shigella and uncultured Phyllobacteiaceae are available in NCBI taxonomy as 1940338 and 257462 respectively. > > Also I found that Escherichia shigella is rightly supposed to be in the “increased abundance” group, not decreased according to Table 2 of the paper.

Kabirat Adeniyi (15:53:50) (in thread): > Thanks

Chioma Onyido (15:55:54) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696882979898809?thread_ts=1696881726.289569&channel=C04RATV9VCY&message_ts=1696882979.898809This video from@Levi Waldronon how to find missing taxa is very detailed. - Attachment: Attachment > At one point I recorded a long video of doing detective work trying to resolve taxonomic nomenclature :sweat_smile: see https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID

Chloe (15:57:10): > which is these is the source respectively? Data from the Surveillance, Epidemiology, and End Results (SEER) program show that the overall incidence of CRCs for African Americans is 41.9 per 100,000 and 37.0 per 100,000 forEuropean Americans[2]. For Egyptians, according to the Egyptian NationalCancer RegistryProgram in 2014 - Attachment (sciencedirect.com): Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients > Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicitie…

Chloe (16:02:04): > which is these is the source respectively? Data from the Surveillance, Epidemiology, and End Results (SEER) program show that the overall incidence of CRCs for African Americans is 41.9 per 100,000 and 37.0 per 100,000 forEuropean Americans[2]. For Egyptians, according to the Egyptian NationalCancer RegistryProgram in 2014 or CRCs and their corresponding normal tissues from Egyptian (n = 17) patients of the Alexandria University Hospital, Egypt, and tissues from AA (n = 18) and EA (n = 19) patients at the University of Alabama at Birmingham were collected. do i take the source for the data or the source for the patients …?sciencedirect.comMicrobiome diversity in African American, European American, and Egyptian colorectal cancer patientsAlthough there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicitie… > > > > are from WaldronLab

U1LCB8WEA (16:02:06) (in thread): > That quote doesn’t sound like it has anything to do with the differential abundance analysis they performed. The question I always ask is: “Which groups were compared in order to produce the signatures of differential abundance that will be reported under this experiment?”

Peace Sandy (16:03:07): > Can a genera be repeated in the signature of multiple experiments, if it is seen in those different experiments@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

U1LCB8WEA (16:07:23) (in thread): > Certainly - some taxa are repeated across many, many experiments in bugsigdb, for exampleEscherichia:https://bugsigdb.org/Special:RunQuery/Taxon?Taxon%5BNCBI%5D=561&Taxon%5BBody%20site%5D=&Taxon%5BCondition%5D=&_run=1. It just means that it was reported to be differentially abundant for more than one different contrast (within a study or in different studies). - Attachment (BugSigDB): Special:RunQuery/Taxon

Nana (16:34:29) (in thread): > This done

Nana (16:35:30) (in thread): > Please<@UBNSEMS3S>how do I figure out the condition used. What I searched is not showing then I went to ontology and I was confused

Paulina Boadiwaa Mensah (16:38:56): > <@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Peroviccan I curate another article after finishing my second contribution and commenting in the issue that I have finished the task?

UBNSEMS3S (16:40:22) (in thread): > You want to curate information about the current study so that would be the latter it looks like.

Paulina Boadiwaa Mensah (16:41:12) (in thread): > Oh I guess I’ve seen the answer in the FAQs. I would have to wait for it to be graded.

Nana (16:42:45): > My people how do I know my article Condition?

UBNSEMS3S (16:44:03) (in thread): > I think what would be helpful is to look at the differential abundance figure which in this case appears to be Fig. 2. What are the two groups being compared in that figure?

U1LCB8WEA (16:44:12) (in thread): > There are other things you could do though if you want to contribute more, under the “TODO for reviewers” or “NCBI cleanup” in the help page on bugsigdb-just post here before making other edits to the wiki.

UBNSEMS3S (16:44:25) (in thread): > The condition is the disease or health condition under study in the differential abundance analysis.

Nana (16:53:21) (in thread): > <@UBNSEMS3S>thanks I really appreciate your time

UBNSEMS3S (16:56:35) (in thread): > I am starting to grade second contributions now and will get to yours soon.

Mildred Anashie (17:04:38) (in thread): > Amplicon sequence variants (ASV) between baseline samples and samples collected following 24 weeks of ART

Peace Sandy (17:07:10) (in thread): > Thank you:blush:@Levi Waldron

Nana (17:07:42) (in thread): > <@UBNSEMS3S>when i put something like this in my control: HIV-associated chronic lung disease (HCLD), no filter for this nature pops up so i cant select it, but if i put something like chronic lung disease, Azithromycin, placebo, which are keywords things starts to pop out

Nana (17:17:59) (in thread): > Or the conditions are these microbial groups[At 48 weeks, fve genera were detected as diferentially abundant between study arms by all methods (Lautropia, Moraxella, Rothia, Treponema and Veilonella) (Figure S24).**** Lautropia, Moraxella, Treponema**, Oribacterium, F0058 and ASV 209 were detected as differentially abundant between the baseline and 48-week samples from participants in the AZM arm by all methods (Figure S25). Moraxella was the only genus detected as diferentially abundant between the 48- and 72-week samples from participants in the AZM arm by all methods (Figure S26). Tere was also a high level of agreement between the diferential abundance testing and the SIMPER analysis of the contribution of taxa to overall dissimilarity

Nana (17:18:42) (in thread): > The microbial groups does not even pop up from the filter

UBNSEMS3S (17:34:30) (in thread): > We want to pick the term that’s closest so I think chronic lung disease would be the best fit for HIV-associated chronic lung disease.

UBNSEMS3S (17:34:56) (in thread): > Microbial groups are not condition. Just checking that you have watched the introductory video on curation? That should define what a condition is I believe.

Peace Sandy (17:35:30): > When Shannon diversity and evenness are not statistically significant,does it mean it is unchanged?

UBNSEMS3S (17:36:56) (in thread): > So that sounds like a longitudinal analysis of two groups (really the same group at two time points). When we are working longitudinally, we use the earlier time point as group 0 and the later time point as group 1. What is the sample size of group 0? If it’s a paired analysis should it differ from the sample size of group 1?

UBNSEMS3S (17:37:03) (in thread): > Correct.

Nana (17:39:14) (in thread): > <@UBNSEMS3S>My own says Shannon diversity is stable. But the select option has only changed, unchanged and declined

UBNSEMS3S (17:40:01) (in thread): > Stable and unchanged mean the same thing.

Peace Sandy (17:40:29) (in thread): > Thank You@C. Mirzayi (please do not tag this account)I’mreally grateful:sunflower:

Nana (17:41:21) (in thread): > Yeah I did…she picked the disease name. My own confusion set in when I put my own disease condition and nothing showed up

Nana (17:43:05) (in thread): > <@UBNSEMS3S>you have saved a soul today..thanks a lot

UBNSEMS3S (17:45:55) (in thread): > Yeah I understand how that can be confusing. I think chronic lung disease is fine. We want as close as possible, even if it isn’t a perfect fit.

Hodan Abdirisak (17:51:17) (in thread): > Thanks for your clarification@C. Mirzayi (please do not tag this account)

Chiagoziem David (18:03:52) (in thread): > Okay,<@UBNSEMS3S>has responded already

Mildred Anashie (18:16:29) (in thread): > Since it is paired i think itshouldn’tdiffer because same participants are being studied till the end of the time and the samples used for the analysis are collected from same participants > > Is this right?

Chiagoziem David (18:16:58): > Hope we are all doing alright and our contributions are not contributing us:grinning::grinning:

Mildred Anashie (18:17:28) (in thread): > I Sincerely apologize for taking up your time and do really appreciate your effort in helping me understand better and figure this out

Joan C. Chukwuemeka (19:43:04): > A total of 57 participants with singleton pregnancy were successfully recruited over the study period, 20 at low risk of PTB and 37 with risk factors for PTB. Multiple swabs were collected from some women depending on clinic visit frequency, accounting for 89 total samples.To control for multiple sampling of some woman and different trimester timepoints, we focused our analysis on single samples for each woman in the second trimester of pregnancy (n = 49).There were no significant differences in the age, race, body mass index, or smoking status of the participants by either the grouping of of risk_PTB, risk_FTB, no-risk_FTB, and no-risk_PTB or the FTB and PTB grouping.Based on the attached table of Patient demographics, and the above phrases, will it be correct to deduce that ******Gestational Age & Sampling Frequency ******were potential confounders controlled for?Or > * Maternal Age > * Race > * Body mass index (BMI) > * Smoking status,are also confounders?** > <@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic - Attachment (Nature): Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth > npj Biofilms and Microbiomes - Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth - File (PNG): image.png

2023-10-11

Fortune Nnamdi (02:11:04): > Hi:wave:everyone. > > Please how long does it take before an account request is approved?

Fortune Nnamdi (02:12:21) (in thread): > I requested for a bugsigdb account yesterday.

Onyewuchi Esther Chikamso (02:53:15) (in thread): > Check your spam. There should be a message there

Nwajei Edgar (02:53:40) (in thread): > Check spam, ifit’snot there, just be patient

Onyewuchi Esther Chikamso (03:00:44): > Greetings to all:hugging_face:In my research paper, it states that the body site is the gut microbiota. But in the create experiment (body site drop down), there is no option for ‘git microbiota’ the options are these - File (JPEG): IMG_20231011_075914.jpg - File (JPEG): IMG_20231011_075929.jpg - File (JPEG): IMG_20231011_075938.jpg - File (JPEG): IMG_20231011_075947.jpg

Fortune Nnamdi (03:31:35) (in thread): > Okay,thank you:blush:

Hodan Abdirisak (04:03:04) (in thread): > Is except few minutes after request no need time check:heavy_check_mark:the spam

Hodan Abdirisak (04:04:52) (in thread): > Read the Methods in your article then you will get sample collection and type of sample

Hodan Abdirisak (04:08:18): > I confused how many experiment needed to add my study, i take this picture as source figure, can you help me to clarify - File (PNG): Screenshot 2023-10-10 224810.png - File (PNG): Screenshot 2023-10-10 224736.png - File (PNG): Screenshot 2023-10-10 224654.png

Hodan Abdirisak (04:09:54): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01516-y - Attachment (BioMed Central): Antibiotic treatment using amoxicillin-clavulanic acid impairs gut mycobiota development through modification of the bacterial ecosystem - Microbiome > Background Effects of antibiotics on gut bacteria have been widely studied, but very little is known about the consequences of such treatments on the fungal microbiota (mycobiota). It is commonly believed that fungal load increases in the gastrointestinal tract following antibiotic treatment, but better characterization is clearly needed of how antibiotics directly or indirectly affect the mycobiota and thus the entire microbiota. Design We used samples from humans (infant cohort) and mice (conventional and human microbiota-associated mice) to study the consequences of antibiotic treatment (amoxicillin-clavulanic acid) on the intestinal microbiota. Bacterial and fungal communities were subjected to qPCR or 16S and ITS2 amplicon-based sequencing for microbiota analysis. In vitro assays further characterized bacterial-fungal interactions, with mixed cultures between specific bacteria and fungi. Results Amoxicillin-clavulanic acid treatment triggered a decrease in the total fungal population in mouse feces, while other antibiotics had opposite effects on the fungal load. This decrease is accompanied by a total remodelling of the fungal population with the enrichment in Aspergillus, Cladosporium, and Valsa genera. In the presence of amoxicillin-clavulanic acid, microbiota analysis showed a remodeling of bacterial microbiota with an increase in specific bacteria belonging to the Enterobacteriaceae. Using in vitro assays, we isolated different Enterobacteriaceae species and explored their effect on different fungal strains. We showed that Enterobacter hormaechei was able to reduce the fungal population in vitro and in vivo through yet unknown mechanisms. Conclusions Bacteria and fungi have strong interactions within the microbiota; hence, the perturbation initiated by an antibiotic treatment targeting the bacterial community can have complex consequences and can induce opposite alterations of the mycobiota. Interestingly, amoxicillin-clavulanic acid treatment has a deleterious effect on the fungal community, which may have been partially due to the overgrowth of specific bacterial strains with inhibiting or competing effects on fungi. This study provides new insights into the interactions between fungi and bacteria of the intestinal microbiota and might offer new strategies to modulate gut microbiota equilibrium. Video Abstract

Nana (04:44:27): > @Svetlana Ugarcina Perovic@Levi Waldron<@UBNSEMS3S>there’s an experiment signature I am supposed to delete. In my first experiment after I saved went back to edit confounders and it went ahead to create a new signature instead of editing. Please how do I edit already saved experiment and delete one.

Svetlana Ugarcina Perovic (04:49:23): > Good morning:teapot:From your previous CLOSED discussions, I added your questions and answers to this tablehttps://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/editKeep up the good work!

Aleru Divine (04:54:51) (in thread): > Or just go to the profile icon:bust_in_silhouette:and click on contributions andyou’llsee the history of every thingyou’vedone. - File (JPEG): Screenshot 2023-10-10 at 14.35.10 - File (PNG): Screenshot 2023-10-10 at 14.35.27

Aleru Divine (04:56:07) (in thread): > Hi@Nanacheck this out, hope it helps.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697014491385089?thread_ts=1696835336.839649&channel=C04RATV9VCY&message_ts=1697014491.385089 - Attachment: Attachment > Or just go to the profile icon :bust_in_silhouette: and click on contributions and you’ll see the history of every thing you’ve done.

Aleru Divine (05:02:54): > My condition isRECURRENT URINARY TRACT INFECTION, but I only seeURINARY TRACT INFECTION, is it okay to just useURINARY TRACT INFECTION?<@U1LCB8WEA>@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Chioma Onyido (05:07:50) (in thread): > Awesome! Thank you, this makes it easier to get through when stuck and also to avoid asking same questions over and over again.:grin::thumbsup:

Chioma Onyido (05:10:55) (in thread): > I don’t think we are authorized to delete yet, but I do know that we can still edit already saved experiment. > If you could share the link to the signature@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldronone of the mentors would help delete.:thumbsup:

Chioma Onyido (05:14:02) (in thread): > To edit your experiment, > Under the specific Experiment you want to edit, click the edit tab, you should be able to edit. - File (JPEG): IMG_4931

Nana (05:14:19) (in thread): > @Chioma Onyidowhen I tried editing one…that one did not edit. It went and created another one. That’s the one I want to delete

Nana (05:14:43) (in thread): > Ok thanks

Chioma Onyido (05:15:27) (in thread): > Created another signature? Or experiment?

Nana (05:17:26) (in thread): > Signature

Chloe (05:17:30): > CRC has a multifactorial pathobiology, includinggenetic mutations; ethnicity; and age, as most CRC patients are older than 50 years (during the last decade, however, there has been an increased rate of early-onset CRC) [4]. Inflammatory intestinal conditions are also a risk factor for CRC [5]. Another risk factor is diet, as low-fiber, high-fatwestern dietsare associated with a higher prevalence of CRC…. Does this:point_up_2:mean the condition is matched on 1. age 2.enthnicity 3.diet 4. inflammatory intestinal some help here - Attachment (sciencedirect.com): Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients > Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicitie… - Attachment (sciencedirect.com): Microbiome diversity in African American, European American, and Egyptian colorectal cancer patients > Although there is an established role for microbiome dysbiosis in the pathobiology of colorectal cancer (CRC), CRC patients of various race/ethnicitie…

Nana (05:17:48) (in thread): > Great.

Nana (05:18:21) (in thread): > @Svetlana Ugarcina Perovicplease I need an administrator to help me delete a signature that I created by mistake

Chioma Onyido (05:20:16) (in thread): > I think a video explaining how to work around this was demonstrated by@Joan C. ChukwuemekaHere’s the link:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696693678091739?thread_ts=1696689928.534139&channel=C04RATV9VCY&message_ts=1696693678.091739 - Attachment: Attachment > An example: The condition being studied is Preterm birth (PTB), while filling it in the autocomplete showed “spontaneous Preterm birth”, as a result I used the “find a term” option to checked on the EFO site. > > When you click the “find a term” it brings a page with another site link. click the new link and input your search term, So here I inputted the preterm birth, different results are shown. Using the filter side bar, type in EFO, it showed “premature birth” as the closest EFO ontology term. Going back to my BugSigDB page. the ” “premature birth” available:blush: > > Alternatively, instead of clicking the “find a term” option, you can open the link in a new tab and search

Chioma Onyido (05:23:52) (in thread): > Alright. Idon’tthinkthere’sany need to be worried okay, you can go ahead with the rest of your curation, they would delete whenthey’reonline.

Chioma Onyido (05:24:23) (in thread): > Have you been able toedityour experiment now?

Chioma Onyido (05:28:59) (in thread): > If after using “ctrl + F” to search for the word “matched” in your paper and you don’t see any results,<@UBNSEMS3S>response here might provide more clarity:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696869162564059?thread_ts=1696867919.650879&channel=C04RATV9VCY&message_ts=1696869162.564059 - Attachment: Attachment > @Chiagoziem David Just remembered that I asked a similar question during the office hour, because matched on wasn’t explicitly stated in the paper I selected and to avoid assumptions, I tried to clarify with the mentors. > > Chloe said to leave it blank, in cases where matched on wasn’t stated in the article. > > For more of @C. Mirzayi (please do not tag this account) ’s response, it’s here at 35:09: > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696529936787429

Hodan Abdirisak (05:31:07) (in thread): > Great and awesome:100:thanks@Svetlana Ugarcina Perovic

Chioma Onyido (05:35:34) (in thread): > @Joan C. ChukwuemekaI encountered the same issue, I had a demographics/ characteristics table but since the confounders controlled for weren’t explicitly stated, I left it blank to avoid assumptions. > > However I am also curious about if we could deduce from the table.:thinking_face:

Peace Sandy (05:36:09) (in thread): > Thank You@Svetlana Ugarcina Perovic

Hodan Abdirisak (05:37:42) (in thread): > I think recurrent is is just frequency but the condition is urinary track infection

Esther Afuape (05:40:13) (in thread): > Thank you!

Spyke Lionel (05:40:17): > Hello, Please adding contributions on Outreachy, should I leave the date accepted blank?

Nana (05:45:31) (in thread): > Yes..I have edited and it’s fine. So what you are saying is that I should create another signature when they come they will delete the particular one I don’t want

Peace Sandy (05:45:48): > If my experiment does not have increased abundance should I enter only signature 2@Svetlana Ugarcina Perovic@Levi Waldron@C. Mirzayi (please do not tag this account)

Onyewuchi Esther Chikamso (05:51:45) (in thread): > I’m not sure I understand you

Svetlana Ugarcina Perovic (05:54:09) (in thread): > @Nanaplease be patient,<@UBNSEMS3S>or<@U1LCB8WEA>will help asap.

Chioma Onyido (05:59:22) (in thread): > @Hodan AbdirisakMakes sense.:thinking_face:

Hodan Abdirisak (06:02:51) (in thread): > It is your first contribution?

Hodan Abdirisak (06:04:38) (in thread): > @C. Mirzayi (please do not tag this account)help me to clarify this

Hodan Abdirisak (06:06:02) (in thread): > What you want to do now?

Chinwendu Enyinna (06:09:33) (in thread): > I’m also interested in the answer for this. My experiment only stated decreased abundance in one of the sample (fecal sample). However, increased abundance was stated for another sample (oral)

Chloe (06:12:37) (in thread): > thanxs@Chioma Onyido

Spyke Lionel (06:14:58) (in thread): > Yes, it is my first contribution

Nana (06:18:07) (in thread): > @Svetlana Ugarcina Perovicok

Nana (06:19:30) (in thread): > Since it’s your first contribution add it

Nana (06:19:51) (in thread): > Same as the date of created if you finished the same day

Spyke Lionel (06:25:59) (in thread): > Alright thanks.

Hodan Abdirisak (07:30:29) (in thread): > Yeah,@Nanaenlighten you

Onyewuchi Esther Chikamso (07:52:22): > Is it okay to use the fill the different temperatures that was used in my research paper for the (Group 1 and 2) text field

Paulina Boadiwaa Mensah (08:05:43) (in thread): > @Aleru Divineif you can’t find Recurrent Urinary Tract Infection you can use Urinary Tract Infection. There is some difference between how the two are managed clinically, but in this instance if you can’t find the former term after searching the EFO site you can use latter as it might be the closest, in principle.

Onyewuchi Esther Chikamso (08:40:40): > I just found an easy way to check if the questions you want to ask have already been answered. > 1. Link on this > 2. Go to the search icon > 3. Click on it and type in relevant keywords to know if the question was already answered. > I hope someone finds this useful - File (PNG): Screenshot_20231011-133646~3.png - File (PNG): Screenshot_20231011-133703~2.png

Hodan Abdirisak (08:47:00) (in thread): > Thanks@Onyewuchi Esther Chikamsoit is realy help full massage

Karen254. Kingecha (09:45:00) (in thread): > @Nanawhat of the second contribution?

Aleru Divine (09:49:55) (in thread): > Thank you so much guys

Nwajei Edgar (09:51:36) (in thread): > Thanks for this

Aleru Divine (10:02:02): > Hi<@UBNSEMS3S>I submitted my curation for review 4 days ago but the ****needs review** ****label has not been added to it yet. I just wanted to bring this to your attention.Here’sthe link:https://github.com/waldronlab/BugSigDBcuration/issues/72Thank you! - Attachment: #72 Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection > Differential Urinary Microbiota Composition Between Women With and Without Recurrent Urinary Tract Infection – Lei Huang et al. – Frontiers in Microbiology 2022
> DOI: 10.3389/fmicb.2022.888681 > > https://www.frontiersin.org/articles/10.3389/fmicb.2022.888681/full

Grace Ogundaini (10:03:54) (in thread): > Did you comment under the article on GitHub, stating it needs review? That’s what I did and mine was marked

Aleru Divine (10:04:49) (in thread): > Yes I left a comment with the link.

Nana (10:09:49) (in thread): > I don’t know have not done that one..I answered for the one I have done

Mildred Anashie (10:18:47): > Hi@Svetlana Ugarcina PerovicMy study says “Bar-coded PCR primers directed at the V4 region of the bacterial 16S rRNA gene were used to generate amplicons from nucleic acid isolated from saliva samples”……Is there a bound region here? I picked V4 for both lower and upper bound region

Svetlana Ugarcina Perovic (10:19:53) (in thread): > It’s under review, thank you for your patience!

Svetlana Ugarcina Perovic (10:20:18) (in thread): > V4 is enough to state

Mildred Anashie (10:29:26) (in thread): > Okay, Thank you

Joan C. Chukwuemeka (11:31:34) (in thread): > <@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicI’m still hoping to a guide on this, please

UBNSEMS3S (11:35:00) (in thread): > @NanaPlease link me to the signature you’d like me to delete.

UBNSEMS3S (11:36:34) (in thread): > That doesn’t sound necessarily like they matched on anything–that sounds like text from the introduction. Generally speaking, there isn’t too much to curate from the introduction. Look specifically for the word “match.” Most of what we want to curate will be found in the methods, results, tables and figures, and supplements.

UBNSEMS3S (11:36:51) (in thread): > That sounds right to me.

U1LCB8WEA (11:37:30) (in thread): > They are claiming to havematchedon age, race, BMI, and smoking status. I think I would include gestational age under this heading as well,<@UBNSEMS3S>?

UBNSEMS3S (11:39:43) (in thread): > Sorry Levi I’m not seeing where there is matching in this paper?

Joan C. Chukwuemeka (11:40:39) (in thread): > Okay,<@U1LCB8WEA>I had the same thought, that those are variables they****“matched on”,****however I was skeptical since it didn’t use the term “matched on”

UBNSEMS3S (11:41:01) (in thread): > They looked at differences between cases and control groups, determined there was none based on their data (which is an incorrect way of assessing potential confounders) and therefore do not appear to have included those variables in their models.

U1LCB8WEA (11:41:51) (in thread): > Sampling frequencydoesn’tmeet the definition of a confounder,and gestational age probablydoesn’teither (something that affects both the exposure and the outcome). Sampling frequency is not even a property of the participants,so I would not include it in either - almost all studies have matched sampling frequency so youdon’tneed to record it just because this study took an extra step to do it.

Joan C. Chukwuemeka (11:42:15) (in thread): > <@UBNSEMS3S>hmm….Okay, I see

U1LCB8WEA (11:43:01) (in thread): > Just from the quote above stating that there was no difference in these factors between cases and controls.

Joan C. Chukwuemeka (11:44:04) (in thread): > Alright. Thanks a lot<@U1LCB8WEA><@UBNSEMS3S>

Nana (11:46:22) (in thread): > <@UBNSEMS3S>good evening, here: Experiment 2https://bugsigdb.org/Study_822 - Attachment (BugSigDB): Study 822

UBNSEMS3S (11:46:30) (in thread): > @Onyewuchi Esther ChikamsoIn the methods, how were samples collected?

UBNSEMS3S (11:47:00) (in thread): > This does not look like a figure we can curate.

Aleru Divine (11:47:49) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

UBNSEMS3S (11:47:55) (in thread): > I’d take a look at figures 2 and 3 instead.

UBNSEMS3S (11:48:28) (in thread): > Yeah Paulina is correct. We want to get the EFO term that is closest even if it’s not a perfect match.

Nana (11:48:34) (in thread): > @Chioma Onyidoafter creating the signature 2 and saved what next? where do i go from there

UBNSEMS3S (11:48:59) (in thread): > Yeah you can just have one signature in the experiment for decreased abundance if there were no taxa that were increased.

Aleru Divine (11:49:31) (in thread): > Alright<@UBNSEMS3S>, thank you so much!

UBNSEMS3S (11:49:40) (in thread): > I will review this today. Thank you for your patience.

UBNSEMS3S (11:50:27) (in thread): > Deleted.

Nana (11:52:38) (in thread): > Thanks seen

Chioma Onyido (11:59:41) (in thread): > Check to see if there are more results of differential abundant taxa to report or experiments to add, if there are none then I believe you are done with your curation. > Cross-check for errors and confirm again that details are accurate. > > After this, Copy the link to your study curation, (it’susually something like bugsigdb.org/Study_xxx), paste this under your GitHub article issue and call the attention of@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovicthatit’sready for review and a “needs review” tag will be subsequently attached.

Hodan Abdirisak (12:02:41) (in thread): > Thanks@C. Mirzayi (please do not tag this account)for your clarification:pray:

Hodan Abdirisak (12:02:55) (in thread): > What about number experiments

Aleru Divine (12:12:18) (in thread): > Thank you so much<@UBNSEMS3S>

Onyewuchi Esther Chikamso (12:42:39) (in thread): > Samples were collected by putting the entire gut (small intestine and colon) into a sterile tube. So what I did was to google the part of the gut the small intestine and colon belonged to. I figured they were part of the midgut and put midgut as my option. I hope that’s okay?

UBNSEMS3S (12:52:11) (in thread): > That sounds right to me.

Onyewuchi Esther Chikamso (12:53:25) (in thread): > Thank you:blush:

UBNSEMS3S (12:57:44) (in thread): > Number of experiments is dependent on the number of contrasts they conducted in the study. Did they compare more than two groups? Did they change the cases or controls for a follow-up analysis? Did they do some type of subgroup analysis?

Joan C. Chukwuemeka (13:12:49): > Please what type of visuals/graphs were used in this Images (a,b,c), to enable interpretation. > Fig A comes across as a stacked bar chart, but a lot of info stacked, making it quite unclear….. > Fig B looks like a bar plot with error bars, the dots ?, seems like scatter plot > Fig c seems to be a heat map, not certain of a and b:thinking_face:.<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic:pray: - File (PNG): image.png

Hodan Abdirisak (13:20:16) (in thread): > There are two Groups group 0 mice before treatment and mice after treatment also there were control infant and amoxicillin treated those the sample transfer to mice collected. As shown in figure one

Hodan Abdirisak (13:20:25) (in thread): > Thats why I confused

Nana (13:28:24) (in thread): > @Chioma Onyidothanks for your time. I have 3 more questions that need clarification: > 1. Experiment to add: do you mean if my article has two sample used as test condition. > 2. Differential abundant taxa.. increased and decreased microbiome > 3. Then GitHub has @ to tag my reviewers. Is it on my worked assigned to me that I will open issues > 4. Then after that I will move to outreachy site to record or until my work is reviewed before I will go to the site

Onyewuchi Esther Chikamso (13:57:14): > Please how can I access the supplementary information mentioned in the research paper? I have used the link that was provided to search for what I want, but I still can’t find it.http://life.scichina.com - File (PNG): Screenshot_20231011-185625.png

Chinwendu Enyinna (14:07:35) (in thread): > Alright, thank you for the clarification<@UBNSEMS3S>.

Paulina Boadiwaa Mensah (14:19:36): > <@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina PerovicI am working on one of the Papers with Missing NCBI id for one of it’s signatures: Study_764. > For the organism termed “Chloroplast” I am finding that the closest scientific name is unclassified Cyanobacteriota. Can I go ahead and edit?

Paulina Boadiwaa Mensah (14:21:44): > <@U1LCB8WEA>asked me to post here before making edits. > Here’s a link that helped me map Chloroplasts to Cyanobacteriota:https://en.wikipedia.org/wiki/Chloroplast - Attachment: Chloroplast > A chloroplast () is a type of membrane-bound organelle known as a plastid that conducts photosynthesis mostly in plant and algal cells. The photosynthetic pigment chlorophyll captures the energy from sunlight, converts it, and stores it in the energy-storage molecules ATP and NADPH while freeing oxygen from water in the cells. The ATP and NADPH is then used to make organic molecules from carbon dioxide in a process known as the Calvin cycle. Chloroplasts carry out a number of other functions, including fatty acid synthesis, amino acid synthesis, and the immune response in plants. The number of chloroplasts per cell varies from one, in unicellular algae, up to 100 in plants like Arabidopsis and wheat. > A chloroplast is characterized by its two membranes and a high concentration of chlorophyll. Other plastid types, such as the leucoplast and the chromoplast, contain little chlorophyll and do not carry out photosynthesis. > Chloroplasts are highly dynamic—they circulate and are moved around within plant cells, and occasionally pinch in two to reproduce. Their behavior is strongly influenced by environmental factors like light color and intensity. Chloroplasts, like mitochondria, contain their own DNA, which is thought to be inherited from their ancestor—a photosynthetic cyanobacterium that was engulfed by an early eukaryotic cell. Chloroplasts cannot be made by the plant cell and must be inherited by each daughter cell during cell division. > With one exception (the amoeboid Paulinella chromatophora), all chloroplasts can probably be traced back to a single endosymbiotic event, when a cyanobacterium was engulfed by the eukaryote. Despite this, chloroplasts can be found in an extremely wide set of organisms, some not even directly related to each other—a consequence of many secondary and even tertiary endosymbiotic events. > The word chloroplast is derived from the Greek words chloros (χλωρός), which means green, and plastes (πλάστης), which means “the one who forms”.

Paulina Boadiwaa Mensah (14:24:49) (in thread): > “Chloroplasts are considered endosymbiotic Cyanobacteria” Ref: doi: > 10.3389/fmicb.2019.01612

Paulina Boadiwaa Mensah (14:54:10) (in thread): > <@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovicalso working on Signature 1/Experiment 1 of Study_730. “Lachnospirales” has a missing NCBI id. After googling and reading a couple of papers, I’m realizing it’s an Order under the Clostridia Class and it’s equivalent toEubacteriales. Can I edit the Signature?

UBNSEMS3S (15:20:12) (in thread): > B is partially curatable. The rest is not. I would check for a supplement or the text if there is easier to curate results than this figure though.

UBNSEMS3S (15:20:44) (in thread): > It looks like Table S4 has what you need in it. Can you link me to the paper?

Onyewuchi Esther Chikamso (15:27:14) (in thread): > https://link.springer.com/article/10.1007/s11427-019-9540-yThis is the link to the paper - Attachment (SpringerLink): Ambient temperature alters body size and gut microbiota of Xenopus tropicalis > Science China Life Sciences - Temperature is important to determine physiological status of ectotherms. However, it is still not fully understood how amphibians and their symbiotic microbiota…

UBNSEMS3S (15:38:25) (in thread): > Makes sense to me.

UBNSEMS3S (15:38:34) (in thread): > Awesome. Please do.

Chioma Onyido (15:52:53) (in thread): > 1. yes, I think there are a couple of situations where You can have more than one experiment. The key thing is to check where differential abundant taxa are reported, check the groups that were contrasted. > 2. I’m not sure what you’re asking here but the differential abundant taxa your experiments (the groups you’re contrasting) is what determines the signatures you’re creating, whether increase or decrease. Check your figures, tables or within the texts > 3. If I get this correctly,you’reasking if you should open a new issue to indicate thatyou’redone reviewing? If this is it, the answer is no, youdon’tneed to open a new issue, same article you commented on for permission to curate,it’sthe same way you comment thatyou’redone curating. > 4. Yesthe mentors are currently still grading. You can go ahead to record on Outreachy, > @NanaI hope I answered your questions, sorry if Ididn’t. The mentors will shed more light whenthey’rehere.:pray:

Mildred Anashie (16:06:49) (in thread): > Thankyou:blush:

Peace Sandy (16:29:08) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Paulina Boadiwaa Mensah (17:21:10): > <@UBNSEMS3S><@U1LCB8WEA>for a study with one main aim and other exploratory aims, must the main aim strictly correspond to Experiment 1 during curation?

UBNSEMS3S (17:34:47): > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499

U02CNMR4YEA (17:35:40): > <@UBNSEMS3S><@U1LCB8WEA>I have a paper that is looking at the ocular microbiome and the authors are stating there are taxon that are significantly higher in one group than the other but I am not seeing where they statistically proved it. Since I am really trying to identify any and all ocular microbiome papers that can be curated, I would really appreciate it if you could take a look and confirm that it’s not curatable.https://pubmed.ncbi.nlm.nih.gov/37803284/ - Attachment (PubMed): Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye - PubMed > The DM-DE group have unique microbial composition and functional metabolic pathways. The dominant species and unique metabolic pathways of the ocular surface in the DM-DE group may be involved in the pathogenesis of dry eye in diabetic children.

Nana (19:07:08) (in thread): > @Chioma Onyidoyeah you answered everything thanks for your time

Esther Afuape (20:14:16): > Hello<@UBNSEMS3S>@Levi Waldronhttps://bugsigdb.org/Study_776has a genus Leptolyngbya in experiment 2/signature 1 with missing NCBI ID. I found it to have an NCBI ID of 47251 on both uniprot and NCBI. Could you confirm if it is correct and if I may go ahead and edit it? - Attachment (BugSigDB): Study 776

Nana (21:26:57): > <@UBNSEMS3S>please for someone who is waiting for their paper to be reviewed, what can be doing during the waiting phase?

2023-10-12

Chiagoziem David (01:45:28) (in thread): > Alrighty

Chiagoziem David (01:46:24) (in thread): > Think of our place in the vastness of the universe

Svetlana Ugarcina Perovic (02:23:57): > Good morning:bouquet:If you want to contribute more, while waiting for your review,under the “TODO for reviewers” or “NCBI cleanup” in the help page on bugsigdb - just POST HERE before making other edits to the wiki. > > Thank you for your patience and have a nice day!@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA>

Mildred Anashie (03:13:42) (in thread): > Noted

Hodan Abdirisak (03:15:41) (in thread): > Good morning sir@Svetlana Ugarcina Perovic:sunrise_over_mountains:

Hodan Abdirisak (03:16:35): > I have questions:question:Is it must to fill two signature in one experiment

Mildred Anashie (03:19:12) (in thread): > @Levi Waldronreplied to that earlier saying….There are other things you could do though if you want to contribute more, under the “TODO for reviewers” or “NCBI cleanup” in the help page on bugsigdb - just post here before making other edits to the wiki.

Nana (03:35:20) (in thread): > Ok

Nwajei Edgar (03:37:46) (in thread): > Good morning:innocent::innocent:

Onyewuchi Esther Chikamso (03:59:37) (in thread): > Hi@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldronplease I’m still not clear on this

Chioma Onyido (04:12:26) (in thread): > No it’s not, if you checked and confirmed thatit’sonly one, you can go ahead and fill in. > Peace Sandy asked a similar question and Chloe answered.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697039339611039?thread_ts=1697017548.668109&channel=C04RATV9VCY&message_ts=1697039339.611039 - Attachment: Attachment > Yeah you can just have one signature in the experiment for decreased abundance if there were no taxa that were increased.

Chioma Onyido (04:13:53) (in thread): > Uhm guysss…@Svetlana Ugarcina Perovic‘s pronouns are she/ her.:sweat_smile:

Peace Sandy (04:31:13) (in thread): > Thank You@Svetlana Ugarcina Perovic

Peace Sandy (04:37:10) (in thread): > Noit’snot compulsory

Peace Sandy (04:37:47) (in thread): > Looking forward to it@C. Mirzayi (please do not tag this account)

Svetlana Ugarcina Perovic (04:39:02) (in thread): > You have it herehttps://link.springer.com/article/10.1007/s11427-019-9540-yin the end, after the literature:https://static-content.springer.com/esm/art%3A10.1007%2Fs11427-019-9540-y/MediaObjects/11427_2019_9540_MOESM1_ESM.pdf

Svetlana Ugarcina Perovic (04:40:14) (in thread): > Tables are hereSupplementary material, approximately 92.0 KB.

Nana (04:47:21) (in thread): > Thank you@Svetlana Ugarcina Perovic

Nana (04:47:50) (in thread): > @Chioma Onyidothanks for pointing that out

Svetlana Ugarcina Perovic (04:48:40) (in thread): > no problem at all:smile:

Chioma Onyido (04:52:50): > Good morning everyone.:sun_with_face:I hope we’re doing well today and making progress with our respective curations. > > Nothing much here, just subtly re-iterating what@Svetlana Ugarcina Perovicposted here yesterday aboutanswers to most of our frequent questions, the mentors have taken their time to answer most of the questions in the word document and it’d be really good if we look through the doc and confirm if our questions have already been answered, it saves us time. > > Rooting for everyone:hugging_face:and don’t forget our weekly teammeeting today by 10:00AM EDT: which is 3:00pm WAT, 5:00pm EAT :thumbsup:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697014163723279:hugging_face: - Attachment: Attachment > Good morning :teapot: > > From your previous CLOSED discussions, I added your questions and answers to this table https://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/edit > > Keep up the good work!

Chiagoziem David (05:02:19) (in thread): > Thanks for the time clarification:smile_cat:, local bois like me:joy::joy::joy::alien:thought it was 10am:smile_cat::smile_cat::smile_cat:

Hodan Abdirisak (05:05:52) (in thread): > Thanks@Peace Sandy@Chioma Onyidofor your clarification

Hodan Abdirisak (05:09:14): > Good morning all of you:sunrise:@Chioma OnyidoI really appreciate the way you clarify Time I was thinking that what the in EAT would be, thanksgiving

Onyewuchi Esther Chikamso (05:19:39) (in thread): > Thank you

Chioma Onyido (05:29:34) (in thread): > Glad it helped.:hugging_face:

Chioma Onyido (05:30:19) (in thread): > I almost mixed it up myself, posting it here to remind myself and others.:sweat_smile:

Wangui Thuo (05:53:38): > Hey@C. Mirzayi (please do not tag this account)and@Levi Waldron. How long do I have to wait before the second contribution is assigned to me?

Chiagoziem David (06:26:50) (in thread): > Alrighty:muscle:

Aleru Divine (06:27:06) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (06:37:05): > Hi@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA>I wanted to bring to your notice that I had previously identified and rectified these taxa names that the original curators couldn’t match with a valid NCBI identifier. My intention was to improve the accuracy and reliability of our data. > I was not aware of this protocol (POST HERE before making other edits to the wiki.), and I apologize for any confusion or inconvenience this may have caused > > Here are the links to them ones I identified:https://bugsigdb.org/Study_716/Experiment_1/Signature_2https://bugsigdb.org/Study_762/Experiment_2/Signature_2https://bugsigdb.org/Study_500/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 716/Experiment 1/Signature 2 - Attachment (BugSigDB): Study 762/Experiment 2/Signature 2 - Attachment (BugSigDB): Study 500/Experiment 1/Signature 2

JulietMadu (07:17:21): > Hello please can someone explain this - File (JPEG): Screenshot_20231012-115208_Chrome.jpg

Esther Afuape (07:29:18) (in thread): > Thank you, Chioma:hugging_face:

Joan C. Chukwuemeka (07:46:25) (in thread): > Hello@JulietMaduthere should be a paragraph that started the question before the point your post started. You may need to include it in the snap shot,so you can be guided.:blush:

Joan C. Chukwuemeka (07:51:16) (in thread): > Yea, B is comparative analysis…. The supplement didn’t have info for that figure and text basically refers to the figures mostly.:woman-shrugging:Trying to interpret the Visual for B- on one hand it’s a bar plot with error bars, just don’t yet know what the dot plots on it are:thinking_face:. > > However, I’ll recheck the supplement and the article again. > Thanks<@UBNSEMS3S>

Hodan Abdirisak (08:32:39): > My study has two experiments, one comparing the faeces of infants before and after treatment with AMOX antibiotics to determine the abundance of bacterial in the samples. According to the highlighted text it explains and increase in the three bacteria after 10days of treatment with AMOX and also a decrease in 2 of the highlighted bacteria before treatment. > > My question is, > Is it okay I record them just like that in the experiment? - File (JPEG): IMG_20231012_132110_572.jpg - File (PNG): Screenshot 2023-10-12 052016.png

JulietMadu (08:35:27) (in thread): > @Joan C. Chukwuemekahere - File (JPEG): Screenshot_20231012-133434_Chrome.jpg

Hodan Abdirisak (08:37:05) (in thread): > Then go to that link you will see where information is then copy one by one

Chioma Onyido (08:38:59) (in thread): > This is valid but I’m afraid it’s probably not enough to conclude that that’s all the reported signatures. > To confirm, you should also look at other figures/ tables too, maybe there’s somewhere with a more detailed report of signatures.

Joan C. Chukwuemeka (08:39:58) (in thread): > Alright@JulietMaduthe annotated article has several differentially abundant bacteria taxa stated within it. > * Identify them and choose any of your choice > * open the web link and search for that taxa. the search result will have the identifier that you are required to fill into the spaces provided as indicated

Chioma Onyido (08:40:35) (in thread): > Also check if there’s Supplementary table/ figure. > But when you check and confirm that this all that’s reported in the paper, then you’re good.:+1:

JulietMadu (08:42:19) (in thread): > @Joan C. Chukwuemekawhat about the last part about “supplement”

Joan C. Chukwuemeka (08:46:21) (in thread): > Search the paper for “supplement” - if present, there will be a URL Link for it. > > Note that it may or may not be present, just as the question specified

Hodan Abdirisak (09:00:13) (in thread): > this the supplemental table - File (PNG): Screenshot 2023-10-10 034818.png

Paulina Boadiwaa Mensah (09:02:01): > @Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>please I am editing Study_814 which I was assigned to curate. I am trying to delete Experiment 1 so I can re-arrange the order of the Experiments according to the order of the Objectives in the study. Can someone with Administrator access delete it for me please?https://bugsigdb.org/Study_814/Experiment_1 - Attachment (BugSigDB): Study 814/Experiment 1

Paulina Boadiwaa Mensah (09:04:52) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>Second question: If a study comparing two groups reports that they were “similar” in terms of some parameters such as age, sex, smoking history, is that equivalent to “matched on”, and can those parameters be used for the “matched on” section in the curation form?

Esther Afuape (09:11:31) (in thread): > Attach a link to the experiment you want deleted so that she just deletes it when she sees your message.

Hodan Abdirisak (09:16:47) (in thread): - File (PNG): Screenshot 2023-10-12 061422.png

Esther Afuape (09:30:28) (in thread): > Please confirm also,https://bugsigdb.org/Study_777/Experiment_3/Signature_2found “saccharimonadaceae” to be “Candidatus Saccharimonadaceae” with taxonomy ID 2171986 - Attachment (BugSigDB): Study 777/Experiment 3/Signature 2

Esther Afuape (09:56:57) (in thread): > https://bugsigdb.org/Study_792/Experiment_1/Signature_1Actinoplanes with tax on ID 1865 on both NCBI and uniprot - Attachment (BugSigDB): Study 792/Experiment 1/Signature 1

Nana (09:57:01): > <!here>meeting time is almost here. Remember to be present

Tolulope Ogunleye (09:59:11): > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499Here’sa gentle reminder of our meeting happening in a minute

Peace Sandy (09:59:55): > Hey Everyone:wave:It’s time for today’s meeting > Kindly find the meeting link attached).https://us02web.zoom.us/j/2737200499

Onyewuchi Esther Chikamso (10:35:18): > Supplementary material, approximately 92.0 KB.

Fortune Nnamdi (10:42:17): > Hi Chloe@C. Mirzayi (please do not tag this account)Will it be possible to get the recording oftoday’smeeting as we did the one of last week?I can barely hearwhat’sbeing said, Ican’teven follow every discussion because of how bad the network is on my end. > > It just logged me out andI’mfinding it difficult to join again:woman-facepalming:I hope to play the recorded version if sent. Thank you for taking out your time to do this. I appreciate.

Chioma Onyido (10:43:22) (in thread): > Yes I think Chloe’s recording already. > So Sorry about your network.

U1LCB8WEA (10:46:21) (in thread): > Great detective work,@Paulina Boadiwaa Mensah!!

U1LCB8WEA (10:46:57) (in thread): > I don’t think the order of experiments is important.

Peace Sandy (11:08:26) (in thread): > Yes, the recording will be shared

Uchechukwu Favour Ojunta (11:55:52): > Hello Everyone, > > I just requested for an account so that I can start my contribution. Please how long will that take?

Fortune Nnamdi (12:06:45) (in thread): > It won’t take long…you’ll receive an email. Mine didn’t take long

Fortune Nnamdi (12:07:15) (in thread): > Alright,thanks guys

Joan C. Chukwuemeka (12:10:00) (in thread): > @Uchechukwu Favour Ojuntafollow this link to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Uchechukwu Favour Ojunta (12:11:51) (in thread): > Thank you@Fortune Nnamdi@Joan C. Chukwuemeka

Peace Sandy (13:41:23) (in thread): > Itwon’ttake long, have you completed the first task

Mildred Anashie (14:06:29) (in thread): > If you have completed the first task be patient, your account will be approved by one of the mentors@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi WaldronMeanwhile check your spam incase the mail has already been sent.

Odigiri Great Alume (15:55:39) (in thread): > Use Ctrl f to find supplementary tables or figures on the work

Odigiri Great Alume (16:06:19) (in thread): > Thanks:pray:

UBNSEMS3S (16:09:46) (in thread): > It looks like all account requests have been approved but let me know if that’s not the case.

Peace Sandy (16:10:57): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldronplease can you explain data transformation, what I’m I supposed to look out for, seems I can’t find anything of that sort in my article, I just want to be sure

UBNSEMS3S (17:02:37): > Today’s recording of office hours - File (MPEG 4 Video): video1118592733.mp4

Chloe (17:05:28): > What is the maximum number of experiences on can create ?

U1LCB8WEA (17:06:17) (in thread): > There’s no maximum enforced, it should be determined just by the number of contrasts made in the study.

U1LCB8WEA (17:09:18): > Someone asked what you can do while waiting for your second contribution to be graded. Here are some suggestions: > 1. double-check your contribution for accuracy and completeness, which is what it will be scored for. > 2. check out theTODO for reviewers- we’d love to have help! > 3. resolve some of theNCBI cleanup- I find this surprisingly fun, like detective work:sweat_smile: > When you first get started reviewing, it’s best if you post proposed changes here to check that you’re on the right track. Actually it’s OK to make edits to the wiki, just post here and we can always roll back changes if needed, and mark a study as reviewed if it seems like you’ve reviewed it sufficiently.

Chloe (17:09:43) (in thread): > ok thanks@Levi Waldron.

UBNSEMS3S (17:11:25) (in thread): > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances ->This is most common.Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio ->Rare.ANCOM > > Arcsine square-root ->Rare. MaAsLin2 sometimes. Some linear models rarely.

UBNSEMS3S (17:14:54) (in thread): > I will note that this is wrong or missing for many previously curated papers and a good cleanup task for an intrepid soul would be to try to update all of these. I’ve found a lot of DESeq2 papers that say they use relative abundances or CLR which do not make sense–DESeq2 uses a negative binomial model which requires counts* or else it will not converge. > > *Or variables that are whole numbers that approximate a negative binomial/poisson distribution.

Peace Sandy (18:05:41) (in thread): > Wow…thank you so much@C. Mirzayi (please do not tag this account)for the clarification

Peace Sandy (18:06:29) (in thread): > Thank you so much for this@C. Mirzayi (please do not tag this account)

Peace Sandy (18:07:19) (in thread): > Thank you so much@Levi Waldronfor the head up, this is helpful

Chioma Onyido (18:52:14) (in thread): > Great! Thank you@Levi Waldron.

Odigiri Great Alume (18:53:58) (in thread): > This is the answer I been looking for. Thank you@Levi Waldron

Chioma Onyido (18:59:07) (in thread): > I think I mixed up data transformation for DeSeq2 during my curation. This is reallyyy helpful<@UBNSEMS3S>thank you:pray:

Ulenyo Attah (19:45:08) (in thread): > Thank you for this, Peace

2023-10-13

Karen254. Kingecha (01:18:46) (in thread): > Thank you@Levi Waldron

Karen254. Kingecha (01:21:05) (in thread): > This is very helpful thank you@C. Mirzayi (please do not tag this account)

Chiagoziem David (01:25:33) (in thread): > Thank you very much<@UBNSEMS3S>, this would be very helpful for those who couldn’t meet up

Chiagoziem David (01:26:21) (in thread): > Thanks<@U1LCB8WEA>:pray:

Chiagoziem David (01:35:05): > It’s a new day guys (at least for those of us in this part of the world:comet::comet::face_with_cowboy_hat:) ,@Svetlana Ugarcina Peroviconce told me to choose quality over quantity - so even as we go about our curating duties, let’s do well to ensure we are doing the right things, ask as many questions as you can too…. it’s not how fast you are .. but how accurate… > > Have a great day.. > David:pray::pray::grinning:. > (PPS: this looks like a campaign mandate text:sweat_smile:)

Hodan Abdirisak (03:03:08) (in thread): > @Chioma Onyido@Odigiri Great Alumethanks:pray:

Hodan Abdirisak (03:07:21) (in thread): > Thanks<@U1LCB8WEA>

Hodan Abdirisak (03:15:34) (in thread): > This helpful information thanks@C. Mirzayi (please do not tag this account):pray::pray:

Hodan Abdirisak (03:18:42) (in thread): > Thanks so much@C. Mirzayi (please do not tag this account)

Peace Sandy (03:26:50) (in thread): > Lol…nice one:blush:Thank You

Mildred Anashie (03:44:23) (in thread): > Thank you for the update@Levi WaldronThis has cleared my confusion:woman-facepalming:regarding this

Fortune Nnamdi (04:25:59) (in thread): > Thanks!!<@UBNSEMS3S>:smiling_face_with_3_hearts:

Esther Afuape (04:48:16) (in thread): > Lol thank you

Esther Afuape (04:49:16) (in thread): > Thank you

Esther Afuape (04:52:38) (in thread): > I just realized that I might have mixed up the data transformation for my curation. Thank you<@UBNSEMS3S>

Esther Afuape (04:55:48) (in thread): > I saw that some of the NCBI clean up tasks are in new curations that applicants just carried out which have not been reviewed yet. Is it okay to solve those too?@Levi Waldron

Svetlana Ugarcina Perovic (05:18:54): > Good morning :teapot:**** & happy Friday!****<@UBNSEMS3S>and I (@Svetlana Ugarcina Perovic) are reviewing your contribution. Thank you for your patience!<@U1LCB8WEA>suggested how you can contribute more while waiting for the results of your contribution herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697144958544289And, more NEWS today:drum_with_drumsticks:I just published a new microbiome digest (a daily digest of scientific microbiome papers, an effort started by Elisabeth Bik & now run by microbiome scientists from all around the world) and featuredYOUR GREAT WORK!https://microbiomedigest.com/2023/10/13/october-13-2023/ - Attachment (Microbiome Digest - Bik’s Picks): October 13, 2023 > Today’s digest features the Chinese Gut Microbiome Resource, plate readers in the anaerobic chamber, seasonal stability of sponge microbiomes, and more. Also, you can support the outreachy bu…

Odigiri Great Alume (05:19:11) (in thread): > https://bugsigdb.org/Study_509/Experiment_2/Signature_2The link above leads to one of the signatures curated by an applicant. Listed among the decreased taxa is MITOCHONDRIA which is not an organism (bacteria) but the power house of a cell. > > It’s okay to delete it right?@Levi Waldron - Attachment (BugSigDB): Study 509/Experiment 2/Signature 2 - File (JPEG): Screenshot_20231013-101606.jpg

Chioma Onyido (05:25:08) (in thread): > @Odigiri Great AlumeI saw this too and you’re right that it’s not a bacteria > but if you check the paper, you’d see that Mitochondria was listed as among the the differential abundant taxa in Table 2 of the paper. Maybethat’swhy the curator added it to the signature. > > I’m curious about how to curate this too. Whether to ignore or include.:thinking_face:

Peace Sandy (05:44:15) (in thread): > Wow…this is awesome

Peace Sandy (05:44:42) (in thread): > Do you have a newsletter@Svetlana Ugarcina Perovic

Nana (05:46:13) (in thread): > Removed mitochondria which when searched on NCBI anduniprot.orgis not a bacteriahttps://bugsigdb.org/Study_509 - Attachment (BugSigDB): Study 509

Peace Sandy (05:53:01): > Are we adding the NCBI clean up task or any other task aside the two contributions to our outreachy task@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:53:24) (in thread): > yes, all the bugsigdb tasks (curations, reviews, clean-ups, etc.) are your outreachy tasks

Peace Sandy (05:55:03) (in thread): > How do I keep track of the clean up task, I did a lot yesterday and it disappeared on the page their after, which shows that the NCBI taxonomy was correctly entered

Peace Sandy (05:55:14) (in thread): > How do I get the link of the ones I did

Svetlana Ugarcina Perovic (05:55:44) (in thread): > That’s a question for<@UBNSEMS3S>/<@U1LCB8WEA>

Svetlana Ugarcina Perovic (05:59:15) (in thread): > I’m pretty sure that is recorded under your name and visible to the admin, let’s wait for Chloe/Levi to point out where you can find your NCBI corrections done there

Svetlana Ugarcina Perovic (06:00:05) (in thread): > not yet:wink:

Peace Sandy (06:01:15) (in thread): > Oh…:blush:

Peace Sandy (06:01:27) (in thread): > Okay

Peace Sandy (06:01:37) (in thread): > Thank You for your response@Svetlana Ugarcina Perovic

Esther Afuape (06:03:13): > Hello@Levi Waldron<@UBNSEMS3S>I made a thread of some of the NCBI clean up I solved (https://community-bioc.slack.com/archives/D05V6NZQ60L/p1697189800793359) and was awaiting permission to edit the changes.@Levi Waldrongave us the permission to go ahead and edit (that was last night over here) and I just saw them this morning.Another applicant has however made those edits unknown to her that I already had them solved. How do we go about this because I need to add the tasks to my contribution. - Attachment: Attachment > Hello @UBNSEMS3S @Levi Waldron https://bugsigdb.org/Study_776 has a genus Leptolyngbya in experiment 2/signature 1 with missing NCBI ID. I found it to have an NCBI ID of 47251 on both uniprot and NCBI. Could you confirm if it is correct and if I may go ahead and edit it?

Chioma Onyido (06:12:27) (in thread): > @Peace SandyOne thing I did was that I saved the link of each of the taxonomic issue I was able to solve, so that I can access them later.:blush:I don’thave the answer for already solved issues (whose linkweren’tsaved) but This is just a suggestion for subsequent contributions.:eyes:

Peace Sandy (06:12:56) (in thread): > Thank You

Mildred Anashie (06:14:24) (in thread): > Good morning > This is great:clap:

Peace Sandy (06:14:36) (in thread): > If you have had them solved completely Idon’tthink they will appear on the NCBI clean up page , however I feel@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldronwill have a better response

Esther Afuape (06:17:46) (in thread): > We were initially told to make posts here before we make edits (https://community-bioc.slack.com/archives/C04RATV9VCY/p1696970652284179?thread_ts=1696970336.230989&channel=C04RATV9VCY&message_ts=1696970652.284179) which was what I did. I was waiting to be given the go ahead to edit andthat’swhy they still appeared on the cleanup page. - Attachment: Attachment > There are other things you could do though if you want to contribute more, under the “TODO for reviewers” or “NCBI cleanup” in the help page on bugsigdb - just post here before making other edits to the wiki.

Peace Sandy (06:20:37) (in thread): > I think@Levi Waldrongave us the go ahead to solve NCBI clean up issues yesterday

Esther Afuape (06:21:28) (in thread): > That was around 10pm and I just saw it this morning.

Peace Sandy (06:27:33) (in thread): > Sorry about that

Hodan Abdirisak (06:31:29) (in thread): > Thanks@Svetlana Ugarcina Perovic:pray::pray::pray:

Nana (06:41:02) (in thread): > Added NCBIhttps://bugsigdb.org/Study_804/Experiment_1/Signature_1 - Attachment (BugSigDB): Study 804/Experiment 1/Signature 1

Nana (06:45:24): > Hello@Levi WaldronI need clarification on this for NCBI clean up: > This person work is mark as incomplete do I have the right to complete it:https://bugsigdb.org/Study_572/Experiment_1/Signature_1About this clostridia group xivClostridiumclusters XIVa and IV are groups of bacteria that have been known as major players in the human microbiome(Hold et al., 2002;Frank et al., 2007;Manson et al., 2008). The designation of these clusters was first proposed byCollins et al. 1994using 16S rRNA phylogeny. > > The genusClostridiumwas a dumping ground for species with certain phenotypes (e.g., anaerobic endospore-forming).Clostridiumclusters XIVa and IV do not represent formal nomenclature nor do they indicate a single taxa such as genus or family. Since 1994, Many of the originally designated species belonging toClostridiumclusters XIVa and IV have been reclassified into new genera. However, there are still misclassified, thereby holding old names,Clostridiumspecies in these clusters. > > Since the definition of these two clusters is not consistent in recent publications and somewhat ambiguous, it is highly recommended to avoid using these terms. There are still manyClostridiumspecies that require re-classification. Perhaps, the genome-based method can resolve this problem in the near future. > What happens to things like this (clostridia) Made some research and this and many more I saw. - Attachment (BugSigDB): Study 572/Experiment 1/Signature 1 - Attachment (PubMed): Assessment of microbial diversity in human colonic samples by 16S rDNA sequence analysis - PubMed > Abstract The bacterial species diversity of three colonic tissue samples from elderly people was investigated by sequence analysis of randomly cloned eubacterial 16S rDNA. The majority of sequences (87%) clustered within three bacterial groups: (1) Bacteroides; (2) low G+C content Gram-positives rel … - Attachment (PubMed): Molecular-phylogenetic characterization of microbial community imbalances in human inflammatory bowel diseases - PubMed > The two primary human inflammatory bowel diseases, Crohn’s disease (CD) and ulcerative colitis (UC), are idiopathic relapsing disorders characterized by chronic inflammation of the intestinal tract. Although several lines of reasoning suggest that gastrointestinal (GI) microbes influence inflammator … - Attachment (PubMed): The commensal microbiology of the gastrointestinal tract - PubMed > The gastrointestinal (GI) tract is a dynamic environment and therefore the stability of the commensal community, or microbiota, is under constant challenge. Microscopic observations have revealed that the majority of bacteria present in the GI tract are not detected using standard culturing techniqu … - Attachment (PubMed): The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations - PubMed > The 16S rRNA gene sequences of 34 named and unnamed clostridial strains were determined by PCR direct sequencing and were compared with more than 80 previously determined clostridial sequences and the previously published sequences of representative species of other low- G + C-content gram-positive …

Iram Jamshed (06:50:38) (in thread): > Hi<@UBNSEMS3S>@Svetlana Ugarcina Perovic, I wanted to ask in yesterday’s meeting itself but there was some problem with the network hence my voice couldn’t reach you guys. The paper I’m curating there is main contrast study on prospective cohort of about 7k individuals between**** non prevalent AFandprevalent AF (Experiment1). During follow up of 14 years around 5k individuals developed AF which they refer to asIncident AF. So they have also studied the contrast in microbiome betweenprevalent AFandcommon generaand also betweenIncident AFandcommon genera. So I believe this would constitute experiment 2 and experiment 3.Am I right? Additionally two sensitivity analyses were conducted, one introducing additional covariates and the other limiting the follow-up time.So these would constitute another experiments? There are other studies also using different computational models so what about them?** ****Could you please guide me on this. It would be really helpful!**** ****Link of paperhttps://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(23)00148-2/fulltext.**** **** - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Nana (06:53:57): > NCBI BLAST name:firmicutes, in this case what will be the ncbi Id since a lot of the firmicutes has some bacterium attached to its end @Levi Waldron:https://bugsigdb.org/Study_804/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 804/Experiment 1/Signature 2

Iram Jamshed (06:55:08) (in thread): > Thank you for the update!@Levi Waldron

Odigiri Great Alume (06:56:36) (in thread): > Ignoring will be best I think

Iram Jamshed (06:59:53) (in thread): > I noticed the same mitochondria confusion!:smile:

Odigiri Great Alume (07:07:06): > When curating my paper. I had no idea how to find missing Ncbi ID. So I added the numbers in front of the phyla (example actinomyces 02.) and recorded them as signatures. > > Afterwards I asked questions on what to do when the phyla appears orange after curating and@Levi WaldronClarified. > > I followed the link to the 2hrs video and went to “help” and corrected found the missing NCBI ID to my own work. > > I just wanted to ask if this counts as a contribution when recording my outreachy contribution:joy:

Peace Sandy (07:12:45) (in thread): > Thank You@Chioma Onyido

Karen254. Kingecha (07:14:53) (in thread): > :sweat_smile:I think it still counts as a contribution.

U1LCB8WEA (07:37:11) (in thread): > Yes it counts!:sweat_smile:nice work@Odigiri Great Alume

Odigiri Great Alume (07:37:55) (in thread): > Thank you sir:blush:

Peace Sandy (07:45:36) (in thread): > Yes@Iram Jamshedmitochondria are membrane-bound cell organelles

Odigiri Great Alume (07:58:53) (in thread): > Again,@Levi Waldronthis study had all signatures missing. I was able to find all the NCBI ID except for three . I searched google for their synonyms and verified them in the NCBI taxonomy browser to be the same as the phyla recorded in the work. I was able to update their ID. > > See image please. > I hope I have done the right thing.:grin:Please@Chioma Onyidocome look at the three I was unable to find their ID.:joy: - File (JPEG): IMG_20231013_125319_119.jpg - File (JPEG): IMG_20231013_125306_403.jpg

Chinwendu Enyinna (08:04:29) (in thread): > Well done@Odigiri Great Alume

Esther Afuape (08:24:49): > @Levi Waldron<@UBNSEMS3S>I markedhttps://bugsigdb.org/Study_567as reviewed. I have reviewed the paper and there are no additional changes to be made to the curation. - Attachment (BugSigDB): Study 567

U1LCB8WEA (08:26:20) (in thread): > Just Signature 1?

Hodan Abdirisak (08:33:15): > these fungus genera are present in my study as increased but when add my signature shows that “This taxon is potentially contaminant” i dont know why. - File (PNG): Screenshot 2023-10-13 045325.png

U1LCB8WEA (08:33:24) (in thread): > Fantasticthat’sa huge improvement!The TM6 is probably Candidatus Dependentiae bacterium, Taxonomy ID: 2030827

Hodan Abdirisak (08:36:02) (in thread): > @Odigiri Great Alumewell done and congrats i also gain more about NCBI

Esther Afuape (08:39:58) (in thread): > :sleepy::pray:is there a way to go about this?It’lllead to a loss of 3 contributions on my part@Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina Perovic

Hodan Abdirisak (08:41:30) (in thread): > <@U1LCB8WEA>can you help me

U1LCB8WEA (08:43:22) (in thread): > There’ssome explanation on the bugsigdb help page - it has been found in negative control samples before

Odigiri Great Alume (08:45:58) (in thread): > @Levi Waldronthank you. I will check to add it, if it hasn’t been added already.

Hodan Abdirisak (08:46:50) (in thread): > okey i am going to read help page

Esther Afuape (09:03:31) (in thread): > Yes, only signature 1. The only other data available is the abundant taxa present in the healthy control group.

Esther Afuape (09:05:13): > I created this second signature by mistake@Levi Waldron<@UBNSEMS3S>please help me to delete it:https://bugsigdb.org/Special:FormEdit/Signature/Study_567/Experiment_1/Signature_2?reload=1&returnto=Study%20567 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 567/Experiment 1/Signature 2

Chloe (09:11:40) (in thread): > @Odigiri Great Alumewell done

UBNSEMS3S (09:33:15) (in thread): > BugSigDB keeps track of your contributions as well so even if you forget to document one or two on Outreachy, we will have a record of it.

UBNSEMS3S (09:33:39) (in thread): > Great work.

UBNSEMS3S (09:34:19) (in thread): > Deleted.

UBNSEMS3S (09:35:03) (in thread): > And just to note that this is automatically added for certain taxa and not something to worry about in terms of your curation.

UBNSEMS3S (09:35:59) (in thread): > Can you post the full name of the taxon you’re trying to identify?

UBNSEMS3S (09:38:22) (in thread): > The clostridium clusters are ones that we have never been able to formally identify.

UBNSEMS3S (09:39:51) (in thread): > As the source you cited notes, many of these species have been reclassified but we don’t know 1) if the particular taxon identified in this paper has been reclassified and 2) if it has been reclassified which genus it has been reclassified into.

UBNSEMS3S (09:40:33) (in thread): > Clostridium clusters taxa cannot be reassigned, at least not without more information–which we don’t have.

Peace Sandy (09:42:04) (in thread): > Thank you so much for the clarification@C. Mirzayi (please do not tag this account)

Peace Sandy (09:42:53) (in thread): > Thank You for the clarification@C. Mirzayi (please do not tag this account)

Mildred Anashie (09:43:30): > Can the group name differ for the experiments being recorded?:thinking_face:

Nana (09:43:36) (in thread): > <@UBNSEMS3S>ok i did not edit it after reading up about clostridium clusters, but when i went back i noticed someone else just gave it NCID ID already. It appeared in two persons curated paper. All same name but ends in different ways like XIVa and IV etc.

UBNSEMS3S (09:45:53) (in thread): > Yeah I reverted one of the changes.

UBNSEMS3S (09:46:18) (in thread): > Yes. Group names and definitions can definitely vary for each experiment.

Mildred Anashie (09:46:52) (in thread): > Okay….Thank you

UBNSEMS3S (09:48:21) (in thread): > <@U1LCB8WEA>I think this might be the first time I’ve ever seen a Cox regression of differential abundance.

U1LCB8WEA (09:48:40) (in thread): > Oh wow me too!

Hodan Abdirisak (09:52:22) (in thread): > Thanks@C. Mirzayi (please do not tag this account)to clarify

Nana (09:54:31) (in thread): > <@UBNSEMS3S>thisfirmicutes, read about it, to know if it has been validated https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.022855-0 - Attachment (microbiologyresearch.org): List of new names and new combinations previously effectively, but not validly, published > The purpose of this announcement is to effect the valid publication of the following effectively published new names and new combinations under the procedure described in the Bacteriological Code (1990 Revision). Authors and other individuals wishing to have new names and/or combinations included in future lists should send three copies of the pertinent reprint or photocopies thereof, or an electronic copy of the published paper, to the IJSEM Editorial Office for confirmation that all of the other requirements for valid publication have been met. It is also a requirement of IJSEM and the ICSP that authors of new species, new subspecies and new combinations provide evidence that types are deposited in two recognized culture collections in two different countries. It should be noted that the date of valid publication of these new names and combinations is the date of publication of this list, not the date of the original publication of the names and combinations. The authors of the new names and combinations are as given below, and these authors' names will be included in the author index of the present issue. Inclusion of a name on these lists validates the publication of the name and thereby makes it available in bacteriological nomenclature. The inclusion of a name on this list is not to be construed as taxonomic acceptance of the taxon to which the name is applied. Indeed, some of these names may, in time, be shown to be synonyms, or the organisms may be transferred to another genus, thus necessitating the creation of a new combination.

UBNSEMS3S (09:55:29) (in thread): > @Iram JamshedTo answer your question, it looks like each of the tables you shared above can be curated. I don’t think fig 2 (the heatmap) can be curated and we don’t curate PCoA results. You may not have the option for the correct statistical test for table 4 so leave it blank for now. Also note that table 4’s model includes a lot of confounders controlled for.

Nana (09:58:23) (in thread): > <@UBNSEMS3S>there’s another place that you supposed to revert i think 3 changes with same name. I left everything about clostridium clusters because of its confusing nature. But someone went ahead to give it NCID Id . in one person curated paper it was one. in another person it was 3. please check because it is wrong to give them wrong NCID Id

Odigiri Great Alume (10:00:01) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Esther Afuape (10:02:52) (in thread): > Thank you

Nancy Wairimu Nyambura (10:09:23): > Hi everyone am Nancy glad to be here

Chioma Onyido (10:20:05) (in thread): > Hi Nancy:wave:Welcome to the community. > Kindly check the pinned:pushpin:messages to get started.

Hodan Abdirisak (10:23:30) (in thread): > Welcome@Nancy Wairimu Nyamburafollow as@Chioma Onyidotell you

Peace Sandy (10:24:39) (in thread): > Welcome Nancy

Peace Sandy (10:25:35) (in thread): > Get started herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Iram Jamshed (10:27:59) (in thread): > Thank you for your response!<@UBNSEMS3S>

UBNSEMS3S (10:42:27) (in thread): > Ok I will find them thanks for the heads up.

UBNSEMS3S (10:42:36) (in thread): > Welcome Nancy!

Nana (10:46:23) (in thread): > Urw

Chloe (11:26:01): > However, age showed a confounding effect on a few species in Egyptians, which includeHerbaspirillum, Prevotella* copri, Leptotrichia, Bacteroides, Prevotella stercorea,andPrevotella intermedia(Fig. 3S). Whereas in AAs and EAs, the species diversity was affected bysex differences. In AAs,Treponema socranskii, Alistipes onderdonkii, Selenomonas, Enterbacteriaceae, Akkermansia muciniphila, Bacteroides, Porphyromonas,andGemellaceaeand, in EAs,Schwartzia, Selenomonas, Enterobacteriaceae, Bacteroides, Flexispira, Porphyromonas, Faecalibacterium prausntitzii,*andBacteroidesshowed differences in diversity coefficients based on sex inmultivariate analyses(Fig. 3S). ………….this is the paragraph i have in the study and am asking my self where do i put the signitures they have written in it…??? because at the end of it , they said that they differences in diversity.

Esther Afuape (11:49:26): > @Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina PerovicI made a complaint on a thread (https://community-bioc.slack.com/archives/C04RATV9VCY/p1697191393132029) andI haven’tgotten a response.Please, kindly look into it. Thank you:pray: - Attachment: Attachment > Hello @Levi Waldron @UBNSEMS3S I made a thread of some of the NCBI clean up I solved (https://community-bioc.slack.com/archives/D05V6NZQ60L/p1697189800793359) and was awaiting permission to edit the changes. @Levi Waldron gave us the permission to go ahead and edit (that was last night over here) and I just saw them this morning. Another applicant has however made those edits unknown to her that I already had them solved. How do we go about this because I need to add the tasks to my contribution.

UBNSEMS3S (11:59:14) (in thread): > Hi@Esther AfuapeI’m sorry this happened. Please feel free to record these as contributions and I’ve made a note that you brought them to our attention.

UBNSEMS3S (11:59:50) (in thread): > I’d look at Figure 3S. That looks like the source of what they’re saying and is likely easier to curate than the text.

Esther Afuape (12:00:25) (in thread): > This is a huge relief:face_holding_back_tears:. Thank you so much<@UBNSEMS3S>

Chioma Onyido (12:27:05) (in thread): > Hi@Odigiri Great Alumeyou did a great job identifying all the missing taxa:clap:, sorry I couldn’t reply earlier, I was on the road. > So I did a google search on one of the you were unable to find “RsaHF231” and I found thatRsaHF231was first isolated and found in the intestines ofReticulitermes santonensis. :thinking_face:* Interestingly, it was also included among wikipedia’slist of taxa with candidatus (uncultured) status, *https://en.wikipedia.org/wiki/List_of_taxa_with_candidatus_status#cite_note-arbsilva-3‘SHA-109’ is enlisted here too. I guess it makes sense why you were unable to find it on ncbi taxonomy and uniprot.:thinking_face: - Attachment: List of taxa with candidatus status > This is a list of taxa with Candidatus status. For taxa not covered by this list, see also: > > the GenBank taxonomy for “effective” names as published; > the Candidatus Lists and LPSN for latinate names, some sanitized to match the Code.

Odigiri Great Alume (12:29:19) (in thread): > Any idea how to solve the other two?@Levi Waldronfound one out of the three which I already updated. So we left with two

U1LCB8WEA (12:32:07) (in thread): > With a Candidatus status bacterium?

U1LCB8WEA (12:32:22) (in thread): > Nice detective work!

Chioma Onyido (12:37:11) (in thread): > @Levi Waldrondo you mean they can be classified as Candidatus status bacteria?

Mildred Anashie (13:03:28): > @C. Mirzayi (please do not tag this account)@Levi WaldronPlease can this be curated, I’m not sure what the experiment is about:confused:

Mildred Anashie (13:04:40) (in thread): > Here’sthe footnote for the figureFig. 3. Bacterial taxa differentially abundant in CD4R low orCD4R high patient saliva. (a) Volcano plots of the log2foldchanges and log10 P values whenever comparing taxaabundances between CD4þ low (< 200 cells/ml) and CD4þhigh (CD4þ >200 cells/ml) samples. Large circles indicatetaxa with FDR significance less than 0.10. (b) Comparisonof ASV with 100% identity to Haemophilus parainfluenzaeidentified with differential abundance testing. Differencesbetween groups were considered statistically significant ifP less than 0.05 using the nonparametric Kruskal–Wallis Testcorrecting for multiple comparisons using the method ofBenjamini, Krieger and Yekutieli. P0.05, P0.01.FDR, false discovery rate.

Mildred Anashie (13:06:31) (in thread): > Sorry, Wrong image > > This is the right one - File (PNG): IMG_4746

Joan C. Chukwuemeka (13:42:14): > Hello all:wave:, > > Here’s a document from the BugSigDB help page that briefly explains each of the sections to be filled as we curate our studies. Hoping it helps someone.:slightly_smiling_face: - File (PDF): Curation Policy - BugSigDB.pdf

Chioma Onyido (13:46:47) (in thread): > Bookmarked.:pushpin:This will come in handy thank you very much@Joan C. Chukwuemeka

Mildred Anashie (13:53:22) (in thread): > Thankyou….Definitely important information

Onalo Deborah (13:58:23): > Thank you@Joan C. Chukwuemeka

Hodan Abdirisak (14:01:21): > In my study there is three fungus genera one of them is Valsa which is not have NCBI in the signature so can I do?

Esther Afuape (14:07:34) (in thread): > This is very useful!Thank you.

Fortune Nnamdi (14:07:59) (in thread): > Thanks Joan, this will be very helpful

Hodan Abdirisak (14:19:17) (in thread): > Thanks@Joan C. Chukwuemekafor helpful document

UBNSEMS3S (14:23:35) (in thread): > https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgiSearch here for valsa - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (14:25:57) (in thread): > @C. Mirzayi (please do not tag this account)please help me look at this:pray:

Hodan Abdirisak (14:28:08) (in thread): > I get it thanks@C. Mirzayi (please do not tag this account)you enlighten me more - File (JPEG): Screenshot_2023-10-13-21-27-12-802_com.android.chrome.jpg

Odigiri Great Alume (14:39:36) (in thread): > @Aleru Divinethank you For your help

Chiagoziem David (15:45:29) (in thread): > If it’s not also here(ncbi database)<@UBNSEMS3S>what do you do?

Paulina Boadiwaa Mensah (16:15:28) (in thread): > <@UBNSEMS3S>can I havehttps://bugsigdb.org/Study_814/Experiment_1deleted please? - Attachment (BugSigDB): Study 814/Experiment 1

Chioma Onyido (16:29:24) (in thread): > @Chiagoziem DavidThen Check uniprot,https://www.uniprot.org@Levi Waldronhas a video where he answered your question in great details.:+1:Here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696882979898809?thread_ts=1696881726.289569&channel=C04RATV9VCY&message_ts=1696882979.898809 - Attachment: Attachment > At one point I recorded a long video of doing detective work trying to resolve taxonomic nomenclature :sweat_smile: see https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID

Odigiri Great Alume (18:52:49) (in thread): > Gracias@Joan C. Chukwuemeka

2023-10-14

Onyewuchi Esther Chikamso (01:40:49) (in thread): > Does this mean any signature with the red symbol is missing?

Hodan Abdirisak (02:00:02) (in thread): > Okey,@Chioma Onyidothanks

Hodan Abdirisak (02:18:33): > Valsa genera is not excepted NCBI name which isascomycete fungior reference txid83174 it became red after when i put there, so else can i do - File (PNG): Screenshot 2023-10-13 231442.png

Hodan Abdirisak (02:19:12): > good saturday first all of you

Hodan Abdirisak (03:17:11): > Is it possible to miss that

Chioma Onyido (03:19:02) (in thread): > Hi@Hodan Abdirisakhave you tried copying the ID itself and pasting? If you copy the ID, then itshouldn’tbe red.

Chioma Onyido (03:19:28) (in thread): > Copy and paste83174

Chioma Onyido (03:21:03) (in thread): > @Onyewuchi Esther ChikamsoYeah.:sweat_smile:

Hodan Abdirisak (03:24:36) (in thread): > Yeah, it works now thank you@Chioma Onyido

Chioma Onyido (03:25:25) (in thread): > @Levi WaldronI am not sure what you meant by “with a Candidatus status bacterium?”, did you mean they can be classified as Candidatus status bacteria?

Hodan Abdirisak (03:25:38) (in thread): > Yeah, it means that name is missing so it needs to recorrect

Chioma Onyido (03:26:24) (in thread): > Yaaay!:smile:

Hodan Abdirisak (03:27:50) (in thread): > now i am completed my experiment what is the next - File (PNG): Screenshot 2023-10-14 002618.png

Hodan Abdirisak (03:28:25) (in thread): > Can I press needs review

Nwajei Edgar (04:01:16) (in thread): > Very useful thank you

Nana (05:00:33) (in thread): > @Hodan Abdirisakcopy your experiment url and to GitHub same place assigned to you. Tag our mentors write needs review and paste the url. Then go to outreachy website and record it

Onyewuchi Esther Chikamso (05:10:30): > Good day everyone,@Svetlana Ugarcina Perovic@Levi Waldron@C. Mirzayi (please do not tag this account)I am currently curating (add experiments) for study I found that was incompletehttps://bugsigdb.org/Study_778I have added an experiment and I’m currently adding signatures - Attachment (BugSigDB): Study 778

Hodan Abdirisak (05:14:34) (in thread): > Thanks,@Nanafor your guidance

Hodan Abdirisak (05:16:03) (in thread): - File (PNG): Screenshot 2023-10-14 021532.png

Hodan Abdirisak (05:17:46) (in thread): > I press the that record your contribution next to final application deadline

Chioma Onyido (05:25:54): > Beautiful weekend to everyone!:wave:I hope we’re all having a restful and pleasant weekend.:blush:<@U1LCB8WEA><@UBNSEMS3S>I identified an ‘incomplete curation’ with no experiments among the list of NCBI clean ups, and I’m currently making some edits and trying to finish curating the paper,bugsigdb.org/Study_768My questions, > 1. for the sequencing platform/ method used, it wasn’t mentioned in the paper but I was directed to another paper where I believe the methodology was discussed in more details but I can’t access the paper, can I get help with this please? The identifier is:doi.10.1136/gutjnl-2022-327156 > 2. I’m not sure about the data transformation used here, and for quality sakes I want to avoid assuming. Maslin2 was used to report the differential abundant taxa and since it’s a linear model, which means it can be classified as ‘linear regression’ understatistical test. > From<@UBNSEMS3S>’s explanation on data transformation yesterday, this is supposed to beraw counts under data transformation, however I don’t see anywhere that is reported in the paper and the term ‘relative abundances’ was used more. Even with that, I don’t see where data transformation was explicitly stated in the paper, > I’m sorry if this seems like a repetition but to be sure, is it still okay to report this as raw counts? - Attachment (Gut): Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer > Objective The incidence of early-onset colorectal cancer (EO-CRC) is steadily increasing. Here, we aimed to characterise the interactions between gut microbiome, metabolites and microbial enzymes in EO-CRC patients and evaluate their potential as non-invasive biomarkers for EO-CRC. > > Design We performed metagenomic and metabolomic analyses, identified multiomics markers and constructed CRC classifiers for the discovery cohort with 130 late-onset CRC (LO-CRC), 114 EO-CRC subjects and age-matched healthy controls (97 LO-Control and 100 EO-Control). An independent cohort of 38 LO-CRC, 24 EO-CRC, 22 LO-Controls and 24 EO-Controls was analysed to validate the results. > > Results Compared with controls, reduced alpha-diversity was apparent in both, LO-CRC and EO-CRC subjects. Although common variations existed, integrative analyses identified distinct microbiome–metabolome associations in LO-CRC and EO-CRC. Fusobacterium nucleatum enrichment and short-chain fatty acid depletion, including reduced microbial GABA biosynthesis and a shift in acetate/acetaldehyde metabolism towards acetyl-CoA production characterises LO-CRC. In comparison, multiomics signatures of EO-CRC tended to be associated with enriched Flavonifractor plauti and increased tryptophan, bile acid and choline metabolism. Notably, elevated red meat intake-related species, choline metabolites and KEGG orthology (KO) pldB and cbh gene axis may be potential tumour stimulators in EO-CRC. The predictive model based on metagenomic, metabolomic and KO gene markers achieved a powerful classification performance for distinguishing EO-CRC from controls. > > Conclusion Our large-sample multiomics data suggest that altered microbiome–metabolome interplay helps explain the pathogenesis of EO-CRC and LO-CRC. The potential of microbiome-derived biomarkers as promising non-invasive tools could be used for the accurate detection and distinction of individuals with EO-CRC. > > All data relevant to the study are included in the article or uploaded as online supplemental information.

Nana (05:30:41) (in thread): > Yes.. Record your contribution…fill it accordingly but do not fill end date until they review it

Nana (05:31:34) (in thread): > Then paste your curated link…in the link option

Hodan Abdirisak (05:32:30) (in thread): > Curated link means the link of my study in GitHub issue

Nana (05:34:50) (in thread): > The add to study link. The link of curated paper you worked on

Hodan Abdirisak (05:36:07) (in thread): > Thanks@Nanafor your clarification

Nana (05:48:01) (in thread): > @Hodan Abdirisakurw

Hodan Abdirisak (05:48:45): > @Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)<@U1LCB8WEA>after when i completed study i did this NCBI Clean uphttps://bugsigdb.org/Study_779/Experiment_2/Signature_1 - Attachment (BugSigDB): Study 779/Experiment 2/Signature 1 - File (PNG): Screenshot 2023-10-14 001113.png - File (PNG): Screenshot 2023-10-13 234228.png

Mildred Anashie (06:55:16): > Hi<@UBNSEMS3S>@Levi WaldronThis is talking about relative abundance of the taxa and not differential abundance, I thinkthere’sa signature here….Is it okay to curate this as experiment 1? > > Similar to previous reports, at baseline the most abundantly detected bacterial phyla in the salivary microbiome were Bacteroidetes, Firmicutes and Proteobacteria, with lower relative abun- dance of Fusobacteria, Spirochaetes, Actinobacteria, and Ternericutes (Fig. 1a). Following 24 weeks of ART, the dominant phyla represented in the saliva remained similar to that found at baseline (Fig. 1b). - File (PNG): IMG_4764

Esther Afuape (07:02:18) (in thread): > I’d like to see the answer to the data transformation question too.In the article was assigned to curate, the relative abundance was measured but it was a linear model so I went with relative abundance for the transformation but raw counts are used for linear models:thinking_face:

Chiagoziem David (07:06:09) (in thread): > Alright thanks

Mildred Anashie (07:09:00) (in thread): > From this figure 2 I noticed three experiments here…1. Comparing ASV with with 91% identity to Muribaculum intestinale at baseline and 100% ID to Treponema lecithinolyticum at week 24. > > My question is which organism is increased and Which is decreased at baseline and at week 24, from the phylum displayed by the side > > 2. I also noticed they could be 2 other experiments in B and C…Can it be curated? And how do I curate this?:pray:@C. Mirzayi (please do not tag this account)@Levi Waldron - File (JPEG): 8e10dc2a-6c32-448d-bae6-4d45f27a70a7

Odigiri Great Alume (07:09:44) (in thread): > I think there’s an experiment here in figure 1.@C. Mirzayi (please do not tag this account)@Levi Waldron

Mildred Anashie (07:34:52): > Also in figure 3@Odigiri Great Alume@Chioma Onyidoand I thinkthere’san experiment here, but we are all confused:satisfied:on if it can be curated and ifthere’san increase or decrease, sinceit’sjust one taxa that was mentioned@Levi Waldron<@UBNSEMS3S>:pray: - File (JPEG): 32f654d1-4dad-401c-9ce8-5a1394dfe74d

Odigiri Great Alume (07:36:04): > Please:pleading_face:@Levi Waldroncome and save the day here please:sweat_smile:

Esther Afuape (07:49:10): > Hello everyoneI’mworking onhttps://bugsigdb.org/Study_717.It’son the incomplete list - Attachment (BugSigDB): Study 717

Chioma Onyido (08:11:40) (in thread): > From thisfigure 2b and c, from the box plots I can tell that there’s a decrease in abundance for M. instestinale at 24weeks compared to the baseline > And an increase in T. lecithinolyticum at 24 weeks.Figure 2a:Also it states somewhere in your paper that larger circles are those that are significant. So if we’re following that, that means (fig 2a) M. intestinale was increased at Baseline and T. lecithinolyticym was increased at 24 weeks. > > Which basically corroborates figure 2b and c,:woman-shrugging:

Chioma Onyido (08:13:36) (in thread): > And M. intestinale belongs to the phylum Bacteriodetes while T. lecithinolyticum belongs to Spirochates.:thinking_face:

Chiagoziem David (08:18:12): > https://bugsigdb.org/Study_804, could you please help me delete the second experiment<@UBNSEMS3S>, thank you. - Attachment (BugSigDB): Study 804

Chioma Onyido (08:20:21) (in thread): > :sweat_smile:I think there’s another experiment here because they compared CD4 low and high at Baseline and at 24 weeks.:eyes:

Nana (09:43:10) (in thread): > <@UBNSEMS3S>here is the link to find that 3 that someone gave NCBI ID > Clostridia clusters IV, XIVa, and XVIII > (https://bugsigdb.org/Study_217/Experiment_2/Signature_1) > Microarray analysis reveals marked intestinal microbiota aberrancy in infants having eczema compared to healthy children in at-risk for atopic disease/Experiment 2/Signature 1 - Attachment (BugSigDB): Study 217/Experiment 2/Signature 1

Nana (09:46:10): > <@UBNSEMS3S>@Levi Waldronyou help me delete this:https://bugsigdb.org/Study_823(shows no experiment) I saw my work saying show no experiment added. but i have completed the experiment and the completed one does not have the same link. so please delete this one - Attachment (BugSigDB): Study 823

Esther Afuape (11:26:41): > Hi Everyone. In the incomplete curation I’m working on, they contrasted Parkinson disease phenotypes; tremor dominant (TD) and postural instability and gait difficulty (PIGD). ANCOM test detected no differentially abundant families or genera, and only 2 OTUs at baseline while DESeq2 detected longer lists of taxa. The data is in the supplementary results (table S8) which I have attached below.@Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina PerovicIt was stated that in all comparisons, p-values <0.05 or adjusted p-values <0.05 were considered significant. Does this mean that any taxa with a p-value less than 0.05 shouldn’t be considered significant and should not be curated? > > Now the problem is that I’m not sure about how to know what taxa is decreasing or increasing for the contrast between TD and PIGD in the supplementary result. - File (PDF): supplementary.parkinson

Sinmi Adesanya (11:31:05) (in thread): > Thank you, Joan. This is super helpful!

Onyewuchi Esther Chikamso (11:36:20) (in thread): > To know the taxa that is increasing or decreasing, check the table S6 C, in the log2fold change, the figures with minus shows a decrease whereas the ones without the minus shows increase. I hope this helps

Esther Afuape (11:39:37) (in thread): > Table S6 is for disease progression…the one I need is for the phenotype.That’sS8

Onyewuchi Esther Chikamso (11:41:00): > Hi@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina PerovicFrom the study I am curatinghttps://link.springer.com/article/10.1007/s10620-020-06415-y, there is something I would like clarity on. In the statistical analysis, it mentioned LEfse, manny-white and krusal-wallis test as the statistical test. Do I put them all in the “statistical test field” - Attachment (SpringerLink): A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients > Digestive Diseases and Sciences - How gastric cancer (GC) incidence is associated with changes in the gastric microbiome has not been firmly established. The present study therefore aims to… - File (PNG): Screenshot_20231014-162639.png

Onyewuchi Esther Chikamso (11:42:44) (in thread): > Check table S8 B

Onyewuchi Esther Chikamso (11:45:10) (in thread): > @Chioma Onyidocan you please point me to the explanation on data transformation by@C. Mirzayi (please do not tag this account)

Esther Afuape (11:47:21) (in thread): > Yeah the problem is that Idon’tknow which one is decreasing or increasing. Is it any one with a p-value less than 0.05? Or is the p-value meant to be up to 0.05 to be significant?

Onyewuchi Esther Chikamso (11:49:18) (in thread): > From what I said earlier, the ones with the minus sign (eg -0.09) on the log2fold column is decreasing, whereas the ones without the minus sign is increasing

Esther Afuape (11:50:00) (in thread): > Thank youuu

Onyewuchi Esther Chikamso (11:51:52) (in thread): > You’re welcome

Chioma Onyido (11:57:20) (in thread): > Hi@Onyewuchi Esther ChikamsoLefse was used to identify the differential abundant taxa. I thinkthat’swhat should be reported.

Chioma Onyido (12:00:06) (in thread): > Here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697145085673689?thread_ts=1697141457.022309&channel=C04RATV9VCY&message_ts=1697145085.673689 - Attachment: Attachment > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio -> Rare. ANCOM > > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

Nana (13:07:39): > <!here>I am working onhttps://bugsigdb.org/Study_503It’s on the incomplete list - Attachment (BugSigDB): Study 503

U1LCB8WEA (13:17:35) (in thread): > I agree - put the test that was used to identify the signatures

U02CNMR4YEA (13:21:30): > Happy Saturday! In one of the papers I am curating, there is a statement that is curious to me as it implies a difference in Shannon Diversity Index with p value=0.56 [“…the microbial diversity in ATD was lower than mixed dry eye (p value= 0.056). However, the difference in diversity was insignificant between MGD and mixed dry eye (p value =0.65)…”]. Would I curate this as the ATD having a decreased Shannon Diversity Index compared to the mixed? They don’t specifically say at what value they set significance but did say it was analyzed by 2-sided Wilcoxan’s rank sum. Thank you in advance for any help:blush:.

U1LCB8WEA (13:25:19) (in thread): > .056 not .56 right?But yes, if the author say it is decreased then record it as such.Did they mention a threshold for differential abundance?Maybe it was .1 for everything.

U02CNMR4YEA (13:27:29): > Yep-0.56. They didn’t mention a threshold. Okay- I will curate it as decreased. THANK YOU!:blush:

U1LCB8WEA (13:28:14): > But you said .056 in your quote from the text?

U1LCB8WEA (14:08:27) (in thread): > Idon’tsee any individual differentially abundant taxa reported there

Onyewuchi Esther Chikamso (14:10:32): > Please@Levi Waldron@Chloe@Svetlana Ugarcina PerovicI noticed there are 3 different figures with different comparison > 1. Cladogram representation of the gastric microbiota taxa associated with superfcial gastritis and gastric cancer > 2. Diferences in functional compositions between the superfcial gastritis and gastric cancer using KO by LEfSe analysis (LDA scores > 3.0). > 3. Non-tumor and tumor comparison > My question is, do I need to 1. create 3 different experiments. 2. Would all the experiment (if there would be) have the values in the field and it’s only when I create signatures that values I enter would be different - File (PNG): Screenshot_20231014-190408.png - File (PNG): Screenshot_20231014-190428.png - File (PNG): Screenshot_20231014-190446.png

Onyewuchi Esther Chikamso (14:13:25): > Please is there any material I can watch or read to know how to remove this from an experiment - File (JPEG): IMG_20231014_191213.jpg

Chioma Onyido (14:14:40) (in thread): > You mean the confounders controlled for? > Ifit’sthat, I thinkit’sto click edit experiment.

Nana (14:26:36): > <@UBNSEMS3S>Please help me delete the experiment 2 ofhttps://bugsigdb.org/Study_503I am re-working on it. - Attachment (BugSigDB): Study 503

U1LCB8WEA (14:27:58) (in thread): > Done

Mildred Anashie (14:33:43) (in thread): > Okay…This means the experimentcan’tbe curated?

Onyewuchi Esther Chikamso (14:35:03) (in thread): > I mean how do I search for the correct “allowed value” for that particular value. Sometimes it might be in the study, but the term in the allowed value might not be the same as the one in the study. I dunno if you get what I mean

U1LCB8WEA (14:40:41) (in thread): > They must have reported on some differential abundance or alpha diversity results somewhere…

U1LCB8WEA (14:43:56) (in thread): > Which study? You should choose the most relevant available EFO term name, and ask if there is one missing in the allowed values.By the way did you see my comments on your talk page?

Mildred Anashie (14:44:51) (in thread): > This is what was said about that - File (JPEG): IMG_4776

Mildred Anashie (14:45:30) (in thread): > Please I asked some other questions…I’lltag you to them again > > Thank you:pray:

Mildred Anashie (14:46:44) (in thread): > @Levi Waldron

Mildred Anashie (14:46:58) (in thread): > @Levi Waldron

Onyewuchi Esther Chikamso (14:47:12) (in thread): > I did. I dropped replies too

Onyewuchi Esther Chikamso (14:50:04) (in thread): > This is the link to the studyhttps://link.springer.com/article/10.1007/s10620-020-06415-y. But it’s the “choose relevant available EFO term name” I don’t quite understand. I’m sorry - Attachment (SpringerLink): A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients > Digestive Diseases and Sciences - How gastric cancer (GC) incidence is associated with changes in the gastric microbiome has not been firmly established. The present study therefore aims to…

Onyewuchi Esther Chikamso (14:51:18) (in thread): > Please can you help me with this@C. Mirzayi (please do not tag this account)@Levi Waldron

Nana (15:14:17) (in thread): > Seen thanks

Paulina Boadiwaa Mensah (15:44:32): > <@U1LCB8WEA><@UBNSEMS3S>can you please give me feedback on this? - Attachment: Attachment > @Svetlana Ugarcina Perovic @U1LCB8WEA @UBNSEMS3S please I am editing Study_814 which I was assigned to curate. I am trying to delete Experiment 1 so I can re-arrange the order of the Experiments according to the order of the Objectives in the study. Can someone with Administrator access delete it for me please? > > https://bugsigdb.org/Study_814/Experiment_1

U1LCB8WEA (15:52:31) (in thread): > There is a lot of data entry here already,Idon’tthink it should be deleted just to change the order of experiments - the order isn’t important anyways.

U1LCB8WEA (15:57:36) (in thread): > noting that the groups are similarisn’tthe same as matching on them, which would be more precise.I was tempted to count it anyways at some point but I think<@UBNSEMS3S>pointed out that “similar” is too subjective, and non-significant differences too dependent on sample size.

U1LCB8WEA (15:58:05) (in thread): > There is a lot of data entry here already, I don’t think it should be deleted just to change the order of experiments - the order isn’t important anyways.

U1LCB8WEA (16:01:16) (in thread): > 1. It’snot clear to me from this description whether they did a contrast or not, and 2. Wedon’trecord functional KOs. 3. definitely looks like an experiment

Chioma Onyido (16:08:01) (in thread): > @Levi Waldronplease I need your help here:pray:

Levi Waldron (16:14:11) (in thread): > The link on bugsigdb? The first of those should be correct, except for the capitalization.The second has to be the name, not EFO ID.

Paulina Boadiwaa Mensah (16:22:42) (in thread): > Alright. Thank you for the clarification.

Onyewuchi Esther Chikamso (16:43:27) (in thread): > Thank you:blush:

U1LCB8WEA (16:43:56) (in thread): > You’rewelcome!

Odigiri Great Alume (17:38:28) (in thread): > @Chioma Onyidoso you think there is one experiment rather than 3 experiments in figure 2?

Chioma Onyido (17:50:45) (in thread): > Yes for figure 2. I think figures 2a,b and c are talking about the same thing.

Chioma Onyido (17:52:33) (in thread): > For figure 1,Can’t find any significant differences,:sweat_smile:not sure how to go about curating figure 1.

Chioma Onyido (17:56:39) (in thread): > @Odigiri Great AlumeWhile we wait for the mentors to clarify, Can we discuss why you think otherwise?:thinking_face:

Odigiri Great Alume (19:20:22) (in thread): > Looking at figure 2a. I think there’s been a comparison between M. Intestinale at 91% at base line and T. Lecithinolyticum at 100% at 24 weeks > Looking at 2b and c. It seems the abundance of each of these taxa were compared both at baseline and week 24. > > That is, abundance of M. Intestinale at base line and week 24. Also, abundance of T.L at baseline and week 24.

Odigiri Great Alume (19:28:30) (in thread): > @Chioma Onyidobut I do think there’s an experiment in fig 1. I say so because it talks about comparing effect of ART at baseline and week 24 and they took into cognizance that after the treatment, there were increase in some bacteria and decrease in others

Peace Sandy (19:33:15) (in thread): > Look for the contrast in the research paper > The figures or diagrams sometimes come in handy

Chioma Onyido (20:56:26) (in thread): > Okay I think I see your perspective on figure 2 now, > Are you saying you would curate as separate experiments meaning; > > Experiment 1: Group 0 (Baseline) vs Week 24 (group 1) > Increase signature: T. lecithi…Decrease: M. intestinale. > > Then > Experiment 2: > increase signature: M. intestinale.. (for group 0) > Decrease signature: T. lecithini…(for group 1)

Chioma Onyido (20:58:00) (in thread): > Hmmm If this is what you’re saying, I think there’s no need to curate as separate experiments since an increase of say M. intestinale at baseline means a decrease for 24 weeks, and so on.. I don’t know if you get me but I feel it’s redundant?:thinking_face:

Chioma Onyido (21:21:04) (in thread): > For fig. 1, I agree, > However here’s an excerpt from the paper > > “Similar to previous reports, at baseline the most abundantly detected bacterial phyla in the salivary microbiome were Bacteroidetes, Firmicutes and Proteobacteria, with lower relative abundance of Fusobacteria, Spirochaetes, Actinobacteria, and Ternericutes (Fig. 1a). Following 24 weeks of ART, the dominant phyla represented in the saliva ******remained similar to that found at baseline *****(Fig. 1b). There was no significant difference in beta diversity whenever comparing baseline samples to those collected following 24 weeks of ART (Fig. 1c, ADONIS test P value: 0.744)… > Similarly, alpha diversity (richness and Shannon diversity) was not significantly different between samples collected at baseline and samples collected following 24 weeks of ART (Figure S3A&B, https://links.lwcom/QAD / B252)*” > > Since the signatures detected in both baseline and 24 weeks are ‘similar’, with no significant difference. I’m not saying it can’t be curated but how would we curate this?:thinking_face:

U1LCB8WEA (22:22:47) (in thread): > There are several things reported changed in that screenshot text that you can record

U1LCB8WEA (22:25:27) (in thread): > Thank you for helping@Onyewuchi Esther Chikamso!

U1LCB8WEA (22:27:44) (in thread): > BTW pvalues less than .05 would be in the signature,greater than .05 not. pvalue is the probability of differential abundance of that size occurring by chance if in truth there is no difference in abundance between the groups.

U1LCB8WEA (22:29:09) (in thread): > Deleted

U1LCB8WEA (22:30:14) (in thread): > Second experiment deleted

U1LCB8WEA (22:35:05) (in thread): > There’san experiment there, with two named differentially abundant species, one increased and the other decreased at week 24.

U1LCB8WEA (22:38:58) (in thread): > Not from the phylum by the side but from whetherthey’reon the left or right of a, and increased or decreased in b/c. Theydon’tdescribe where more than one experiment,just give a more detailed view in bc on two top “hits” - smallest pvalues. Remember, experiments are defined by what is being contrasted, not by different ways of showing the results.

U1LCB8WEA (22:39:44) (in thread): > Nice work!

U1LCB8WEA (22:42:23) (in thread): > If they say they used relative abundance then record what they said,it’sperfectly possible to fit a linear model also to relative abundance

U1LCB8WEA (22:47:43) (in thread): > The paywalled article - File (PDF): 516b4039-d857-4354-a541-7a98c74df1c5

U1LCB8WEA (22:50:11) (in thread): > Why all the “not specified “ In Experiment 2?

U1LCB8WEA (22:55:04) (in thread): > But youdidn’treview experiment 1 or the study?

U1LCB8WEA (23:02:20) (in thread): > @NanaI’mcomfortable with you rolling back an incorrect edit that you found.

Nana (23:13:15) (in thread): > Thanks

2023-10-15

Nana (00:51:58) (in thread): > @Levi WaldronThank you.

Mildred Anashie (00:57:50) (in thread): > If I understand you, there are no differential abundant taxas to report but other things can be reported. So an experiment can be reported without signatures?

Mildred Anashie (01:24:54) (in thread): > It talks about alpha diversity being unchanged but abundance being detected…Are you saying even though there was detection of abundance, since the diversity was not significant weshouldn’tcurate? > > Because I think it can be curated stating the signatures identified as increase and decrease and alpha diversity stated as unchanged?

Mildred Anashie (01:38:06) (in thread): > Figure 2 seems clearer from what@Levi Waldronis saying a,b and c are talking about the same thing but reported differently…

Hodan Abdirisak (02:07:05) (in thread): > I don’t know why? I see in NCBi clean up then I fix

Chioma Onyido (02:11:06) (in thread): > Thank you so much<@U1LCB8WEA>:blush:

Chioma Onyido (02:16:46) (in thread): > @Mildred Anashie, yes according towhat hewrote figures 2a,b and cshouldn’tbe curated as separate experiments. > “…experiments are defined by what is being contrasted not by different ways of showing the results”.

Chioma Onyido (02:17:59) (in thread): > So thanks to<@U1LCB8WEA>we’re clear on figure 2 now:clap:Figure 1 tho?:thinking_face:

Sinmi Adesanya (05:20:46): > Hello, everyone, and happy Sunday! I hope you don’t mind me reaching out on the weekend, but I could really use some guidance on the taxa I’m curating for my study. The paper I’m working with has organized results in three tables, each corresponding to a different taxonomic rank (phylum, genus, and species). In the attached PDF from@Joan C. Chukwuemeka, we were instructed to enter only the highest taxonomic rank mentioned in the paper. > > For this particular paper, I’ve selected “Phylum” as it’s the highest rank, but I’m uncertain about how to interpret the abundance levels of the microbiomes from the tables. To gain clarity, I usedonlythe information in the paper (I’ve included text and images from the tables below). I want to make sure I’m on the right track and, if possible, receive some guidance on reading the abundance data from the tables so I can confirm the information in the paper. This is the final step before marking my signature sections as complete, so any assistance would be greatly appreciated. Thank you!<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina Perovic - File (PNG): Screen Shot 2023-10-15 at 10.14.28 AM.png - File (PNG): Screen Shot 2023-10-15 at 10.14.46 AM.png

U1LCB8WEA (05:21:59) (in thread): > You’vestudied this paper more closely than me but figure 1 looks like the same baseline vs week 24 no? But without reporting differential abundance of individual taxa.

U1LCB8WEA (05:24:01) (in thread): > This sounds like a misunderstanding because you should record any taxonomic rank that is reported as differentially abundant

U1LCB8WEA (05:27:25) (in thread): > What they refer to as “adjusted p value” in the text is “qval” in the tables

Sinmi Adesanya (05:30:12) (in thread): > Thank you for the feedback, Levi.

Odigiri Great Alume (05:42:10) (in thread): > @Chioma OnyidoI see what you mean. But there could still be an increase and decrease in taxas even tho it might not be a ” significant increase” > > I don’t know if this makes sense. > Just something I picked up from biostatistics class .:laughing:

Odigiri Great Alume (05:44:59) (in thread): > @Levi Waldronwhile figure 1. Didn’t report differential abundance, it did report relative abundance of these taxa. > Does this mean that there is a difference between relative abundance and differential abundance? > And relative abundance can be recorded as signatures in a experiments?

Chioma Onyido (05:45:24) (in thread): > Yes<@U1LCB8WEA>the paper reported that the increase and decrease is similar, as in the same taxa at both baseline and 24 weeks.

Chioma Onyido (05:49:47) (in thread): > @Odigiri Great AlumeAccording to figure 1a and the excerpt: > Baseline: Bacteriodetes, firmicutes and Proteobacteria (increase)Decrease(fusobacteria, spirochates, actino.. and ternericutes. > Same for 24 weeks > > Say you want to curate figure 1, how would you curate this?

Odigiri Great Alume (05:55:43) (in thread): > Wait, doesn’t this mean that…. > At baseline( before the samples received ART) bacteriodetes, firmicutes, and proteobacteria taxa showed an increase. Also at 24 weeks (After samples received ART) Fuso, Spiro, terner and actino Showed to be less abundant (decreased)?@Chioma Onyido

Chioma Onyido (05:58:38) (in thread): > Yes they both have similar signatures. Both at Baseline and post treatment.

Odigiri Great Alume (06:00:01) (in thread): > I’m saying this because the samples were a paired sample. And hence I thought it make sense to record increase taxa for samples at baseline and decrease at 24weeks showing the effect of the ART Treatment on the samples. > > Uhmmmm:thinking_face:

Chioma Onyido (06:03:32) (in thread): > @Odigiri Great AlumeI getyour perspective and I thought the same at first butlet’slook at it this way, If the salivary microbiome remained the sameboth before and after ART treatment, should this be curated? > Rememberwe’resupposed to curate ’differentially abundant taxa’.

Sinmi Adesanya (06:09:47) (in thread): > @Chioma Onyidohere

Odigiri Great Alume (06:10:22) (in thread): > @Chioma Onyidothis brings me to the question on the difference between relative abundance and differential abundance. > Maybe@Levi Waldroncan clarify. > > On your question on “if the salivary microbiome remained the same ******both before and after ART treatment*******, should this be curated? > Remember we’re supposed to curate ‘*******differentially abundant taxa’. > **I really do not have an accurate answer to be honest. But I do think however that, there was increase and decrease in this taxa at diff points (before and after) however it wasn’t significant. > > As to whether we can curate, I think@Levi Waldronand@C. Mirzayi (please do not tag this account)will be in the position to give definite answers.:sweat_smile:

Chioma Onyido (06:15:58) (in thread): > I’mcurious about this too.:thinking_face:

Chioma Onyido (07:14:20) (in thread): > I think I figured it out. Your adjusted pvalue is < 0.05, and following what<@U1LCB8WEA>if you checkthe “qval” column, you’d see that those highlighted in green are those < 0.05. > I think those are what you should curate.

Chioma Onyido (07:28:40) (in thread): > If onlyallpapers can highlightit like this to make it easier to filter.:sneezing_face::sweat_smile:

Sinmi Adesanya (07:29:36) (in thread): > Thank you so much, Chioma!

U1LCB8WEA (07:33:42) (in thread): > This experiment does name at least two differentially abundant taxa (although not in figure 1). In an experiment with only non-significant results you could still report alpha diversity unchanged and no signatures under the experiment.

Odigiri Great Alume (07:36:28) (in thread): > @Levi Waldronthank you > This makes it clear

Chioma Onyido (07:37:53) (in thread): > Clearer now. Thank you<@U1LCB8WEA>Also sorry for disturbing your weekend.:sweat_smile:

U1LCB8WEA (07:38:25) (in thread): > No problem:wink:

Mildred Anashie (08:57:32) (in thread): > Thank you so much@Levi Waldronfor the clarification and your time@Odigiri Great Alumeand@Chioma OnyidoI really appreciate your help with this:pray:

Odigiri Great Alume (09:46:42) (in thread): > @Levi Waldron:blush:

Peace Sandy (10:33:03) (in thread): > Your paper really made it easy to see the adjusted value

Joan C. Chukwuemeka (10:43:06): > Good day all, > > I need help here: > > Trying to determine the experiment groups and microbial signature for the condition of interest (Spontaneous Preterm Birth) has not been sorted yet. I see a possibility of one experiment group, However, some few sentences seems to have comparisons. But, then I came across a phrase which seems like the study had no distinct microbial signatures that is curatable based on BugSigDB curation need. > > Here it is:A distinct variation in both the taxonomic and functional potential of the preterm linked vaginal microbiome reinforces the concept of a microbiome role in PTB. ******However, the inability of both this study and others to determine a strict signature******* highlights the need for much larger controlled studies with the ability to examine confounding factors like ethnicity, biogeography, and predetermined risk factors using high-resolution, strain level analysis. <@UBNSEMS3S> <@U1LCB8WEA> @Svetlana Ugarcina Perovic *would it be feasible to help me scan through the article to know the number of potential experiment groups with microbial signature for the condition of interest (Spontaneous Preterm Birth) that can be curated? If so, then I dig deeper, If not, I could move to other ones. > > Article:https://github.com/waldronlab/BugSigDBcuration/issues/76 - Attachment: #76 Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth > Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily et al. – npj Biofilms and Microbiomes 2020
> DOI: 10.1038/s41522-020-00162-8
> https://www.nature.com/articles/s41522-020-00162-8

Sinmi Adesanya (10:45:01) (in thread): > Yes. Levi and Chioma shed more light and its much clearer to me now. Thanks a bunch guys!

Peace Sandy (10:45:41) (in thread): > Glad you got help

Peace Sandy (10:46:29) (in thread): > @Joan C. Chukwuemekacan you share the link to your article, let me take a look

Sinmi Adesanya (10:47:00) (in thread): > Thanks!

Peace Sandy (10:50:16): > @Mariam Taleebyou can get started herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Joan C. Chukwuemeka (10:54:53) (in thread): > @Peace Sandyhere is ithttps://github.com/waldronlab/BugSigDBcuration/issues/76https://www.nature.com/articles/s41522-020-00162-8 - Attachment (Nature): Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth > npj Biofilms and Microbiomes - Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth

Peace Sandy (11:44:50) (in thread): > Okay

Peace Sandy (11:45:54): > Can antibiotic exclusion be recorded indays let’ssay 14days or so, if is written as 30days in the article should it be converted to 1 month@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron

Esther Afuape (12:42:31) (in thread): > Thank you@Levi Waldrongot it!

U02CNMR4YEA (12:53:19) (in thread): > My apologies - it was 0.056. This paper is challenging because they used Principal coordinates analysis to focus on the species seen in greater than 10% of the ocular microbiome in DED patients. Each rereading, I see something different:grinning:. Thank you!

Chiagoziem David (12:57:19) (in thread): > Does it matter what convention you use to record duration (at least the basic day and month)

Chiagoziem David (12:57:49) (in thread): > Thank you very much

Peace Sandy (13:05:48) (in thread): > Idon’tknow,just asking for clarification

Chiagoziem David (13:09:48) (in thread): > Okay, I don’t think it matters (as long as you are not saying 4000 hours 43 min:sweat_smile::sweat_smile:) I think the conventional 1 months or its 30 days variant would suffice.

U02CNMR4YEA (13:14:54) (in thread): > I have always curated it however it is written in the article (so if it says 30 days, I put 30 days).:grinning:

Chiagoziem David (13:16:28) (in thread): > This works too

Levi Waldron (15:23:09) (in thread): > > I saw that some of the NCBI clean up tasks are in new curations that applicants just carried out which have not been reviewed yet. Is it okay to solve those too? > @Esther Afuapeyes I don’t mind you doing cleanup tasks, just let us know here what you’ve done and if you have any doubts so we can confirm correctness of the corrections:slightly_smiling_face:

Esther Afuape (15:23:44) (in thread): > Got it!@Levi Waldron

Levi Waldron (15:25:41) (in thread): > @Chiagoziem David@Peace SandyI appreciate your preference for standards! We’ve allowed antibiotics exclusion criteria to be free-form, and converted these to a uniform scale with code afterwards, as long as it’s clear whether it’s days, weeks, months, or current use only.

Chiagoziem David (15:26:45) (in thread): > Alrighty

Levi Waldron (15:32:01) (in thread): > I can’t read what the y-axis is in figure (b) to know whether it’s a taxon or something else represented in the plot. It is showing two different contrasts ofsomethingas@Chioma Onyidosaid, and if this is abundance of something then they would reported in siguatures under two different experiments.

Chloe (15:33:18): > while making location for experiments …… i have European American & African American,…… but on the location they are not there….. though the samples of both were from the University of Alabama at Birmingham > do i make USA the location for both experiments?..

Chioma Onyido (15:35:19) (in thread): > Our thoughts exactly Prof. This is the full figure<@U1LCB8WEA> - File (PNG): IMG_4989

Onyewuchi Esther Chikamso (15:35:57) (in thread): > I think this thread would answer your questionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696946728275149?thread_ts=1696946728.275149&cid=C04RATV9VCY - Attachment: Attachment > @Levi Waldron @Svetlana Ugarcina Perovic (this question is a blocker for me) my location of subjects is in Africa. However there’s no African rather than Central African Republic and South Africa that pops out that I can choose from, in this type of suitation what do I do. For I can’t even type

Onyewuchi Esther Chikamso (15:36:55) (in thread): > You should be able to add multiple countries to your curation like@C. Mirzayi (please do not tag this account)said

Chloe (15:38:39) (in thread): > ok@Onyewuchi Esther Chikamsohow do i add multiple countries

Onyewuchi Esther Chikamso (15:41:09) (in thread): > I’m not sure:thinking_face:But can you try this; when you add one country, hit the enter button (if you’re using your system). Then try to type the second country in the same place.

Mildred Anashie (15:45:34) (in thread): > This is the information for figure 3@Levi Waldronit talks about differential abundance in the groups, also indicating two experiments were done @baseline and at week 24 for CD4 low and CD4 high samples. Although only Haemophilus parainfluenzae was mentioned - File (JPEG): photo-output

Chioma Onyido (15:47:52) (in thread): > @Mildred AnashieYes he is saying this should be curated under 2 different experiments.

Chloe (15:49:01) (in thread): > i tried that.@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovicplease come to our assistance

Mildred Anashie (15:49:25) (in thread): > Yea I think I get that@Chioma Onyido….My question though is based on the mention of just one organism

U02CNMR4YEA (17:58:51): > Hi All! Happy Sunday! I can’t remember if, when the authors report out results with different p values (e.g. P < 0.05, P < 0.01, ****P < 0.001). Do we have to curate each as a different experiment with a different p-value or just set it at P<0.05 and enter all taxon in one experiment? Thank you!

U1LCB8WEA (18:01:33) (in thread): > In theory you could make these different experiments but I think it’s too redundant and think you should just pick the largest signature, P < 0.05 (which would then include also anything that is P < 0.01 or 0.001)

U02CNMR4YEA (18:02:08) (in thread): > Great! (I like that answer:smile:) Thank you!

U1LCB8WEA (18:03:41) (in thread): > And honestly if that signature were huge, I’d pick a more stringent one like .01:sweat_smile:- p-value thresholds are arbitrary anyways!

Joan C. Chukwuemeka (18:08:54) (in thread): > Still hoping to get help with this@Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina Perovic

U1LCB8WEA (18:24:32): > Thank you to those who are now reviewing previously unreviewed pages on bugsigdb! I just reviewed this page (https://bugsigdb.org/Study_597(Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination) and saw a couple things that can benefit everyone: > 1. in the Group 0 and 1 names, try to pick names that will be informative to someone seeing only that name without having read the paper, without using abbreviations or table references. Here the use of “S1 Table (control group)” shouldn’t refer to the table # and ideally would say something about what kind of controls they are (healthy unvaccinated controls?) “T1, T2, T3, T4,(experimental group)” doesn’t tell me anything unless I read the paper, and we’re trying to make these data analyzable while rarely having to read the papers in detail. UseGroup 1 definition to make clear what distinguishes Group 1 from Group 0. > 2. The “Condition” should refer to what condition is being studiedby the contrastmade in this experiment. If the contrast is response to an HIV vaccine, then the condition is “response to vaccine” and not “HIV infection”. Even if the contrast were response to a vaccine among HIV infected individuals, HIV infection is not a condition of study if the controls have the same condition. Choosing the correct Condition is critical to being able to group together experiments that are making the same or similar contrasts to produce their signatures. > 3. Since there is only one microbiome sample from each participant, this is not a time series / longitudinal observational study. It appears to be cross-sectional observational, not case-control study (everyone was vaccinated, and the contrast is of immunological response to the vaccine) (“Samples from the earliest available sample (day 0 for 3 participants, month 6.5 for 11 participants and month 12 for 7 participants;S1 Table) were amplified with barcoded primers that targeted the hypervariable sequence containing V3-V4 region of the 16S rRNA gene and sequenced on a Roche 454”) > 4. It’s not clear how signatures were extracted from Figures 4A-D; this would be good to explain in the “Description” of these signatures. > 5. Different rank of taxa should be combined into a single signature rather than creating different signature for each rank as this paper did. In fact it looks like a separate Experiment 2 was created here for the same contrast, just to report taxa of different rank. Remember: an experiment is defined by the contrast between two groups, and signatures are the taxa that are either increased (one signature) or decreased (one signature) in Group 1 compared to Group 0 of that experiment. > @Nanalet me know when you’ve made new edits and I’ll check and mark reviewed. - Attachment (journals.plos.org): Human gut microbiota is associated with HIV-reactive immunoglobulin at baseline and following HIV vaccination > Antibodies that recognize commensal microbial antigens may be cross reactive with a part of the human immunodeficiency virus (HIV) envelope glycoprotein gp41. To improve understanding of the role of the microbiota in modulating the immune response to HIV vaccines, we studied the associations of the gut microbiota composition of participants in the HIV Vaccine Trials Network 096 clinical trial with their HIV-specific immune responses in response to vaccination with a DNA-prime, pox virus boost strategy designed to recapitulate the only efficacious HIV-vaccine trial (RV144). We observed that both levels of IgG antibodies to gp41 at baseline and post-vaccination levels of IgG antibodies to the Con.6.gp120.B, ZM96.gp140 and gp70 B.CaseA V1-V2 antigens were associated with three co-occurring clusters of family level microbial taxa. One cluster contained several families positively associated with gp41-specific IgG and negatively associated with vaccine-matched gp120, gp140 and V1-V2-specific IgG responses. A second cluster contained families that negatively associated with gp41 and positively associated with gp120, gp140 and V1-V2-specific IgG responses. A third cluster contained microbial groups that did not correlate with any immune responses. Baseline and post-vaccination levels of gp41 IgG were not significantly correlated, suggesting that factors beyond the microbiome that contribute to immune response heterogeneity. Sequence variant richness was positively associated with gp41, p24, pg140 and V1-V2 specific IgG responses, gp41 and p24 IgA responses, and CD4+ T cell responses to HIV-1 proteins. Our findings provide preliminary evidence that the gut microbiota may be an important predictor of vaccine response.

Tolulope Ogunleye (18:30:02): > Hi@Levi Waldronplease I would like to confirm that each experiment would have 2 signatures;one for the control and one group 1

U1LCB8WEA (18:35:42) (in thread): > Here is another example for Condition:https://bugsigdb.org/Study_503says that Group 1 isExposed group (Amoxicillin Group)and Group 0 isUnexposed group that did not receive antibiotics. (control group). These names are clear and good, although they could be a little more concise like “Amoxicillin-exposed” and “Controls not exposed to Amoxicillin”. These names tell me that the study Condition isamoxicillin, not “otitis media with effusion”. Condition of study is what distinguishes the case/exposed group 1 from the control group 0, not something shared by everyone in the study.@Chinwendu Enyinna

U1LCB8WEA (18:36:43) (in thread): > an experiment can have 0, 1, or 2 signatures depending on how many significant results are reported for that contrast.

Tolulope Ogunleye (18:38:54) (in thread): > This is helpful..Thank you

U1LCB8WEA (18:53:10) (in thread): > @Joan C. Chukwuemekais the advice I just gave on some other articles about what constitutes an Experiment helpful? The key message is thatexperiments are defined by the contrasts made, and signatures are defined by the results of those experiments. So it is perfectly possible to perform one or more experiments and find no statistically significant results, such as unchanged alpha diversity and no signatures of differentially abundant taxa.

Chioma Onyido (19:04:57) (in thread): > Thank you for taking the time to provide such a comprehensive explanation. I was saving a question to drop on the channel tomorrow:sweat_smile:but your detailed response here has given me a great starting point. Your guidance is deeply appreciated!

U1LCB8WEA (19:05:51) (in thread): > You are welcome!:blush:

Chioma Onyido (19:10:40) (in thread): > I’mcurious to learn more about study designs if youdon’tmind me asking, from the example study you gave innumber 3, (without seeing this info), honestly Iwould’vecurated as longitudinal because of the different time points of sample collection, I guess my question**** is ****what is the major difference between cross-sectional observational and longitudinal?

U1LCB8WEA (19:12:22) (in thread): > The different time points were fordifferentindividuals (and this was a shortcoming of the study, only because they happened to be able to collect specimens for different individuals at different times with respect to vaccination, which is fine as long as the microbiome is relatively stable and unaffected by the exposure), and each individual was sampled at only one time point. The contrasts were between the measurements of different individuals at their single time of measurement, making it a cross-sectional observational study. In a time series-longitudinal study, you investigate changes within each individual over time, then typically average those trends over multiple individuals. A classic simple longitudinal study would be taking microbiome measurements before and after a treatment, and estimating average differential abundance from before to after treatmentwithin each participant. The corresponding cross-sectional design would be comparing control subjects who were unexposed to study subjects who were exposed.

Chioma Onyido (19:26:03) (in thread): > This Makes sense and much clearer now. > I’ve a confession:eyes:After my first curation, I tried to avoid papers that’s not case-control or prospective cohort as much as possible because at the time, these study designs were easier to identify:sweat_smile:With these explanations you’ve provided, I’m now more interested in exploring further. Very grateful!:pray::blush:

Desire Oluwarotimi (21:59:25): > Hi@Levi Waldron@C. Mirzayi (please do not tag this account)From the paper I’m currently reviewing, there are samples from various sources used in the study. > > Mothers’ skin, oral mucosa, and vagina were sampled 1 h before delivery, and neonates’ skin, oral mucosa, and nasopharyngeal aspirate were sampled <5 min, and meconium <24 h, after delivery. > > Do all of these body sites get to be in the curation?

Chioma Onyido (23:03:46) (in thread): > Hi@Desire OluwarotimiSomeone asked same question some days ago, Here’s a response from<@UBNSEMS3S>https://community-bioc.slack.com/archives/C04RATV9VCY/p1696863436081849?thread_ts=1696773203.432559&channel=C04RATV9VCY&message_ts=1696863436.081849 - Attachment: Attachment > @Chinwendu Enyinna Correct. Some studies with do oral + gut, for instance. Those would be entered as separate experiments.

2023-10-16

Desire Oluwarotimi (00:50:26) (in thread): > Thank you.

Chiagoziem David (02:54:49) (in thread): > @Chioma Onyidono dey disappoint , chioma no be amaka:sweat_smile::sweat_smile::sweat_smile::sweat_smile:

Karen254. Kingecha (02:55:44) (in thread): > This has been so helpful thank you@Levi Waldronfor the detailed explanation

Odigiri Great Alume (03:55:30) (in thread): > Thank you for the details@Levi Waldron

Joan C. Chukwuemeka (03:56:46) (in thread): > <@U1LCB8WEA>Okay, I’ll go through your response to the other article and revert back. Thanks

Peace Sandy (04:03:58) (in thread): > Thank you so much for the detailed explanation@Levi Waldron

Peace Sandy (04:04:26) (in thread): > Thank you so much@Levi Waldron

Esther Afuape (04:08:10) (in thread): > Thank you so much@Levi WaldronThis has cleared a lot of my confusion, especially with picking the right condition and study design.I’dlike if you could give us a comprehensive summary like this on just study designs:face_holding_back_tears::pray:

Peace Sandy (04:15:16): > For those looking for how to make more contributionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697144958544289 - Attachment: Attachment > Someone asked what you can do while waiting for your second contribution to be graded. Here are some suggestions: > 1. double-check your contribution for accuracy and completeness, which is what it will be scored for. > 2. check out the <https://bugsigdb.org/Help:Contents#TODO_for_reviewers|TODO for reviewers> - we’d love to have help! > 3. resolve some of the <https://bugsigdb.org/Help:Contents#NCBI_cleanup|NCBI cleanup> - I find this surprisingly fun, like detective work :sweat_smile: > When you first get started reviewing, it’s best if you post proposed changes here to check that you’re on the right track. Actually it’s OK to make edits to the wiki, just post here and we can always roll back changes if needed, and mark a study as reviewed if it seems like you’ve reviewed it sufficiently.

Peace Sandy (04:15:28) (in thread): > @Chiagoziem David

Nana (04:18:54) (in thread): > Ok@Levi Waldronthanks for the clarification. I have taken up the correction and I will make adjustments. You nailed the explanation:+1::+1:

Kabirat Adeniyi (04:20:03) (in thread): > After we’re done with the second contribution is there a method of submission or we just wait until its graded

Peace Sandy (04:22:45) (in thread): > @Kabirat Adeniyitag any of the mentors to your paper on GitHub,it will be marked as needs review

Chiagoziem David (04:23:07) (in thread): > Tag to GitHub? How so?

Peace Sandy (04:24:05) (in thread): > The way you claimed a paper to curate

Peace Sandy (04:24:20) (in thread): > Go to the paper and tag the mentors

Chiagoziem David (04:25:16) (in thread): > Oh, okay, thanks

Kabirat Adeniyi (04:25:48) (in thread): > Thanks

Peace Sandy (04:34:16) (in thread): > You are welcome

Sinmi Adesanya (04:34:50) (in thread): > Thank you for the detailed feedback!@Levi Waldron

Nana (04:52:02) (in thread): > @Levi Waldronplease help me delete the experiment 2 ofhttps://bugsigdb.org/Study_597 - Attachment (BugSigDB): Study 597

Nana (05:37:01) (in thread): > Ok..thanks@Peace Sandy

Chloe (05:45:22): > how do i add multiple countries…?@C. Mirzayi (please do not tag this account)<@U1LCB8WEA>@Svetlana Ugarcina Perovicsince under location there is no european america nor African America……..but the samples of both were from the University of Alabama at Birmingham > do i make USA the location for both experiments?..

Odigiri Great Alume (05:55:55): > @Chloecheck the author affiliation. Usually the first and last author location should be thesame. That’s where the location of the study is. > > Also University of Alabama at Birmingham Is located in the United States so I believe your location should be USA for both experiments - File (JPEG): Screenshot_20231016-105438.jpg

Odigiri Great Alume (05:56:02): > @Chloecheck the author affiliation. Usually the first and last author location should be thesame. That’s where the location of the study is. > > Also University of Alabama at Birmingham Is located in the United States so I believe your location should be USA for both experiments - File (JPEG): Screenshot_20231016-105438.jpg

Odigiri Great Alume (05:58:24): > @Levi Waldronplease I don’t mean to bother, but I am still confused about relative abundance and differential abundance. I want to contribute more but some of the studies I see here talks of relative abundance and not differential abundance. So I want clarification on whether figures and tables about relative abundance can be curated as experiments:pleading_face:

Chloe (06:03:51) (in thread): > Thanks@Odigiri Great Alume

Odigiri Great Alume (06:04:09) (in thread): > Welcome:hugging_face:

Taiwo Adeyombo (06:07:12): > Hello@Levi Waldron@C. Mirzayi (please do not tag this account)I have been experiencing a particular issue in the course of my curation. My paper has three experiments but the edits I’ve been making to the second and third aren’t rendering. I’ve cleared my browser cache and even logged out and logged in again but the issue still persists.

Mildred Anashie (06:32:46): > Hi<@UBNSEMS3S>@Levi Waldroncan signature 1 be recorded as decreased and signature 2 increased?

Peace Sandy (06:35:24) (in thread): > Where is the University of Albama located, it could be that the samples where taken from people that are resident in the environment

Desire Oluwarotimi (06:35:38) (in thread): > I’m not sure about this but according to the introductory videos, signature 1 should be increased while signature 2 decreased. > > I think it’s just best to stick to that.

Peace Sandy (06:36:59) (in thread): > Signature 1 is always used as increased, while signature two as decrease.In a case where you have just increased or decreased abundance you will use signature 1

Peace Sandy (06:37:27) (in thread): > You are welcome@Nana

Kabirat Adeniyi (06:43:59) (in thread): > So if we want to contribute in the TODO for reviewers, is there any specific one we shouldn’t go for?

U1LCB8WEA (06:57:36) (in thread): > I don’tthinkthere’sa rule about order of signatures even though we usually do it one way, Iwouldn’tredo work

Nana (06:59:56) (in thread): > @Kabirat Adeniyidon’t review the one that was curated by 2023 Oct outreachy look for older year

Mildred Anashie (07:02:11) (in thread): > Okay…Thank you:pray:

U1LCB8WEA (07:03:29) (in thread): > Can you provide the link to the study?I think there is a bug in displaying some experiments.

Mildred Anashie (07:05:56) (in thread): > @Levi Waldronplease i dropped a comment herehttps://github.com/waldronlab/BugSigDBcuration/issues/97I’ll like help with that:pray: - Attachment: #97 Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status > Presti, Rachel M.a; Handley, Scott A.a; Droit, Lindsaya; Ghannoum, Mahmoudb; Jacobson, Markc; Shiboski, Caroline H.c; Webster-Cyriaque, Jenniferd; Brown, Todde; Yin, Michael T.f; Overton, Edgar T.g. Alterations in the oral microbiome in HIV-infected participants after antiretroviral therapy administration are influenced by immune status. AIDS 32(10):p 1279-1287, June 19, 2018. | DOI: 10.1097/QAD.0000000000001811 > > https://journals.lww.com/aidsonline/Fulltext/2018/06190/Alterations_in_the_oral_microbiome_in_HIV_infected.8.aspx

Taiwo Adeyombo (07:08:51) (in thread): > Surehttps://bugsigdb.org/Study_825 - Attachment (BugSigDB): Study 825

U1LCB8WEA (07:26:43) (in thread): > @Peace Sandyis correct,it is the country where the study was conducted

U1LCB8WEA (07:27:48) (in thread): > @Svetlana Ugarcina Perovicwill you report this one as well?https://bugsigdb.org/Study_825 - Attachment (BugSigDB): Study 825

U1LCB8WEA (07:28:46) (in thread): > @Taiwo Adeyomboyou can still type in the experiment and study URLs manually to see or edit them in the meantime.

Desire Oluwarotimi (07:30:20): > @Levi Waldron@C. Mirzayi (please do not tag this account)The options available for sequencing type doesn’t include metagenomic shotgun sequencing. > What is to be done?

U1LCB8WEA (07:31:51) (in thread): > I believe this is in the policy documents- let us know if what’s written there is insufficient

Nana (07:36:01): > @Levi Waldronthere’s an experiment 2 I pointed out for you to help delete. And when you redo an old curated paper you so on Todo reviews how do you find it and tag it on the GitHub to show it needs review. Like our own curated paper is showing

Joan C. Chukwuemeka (07:46:45) (in thread): > @Desire OluwarotimiI think shotgun sequencing is a type of Whole Metagenome Sequencing (WMS)

Taiwo Adeyombo (07:47:21) (in thread): > Alright. Thank you@Levi Waldron

Desire Oluwarotimi (08:07:37) (in thread): > @Joan C. ChukwuemekaI think so too seeing that Levi directed me to that document. > > Thank You!

Desire Oluwarotimi (08:07:45) (in thread): > Thank you Levi

Odigiri Great Alume (08:35:26) (in thread): > @Chioma Onyido@Levi Waldron@C. Mirzayi (please do not tag this account):pleading_face:

Chioma Onyido (08:55:06) (in thread): > Can you share the figures/ tables?

Chioma Onyido (09:18:22): > Hello<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovicand everyone:wave:. I just finished curatingbugsigdb.org/Study_768which I found under the ‘studies without experiments’ section in the NCBI cleanups. > It’s supposed to be 211 for signature 1, and I’ve cross checked over and over again to make sureit’scomplete. I could use a second pair of eyes to review my work for errors as this was an exhaustive curation, particularly experiment 1. > > Also I am not sure about the study design I picked for experiment 1, since the comparison was between DNA mismatch repair status (pMMR vs dMMR), should this be cross- sectional instead?:thinking_face:I think Experiments 2 and 3 are case-control since each MMR status was compared with healthy controls, respectively.

Chioma Onyido (09:21:33) (in thread): > Hmmm@NanaIdon’tknow ifthere’sa way to find old curated papers on GitHub. But I do know that whenyou’redone with a cleanup task, you should post here and tag the mentors so that they can review for errors and ensure that everything is accurate.

Chioma Onyido (09:24:30) (in thread): > Also antibiotic resistancewasn’tmentioned in the study, however Immune checkpoint inhibitor (ICI) was reported, should I leave the antibiotics section blank or is there a way to curate ICI? - File (JPEG): IMG_5089

Svetlana Ugarcina Perovic (09:26:51) (in thread): > @Taiwo Adeyombocould you please specify which parts of the second and third experiments aren’t rendering?

Nana (09:30:43) (in thread): > Ok..thanks chioma

Peace Sandy (09:36:04) (in thread): > This thing can be tricky, not all figures and tables should be curated as experiments, if you can post the study here, it will help people provide a better response

Esther Afuape (09:50:59): > Hello@Levi Waldron<@UBNSEMS3S>and everyone. Hope y’all had a great weekend. I just concluded an old curation that was marked incomplete:https://bugsigdb.org/Study_717. The location of the participants wasn’t stated but they were recruited from an initial experiment that took place in Finland. The study was also approved by a body in Finland so I included Finland as the location. 3 different statistical tests were done from what I saw so I included the other 2. I’m not sure about the data transformation as none was clearly stated in the paper so I left that out. > I think this signature:https://bugsigdb.org/Special:FormEdit/Signature/Study_717/Experiment_1/Signature_3?reload=1&returnto=Study%20717, and this:https://bugsigdb.org/Special:FormEdit/Signature/Study_717/Experiment_1/Signature_4?reload=1&returnto=Study%20717should be deleted. They’re already signatures of another experiment. > I created experiments 6&7 in some kind of error and I’d like those deleted too:https://bugsigdb.org/Special:FormEdit/Experiment/Study_717/Experiment_7?reload=1&returnto=Study_717,,https://bugsigdb.org/Special:FormEdit/Experiment/Study_717/Experiment_7?reload=1&returnto=Study_717. > One of the confounders controlled for was Rome III score. I saw that it’s a diagnostic criteria for IBS so I changed that. > I created experiments 4&5 but I’m unsure of the quality of the signatures. They were included in the supplementary result and some of them appeared in both increased and decreased abundance. Please, help me to check out both experiments and their signatures. - Attachment (BugSigDB): Study 717 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 717/Experiment 1/Signature 3 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 717/Experiment 1/Signature 4 - Attachment (BugSigDB): Special:FormEdit/Experiment/Study 717/Experiment 7

Esther Afuape (09:51:52) (in thread): > Well done,Chioma:raised_hands:

UBNSEMS3S (10:34:30) (in thread): > I would look to see if there’s a supplemental table that contains the taxa presented in the A part of the figure.

UBNSEMS3S (10:37:03) (in thread): > I don’t think I would curate something with a p-value of 0.56 as decreased so I just want to be very sure that it’s 0.56 and not 0.056 since both appear in the paragraph you posted.

UBNSEMS3S (10:37:15) (in thread): > Oh nevermind Levi already responded.

UBNSEMS3S (10:39:45) (in thread): > @Onyewuchi Esther ChikamsoHow are you identifying these confounders? I don’t think you can really adjust for “ethical considerations” for instance.

UBNSEMS3S (10:45:27) (in thread): > You should be able to just select them from the list. - File (PNG): image.png

UBNSEMS3S (10:58:08) (in thread): > Please note that the author location should be used as last resort for identifying location. Most articles should state in the methods or results where participants were recruited from.

Onyewuchi Esther Chikamso (10:59:02) (in thread): > Hi@C. Mirzayi (please do not tag this account), I have taken the corrections<@U1LCB8WEA>left on the talk page. I thought having the consent of the participants before carrying out the research would be noted for what co-founders controlled for but now I know better:sweat_smile:. Thank you for your guidance

U1LCB8WEA (11:01:12) (in thread): > That’s what I said too, or at least tried to:sweat_smile:Ethical considerations is not a confounding factor.

UBNSEMS3S (11:01:34) (in thread): > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

UBNSEMS3S (11:02:37) (in thread): > ICIs are not antibiotics@Chioma Onyido. I would leave it blank if they do not mention any antibiotics exclusions.

UBNSEMS3S (11:10:17) (in thread): > I’ve deleted the extra experiments and signatures.

UBNSEMS3S (11:11:13) (in thread): > @Onyewuchi Esther ChikamsoIf you watch toward the end of the recording of last week’s office hours I talk about how to identify confounders.

Odigiri Great Alume (11:14:24) (in thread): > Thank you so much@C. Mirzayi (please do not tag this account):pleading_face:Grateful

Esther Afuape (11:19:11) (in thread): > Thank you. > Kindly review the curation@Levi Waldron

Chioma Onyido (11:21:15) (in thread): > This is noted, thank you<@UBNSEMS3S>What about the study design please:pleading_face:?

UBNSEMS3S (11:34:19) (in thread): > I can’t tell from the screenshot of the start of the methods. It depends on how participants were recruited–did they recruit cases and controls separately? That’s probably a case-control. Did they select a sample and follow them over time? Probably a prospective cohort. Did they select a sample and assign them the condition as an experimental treatment? That’s an RCT.

U1LCB8WEA (11:35:37) (in thread): > <@UBNSEMS3S>it’dbe good to add some detail on questions about study design,confounding/matched on, sequencing strategy, tohttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy

UBNSEMS3S (11:35:53) (in thread): > I will do that.

Chioma Onyido (11:44:18) (in thread): > Yes<@UBNSEMS3S>cases and controls were recruited separately. I think the answer is clear now. And that would be super helpful<@U1LCB8WEA>because most of the questions lately are study design- related. Thank you so much.:blush::pray:This curation is now complete. Hoping to get a review on the signatures.:hand_with_index_and_middle_fingers_crossed: - File (QuickTime Movie): Video Clip (2023-10-16 16:41:25)

Hodan Abdirisak (11:54:52) (in thread): > Thanks<@U1LCB8WEA>for this farther information

Mildred Anashie (12:02:47) (in thread): > There is one<@UBNSEMS3S>

Chinwendu Enyinna (12:29:36) (in thread): > Thank you for this detailed explanation<@U1LCB8WEA>

Nana (12:34:22) (in thread): > @Levi Waldronthis taskhttps://bugsigdb.org/Study_503you tagged@Chinwendu EnyinnaI am already reworking it. Please kindly check back for they could be a mistake somewhere. - Attachment (BugSigDB): Study 503

Peace Sandy (12:37:31): > I just identified this incomplete study and would and one without signature, I would like to work on ithttps://bugsigdb.org/Study_796https://bugsigdb.org/Study_765 - Attachment (BugSigDB): Study 796 - Attachment (BugSigDB): Study 765

Chinwendu Enyinna (12:38:56) (in thread): > @NanaYeah, I think the tag was for you.

Nana (12:41:27) (in thread): > @Chinwendu Enyinnaok:+1:

U1LCB8WEA (12:44:37) (in thread): > Sorry about that, it’stricky translating usernames between Slack and bugsigdb!

Mildred Anashie (13:00:06) (in thread): > Also I have a better understanding of it now > > Thank you<@UBNSEMS3S>

Nana (13:28:07) (in thread): > @Levi Waldronplease help me delete experiment 2 and it’s signature of this. Secondly when I review a paper on the Todo how do I find and tag it at GitHub so that it can be reviewed?https://bugsigdb.org/Study_597 - Attachment (BugSigDB): Study 597

U1LCB8WEA (13:41:30) (in thread): > @Nanawhy do you want to delete experiment 2 and its signatures? I avoid deleting things unless they were created in error and can’t be corrected through editing.

U1LCB8WEA (13:44:09) (in thread): > > Secondly when I review a paper on the Todo how do I find and tag it at GitHub so that it can be reviewed? > For reviewing/cleanup we don’t normally use GitHub, unless there’s an existing open issue that can be closed.

Nana (13:50:04) (in thread): > @Levi WaldronThe experiment i asked you to delete was based on the correction you pointed out to me. You reviewed the paper i was reworking on and you said that they was no need for exp 2 and its signature since the signature could all be contained in exp 1. So i wanted it deleted based on the correction you gave me. for you said after i made the correction you pointed out i should let you know.

Nana (13:50:22) (in thread): > ok

Joan C. Chukwuemeka (14:30:07) (in thread): > Thanks<@U1LCB8WEA>the response was helpful

U1LCB8WEA (14:34:04) (in thread): > Why do you want these signatures deleted? I only delete a page if it was added in error and doesn’t belong there at all. If it’s something that can be fixed through editing, that’s usually preferable.

U1LCB8WEA (14:48:36) (in thread): > @Chioma OnyidoI’m not too sure what I meant either, just something withCandidatusandbacteriumin the name:sweat_smile:

Mildred Anashie (14:51:49) (in thread): > I want it deleted because I think it was done in error….This talked about relative abundance and not differential abundance and when I read further it also stated that there was no significant difference in the signaturesHere’s an excerpt from the paper“Similar to previous reports, at baseline the most abundantly detected bacterial phyla in the salivary microbiome were* Bacteroidetes, Firmicutes and Proteobacteria, with lower relative abundance of Fusobacteria, Spirochaetes, Actinobacteria, and Ternericutes (Fig. 1a). Following 24 weeks of ART, the dominant phyla represented in the saliva *****remained similar to that found at baseline ******(Fig. 1b). There was no significant difference in beta diversity whenever comparing baseline samples to those collected following 24 weeks of ART (Fig. 1c, ADONIS test P value: 0.744)… > Similarly, alpha diversity (richness and Shannon diversity) was not significantly different between samples collected at baseline and samples collected following 24 weeks of ART (Figure S3A&B, https://links.lwcom/QAD* / B252)*”Since the signatures detected in both baseline and 24 weeks are ‘similar’, with no significant differenceand the previous replies given from all the questions I have been asking:smiley:, I understood the experiment can be curated but not the mentioned taxas, Is this wrong?:thinking_face:<@U1LCB8WEA>

U1LCB8WEA (14:54:28) (in thread): > Yes that’s a good reason, I’ll delete. What about the “incomplete” Signature 1 of Experiment 3?

Mildred Anashie (14:55:03) (in thread): > Thank you:pray:I’mstill working on that please

Odigiri Great Alume (16:17:52): > So, I started working on study #575 with the linkhttps://bugsigdb.org/Study_575the study’s title is “Antibiotics at birth and later antibiotics course: effects on gut microbiota”
> > the study’s participants were divided Into
> > 1. control (did not receive any IAP, or postnatal antibiotics during first week of life or any maternal antibiotics withing one week before delivery) > > 2. Intrapartum antibiotic prophylaxis IAP group (participants received only IAP) > > 3. postnatal group (received IV antibiotics 24hrs after birth) > > 4. IAP + postnatal group (received both IAP and IV antibiotics) > >
> > this study speaks more on participants “response to antibiotics” so I changed the study condition from “antimicrobial agent to response to antibiotics”
> >
>
> > Secondly, group one definition in the first experiment was defined as “Postnatal antibiotics during the first week of life, or to any maternal antibiotics within 1 week before delivery, the IAP group received only IAP (n=27), the postnatal group was exposed to empirical postnatal intravenous antibiotics within 24 h after birth (n=24), and the IAP + postnatal group received both IAP and postnatal intravenous antibiotics (n=22)”
> > However, the first experiment compared a combo of all antibiotics group (perinatal antibiotic group) with the control group, I think the most appropriate definition of group 1 in the first experiment is “participants who received any perinatal antibiotics” Hence, I effected the change. > >
> > Thirdly, only infants delivered by vaginal were eligible for inclusion hence I set the confounder controlled for to be “method of delivery, severe congenital disorders (as they were excluded for from the study) and neurological or developmental problem” > >
> > Lastly, I added two signatures for experiment 1. > > Prevotella, clostridium. Faecalibacteriuym, E.coli increased in group 1 while bacteroides decreased. > > I just want to confirm I’m doing the right thing before I move on to add other experiments.@C. Mirzayi (please do not tag this account)@Levi Waldron - Attachment (BugSigDB): Study 575 - File (JPEG): IMG_20231016_172549.jpg - File (JPEG): IMG_20231016_184348.jpg

U1LCB8WEA (17:10:38) (in thread): > Doing great@Esther Afuape! I agree that the location is Finland, and your conversion of Rome Score -> “irritable bowel syndrome” is an excellent standardization to the ontology. One question, are the “matched on” and “Confounders controlled for” really different for Experiment 2+ than they are for Experiment 1? 2 is different, then 4-5 unspecified.

Peace Sandy (17:26:40): > Can selected covariates such as ( infant age, maternal work outside the home etc ) be use as controls matched for ?@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

UBNSEMS3S (17:38:35) (in thread): > If those covariates were entered into a model they almost certainly weren’t matched on. You can’t include in a model a variable you matched on.

UBNSEMS3S (17:38:51) (in thread): > I will take a look at this tomorrow.

Odigiri Great Alume (18:27:33) (in thread): > Thank you ma’am

saskia (18:30:48): > This looks like a really active channel! Would someone from your community be interested in joining the Code of Conduct Committee for the Bioconductor project. We also strive to have as much diverse representation of the community as we can, so please consider this. Applications are due on the 31st of October via this linkhttps://docs.google.com/forms/d/e/1FAIpQLSeTRs3m3-XNM7iGs0kyHfoaXNiwRVsgebmce10t0ieKfamaPg/viewform?usp=sf_link

saskia (18:31:03) (in thread): > Let me know if you want more information

Tolulope Ogunleye (18:38:32): > @C. Mirzayi (please do not tag this account)Hi, I can’t seem to find the name for the code in Fig 2A in the taxon identifier , please,how do I proceed? - File (JPEG): IMG_8815

Esther Afuape (19:09:06) (in thread): > Thank you@Levi WaldronThe participants were originally recruited for a pilot study in Parkinson’s disease and they were age and sex matched then. The participants in all of the experiments in this current study are from the set invited back for the follow-up, just divided into subgroups so I believe the “matched on” is the same for all the experiments. > The “confounders controlled” for are different though. COMT inhibitor was only used for the experiment on progression since only PD patients take the medication. Experiments 4&5 were not corrected for confounders due to the small number of subjects included in the analysis.

Esther Afuape (19:13:22) (in thread): > Have you checked uniprot and NCBI?

Esther Afuape (19:27:59) (in thread): > This might be helpfulhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696874309029659 - Attachment: Attachment > Can covariates be filled in for confounders controlled for? @Levi Waldron

Esther Afuape (19:49:25): > Hi,@Levi Waldron<@UBNSEMS3S>how can I get the full paper for this study?https://bugsigdb.org/Study_739 - Attachment (BugSigDB): Study 739

Peace Sandy (20:57:25) (in thread): > What is the community all about ?

Peace Sandy (20:58:22) (in thread): > Oh…Thank you so much@C. Mirzayi (please do not tag this account)

Peace Sandy (20:58:32) (in thread): > Thank You@Esther Afuape

saskia (21:11:13) (in thread): > The Bioconductor project is a repository of R packages geared for the analysis of biological assays (new and emerging), including mircobial data. The community around the project includes the community-bioc workspace which this channel is connected to. The Code of Conduct Committee oversees any complaints about personal interactions that are being made.

saskia (21:12:24) (in thread): > Levi Waldron used to be part of the Code of Conduct Committee when it was first formed. Being part of the Committee is a great way to learn more about the project, become part of the community and also practice your leadership skills.

Chiagoziem David (21:35:23): > ….

U1LCB8WEA (21:51:23): > https://bugsigdb.org/Study_739Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease - Attachment (BugSigDB): Study 739 - File (PDF): d53da1fe-ccfb-047e-9e6a-4ef064f7b0c6

U1LCB8WEA (21:53:08) (in thread): > If youcan’tfind the valid NCBI ID, just enter the taxon name as it appears.

U1LCB8WEA (21:54:55) (in thread): > I can confirm it was a great experience on the code of conduct committee!It’sessential to the Bioconductor project.

Peace Sandy (21:56:09) (in thread): > Sounds great!:clap:

U1LCB8WEA (22:15:33) (in thread): > Good study of the paper! Just check that the experiments on bugsigdb match whatyou’resaying.

Sinmi Adesanya (22:42:02) (in thread): > This sounds like a great opportunity@saskia. I studied law but branched into the sciences recently so I am very excited about this!

Sinmi Adesanya (22:46:42) (in thread): > Hi@saskia, access to the PPT is restricted. Can you please grant access? I’d be happy to provide any information you need to facilitate the process. Thanks!

Sinmi Adesanya (23:20:27) (in thread): > Got it. Thanks!

2023-10-17

Chioma Onyido (01:07:10) (in thread): > Wow, this opportunity sounds interesting,@saskia:grin:I sent a request to access the PPT.

Onyewuchi Esther Chikamso (01:30:24) (in thread): > @Joan C. Chukwuemekaif I have a second experiment, would all the values for the experiment be the same as the first, while only the signatures entered would be different?

Chioma Onyido (01:38:46) (in thread): > Seen, thanks!

Karen254. Kingecha (01:43:46) (in thread): > @saskiasounds great:blush:

Onyewuchi Esther Chikamso (02:09:28) (in thread): > This sounds exciting@saskia. I sent a request access to the PPT

Tolulope Ogunleye (02:29:05) (in thread): > Alright,thanks

Onyewuchi Esther Chikamso (02:44:11) (in thread): > Thanks@C. Mirzayi (please do not tag this account). So I had to cross-check the study, and I realised there were no words like matched on, controlled for, adjusted for, entered as co-variant, included in the model. But the statement ’no statistical difference” was used. So this means I have no “confounders controlled” for and “matched on” in my study. Is this really possible?:thinking_face:Link the paperhttps://pubmed.ncbi.nlm.nih.gov/32591968/ - Attachment (PubMed): A Comparison of Tumor-Associated and Non-Tumor-Associated Gastric Microbiota in Gastric Cancer Patients - PubMed > GC patients exhibited a gastric microbiome profile distinct from that observed in SG patients, with these differences being evident in both tumor and paracancerous tissues. Differences in the relative abundance of Helicobacter spp. may be the primary driver of gastric dysbiosis in GC patients. - File (PNG): Screenshot_20231017-074352.png

Nana (03:50:07): > @Levi Waldron<@UBNSEMS3S>Good morning, found this incomplete study in TODO for reviewers and I want to complete.https://bugsigdb.org/Study_454have some questions regarding creating of signature so many look alike figures confused about the right one to curate. here is a screenshot of the figures and tables - Attachment (BugSigDB): Study 454

Mildred Anashie (04:45:47) (in thread): > There seem to be a lot of supplemental tables and figures for this study…Maybe you could look at them if you haven’t, I think you might find something there while you await response from the mentors…. > My opinion though:blush:

Odigiri Great Alume (04:58:32) (in thread): > I requested an access to the slides. Awaiting approval. Thanks@saskia

Esther Afuape (05:24:01) (in thread): > Thank you!I’llbe working on this

Esther Afuape (05:28:44) (in thread): > Will do:saluting_face:

Esther Afuape (05:33:05) (in thread): > Sounds exciting. Just went through the presentation slides

Chioma Onyido (05:46:08) (in thread): > In addition to Mildred’s suggestions, Also try to focus more on the tables/ figures where groups were contrasted for the signatures, remember that’s also where our ‘experiments’ come from.

Hodan Abdirisak (05:51:53): > https://doi.org/10.1038/s41598-020-60794-w@C. Mirzayi (please do not tag this account)<@U1LCB8WEA>this study is marked as incomplete because of missing study design and is not mentioned in the study, in my understand i get that it is Case study can I fix this? I - File (PNG): Screenshot 2023-10-17 023942.png

Peace Sandy (06:00:00) (in thread): > Let me share a post where the mentors talked about study designs

Peace Sandy (06:02:39) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1697411542396799?thread_ts=1697408672.849819&channel=C04RATV9VCY&message_ts=1697411542.396799@Hodan Abdirisak - Attachment: Attachment > The different time points were for different individuals (and this was a shortcoming of the study, only because they happened to be able to collect specimens for different individuals at different times with respect to vaccination, which is fine as long as the microbiome is relatively stable and unaffected by the exposure), and each individual was sampled at only one time point. The contrasts were between the measurements of different individuals at their single time of measurement, making it a cross-sectional observational study. In a time series-longitudinal study, you investigate changes within each individual over time, then typically average those trends over multiple individuals. A classic simple longitudinal study would be taking microbiome measurements before and after a treatment, and estimating average differential abundance from before to after treatment within each participant. The corresponding cross-sectional design would be comparing control subjects who were unexposed to study subjects who were exposed.

Joan C. Chukwuemeka (06:47:50) (in thread): > Hello@Onyewuchi Esther Chikamso, > The information on the each experiment depends on what is recorded in the study. > > According to<@U1LCB8WEA>, “The key message is that ******experiments are defined by the contrasts made, and signatures are defined by the results of those experiments********.”**So, 2 experiments means you have 2 pairs of contrast investigated in the study. The values for each experiment will come from what the paper recorded accordingly.

Onyewuchi Esther Chikamso (07:18:55) (in thread): > Thank you@Joan C. Chukwuemeka

Chiagoziem David (07:29:35): > Guys I am working on study_717 on the NCBI clean up

Chiagoziem David (07:41:59) (in thread): > Sounds interesting:thinking_face::smiley:, thanks

Kabirat Adeniyi (08:48:14): > Hey Guys, Im working on thehttps://bugsigdb.org/Study_761in the NCBI cleanup - Attachment (BugSigDB): Study 761

UBNSEMS3S (09:53:25) (in thread): > This appears to be the full version:https://www.sciencedirect.com/science/article/pii/S1075996422001457?casa_token=3xJkyhfl[…]vY8p8BfY0SaqjnfEBLYe4QdckbqVbX4WbJaPiQtIr_1BPTrG70taFKMiLQ - Attachment (sciencedirect.com): Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease > To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients.Patients were randomly allocated t…

Esther Afuape (09:53:59) (in thread): > Thank you

Peace Sandy (10:37:48) (in thread): > This explanation is really helpful@C. Mirzayi (please do not tag this account)

Odigiri Great Alume (11:36:15) (in thread): > Good evening@C. Mirzayi (please do not tag this account)@Levi WaldronI need clarification here before I proceed with the second experiment. Thank you. > I figured@C. Mirzayi (please do not tag this account)is caught up with work and forgot me.:pleading_face:

Joan C. Chukwuemeka (11:40:05): > Good day all, > Has all studies requiring matching NCBI ID been taken?:thinking_face:didn’t see an outstanding one on the link..

Peace Sandy (11:58:10) (in thread): > If they are no study with NCBI ID issues on the link,it means they have all been corrected that is whyit’sno longer available.

Joan C. Chukwuemeka (12:01:26) (in thread): > Alright@Peace Sandy, I saw just one and it seemed like you were working on it..

Peace Sandy (12:02:52) (in thread): > Yes, butit’sa Clostridium cluster@C. Mirzayi (please do not tag this account)addressed it herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697204302943869?thread_ts=1697193924.756799&channel=C04RATV9VCY&message_ts=1697204302.943869 - Attachment: Attachment > The clostridium clusters are ones that we have never been able to formally identify.

Hodan Abdirisak (12:04:02) (in thread): > @Joan C. Chukwuemekait will be not empty when some one misses NCBI ID immediately come to there

Joan C. Chukwuemeka (12:08:01) (in thread): > Here’s it is@Peace Sandy - File (PNG): image.png - File (PNG): image.png

Peace Sandy (12:08:23) (in thread): > I’veresponded

Peace Sandy (12:08:49) (in thread): > I saidit’sa clostridium clusterthat’swhyI couldn’tedit it@Joan C. Chukwuemeka

Peace Sandy (12:09:56) (in thread): > @C. Mirzayi (please do not tag this account)explained it herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697204302943869?thread_ts=1697193924.756799&channel=C04RATV9VCY&message_ts=1697204302.943869

Joan C. Chukwuemeka (12:10:19) (in thread): > @Peace SandyStudy 717. it’s different from the one you referred to. Are you working on this currently?

Joan C. Chukwuemeka (12:12:35) (in thread): > Okay@Peace Sandy… When I opened the thread you referred to, I saw study 572. I get it now. It’s all good:+1:

Peace Sandy (12:13:10) (in thread): > Alright

UBNSEMS3S (15:27:20) (in thread): > I didn’t forget! Ok a few quick thoughts: > > I understand why you updated the condition but I do think “antimicrobial agent” is the more fitting condition. “Response to antibiotics” is something I would use if they were contrasting on side effects or some measure of the biological mechanisms that changed in the body as a result of antibiotics exposure. > > Group 1 change makes sense. > > Inclusion criteria are not the same thing as controlling for confounders. I just skimmed the paper but it does not look like to me that they controlled for any confounders, nor did they match on any variables. > > You are missing Faith and Richness diversity measures. > > Missing from signatures: Bacteroidetes, Firmicutes. Right now only differences on the genus level were curated but there’s no reason you can’t curate the phylum level results. > > I think these are some fairly important elements to have a clear understanding of before continuing to review other studies.

UBNSEMS3S (15:29:45) (in thread): > It is common, unfortunately, for many published articles to require you to read between the lines. It sounds like you’re making good progress in figuring this out.

UBNSEMS3S (15:30:35) (in thread): > Yeah I’d look for a supplemental table. The figures you’ve shown do have some differential abundance results in them but I wouldn’t want to try to curate them.

UBNSEMS3S (15:31:50) (in thread): > It’s not only possible, it’s common for studies of the microbiome to not adjust for confounders.

Odigiri Great Alume (15:43:52) (in thread): > @C. Mirzayi (please do not tag this account)thank you so much for this details. I will look at the study and effect the necessary changes. Begining with the condition, confounder and matched on. > > Thank you

Nana (15:46:04) (in thread): > <@UBNSEMS3S>is your suggestion saying that having just experiment without signature for that 454 is ok

UBNSEMS3S (15:53:16) (in thread): > I’d have to take a closer look at the paper.

Nana (15:55:24) (in thread): > Ok. Thanks in advance

Odigiri Great Alume (16:48:33) (in thread): > So I have effected the following corrections on the study@C. Mirzayi (please do not tag this account) > 1. I changed the condition back to “antimicrobial agent” > 2. I have also taken out the inclusion and exclusion criteria I mistook for confounder > 3. I looked again in the study to confirm your submission on Bacteroidetes and Firmicutes from the text below:point_down: > Effects of the perinatal antibiotics and courses of antibiotics on the three main bacterial phyla, Bacteroidetes, Firmicutes, and Proteo bacteria of the infant’s gut microbiota, were compared using the linear mixed-model analysis adjusted for different antibiotic exposure groups: IAP, postnatal, IAP + postnatal, and courses of oral antibiotics (any vs. none). Relative abundance of the Bacteroidetes was inversely associated with the exposure to IAP (P = 0.045), to postnatal antibiotics (P = 0.02), and to IAP + postnatal antibiotics (P = 0.005). Relative abundance of the Firmicutes was linearly associated with the postnatal group (P = 0.02) and the IAP + postnatal group (P = 0.01), but no associations were seen in the IAP group (P = 0.09) nor exposing to any courses of antibiotics (P = 0.99). No statistically significant associations were seen in the relative abundance of Proteobacteria and exposures to perinatal antibiotics or courses of antibiotics
> I saw that while the abundance of Bacteriodetes increased in the control group it decreased in the group 1 ( because of the inverse association) > Also, Firmicutes had a linear association with controls hence, it increased in group 1 as a result. > I have curated for both. > > 4. Finally, I looked again for “faiths diversity” and saw that it was not statistically significant > hence I have added it to the alpha diversity and marked it unchanged as it wasn’t statistically significant either. However, I did not see that they used Richness in alpha diversity. > > > This is the changes I have done so far. > Please@C. Mirzayi (please do not tag this account)

Chiagoziem David (17:56:08) (in thread): > I said I was working on study 717 earlier, but what@Peace Sandysaid holds

Chiagoziem David (20:07:45): > https://bugsigdb.org/Special:FormEdit/Signature/Study_831/Experiment_2/Signature_1?reload=1&returnto=Study%20831%2FExperiment%202%2FSignature%201 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 831/Experiment 2/Signature 1

Chiagoziem David (20:07:55): > I am working on this guys

Chiagoziem David (20:17:00): > <@U1LCB8WEA>hello sir, please if a genera is unassigned but the family name is given, should we go with the family name, or put down the unassigned genera like that

U1LCB8WEA (20:20:45) (in thread): > Did they specify that it is of rank genus? Because sometimes you can find an unspecified species withbacteriumin the name, of the correct family.

U1LCB8WEA (20:22:25) (in thread): > I would rather err on the side of putting aBacteriumof species rank than of putting the family name, because they’re not claiming that the entire family is differentially abundant. Whether there is one or several species of that family, unnamedBacteriumis not too bad a description of what they’re saying (if I understand the context correctly)

Chiagoziem David (20:24:12) (in thread): > This is a snapshot sir.. “……decrease in the abundance of two unassigned genera (PAC001138 and PAC001046) in Lachnospiraceae family,…”

Chiagoziem David (20:26:32) (in thread): > PAC001138 and PAC001046 are not in the NCBI database(yet), I am asking if we can specify it this way, or use the more generic family name (although that would be wrong I guess)

U1LCB8WEA (20:34:06) (in thread): > Using a code like PAC001138 isn’t wrong, but it also will just be ignored in all analyses. You could summarize these both asLachnospiraceae incertae sedis (Taxonomy ID: 2840493), and leave comments next to the taxa in this signatures that this was orriginally recorded as two unassigned genera (PAC001138 and PAC001046) inLachnospiraceaefamily.

Chiagoziem David (20:36:03) (in thread): > Alright sir, thank you, I am not clear on the comment part though….

Chiagoziem David (20:37:14) (in thread): > Also, how did you get to summarize them as lachnospiraceae invertase sedis?

Mildred Anashie (20:48:09): > Hello sir<@U1LCB8WEA>When curating, can Matched on and confounders controlled for be left out if it wasn’t explicitly mentioned in the paper?……..Although the inclusion criteria were stated, can this account for them?

U1LCB8WEA (20:51:01) (in thread): > Inclusion criteria that apply to everyone can be described in the group names (if critical, like infants, people living with HIV) or group 1 description.If there was no matching or confounders controlled for thendon’tmake any up just to fill the space:grin:

U1LCB8WEA (20:52:20) (in thread): > You’llhave to read about what incertae sedia means.There’sa comment icon next to every taxon in the signature

Mildred Anashie (20:54:24) (in thread): > :sweat_smile:Thank you sir

Chiagoziem David (21:26:25) (in thread): > Okay, thank you very much

Chiagoziem David (21:38:37): > Sir<@U1LCB8WEA>please can this be deleted, there’s nothing therehttps://bugsigdb.org/Study_769 - Attachment (BugSigDB): Study 769

U1LCB8WEA (21:46:41) (in thread): > Done

Mildred Anashie (21:58:15): > Same as thishttps://bugsigdb.org/Study_824Although theres a study design but no PMID or DOI@Levi Waldron - Attachment (BugSigDB): Study 824

Mildred Anashie (22:01:11): > https://bugsigdb.org/Study_813this also - Attachment (BugSigDB): Study 813

Mildred Anashie (22:13:43): > Hi sir<@U1LCB8WEA>https://bugsigdb.org/Study_807https://bugsigdb.org/Study_808https://bugsigdb.org/Study_826all three studies have the same DOI:http://dx.doi.org/https://doi.org/10.1016/j.xcrm.2022.100753should it be so? - Attachment (BugSigDB): Study 807 - Attachment (BugSigDB): Study 808 - Attachment (BugSigDB): Study 826 - Attachment (sciencedirect.com): Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome > Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary en…

U1LCB8WEA (22:16:44) (in thread): > Thank you for pointing all these out, and the blank ones above.All deleted.

U1LCB8WEA (22:43:43) (in thread): > The screenshot of text provides some signatures for the cancer vs controls contrast directly in the text, so there is at least one experiment with two signatures.It also refers to supplements with more information, so see if they list additional differentially abundant taxa.

Mildred Anashie (22:50:21) (in thread): > Thank you too, Apologies for disturbing

Levi Waldron (22:57:37): > <!channel>apologies for the late notice, but I will be hosting tomorrow’s (Oct 17) Microbiome Virtual International Forum, with: > * a keynote talk “Advances and Challenges in Understanding the Virosphere”, and selected talks: > * “Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease” > * “Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut” > * “No evidence for a common blood microbiome based on a population study of 9,770 healthy humans”, and research highlights: > * “Probing the Metatranscriptome of the House Mosquito Culex tritaeniorhynchus from the Philippines” > * “Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift” > It’s free, 3h in total, happens every month, is a good way to learn about the latest microbiome research, and has opportunities for networking. You can register for free athttps://microbiome-vif.org - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Chiagoziem David (23:28:08) (in thread): > Thank you.

Chiagoziem David (23:29:24) (in thread): > :partying_face::tada:

2023-10-18

Peace Sandy (01:23:17) (in thread): > Thank you for the notice@Levi Waldron

Fortune Nnamdi (01:59:29) (in thread): > Thanks for the notice!:blush:

Odigiri Great Alume (03:23:12): > Good morning everyone. > Please I need help with alpha diversity in my study.

Peace Sandy (03:24:04) (in thread): > What kind of hep ?

Sinmi Adesanya (03:28:24) (in thread): > Amazing. Thank you for sharing@Levi Waldron!

Odigiri Great Alume (03:29:29) (in thread): > So here’s a link to my study@Peace SandyDOI 10.1099/acmi.0.000497.v3First I was sure CHAO1 and Inverse Simpson was used. While Chao1 decreased, Simpson increased. > > But then I’m no longer sure. Cos I’m now seeing Faith diversity. And I’m not sure what the status of all three would be. > > So here’s it. If you can help me look into the study and help confirm which alpha diversity was tested for and what the status is - Attachment (microbiologyresearch.org): Lower respiratory tract microbiome composition and community interactions in smokers > The lung microbiome impacts on lung function, making any smoking-induced changes in the lung microbiome potentially significant. The complex co-occurrence and co-avoidance patterns between the bacterial taxa in the lower respiratory tract (LRT) microbiome were explored for a cohort of active (AS), former (FS) and never (NS) smokers. Bronchoalveolar lavages (BALs) were collected from 55 volunteer subjects (9 NS, 24 FS and 22 AS). The LRT microbiome composition was assessed using 16S rRNA amplicon sequencing. Identification of differentially abundant taxa and co-occurrence patterns, discriminant analysis and biomarker inferences were performed. The data show that smoking results in a loss in the diversity of the LRT microbiome, change in the co-occurrence patterns and a weakening of the tight community structure present in healthy microbiomes. The increased abundance of the genus > Ralstonia > in the lung microbiomes of both former and active smokers is significant. Partial least square discriminant and DESeq2 analyses suggested a compositional difference between the cohorts in the LRT microbiome. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS. The linear discriminant analysis effect size (LEfSe) analyses identified several bacterial taxa as potential biomarkers of smoking status. Network-based clustering analysis highlighted different co-occurring and co-avoiding microbial taxa in the three groups. The analysis found a cluster of bacterial taxa that co-occur in smokers and non-smokers alike. The clusters exhibited tighter and more significant associations in NS compared to FS and AS. Higher degree of rivalry between clusters was observed in the AS. The groups were sufficiently distinct from each other to suggest that cessation of smoking may not be sufficient for the lung microbiota to return to a similar composition to that of NS.

Nana (03:39:00) (in thread): > @Levi Waldronthanks for sharing but today is 18 and the date said 17

Nana (03:42:25) (in thread): > @Levi Waldronthanks I now know exactly what to do

Esther Afuape (03:52:47) (in thread): > I think it was for 2am WAT:sweat_smile:

Peace Sandy (03:54:59) (in thread): > Is it not possible that your study can have more than 3 alpha diversity

Odigiri Great Alume (03:57:04) (in thread): > It is possible but how do I know which ones apply > And know if they increase or decrease. > I know it should be stated but it’s rather confusing that’s why I need extra pair of eyes

Odigiri Great Alume (04:01:17) (in thread): > Wait. The date says October 17th:thinking_face:

Peace Sandy (04:02:03) (in thread): > Most times it is not clearly stated, like in my paper, and then I think any alpha diversity mentioned in your study was applied

Odigiri Great Alume (04:03:06) (in thread): > Okay thank you.

Grace Ogundaini (04:54:05): > Hello everyone, > I found this articlehttps://bugsigdb.org/Study_766under “incomplete pages” and identified the DOI and Case study. All fields are now marked for review.<@UBNSEMS3S>@Svetlana Ugarcina PerovicI am not really sure on the next steps to take after completing an incomplete curation, when we complete papers like this, do we need to drop an update here for tracking or we don’t? - Attachment (BugSigDB): Study 766

Esther Afuape (04:58:58) (in thread): > Yes, you drop an update here so that it can be reviewed

Chiagoziem David (05:11:03): > https://bugsigdb.org/Study_796 - Attachment (BugSigDB): Study 796

Chiagoziem David (05:11:20): > Hello guys I am working on adding experiments to this guy

Chiagoziem David (05:19:50): > Although I am having issues formulating what the condition would be

Joan C. Chukwuemeka (06:28:29): > Hello<!here>How has our Microbiome study curation been?:blush:Mine has been an interesting learning & growth experience, that I sure will ever be grateful for. Thanks<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovicfor your wonderful guide and help:gratitude-asl:To work on Incomplete Study curations, Is there a way to filter out the ones no one is working on? Or I just select one and post here first to check for that?

Joan C. Chukwuemeka (06:30:13) (in thread): > @Chiagoziem Davidwhat is the challenge you’re facing in determining the condition?

Paulina Boadiwaa Mensah (06:43:08) (in thread): > Insightful!

Chioma Onyido (06:54:53) (in thread): > Hi@Joan C. ChukwuemekaI don’t know if there’s a way to automatically filter out what someone is currently working on but I noticed our colleagues posting the curations they’re reviewing. And they’ve been doing this since Saturday, some people even posted yesterday and the day before. > > Maybe scrolling and scanning through recent chats would help.:sweat_smile:

Joan C. Chukwuemeka (07:01:04) (in thread): > Scrolling and scanning through…hmmm…:thinking_face:That’s one way to go about it@Chioma Onyido. > Just got an idea - I think I’ll pick one and ctrl + F, to see if it has been mentioned in the channel. > Thanks:smiley:

Chioma Onyido (07:02:09) (in thread): > Great!That’seven an easier way to go about it.:+1:

Chiagoziem David (07:06:59) (in thread): > @Joan C. Chukwuemekawhat should be the condition

Chiagoziem David (07:07:24) (in thread): > Hello<@U1LCB8WEA>your help Is needed here

U1LCB8WEA (07:21:51) (in thread): > There are two dates for each event, the second date for this event is today, starting 9am NYC time

Esther Afuape (07:23:55) (in thread): > Thank you.Thatshouldbe 2pm WAT.

Joan C. Chukwuemeka (07:28:18) (in thread): > @Chiagoziem DavidAn Excerpt from the study:******“In this study, we applied these validated techniques to characterize how the small intestinal microbiome changes with increasing age, in adult subjects from 18 to 80 years of age.”**********“Aging and duodenal microbiome changes” ****seems to be the condition, however would need to confirm a close match in the EFO ontology

Chiagoziem David (07:29:19) (in thread): > Okay, thank you Very much

U1LCB8WEA (07:45:06) (in thread): > The condition is what is contrasted-which is age/aging. The body site would be small intestine.

Mildred Anashie (07:54:49): > Hello<@U1LCB8WEA><@UBNSEMS3S>I’m working on this for an experiment and it says there was a decreased abundance of H. Influenzae in the CD4+ low samples following 24 weeks and my Group name is as follows; > Group 0= Week 24 CD4+ low samples > Group 1 = Week 24 CD4+ high samples > > When entering my signatures the Group 1 abundance is showing decrease in CD4+ high samples sincethat’swhat is used as Group 1 > > My question is, can I swap the Group names so that the CD4+ low samples will be the Group 1 and CD4+ high samples will be the Group 0 that wayI’llbetter represent the abundance as decreased in CD4+ low samples? - File (PNG): image.png

Joan C. Chukwuemeka (07:56:07) (in thread): > Thanks<@U1LCB8WEA>.@Chiagoziem DavidSeen this response?

Chiagoziem David (07:56:48) (in thread): > Thank you very much<@U1LCB8WEA>and@Joan C. Chukwuemeka

U1LCB8WEA (07:59:01) (in thread): > (As Joan said, the exact terms from ontologies/drop-down menus, that was just off the top of my head!)

Chiagoziem David (08:05:20) (in thread): > Alright sire

Joan C. Chukwuemeka (08:06:25) (in thread): > Hello@Odigiri Great Alume, > Have you sorted this yet?

Odigiri Great Alume (08:07:51) (in thread): > Not yet. I sent a question to@Levi Waldronhe’s yet to respond. Are you free

U1LCB8WEA (08:09:18) (in thread): > The “normal” CD4 condition should probably be group 0. Looks like there are multiple experiments,some contrasting CD4, others contrasting time.

U1LCB8WEA (08:10:14) (in thread): > So I think you are right to do it as you propose

Joan C. Chukwuemeka (08:14:19) (in thread): > Here’s an excerpt from the study that i think would be helpful to determine that: a kind of question and answer section******L210: Were any statistical tests used to look for significant differences in alpha diversity? It appears as though NS have a higher alpha diversity than the other groups but I would like to see this tested using a One-Way ANOVA or Kruskal-Wallis test (whichever is more appropriate)******.Response:Added the statistical tests you mentioned, using ANOVA.******Changed**********:****Never smokers exhibited markedly higher average and diversity compared to FS and AS (Figs. 4A and 4B)T******o: Never smokers exhibited markedly higher average richness (ANOVA (32), p=1e-9) and diversity (ANOVA, p=0.00075) compared to FS and AS (Figs. 4A and 4B)************L211: In my opinion, Simpson’s index better measures species evenness than diversity. Was any difference observed between the groups using Faith’s Phylogenetic Diversity? **********Response: ****We computed Faith‟s Phylogenetic Diversity index among the three groups, and also a higher phylogenetic diversity was observed for Never smokers. This is now our new Fig. 4D, and we added: Faith‟s Phylogenetic Diversity index (33) also showed a higher value within errors (ANOVA, p=2e-8) for Never smokers compared to Active and Former (Fig. 4D).

Mildred Anashie (08:15:35) (in thread): > @Levi WaldronCan I get an insight into what you mean by Contrasting CD4 and some contrasting time? > > I curated as two experiments CD4 low and CD4 high at baseline and CD4 low and CD4 high at Week 24

Svetlana Ugarcina Perovic (08:16:04) (in thread): > @Grace Ogundainithanks!

Joan C. Chukwuemeka (08:18:51) (in thread): > I noticed the pdf had preprint watermark, perhaps that explains why there’s a sort of question and answer section:thinking_face:@Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina PerovicIs this usual for a published paper? a sort of question and answer section?

Chiagoziem David (08:20:38) (in thread): > Hmmm

Chiagoziem David (08:20:45) (in thread): > Ctrl f?

Joan C. Chukwuemeka (08:22:21) (in thread): > Yes@Chiagoziem DavidSee an example - File (PNG): image.png

Chiagoziem David (08:23:01) (in thread): > Mad oh:sweat_smile::sweat_smile:, that’s smart

Svetlana Ugarcina Perovic (08:23:34) (in thread): > @Joan C. Chukwuemekathat’sPeer review historyprovided in the end of the final version of published paper. When scientists want to publish their work, they first submit it for reviewing: this process is a communication between reviewers (your colleagues out of your university/institute, often anonymously) and scientists who want to publish their work. They have a mutual goal: to improve the paper to publish the most precise, concise and up-to-date work.

Mildred Anashie (08:24:17): > I’m working on this studyhttps://bugsigdb.org/Study_785from the NCBI cleanup, under studies without experiments and when I input the PMID the first image shows what I get > > I had to input it manually and what is in the second image is the outcome…I just want to know if I’m on track or if there’s another way to go about it@Levi Waldron - Attachment (BugSigDB): Study 785 - File (JPEG): IMG_4833 - File (JPEG): IMG_4831

Svetlana Ugarcina Perovic (08:25:15) (in thread): > Some journals have this option of visible/open reviewing process.

Joan C. Chukwuemeka (08:26:36) (in thread): > Oh wow!….That’s interesting and nice to make that part of the publication process public. It would be helpful for curation. Thanks@Svetlana Ugarcina Perovic:blush:@Odigiri Great AlumeI do hope the section helps your curation?

Svetlana Ugarcina Perovic (08:27:33) (in thread): > Actually yes,@Odigiri Great Alume, their discussion with the reviewer about apha diversity can help you:wink:

Svetlana Ugarcina Perovic (08:34:00) (in thread): > @Joan C. Chukwuemekasee this nice example > published paper:https://elifesciences.org/articles/83152review communication:https://elifesciences.org/articles/83152#sa1

Odigiri Great Alume (08:36:10) (in thread): > @Svetlana Ugarcina PerovicI will read through now. > However here’s what I’m confused about. > > So I have 5 experiments but I don’t know if each experiment is supposed to have a different alpha diversity measure according to the text below:point_down:(image 1). > > Also I’m not sure what increases and what decreases. And which diversity measures were used (faith, chao1 and Simpson in image 2) > > And lastly image 3 stated clearly that Chao and Simpsons were used. > > > > The experiments are > Active smokers vs Never smokers > Active smoked vs Former smokers > Former smokers vs Never smokers > Active smokers vs Former smokers and never smokers > Never smokers vs Active smokers and former smokers - File (JPEG): IMG_20231018_095608.jpg - File (JPEG): IMG_20231018_095825.jpg - File (JPEG): Screenshot_20231018-094813.jpg

Joan C. Chukwuemeka (08:38:54) (in thread): > Oh Yea….I see the review section here too… Thanks@Svetlana Ugarcina Perovic

Odigiri Great Alume (08:47:52) (in thread): > @Joan C. Chukwuemekado you get the question I justed posted?:pleading_face:If you can read it it can provide context > Thanks dear

Svetlana Ugarcina Perovic (08:48:30) (in thread): > @Odigiri Great Alumeyes, it looks like the experiments have a diff alpha diversity

Joan C. Chukwuemeka (08:48:43) (in thread): > Okay@Odigiri Great AlumeLet me check through.

Odigiri Great Alume (08:52:20) (in thread): > @Svetlana Ugarcina PerovicI think so too. However it’s confusing which ones to use for which experiments and what status to mark them as (decrease, increase or unchanged)

Nana (08:54:51) (in thread): > ok..noted

Joan C. Chukwuemeka (09:04:16) (in thread): > @Odigiri Great Alume******“Never smokers *****exhibited *******markedly higher average richness ******(ANOVA (32), p=1e-9) and******* diversity (*******ANOVA, p=0.00075)******* compared to FS and AS (Figs. 4A and 4B)”*****The statement above from the paper would suggest: > * decreased diversity & richnessfor ******FS (former smokers) and AS(Active smokers) *****which are *******the exposed groups****** > * Experiment would be -***** ********Never smokers vs Active smokers and former smokers > ** [see a snippet from the curation policy on alpha diversity below]***** - File (PNG): image.png

Chiagoziem David (09:08:16): > The event is still by 2 yeah?

Onyewuchi Esther Chikamso (09:08:53) (in thread): > What event@Chiagoziem David

Esther Afuape (09:14:36): > The virtual forum has started if anyone would like to join.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697597857987569 - Attachment: Attachment > <!channel> apologies for the late notice, but I will be hosting tomorrow’s (Oct 17) Microbiome Virtual International Forum, with: > • a keynote talk “Advances and Challenges in Understanding the Virosphere”, and selected talks: > • “Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease” > • “Personalized Clostridioides difficile engraftment risk prediction and probiotic therapy assessment in the human gut” > • “No evidence for a common blood microbiome based on a population study of 9,770 healthy humans”, and research highlights: > • “Probing the Metatranscriptome of the House Mosquito Culex tritaeniorhynchus from the Philippines” > • “Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift” > It’s free, 3h in total, happens every month, is a good way to learn about the latest microbiome research, and has opportunities for networking. You can register for free at https://microbiome-vif.org

Odigiri Great Alume (09:16:17) (in thread): > @Joan C. Chukwuemekathank you a bunch for this. > In essence for the experiment NS vs AS and FS > > they used chao1 and Simpson and they both showed decreased diversity

Joan C. Chukwuemeka (09:33:43): > Hello all, > I’ll be working to complete this incomplete study:slightly_smiling_face:https://bugsigdb.org/Study_542 - Attachment (BugSigDB): Study 542

Chiagoziem David (09:34:27) (in thread): > This :https://app.hopin.com/events/microbiome-vif-n-22/stages/7a09da98-cade-4102-8a8f-caefa2ea92fe@Onyewuchi Esther Chikamso

Odigiri Great Alume (09:37:19) (in thread): > @Joan C. ChukwuemekaI am thinking that that if NS exhibited higher richness and diversity compared to FS and AS. and judging from our conclusion on have a decreased diversity (Both Chao and Simpson) for the experiment NS vs AS and FS. > > Since NS showed increased diversity, I think the experiments > > FS vs NS will also show decreased diversity too. > Since according to them they said FS showed weaker correlation (FS is the exposed group) and we already know that NS showed higher correlation. > > AS vs NS will show Unchanged diversity for both Chao and Simpson too as AS is the exposed group and NS already showed increased diversity. I am thinking this because they stated here too that “the AS experienced almost no correlation at all (0.09, p = 0.69).”AS vs FS will also show unchanged diversity still based on the statement that”the AS experienced almost no correlation at all (0.09, p = 0.69)” > AS vs NS and FS will also show unchanged since AS experience no correlation > > Finally, if my thinking is correct, what do I do with “Across the entire set, a statistically significant (P=3e-7) positive correlation of 0.63 was observed between rich ness and diversity. Faith’s phylogenetic diversity index [47] also showed a higher value within errors for NS (ANOVA, P=2e-8) compared to AS and FS (Fig. 4d).”@Levi Waldron@Joan C. Chukwuemeka@Svetlana Ugarcina Perovic@Chioma Onyido:sob:Please does this make sense? - File (JPEG): IMG_20231018_095608.jpg

Joan C. Chukwuemeka (09:51:29) (in thread): > :thinking_face:@Odigiri Great AlumeI don’t think******correlation******is the same as the******richness and diversity measures******

UBNSEMS3S (09:54:10) (in thread): > We don’t curate correlations between different diversity measures.

UBNSEMS3S (09:55:14) (in thread): > “No. of OTUs” is a synonym of richness.

Odigiri Great Alume (10:02:57) (in thread): > @C. Mirzayi (please do not tag this account)I didn’t know how to go about it. So I started putting all my thoughts down:thought_balloon::pleading_face:Thanks for clarifying > > But please can you help me look at it for insight ma’am ? Because I know, they stated explicitly that they used Chao1 and Simpson for alpha diversity but it is not stated how each experiment increased, decreased or was not statistically significant(unchanged).

Joan C. Chukwuemeka (10:18:32) (in thread): > @Odigiri Great AlumeIn response to a question I once had,<@U1LCB8WEA>stated that“********experiments are defined by the contrasts made, and signatures are defined by the results of those experiments********.”Perhaps, you need to study & re-read through the paper“in-between the lines”.Possibly, check to be sure those number of experiments are the contrasts that were made, with respective resulting signatures.:shrug:Alpha diversity may be stated for just the group of contrasted conditions:thinking_face:

Chioma Onyido (10:26:05) (in thread): > In his previous questions on this same curation,We’vetried to look through the paper and the alpha diversity reported actually looks confusing to me, I mean they explicitly stated the chao and Simpson estimators used but what wecan’tseem to figure out if theres an increase or decrease in thegroups contrasted, becauseit’sreported in different places within the texts.

Odigiri Great Alume (10:29:24) (in thread): > @Chioma Onyidoexactly

Joan C. Chukwuemeka (10:29:55) (in thread): > I see:thinking_face:@Chioma OnyidoI think already spotted one though:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697634256412309?thread_ts=1697613792.054029&cid=C04RATV9VCY - Attachment: Attachment > @Odigiri Great Alume > “Never smokers* exhibited markedly higher average richness** (ANOVA (32), p=1e-9) and diversity (ANOVA, p=0.00075) compared to FS and AS (Figs. 4A and 4B)“ > > The statement above from the paper would suggest: > • decreased diversity & richness for FS (former smokers) and AS(Active smokers)** which are *the exposed groups > • Experiment would be - Never smokers vs Active smokers and former smokers > [see a snippet from the curation policy on alpha diversity below]**

Odigiri Great Alume (10:30:51) (in thread): > Yes@Joan C. Chukwuemekadid NS vs AS and FS

Joan C. Chukwuemeka (10:34:25) (in thread): > Alright@Odigiri Great Alume, I have an incomplete study I’m currently working on completing. .however, I’d try to spare some time to check & read the paper… hopefully we can sort this out:slightly_smiling_face:

Odigiri Great Alume (10:36:51) (in thread): > Thanks@Joan C. Chukwuemeka

Levi Waldron (11:10:42) (in thread): > And noted that today is Oct 18 - it was late when I composed the message!:smile:

Sinmi Adesanya (11:12:00) (in thread): > Yes. It started a while ago but is still ongoing so feel free to join in@Chiagoziem David

Sinmi Adesanya (11:14:22) (in thread): > Very insightful event so far@Levi Waldron. Well done!

Joan C. Chukwuemeka (11:17:21) (in thread): > Ok

UBNSEMS3S (11:39:30) (in thread): > Many studies include multiple experiments with different contrasts. > > If I compare baseline to 24M, I am contrasting on time. > If I compare low CD4 to high CD4, I am contrasting on CD4 count.

Joan C. Chukwuemeka (11:47:18) (in thread): > <@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina PerovicI’ve updated the study design for this study which was not previously captured to make the 1st section complete and marked as “Needs review” > > Proceeding to work on the Experiment section which is currently incomplete too

Chiagoziem David (11:57:06) (in thread): > Yeah, I had joined already:grin::smile_cat::grin:, was putting the link up for@Onyewuchi Esther Chikamso

Hodan Abdirisak (12:07:34) (in thread): > Today I was not in the network 🛜:disappointed:I am sorry to see late,<@U1LCB8WEA>:pray:thanks

Chiagoziem David (12:09:40) (in thread): > @Hodan Abdirisak, I think some sessions were recorded, maybe<@U1LCB8WEA>could help with that

Hodan Abdirisak (12:10:29) (in thread): > @Chiagoziem DavidThat is a good news

Sinmi Adesanya (12:10:35) (in thread): > I see:grin:

PATIENCE ONAH (12:12:39): > @PATIENCE ONAH has left the channel

Hodan Abdirisak (12:54:46): > I am working on NCBI clean up of this study Clostridium sensu stricto 1 is missing in signature what if i take only genera name which clostridium - File (PNG): Screenshot 2023-10-18 095029.png - File (JPEG): bmb-56-7-404-f3.jpg

Joan C. Chukwuemeka (12:57:13) (in thread): > @Hodan AbdirisakCheck this… I think it’s relatedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697204302943869?thread_ts=1697193924.756799&channel=C04RATV9VCY&message_ts=1697204302.943869 - Attachment: Attachment > The clostridium clusters are ones that we have never been able to formally identify.

Hodan Abdirisak (13:06:40) (in thread): > thanks@Joan C. Chukwuemeka

Hodan Abdirisak (13:08:25): > https://bugsigdb.org/Study_802/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 802/Experiment 1/Signature 2

Hodan Abdirisak (13:08:49): > https://bugsigdb.org/Study_717/Experiment_5/Signature_1 - Attachment (BugSigDB): Study 717/Experiment 5/Signature 1

Chloe (13:43:05) (in thread): > woooowu am really so excited about this …..i feel like a proffesional scientist already:innocent:

Joan C. Chukwuemeka (14:01:54) (in thread): > @Odigiri Great AlumeGoing through… > I think the Body site should be Lower Respiratory tract. > > Secondly, So far seen possibility of 3 experiments/contrasts > 1. Active smokers and former smokers (AS/FS) vs. Never smokers (NS): > Chao1 - decreased Inverse Simpson diversity - decreasedFaith’s Phylogenetic Diversity index - decreased2. Active smokers and Never smokers (AS/NS) vs. Former smokers (FS)3. Former smokers and Never smokers (FS/NS) vs. Active smokers (AS)Trying to see what the alpha diversity is forAS/NS vs. FSandFS/NS vs. AS?

Peace Sandy (14:29:20) (in thread): > @Hodan Abdirisakthis was addressed,I just saw that Joan shared the link with you ?

Joan C. Chukwuemeka (14:32:34) (in thread): > Based on the curation policy, alpha diversity is for the******exposed group - Group 1******Here, I see 3 groupings in the study, such that each group is compared with the other pair. > So here’s my perspective/deductions in terms of Alpha diversityExperiment 1Group 0: Active smokers and former smokers (AS/FS) Group 1: Never smokers (NS)Chao1 - IncreasedInverse Simpson diversity - IncreasedFaith’s Phylogenetic Diversity index - IncreasedExperiment 2Group 0: Active smokers and Never smokers (AS/NS) Group 1: Former smokers (FS)Chao1 - decreasedInverse Simpson diversity - decreasedFaith’s Phylogenetic Diversity index - decreasedExperiment 3Group 0: Former smokers and Never smokers (FS/NS) Group 1: Active smokers (AS)Chao1 -* decreased****Inverse Simpson diversity -*****decreased*****Faith’s Phylogenetic Diversity index - *****decreased**

U1LCB8WEA (14:33:06): > Hi<!channel>- I am unclear how the pages with missing NCBI ID (https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID) have all been resolved, even those on theTalk pagethat I’d previously found to be unresolvable? Orange names that cannot be mapped somehow to the NCBI taxonomy should be left alone and can have comments added, but not deleted. Can those who have been working on this help clarify? I can start studying histories but it will be easier if you can help me understand how so many NCBI IDs have been resolved. I see some names on this talk page have been solved (Gemellaceae= 539738, yeah!!) - if you solved something, please update the talk page to move that section to a “solved” section. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Odigiri Great Alume (14:35:31) (in thread): > @Joan C. Chukwuemekathank you > I will look at it now. Thanks a million

Joan C. Chukwuemeka (14:37:41) (in thread): > You’re welcome:+1:@Odigiri Great Alume

Chiagoziem David (14:39:56) (in thread): > Alright sire

Joan C. Chukwuemeka (14:48:35) (in thread): > <@U1LCB8WEA>I didn’t see any to work on for Missing NCBI IDs when I checked, however should we do the update on talk page forincomplete experiments that we complete?

U1LCB8WEA (14:50:42) (in thread): > The Talk page of a study is a great place to leave a record of any issues, uncertainties, or tricky decisions you had to make for that study, but you don’t need to use it. I used this particular talk page to discuss some of the taxonomic issues that may affect multiple signatures across the database.

Joan C. Chukwuemeka (14:51:34) (in thread): > Alright:gratitude-asl:

Esther Afuape (14:53:35) (in thread): > Hello everyone. I think clostridium XIVa should always be left as it is and not changed to Clostridium becausethey’renot the same.It’sbeen changed severally in an incomplete curation that I worked on by my colleagues.

Chioma Onyido (14:54:04) (in thread): > Thank you for this detailed answer@Joan C. Chukwuemekathis corroborated the previous experiments identified with an additional one. > > However don’t you think there’s more experiments to curate from table 3?:thinking_face:I think there’s 3 more; > AS vs NS > AS vs FS > FS vs NS

Chiagoziem David (14:56:01) (in thread): > Hmmmm

Peace Sandy (14:56:47) (in thread): > Should incomplete study be done on talk page as well

U1LCB8WEA (14:57:03) (in thread): > Thank you@Esther Afuape- yes, taxonomic edits should not introduce unwarranted confidence in the taxon or change its identity.

Chiagoziem David (14:57:44) (in thread): > Noted

Chioma Onyido (14:59:21) (in thread): > Table 3. Genera that were found to be significantly more abundant in each of the study groups using DESeq2. ******For each column, taxa differentially abundant with respect to one other group have the second group provided in parentheses*******… > > * - File (PNG): IMG_5288 - File (PNG): IMG_5289

Esther Afuape (15:13:31): > @Levi WaldronI just completed this study marked incomplete:https://bugsigdb.org/Study_739it’s a quite “minimalistic” study. The alpha and beta diversities were not mentioned. There were no confounders controlled for, neither were therevariables matched on. The participants were within a certain age range,I’mwondering if this could be used as a confounder controlled for?I’veadded the 2 experiments performed in the study and added their respective signatures. Please, review the curation and also confirm the condition I assigned to it. I had a bit of doubt about that. - Attachment (BugSigDB): Study 739

U1LCB8WEA (15:18:45) (in thread): > Inclusion criteria applied to everyone could be described in the Group 1 description or fit into the group names. I do have a question - the contrasts here are very unusual, because in an RCT you would normally compare the treatment group to the placebo group after treatment. But here the treatment group is never compared to the placebo group, instead both placebo and treatment groups are compared to themselves before and after treatment (even though by definition, the placebo group should not be any different after treatment).

Chioma Onyido (15:19:06) (in thread): > This is noted. Thanks!

U1LCB8WEA (15:20:07) (in thread): > The abstract only states one contrast, and it matches with my expectations of a normal RCT: “A significant increase was observed in the abundance of anaerobic bacterial genera Lactobacillus, Bifidobacterium and Faecalibacterium in the probiotic treated group (p < 0.01) as compared to placebo group.”

U1LCB8WEA (15:23:42) (in thread): > Remember, the Condition is what is being contrasted in the experiment,notsomething shared by both groups. From the objective:To assess the effect of a probiotic strain ******Bacillus clausii********** UBBC-07**~on gut microbiota and cytokines in IBD patients.~

U1LCB8WEA (15:28:18) (in thread): > Figure 2 isn’t reporting differential abundance, only abundant phyla

Nana (15:28:27) (in thread): > @Levi Waldronthe abstract only states one contrast which is? Please I need answer to this. It will make understand condition better

U1LCB8WEA (15:28:56) (in thread): > neither are figures 3-4.

Nana (15:28:59) (in thread): > And must all conditions be checked at OLS?

Esther Afuape (15:29:26) (in thread): > My apologies. I directly interpreted the results which accounts for the abundance in both the placebo and treatment groups. That was why I thought I needed to curate the signatures for both.I’llbe redoing this:pray:

U1LCB8WEA (15:29:31) (in thread): > A significant increase was observed in the abundance of anaerobic bacterial genera Lactobacillus, Bifidobacterium and Faecalibacterium ******in the probiotic treated group (p < 0.01) as compared to placebo group********.**

Esther Afuape (15:29:51) (in thread): > NowI’mconfused:sweat_smile:

U1LCB8WEA (15:30:02) (in thread): > ie purpose of the study is to contrasting the probiotic treated group to the placebo group.

Nana (15:31:35) (in thread): > So is ok to say that probiotic is the condition?

Nana (15:33:08) (in thread): > Is it ok to say my group 0 is placebo or placebo arm in my RTC arm was attached to each group through out the article

Esther Afuape (15:42:02) (in thread): > @Nanayeah, the group 0 should be placebo

Esther Afuape (15:44:44) (in thread): > @Levi Waldronthose are the only figures showing any kind of result in the study.. did I miss where the right differential abundances are stated in the paper or is it just those that are mentioned in the abstract (lactobacillus, bifidobacterium, and faecalibacterium)?

U1LCB8WEA (15:53:53) (in thread): > If results are mentioned in the abstract they must also be presented somewhere in the results, potentially along with other taxa that they found less interesting. These figures 2-4 show taxa, but they are not the results of a contrast. Ask:1. What contrasts are made?(one contrast = one experiment). Then2. What taxa are differentially abundant in that contrast? (this defines the signatures)

U1LCB8WEA (15:54:08) (in thread): > (thumbs up added to questions above)

Esther Afuape (15:57:10) (in thread): > @Levi WaldronGot that! But those results in the abstract were shown in figure 3 only throughout the study…

Odigiri Great Alume (16:15:30) (in thread): > I have looked at this again and I am sure there are five experiments in my study.@Joan C. ChukwuemekaThank you for helping. I’m really grateful. Your contribution gave me insights and made a lot clearer. > You guys are truly the best. > > However I am still going to find the answers to the alpha diversity and I will state them here when I’m done.:blush:@Joan C. Chukwuemekaalready found one for me. I will use that to find the rest. > > Again thanks to everyone

U1LCB8WEA (16:22:59) (in thread): > You’re right, yes it’s possible to use these figures to compare the treatment group to placebo group post-treatment, and to compare the treatment group post- to pre-treatment. But since there’s no indication of statistical significance in these tables, it seems the only way to know what are the statistically significant differential abundance is from the text of the Results. Signatures can be reported in text, sometimes not from figures or tables.

Chioma Onyido (16:23:15) (in thread): > Great! Well done.

Esther Afuape (16:27:03) (in thread): > Okay. So the 2 experiments ought to be placebo group as group 0 (after treatment) vs treatment group (after treatment) and treatment group (before treatment) as group 0 vs treatment group (after treatment)? These seem like they’ll end up having the same signatures@Levi Waldron

Joan C. Chukwuemeka (16:27:36) (in thread): > ******“Signatures can be reported in text, sometimes not from figures or tables.”******:thinking_face:Noted:pushpin:

Peace Sandy (16:29:08): > If they is something like uncultured bacterium in the increase group how should it be entered@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (16:29:15) (in thread): > Glad to help@Odigiri Great Alume, all the best.:grinning:

Odigiri Great Alume (16:30:42) (in thread): > Thanks!

U1LCB8WEA (16:36:24) (in thread): > @Esther AfuapeI think a good strategy would be for you to use the PDF article to highlight every sentence in the Results that reports a differential abundance result, then summarize all the contrasts they resulted from. I think they did make some contrasts of very limited scientific value (other than to show they are getting false positives), and we could make an editorial decision to skip those.

Esther Afuape (16:38:13) (in thread): > @Levi WaldronThank you so much for your time, Levi.I’llstart the curation afresh and revert.

Chioma Onyido (16:38:44) (in thread): > Hi@Peace Sandy, uncultured bacterium pops up just fine when entering signatures during curation, but if it doesn’t, you can go through another route by using the taxonomy browser.

U1LCB8WEA (16:39:26) (in thread): > You are welcome! I did notice that the experiments there are contrasts they made, although they seem to be larger than what is reported in the results, but the most important experiment - treatment vs placebo - is missing.

Chioma Onyido (16:39:38) (in thread): - File (JPEG): IMG_5292

Esther Afuape (16:40:40) (in thread): > The paper seems to be missing quite a number of information.I wonder if that one is incomplete or it justwasn’twell documented.

Peace Sandy (16:42:11) (in thread): > Thank You

Esther Afuape (16:43:57) (in thread): > We could use Bacillus clausii UBBC-07 as the signature for treatment vs placebo:thinking_face:

U1LCB8WEA (16:44:20) (in thread): > I haven’t reviewed it carefully - what is missing? But my scientific opinion about the analyses are that 1) the placebo pre vs placebo post should have no differential abundance, so this contrast serves only to show that they are seeing false positives. I wouldn’t enter these into bugsigdb because this isn’t a biologically meaningful contrast. 2) as a result of 1), I would not trust the treatment pre vs treatment post contrast, since it could be subject to the same false positives. My opinion would be to go only with the treatment post vs placebo pre, and hope that they haven’t created false positives in whatever same way they were created for the placebo vs placebo contrast.

U1LCB8WEA (16:47:50) (in thread): > Just keep in mind this ID says nothing other than that it is an unknown bacterium. There are many other “bacterium” in NCBI that specify which genus, family, … the bacterium belongs to, so if you have some taxonomic information you should try to use one of those instead.

Peace Sandy (16:49:29) (in thread): > Yes this is my confusion, should uncultured bacterium be entered as either increase or decrease or should they be left alone and not included

Peace Sandy (16:50:47) (in thread): > What was written is just s_uncultured bacterium

Chioma Onyido (16:51:23) (in thread): > Hmm but Your question says thatit’sin the increase group.

Peace Sandy (16:53:57) (in thread): > That’san instance,it can either be in the increase or decrease group, the emphasis is on the uncultured bacterium,I’vegone through previous studies andcan’tsee anyone with just uncultured bacterium.

Peace Sandy (16:54:38) (in thread): > If you enter the NCBI taxonomy ID , when you save it will appear as uncultured bacterium

Chioma Onyido (16:57:45) (in thread): > I do know that uncultured bacterium nomenclature is used when the species is unknown maybe due to lack of pure culture. > So if you have some additional taxonomic info you should use one of those instead like@Levi Waldronsaid.

Peace Sandy (16:58:58) (in thread): > Yes I have, I just wanted to be sure

Peace Sandy (16:59:00) (in thread): > Thank You

Chioma Onyido (16:59:41) (in thread): > I think I might have seen one or two studies with uncultured bacterium:thinking_face:

saskia (17:04:28): > @saskia has left the channel

Chioma Onyido (17:05:56) (in thread): > https://bugsigdb.org/Study_424/Experiment_1/Signature_2https://bugsigdb.org/Study_695/Experiment_4/Signature_2 - Attachment (BugSigDB): Study 424/Experiment 1/Signature 2 - Attachment (BugSigDB): Study 695/Experiment 4/Signature 2

Peace Sandy (17:11:56) (in thread): > Okay

Hodan Abdirisak (17:27:14) (in thread): > <@U1LCB8WEA>thanks for your clarification, so it means if you see clostridium NCBI that is missing in signature leave as it, red sign have no problems

Joan C. Chukwuemeka (17:34:51) (in thread): > From@Odigiri Great AlumeSo here’s the interpretation of table 3.:point_down:Genera that were found to be significantly more abundant in each of the study groups using DESeq2. For each column, taxa differentially abundant with respect to one other group have the second group provided in parentheses (taxa differentially abundant with respect to both the remaining groups do not have any cohorts mentioned in parentheses and are marked in bold. Highlighted taxa distinguish two different groups from the same third groupGenera that were found to be significantly more abundant: This part of the statement refers to the specific microbial genera (groups of related species) that were identified as having significantly different levels of abundance between different subject groups. The analysis likely used DESeq2, a statistical method, to determine these differences.For each column: The results are likely organized into columns, with each column corresponding to one of the subject groups being compared. In this case, the subject groups are “Never Smokers (NS),” “Former Smokers (FS),” and “Active Smokers (AS).”Taxa differentially abundant with respect to one other group have the second group provided in parentheses: This part of the statement clarifies that when a microbial genus is found to be significantly more abundant in one group compared to another, the second group (the reference group) is provided in parentheses. For example, if a genus is more abundant in AS compared to NS, you would see “Streptococcus.03 (AS)” to indicate that Streptococcus.03 is more abundant in AS than in NS.Taxa differentially abundant with respect to both the remaining groups do not have any cohorts mentioned in parentheses and are marked in bold:When a microbial genus is significantly more abundant in one group compared to both of the other groups, it is marked in bold and does not have any groups mentioned in parentheses. This is done to highlight these genera as they distinguish the group they are associated with from both of the other groups. > > In summary, the statement is describing how the results of the analysis were presented in a table, making it clear which genera are significantly more abundant in one group compared to another, and which genera stand out by being more abundant in one group compared to both of the other groups.

Joan C. Chukwuemeka (17:37:59) (in thread): > @Chioma OnyidoI get the idea of having other experiments asides what I deduced previously, based the post above I got from@Odigiri Great Alume. > I was looking at contrasts/ experiments with alpha diversity based on his question. > > However, from the curation policy,******absence of an alpha diversity is possible for an experiment, in which case it is left blank******- I stand to be corrected though -<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697634256412309?thread_ts=1697613792.054029&cid=C04RATV9VCY - Attachment: Attachment > @Odigiri Great Alume > “Never smokers* exhibited markedly higher average richness** (ANOVA (32), p=1e-9) and diversity (ANOVA, p=0.00075) compared to FS and AS (Figs. 4A and 4B)“ > > The statement above from the paper would suggest: > • decreased diversity & richness for FS (former smokers) and AS(Active smokers)** which are *the exposed groups > • Experiment would be - Never smokers vs Active smokers and former smokers > [see a snippet from the curation policy on alpha diversity below]**

Chioma Onyido (17:50:04) (in thread): > I’mnot sure but Idon’tthink I have access to the talk page? I only see@Levi Waldronwelcome message but Ican’tseem to reply or drop a comment.

Esther Afuape (18:21:26) (in thread): > @Levi Waldronso I have gone through the results again. The contrasts in the results text were between post intervention in the treatment group and post intervention in placebo. The only parts that have a “pre-placebo” are the parts I highlighted in green that have a percentage for pre and post intervention in both groups. To get a pre-intervention placebo result, I’ll have to pick the pre percentages in those parts and ignore the post but I doubt they’re reliable. > In the discussion and conclusion however, emphasis was on faecalibacterium, lactobacillus and bifidobacterium because they correlate with results in other studies. But they still referred to them as though they compared results from post-intervention for both groups. Should I curate this and assume it’s pre-placebo(as group 0) vs post-intervention in treatment group? - File (JPEG): de9cd4e3-5451-4c02-9e87-ab28df540ad0 - File (JPEG): cbff2f15-449c-4588-8d17-363a32370dc7 - File (JPEG): 763d1be6-1024-48ff-b87c-45dbce16cb38

Odigiri Great Alume (18:29:39) (in thread): > Since it states that NS (unexposed group) exhibited markedly higher average richness and diversity compared to AS and FS (exposed groups)Flipping the statement around, > I Believe it is then safe to say AS and FS exhibited lower (decreased) richness and diversity compared to NS. > > Hence since according to the curation policy we focus on the group one (exposed group) while assigning for decrease and increase: > > AS (exposed group) vs NS > FS (exposed group) vs NS > AS (exposed group) vs FS > AS and FS (exposed groups) vs NS > AS (exposed group) vs NS and FS > > All these will probably show decreased in chao1 and Simpson diversity. And I also think that Faiths diversity will decrease across all exposed groups too as it is statedthat Faith’s phylogenetic diversity showed a higher value within ******errors for NS compared to AS and FS******I STILL STAND CORRECTED:cry:@C. Mirzayi (please do not tag this account)@Levi Waldron@Joan C. Chukwuemeka@Chioma Onyido

Mildred Anashie (19:16:23) (in thread): > Okay….This is clear, Thank you<@UBNSEMS3S>Idon’tthink there was a seperate experiment for Baseline and week 24 for the CD4 condition:thinking_face:What I observed was CD4 low and CD4 high at baseline and at week 24 and I thinkthat’swhat differential abundance was reported forI’mwondering if the way I reported the experiment still represents the contrast I.e time and CD4

Mildred Anashie (19:20:23) (in thread): > @Levi Waldron<@UBNSEMS3S>:pray:

2023-10-19

Odigiri Great Alume (02:21:29) (in thread): > Oh my world:blush:@C. Mirzayi (please do not tag this account). > I understand now. OTU (Richness did not differ between the control group and the perinatal group) so it stays unchanged too. > > Thank you so much. > > > Please ma’am, I asked another question and tagged you,@Chioma Onyido@Joan C. Chukwuemekaand I have been on it for over a day now. Even though we have made some progress we still need clarity from the @mentors ma’am. > > Thank you for your patience. > Thank you a billion.:raised_hands:

Shruti Pal (03:41:21): > Hello community, I am Shruti. I have completed the first contribution and was looking for papers to curate as my second contribution. But I all present on github issues are already assigned. Can somebody tell me when will new tasks will be created?

Chiagoziem David (03:41:32) (in thread): > Omo:sweat_smile:

Joan C. Chukwuemeka (03:52:08) (in thread): > welcome@Shruti Pal:blush:

Joan C. Chukwuemeka (04:09:25) (in thread): > @Shruti PalThere are still few unassigned papers on the GitHub page > > Here’s a video/text guide on how you can filter out unassigned ones: > * Go to the******GitHub link (******https://github.com/waldronlab/BugSigDBcuration/issues/94) > * Click on the******“papers to curate” ****link > * On the view of “papers to curate”, click the drop down for******“Assignee”******at the top right side and choose the******“Assigned to Nobody” ****option > All the best:slightly_smiling_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. You’re also welcome to introduce yourself on the Bioconductor Slack channel #outreachy. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channels #bugsigdb and #outreachy. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation. - File (MPEG 4 Video): Finding BugSigDB GitHub unassigned papers.mp4

Fortune Nnamdi (04:30:17) (in thread): > You’rewelcome@Shruti PalDo well to ask questions as you continue your second contribution.This channel is quite active:sweat_smile:All the best!

Joan C. Chukwuemeka (04:31:03): > Hello<!here>:blush:Looking forward to our weekly office hour**** today at: ****https://us02web.zoom.us/j/2737200499Time: 10:00AM EDT / 3:00PM WAT/ 5:00PM EAT

Peace Sandy (05:32:09) (in thread): > Welcome

Peace Sandy (05:32:29) (in thread): > Glad you have been able to navigate through the first contribution

Peace Sandy (05:32:45) (in thread): > Please feel free to ask questions if you are stuck

Shruti Pal (05:32:53) (in thread): > Can I take the issues which do not have the labels “outreachy” or “second contribution”? Will those ones be counted?

Peace Sandy (05:34:51) (in thread): > No I think you can only take the issues labeled outreachy and second contribution, if they are no issues like that, kindly call the attention of the mentors

Shruti Pal (05:43:27) (in thread): > Okay

Chiagoziem David (06:16:06): > Hello guys , who here attended UNN:sweat_smile::sweat_smile:

Peace Sandy (06:26:54) (in thread): > Thanks for the reminder@Joan C. Chukwuemeka

Joan C. Chukwuemeka (06:36:59) (in thread): > @Shruti PalYou’ll also need to request for an account to be created for you first. The link for that is also on the same GitHub “welcome page”. This is important for carrying out the 2nd contribution. Cheers:slightly_smiling_face:

Shruti Pal (07:07:55) (in thread): > Thankyou@Joan C. Chukwuemeka

UBNSEMS3S (09:15:12) (in thread): > Thanks for the reminder. I was just about to post this.

UBNSEMS3S (09:15:58): > Hi apologies for the late notice but we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT today (in 45 minutes).https://us02web.zoom.us/j/2737200499

Hodan Abdirisak (09:34:12) (in thread): > Congratulations@Shruti Pal:clap::tada:go ahead

Peace Sandy (09:40:05) (in thread): > Thanks for the notice:rocket:

Nana (09:58:01) (in thread): > ok

Hodan Abdirisak (10:01:52): > It 5:00 PM the meeting started so Join please

Sinmi Adesanya (10:05:43) (in thread): > Noted Chloe. Thanks for the notice!

Esther Afuape (11:01:25): > https://bugsigdb.org/Study_739Hi<@UBNSEMS3S>please, help me to delete experiment 2 and the signatures in it - Attachment (BugSigDB): Study 739

Chioma Onyido (11:03:01): > Wheww! What an interesting discussion today!:grin:If you weren’t able to attend the meeting today, Here’s a summary of what I gathered from the office hour today: > -“Hallmarks of Study Designs”- by<@UBNSEMS3S> > 1. Randomized controlled trial (RCT): participants are randomly divided into groups. The treatment group receives the intervention while control group don’t. Here, researchersrandomly assign the conditions to people. > Classical example:50 people receive the real vaccine, 50 receive the placebo. Other examples: diet, exercise, etc. > > 2.Laboratory experiment: done using animal models, such as rats, pigs, mice, etc. > You’re not randomizing here because they’re all in the same condition. > > 3.Meta-analysis: this is a study design where researchers combine results from different studies. Meta analysis also means Pooling of results. > > 4.Prospective cohort studies: this is a study where researchers recruit a group of people based on a common characteristic (e.g. based on residence) and follow them up over time.Classical example #1: all patients recruited in a study who showed signs of depression in the month of October.Classical example #2: 100 people develop some diseases of interest (cases) and some people don’t (control) > > 5.Longitudinal observational study: time series studies. There is no intervention by the researcher in this kind of study.Data is collected at multiple time points.Classical example: observing COVID participants before and after the event.**** > 6. Case control: when you recruit cases ( people with a disease of interest) and controls (people without) similar on some characteristics. You would sometimes see matched on: age, bmi, sex, etc.Classical example: Healthy control group (control) and JIA group (case) > > 7.Cross-sectional observational: Contrasting 2 geographical areas or based on some socio-demographical characteristic (for example),usually at a single time point.*****Classical example***: community studies where they took 100 people from a neighborhood and contrasted with people from another neighborhood. > > Apologies if I left anything out, the recording will be posted soon.:pray:

Chiagoziem David (11:06:33) (in thread): > Thank you very much

Sinmi Adesanya (11:06:46): > Thank you so much<@UBNSEMS3S>and@Levi Waldronfor going over the curation process today. I’m sharing my paper here for thoughts on one of the first issues discussed.My question:In the study it is stated that it is a cross-sectional study. However, they used participants from the Framingham Heart Study which indicates a prospective cohort study design. Am I to add both the cross-sectional and prospective cohort to the study design section or just go with only what was stated in the paper?Here is a link to the paper:https://bugsigdb.org/Study_793 - Attachment (BugSigDB): Study 793

Sinmi Adesanya (11:07:27) (in thread): > Thank you@Chioma Onyido!:slightly_smiling_face:

Esther Afuape (11:08:54) (in thread): > Thank youuu:heart:

Desire Oluwarotimi (11:13:44): > @C. Mirzayi (please do not tag this account)@Levi WaldronI have asked this question before and Levi redirected me to the curation policy. It says there are two main sequencing types; 16S and WMS. > > How is metagenomic sequencing supposed to be curated? Is it considered a type of WMS? > > I’m looking forward to seeing Chloe’s update with the curation policy too.

Chinwendu Enyinna (11:18:41): > Hi<@UBNSEMS3S><@U1LCB8WEA>.Thank you for the insightful session. I would love to get clarity on this. In the paper I’m curating, oral, fecal, and serum samples were collected and analyzed. I am curating these as separate experiments. However, in reporting the data for the oral sample results, the sequencing used is a novel technology (2bRAD-M to be precise), and this wasn’t included as part of the sequencing options I can select from. How do I navigate this? Is it okay to select WMS for this? > > Here’s the paper for more contexthttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10355065/ - Attachment (PubMed Central (PMC)): Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites > Since the coronavirus disease 2019 (COVID-19) outbreak, many COVID-19 variants have emerged, causing several waves of pandemics and many infections. Long COVID-19, or long-term sequelae after recovery from COVID-19, has aroused worldwide concern because …

U05T2TFALH4 (11:19:46): > <@UBNSEMS3S>could you please delete experiments 4 & 5 for this study? Thank you

Joan C. Chukwuemeka (11:29:56) (in thread): > @Desire OluwarotimiWMS means Whole Metagenome Sequencing. The study I curated used Shotgun metagenomic sequencing, which I captured under the WMS. > > Here’s info I got from research on that:******Whole metagenome sequencing (WMS) ****is a powerful sequencing approach that provides insight into community biodiversity and function. It involves the******sequencing of all of the DNA in a sample******, regardless of the species or organism that it comes from.******Shotgun metagenomic sequencing******allows researchers to***** comprehensively sample all genes in all organisms present *****in a given complex sample. The method enables microbiologists to evaluate bacterial diversity and detect the abundance of microbes in various environments. Shotgun metagenomics also provides a means to study unculturable microorganisms that are otherwise difficult or impossible to analyze.

Joan C. Chukwuemeka (11:34:18) (in thread): > This incomplete study I’m working to complete is for 3 healthy individuals. > > If the group 0 is “before intake of the antibiotic” and group 1 is for “during or after intake”, what will be number for the groups? should it be 3 for both?<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicHere’s an excerpt: > In the present study, we used pyrosequencing tags spanning the V6 and V3 regions as well as full-length 16S rRNA sequences to analyze the bacterial community composition in a time series of stool samples obtained from three healthy adults before, during, and after a short course of the antibiotic ciprofloxacin (Cp).

Desire Oluwarotimi (11:43:48) (in thread): > Thank you@Joan C. ChukwuemekaI’ve done a bit of research on my part too but I just thought it best to hear also from the mentors.

Joan C. Chukwuemeka (11:44:17) (in thread): > Okay

Odigiri Great Alume (11:50:22) (in thread): > Looking at your study, I think they used alongitudinal cohort study design. This is because it involved the continuous follow-up of a specific group of individuals (cohorts) over an extended period of time to investigate various health-related factors, starting in 1948 with the Original Cohort and later expanding to include the Offspring Cohort and the 3rd Generation cohort. > > Cross-sectional study is conducted with different samples.Longitudinal study is conducted with the same sample over the years. > @Sinmi Adesanya** hope this helps**

UBNSEMS3S (11:54:35): > Recording of today’s office hours - File (MPEG 4 Video): video1222635148.mp4

Sinmi Adesanya (12:06:12) (in thread): > I see. Thank you@Odigiri Great Alume. I’ll look through it again.

Peace Sandy (12:27:58) (in thread): > Thank you so much for the recording,can’twait to go over it again.Today’ssession was really insightful > > Thank You@C. Mirzayi (please do not tag this account)and@Levi Waldron

Esther Afuape (13:45:58): > @Levi Waldron<@UBNSEMS3S>concerning this study:sweat_smile::https://bugsigdb.org/Study_739, I decided to go with just one experiment contrasting the placebo group before intervention and the treatment group after intervention. For the signatures, I picked those that were emphasized on in the abstract and discussion. They were found to be in line with similar studies and I guess that’s why they focused on those. I’ll like to delete experiment 2 and its signatures. Please review and let me know if this is fine. - Attachment (BugSigDB): Study 739

Chiagoziem David (19:30:35) (in thread): > Thank you very much<@UBNSEMS3S>and<@U1LCB8WEA>

2023-10-20

Karen254. Kingecha (00:20:49) (in thread): > Thank you for the recording

Peace Sandy (02:22:47) (in thread): > Thank You@Chioma Onyidothis is really nice:+1:

Chiagoziem David (03:39:16): > Good morning all. > It’s Friday:comet:, endeavour to rest and have some fun today.. > Remember also to watch what you eat , as it gets to your gut and affects your gut microbiome:face_with_peeking_eye:….. You wouldn’t want us calculating alpha diversity changes on you:smile_cat:…:v:

Hodan Abdirisak (06:44:18) (in thread): > Thanksgiving@Chioma Onyido

Peace Sandy (06:45:10) (in thread): > @Chiagoziem DavidI pointed out that I was working on this study, went back to check and found out that you had worked on it

Peace Sandy (06:45:58) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1697474251938029 - Attachment: Attachment > I just identified this incomplete study and would and one without signature, I would like to work on it > > https://bugsigdb.org/Study_796 > > https://bugsigdb.org/Study_765

Peace Sandy (06:46:23) (in thread): > Please can we check through the messages,before going ahead to work on studies

Chiagoziem David (06:47:27) (in thread): > I am really sorry@Peace Sandy, my bad. I will try to cross check next time:pray::pray:

Nana (06:50:04): > @Levi Waldronplease help delete experiment 2 and it’s signature of this experimenthttps://bugsigdb.org/Study_597 - Attachment (BugSigDB): Study 597

Peace Sandy (06:55:23): > Hello @everyoneI’llbe working on this study with no experimentshttps://bugsigdb.org/Study_810 - Attachment (BugSigDB): Study 810

Peace Sandy (07:16:28) (in thread): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi WaldronIcan’tfind the full article to this study

Peace Sandy (07:16:57) (in thread): > It’sfine@Chiagoziem David

Svetlana Ugarcina Perovic (08:37:50) (in thread): > ****Microbial community sequencing**** > includes 2 methodological approaches: > > 1. microbial community amplicon sequencing == MARKER GENE SEQUENCING > *most commonly sequenced marker gene is 16S rRNA gene > > AND > > 2. microbial community whole genome shotgun sequencing == METAGENOMICS > > See this threadhttps://twitter.com/svetlana_up/status/1394613676875915268 - Attachment (X (formerly Twitter)): Svetlana U. Perović on X > “shotgun and 16S metagenomics data” > > 16S metagenomics is a misnomer – a wrong or inaccurate use of a name or term > > TL;DR 16S rRNA gene sequencing is NOT metagenomics > > Well if you are still in doubt, you should read the thread below. > 1/5

Svetlana Ugarcina Perovic (08:39:34) (in thread): > Still most scientists are using “metagenomic sequencing” when they talk aboutMicrobial community sequencing

Svetlana Ugarcina Perovic (08:44:50) (in thread): > https://bugsigdb.org/Curation_Policysays: > > Two main types: 16S and WMS (Whole Metagenome Sequencing) > > 16S -> 16S rRNA gene sequencing (type of microbial community amplicon sequencing) > > AND > > Whole Metagenome Sequencing -> microbial community whole genome shotgun sequencing or whole metagenome sequencing

Svetlana Ugarcina Perovic (08:46:00) (in thread): > Hope this helps@Desire Oluwarotimi@Joan C. Chukwuemeka

Svetlana Ugarcina Perovic (08:52:07) (in thread): > It’s with incorrect DOI. And indeed it seems not available.

Peace Sandy (08:52:45) (in thread): > Oh Okay…Thank you

Svetlana Ugarcina Perovic (08:54:54) (in thread): > But we should reported/recorded this. What’s the protocol for this case?<@UBNSEMS3S>@Levi Waldron

Svetlana Ugarcina Perovic (08:57:33): > Happy Friday!https://twitter.com/svetlana_up/status/1715344373930475623 - Attachment (X (formerly Twitter)): Svetlana U. Perović on X > Together w/@outreachy, #BugSigDB is supporting & CELEBRATING* diversity in open source & open science! > > Right now, >30 applicants are active in curating microbiome studies during contribution stage https://t.co/V60qzB8x6X > > :clap:@outreachy, congrats on >1000 successful internships!

PATIENCE ONAH (09:12:39): > Hi@C. Mirzayi (please do not tag this account), I requested to be assigned to an article for my second contribution on GitHub. Can you please look it up.

Joan C. Chukwuemeka (09:22:16) (in thread): > Sure:+1:@Svetlana Ugarcina Perovic. Thanks

Svetlana Ugarcina Perovic (09:40:23) (in thread): > Could you please provide a link to it?

UBNSEMS3S (10:05:51) (in thread): > Done.

UBNSEMS3S (10:08:29) (in thread): > I think this paper was never curated due to not having any differential abundance results with statistical significance testing.

UBNSEMS3S (10:08:43) (in thread): > So it might not be one that can be curated, unless you’re seeing results somewhere I am not?

PATIENCE ONAH (10:09:51) (in thread): > Thank for your response.https://github.com/waldronlab/BugSigDBcuration/issues/129 - Attachment: #129 Association Between Breastmilk Microbiota and Food Allergy in Infants. > Association Between Breastmilk Microbiota and Food Allergy in Infants – Shuo Wang et al. — Front Cell Infect Microbiol.
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8790183/

UBNSEMS3S (10:10:40) (in thread): > Sounds good. Deleted.

UBNSEMS3S (10:11:11) (in thread): > Deleted.

Svetlana Ugarcina Perovic (10:11:57) (in thread): > Ok, I see it now.<@UBNSEMS3S>will assign it once your 1st contribution checked. Thank you for your patience!

UBNSEMS3S (10:12:43) (in thread): > Looks like the incorrect study is not a microbiome study and the correct article has already been curated. Deleted.

UBNSEMS3S (10:13:15) (in thread): > Checking first contributions now!

Svetlana Ugarcina Perovic (10:13:28) (in thread): > Thanks<@UBNSEMS3S>

PATIENCE ONAH (10:15:08) (in thread): > Alright,@Svetlana Ugarcina Perovicthank you so much for your support.

Nana (10:20:38) (in thread): > <@UBNSEMS3S>thanks

PATIENCE ONAH (10:30:33) (in thread): > Thank you@C. Mirzayi (please do not tag this account), I’m waiting for your feedback

Hodan Abdirisak (10:36:46) (in thread): > https://twitter.com/HodanAbdirazak/status/1714367604003831844?t=GoBw-8P9UrfDYcxKrrd0AA&s=19 - Attachment (X (formerly Twitter)): Hodan Abdirazak on X > I am glad to pass the contribution stage of @outreachy by curation of microbiome studies, it is the third week & it was a great to join supportive community that help each other @Bioconductor #bugsigdb @outreachy

Peace Sandy (10:37:39) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:blush:

Peace Sandy (10:38:09) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Joan C. Chukwuemeka (10:45:42) (in thread): > Okay<@UBNSEMS3S>, wow. I saw a figure with statistical diversity info below, and thought it will be curatable. > I’ll leave it then and check another one - File (PNG): image.png

UBNSEMS3S (11:15:54) (in thread): > This is alpha diversity but not differential abundance.

Chioma Onyido (11:24:41): > Hi<!here>:wave:I’ll beworking to completebugsigdb.org/Study_805which currently has no experiments.

Joan C. Chukwuemeka (11:25:23) (in thread): > Yes…Was expecting that differential abundance will be listed, since alpha diversity was done. > Thanks:blush:<@UBNSEMS3S>

UBNSEMS3S (11:36:15) (in thread): > @PATIENCE ONAHThe article has been assigned.

Joan C. Chukwuemeka (11:37:54) (in thread): > <@UBNSEMS3S>I’d like to ask though: What does V3refOTU Abundance mean? there’s a supplement excel file with that info.******Dataset S5. Comparison of V3refOTUAbundance between Participants************The file contains EDGE software output listing individual P values************and cumulative FDRs (known as Q values) for a test of interindividual************variation in V3 refOTU abundance.************Found at doi:10.1371/journal.pbio.0060280.sd005 (189 KB XLS).******

UBNSEMS3S (11:41:16) (in thread): > Ok this could be curated but it has 528 significant results. It looks like perhaps table 7 includes only significant results (as well as one not significant result) fromt he Bacteroides genus. I still don’t know that this is easily curatable or worth the effort.

Joan C. Chukwuemeka (11:43:57) (in thread): > Okay.

Joan C. Chukwuemeka (12:23:41): > Good day<!here>I’ve selected the incomplete study @https://bugsigdb.org/Study_767, with the goal to complete it:seedling: - Attachment (BugSigDB): Study 767

Esther Afuape (12:33:01): > Hello everyone.I’llbe completinghttps://bugsigdb.org/Study_835 - Attachment (BugSigDB): Study 835

PATIENCE ONAH (12:41:52) (in thread): > Thank you so much@C. Mirzayi (please do not tag this account)

Nana (13:54:52): > <!here>..hello family..TGIF.. happy weekend all..enjoy the rest of your night

Nana (13:58:04): > <!here>hello all..I will be working to complete this incomplete studyhttps://bugsigdb.org/Study_454 - Attachment (BugSigDB): Study 454

Chioma Onyido (15:55:04) (in thread): > Study 805 seems to be a duplicate curation forbugsigdb.org/Study_804. I confirmed this after I tried to add the PMID and it flagged as “must be unique”. > The curator probably added 2 new studies during curation, focused on one (study 804) andmust’veforgotten about the other one (study 805).:thinking_face:Could you help delete thishttp://bugsigdb.org/Study_805please?@Levi Waldron<@UBNSEMS3S> - Attachment (BugSigDB): Study 805

2023-10-21

Chiagoziem David (01:46:52) (in thread): > 1000:eyes::exploding_head:

Joan C. Chukwuemeka (02:53:46): > I’m thrilled to be part of this Bioconductor BugSigDB Community. > > The BugSigDB project truly stands out as a remarkable & timely solution.******Imagine having all host-associated microbiome differential abundance signatures in one place ****:smiley:******- it saves time spent in going through research publications one after the other, enhances data analytics, and offers numerous efficiency benefits.******While I acknowledge that the BugSigDB team doesn’t focus on“policing”authors as some errors are uncovered during study curation, I envision a future where authors adopt standardized practices, making their research curatable & readily available on BugSigDB. > > I’m deeply grateful for the privilege to contribute to what I see as the future****“Google of microbial signatures.”****:seedling:My heartfelt thanks go out to our mentors<@UBNSEMS3S><@U1LCB8WEA>and@Svetlana Ugarcina Perovicand fellow contributors. > > Since it’s the weekend, let’s exercise patience when waiting for responses from our mentors, considering the time zone differences. > > And don’t forget to set aside time for self-care and rejuvenation, as it’s essential for productivity and overall well-being. > > Wishing everyone a wonderful and restful weekend.:blush:

Odigiri Great Alume (05:04:04): > Good morning and happy weekend everyone. > So I finished adding signatures to the study #575 that Also needed some corrections. > > Here’s what I found. > > There were two experiment recorded. One experiment compared control groups (infants who received no antibiotics) and perinatal groups ( all 3 groups exposed to antibiotics i.e, Intrapartum antibiotics prophylaxis group, postnatal group and IAP + Postnatal group). In this experiment they used student t-test to compare each group with the control and then used one way ANOVA to compare perinatal groups ( all groups combined) with the control. > They found that all taxa abundant in each group were same taxa abundant in all group combined when compared with the controls. Hence I decided to record only one experiment here (perinatal vs control) as it broadly contains all the result). I also recorded the signatures > > in the second experiment, all the perinatal groups (IAP, postnatal, postnal + IAP) were exposed to courses of antibiotics (No course, one or two courses, and three or more courses) and then compared with control group. This experiment did not yield any statistical significance between these courses and control. > Hence I have proceeded to record the experiment without signatures (please correct me if I’m wrong to do this) > > I’m recording the second experiment as ” Control group vs perinatal groups with antibiotics courses) > > The study link ishttps://bugsigdb.org/Study_575Please if you have time help look at this.@C. Mirzayi (please do not tag this account)@Levi Waldron@Chioma Onyido@Joan C. Chukwuemeka@Svetlana Ugarcina Perovic - Attachment (BugSigDB): Study 575

Mildred Anashie (08:57:01) (in thread): > I had the same issue for study 785 earlier on and was wondering why and stopped working on it, I asked a question concerning that but I guess the mentors missed it. > > Aftter seeing this@Chioma OnyidoI just realized that it’s a duplicate study and the curator has completed it already as Study 786 so please deletehttps://bugsigdb.org/Study_785<@UBNSEMS3S>@Levi Waldron:pray: - Attachment (BugSigDB): Study 785

Peace Sandy (09:30:37) (in thread): > Hi@Odigiri Great AlumeI tried clicking on the link andit’svalid, can you share the correct link

Odigiri Great Alume (09:34:24) (in thread): > http://dx.doi.org/10.1038/s41390-021-01494-7@Peace SandyI will share the curation link now however that’s the study

Peace Sandy (09:34:58) (in thread): > Okay

Odigiri Great Alume (09:45:01) (in thread): > @Peace Sandyhttps://bugsigdb.org/Study_575Thank you

Peace Sandy (10:08:00) (in thread): > Okay

Nana (12:47:44): > can 2 body sites be reported for one experiment ?

Chioma Onyido (13:02:33) (in thread): > Hi@Odigiri Great Alume, > So I read through the paper and also checked your curations. > > I think experiment 1 and experiment 2 are accurate.:+1:However for experiment 1, I think you’re missing a signature “firmicutes” which was found to be more abundant in perinatal group (at p < .002) > > Also I agree that experiment 2 has no signatures because there was no statistical significance, both in figures/tables and within texts, which is still okay. > > According to<@UBNSEMS3S>, > “Differential abundance is when you compare relative abundances between groups to see if there was astatistically significant difference”.And in<@U1LCB8WEA>’s words, > > “an experiment can have 0, 1, or 2 signatures depending on how many significant results are reported for that contrast”https://community-bioc.slack.com/archives/C04RATV9VCY/p1697409403682259?thread_ts=1697409002.869499&channel=C04RATV9VCY&message_ts=1697409403.682259“…So it is perfectly possible to perform one or more experiments and find no statistically significant results, such as unchanged alpha diversity and no signatures of differentially abundant taxa”https://community-bioc.slack.com/archives/C04RATV9VCY/p1697410390867449?thread_ts=1697380986.698779&channel=C04RATV9VCY&message_ts=1697410390.867449My thoughts. I hope this helps. - Attachment: Attachment > an experiment can have 0, 1, or 2 signatures depending on how many significant results are reported for that contrast. - Attachment: Attachment > @Joan C. Chukwuemeka is the advice I just gave on some other articles about what constitutes an Experiment helpful? The key message is that experiments are defined by the contrasts made, and signatures are defined by the results of those experiments. So it is perfectly possible to perform one or more experiments and find no statistically significant results, such as unchanged alpha diversity and no signatures of differentially abundant taxa.

Odigiri Great Alume (13:05:45) (in thread): > You don’t curate signatures for ctrl groups. Only for exposed groups.

Joan C. Chukwuemeka (13:10:57) (in thread): > @NanaI think it’s possible for an experiment to have 2 body sites…the study I curated as second contribution did and<@UBNSEMS3S>confirmed I could curate both. I’m uncertain about curating signature for controls. Let’s wait to hear from<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic

Odigiri Great Alume (13:16:31) (in thread): > Bugsigdb won’t even let you curate for ctrl groups. It automatically records signatures for group 1 and group 1 is usually the exposed group@Joan C. Chukwuemekabut I’m sure the mentors can clarify.:blush:

Odigiri Great Alume (13:19:08) (in thread): - File (JPEG): Screenshot_20231021-181404.jpg

Odigiri Great Alume (13:20:47) (in thread): > Thank you@Chioma OnyidoI will look through the paper and add it. Thanks

Nana (13:22:08) (in thread): > @Joan C. Chukwuemekaso I can have 2 body sites in one experiment?

Odigiri Great Alume (13:22:57) (in thread): > Yes you can from what@Joan C. Chukwuemekaexplained I guess

Chioma Onyido (13:25:01) (in thread): > You’re welcome. This paper required some between the lines reading tho!:sweat_smile:Well done.:+1:

Joan C. Chukwuemeka (13:46:31) (in thread): > Yea,@Odigiri Great AlumeBugSigDB signature prompt is usually for group 1, the exposed group, hence why I said I’m uncertain about the possibility of that for control groups:blush:I also believe signatures for the exposed group are usually the focus of most studies, as that shows the deviation from what is known to be “normal”(control groups), and informs decision on possible therapeutic interventions where needed.

Joan C. Chukwuemeka (13:54:40) (in thread): > So,@Nanacurating signature for controls may not be needed.:+1:@Odigiri Great Alume

Nana (13:59:11) (in thread): > Ok .thanks guys

Doreen Wanyama (14:19:40): > Good day everyone. My name is Doreen Wanyama. I just saw this project on the outreachy site and got interested. I just hope I have not missed out on a lot. I have always wanted to contribute in the health field and share my ideas with others. I like the work going on at#bugsigdband I can’t wait to make positive impact to human health. I just started going through the resource materials now. Any tips or advise or directions I from this community will be highly appreciated. Thank you in advance.

Chioma Onyido (14:21:53) (in thread): > Hi@Doreen Wanyamawelcome to the community!:blush:It’swarm over here and really active too! > Kindly go through the pinned messages to get started.

Chioma Onyido (14:22:37) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939 - Attachment: Attachment > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on Github for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. If you have any questions, please post them in this channel so that all applicants can see the answers. Thank you so much for your interest and we look forward to working with you.

Doreen Wanyama (14:22:47) (in thread): > Thanks a lot@Chioma Onyido

Chioma Onyido (14:23:18) (in thread): > This one too.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Tolulope Ogunleye (14:26:49) (in thread): > Hi Doreen, you’re welcome. You will getinstructions about how to makeyourfirst contributionherehttps://github.com/waldronlab/BugSigDBcuration/issues/94and you can ask help to us every time you need - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identify common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_7UTYhqDc3qYwiEu > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration Github issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. You’re also welcome to introduce yourself on the Bioconductor Slack channel #outreachy. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channels #bugsigdb and #outreachy. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 10 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20230929T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-december-2023-internship-round/communities/bioconductor/microbiome-study-curation/contributions/.

Odigiri Great Alume (14:28:32) (in thread): > :+1:

Esther Afuape (14:31:20) (in thread): > Welcome, Doreen:hugging_face:

Odigiri Great Alume (15:37:14) (in thread): > True, it took my some time to figure out much. Again thanks for aways helping out.@Chioma Onyido

Joan C. Chukwuemeka (15:42:33) (in thread): > Welcome to the community@Doreen Wanyama:blush:

Peace Sandy (16:06:30) (in thread): > Welcome@Doreen Wanyama

Mildred Anashie (16:29:36) (in thread): > Welcome@Doreen Wanyama

Odigiri Great Alume (18:58:33) (in thread): > Welcome onboard. We all here to help you get started.

Esther Afuape (19:41:21): > Hello everyone. I have a bit of confusion on the results in the paper I’m working on. The study is about the effect of Covid vaccine on breast milk micobiota. Samples were collected pre-vaccination, one week post first-dose, one week post-second dose and one month post-second dose. Over 100 differentially abundant taxa were identified between pre and post vaccination time points, 10 of which remained differentially abundant throughout all three post-vaccination timepoints. > There’s a long list in the supplementary file that shows the abundant species at each time point and it also shows those that were present at all the time points. > My question now is should I be creating an experiment for each time point and creating individual signatures for them or should I create a single experiment and curate the abundances that occurred at all the time points? There’s a Venn diagram (attached below) that shows how the abundant species are distributed amongst the time points, with some occurring between 2 times points. This didn’t seem like the main focus of the study, I also attached the abstract. I’m leaning towards using the abundance at all time points but I also don’t want to underrepresent the information in the paper.@Levi Waldron<@UBNSEMS3S> - File (JPEG): 8f986601-8a6f-48b2-a38b-e2d32abc3a0a - File (JPEG): aeaffe4c-9d3d-4a15-922d-784bcfe48c8c

Sinmi Adesanya (22:03:39) (in thread): > Welcome@Doreen Wanyama!:slightly_smiling_face:

Onyewuchi Esther Chikamso (22:40:14) (in thread): > Did you click on this edit icon? You should be able to drop a comment there@Chioma Onyido - File (JPEG): IMG_20231022_033924.jpg

Chioma Onyido (23:11:21) (in thread): > When I clicked, it tried to edit the message. ???

Chioma Onyido (23:50:07) (in thread): > I think I figured it out, I clicked on the discussion (within the three dots). Thank you!

2023-10-22

Hodan Abdirisak (02:07:32) (in thread): > @Doreen Wanyamawelcome:hugging_face:

Hodan Abdirisak (02:33:57): > Happy Sunday:sunny:all of you:pray:I wish you bright and joyful day

Esther Afuape (02:56:40) (in thread): - File (PNG): IMG_3575

Esther Afuape (02:57:30) (in thread): > I still need help with this:face_holding_back_tears:@Levi Waldron<@UBNSEMS3S>@Chioma Onyido

Hodan Abdirisak (03:03:06): > https://bugsigdb.org/Study_807this study form was completed but marked as incomplete then I reviewed and I didn’t get any corrections in my understanding then I marked complete - Attachment (BugSigDB): Study 807

Odigiri Great Alume (07:13:52) (in thread): > Can you provide the link to the study so I’d go through it pls.@Esther Afuape

Peace Sandy (08:15:57) (in thread): > I think you should look out for the contrast in the experiment

Peace Sandy (08:16:14) (in thread): > First look out for what is being contrasted in the paper

Chioma Onyido (08:27:03) (in thread): > Hi@Esther Afuape. If you can provide a link to the paper so that we’ll help look at it.

Esther Afuape (08:27:46) (in thread): > https://www.nature.com/articles/s41541-023-00745-4 - Attachment (Nature): COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition > npj Vaccines - COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition

Peace Sandy (08:38:50) (in thread): > Hi@Esther AfuapeI think one of your experiments should be on pre and post vaccination timepoint, from this part of the paper - File (JPEG): IMG_5785

Peace Sandy (08:39:40) (in thread): > Let me point you to some explanations by the mentors too that might help

Esther Afuape (08:39:46) (in thread): > Yes I know that.I’masking ifit’salso necessary to create experiments for each time point separately

Peace Sandy (08:40:11) (in thread): > Do the time point have any contrast ?

Peace Sandy (08:40:38) (in thread): > If you are creating any experiments,they should be some form of contrast

Esther Afuape (08:42:03) (in thread): > Pre-vaccination(baseline) versus each of the time points?

Peace Sandy (08:43:43) (in thread): > Okay, let me check the figures

Esther Afuape (08:47:03) (in thread): > The figures are here - File (PDF): d53da1fe-ccfb-047e-9e6a-4ef064f7b0c6

Peace Sandy (08:48:25) (in thread): > See this@Esther Afuapehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697410390867449?thread_ts=1697380986.698779&channel=C04RATV9VCY&message_ts=1697410390.867449 - Attachment: Attachment > @Joan C. Chukwuemeka is the advice I just gave on some other articles about what constitutes an Experiment helpful? The key message is that experiments are defined by the contrasts made, and signatures are defined by the results of those experiments. So it is perfectly possible to perform one or more experiments and find no statistically significant results, such as unchanged alpha diversity and no signatures of differentially abundant taxa.

Peace Sandy (08:49:17) (in thread): > Let me go through the article again

Peace Sandy (08:50:15) (in thread): > Thank You:pray:

Odigiri Great Alume (09:23:24) (in thread): > @Esther AfuapeI think you should create three experiments like you said earlier. As the study compares baseline vs each time point. > > Prevaccination samples represented the baseline samples here I guess. While post vaccination samples represented the different time points. > > I think you are on track comparing basline to each time point. > > I’m not sure the study compared baseline to all time points combined. > > > These separate comparisons allowed the researcher to assess how breast milk microbiota changed at different stages of vaccination and to identify specific time points at which significant changes in microbial composition and diversity occured. > > So I guess you are on tract. > > Well done > I hope this helps a little

Esther Afuape (09:31:08) (in thread): > Thank you:pray:

Nana (09:56:08) (in thread): > @Esther Afuapei would take a look:https://www.nature.com/articles/s41541-023-00745-4 - Attachment (Nature): COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition > npj Vaccines - COVID-19 mRNA vaccine-mediated antibodies in human breast milk and their association with breast milk microbiota composition

Joan C. Chukwuemeka (11:13:22) (in thread): > Good day all, > I need help with this incomplete studyhttps://bugsigdb.org/Study_767on******identifying the signature taxa that are increased abundance vs decreased abundance******So from the study, I see 2 contrast / experiments: > * Mild Cognitive Impairment (MCI) group Vs Control > * Alzheimer’s disease (AD) group vs Control > The figure 1 (below) that shows the relative abundance is not clear enough for curation for increased/decreased abundance. > and I’m not clear on how I can determine that from the supplement excel table provided athttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8823292/bin/msystems.00004-22-st002.xlsxAny help will be appreciated<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicPlease how do I go about this? - File (PNG): image.png

Hodan Abdirisak (13:18:43) (in thread): > In my understanding this is a color keys so FIG 1A shows firmcutes bacterioidetes and protecteobacteria are increased and the stund the most increased three color(green, orange and navy:large_blue_circle:blue)

Hodan Abdirisak (13:21:09) (in thread): > And yellow:large_yellow_circle:which is MCI firmcutes is highest

Sara Mohammed (13:45:40): > Hello everyone. I’m having trouble signing in to Bugsibdb and for some reason I can’t. What should I do now?

Onyewuchi Esther Chikamso (13:47:07) (in thread): > Have you requested access?

Sara Mohammed (13:48:40) (in thread): > Is signing up not enough?

Onyewuchi Esther Chikamso (13:56:28) (in thread): > I just want to be sure you’ve signed up before that’s all. If you have and you have difficulty logging in, what I do is that I manually input the password myself instead of relying on the auto fill. If it still doesn’t work, perhaps try to change the password

Sara Mohammed (13:59:08) (in thread): > I tried to manually put the password. Doesn’t work. So I tried to change the password and pressed forgot my password so it can send me an email with link to change it but I didn’t receive any emails. And it didn’t go to spam. I really don’t know what to do now

Onyewuchi Esther Chikamso (14:01:11) (in thread): > Hmmmmm. Please we need your help<@U1LCB8WEA>:pray:

Onyewuchi Esther Chikamso (14:10:54) (in thread): > When did you request for a temporary password? If it’s not been long perhaps you should wait a while, at least to the end of the day

Sara Mohammed (14:12:33) (in thread): > I requested it in the morning. I will wait for few more hours and see if I get it.

Peace Sandy (14:36:19) (in thread): > I think you need to request for an account and wait for it to be approved

Esther Afuape (14:42:39) (in thread): > Check your spam folder. Account confirmation and temporary password emails go there sometimes.

Sara Mohammed (14:46:48) (in thread): > I will do that.

Sara Mohammed (14:47:51) (in thread): > Thank you all.

Chioma Onyido (15:07:06) (in thread): > Thank you:hugging_face:

Esther Afuape (16:09:26): > Are differential abundances always increasing or decreasing?Or can we simply have a differential abundance without it necessarily increasing or decreasing?

U1LCB8WEA (22:49:27) (in thread): > Welcome@Sara Mohammed! I just approved your account.

2023-10-23

Peace Sandy (02:53:35) (in thread): > Differential abundance can either decrease or increase, it depends on the paper you are curating

Chiagoziem David (02:53:51) (in thread): > I think it should either decrease or increase

Peace Sandy (02:55:22) (in thread): > See@Esther Afuapehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697468494614279?thread_ts=1697450304.857849&channel=C04RATV9VCY&message_ts=1697468494.614279 - Attachment: Attachment > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

Esther Afuape (03:47:13) (in thread): > Thank you

Svetlana Ugarcina Perovic (06:14:35): > As we count down to the end of the contribution, this is a kindly reminder to record your contributions in preparation for the final application.Happy Monday!:tulip:

Nwajei Edgar (06:15:03) (in thread): > Happy Monday:partying_face::partying_face:

Peace Sandy (06:15:20) (in thread): > Happy Monday

Nana (06:16:49) (in thread): > ok..Happy Monday too

Chioma Onyido (06:17:08) (in thread): > Yesma’am. Would we receive instructions on how to go about thefinal application?It’snot so clear me.

Peace Sandy (06:18:10) (in thread): > True, this will be a great discourse during the office hour

Nana (06:18:28) (in thread): > same here as@Chioma Onyidopointed out

Nana (06:21:09): > Hope we had a great weekend > > Greetings to my fellow contributors, > > I’d like to draw your attention to an important observation and a point for correction in our curation practices. It’s better to refrain from providing an NCBI ID (Pages with missing NCBI ID) when uncertain, rather than offering an incorrect one. > > Let me illustrate with a few examples. When we encounter cases like ASV-62 (Lachnospiraceae), attempting to find an NCBI ID for this specific ASV could lead us to a broader category like Lachnospiraceae, which is not the same thing. Providing an NCBI ID for the larger group instead of the specific ASV is misleading because an NCBI ID should be unique to an individual entity and cannot be shared by two different entities. > > Similarly, the case of Clostridia XIVa, ASV_205 (Clostridia) is distinct from Clostridia. Assigning a Clostridia NCBI ID to Clostridia XIVa or ASV_205 (Clostridia) is also incorrect and can lead to confusion. > > Another example is ASV_157 (Absconditabacteria), which is not the same as Candidatus Absconditabacteria. > > I could continue with more examples, but the central point I wish to emphasize is that it’s better to leave the field blank if we cannot provide an accurate NCBI ID. Using incorrect IDs can lead to misunderstandings and misrepresentations. Let’s prioritize accuracy in our curation efforts. > > Thank you for your attention and understanding. > Best regards,

Sinmi Adesanya (06:23:07) (in thread): > Happy Monday@Svetlana Ugarcina Perovic! Thank you for the update. Looking forward to hearing more on how to submit a final application as well. Thank you!

Nana (06:36:42): > @Levi Waldron@Svetlana Ugarcina Perovic<@UBNSEMS3S> > 1. when I searched for PPROM on EFO it showed up but the url had /MONDO_0012511 rather the /EFO as the condition i am contrasting for. thou Preterm birth showed with correct EFO url please which should i use. - File (PNG): condition pp.png

Karen254. Kingecha (06:37:37) (in thread): > @Svetlana Ugarcina PerovicThank you for the update.

Joan C. Chukwuemeka (06:37:44) (in thread): > <@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicPlease I’m still hoping to get a guide on this?

Nana (06:47:07): > @Levi Waldron@Svetlana Ugarcina Perovic<@UBNSEMS3S>2. from the image below choosing body site for cervical swab (can it be replaced with Uterine cervix, that was the closest i found when i use find term on uberon) Also can lateral and anterior vaginal wall be replaced (Lateral fornix of vagina) that was also the closest found when using find term link > 3. is PPROM best suited for the condition or respiratory distress syndrome (RDS), from the image below. > waiting for your kind response - File (PNG): body site.png - File (PNG): condition pprom.png

Peace Sandy (07:06:02): > Is it possible for a study not to have 16s variable region specified, if yes, what should be the next line of action@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (07:09:33) (in thread): > Could you please send me a link of paper?

Svetlana Ugarcina Perovic (07:11:33) (in thread): > It can be also that thefulllength (V1 to V9)16S rRNA gene sequenceanalysis was performed

Peace Sandy (07:12:10) (in thread): > Okay

Peace Sandy (07:12:48) (in thread): > Here is the link to the paper@Svetlana Ugarcina Perovichttps://journals.plos.org/plosone/article?id=10.1371/journal.pone.0145274 - Attachment (journals.plos.org): Gut Dysbiosis in Patients with Anorexia Nervosa > Anorexia nervosa (AN) is a psychological illness with devastating physical consequences; however, its pathophysiological mechanism remains unclear. Because numerous reports have indicated the importance of gut microbiota in the regulation of weight gain, it is reasonable to speculate that AN patients might have a microbial imbalance, i.e. dysbiosis, in their gut. In this study, we compared the fecal microbiota of female patients with AN (n = 25), including restrictive (ANR, n = 14) and binge-eating (ANBP, n = 11) subtypes, with those of age-matched healthy female controls (n = 21) using the Yakult Intestinal Flora-SCAN based on 16S or 23S rRNA–targeted RT–quantitative PCR technology. AN patients had significantly lower amounts of total bacteria and obligate anaerobes including those from the Clostridium coccoides group, Clostridium leptum subgroup, and Bacteroides fragilis group than the age-matched healthy women. Lower numbers of Streptococcus were also found in the AN group than in the control group. In the analysis based on AN subtypes, the counts of the Bacteroides fragilis group in the ANR and ANBP groups and the counts of the Clostridium coccoides group in the ANR group were significantly lower than those in the control group. The detection rate of the Lactobacillus plantarum subgroup was significantly lower in the AN group than in the control group. The AN group had significantly lower acetic and propionic acid concentrations in the feces than the control group. Moreover, the subtype analysis showed that the fecal concentrations of acetic acid were lower in the ANR group than in the control group. Principal component analysis confirmed a clear difference in the bacterial components between the AN patients and healthy women. Collectively, these results clearly indicate the existence of dysbiosis in the gut of AN patients.

Svetlana Ugarcina Perovic (07:17:42) (in thread): > The specificity of the RT-qPCR assay, the sequences of the primers, and the lower detection limit for each bacterium were thoroughly checked and determined (S1 Table), as previously described [18–23].

Svetlana Ugarcina Perovic (07:20:39) (in thread): > I do not see that this is a microbial community study… If you go to S1 table you will see that the study focuses on specific bacteria by selecting species/group-specific primers for sequencing

Peace Sandy (07:24:12) (in thread): > True, I noticed the study has been curated and reviewed

Peace Sandy (07:24:47) (in thread): > And the 16s variable region was written as not specified by the curator

Svetlana Ugarcina Perovic (07:24:52) (in thread): > Take a look at this one as wellhttps://bugsigdb.org/Study_216 - Attachment (BugSigDB): Study 216

Svetlana Ugarcina Perovic (07:25:33) (in thread): > It saysSequencing type16SNot specifiedAnd the signatures are recorded. - Attachment (BugSigDB): Special:RunQuery/Quick filter

Peace Sandy (07:26:31) (in thread): > Wow…this is really nice to know

Esther Afuape (07:42:45): > @Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina PerovicHello everyone and happy new week! I’m currently working on this incomplete study without experimentshttps://bugsigdb.org/Study_835. The study is on how COVID-19 mRNA vaccine-mediated antibodies affect breast milk microbiota. They conducted conducted LEfSe to identify differentially abundant bacterial taxa between timepoints and found 109 differentially abundant species identified between pre- and post-vaccination timepoints, ten of which remained differentially abundant throughout all three post-vaccination timepoints. I created an experiment for this and added the 10 taxa that were abundant throughout all the timepoints as a signature. > They found baseline breast milk microbiota differential groups to find out how it predicts the spike in IgA. The spike in IgA occurred at one week post second-dose so this group was subdivided into high IgA and low IgA groups. I created an experiment for this and added the signatures. > The taxonomic differences in microbiota one week post-second dose between high-IgA and low-IgA subjects were also identified but I couldn’t find a significance value for it so I didn’t create an experiment for this. > Can you review what I have done so far and let me know the corrections please? I’ve had a bit of a hard time interpreting the results. I’d also like to know if I ought to create experiments for the differential abundance in each of the time points as provided in the supplementary file. - Attachment (BugSigDB): Study 835

USLACKBOT (08:00:00): > This message was deleted.

Chioma Onyido (08:10:45) (in thread): > From this excerpt, age is one, thenthere’sgestational age which is the second matched on. > I thinktheyshould both be recorded.

Esther Afuape (08:29:13) (in thread): > Both should be recorded. Age and gestational age

Chioma Onyido (08:44:10): > Understudies that have no experiments: > –study 774 has already been curated as 775 > –study 806 has already been curated as 795 > – study 784 has already been curated as 786 > – study 809 has already been curated as 812 > – study 827 has already been curated as 814 > — study 816 has already been curated as 817 > > –I have completed study 801, but I mistakenly created another Experiment (Expt. 2), could this be deleted too? > – study 789 seems to me like an incomplete duplicate of 788, with an incorrect doi as well. I think it’s a duplicate because they both have similar doi’s (from mdpi too). > > In summary, please can I get help with the following:<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>HelpDelete:bugsigdb.org/Study_774bugsigdb.org/Study_806bugsigdb.org/Study_784bugsigdb.org/Study_789bugsigdb.org/Study_809bugsigdb.org/Study_827bugsigdb.org/Study_816https://bugsigdb.org/Study_801/Experiment_2HelpRemove801 (“Metagenomics reveals a core macro life resistive related to microbiota in chronic respiratory disease”) from the “studies with no experiments” category since it’s been fully curated.

Karen254. Kingecha (09:13:31) (in thread): > Both should be included

Esther Afuape (09:41:29) (in thread): > Studies 212 which has been curated and reviewed was also duplicated as 211 and 213

Nana (09:56:30) (in thread): > Noted

Esther Afuape (10:25:00) (in thread): > Thank you

Joan C. Chukwuemeka (11:09:17) (in thread): > <!here>Please i need assistance with this<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Hodan Abdirisak (11:33:00) (in thread): > Happy Monday too ma’am@Svetlana Ugarcina Perovicthanks for your update I have question same to@Chioma Onyidoone

Chiagoziem David (12:01:36): > They’re 13 pages with missing NCBI ID, is anyone working on any of them?

Chioma Onyido (12:04:30) (in thread): > Hi@Chiagoziem David, some of our colleagues have already worked on/ are still working on some. Onegood way to confirm is to ctrl + f (the study you’re interested in identifying the missing ID) here,if nothing pops up, that means nobody is working on it and you can go ahead.

Chiagoziem David (12:04:57) (in thread): > I am using my pc,

Chiagoziem David (12:04:59) (in thread): > Emmm

Chiagoziem David (12:05:13) (in thread): > Let me see if I can log in the slack channel on my pc

Chioma Onyido (12:07:33) (in thread): > If you’re using your phone, go to the activity section on slack and type the study in the search bar. For example, study 801… - File (PNG): IMG_5435 - File (JPEG): IMG_5436

Joan C. Chukwuemeka (12:08:52) (in thread): > Please i need assistance with this<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Chiagoziem David (12:08:56) (in thread): > Oh, this is beautiful:melting_face:, imela Chioma

Chioma Onyido (12:12:00) (in thread): > :sweat_smile:Did it work tho?

Chiagoziem David (12:12:33) (in thread): > Emm, if a person is working on one experiment, can you work on another, if they are both the same study

Chiagoziem David (12:12:46) (in thread): > Yeah:sweat_smile:, kind of

Hodan Abdirisak (12:13:39): > https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy

Chioma Onyido (12:20:02) (in thread): > I think to avoid conflict, maybe you should look for another taxonomic issue or clean up task to solve. We’ve lots of them on BugSigDB!:wink:Here:https://bugsigdb.org/Help:Contents#NCBI_cleanup - Attachment (BugSigDB): Help:Contents

Chiagoziem David (12:21:09) (in thread): > Emmm

Chiagoziem David (12:21:30) (in thread): > The are all subsets of the same 2 or 3 papers

Chioma Onyido (12:21:48) (in thread): > https://bugsigdb.org/Help:Contents#TODO_for_reviewers - Attachment (BugSigDB): Help:Contents

Chiagoziem David (12:23:07) (in thread): > I know:joy::joy:, I am staring at it on my pc now:joy::pray::grin::grin:

Doreen Wanyama (12:32:23) (in thread): > Thank you all for the warm welcome. I appreciate

Chiagoziem David (12:33:03): > Hello guys , seems nobody is working on this :

Chiagoziem David (12:33:06): > https://bugsigdb.org/Study_1/Experiment_5/Signature_1 - Attachment (BugSigDB): Study 1/Experiment 5/Signature 1

Chiagoziem David (12:33:20): > id be trying to do that

U01MW62UDQR (12:53:29): > <@UBNSEMS3S>@Svetlana Ugarcina PerovicI know you’re both pretty busy right now. I need help from an experienced curator to assess the validity ofhttps://github.com/waldronlab/BugSigDBExports/blob/devel/full_dump.csv, which has NAs forBody siteandConditionfor coming release.@Ludwig Geistlingerhas guidance athttps://github.com/waldronlab/bugsigdbr/issues/49#issuecomment-1764503625. Could either one of you help me out when you have time? - Attachment: Comment on #49 Release 3.18

Hodan Abdirisak (12:53:51) (in thread): > It is flagged as reviewed:face_holding_back_tears:

Chiagoziem David (12:55:48): > Hello<@U1LCB8WEA>and<@UBNSEMS3S>, how do i add a signature that’s not on the ncbi database but actually exist ( saw it on another website -namesforlife.com- ) but it has no ID there. Thanks

Peace Sandy (12:59:07): > How do I identify specific microbial taxa that was different between placebo and letrozole from this supporting material , it’s pretty confusing.@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron - File (PNG): supportingmaterial

Odigiri Great Alume (13:23:56) (in thread): > You’re welcome

Chioma Onyido (16:06:51) (in thread): > Hi@Peace Sandy, I curated something similar in the past and I used the ‘mean’ to differentiate, when I didn’t find any other supporting figure or table. > For the taxa, I think they just listed the full taxonomy each, instead of doing it separately. > > For example, for the first taxon on your list, > bacteroidetes (phylum) > bacteroidia (class) > bacteroidales (order) > S24-7 (probably family) > > WhatI’mnot sure of is ifit’sright to curate all of the taxon. classification for each. Or to go with one.:thinking_face:

Chioma Onyido (17:09:28) (in thread): > @Chiagoziem DavidHave you looked it up on uniprot?

Esther Afuape (17:43:09) (in thread): > That makes sense. The group that has the highest mean will be the enriched one. I think the whole taxon should be curated. Sometimes they provide the results for abundance from phylum to species

Esther Afuape (19:47:30): > Hi everyone<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina PerovicI just added experiments and signatures to this study under the list of studies with no experiments.https://bugsigdb.org/Study_788 - Attachment (BugSigDB): Differential Dynamics of the Ruminal Microbiome of Jersey Cows in a Heat Stress Environment - BugSigDB > The microbial community within the rumen can be changed and shaped by heat stress. Accumulating data have suggested that different breeds of dairy cows have differential heat stress resistance; however, the underlying mechanism by which nonanimal factors contribute to heat stress are yet to be understood. This study is designed to determine changes in the rumen microbiome of Holstein and Jersey cows to normal and heat stress conditions. Under heat stress conditions, Holstein cows had a significantly higher respiration rate than Jersey cows. Heat stress increased the rectal temperature of Holstein but not Jersey cows. In the Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis, Jersey cows had a significantly higher proportion of genes associated with energy metabolism in the normal condition than that with other treatments. Linear discriminant analysis effect size (LEfSe) results identified six taxa as distinguishing taxa between normal and heat stress conditions in Holstein cows; in Jersey cows, 29 such taxa were identified. Changes in the rumen bacterial taxa were more sensitive to heat stress in Jersey cows than in Holstein cows, suggesting that the rumen mechanism is different in both breeds in adapting to heat stress. Collectively, distinct changes in rumen bacterial taxa and functional gene abundance in Jersey cows may be associated with better adaptation ability to heat stress.

Chioma Onyido (20:10:50) (in thread): > Hi@Joan C. Chukwuemeka, from the supplemental file you provided, I see log fold change (logFC) values reported for AD vs C and MCI vs C, and from previous discussions with the mentors, I know that a negative logfc means a decrease while a positive logfc means an increase.

Chioma Onyido (20:18:30) (in thread): > Fpund it!:smiley:https://community-bioc.slack.com/archives/C04RATV9VCY/p1696954274418709?thread_ts=1696934289.503959&cid=C04RATV9VCY - Attachment: Attachment > Good question. Log fold change is a measure of effect size. A negative log fold change generally indicates a decrease in cases relative to controls and a positive log fold change generally indicates an increase in cases relative to controls.

Esther Afuape (21:07:31): > Does anyone know whyI’mgetting this error with the PMID even thoughI’veconfirmedit’scorrect? - File (JPEG): cc62a8ff-d83b-42f9-9ebb-30e5ed3a193d

U01MW62UDQR (21:17:55) (in thread): > It looks like a study with that PMID already exists athttps://bugsigdb.org/Study_804

Chioma Onyido (21:30:44) (in thread): > Yes that’s true. Whenever it flags “must be unique”, it means it already exists in BugSigDB like@Andres Wokatypointed.:sweat_smile:

Chioma Onyido (21:38:09) (in thread): > @Esther AfuapeAlready called the mentors attention to help delete some days ago.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697831704845229?thread_ts=1697815481.087259&channel=C04RATV9VCY&message_ts=1697831704.845229 - Attachment: Attachment > Study 805 seems to be a duplicate curation for bugsigdb.org/Study_804 . I confirmed this after I tried to add the PMID and it flagged as “must be unique”. > The curator probably added 2 new studies during curation, focused on one (study 804) and must’ve forgotten about the other one (study 805). :thinking_face: > > Could you help delete this http://bugsigdb.org/Study_805 please? @Levi Waldron @UBNSEMS3S

Hodan Abdirisak (23:37:49) (in thread): > Thanks<@U01MW62UDQR>for your clarification, I don’t know this before

2023-10-24

Grace Ogundaini (00:04:08): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicGood morning, I just got an email nudge to submit my final contribution. For the internship project timeline,what should I fill in, December 2023 to May 2024?

Taiwo Adeyombo (00:16:03): > Good morning@Levi Waldron@Svetlana Ugarcina Perovic<@UBNSEMS3S>I’m still experiencing the problem with my changes not being rendered in experiments 2 and 3, so I’m unsure if I’m doing something wrong.https://bugsigdb.org/Study_825I’m also stuck regarding my curation. My main problem is there is no clearly defined group of increased or decreased abundance between groups 0 and 1. And there are three experiments, although it’s a meta-analysis. I’ve been trying to figure it out for a while now but I realize I’ve taken a lot of time. > > This is the link to the article I’m curating:https://www.frontiersin.org/articles/10.3389/fmolb.2023.1210225/full#B9I really look forward to your advice and guidance. Thank you very much. - Attachment (BugSigDB): Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease - BugSigDB > Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear. Delineating the contribution of rare and common phylotypes to urinary stone disease is important for the development of bacteriotherapies to promote urologic health. Methods: The objectives of the current report were to conduct a metaanalysis of 16S rRNA datasets derived from the kidney stone, stool, and urine samples of participants with or without urinary stone disease. To delineate the impact of rare and common phylotypes, metaanalyses were conducted by first separating rare and common taxa determined by both the frequency and abundance of amplicon sequence variants. Results: Consistent with previous analyses, we found that gut, upper urinary, and lower urinary tract microbiomes were all unique. Rare phylotypes comprised the majority of species observed in all sample types, with kidney stones exhibiting the greatest bias toward rarity, followed by urine and stool. Both rare and common fractions contributed significantly to the differences observed between sample types and health disparity. Furthermore, the rare and common fractions were taxonomically unique across all sample types. A total of 222 and 320 unique rare phylotypes from urine and stool samples were found to be significantly associated with USD. A co-occurrence correlation analysis revealed that rare phylotypes are most important for microbiome structure in stones, followed by urine and stool. Discussion: Collectively, the results indicate that rare phylotypes may be important for the pathophysiology of USD, particularly in the kidney stone matrix, which is inherently a very low microbial biomass niche that can have implications for the diagnosis and treatment of kidney stones. Further studies are needed to investigate the functional significance of rare phylotypes in kidney stone pathogenesis. - Attachment (Frontiers): Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease > Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized. Clinical microbiome studies on urinary stone disease (USD) have indicated that both the gut and urinary tract microbiota are associated with the onset of the disease and that kidney stones them-selves harbor a complex, yet consistent and viable, microbiome. However, how rare phylotypes contribute to this association remains unclear. Delineating the contribution of rare and common phylotypes to urinary stone disease is important for the development of bacteriotherapies to promote urologic health.Methods: The objectives of the current report were to conduct a metaanalysis of 16S rRNA datasets derived from the kidney stone, stool, and urine samples of participants with or without urinary stone disease. To delineate the impact of rare and common phylotypes, metaanalyses were conducted by first separating rare and common taxa determined by both the frequency and abundance of amplicon sequence variants.Results: Consistent with previous analyses, we found that gut, upper urinary, and lower urinary tract microbiomes were all unique. Rare phylotypes comprised the majority of species observed in all sample types, with kidney stones exhibiting the greatest bias toward rarity, followed by urine and stool. Both rare and common fractions contributed significantly to the differe…

Peace Sandy (02:26:16) (in thread): > Thank you

Peace Sandy (02:30:40) (in thread): > Hi@Taiwo Adeyombonot all experiments are curatable. For the increase and decrease abundance it might not be clearly defined most times,you’llneed to read in between lines.

Peace Sandy (02:33:04) (in thread): > @Taiwo Adeyombocheck out this

Peace Sandy (02:34:12) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696823157796939?thread_ts=1696792402.846789&channel=C04RATV9VCY&message_ts=1696823157.796939 - Attachment: Attachment > @Joan C. Chukwuemeka summarizes the discussion well. Usually the authors will identify a control/reference group, and increased or decreased abundance is reported relative to that reference group. In some comparative studies it is arbitrary which is the reference group (such as a comparison of males against females, and maybe in this case you bring up), in such cases it’s best just follow the lead of the paper.

Chiagoziem David (04:01:27) (in thread): > Let me do that now, thanks

Esther Afuape (04:13:20) (in thread): > Oh thank you!

Joan C. Chukwuemeka (04:15:03) (in thread): > Okay .. Thanks@Chioma Onyido:gratitude-asl::relaxed:

Hodan Abdirisak (04:46:23): > Happy Tuesday all of you:smiling_face_with_3_hearts:i see this missing NCBI for ruminoc….. so can i write like this uncultured Oscillospiraceae bacterium. as mention how to resole in discussion page

Hodan Abdirisak (04:46:35): - File (PNG): Screenshot 2023-10-23 220602.png - File (PNG): Screenshot 2023-10-23 220517.png

Peace Sandy (05:05:09) (in thread): > I think this has been addressed, let me check for it

Peace Sandy (05:06:03) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1697662070165049?thread_ts=1697660948.295849&channel=C04RATV9VCY&message_ts=1697662070.165049 - Attachment: Attachment > Just keep in mind this ID says nothing other than that it is an unknown bacterium. There are many other “bacterium” in NCBI that specify which genus, family, … the bacterium belongs to, so if you have some taxonomic information you should try to use one of those instead.

Joan C. Chukwuemeka (05:24:11) (in thread): > Yea..@Grace OgundainiThere are actually 2 main aspects of the final application, among others, that we’ll need our mentors guidance: > 1. ****(Optional) Community-specific Questions: *****Some communities or projects may want you to answer additional questions. *******Please check with your mentor and community coordinator ******to see if you need to provide any additional information after you save your final application. > 2. Outreachy internship project timeline: ********Please work with your mentor******* to provide a timeline of the work you plan to accomplish on the project and what tasks you will finish at each step. Make sure take into account any time commitments you have during the Outreachy internship round. If you are still working on your contributions and need more time, you can leave this blank and edit your application later.*<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovicwill respond to us once they are available. > > Perhaps, It may also be part of our Office hour discourse this Thursday as someone previously suggested.

Hodan Abdirisak (05:40:14) (in thread): > @Peace Sandyso it means I am right to put that

Chiagoziem David (05:46:19) (in thread): > So we should probably wait till Thursday before we apply yeah?

Chiagoziem David (05:47:49): > I also have a question, is it of importance that we apply for the Google summer of code? The memo is that it increases your chances of getting accepted as an intern.

Joan C. Chukwuemeka (05:58:45): > @Chiagoziem DavidThere’s a caveat for that one you may have missed:slightly_smiling_face::******“If this application is for the December to March internship period, or you are not applying to Google Summer of Code, please leave this question blank.”****** - File (PNG): image.png

Chiagoziem David (06:05:41): > Alrighty, thanks

Joan C. Chukwuemeka (06:06:15) (in thread): > @Chiagoziem David***** “Making it part of our Office hour discourse this Thursday” *****is a suggestion, which is yet to be affirmed by our mentors.

Fortune Nnamdi (06:36:18): > <@UBNSEMS3S>@Svetlana Ugarcina PerovicHi, please can you guys help me out by deleting signature 3 in Experement 1.Here’sthe link:https://bugsigdb.org/Study_828I put it in by mistake.Alsoit’sthe only one marked incomplete. - Attachment (BugSigDB): Uncover a microbiota signature of upper respiratory tract in patients with SARS-CoV-2 +  - BugSigDB > The outbreak of Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2, forced us to face a pandemic with unprecedented social, economic, and public health consequences. Several nations have launched campaigns to immunize millions of people using various vaccines to prevent infections. Meanwhile, therapeutic approaches and discoveries continuously arise; however, identifying infected patients that are going to experience the more severe outcomes of COVID-19 is still a major need, to focus therapeutic efforts, reducing hospitalization and mitigating drug adverse effects. Microbial communities colonizing the respiratory tract exert significant effects on host immune responses, influencing the susceptibility to infectious agents. Through 16S rDNAseq we characterized the upper airways’ microbiota of 192 subjects with nasopharyngeal swab positive for SARS-CoV-2. Patients were divided into groups based on the presence of symptoms, pneumonia severity, and need for oxygen therapy or intubation. Indeed, unlike most of the literature, our study focuses on identifying microbial signatures predictive of disease progression rather than on the probability of infection itself, for which a consensus is lacking. Diversity, differential abundance, and network analysis at different taxonomic levels were synergistically adopted, in a robust bioinformatic pipeline, highlighting novel possible taxa correlated with patients’ disease progression to intubation.

Chiagoziem David (06:37:50) (in thread): > Okay okay

Peace Sandy (06:38:36) (in thread): > @Chiagoziem DavidGoogle summer of code is a different program from outreachy

Peace Sandy (06:39:28) (in thread): > @Grace OgundainiI think you should wait for the mentors reply to be on a safe side

Chiagoziem David (06:40:13) (in thread): > Okay okay, thanks.:sweat_smile::sweat_smile:

Taiwo Adeyombo (07:54:01) (in thread): > Thank you@Peace Sandy. I don’t think there’s an actual reference group, and there’s mention of rare and common taxa but it’s all really interwoven.

Svetlana Ugarcina Perovic (08:18:32) (in thread): > Deleted.

Peace Sandy (08:20:34) (in thread): > Oh…Okay,just try to read in between lines,you’vegot this

Svetlana Ugarcina Perovic (08:54:15) (in thread): > @Chioma Onyidohttp://bugsigdb.org/Study_805is deleted now.

Svetlana Ugarcina Perovic (08:55:23) (in thread): > @Mildred Anashiehttps://bugsigdb.org/Study_785is deleted.

Chioma Onyido (10:27:17) (in thread): > @Svetlana Ugarcina Perovichere please.:pray:

Chioma Onyido (10:28:30) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:46:27) (in thread): > 774 > 806 > 784 > 789 > 809 > 827 > 816 > studies deleted@Chioma Onyido

Svetlana Ugarcina Perovic (10:47:07) (in thread): > https://bugsigdb.org/Study_801/Experiment_2deleted@Chioma Onyido

Chioma Onyido (10:48:23) (in thread): > Thanksma’am.:blush:

Svetlana Ugarcina Perovic (10:50:17) (in thread): > @Chioma Onyidohttps://bugsigdb.org/Study_801where do you see the “studies with no experiments” category?

Chioma Onyido (10:52:18) (in thread): > Here,https://bugsigdb.org/Help:Cleanup - Attachment (BugSigDB): Help:Cleanup - File (JPEG): IMG_5483

Svetlana Ugarcina Perovic (10:55:25) (in thread): > I see, ok

Svetlana Ugarcina Perovic (10:57:29) (in thread): > @Esther Afuapewhat abouthttps://bugsigdb.org/Study_212https://bugsigdb.org/Study_211https://bugsigdb.org/Study_213? - Attachment (BugSigDB): Association of dietary fibre intake and gut microbiota in adults - BugSigDB > Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies. - Attachment (BugSigDB): Association of dietary fibre intake and gut microbiota in adults - BugSigDB > Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies. - Attachment (BugSigDB): Association of dietary fibre intake and gut microbiota in adults - BugSigDB > Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies.

Esther Afuape (11:00:03) (in thread): > https://bugsigdb.org/Project:Duplicate_studies - Attachment (BugSigDB): Project:Duplicate studies

Svetlana Ugarcina Perovic (11:01:03) (in thread): > I see I see:slightly_smiling_face:

Svetlana Ugarcina Perovic (11:01:17) (in thread): > but which one is the correct one that you reviewed?

Svetlana Ugarcina Perovic (11:01:28) (in thread): > 212?

Esther Afuape (11:02:36) (in thread): > Yesma’am. Ididn’treview it butit’sbeen completely reviewed unlike its duplicates.

Svetlana Ugarcina Perovic (11:04:08) (in thread): > Thank you very much@Esther Afuape@Chioma OnyidoAll fixed!

Mildred Anashie (11:26:46) (in thread): > Okay > > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (11:31:42): > Hi<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina Perovic…I’m curating study 782 from the studies that have no experiment > > I’m not sure what the LDA score is from this. The screenshot of text shows where LDA was mentioned asides the figure - File (PNG): IMG_4928 - File (PNG): IMG_4929

Joan C. Chukwuemeka (11:41:07) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>I’ve completed the curation of this previously incomplete studyhttps://bugsigdb.org/Study_767, however, the signature sections for the 2 experiments got listed in the******“Pages with missing NCBI ID******” due to certain signatures from the study. Currently working on that aspect to see how many I can resolve. - Attachment (BugSigDB): Stratification of the Gut Microbiota Composition Landscape across the Alzheimer’s Disease Continuum in a Turkish Cohort - BugSigDB > Alzheimer’s disease (AD) is a heterogeneous disorder that spans a continuum with multiple phases, including preclinical, mild cognitive impairment, and dementia. Unlike for most other chronic diseases, human studies reporting on AD gut microbiota in the literature are very limited. With the scarcity of approved drugs for AD therapies, the rational and precise modulation of gut microbiota composition using diet and other tools is a promising approach to the management of AD. Such an approach could be personalized if an AD continuum can first be deconstructed into multiple strata based on specific microbiota features by using single or multiomics techniques. However, stratification of AD gut microbiota has not been systematically investigated before, leaving an important research gap for gut microbiota-based therapeutic approaches. Here, we analyze 16S rRNA amplicon sequencing of stool samples from 27 patients with mild cognitive impairment, 47 patients with AD, and 51 nondemented control subjects by using tools compatible with the compositional nature of microbiota. To stratify the AD gut microbiota community, we applied four machine learning techniques, including partitioning around the medoid clustering and fitting a probabilistic Dirichlet mixture model, the latent Dirichlet allocation model, and we performed topological data analysis for population-scale microbiome stratification based on the Mapper algorithm. These four distinct techniques all converge on Prevotella and Bacteroides stratification of the gut microbiota across the AD continuum, while some methods provided fine-scale resolution in stratifying the community landscape. Finally, we demonstrate that the signature taxa and neuropsychometric parameters together robustly classify the groups. Our results provide a framework for precision nutrition approaches aiming to modulate the AD gut microbiota. IMPORTANCE The prevalence of AD worldwide is estimated to reach 131 million by 2050. Most disease-modifying treatments and drug trials have failed, due partly to the heterogeneous and complex nature of the disease. Recent studies demonstrated that gut dybiosis can influence normal brain function through the so-called “gut-brain axis.” Modulation of the gut microbiota, therefore, has drawn strong interest in the clinic in the management of the disease. However, there is unmet need for microbiota-informed stratification of AD clinical cohorts for intervention studies aiming to modulate the gut microbiota. Our study fills in this gap and draws attention to the need for microbiota stratification as the first step for microbiota-based therapy. We demonstrate that while Prevotella and Bacteroides clusters are the consensus partitions, the newly developed probabilistic methods can provide fine-scale resolution in partitioning the AD gut microbiome landscape. - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Chioma Onyido (11:41:09) (in thread): > Hi@Mildred AnashieFrom the images and within text, I see LDA score >= 2. - File (JPEG): IMG_5485

Chioma Onyido (11:44:56) (in thread): > Also I noticed that you shared images and texts for the results of differential microbial function. > I don’t think we curate microbial function on BugSigDB, but instead it’smicrobial taxa. :sweat_smile:**** > > ****In that case, I believe**** ****you should record the LDA score for thedifferential microbial taxain your study.

Mildred Anashie (11:54:55) (in thread): > @Chioma OnyidoI shared images of the only places LDA was mentioned in the study

Chioma Onyido (11:56:18) (in thread): > Okay I see. Can you share images of your differential abundant taxa results? Maybe we can figure it out from there.

Mildred Anashie (12:02:48) (in thread): > Yea…I noticed the >=2 and I think LDA scores should be greater than 2 unless in the case of Negative scores….I’mnot sure whatI’msaying:sweat_smile:

Mildred Anashie (12:03:31) (in thread): > Okay let me screenshot the figures…Although I think the differential taxas were emphasised in text more

Mildred Anashie (12:06:51) (in thread): > Here’sthe link to the paper alsohttps://static-content.springer.com/esm/art%3A10.1186%2Fs40168-022-01447-0/MediaObjects/40168_2022_1447_MOESM1_ESM.pdf - File (JPEG): IMG_4933 - File (JPEG): IMG_4931 - File (PNG): IMG_4929

Fortune Nnamdi (12:06:56) (in thread): > Thanks

Esther Afuape (12:18:28): > Are compared groups always relative? For example, if the enriched taxa in group 1 were mentioned but the ones that decreased weren’t, do I only create a single signature for the enriched ones? or do I create a second signature for the group 1 using the taxa that were enriched in group 0 as decreased for group 1? > I hope I’ve not confused everyone:sweat_smile:<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina Perovic

Chioma Onyido (12:31:10) (in thread): > @Mildred AnashieNot sure this is the link to the full paper, but I see curatable figures in the supplemental file link you shared.

Odigiri Great Alume (12:44:48) (in thread): > @Chioma Onyidofig 1 D, F and E right? > We figured these ones out. However, what we not sure of is the LDA score. > > I still don’t find a place where it mentions LDA other than those figures and the text too

Odigiri Great Alume (12:47:03) (in thread): > If they recorded enriched taxa in group 0, then they could mean decreased for group 1.:thinking_face:

Esther Afuape (12:50:10) (in thread): > Iwant to be sureit’salways relative like that or you just curate what was clearly stated

Joan C. Chukwuemeka (12:51:58) (in thread): > @here Experiment 1/Signature 1 resolved, with details provided on the discussion/talk pagehttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID#Resolution_of_Stratification_of_the_Gut_M[…]urkish_Cohort.2FExperiment_1.2FSignature_1

Odigiri Great Alume (12:53:13) (in thread): > I get, it should be.

Esther Afuape (12:54:10) (in thread): > Thank you

Odigiri Great Alume (12:54:47) (in thread): > You’re welcome

Chioma Onyido (13:16:16) (in thread): > YesI don’tsee where too. I think it should be left blank since itwasn’texplicitly stated.

Odigiri Great Alume (13:18:07) (in thread): > Okay then or she should record 2 as LDA score is greater than or equal to 2

Chioma Onyido (13:20:03) (in thread): > The LDA score >= 2 was reported for microbial function not taxa.:thinking_face:

Chioma Onyido (13:20:39) (in thread): > And wedon’trecord microbial function in bugsigdb, soI’mnot sure if their LDA score can be used interchangeably.

Odigiri Great Alume (13:21:06) (in thread): > Oh I get it now.:thinking_face:

Odigiri Great Alume (13:31:47): > https://www.nature.com/articles/srep36666I will be working on this - Attachment (Nature): Composition of gut microbiota in infants in China and global comparison > Scientific Reports - Composition of gut microbiota in infants in China and global comparison

Mildred Anashie (14:24:32) (in thread): > >=2 is not a valid number for that field > > > Tried it, itdidn’t record

Odigiri Great Alume (14:26:21) (in thread): > She’s saying you leave it blank since it wasn’t mentioned explicitly.

Mildred Anashie (14:30:22) (in thread): > Okay

UBNSEMS3S (16:01:17) (in thread): > I’m happy to help but could you clarify what “assess the validity” should entail?

UBNSEMS3S (16:03:35) (in thread): > Please only curate the lowest taxonomic rank. That is to say in this case for the first row do not curate Bacteroidetes, bacteroidia, or bacteroidales–instead curate S24-7 which is a family better known as muribaculaceae (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2005473&lvl=3&lin=f&keep=1&srchmode=1&unlock) - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Peace Sandy (16:04:51) (in thread): > Wow…Thank You…I thought as much,it was pretty confusing earlier,thanks for the clarification@C. Mirzayi (please do not tag this account)

UBNSEMS3S (16:07:01) (in thread): > Application Timeline Guidelines:Thank you for your patience as we developed guidelines for the timeline section of your applications. To remind you, the internship begins on Monday, December 4th and runs until Friday, March 1st and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > * Fixing curation issues. As presented on this page:https://bugsigdb.org/Help:Contents#TODO_for_reviewers > * Reviewing existing curations that are marked as needs review > * The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > * Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > * Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > Our hope is that our intern can spend a lot of their time working on curation issues and reviewing curations (bullet point numbers one and two) so I would recommend emphasizing that in your timeline.Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project. - Attachment (BugSigDB): Help:Contents

UBNSEMS3S (16:08:18): > Application Timeline Guidelines:Thank you for your patience as we developed guidelines for the timeline section of your applications. To remind you, the internship begins on Monday, December 4th and runs until Friday, March 1st and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > * Fixing curation issues. As presented on this page:https://bugsigdb.org/Help:Contents#TODO_for_reviewers > * Reviewing existing curations that are marked as needs review > * The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > * Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > * Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > Our hope is that our intern can spend a lot of their time working on curation issues and reviewing curations (bullet point numbers one and two) so I would recommend emphasizing that in your timeline.Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Chiagoziem David (16:08:56) (in thread): > Thank you very much<@UBNSEMS3S>

UBNSEMS3S (16:09:22) (in thread): > Yes you don’t need to double enter as everything should be curated as relative to group 0

UBNSEMS3S (16:10:17) (in thread): > It’s ok for some NCBI IDs to be missing as long as you put in a good effort to try to identify them. There will always be some missing NCBI IDs

UBNSEMS3S (16:11:47) (in thread): > @Mildred AnashieYou can just enter a “2” as the LDA score threshold. You do not need to include the inequality sign as that will cause an error. It expects a numeric value for LDA score.

UBNSEMS3S (16:13:00) (in thread): > We do not receive information on your status with Google’s Summer of Code as part of your application and I can say it absolutely will not have any bearing on our decision.

Chioma Onyido (16:13:42) (in thread): > <@UBNSEMS3S>that means LDA scores for microbial functions can also be used for microbial taxa?:thinking_face:

Chiagoziem David (16:14:31) (in thread): > Alrighty, thank you very much

Joan C. Chukwuemeka (16:14:58) (in thread): > Thanks a lot<@UBNSEMS3S>There’s a part of the final application with the question below:****(Optional) Community-specific Questions:****Some communities or projects may want you to answer additional questions. Please check with your mentor and community coordinator.******So, do we need to provide any additional information after saving our final application?******

UBNSEMS3S (16:15:22) (in thread): > Looking at this, Figures 6 and 7 are curateable. These information appear to be also present in the supplements in a potentially easier to curate format.

UBNSEMS3S (16:16:04) (in thread): > It should be relatively rare but yes there can be two body sites in a single experiment if they combined samples across body sites for some reason.

UBNSEMS3S (16:16:55) (in thread): > No you do not need to provide any additional information unless there’s something else you would like us to consider or know about you.

UBNSEMS3S (16:17:32) (in thread): > Oh I didn’t even see those were functional analyses not bacteria oops. Yeah we don’t curate those.

UBNSEMS3S (16:17:47) (in thread): > Let me take a closer look at the paper.

Mildred Anashie (16:21:04) (in thread): > https://bugsigdb.org/Study_782 - Attachment (BugSigDB): Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection - BugSigDB > BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system. Connections and interactions have been found between the microbiome of the gut and oral pharynx in the context of SARS-CoV-2 and other viral infections; hence, to broaden our understanding of host-viral responses in general and to deepen our knowledge of COVID-19, we performed a large-scale, systematic evaluation of the effect of SARS-CoV-2 infection on human microbiota in patients with varying disease severity. RESULTS: We processed 521 samples from 203 COVID-19 patients with varying disease severity and 94 samples from 31 healthy donors, consisting of 213 pharyngeal swabs, 250 sputa, and 152 fecal samples, and obtained meta-transcriptomes as well as SARS-CoV-2 sequences from each sample. Detailed assessment of these samples revealed altered microbial composition and function in the upper respiratory tract (URT) and gut of COVID-19 patients, and these changes are significantly associated with disease severity. Moreover, URT and gut microbiota show different patterns of alteration, where gut microbiome seems to be more variable and in direct correlation with viral load; and microbial community in the upper respiratory tract renders a high risk of antibiotic resistance. Longitudinally, the microbial composition remains relatively stable during the study period. CONCLUSIONS: Our study has revealed different trends and the relative sensitivity of microbiome in different body sites to SARS-CoV-2 infection. Furthermore, while the use of antibiotics is often essential for the prevention and treatment of secondary infections, our results indicate a need to evaluate potential antibiotic resistance in the management of COVID-19 patients in the ongoing pandemic. Moreover, a longitudinal follow-up to monitor the restoration of the microbiome could enhance our understanding of the long-term effects of COVID-19. Video Abstract.

UBNSEMS3S (16:21:21) (in thread): > They still used LEfSe for the differential abundance analysis (the results are presented in the text of the results section but they did not use an LDA threshold so it should be left blank.

UBNSEMS3S (16:21:36) (in thread): > I apologize for the confusion.

Odigiri Great Alume (16:24:31) (in thread): > Thank you for clarifying ma’am. Well done

Mildred Anashie (16:24:55) (in thread): > Okay > > Thank you<@UBNSEMS3S>:blush:

Mildred Anashie (16:26:11) (in thread): > @Chioma Onyidoand@Odigiri Great AlumeThank you too:blush:

Joan C. Chukwuemeka (16:33:21) (in thread): > Alright… Thanks:blush:

U01MW62UDQR (16:39:32) (in thread): > @Ludwig GeistlingerTried to describe this in the comment I linked to. It seems that generally theBody siteandConditioncolumns should not haveNA. So I need someone to check the rows where these columns haveNAin thehttps://github.com/waldronlab/BugSigDBExports/blob/devel/full_dump.csvto determine that they should be kept asNAor corrected to another value. If they need to be corrected then I think the study should be corrected in bugsigdb.

Nana (16:41:43) (in thread): > ok thank you

UBNSEMS3S (17:14:21) (in thread): > Ok I’ll see what I can do. Is there a deadline? I have a lot on my plate and I would love to be able to triage accordingly.

UBNSEMS3S (17:15:15): > Also hi everyone sorry I was not around yesterday–I was out of the office. Please continue posting questions. I know many of you are waiting on reviews. We are going to get a lot of those reviews done this week.

Peace Sandy (17:30:19) (in thread): > Thank you so much@C. Mirzayi (please do not tag this account)

Peace Sandy (17:31:59) (in thread): > Thank you so much for the detailed response

Nana (17:35:04) (in thread): > Noted<@UBNSEMS3S>:+1:

Joan C. Chukwuemeka (17:39:11) (in thread): > Alright… Thanks for all you do:blush:. Much appreciated

Grace Ogundaini (18:10:14) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Odigiri Great Alume (18:23:00): > Good evening@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina PerovicI’m working on a study with linkhttps://www.nature.com/articles/srep36666After adding study and creating my first experiment, noticed that this study has 3unrelated experiments created already. My own experiment came as experiment 4. > > Here’s a the curation linkbugsigdb.org/Study_213Please what do I do? > If the experiments has to be deleted please help me delete them so I can go on with the curation please:pleading_face: - Attachment (Nature): Composition of gut microbiota in infants in China and global comparison > Scientific Reports - Composition of gut microbiota in infants in China and global comparison

Odigiri Great Alume (18:23:27) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Esther Afuape (18:34:55) (in thread): > Thank you

Esther Afuape (18:39:49) (in thread): > <@UBNSEMS3S>I’msorry, Ididn’treally get you. Idon’thave to double enter in the sense that Idon’thave to curate what has already been stated as enriched for 0 as a decrease for group 1?

Peace Sandy (18:49:27): > I’llbe completing this incomplete studyhttps://bugsigdb.org/Study_555 - Attachment (BugSigDB): Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis - BugSigDB > We sought to characterize and assess differences in compositions of intestinal flora between patients with rheumatoid arthritis (RA) and their respective spouses. Eighty volunteers were recruited, including 30 pairs of RA patients and their spouses, and 20 healthy individuals. Fresh stool samples were collected, processed, and 16S rRNA-sequencing was performed. Data were analyzed using an operational taxonomic units-based method, and community structure assessments were performed. Community composition analysis indicated that there were similar intestinal microbiota structures in RA and in their respective spouses. Gut microbiota in spouses of RA were different from those of the healthy controls group, but these differences were not significant. We found that Blautia spp. and Streptococcus spp. were two most associated species in RA and these taxa were significantly higher in comparison to healthy controls. In contrast, our findings suggested that Roseburia spp. and Lachnoclostridium spp. were significantly lower in the RA in comparison to healthy controls. In conclusion, RA patients shared similar gut microbiota pattern with their spouses which were different from healthy individuals. The findings suggest that disturbance of the balance of gut microbiota may play an important role in the dynamics of pathogenesis of RA.

Odigiri Great Alume (18:52:59) (in thread): > @C. Mirzayi (please do not tag this account)

Esther Afuape (18:57:58): > https://bugsigdb.org/Study_563I’ll be completing this. - Attachment (BugSigDB): The conjunctival microbiome in health and trachomatous disease: a case control study - BugSigDB > BACKGROUND: Trachoma, caused by Chlamydia trachomatis, remains the world’s leading infectious cause of blindness. Repeated ocular infection during childhood leads to scarring of the conjunctiva, in-turning of the eyelashes (trichiasis) and corneal opacity in later life. There is a growing body of evidence to suggest non-chlamydial bacteria are associated with clinical signs of trachoma, independent of C. trachomatis infection. METHODS: We used deep sequencing of the V1-V3 region of the bacterial 16S rRNA gene to characterize the microbiome of the conjunctiva of 220 residents of The Gambia, 105 with healthy conjunctivae and 115 with clinical signs of trachoma in the absence of detectable C. trachomatis infection. Deep sequencing was carried out using the Roche-454 platform. Sequence data were processed and analyzed through a pipeline developed by the Human Microbiome Project. RESULTS: The microbiome of healthy participants was influenced by age and season of sample collection with increased richness and diversity seen in younger participants and in samples collected during the dry season. Decreased diversity and an increased abundance of Corynebacterium and Streptococcus were seen in participants with conjunctival scarring compared to normal controls. Abundance of Corynebacterium was higher still in adults with scarring and trichiasis compared to adults with scarring only. CONCLUSIONS: Our results indicate that changes in the conjunctival microbiome occur in trachomatous disease; whether these are a cause or a consequence is yet unknown.

Chiagoziem David (19:51:50) (in thread): > I have a question<@UBNSEMS3S>, the part where we are to develop our timelines, are you saying we should give a breakdown of how we intend to complete the bulleted points in three months( the duration of the internship), or a breakdown of how we intend to spend our time contributing… > > In my head I’m like ” as much work that needs to be done during the internship would be done…. And more” , I am finding it difficult to put that into a “timeline”

Odigiri Great Alume (20:27:20) (in thread): > @C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic@Chioma Onyido@Joan C. ChukwuemekaPlease help with this:point_down:I understand that there are two experiments in figure 5 of my study and I’m confused on what exactly they are comparing. > > From the text below and the image attached:point_down:On the compositional profiles, Bacteroidetes was more likely to occur in vaginally delivered babies (7% vs. 0% in neonates and 13% vs. 5% in 2-month-old infants). For families within the phylum Bacteroidetes, Bacteroidaceae (mainly represented by the genera Bacteroides and Parabacteroides) tended to be enriched in vaginally delivered subjects. In contrast, Prevotellaceae (mainly represented by Prevotella) tended to be enriched in cesarean deliv ered subjects (Fig. 5). For other families and genera, Streptococcus (p= 0.0044, Student’s t test) and Trabulsiella (p= 0.0091) were significantly enriched in cesarean delivered neonates, and Clostridium (p= 0.0032) was sig nificantly enriched in cesarean delivered 2-month-old infants. Another genus, Megamonas was only found in vaginally delivered neonates (mean relative abundance=1.4%) and 2-month-old infants (0.3%).I was thinking rather that, it will beExperiment A: Neonates delivered by cesarean section vs Neonates delivered by vaginal > ****Experiment B: Infants delivered by cesarean section vs infants delivered by vagina > ****But I’m noy sure, because if I do this, I don’t know which will be group 0 and group 1. Wether Cesarean section or Vaginal delivery. > > Speaking with@Esther Afuapeshe suggested that it could beExperiment A: Vaginally delivered Neonats (group 0) vs Vaginally delivered infants (group 1) > ****Experiment B: Neonats delivered by CS (group0) vs infants delivered by CS (group 1) > ****Please I need help. - File (JPEG): Screenshot_20231025-005140.jpg

UBNSEMS3S (20:58:42) (in thread): > Correct.

Peace Sandy (21:11:10): > In a case were in the RA treatment group alpha diversity was decreased, but however when comparing the RA, SP, and HC treatment groups there were no significant differences between these groups, does it mean the alpha diversity is unchanged@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron

Chioma Onyido (22:16:36) (in thread): > Hmmm… > This is a tricky one because I was confused initially but I read through the texts again and I found:point_down: > 1. From an excerpt under theEffects of delivery modes on infant gut microbiota section: > “Despite high variability between neonates and 2-month-old infants, we were able to find discernable *******differences between vaginally and cesarean delivered subjects********…”2. From an excerpt under thediscussion section: > “The differences observed in within-sample diversity and UniFrac distance between ******vaginally and cesarean delivered infants *****suggested that delivery mode might affect composition of infant gut bacterial communities. Bacteroidetes was more abundant in the gut microbiota of *******vaginally delivered infants than in cesarean delivered infants,******* which is consistent with previous reports in Canadian and Italian infants…”These within-text explanations of figure 5 make clear the direction of the comparison made, which isdifferences in the microbiota of vaginally-delivered infants vs caesarean-delivered infants,**same comparison goes for neonates. With these, I think it makes more sense to curate just like you said.

Chioma Onyido (22:52:38) (in thread): > @Esther Afuapehas an interesting POV, that would yield a completely different curation for groups 0 and 1. Maybe they can both be curated?:thinking_face:Not sure… > > But I don’t think this is right for this curation, another reason is because comparisons between neo and infants have already been documented in**** Figure 3b**(which I believe should be another experiment). > Whereas Figure 5 focuses on delivery mode. > A clarification from<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovicshould clear things up.

Taiwo Adeyombo (23:33:57) (in thread): > Okay. Thank you. But there’s still the rendering issue. > > And the thing with the signatures is that although there’s supplemental material containing them, this is my challenge (apart from having to manually figure out which taxa have increased abundance). > * It was mentioned in the paper that there is differential abundance between rare and common taxa in groups 0 and 1. And this is reflected in the supplementary material. So going by that will I have four signatures for each body site. Or should I only record signatures for rare phylotypes. > Then from my understanding there are three experiments, because > three different body site microbiomes were analyzed. However the signatures for the stool microbiomes are essentially uncuratable. I have no way of knowing what belongs to what group. I’ve the relevant supplementary information for for the stool microbiome signatures below. Thank you very much for your patience & guidance and I look forward to hearing from you. - File (PDF): Data Sheet 3.pdf - File (PDF): Data Sheet 4.pdf

2023-10-25

Chioma Onyido (00:24:25): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698186180847909Hi:wave:<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina PerovicCalling your attention tobugsigdb.org/Study_213which is currently being curated by@Odigiri Great AlumeSo I noticed the mix with Great’s curation, > Another curation with the correct paper title, doi and other details already exists ashttp://bugsigdb.org/Study_212However, the signatures under experiment 1 for (Study 212) are incorrect whereas the experiments (1 to 3) under study213 are correct, (but incomplete -2 signatures missing from expt. 1/sig. 2 and one missing from expt/Sig.1) > > Since study212 has the correct study details but incorrect signatures, and study213 has the correct signatures but incorrect study details, > > What’s the best way to go about this? is there a way to maybe switch/ move the experiments (1 to 3) from 213 to 212?:sweat_smile:If that’s not possible, > > Another way is to have study212 signatures edited and experiments curated again, which I am willing to help with. - Attachment: Attachment > Good evening @C. Mirzayi (please do not tag this account) @Levi Waldron @Svetlana Ugarcina Perovic > > I’m working on a study with link https://www.nature.com/articles/srep36666 > > After adding study and creating my first experiment, noticed that this study has 3 unrelated experiments created already. My own experiment came as experiment 4. > > Here’s a the curation link > bugsigdb.org/Study_213 > > Please what do I do? > If the experiments has to be deleted please help me delete them so I can go on with the curation please :pleading_face: - Attachment (BugSigDB): Association of dietary fibre intake and gut microbiota in adults - BugSigDB > Increasing evidence indicates that gut microbiota may influence colorectal cancer risk. Diet, particularly fibre intake, may modify gut microbiota composition, which may affect cancer risk. We investigated the relationship between dietary fibre intake and gut microbiota in adults. Using 16S rRNA gene sequencing, we assessed gut microbiota in faecal samples from 151 adults in two independent study populations: National Cancer Institute (NCI), n 75, and New York University (NYU), n 76. We calculated energy-adjusted fibre intake based on FFQ. For each study population with adjustment for age, sex, race, BMI and smoking, we evaluated the relationship between fibre intake and gut microbiota community composition and taxon abundance. Total fibre intake was significantly associated with overall microbial community composition in NYU (P=0·008) but not in NCI (P=0·81). In a meta-analysis of both study populations, higher fibre intake tended to be associated with genera of class Clostridia, including higher abundance of SMB53 (fold change (FC)=1·04, P=0·04), Lachnospira (FC=1·03, P=0·05) and Faecalibacterium (FC=1·03, P=0·06), and lower abundance of Actinomyces (FC=0·95, P=0·002), Odoribacter (FC=0·95, P=0·03) and Oscillospira (FC=0·96, P=0·06). A species-level meta-analysis showed that higher fibre intake was marginally associated with greater abundance of Faecalibacterium prausnitzii (FC=1·03, P=0·07) and lower abundance of Eubacterium dolichum (FC=0·96, P=0·04) and Bacteroides uniformis (FC=0·97, P=0·05). Thus, dietary fibre intake may impact gut microbiota composition, particularly class Clostridia, and may favour putatively beneficial bacteria such as F. prausnitzii. These findings warrant further understanding of diet-microbiota relationships for future development of colorectal cancer prevention strategies.

Chioma Onyido (00:28:58) (in thread): > Also this same study seems to be duplicated inbugsigdb.org/Study_211Correct study details:white_check_mark:but incorrect experiment. Can you help delete experiment 1 please?:pray:

Sinmi Adesanya (01:43:05) (in thread): > Thank you for this, Chloe!

Hodan Abdirisak (02:49:24) (in thread): > Noted thanks@C. Mirzayi (please do not tag this account)

Hodan Abdirisak (02:52:45) (in thread): > Thanks:pray:@C. Mirzayi (please do not tag this account)

Odigiri Great Alume (02:56:11) (in thread): > @Chioma Onyidothank you so much. However, if we compare like you and I have suggested,@Esther Afuapeconcern is that, WHAT WILL BE GROUP 1 and 0 > > Tho I’m thinking CS will be group 0 and Vaginally delivery will be group 1 > > Thank you@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic

Odigiri Great Alume (02:58:12) (in thread): > @Chioma Onyidothank you a lot

Karen254. Kingecha (03:15:16) (in thread): > Not really, if the RA treatment group showed a decrease in alpha diversity compared to its own baseline but there were no significant differences when comparing the RA, SP, and HC treatment groups, it means that the alpha diversity didn’t change significantly between those groups. However, it doesn’t imply that alpha diversity is unchanged in an absolute sense. It’s possible that alpha diversity is altered within the RA group but remains relatively consistent across all treatment groups when compared to each other. > (my thoughts)

Karen254. Kingecha (03:16:38) (in thread): > Noted<@UBNSEMS3S>

Peace Sandy (03:30:07) (in thread): > This is not what I mean exactly, but thank you.

Esther Afuape (04:00:13) (in thread): > Ah:sweat_smile:I thought we deleted 213 yesterday?

Odigiri Great Alume (05:22:52) (in thread): > @C. Mirzayi (please do not tag this account)@Levi Waldron@Chioma Onyido@Esther AfuapeAlso it the study reads that “prevotella, bacteriodes and parabacteriodes TENDED to be enriched in the Vaginal delivery” > > When the same word TENDED was used earlier in the study it stated that there was no statistical significance in the taxa involved. Hence, could it be that prevotella, bacteriodes and parabacteriodes also didn’t not show a statistical significance between comparison groups? > > If I am correct then I will also plead that signature 1for both experiment 5 and 6 be deleted and it shouldn’t be curated since “the taxa abundance isn’t statistically significant”. > > > Thank you again so everyone

Esther Afuape (05:30:52) (in thread): > The significant taxa were clearly selected with the asterisks in the figures so I’ll say you go with only the ones that have been clearly stated to be significant.

Hodan Abdirisak (05:37:19): > Have nice day:two_hearts:all of you@C. Mirzayi (please do not tag this account)I have question about final application in project timeline you mentioned bugsigDB contribution intern will do during that time > but is it must to divide project timeline into weeks or I write as general overview like the way you write?https://community-bioc.slack.com/archives/C04RATV9VCY/p1698178098103179?thread_ts=1698178098.103179&cid=C04RATV9VCY - Attachment: Attachment > Application Timeline Guidelines: Thank you for your patience as we developed guidelines for the timeline section of your applications. To remind you, the internship begins on Monday, December 4th and runs until Friday, March 1st and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Fixing curation issues. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • Reviewing existing curations that are marked as needs review > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > Our hope is that our intern can spend a lot of their time working on curation issues and reviewing curations (bullet point numbers one and two) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Esther Afuape (06:01:00): > Good morning<@UBNSEMS3S>please help delete:https://bugsigdb.org/Special:FormEdit/Signature/Study_835/Experiment_4/Signature_2?reload=1&returnto=Study%20835https://bugsigdb.org/Special:FormEdit/Experiment/Study_835/Experiment_5?reload=1&returnto=Study_835 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 835/Experiment 4/Signature 2 - Attachment (BugSigDB): Special:FormEdit/Experiment/Study 835/Experiment 5

Chioma Onyido (06:33:16) (in thread): > I agree with@Esther Afuape, the asterisks in the figure indicates significance.

Chioma Onyido (07:51:37) (in thread): > Hi@Peace Sandy, I think the best way to to approach this is to look at the groups that were contrasted, that’s what determines if you have an experiment. > Yes, when there’s no significant difference in alpha diversity between groups contrasted, that means the alpha diversity would be recorded asunchanged. > Is there another experiment that contrasted RA treatment to another group (maybe healthy controls)? Then the alpha diversity should be recorded for that particular experiment. > > But if no alpha diversity was stated, It should be left blank (from the curation policy). > I hope I didn’t confuse you.:sweat_smile:

Odigiri Great Alume (07:56:24) (in thread): > Yes it indicates significance. However in the text explanation, not all the microbes in the asterisks were mentioned. So do you think I should add the ones marked asterisk* in my differentially abundant even tho they aren’t mentioned in the text but in the figure 5?:thinking_face:Example is Ruminococcoceae marked asteric for significance but not in the text.@Chioma Onyido@Esther Afuape

Chiagoziem David (08:12:42): > Emmm guys, has anyone applied with the whole timeline stuff, could you please share

Chioma Onyido (08:18:13) (in thread): > I think you should.

Esther Afuape (08:28:46) (in thread): > I’dcurate them too

Odigiri Great Alume (08:39:29) (in thread): > Thank you both. I just updated them@Chioma Onyido@Esther Afuape

Peace Sandy (08:57:35) (in thread): > Lol…no you did not, probably I did not ask the question in the correct way,butI’llfigure it out:joy:

Chioma Onyido (09:45:03) (in thread): > Thats@Odigiri Great Alume’s current curation, I doubt it was deleted.@Svetlana Ugarcina Perovic<@UBNSEMS3S>we need your help here.:pray:

edilawit (09:55:51) (in thread): > thank you!

Svetlana Ugarcina Perovic (11:17:08) (in thread): > Hello@Esther Afuapewhat’s the reason to delete signature 2 and experiment 5 in this study?

Svetlana Ugarcina Perovic (11:23:31) (in thread): > Sure@Chioma Onyidoplease send me the latest update what and why should be deleted. thanks

Esther Afuape (11:24:41) (in thread): > I meant to delete signature 2 of experiment 4, and signature 2 of experiment 5. Not experiment 5 itself:pray:The taxa I entered there as decreased were the taxa that were enriched in the baseline.<@UBNSEMS3S>said there’s no need to double enter and curate what was stated as enriched in the group 0 as decreased for group 1.

Svetlana Ugarcina Perovic (11:28:19) (in thread): > All clear. Deleted.

Doreen Wanyama (11:36:26): > Good day everyone! How many contributions are we exactly supposed to submit for outreachy application? Thanks in advance

Uchechukwu Favour Ojunta (11:57:03): > Good evening everyone,@C. Mirzayi (please do not tag this account)please I just finished my contributions so I am about to start my final application, please I need help on where to start from, Thanks

Uchechukwu Favour Ojunta (12:09:21): > Hello@C. Mirzayi (please do not tag this account)<@U1LCB8WEA>please I just added an experiment to this studybugsigdb.org/Study_761/Experiment_2I will appreciate a review of my work, thanks

Esther Afuape (12:13:15): > <@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina PerovicI just finished completing and reviewinghttps://bugsigdb.org/Study_563. Experiments 5 and 7 were carried out in the paper but they had no differentially abundant taxa. I think they should be deleted since they have no signatures. - Attachment (BugSigDB): The conjunctival microbiome in health and trachomatous disease: a case control study - BugSigDB > BACKGROUND: Trachoma, caused by Chlamydia trachomatis, remains the world’s leading infectious cause of blindness. Repeated ocular infection during childhood leads to scarring of the conjunctiva, in-turning of the eyelashes (trichiasis) and corneal opacity in later life. There is a growing body of evidence to suggest non-chlamydial bacteria are associated with clinical signs of trachoma, independent of C. trachomatis infection. METHODS: We used deep sequencing of the V1-V3 region of the bacterial 16S rRNA gene to characterize the microbiome of the conjunctiva of 220 residents of The Gambia, 105 with healthy conjunctivae and 115 with clinical signs of trachoma in the absence of detectable C. trachomatis infection. Deep sequencing was carried out using the Roche-454 platform. Sequence data were processed and analyzed through a pipeline developed by the Human Microbiome Project. RESULTS: The microbiome of healthy participants was influenced by age and season of sample collection with increased richness and diversity seen in younger participants and in samples collected during the dry season. Decreased diversity and an increased abundance of Corynebacterium and Streptococcus were seen in participants with conjunctival scarring compared to normal controls. Abundance of Corynebacterium was higher still in adults with scarring and trichiasis compared to adults with scarring only. CONCLUSIONS: Our results indicate that changes in the conjunctival microbiome occur in trachomatous disease; whether these are a cause or a consequence is yet unknown.

Chioma Onyido (12:15:39) (in thread): > @Svetlana Ugarcina PerovicTo help delete: > study 212 experiment 1 (because of incorrect signatures). > Study 211 experiment 1 (because of incorrect) > Study 213 experiments 1 to 3 (because it is conflicting with@Odigiri Great Alume‘s curation):pray:

Chioma Onyido (12:20:52) (in thread): > Hi@Uchechukwu Favour Ojunta, this should help:https://community-bioc.slack.com/archives/C04RATV9VCY/p1698178098103179 - Attachment: Attachment > Application Timeline Guidelines: Thank you for your patience as we developed guidelines for the timeline section of your applications. To remind you, the internship begins on Monday, December 4th and runs until Friday, March 1st and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Fixing curation issues. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • Reviewing existing curations that are marked as needs review > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > Our hope is that our intern can spend a lot of their time working on curation issues and reviewing curations (bullet point numbers one and two) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Uchechukwu Favour Ojunta (12:22:32) (in thread): > Thank you so much@Chioma Onyido

Chioma Onyido (12:32:45) (in thread): > Hmmm…@Esther AfuapeFrom my understanding, I think its possible to have experiments without signatures. > > Let me share a response from<@U1LCB8WEA>,https://community-bioc.slack.com/archives/C04RATV9VCY/p1697410390867449?thread_ts=1697380986.698779&channel=C04RATV9VCY&message_ts=1697410390.867449 - Attachment: Attachment > @Joan C. Chukwuemeka is the advice I just gave on some other articles about what constitutes an Experiment helpful? The key message is that experiments are defined by the contrasts made, and signatures are defined by the results of those experiments. So it is perfectly possible to perform one or more experiments and find no statistically significant results, such as unchanged alpha diversity and no signatures of differentially abundant taxa.

Chioma Onyido (12:35:43): > Hi:wave:@Svetlana Ugarcina Perovic<@UBNSEMS3S>bugsigdb.org/Study_10andhttp://bugsigdb.org/Study_11are duplicates

UBNSEMS3S (12:41:33) (in thread): > @Chiagoziem DavidOur expectation is not that if selected as an intern you will make progress but we don’t expect you tocomplete any of the bulleted items as they will be ongoing for as long as the project exists. > > I will say what we look for in the timeline is that you have an understanding of how BugSigDB works and how as an intern you can contribute to the project. Realistic goals are preferred.

Chiagoziem David (12:48:55) (in thread): > Exactly, the bulleted points are for the duration of the project not the internship… > > Thank you very much<@UBNSEMS3S>, I am better equipped with this clarification. > > Thanks.

UBNSEMS3S (12:48:59) (in thread): > I’m not having an issue updating experiments 2 and 3. What updates are you trying to make to them that isn’t working? > > Those supplementary figures you linked are not curateable from the looks of things. You want to curate Supplementary Tables 3 and 4 which are excel spreadsheets.

Esther Afuape (12:56:43) (in thread): > Thank you so much ! Ididn’tknow it was okay to leave experiments without signatures.I’llreview and complete those 2 experiments then

Ludwig Geistlinger (13:07:23) (in thread): > Note the difference in study design for Study 10 and Study 11. Sometimes there can be several “studies” within one article in the sense that the authors studied different cohorts in a different study design within one publication. This is the case here.

Taiwo Adeyombo (13:09:51) (in thread): > Okay. For the experiments, I have filled in info under subjects such as group sizes and also statistical analysis. But each time I save the form it doesn’t show those things.

Chioma Onyido (13:10:59) (in thread): > Ohh I see. Got it! Thank you.

Chioma Onyido (13:35:22): > I have a question, > Forbugsigdb.org/Study_774whichI’mcurrently curating, the study was performed on Cohorts from the American Gut Project, I checked the link to the Project and saw that the participants were recruited from the US, UK and Australia. > > Should these countries be recorded in the location section in my curation?

Peace Sandy (13:37:20) (in thread): > I think this has been addressed by@C. Mirzayi (please do not tag this account)

Peace Sandy (13:37:52) (in thread): > Let me look for it

Peace Sandy (13:38:34) (in thread): > I noticed this too@Ludwig Geistlinger

Chioma Onyido (13:43:21) (in thread): > In my current curation, the authors studied anadditionalvalidation cohort within the same article, but same study design and matched on. > > I was thinking of curating as a new experiment. But seeing your discussion now, should this be curated as a different study?

Chioma Onyido (13:45:15) (in thread): > Alright. Waiting:blush:

Esther Afuape (13:49:02) (in thread): > This might helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696957404413579?thread_ts=1696946728.275149&channel=C04RATV9VCY&message_ts=1696957404.413579 - Attachment: Attachment > Look carefully at the Methods > Study design section. The locations are listed there and you should be able to add multiple countries in your curation.

Esther Afuape (13:55:38) (in thread): > I also had to select the location of a previous study for a new one in one of my previous curations and one of the mentors said it was fine

Chioma Onyido (14:00:23) (in thread): > @Esther AfuapeIt’sclear now, thank you so much!

Ludwig Geistlinger (14:01:03) (in thread): > If it is the same study design then it is likely easiest to add it as an additional experiment. It also seems that it was at some point possible to have two different studies associated with the same PMID. But this is not possible anymore as the “create study” form will prevent you from entering the same PMID again.

Svetlana Ugarcina Perovic (14:01:10) (in thread): > Deleted, thanks@Chioma Onyido

Esther Afuape (14:01:31) (in thread): > You’rewelcome

Chioma Onyido (14:02:28) (in thread): > Yes this is true, only unique PMID values are allowed. Thanks for the clarification.:pray:

Chioma Onyido (14:05:38) (in thread): > Thanks a bunch.:pray:Recurating it now.

Odigiri Great Alume (14:38:25) (in thread): > Thank you a lot@Svetlana Ugarcina Perovic@Chioma Onyido

Peace Sandy (14:48:22) (in thread): > Thanks for the clarification@Ludwig Geistlinger

UBNSEMS3S (16:37:54) (in thread): > Yes it is common for studies to recruit participants from within larger studies.

Chioma Onyido (16:39:56) (in thread): > Got it. Thanks for the clarification ma’am.

UBNSEMS3S (16:43:29): > Hi everyone we will be having our weekly team meeting and Outreachy office hours at 10 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499

Chioma Onyido (16:47:32) (in thread): > Thanks for the reminder. Looking forward to it!

Peace Sandy (17:25:04) (in thread): > Thank You@C. Mirzayi (please do not tag this account):confetti_ball:

Nana (17:31:48) (in thread): > <@UBNSEMS3S>Noted:white_check_mark:I will be there as usual

Peace Sandy (17:39:19): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldronplease can you help delete signatures 3 to 10 of this studyhttps://bugsigdb.org/Study_555I’m currently curating and i noticed that the initial curator entered multiple incomplete signatures - Attachment (BugSigDB): Self-Balance of Intestinal Flora in Spouses of Patients With Rheumatoid Arthritis - BugSigDB > We sought to characterize and assess differences in compositions of intestinal flora between patients with rheumatoid arthritis (RA) and their respective spouses. Eighty volunteers were recruited, including 30 pairs of RA patients and their spouses, and 20 healthy individuals. Fresh stool samples were collected, processed, and 16S rRNA-sequencing was performed. Data were analyzed using an operational taxonomic units-based method, and community structure assessments were performed. Community composition analysis indicated that there were similar intestinal microbiota structures in RA and in their respective spouses. Gut microbiota in spouses of RA were different from those of the healthy controls group, but these differences were not significant. We found that Blautia spp. and Streptococcus spp. were two most associated species in RA and these taxa were significantly higher in comparison to healthy controls. In contrast, our findings suggested that Roseburia spp. and Lachnoclostridium spp. were significantly lower in the RA in comparison to healthy controls. In conclusion, RA patients shared similar gut microbiota pattern with their spouses which were different from healthy individuals. The findings suggest that disturbance of the balance of gut microbiota may play an important role in the dynamics of pathogenesis of RA.

Esther Afuape (17:44:54) (in thread): > Thanks for the reminder

Esther Afuape (19:42:09): > I’llbe working on this study marked incomplete:https://bugsigdb.org/Study_826 - Attachment (BugSigDB): Long-term follow-up of colorectal cancer screening attendees identifies differences in Phascolarctobacterium spp. using 16S rRNA and metagenome sequencing - BugSigDB > BACKGROUND: The microbiome has been implicated in the initiation and progression of colorectal cancer (CRC) in cross-sectional studies. However, there is a lack of studies using prospectively collected samples. METHODS: From the Norwegian Colorectal Cancer Prevention (NORCCAP) trial, we analyzed 144 archived fecal samples from participants who were diagnosed with CRC or high-risk adenoma (HRA) at screening and from participants who remained cancer-free during 17 years of follow-up. We performed 16S rRNA sequencing of all the samples and metagenome sequencing on a subset of 47 samples. Differences in taxonomy and gene content between outcome groups were assessed for alpha and beta diversity and differential abundance. RESULTS: Diversity and composition analyses showed no significant differences between CRC, HRA, and healthy controls. Phascolarctobacterium succinatutens was more abundant in CRC compared with healthy controls in both the 16S and metagenome data. The abundance of Bifidobacterium and Lachnospiraceae spp. was associated with time to CRC diagnosis. CONCLUSION: Using a longitudinal study design, we identified three taxa as being potentially associated with CRC. These should be the focus of further studies of microbial changes occurring prior to CRC diagnosis.

2023-10-26

Chiagoziem David (01:45:27) (in thread): > Thanks

Karen254. Kingecha (02:26:18) (in thread): > Noted, thanks for the reminder

Svetlana Ugarcina Perovic (04:30:10) (in thread): > @Peace Sandygood morning, could you please confirm the request to delete signatures?

Grace Ogundaini (04:53:29): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina PerovicGood morning, for the final application are we supposed to record only the first two contributions we made I.e the mini-curation and the optional task, or are we supposed to record all contributions made to BugSigDB?

Peace Sandy (04:53:56) (in thread): > Good Morning@Svetlana Ugarcina Perovicyes please. > > Please delete signatures 3 to 10, they are incorrect

Mildred Anashie (05:16:27) (in thread): > I think we can record every contribution we made during the contribution phase not just the mini-curation and optional task

Peace Sandy (05:19:07) (in thread): > We are to record all the contributions we made

Peace Sandy (05:23:27) (in thread): > @Grace Ogundainisee our mentors replyhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697190804622469?thread_ts=1697190781.971739&channel=C04RATV9VCY&message_ts=1697190804.622469 - Attachment: Attachment > yes, all the bugsigdb tasks (curations, reviews, clean-ups, etc.) are your outreachy tasks

Mildred Anashie (05:35:23) (in thread): > Also, if youhaven’tbeen keeping track of your contributions, you can find them from the user icon when you login > I noticed Bugsigdb keeps track of the contributions you have made - File (PNG): IMG_4976

Grace Ogundaini (05:36:21) (in thread): > Thanks a lot

Peace Sandy (05:36:56) (in thread): > You are welcome@Grace Ogundaini

Mildred Anashie (05:39:48) (in thread): > You are welcome@Grace Ogundaini

Svetlana Ugarcina Perovic (05:43:29) (in thread): > Deleted. Thanks@Peace Sandy

Hodan Abdirisak (05:49:07) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Peace Sandy (06:08:19) (in thread): > Thank You@Svetlana Ugarcina Perovic

Grace Ogundaini (06:14:28): > Hello everyone! I will be working on this studyhttps://bugsigdb.org/Study_772under incomplete pages. - Attachment (BugSigDB): Differential Responses to Dietary Protein and Carbohydrate Ratio on Gut Microbiome in Obese vs. Lean Cats - BugSigDB > More than 60% of domestic cats in the United States are either overweight or obese (OW). High-protein low-carbohydrate (HPLC) diets have been recommended for weight management for humans and pets. Gut microbes can influence the host’s health and metabolism. Less is known about feline gut microbiomes compared to other species. Thirty-nine lean (LN) and OW domestic short-haired cats (median age, 7.2 years) with median body fat of 15.8 and 32.5%, respectively, were enrolled in a two-phase study. All cats were fed the control diet (CON) with 32.4% protein and 32.3% carbohydrate for 8 weeks followed by another 8 weeks of intervention where half of the cats continued the CON diet while the other half were switched to a HPLC diet with 51.4% protein and 11.6% carbohydrate. The goal was to understand how the HPLC diet influenced gut microbiota in obese vs. lean cats. The 16S rRNA gene profiling study revealed a significant impact on gut microbiome by dietary protein and carbohydrate ratio. The effect was more pronounced in OW cats than LN cats. While no microbial taxon was different between groups in LN cats, compositional changes occurred at different taxonomical ranks in OW cats. At the phylum level, Fusobacteria became more abundant in HPLC-fed cats than in CON-fed cats. At the genus level, five short-chain fatty acid (SCFA) producers had altered compositions in response to the diets: Faecalibacterium and Fusobacterium are more abundant in HPLC-fed cats while the abundances of Megasphaera, Bifidobacterium, and Veillonella increased in CON-fed cats. Predicted microbial gene networks showed changes in energy metabolism and one-carbon metabolism pathways. Our study demonstrated differential responses to HPLC diet between obese vs. lean cats and opportunities to explore these SCFA-producers for weight management in cats.

Esther Afuape (07:53:12): > Hi everyone > How do you guys fill the date contribution started and date contribution was accepted or merged whenyou’rerecording your contributions?

Chioma Onyido (08:22:43): > Hello<!here>I’m currently curatingbugsigdb.org/Study_774Some of my taxa are showing as orange because they weren’t yielding any results on the taxon browser page, uniprot and wiki. > Especially For theuncultured taxa (UCG), I wasn’t able to get IDs for them. For example, oscillospiraceae_ucg_003, I saw an ID for “uncultured oscillospiraceae” but the rank is not the same with the one in the paper (the rank on NCBI is species while mine is supposed to begenus), that’s why I entered it as I saw in the paper. Same goes for 15+ other orange taxa in my curation. The mentors advised to curate as is when we are unable to get IDs, > > But I need a second pair of eyes to be sure about this. Would anyone be willling to offer their assistance please? - File (Excel Spreadsheet): Supplementary Table 3 - File (Excel Spreadsheet): Supplementary Table 4

Chioma Onyido (08:27:25) (in thread): > I filled mine as when I started my curation (date started) and when I finished and submitted for review (date accepted/ merged).

Chiagoziem David (08:38:05) (in thread): > Alright

Chiagoziem David (08:38:10) (in thread): > Let me see

Chiagoziem David (08:41:04) (in thread): > Omo, all the contributions?

Chiagoziem David (08:41:20) (in thread): > If you made quite a lot ?

Esther Afuape (08:45:02) (in thread): > The UCG nomenclature is said to be treated as an uncultured Oscillospiraceae on the talk page but since the rankisn’tthe same, I think you should just curate it as it is. The other orange taxa I can see have a combinations of letters and numbers behind them that makes them very specific so I think you should leave those as they are too.

Chioma Onyido (08:46:17) (in thread): > Thank you so much:pray:@Chiagoziem David@Esther Afuape

Grace Ogundaini (08:54:09) (in thread): > :raised_hands:

Esther Afuape (09:14:21) (in thread): > Thank you so much

Chiagoziem David (09:23:27) (in thread): > I am asking:sweat_smile::sweat_smile::sweat_smile:, I’d bring it up today after office hours

Joan C. Chukwuemeka (09:35:35): > Good day all, > If part or all signatures you curate are within the text, how do you indicate it in the “Source” category?<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic

Peace Sandy (09:36:20) (in thread): > Most times they is always a figure or supplementary material for it, in very very few cases,I’veseen people include text in their source, butI’mnot sure about that yet.

Nana (09:36:50) (in thread): > i will take a look too

Nana (09:38:21): > <!here>gentle reminder of our townhall meeting happening by 3pm WAT

Joan C. Chukwuemeka (09:39:03) (in thread): > okay…..:thinking_face:

Peace Sandy (09:41:48) (in thread): > But is they any supporting material or figures,in most cases they is

Peace Sandy (09:42:30) (in thread): > Thank You for the reminder

Nwajei Edgar (09:43:49) (in thread): > Thanks for the reminder

Peace Sandy (09:44:34): > Here is the link for easy access:wave:https://us02web.zoom.us/j/2737200499

Hodan Abdirisak (09:44:36) (in thread): > Some times there additional file in lower pages of the study that explains figure or table which can be the source

Hodan Abdirisak (09:45:15): > Thanks:pray:15 min to go

Joan C. Chukwuemeka (09:45:19) (in thread): > In an excerpt like this: > > The species******Sneathia amnii******* and*****Prevotella******* *******amnii ****have recently been identified as emerging candidates for poor pregnancy > outcomes.******In our study, both of these were increased and had a significant association with PTB (q-value 0.02 and 0.05,************respectively; Table 2).*********Will the source be text or table 2?******note: ***Table 2 presents the results from several different contrasts at once, making it confusing

Peace Sandy (09:47:11) (in thread): > Oh…can you post table 2, just a snippet

UBNSEMS3S (09:47:30) (in thread): > Yes please record the contributions you’ve made. If you’ve made lots of small contributions to existing curations, you can summarize that without having to enter a contribution for each and every one.

UBNSEMS3S (09:48:13) (in thread): > Yeah you can have some orange taxa. “Uncultured” usually means that it can’t really be identified specifically.

Joan C. Chukwuemeka (09:48:24) (in thread): > Here@Peace Sandy - File (PNG): image.png

UBNSEMS3S (09:48:41) (in thread): > If it is only in the body of the text you can say “Results text” as the source

Chiagoziem David (09:49:00) (in thread): > Okay, that’s fair, thank you very much.

Chioma Onyido (09:49:51) (in thread): > Noted. Thank you:grin:<@UBNSEMS3S>

Peace Sandy (09:52:16) (in thread): > In the paper did they identify specific microbial taxa that were different between groups using some sort of statistical test

Esther Afuape (09:52:34) (in thread): > Were you an altschooler by chance?:sweat_smile:@Nana

Chiagoziem David (09:53:07) (in thread): > <@UBNSEMS3S>how do you link the summarised contributions though, what URL should you put for that

Joan C. Chukwuemeka (09:54:56) (in thread): > Okay<@UBNSEMS3S>Thanks. Could you suggest a resource that could help with understanding how to interpret heatmaps and bar plots as relates to microbiome studies? > > The one below in my curation is quite tasking, and I’m looking to consolidate my 2nd contribution based on feedback received. - File (PNG): image.png

Peace Sandy (09:55:39) (in thread): > Looking forward to the response too@C. Mirzayi (please do not tag this account)

Svetlana Ugarcina Perovic (09:57:07) (in thread): > <@UBNSEMS3S>for your referencehttps://github.com/waldronlab/BugSigDBcuration/issues/76 - Attachment: #76 Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth > Shotgun sequencing of the vaginal microbiome reveals both a species and functional potential signature of preterm birth – Conor Feehily et al. – npj Biofilms and Microbiomes 2020
> DOI: 10.1038/s41522-020-00162-8
> https://www.nature.com/articles/s41522-020-00162-8

Nana (10:00:03) (in thread): > @Esther Afuapeleave me alone:grinning::smile:how funny

Nana (10:00:09) (in thread): > una welcome

Chiagoziem David (10:00:41): > It’s time

Esther Afuape (10:06:14) (in thread): > I use “results (text)” whenit’sthat way

Esther Afuape (11:05:06) (in thread): > This was coincidentally presented today!:sweat_smile:I’llbe looking for something else to work on

Joan C. Chukwuemeka (12:10:17) (in thread): > <@U1LCB8WEA>thanks for the clarity during the office hour. > the figure description text for fig 2c says:******MaAsLiN analysis correlating species multiple metadata fixed effects. Heatmap displays the top 50 species with a significant association to either fixed effect with q-value < 0.25.******Will it be correct then, to say that threshold used is q < 0.25? > > Secondly, I’m starting to see that table 2 seems to consolidates fig 2c? Is that right?<@UBNSEMS3S>@Svetlana Ugarcina Perovic

UBNSEMS3S (16:52:13) (in thread): > This is a tough curation. Table 2 is what I would focus on curating but it has several experiments presented in it. Looking at it, it looks like there’s: > > Experiment 1: Previous PTB vs no > Experiment 2: Risk group vs not in risk group > Experiment 3: PTB vs. normal birth > Experiment 4: No-risk PTB vs. (some other group I can’t identify from the table so examine the text of the paper carefully)

UBNSEMS3S (16:52:32) (in thread): > And a q value of 0.25 does indeed appear to be their cutoff.

UBNSEMS3S (16:53:19): > Recording of today’s office hours. Apologies that I forgot to record the first 10 or so minutes. - File (MPEG 4 Audio): audio1125883594.m4a

UBNSEMS3S (16:54:58) (in thread): > https://bugsigdb.org/Special:Contributions/ > > If you want to link to every contribution you’ve made to BugSigDB. - Attachment (BugSigDB): Special:Contributions/

UBNSEMS3S (16:55:07) (in thread): > For instance, here’s mine:https://bugsigdb.org/Special:Contributions/Chloe - Attachment (BugSigDB): Special:Contributions/Chloe

Chiagoziem David (16:56:29) (in thread): > Thank you very much:blush:<@UBNSEMS3S>

Chioma Onyido (16:58:19) (in thread): > Very helpful! Thank you<@UBNSEMS3S>

Chiagoziem David (17:10:26) (in thread): > Thank you very much:blush:

Joan C. Chukwuemeka (17:41:08) (in thread): > Alright. Thanks<@UBNSEMS3S>In the context of MaAsLiN, I found out from further research that fixed effects are variables that are constant across individuals. They are also known as categorical variables or factors. > In the study, the fixed effects were risk group, delivery outcome, and previous PTB.Risk group: no-risk PTB, no-risk FTB, risk PTB, or risk FTB,(contrast stated within text is risk_FTB group vs non-risk FTB)Delivery outcome: preterm birth or full-term birthPrevious PTB: yes or no > > I’ll re-analyse the study, and believe the outcome will be better with the new knowledge gained,

Odigiri Great Alume (18:07:29): > Good evening@C. Mirzayi (please do not tag this account)@Levi WaldronI looked through the link for pages with missing NCBI taxa and saw that the study with the linkbugsigdb.org/Study_761was listed. I opened it and saw thatRothia” was listed in orange. After resolving the NCBI ID. I looked further to see what the study was about but noticed that the study was marked incomplete, and on trying to access the paper I again noticed that I can’t access the paper. It said something like paying to access the paper, however the person who curated that paper went ahead with the information visible and made an incomplete curation. > > What should be done here please ? > Thank you

Esther Afuape (18:16:33) (in thread): > paste the DOI of the paper in sci hub to see if you can get it there

Peace Sandy (18:42:19) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Odigiri Great Alume (21:37:37) (in thread): > I found the article however I don’t have access to the supplementary figures. Any ideas?

Mildred Anashie (21:39:45) (in thread): > Paste PMID or DOI on Pubmed you might get it there

Odigiri Great Alume (21:40:59) (in thread): > Thank you@Mildred AnashieI found the supplementary figure but I’m not able to find anything on statistical test. It’s not in the text either. > > But in all I am able to make corrections to the work and have curated some signatures and completed the missing information left blank

Mildred Anashie (21:52:55): > Hi<@U1LCB8WEA><@UBNSEMS3S>I’m working on this studyhttps://bugsigdb.org/Study_782from the studies without experiment and I duplicated Signature 2, please I need help deleting signature 3 for Experiment 2:pray: - Attachment (BugSigDB): Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection - BugSigDB > BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system.

Odigiri Great Alume (23:31:41) (in thread): > In the study I worked on, the curator used two study designs (prospective cohort and cross-sectional observational, not case-control study) at once. but after reading through the paper i noticed the correct study design employed was prospective cohort. Hence, I made changes. > > Also I filled in all the missing information for the study after finding the free paper on sc hub and pubmed and curated the missing data. However, I was unable to find the statistical test used for the study. > > The study made four comparisons in figure 2. but the curator did not correctly represent experiments 1 as he left Group 1 blank and then went on not to curate any signatures. > > For his second experiment, he compared healthy controls with all patients combined, and created three signatures, however the study does not seem to do that. Rather the study made for comparisons below; > 1. Controls vs SJS > 2. Controls vs GVHD > 3. Controls vs FES > 4. Controls vs DED > > I have decided to leave his second experiment and signatures for the mentors to review and decide to delete or not. > I then proceeded to add the rest of the experiment above. > > Here’s the link to the curation@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina PerovicBugsigdb.org/Study_761

Sinmi Adesanya (23:42:03) (in thread): > Thanks Chloe!

2023-10-27

Hodan Abdirisak (02:11:21) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Fortune Nnamdi (02:33:32) (in thread): > Thanks!<@UBNSEMS3S>

Svetlana Ugarcina Perovic (05:55:43) (in thread): > deleted.

Mildred Anashie (06:58:19): > Thankyou:pray:

Joan C. Chukwuemeka (10:50:08): > Good day all, > > Please can species dominance be curated as per increased abundance?<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic

Odigiri Great Alume (12:11:03) (in thread): > @Svetlana Ugarcina Perovicplease could you look at this for me to delete experiment two and it’s signatures.http://bugsigdb.org/Study_761 - Attachment (BugSigDB): Assessing the ocular surface microbiome in severe ocular surface diseases - BugSigDB > PURPOSE: There is growing evidence for a critical role of the microbiome in ocular health and disease.We performed a prospective, observational study to characterize the ocular surface microbiome (OSM) in four chronic ocular surface diseases (OSDs) and healthy controls.

Mildred Anashie (12:14:29) (in thread): > Thank you:pray:

UBNSEMS3S (12:38:11) (in thread): > Could you show us the context? Dominance does not necessarily mean increased abundance.

Joan C. Chukwuemeka (12:45:25) (in thread): > Here’s the Excerpt<@UBNSEMS3S>Taxonomic classification revealed that lactobacilli were dominant > across all groups at 59.13% mean relative abundance (Fig. 2a), with a greater proportion observed in full-term pregnancies (61.86%) compared to preterm (45.11%).******This dominance was greatest in the no-risk_FTB group (71.32%) where both Lactobacillus crispatus (50.86%) and Lactobacillus iners (21.27%) were************dominant. Within the risk_FTB group, L. crispatus (25.83%), L. iners************(14.83%), Lactobacillus gasseri (11.70%), and L. gasseri A (7.30%)************were the dominant species detected.******L. crispatus was never 0.03% relative abundance in the risk_PTB group. In addition, L. gasseri was only detected in two samples in the risk_PTB group, accounting for just 0.01% mean relative abundance. Although L. iners (30.82%) accounted for a greater proportion of the mean population in the risk_PTB group compared to both FTB groups, this increase was not statistically significant.

UBNSEMS3S (14:05:16) (in thread): > Can I see Fig. 2A please?

Joan C. Chukwuemeka (14:07:08) (in thread): > This is it - File (PNG): image.png

UBNSEMS3S (14:26:08) (in thread): > That doesn’t look like something curatable to me. Looking at the text, it also doesn’t seem to state that they did statistical testing for those differences aside from the last one. I’d look for a different figure or table to curate.

Joan C. Chukwuemeka (14:28:09) (in thread): > Alright. Thanks a lot:blush:<@UBNSEMS3S>

Joan C. Chukwuemeka (19:14:47): > After curating signatures for a study experiment, a couple of them were marked****“red”****due to******missing NCBI ID******. I didn’t see them in NCBI initially, however, I recalled that the study mentioned Genome Taxonomy Database (GTDB) > > So I googled it and searched for the taxa names. Interestingly, it shows taxon history (which is helpful for obsolete names) and also the corresponding name in NCBI. > > Here’s a video example of how I resolved them, using one of the signatures as an instance.<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicPlease, would want to check if this step I took is okay and still in line with the required“detective”approach:blush:toresolving Missing NCBI ID issues? - File (MPEG 4 Video): Missing NCBI ID resolution.mp4

2023-10-28

Chioma Onyido (02:59:52): > Happy weekend all<!here>bugsigdb.org/Study_633I changed the description for signatures 1 and 2 (under experiment 1) to “Comparison of Gut Microbiota between proximal colon cancer and distal colorectal cancer based on principal component analysis scores (97% similarity level)”. It was previously “Principal component analysis scores plot based on the relative abundance of otus (97% similarity level)”. Let me know if this is okay<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina PerovicNot sure why the curator marked as incomplete but I reviewed the paper and confirmed that the signatures were accurate, so I proceeded to mark as complete.

Chioma Onyido (04:18:16): > bugsigdb.org/Study_774A subset of IBS patients had a diagnosis of depression which is one of the psycosocial factors usually associated with worse prognosis of IBS. This formed my experiment 4, where a contrast was made between IBS patients with depression and IBS patients without. > I’m looking for the best EFO to describe this condition, Ididn’tgo with IBS because both groups had IBS, the condition that differentiates them is “depression”:sweat_smile:Can you advise me on the closest match?irritable bowel syndrome symptom measurementor simply,depressive disorder?

Joan C. Chukwuemeka (04:29:55) (in thread): > Good morning@Chioma OnyidoChecking it out:slightly_smiling_face:

Joan C. Chukwuemeka (05:31:06) (in thread): > I think using a different condition may not be needed. > Considering this Excerpt:*****A total of 942 subjects with IBS-Diarrhea (IBS-D), IBS-Constipation (IBS-C), unclassified IBS (IBS-U), and 942 non-IBS controls were included. > *****I think the depression grouping is still an IBS subtype like the ones listed above, except it was not initially listed. > Something like******IBS-depressed******

Chioma Onyido (05:39:14) (in thread): > I know right? I wanted to go with this initially but I remember<@U1LCB8WEA>’s explanation sometime ago thatcondition is based on what is being contrasted not what is shared by both groups. Made me reconsider using a different condition since both groups had IBS.:thinking_face:The excerpt you shared was what they used for the general contrast which formed by experiments 1 to 3. > > However, Depression was what they used to contrast groups for my experiment 4. > Hmmm I don’t think depression is a subtype because the paper says that they selected a subset of patients (all subtypes) that had a diagnosis of depression. > > Excerpt:A subset of patients with IBS had a diagnosis of depression (IBS-D, n = 36; IBS-U, n = 63; IBS-C, n = 35). We paired patients with IBS on depression, with others without depression using the above matching algorithm adjusting for age, BMI, country, diet (including alcohol), and sex. https://community-bioc.slack.com/archives/C04RATV9VCY/p1697657022574859?thread_ts=1697656411.851839&channel=C04RATV9VCY&message_ts=1697657022.574859 - Attachment: Attachment > Remember, the Condition is what is being contrasted in the experiment, not something shared by both groups. From the objective: To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients.

Odigiri Great Alume (05:39:18) (in thread): > @Joan C. Chukwuemekawell done. But I want to ask, is it okay to use a condition that’s common to the Groups ? > I think that’s the angle @chioma@Chioma Onyidois taking it from. > > I read some where that to decide the condition you should look for what is been compared in both groups 1 and 0 > > I don’t know if it makes sense:blush:

Khadija (05:59:48): > Hey there, i have completed my first contribution and recorded the contribution on outreachy. When should i submit my final application on outreachy? After 2nd contribution? What to write in it?

Chioma Onyido (06:00:56) (in thread): > Hi@Khadijayesit’sadvisable to finish and record your second contribution before submitting your final application.

Chioma Onyido (06:04:22) (in thread): > 1. Here’s a guide on how you can start out with your second contribution. > https://community-bioc.slack.com/archives/C04RATV9VCY/p16964363062173492. When you’ve done that and you’re ready for your final application on Outreachy, here’s a guide on how to go about that.https://community-bioc.slack.com/archives/C04RATV9VCY/p1698178098103179 - Attachment: Attachment > Application Timeline Guidelines: Thank you for your patience as we developed guidelines for the timeline section of your applications. To remind you, the internship begins on Monday, December 4th and runs until Friday, March 1st and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Fixing curation issues. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • Reviewing existing curations that are marked as needs review > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > Our hope is that our intern can spend a lot of their time working on curation issues and reviewing curations (bullet point numbers one and two) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Tolulope Ogunleye (06:06:21): > Hi everyone, as the contribution period draws to a close, you can find all of the contributions you have made in one place by searching for your user name on BugSigDB .

Joan C. Chukwuemeka (06:13:57) (in thread): > Hmmm…I see:thinking_face:@Odigiri Great AlumeHowever, IBS is the primary condition here, hence why each is prefixed with IBS… > > Every sub condition is on the basis of having IBS. > We have IBS patients having diarrhea,those having constipation, those depressed and not, and then non-IBS. The authors here probably wants to see if the microbiome is affected by this sub-conditions.

Peace Sandy (06:27:07) (in thread): > Have you been able to do your second contribution

Peace Sandy (06:27:41) (in thread): > Thank you so much,I realized I did some contributions Ididn’trecord

Joan C. Chukwuemeka (06:28:12) (in thread): > Constipation and diarrhea are symptoms of IBS, depression may be experienced too by some persons

Chiagoziem David (06:28:45) (in thread): > Follow through the link that@Chioma Onyidodropped , if you have any extra questions drop em here

Chioma Onyido (06:36:06) (in thread): > @Joan C. ChukwuemekaYes you’re right but Depression wasn’t prefixed with IBS in this paper. The groupwith depression wasn’t compared with Non-IBS, they were compared with IBS patientswithoutdepression. > > Can you read through the results section again, carefully? - File (JPEG): IMG_5587

Chioma Onyido (06:41:57) (in thread): > Hmmm okay@Joan C. Chukwuemekayou’resaying depression is a symptom yeah? > > So that meansIBS symptom measurementmight be the nearest EFO?:thinking_face:

Odigiri Great Alume (06:47:25) (in thread): > @Chioma OnyidoI think the condition will have to change for each experiments:thinking_face:I’m not sure bout this but let’s see. > Can you state the experiments carried out in the study please

Chioma Onyido (06:48:28) (in thread): > @Odigiri Great AlumeSame. Andthat’sexactly what I did.I’mjust confused about the ontology to use for experiment 4

Odigiri Great Alume (06:48:49) (in thread): > What does experiment four compare

Odigiri Great Alume (06:49:22) (in thread): > I mean what variables were compared in experiment 4

Chioma Onyido (06:50:35) (in thread): > Experiments 1 to 3; > IBS-C vs Non-IBS1 > IBS-D vs Non-IBS2 > IBS-U vs Non-IBS3 > > Then they selected a subset from patients with IBS and compared IBS patients with depression and IBS patients without depression. > > Experiment 4; > IBS patients (IBS-C, IBS-D, IBS-U) with depression vs IBS patients without depression.

Chioma Onyido (06:52:37) (in thread): > Condition for Experiments 1 to 3 is clear, which is IBS, because that is what they used for the contrast. > > However for Experiment 4, what was used for contrast wasn’t IBS but depression, Im thinking to go with a different condition for this because the contrast was not IBS, but I’m not sure how to go about this because the ontology provides different terms,IBS symptom measurement ordepressive disorder? > > Since depression is a symptom, should I go with IBS symptom measurement?

Joan C. Chukwuemeka (06:53:30) (in thread): > ******IBS symptom measurement ****@Chioma Onyido***** *****

Odigiri Great Alume (06:54:24) (in thread): > @Chioma Onyidoin my opinion, the condition in studied here is depression related and if depression is a symptom of IBS then I agree with IBS symptom management

Chioma Onyido (06:55:36) (in thread): > Thank you for your time@Joan C. Chukwuemeka@Odigiri Great Alume:smiling_face_with_3_hearts::pray:

Odigiri Great Alume (06:56:23) (in thread): > Well done:+1:@Chioma OnyidoYou make it easy being here. God bless you

Joan C. Chukwuemeka (06:57:33) (in thread): > You’re welcome@Chioma Onyido.:blush:we grow together through collaboration

Esther Afuape (07:13:55) (in thread): > Well done guys. Came late to the party:sweat_smile:

Chioma Onyido (07:18:18) (in thread): > I tried typing “irritable bowel syndrome symptom measurement”, it says result not found but I see it clearly on the EFO browser!:tired_face: - File (JPEG): IMG_5588

Odigiri Great Alume (07:19:38) (in thread): > Why not try IBS symptom measurements

Odigiri Great Alume (07:19:44) (in thread): > Not the full meaning

Chioma Onyido (07:20:14) (in thread): > Still not showing.

Joan C. Chukwuemeka (07:21:14) (in thread): > wow.. let me check:thinking_face:

Karen254. Kingecha (07:27:26) (in thread): > Thanks alot

Karen254. Kingecha (07:29:11) (in thread): > This whole conversation was insightful

Joan C. Chukwuemeka (07:31:44) (in thread): > Still same thing here… just wondering why the bugsigdb isn’t having it:thinking_face:

Odigiri Great Alume (07:33:04) (in thread): > I think the closest thing here is to use IBS

Esther Afuape (07:33:55) (in thread): > Can you copy and paste the EFO ID instead?

Joan C. Chukwuemeka (07:34:05) (in thread): > Yes@Odigiri Great Alume, however, it’d be nice to let the mentors know to clarify it

Joan C. Chukwuemeka (07:34:26) (in thread): > @Esther Afuapetried that, didn’t work

Karen254. Kingecha (07:36:41) (in thread): > I’d also choose IBS just as@Odigiri Great Alumehas said I think its the closest match. > But let’s wait and hear from our mentors@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic

Esther Afuape (07:37:37) (in thread): > It’spossible to select 2 conditions.SoI’dchoose IBS and depressive disorder

Odigiri Great Alume (07:39:05) (in thread): > Makes sense if itz possible

Joan C. Chukwuemeka (07:42:23) (in thread): > @Chioma OnyidoI’m thinking perhaps its because IBS symptom measurements is not listed as a disease condition in EFO, but a measurement:thinking_face:. compare the 2 images below showing their tree designation on EFO:@Esther Afuape’s suggestion its workable though, but I’d love to get the perspective of our mentors<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic - File (PNG): image.png - File (PNG): image.png

Chioma Onyido (07:47:35) (in thread): > Ohh I see.

Chioma Onyido (07:49:46) (in thread): > Esther’ssuggestion to select 2 conditions makes sense butI’llwait for clarification from the mentors.:pray:

Esther Afuape (07:51:45) (in thread): > Yes. Their clarification will sort it out. Well done:hugging_face:

Chioma Onyido (07:52:59) (in thread): > @Joan C. Chukwuemekayou’re right, That’s probably why it didn’t reflect on bugsigdb since it’s a measurement not a condition.:sweat_smile:In the words of@Levi Waldron<@UBNSEMS3S>,good detective jobeveryone! And thank you for your time!:clap:

Hodan Abdirisak (08:12:37) (in thread): > I did first contribution and second contribution is there any other contribution needed to record

Hodan Abdirisak (08:14:37) (in thread): > @Khadijado final application after the second contribution and follow that guidelines@Chioma Onyidogives

Karen254. Kingecha (08:17:23): > Hey everyone, when recording my contribution in the outreachy website I accidentally recorded one project twice any ideas how i can delete one.

Desire Oluwarotimi (08:22:53) (in thread): > I’m not quite sure if there a way to perform the delete function but I’d say if you have other contributions yet to be recorded, you can simply edit the mistake instead of creating a new contribution.

Peace Sandy (08:26:16) (in thread): > Idon’tthink you can delete

Odigiri Great Alume (08:39:37): > Hello, please during the final application, for those who didn’t list any time commitments, can we go ahead to check the box that says “are the time commitment listed above correct?” > > Also, do we need to send our project timeline to the mentors for a review before final application?@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic

Hodan Abdirisak (08:53:09): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovicwhat I enter the end date of second contribution

Nana (09:25:23) (in thread): > If is not you final contribution click on edit contribution and manually remove the one you don’t want

Chioma Onyido (09:34:51) (in thread): > @Hodan AbdirisakIfilled mineas,when I started my curation (date started) and when I finished and submitted for review (date accepted/ merged).

U1LCB8WEA (09:37:45) (in thread): > This is excellent “detective” work,@Joan C. Chukwuemeka!!!:clap:

U1LCB8WEA (09:39:31) (in thread): > Great,@Chioma Onyido! I marked 633 as reviewed.

U1LCB8WEA (09:45:51) (in thread): > It’s wonderful to see this collaboration! Like@Chioma Onyidorecalled that I said, “condition is based on what is being contrasted not what is shared by both groups.” So forexperiment 4, where a contrast was made between IBS patients with depression and IBS patients without,the Condition would bedepressive disorder.

U1LCB8WEA (09:47:32) (in thread): > And in this contrast, what is being contrasted is location in the colon: - File (PNG): image.png

Peace Sandy (09:47:46) (in thread): > Here for the response

U1LCB8WEA (09:48:07) (in thread): > (oh, that last screenshot was from 633)

Esther Afuape (09:49:38) (in thread): > So for a study between trachoma participants that were sampled in wet and dry season, the condition is season?

U1LCB8WEA (09:52:06) (in thread): > Note though that for this experiment, the location is location of the cancer, but if that’s not in EFO, then just colorectal cancer might be the closest available. - File (PNG): image.png

U1LCB8WEA (09:53:07) (in thread): > yes:sweat_smile:

Karen254. Kingecha (09:53:31) (in thread): > @Esther AfuapeIn your study, it seems like the condition being investigated is the effect of the season (wet season vs. dry season) on participants with trachoma. So, yes, the condition in this context is the season.

U1LCB8WEA (09:54:22) (in thread): > unless there is a known difference between trachoma in those two seasons that is reflected in EFO, like “wet season trachoma”

Joan C. Chukwuemeka (09:55:20) (in thread): > Thanks<@U1LCB8WEA>, So it’s possible then for a study to have experiments with different conditions?

U1LCB8WEA (09:55:31) (in thread): > Yes definitely!

Esther Afuape (09:58:31) (in thread): > Got it!

Joan C. Chukwuemeka (10:01:11) (in thread): > Thanks<@U1LCB8WEA>:gratitude-asl:

Chioma Onyido (10:05:50) (in thread): > Yes<@U1LCB8WEA>I checked and locationwasn’tin EFO,that’swhy I left it as the initial condition the curator selected which is colorectal cancer.

Chioma Onyido (10:08:05) (in thread): > Actually just searched EFO again and I seesigmoid neoplasm:thinking_face:

Chioma Onyido (10:19:07) (in thread): > Same.

Tolulope Ogunleye (11:30:34) (in thread): > You can still work on other contributions if you’ll like…. Click on “to do for reviewers” you’ll find some tasks that you can do and record it the contributions.

Odigiri Great Alume (12:00:37) (in thread): > Me too.:joy:

Odigiri Great Alume (12:05:39): > Please@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovicplease can you help me look at experiment 2 and it’s signatures for possible delete?http://bugsigdb.org/Study_761The curator curated 3 signatures and then created an experiment that wasn’t in the study. > > I had previously asked for this but it seems because of the overwhelming schedule lately it was not attended to. > > Here’s the link to the message I raised this concern originallyhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1698377501197979?thread_ts=1698358049.109889&cid=C04RATV9VCY - Attachment (BugSigDB): Assessing the ocular surface microbiome in severe ocular surface diseases - BugSigDB > PURPOSE: There is growing evidence for a critical role of the microbiome in ocular health and disease.We performed a prospective, observational study to characterize the ocular surface microbiome (OSM) in four chronic ocular surface diseases (OSDs) and healthy controls. - Attachment: Attachment > In the study I worked on, the curator used two study designs (prospective cohort and cross-sectional observational, not case-control study) at once. but after reading through the paper i noticed the correct study design employed was prospective cohort. Hence, I made changes. > > Also I filled in all the missing information for the study after finding the free paper on sc hub and pubmed and curated the missing data. However, I was unable to find the statistical test used for the study. > > The study made four comparisons in figure 2. but the curator did not correctly represent experiments 1 as he left Group 1 blank and then went on not to curate any signatures. > > For his second experiment, he compared healthy controls with all patients combined, and created three signatures, however the study does not seem to do that. Rather the study made for comparisons below; > 1. Controls vs SJS > 2. Controls vs GVHD > 3. Controls vs FES > 4. Controls vs DED > > I have decided to leave his second experiment and signatures for the mentors to review and decide to delete or not. > I then proceeded to add the rest of the experiment above. > > Here’s the link to the curation > @C. Mirzayi (please do not tag this account) @Levi Waldron @Svetlana Ugarcina Perovic > > Bugsigdb.org/Study_761

Esther Afuape (15:28:55): > Is it still possible to add contributions after making your final application?Before the deadline of course

Hodan Abdirisak (15:53:04) (in thread): > @Chioma Onyidothanks but is not merged yet

Hodan Abdirisak (15:53:20) (in thread): - File (PNG): Screenshot 2023-10-28 125157.png

Chioma Onyido (15:58:49) (in thread): > Did you put a date in the slot for “date contribution was accepted or merged”? - File (JPEG): IMG_5602

Chioma Onyido (16:02:27) (in thread): > You mean add contributions to bugsigdb or to record on Outreachy?

Esther Afuape (16:03:02) (in thread): > To record on outreachy

Chioma Onyido (16:03:13) (in thread): > Ifit’stoo add to BugSigDB, I think we can keep contributing, (I hope we can) > > But ifit’srecording on Outreachy, not sure.:eyes:

Esther Afuape (16:04:05) (in thread): > Hmm okay > Thank you

Hodan Abdirisak (16:21:30) (in thread): > Not yet

Chioma Onyido (16:25:44) (in thread): > We were advisedthatthere’sno need to wait for review by the mentors before we can insert the date, Ifyou’vefinished your second curation, you should record a date there so that itwon’tflag asnot accepted or merged.

Hodan Abdirisak (16:27:28) (in thread): > So I can enter any date

Hodan Abdirisak (16:27:44) (in thread): > Or the date I start

Chioma Onyido (16:27:51) (in thread): > Yes@Hodan Abdirisak, the date you finished your second curation.

Hodan Abdirisak (16:28:25) (in thread): > Thanks@Chioma Onyidoyou enlighten me more

Chioma Onyido (16:31:28) (in thread): > I hope this image makes it clearer@Hodan Abdirisak:sweat_smile:

Chioma Onyido (16:33:14) (in thread): - File (JPEG): IMG_5604

Fortune Nnamdi (17:09:53) (in thread): > Yeah, Chioma is right. > > After the final application deadline,it’simpossible to record more contributions on outreachy. Hopefullyit’llbe possible to do so on BugSigDB.

Odigiri Great Alume (17:23:05) (in thread): > You can keep recording your contributions after submitting final application so long as it’s before 30th October 4pm. > > So if you haven’t finished a contribution and you know it’s ongoing and might not finish before the date, I think you can record it while you work to finish it. > > My opinion.

Esther Afuape (17:32:31) (in thread): > Yeah I just saw it in the reminder email that was was sent that you can keep recording or editing contributions till November 20th

Odigiri Great Alume (17:58:54) (in thread): > Very good then

Odigiri Great Alume (17:59:17) (in thread): > Quality over quantity:joy:

Chioma Onyido (18:02:12) (in thread): > Awesome!

Peace Sandy (18:48:17) (in thread): > Great:+1:

Hodan Abdirisak (23:01:45) (in thread): > :laughing:yeah it really makes sense

2023-10-29

Khadija (05:35:32) (in thread): > I am waiting for my account approval.@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Odigiri Great Alume (07:10:51): > Good Afternoon everyone. Please I need help. > The Figure below shows increase and decrease in taxa for H vs PD. > How do I record these signatures. Eg. ASV7: STREPTOCOCCUS, ASV1580: STREPTOCOCCUS and ASV415: STREPTOCOCCUS.https://journals.asm.org/doi/10.1128/msystems.01489-21@Levi Waldron@C. Mirzayi (please do not tag this account) - File (JPEG): IMG_20231029_120614.jpg

Mildred Anashie (07:54:29) (in thread): > ASV (Amplicon Sequence Variance) could have been what was used to identify the bacterial species, probably giving it molecular identityMy thoughtsare ASV7 should be omitted when curating for ASV 7: STREPTOCOCCUSI’m interested in this too because I came across a study where ASV was being contrasted between groups although the taxasweren’tpresented this way > > > But weshouldwait for the mentors@Levi Waldron<@UBNSEMS3S>to clarify this

Odigiri Great Alume (07:59:08) (in thread): > @Mildred Anashiethank you. However there are three different ASV ID for streptococcus. If we leave it out, does that mean to record streptococcus three times (I don’t think so) so I’d wait for more clarification from the mentors@C. Mirzayi (please do not tag this account)@Levi Waldronand other team mates who have come across this before@Chioma Onyido@Esther Afuapeetc > > Thanks:pray:

Mildred Anashie (08:05:03) (in thread): > Okay@Odigiri Great Alumemy apologies Ididn’tnotice that > > We’d have to wait for their response to know what to do > Maybe you could share a link to the paper to go through while we wait

Odigiri Great Alume (08:07:15) (in thread): > :joy:@Mildred Anashieyou don’t need to apologize dear. I should be thanking you for helping. Also thanks for the suggestion. > I will add the link to the study now

Esther Afuape (08:15:59) (in thread): > It looks similar to this. This one was a linear discriminant analysis from one of my curations. Everything in front of the green lines are for low IgA while everything in front of the orange lines are for High IgA - File (JPEG): 8db7bfcb-3df9-44e0-a0f4-57af22f0e4e8

Esther Afuape (08:17:18) (in thread): > For yours, I can’t see the labels but ASV16: corynebacterium_1 is for whatever was labeled in red

Odigiri Great Alume (08:20:16) (in thread): > Uhmmm@Esther AfuapeI don’t understand:thinking_face:. > I was thinking ASV16: Corynebacterium increased for the H. while the rest of the taxa increased for PD. > Are we saying same thing?

Esther Afuape (08:21:32) (in thread): > Can you send the link to the study?

Esther Afuape (08:22:29) (in thread): > Yes,we’resaying the same thing@Odigiri Great Alume

Mildred Anashie (08:22:32) (in thread): > @Esther AfuapeHis question seems to be based on how he’ll curate for the identified taxas. All are Streptococcus with ASV7, ASV1580 and ASV415

Odigiri Great Alume (08:22:37) (in thread): > :blush:

Odigiri Great Alume (08:22:58) (in thread): > Oh thanks:pray:.. just sent the link to your dm

Hodan Abdirisak (08:26:45) (in thread): > @Khadijacheck:heavy_check_mark:your spam in email

Hodan Abdirisak (08:26:54) (in thread): > Then verify your account

Esther Afuape (08:32:47) (in thread): > Seems ASV was only a label to identify abundant species. Itdoesn’tseem to be necessarily referring to different species or strains.I’djust curate streptococcus once for the three - File (PNG): IMG_3678

Odigiri Great Alume (08:37:16) (in thread): > @Esther Afuapethis makes sense. Thanks@Mildred Anashiethanks too

Peace Sandy (08:49:10): > Hey Everyone:wave:Deadline for final application is tomorrow 30th, 5pm Nigerian time. > > If you have any questions or doubts as regards the final application,feel free to drop your concerns and ask those questions. > > Good Luck Everyone:bouquet:

Zoyander Street (09:56:29): > Hi! I’m joining late, but hoping to make and record a contribution by the deadline tomorrow. I’m very interested in the microbiome, so I’m excited to give this a shot!

Hodan Abdirisak (11:05:10): > i fill final application form and press submit here is the next i think that would be the last step, is there any other requirement? - File (PNG): Screenshot 2023-10-29 080243.png

Mildred Anashie (11:26:43) (in thread): > Welcome@Zoyander Street

Chioma Onyido (11:34:22) (in thread): > ASV stands for Amplicon sequence variant just as@Mildred Anashieand@Esther Afuapeexplained. Similar to OTUs, It’s another method (more detailed actually) used to identify and characterize microbes. Researchers use ASVs when studying complex microbial ecosystems for more accurate rep of diversity (Source: ChatGPT) > > So the ASVs you see are what the Authors decided to use as labels.:thumbsup:Also, I would curateStreptococcusonce too, but with “spp.” to collectively represent the species. -Streptcoccus spp.(that’s if it’s available on NCBI)

Fortune Nnamdi (12:46:48) (in thread): > Hi@Zoyander StreetYou’re welcome. > > Check this link to see how you can go about the first contribution:https://github.com/waldronlab/BugSigDBcuration/issues/94And for the second contribution, read through this shared by Chioma.https://community-bioc.slack.com/archives/C04RATV9VCY/p1698487462625409?thread_ts=1698487188.036549&channel=C04RATV9VCY&message_ts=1698487462.625409 - Attachment: Attachment > 1. Here’s a guide on how you can start out with your second contribution. > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 > > 2. When you’ve done that and you’re ready for your final application on Outreachy, here’s a guide on how to go about that. > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698178098103179

Fortune Nnamdi (13:02:41) (in thread): > If we want to fill this how do we go about it? It says it’s optional, yeah…but it says some communities might want us to answer additional questions.Do we have such questions in our community? - File (JPEG): IMG_5971

Zoyander Street (13:04:44) (in thread): > Thanks so much!

Fortune Nnamdi (13:35:12) (in thread): > @Odigiri Great AlumeI also didn’t list any time commitments,I’malso a little bit confused as to whether checking the box is okay

Peace Sandy (13:37:20) (in thread): > I think this is it

Peace Sandy (13:37:42) (in thread): > Let me share@C. Mirzayi (please do not tag this account)response

Peace Sandy (13:38:53) (in thread): > @Fortune Nnamdihttps://community-bioc.slack.com/archives/C04RATV9VCY/p1698178615108109?thread_ts=1698120248.862859&channel=C04RATV9VCY&message_ts=1698178615.108109 - Attachment: Attachment > No you do not need to provide any additional information unless there’s something else you would like us to consider or know about you.

Peace Sandy (13:39:28) (in thread): > Welcome, all the best

Fortune Nnamdi (13:52:06) (in thread): > Alright, thanks!:blush:

Hodan Abdirisak (13:55:49) (in thread): > :pray:thanks

Peace Sandy (14:15:32) (in thread): > You are welcome

Nana (14:30:19) (in thread): > @Hodan Abdirisakwas it on edit or create a final application you clicked on to record that

Nana (14:33:01) (in thread): > @Peace Sandyshabi na final application i go click on, then about the merged date<@UBNSEMS3S>mentioned we should fill it by ourself

Peace Sandy (14:33:38) (in thread): > You will click on create final application

Peace Sandy (14:34:24) (in thread): > Yes, click on final application

Nana (14:43:51) (in thread): > About merged date nko

Nana (14:44:31) (in thread): > ok

Fortune Nnamdi (14:45:04) (in thread): > @Nanajust put in the date you finished that particular contribution

Nana (14:45:27) (in thread): > @Fortune Nnamdiok thanks

Odigiri Great Alume (14:47:24) (in thread): > To be on a safer side please check that box okay. Checking the box could also mean that your previous response of not listing a time commitment still stands@Fortune Nnamdi

Fortune Nnamdi (14:47:58) (in thread): > Thanks

Odigiri Great Alume (15:01:05): > Please@C. Mirzayi (please do not tag this account)@Levi Waldronis there any specific community questions that needs to be added to our final application.

Hodan Abdirisak (15:13:50) (in thread): > Yeah@Nanaas@Peace Sandytold you

Nana (15:21:43): > @Odigiri Great Alumeread previous chat she has answered it.

Odigiri Great Alume (15:24:08) (in thread): > I did before asking, just didn’t find anything. Please:pleading_face:if you can point me to it I’d be happy .@Nana

Fortune Nnamdi (15:34:08) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698601133769159?thread_ts=1698583750.178099&channel=C04RATV9VCY&message_ts=1698601133.769159 - Attachment: Attachment > @Fortune Nnamdi https://community-bioc.slack.com/archives/C04RATV9VCY/p1698178615108109?thread_ts=1698120248.862859&channel=C04RATV9VCY&message_ts=1698178615.108109

Fortune Nnamdi (15:34:42) (in thread): > @Odigiri Great AlumeI asked this question and Peace answered:sweat_smile:

Fortune Nnamdi (15:35:07) (in thread): > None

Odigiri Great Alume (15:35:13) (in thread): > Thanks@Fortune Nnamdi

Fortune Nnamdi (15:35:59) (in thread): > You’rewelcome:innocent:

Peace Sandy (16:05:47) (in thread): > Theyisn’t

Peace Sandy (16:05:53) (in thread): > Check this out

Peace Sandy (16:06:39) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698178615108109?thread_ts=1698120248.862859&channel=C04RATV9VCY&message_ts=1698178615.108109 - Attachment: Attachment > No you do not need to provide any additional information unless there’s something else you would like us to consider or know about you.

Fortune Nnamdi (17:08:40): > Guys, I filled my final application using my phone and this is what it looked like. > > Does anyone else have this withdrawal application button? Is this what it’s meant to look like or I really haven’t submitted properly?:sweat_smile: - File (PNG): IMG_5981

Uchechukwu Favour Ojunta (18:49:22): > Good day everyone, please I just finished completing my final application and I pressedsave, is there anything we are to do after that?

Paulina Boadiwaa Mensah (19:04:02): > @Tolulope OgunleyeI was originally assigned tohttps://bugsigdb.org/Study_814/Experiment_1as my second contribution and I see you made some changes to Experiment 1 and Signature 1 that I don’t agree with so I have modified those and will resubmit for the second review. - Attachment (BugSigDB): Study 814/Experiment 1 > …

Paulina Boadiwaa Mensah (19:16:36) (in thread): > @Hodan Abdirisak@Peace Sandysame for Experiment 2 of this study. I do not agree with the changes made. Could you please let me have the opportunity to effect the changes<@UBNSEMS3S>directed me to, during her first review and then resubmit?

Peace Sandy (20:07:30) (in thread): > I’m so sorry about this I think the only change I tried to make on this was when it appeared on the NCBI cleanup page, it didn’t work because the organisms are still showing orange, so I left it.

Peace Sandy (20:09:13) (in thread): > Of course you can make your changes and ask the admin to delete any experiment or signature you do not want. > > Sorry about all these:heartpulse:

Peace Sandy (20:11:58) (in thread): > Since a Withdraw application button is showing,it seems you have submitted an application.

Peace Sandy (20:12:36) (in thread): > I thinkthat’sall, you still have the opportunity to edit it till the deadline

2023-10-30

Fortune Nnamdi (02:08:01) (in thread): > :joy:…thanks Peace

Hodan Abdirisak (03:19:41) (in thread): > You have completed successfully@Fortune Nnamdi

Hodan Abdirisak (03:20:10) (in thread): > Save or submit?

Tolulope Ogunleye (03:42:18) (in thread): > I’m sorry this happened,I found the curation under‘incompletepages ´ , made some revision edits and submitted as completed.

Hodan Abdirisak (04:07:14): > Good Monday all:heart:

Hodan Abdirisak (04:09:15): > today is the last day of contribution period hope you are doing well and do not forget to submit your final application before the deadline if you have any problem for submitting do not hesitate to ask us

Hodan Abdirisak (04:10:26): > have nice day all

Mildred Anashie (04:29:37): > Hello everyone… > > Hope we have all filled out our Final applications… > I’m currently trying to record a taxa (Leuconostocaceae) and I found it under Lactobacillaceae on the NCBI taxonomy browser. > > My question is if I could post the ID for the Lactobacillaceae or I leave it as Leuconostocaceae which is displayed in orange when I save the page - File (JPEG): IMG_5077

Chioma Onyido (04:35:18) (in thread): > Hi@Mildred Anashie, in the screenshot of the NCBI browser you shared, Leuconostocaceae is listed as a heterotypic synonym (which basically means diff scientific names but same taxon) of Lactobacillacaeae, I think it’s okay to record the ID of Lactobacillacaeae.

Mildred Anashie (04:46:14) (in thread): > Okay > > Thanks@Chioma Onyido:blush:I did that but I needed to share whatI’vedone:smile:

Chioma Onyido (04:49:22) (in thread): > Well done.:thumbsup:

Chiagoziem David (06:19:43) (in thread): > Okay, thanks@Chioma Onyidofor the clarity

Chiagoziem David (06:20:15) (in thread): > Exactly, save or submit?

Zoyander Street (06:58:07): > Hi! I’m putting together my final application. I have two questions: 1) would it be possible to get my BugSigDB account request approved so that I can make the second contribution before the deadline? and 2) what should I do to create a project timeline?<@UBNSEMS3S>@Levi Waldron<@U1LCB8WEA>@Svetlana Ugarcina Perovic

Mildred Anashie (07:07:48): > Hi, Has anyone come across Single center observational study in any study, I don’t know if it’ll be right to pick Cross-sectional observational, not case control for this because I’ve gone through the paper and the other study designs do not fit > > Please I need help with this<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic:pray: - File (JPEG): IMG_5090

Peace Sandy (07:28:40) (in thread): > Hi:wave:I think you should tag the mentors

Chioma Onyido (07:36:48) (in thread): > Can you also share the link to your paper? That wayIt’llbe easier for members to help.

Mildred Anashie (07:38:53) (in thread): > Sure

Mildred Anashie (07:38:59) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537781/pdf/12920_2015_Article_121.pdfThank you:pray:

Zoyander Street (07:39:03) (in thread): > Ah, thanks!

Peace Sandy (07:59:36) (in thread): > You are welcome

Peace Sandy (08:00:58) (in thread): > You are welcome@Fortune NnamdiAll the best:balloon:

Fortune Nnamdi (08:01:45) (in thread): > Thanks. You too@Peace Sandy

Fortune Nnamdi (08:02:03) (in thread): > @Hodan Abdirisakall the best:heart:

Odigiri Great Alume (08:02:06): > Hehehe > I hope I’m not the only one not including weekends in my timeline:joy:

Peace Sandy (08:02:44) (in thread): > :joy::joy::joy:… You are doing well > Try to summit before the deadline

Fortune Nnamdi (08:03:37) (in thread): > :sweat_smile:

Odigiri Great Alume (08:05:55) (in thread): > I have submitted:joy:I’m just checking something:joy:

Peace Sandy (08:39:15) (in thread): > Okay:relaxed:

Chioma Onyido (08:39:34) (in thread): > I agree with your selected study design being cross-sectional observational because most of the characteristics align with that of a cross-sectional study design. > > “physician-diagnosed asthma for at least one year prior to the time of recruitment,” that’s for cases > and for controls “were confirmed not to have asthma” at the time of recruitment (in a specific age group). Meaning that the study assessed asthma status at a particular point in time which aligns with<@UBNSEMS3S>’s explanation on cross-sectional study designs during the office hour.:thinking_face:Also, theydidn’tcompare (or match on) past exposure (smoking or other factors) btw the cases and controls, thiswould’veprobably made it a case-control study design. >
> Not sure if I’m looking at this from the right perspective but I stand to be corrected.:sweat_smile::eyes:

Mildred Anashie (08:45:22) (in thread): > I’dgo with that for now > > I could still edit it, incase the mentors opinions are different from ours > > Thank you:blush:

USLACKBOT (09:37:43): > This message was deleted.

Onyewuchi Esther Chikamso (09:40:08) (in thread): > Click on the apply button, that’s the final application button - File (PNG): Screenshot_20231030-143921.png

Hodan Abdirisak (09:58:50): - File (PNG): Screenshot 2023-10-30 065707.png

Odigiri Great Alume (10:03:52): > You will need to scroll down to last box that asked you to fill your timeline@Nanathat’s were submit is. It’s saves your application and that’s all you need.. > > > I hope everyone is good as it’s an hour or two to the deadline. > > Please reach out if you are stuck so you can get help. > > It’s been a pleasure collaborating with you all. I look forward to doing more of this with y’all.:blush:.

Hodan Abdirisak (10:06:31) (in thread): > Click apply for this project

Taiwo Adeyombo (10:10:00): > Hello everyone. > > @sveltlana_up @lwaldron @Chloe Mirzayi > > Please can you help me delete experiment 3 of this study.https://bugsigdb.org/Study_825Thank you very much. - Attachment (BugSigDB): Rare phylotypes in stone, stool, and urine microbiomes are associated with urinary stone disease - BugSigDB > Introduction: In complex microbial communities, the importance of microbial species at very low abundance levels and their prevalence for overall community structure and function is increasingly being recognized.

Iram Jamshed (11:29:07): > Hi,@Svetlana Ugarcina Perovic@Levi Waldron@Levi Waldronplease delete the third signature.https://bugsigdb.org/Special:FormEdit/Signature/Study_832/Experiment_1/Signature_3?reload=1&returnto=Study%20832. I accidentally duplicated it. - Attachment (BugSigDB): Special:FormEdit/Signature/Study 832/Experiment 1/Signature 3

UBNSEMS3S (11:56:16) (in thread): > Thanks for the explanation Chioma but I would curate it as written asStreptococcus. There’s an important difference between curating the Streptococcus genus and “Streptococcus spp.” which means multiple species contained within the Streptococcus genus.

Joan C. Chukwuemeka (11:57:23): > Hello all, > Trust no one was behind schedule in submission. > Well done everyone and all the best:slightly_smiling_face:.

Esther Afuape (11:59:49) (in thread): > But the screenshot above says that ASVs 7 and 415 represent Streptococcus species:thinking_face:. Seems to me like they were different species of Streptococcus<@UBNSEMS3S>

Esther Afuape (12:02:04): > Good luck everyone.It’sbeen great collaborating withy’all:hugging_face:

Odigiri Great Alume (12:03:30) (in thread): > @C. Mirzayi (please do not tag this account)thanks for the clarity buy@Esther Afuaperaised a point from the screenshot too ma’am.

UBNSEMS3S (12:18:32) (in thread): > Oh my bad. I didn’t see that follow-up screenshot.

UBNSEMS3S (12:18:40) (in thread): > Yeah Streptococcus spp. then

UBNSEMS3S (12:23:50) (in thread): > Deleted.

UBNSEMS3S (12:24:05) (in thread): > Deleted.

UBNSEMS3S (12:24:51) (in thread): > Thanks for the good advice. This is in fact a case-control study from the sound of things.

UBNSEMS3S (12:25:11) (in thread): > All account requests were approved early this morning it looks like.

Taiwo Adeyombo (12:27:54) (in thread): > Thank you:raised_hands:

Chioma Onyido (13:07:43) (in thread): > @Mildred Anashie

Mildred Anashie (13:12:18) (in thread): > Wow….This is interesting > > Thank you<@UBNSEMS3S>that means I shouldn’t ignore the obvious cases and controls even though it was an observational study and there was no mention of variables matched on or controlled for

Odigiri Great Alume (13:43:49) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Karen254. Kingecha (14:16:21): > Good luck everyone, it was fun collaborating with you all I’ve really gained alot being in this community.

Odigiri Great Alume (14:52:34) (in thread): > @Mildred Anashiediscussing this with@Chioma Onyidowe found these from your study. > It’s a case control study matched on age and gender. But there were no confounders ctrld for that we know so far - File (JPEG): Screenshot_20231030-185919.jpg - File (JPEG): Screenshot_20231030-185603.jpg - File (JPEG): Screenshot_20231030-185125.jpg

Mildred Anashie (14:57:29) (in thread): > Asides the Table showing the Demographic data of subjects,I’mnot sure what you are pointing out in the other two images

Mildred Anashie (14:57:40) (in thread): > @Odigiri Great Alume

Odigiri Great Alume (15:02:10) (in thread): > The other two images explicitly stated cases and control

Mildred Anashie (15:02:24) (in thread): > Also how did you figure out that was what was used to match on participants because I assumed age was one of the inclusion criteria for participants

Chioma Onyido (15:02:26) (in thread): > Found these as well where case and control was explicitly stated.@Mildred Anashie - File (JPEG): IMG_5678 - File (JPEG): IMG_5679

Mildred Anashie (15:09:16) (in thread): > @Chioma OnyidoThank you so much for always coming through > > I saw all of this but was a bit confused although<@UBNSEMS3S>has pointed my eyes in the right direction:blush:

Mildred Anashie (15:10:08) (in thread): > @Odigiri Great AlumeThank you too > > Are you suggesting the inclusion criteria is what was matched on?

Odigiri Great Alume (15:18:34) (in thread): > @Mildred Anashiethat’s not what I’m suggesting tho. > > In case control studies, subjects are matched on characteristics to ensure that cases and controls are similar in these selected characteristics. > Gender because they wanted cases and control to have same xtics (male) > Age because they wanted case and control to have same xtics (adolescent). That is saying same age range > > Basically both groups should be well matched to control for possible confounders . > > My opinion from what I know:thinking_face:

Odigiri Great Alume (15:18:59) (in thread): > Thank God@C. Mirzayi (please do not tag this account)is typing:joy:

Mildred Anashie (15:20:18) (in thread): > @Odigiri Great AlumeI get your point

UBNSEMS3S (15:20:34) (in thread): > The vast majority of studies we curate are case-control studies, even without any matching and even if they say that the case and control groups differed on some variables. The hallmarks of a case control study is that they selected a group of cases based on having some condition of interest then tried to find a group of similar people for the controls. That doesn’t mean they have to be matched or that the groups have to be in fact similar at all to the cases. Matching is difficult and expensive so many do not trouble themselves to do it.

UBNSEMS3S (15:22:28) (in thread): > > Nasal epithelial cells were collected from 8 children and adolescents with asthma and 6 healthy controls by brushing the medial aspect of the inferior turbinate of each nare using a cytology brush. > This is classic case control study design.

Odigiri Great Alume (15:23:25) (in thread): > @Mildred AnashieI’m sure this clarify things:blush:Thank you@C. Mirzayi (please do not tag this account)However, in her study, is it safe to say they were matched on age and gender?

Mildred Anashie (15:23:30) (in thread): > Thank you so much<@UBNSEMS3S>….This explanation clears a lot of confusion for me

UBNSEMS3S (15:24:20) (in thread): > Basically if you aren’t sure if it’s case-control or cross-sectional observational, it’s probably case-control. Cross-sectional observational is really only true in situations where there is no clear case group. This could be a study of two different neighborhoods or classes or perhaps a study of different racial groups. There really isn’t a “case” or a control in these situations.

UBNSEMS3S (15:27:22) (in thread): > > However, in her study, is it safe to say they were matched on age and gender? > Unless they explicitly say that they matched on age and gender, then no we cannot safely conclude that. Even if they do an analysis to show that there was no stat. sig. difference in age and gender between cases and controls that is not the same thing as matching. Matching has to be something that is specifically and deliberately done prior to data analysis. > > Typically. There are ways to do matching during data analysis but I think of the 100s of papers we’ve curated I’ve seen exactly 1 do so.

Mildred Anashie (15:28:03) (in thread): > Okay this is much clearer > > > I always felt it was safer to go with cross sectional observational when not sure but now I know when cases and controls are clearly definedit’ssafer to go with case-control

Odigiri Great Alume (15:29:22) (in thread): > @C. Mirzayi (please do not tag this account)Thank you for clarifying things.

Chioma Onyido (15:30:36) (in thread): > Enlightening discussion:blush:Thank you for your patience and clear explanations<@UBNSEMS3S>

UBNSEMS3S (15:30:47) (in thread): > Always happy to help. You are asking good questions. My hope is to clean up our curation policy in the coming days to make this much clearer; however, it’s always going to be difficult because many researchers do not describe their study design very clearly at all.

Mildred Anashie (15:33:29) (in thread): > <@UBNSEMS3S>Thank you so much > > Yes, some studies can be really confusing, but insightful conversations like this are really helpful

Odigiri Great Alume (15:45:16) (in thread): > @C. Mirzayi (please do not tag this account)Looking from a study I curated yesterday, I used Cross sectional study as study design. > > > Here’s an excerptWe analyzed and compared the resident bacterial taxa of histologically normal breast tissue (healthy, H, n = 49) with those of tissues donated prior to (prediagnostic, PD, n = 15) and after (adjacent normal, AN, n = 49, and tumor, T, n = 46) breast cancer diagnosis (n total = 159). > Breast tissue cores were collected from 141 women, including 65 healthy (H) women and 76 breast cancer patients who donated adjacent normal (AN) and/or tumor (T) tissue (Fig. 1) (11). ****The healthy cohort included 15 women who were subsequently diagnosed with breast cancer. Therefore, their breast biopsy specimens are classified as prediagnostic (PD) tissue (Fig. 1).******* The tumor-bearing cohort included 24 women who donated both tumor and adjacent normal tissue and an additional 52 women who donated either AN or T tissue. > *In the study H and PD were compared for differentially abundant taxa (even though bold text above suggest these samples come from the healthy cohorts ) > > Hope I’m correct to not chose a case control study design?:blush:https://journals.asm.org/doi/10.1128/msystems.01489-21

Esther Afuape (17:55:09): > Hello > I’m currently working on this paperhttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02557-3. I’m having a hard time deducing the alpha diversities for each of the experiments. All of the alpha diversities utilized seem to be in figure 1. To investigate whether the individual relative abundance of microbiota was associated with prognosis, univariate/multivariate Cox regression was carried out (table 3). However, there was also evaluation of threshold value of individual microbiota relative abundance for prognosis. I expected the results to be similar, with the threshold experiment showing the good/poor prognosis factors amongst the taxa that were gotten from the multivariate Cox regression taxa but the taxa are different in both experiments. I can’t seem to be able to interpret the result in the threshold experiment table too (table 4). I’ve attached screenshots of some pointers. Please help:pray:<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina Perovic - Attachment (BioMed Central): Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis - BMC Microbiology > Background The microbial population of the intestinal tract and its relationship to specific diseases has been extensively studied during the past decade. However, reports characterizing the bile microbiota are rare. This study aims to investigate the microbiota composition in patients with pancreaticobiliary cancers and benign diseases by 16S rRNA gene amplicon sequencing and to evaluate its potential value as a biomarker for the cancer of the bile duct, pancreas, and gallbladder. Results We enrolled patients who were diagnosed with cancer, cystic lesions, and inflammation of the pancreaticobiliary tract. The study cohort comprised 244 patients. We extracted microbiome-derived DNA from the bile juice in surgically resected gallbladders. The microbiome composition was not significantly different according to lesion position and cancer type in terms of alpha and beta diversity. We found a significant difference in the relative abundance of Campylobacter, Citrobacter, Leptotrichia, Enterobacter, Hungatella, Mycolicibacterium, Phyllobacterium and Sphingomonas between patients without and with lymph node metastasis. Conclusions There was a significant association between the relative abundance of certain microbes and overall survival prognosis. These microbes showed association with good prognosis in cholangiocarcinoma, but with poor prognosis in pancreatic adenocarcinoma, and vice versa. Our findings suggest that pancreaticobiliary tract cancer patients have an altered microbiome composition, which might be a biomarker for distinguishing malignancy.

2023-10-31

Fortune Nnamdi (02:34:14) (in thread): > :relaxed:

Fortune Nnamdi (02:34:21) (in thread): > :relaxed:

Fortune Nnamdi (02:34:29) (in thread): > :relaxed:

Odigiri Great Alume (02:43:02) (in thread): > Good morning@Esther AfuapeI glanced through the paper and here are my thoughts while we wait on the mentors@C. Mirzayi (please do not tag this account) > 1. I think they made comparisons based onlesion location and types. > 2. For location: the alpha diversities came out not significant across all comparisons except for Shannon with p value less than 0.05 as seen in the screenshot below. > 3. For types: the alpha diversities came out not significant across all comparisons including Shannon as all p values were greater than 0.05. > I hope this helps. > We can discuss further if I’m missing anything ok. - File (JPEG): Screenshot_20231031-073327.jpg - File (JPEG): Screenshot_20231031-072741.jpg

Joan C. Chukwuemeka (03:37:27) (in thread): > Hi@Esther AfuapeBased on this excerpt from the study:“The microbiome composition was *******not significantly different******* according to lesion position and cancer type in terms of alpha and beta diversity.”I think the alpha diversity were unchanged.

Odigiri Great Alume (03:40:40) (in thread): > @Joan C. ChukwuemekaI think so too, please look at the Shannon diversity forlocation, I think :thinking_face:**** it’s stated their that there was a difference hence p < 0.05 > ****The rest are unchanged I guess. > Whereas looking at the plots for Shannon you can tell what decreased and increased

Esther Afuape (04:31:47) (in thread): > Thank you..but there are other experiments in the paper. Theydon’thave their diversities stated. Like the experiment for prognosis and the one for progression

Joan C. Chukwuemeka (04:58:56) (in thread): > Okay?:thinking_face:I’d give it a second look

Esther Afuape (05:20:00) (in thread): > I just realized that Ididn’tattach the screenshots - File (JPEG): 8f9030ce-8300-4fb9-8eda-a3f430877d02 - File (JPEG): e9ec6bb5-c495-44b1-ba4e-9c0c84bf5ce9

Joan C. Chukwuemeka (07:16:04) (in thread): > @Esther Afuapelet’s do this together, one step at a time.******I tried to rephrase the abstract in simpler terms below******: > In the last ten years, scientists have studied the microorganisms living in our gut and their connection to various diseases quite extensively. However, not much research has focused on the microorganisms in the bile, which is a fluid produced by the liver and stored in the gallbladder.******This study set out to examine the types of microorganisms present in the bile of patients with cancers in the pancreas, bile duct, and gallbladder, as well as in people with non-cancerous bile issues. ****The goal was to see if these microorganisms could be used as a marker to identify these cancers. > > Here’s what we did:******We included 244 patients who were diagnosed with different conditions related to the pancreas and bile system, including cancer, cysts, and inflammation.********** ****We collected samples of the microorganisms found in the bile during surgery to remove the gallbladder. > > When we looked at the types of microorganisms in the bile, we didn’t find a significant difference between the different types of cancer (type)or where the issue was in the pancreas or bile duct(location). > > However, we did notice some differences in the types and amounts of certain microorganisms(significant difference in the relative abundance) in patients with or without the spread of cancer to nearby lymph nodes (without and with lymph node metastasis.)In summary, we found that certain microorganisms in the bile were linked tohow long patients survived after their cancer diagnosis(survival prognosis******)*******. Some of these microorganisms were associated with better outcomes in bile duct cancer(good prognosis in cholangiocarcinoma), but worse outcomes in pancreatic cancer(poor prognosis in pancreatic adenocarcinoma), and vice versa. > Our results suggest that the makeup of microorganisms in the bile may be a useful marker for identifying these types of cancers.*****so question 1: What condition(s) is(are) being contrasted******?:blush:this will define the experiments

Joan C. Chukwuemeka (07:17:29) (in thread): > ****“Prognosis” refers to the** likely course or outcome of a medical condition**, particularly a disease or illness. It’s an estimate of how the condition is expected to progress and what the expected outcome, recovery, or survival chances are. In simpler terms, it’s a prediction or forecast about what might happen to a person’s health based on their current condition and the available medical information. > For example, a* good prognosis indicates that a person is likely to recover or have a positive outcome, while a poor prognosis suggests that the outlook may not be very favorable.*

Esther Afuape (07:33:37) (in thread): > Thank you so much for taking your time to help me with this@Joan C. Chukwuemekahere are the experimentsI’vedocumented so far:https://bugsigdb.org/Study_827. I documented experiments for disease progression (significant microbiota in patients with/without lymph node metastasis) and for non-cancerous conditions (IPMC and IPMN). > The prognosis part is whereI’mconfused. They carried out two different experiments. They also found overall prognosis (total cases) and then for bile duct lesion and for pancreatic lesion. > > Now my question is which of the 2 experiments (Cox regression analysis, and Cox proportional hazards model analysis (to get the threshold)) is really determining the prognosis?If you check the discussion,there’sa part that lists the taxa found to be significant in prognosis. Thenthere’sa part that says“furthermore, we found that the threshold value of relative abundance of microbiota is a significant marker for the prognosis of pancreaticobiliary tract cancer” and the results are different. - Attachment (BugSigDB): Gallbladder microbiota composition is associated with pancreaticobiliary and gallbladder cancer prognosis - BugSigDB > BACKGROUND: The microbial population of the intestinal tract and its relationship to specific diseases has been extensively studied during the past decade.However, reports characterizing the bile microbiota are rare.

Joan C. Chukwuemeka (08:15:59) (in thread): > okay… on it.. > > meanwhile looking at this excerpt:There were no differences in the alpha diversity ******among the lesion locations *****(Pielou evenness index: p = 0.431; Faith PD: p = 0.703 and Chao1: p = 0.403) *******without Shannon index (p = 0.024) *****or lesion type (Pielou evenness index: p = 0.902; FaithPD: p = 0.853; Chao1: p = 0.403 and Shannon index: p = 0.131) The Shannon index was the only measure of alpha diversity that showed a statistically significant difference between different****** lesion locations (p = 0.024). *****This means that the microbiome in the gallbladder was more diverse in patients with lesions in the pancreaticobiliary tract than it was in patients with lesions in the gallbladder:thinking_face:

Joan C. Chukwuemeka (08:18:36) (in thread): > The analysis seems to be about location and type of lesion:eyes:…as@Odigiri Great Alumealso statedThe Supplementary table 3. Cross-analysis between threshold value of relative abundance (permyriad) and clinical information, may be curatable. trying to figure the analysis meaning

Chiagoziem David (08:19:47): > Hello guys, if you have an article that conducted 4 different experiments, but one had alpha diversity calculated for one of the experiments, should you still record the remaining experiments?

Esther Afuape (08:27:55) (in thread): > I’mnot surethat’sthe right interpretation for the diversity. Pancreaticobiliary tract itself is made up of the pancreas, bile duct and gallbladder. These are the locations. > Then there are different types of lesions. It was shown more clearly in figure 1.

Chiagoziem David (08:56:13): > <@U1LCB8WEA>could you please delete experiment 1-3 for this study :https://bugsigdb.org/Study_213 - Attachment (BugSigDB): Composition of gut microbiota in infants in China and global comparison - BugSigDB > Symbiotic gut microbiota is essential for human health, and its compositional changes have been associated with various complex disorders

Chioma Onyido (08:58:08) (in thread): > Yes, experiments are based on the contrasts between groups. So if differential abundance results were reported but no alpha diversity was stated, it’s still okay to record the experiments but You’d leave the alpha diversity section blank (for those experiments without), according to the curation policy.

Chiagoziem David (09:00:59) (in thread): > There were no “differential abundance” recorded. the whole discuss was still centered mainly on the one experiment that had alpha diversity calculated for

Chioma Onyido (09:01:21) (in thread): > Hmmm Can you share a link to your paper?

Chioma Onyido (09:05:06) (in thread): > I do know that it’s possible to curate experiments without signatures. But sharing a link to your paper would be helpful so we can take a look.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697410390867449?thread_ts=1697380986.698779&channel=C04RATV9VCY&message_ts=1697410390.867449 - Attachment: Attachment > @Joan C. Chukwuemeka is the advice I just gave on some other articles about what constitutes an Experiment helpful? The key message is that experiments are defined by the contrasts made, and signatures are defined by the results of those experiments. So it is perfectly possible to perform one or more experiments and find no statistically significant results, such as unchanged alpha diversity and no signatures of differentially abundant taxa.

Chiagoziem David (09:21:43) (in thread): > alright, thanks

Nana (10:11:32): > <@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina Perovicin the Studies that have no signature they are study with numbers that are empty, 3 of them, can you help delete them below is a screenshot - File (PNG): exp.png

Zoyander Street (10:21:59) (in thread): > Thanks - for whatever reason, I didn’t get my account until the afternoon, but regardless of the outcome I’m excited to learn more and make some contributions

Nana (10:22:18): > <@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina PerovicI don’t know how this works but this experiment has been reviewed yet it still appears on Studies that have no ExperimentGut Microbiota Signatures in Gestational Anemia - File (PNG): exp.png

Nana (10:25:44): > <@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina PerovicHere they have experiment and have been reviewed

Chioma Onyido (10:46:25): > For this study,bugsigdb.org/Study_211Solved these under experiment 2, signature 2. - File (JPEG): IMG_5697 - File (JPEG): IMG_5693 - File (JPEG): IMG_5695 - File (JPEG): IMG_5694

Joan C. Chukwuemeka (12:41:36) (in thread): > @Esther AfuapeI have done a first time complete read of the article and did a bit of research. These are my findings. > > Using table 2 as signature source seen so far, and the first set of contrasts to explain it: > > The table presents a comparison of the relative abundance of specific microbiota in patients with Cholangiocarcinoma (BDAC) based on different clinical information, specifically the cancer stage (Early vs. Advance). Here’s how to interpret the table: > > - The first column lists the microbiota being analyzed (e.g., Campylobacter, Citrobacter, Leptotrichia). > - The next two columns show the mean and standard deviation (sd) of the relative abundance of each microbiota in patients with early-stage (left) and advanced-stage (right) Cholangiocarcinoma. > - The “p” column indicates the p-value, which is the result of a Wilcoxon test, a statistical test used to compare the means of two groups (in this case, early and advanced-stage Cholangiocarcinoma patients). A low p-value (typically below 0.05) suggests a significant difference. > - The “Cliff’s delta” column provides a measure of effect size, indicating the magnitude of the difference. A negative value indicates a decrease in relative abundance in advanced-stage Cholangiocarcinoma patients. > - The “CI95” column represents the 95% confidence interval for the effect size. > > For instance, looking at the data for Campylobacter: > - In patients with early-stage Cholangiocarcinoma, the mean relative abundance of Campylobacter is 8.3 per myriad with a standard deviation of 36.9 per myriad. > - In patients with advanced-stage Cholangiocarcinoma, the mean relative abundance of Campylobacter is 32.5 per myriad with a standard deviation of 86.7 per myriad. > - The p-value is 0.025, which is below the typical significance level of 0.05, indicating a statistically significant difference. > -******The Cliff’s delta is -0.212, suggesting a decrease in relative abundance in advanced-stage Cholangiocarcinoma patients.******- The 95% confidence interval for the effect size ranges from -0.40 to -0.01.

Joan C. Chukwuemeka (12:42:41) (in thread): > for alpha diversity: > Alpha diversity was done for lesion type and lesion location. The Shannon index was the only measure of alpha diversity that showed a statistically significant difference between different lesion locations (p = 0.024). > However, the experiment/contrasts see in table 2 were for lesion type, which had no differences in the alpha diversity (Pielou evenness index: p = 0.902; Faith PD: p = 0.853; Chao1: p = 0.403 and Shannon index: p = 0.131) (Fig. 1C).

Joan C. Chukwuemeka (12:46:26) (in thread): > Experiment 1Group 0 name: Early CholangiocarcinomaGroup 1 name: Advanced CholangiocarcinomaGroup 1 definition: Cholangiocarcinoma patients with lymph node metastasisGroup 0 sample size: ?Not seen yet in the study(total for both groups =92)Group 1 sample size:?Not seen yet in the study (total for both groups =92)Antibiotics exclusion - Not doneStatistical AnalysisData transformation:relative abundancesStatistical test: Wilcoxon testSignificance threshold - 0.05Alpha DiversityPielou: unchanged > Shannon: unchanged
> Chao1: unchanged > Faith: unchangedSignature 1 - increased abundance in Advanced Cholangiocarcinoma(need to restudy text to check)Signature 2 -decreased abundance in Advanced Cholangiocarcinomasource - table 2CampylobacterCitrobacterLeptotrichia

Joan C. Chukwuemeka (12:50:24) (in thread): > Experiment 2Group 0 name: Early Pancreatic ductal adenocarcinomaGroup 1 name:Advanced Pancreatic ductal adenocarcinomaGroup 1 definition: Pancreatic ductal adenocarcinoma patients with lymph node metastasisGroup 0 sample size: ?Not seen yet in the study(total for both groups =105)Group 1 sample size: ?Not seen yet in the study (total for both groups =105)Antibiotics exclusion- Not doneStatistical AnalysisData transformation: relative abundancesStatistical test: Wilcoxon testSignificance threshold- 0.05Alpha DiversityPielou: unchanged > Shannon: unchanged
> Chao1: unchanged > Faith: unchangedSignature 1 - increased abundance in Advanced Pancreatic ductal adenocarcinomasource - table 2Enterobacter Hungatella Mycobacterium Signature 2 -decreased abundance in Advanced Pancreatic ductal adenocarcinomasource - table 2Phyllobacterium Sphingomonas

Esther Afuape (12:51:35) (in thread): > Got it! It makes much sense now. Thank you so much@Joan C. Chukwuemeka

Esther Afuape (12:53:13) (in thread): > I have done the comparisons from table 2 althoughI’llbe correcting some of the values. > My main concern is still the prognosis experiment and which of the two experiments really explains it@Joan C. Chukwuemeka

Joan C. Chukwuemeka (12:57:12) (in thread): > Experiment 3Group 0 name:Intraductal papillary mucinous neoplasmGroup 1 name:Intraductal papillary mucinous carcinomaGroup 1 definition:Patients with advanced stage of a cystic pancreatic lesionsGroup 0 sample size: ?Not seen yet in the studyGroup 1 sample size: ?Not seen yet in the studyAntibiotics exclusion- Not doneStatistical AnalysisData transformation: relative abundancesStatistical test: Wilcoxon testSignificance threshold - 0.05Alpha DiversityPielou: unchanged > Shannon: unchanged
> Chao1: unchanged > Simpson:
> Inverse Simpson:
> Richness:
> Faith: unchangedSignature 1 - increased abundance in Intraductal papillary mucinous carcinoma(need to restudy text to check)Signature 2 -decreased abundance in Intraductal papillary mucinous carcinomasource - table 2ActinomycesAlloprevotella Bilophila Dialister Eggerthella Selenomonas****Streptococcus**

Joan C. Chukwuemeka (12:59:55) (in thread): > @Esther Afuapedidn’t see a contrast for the prognosis your referring to.https://community-bioc.slack.com/archives/C04RATV9VCY/p1698751049045499?thread_ts=1698702909.878569&cid=C04RATV9VCY - Attachment: Attachment > “Prognosis” refers to the likely course or outcome of a medical condition, particularly a disease or illness. It’s an estimate of how the condition is expected to progress and what the expected outcome, recovery, or survival chances are. In simpler terms, it’s a prediction or forecast about what might happen to a person’s health based on their current condition and the available medical information. > For example, a good prognosis indicates that a person is likely to recover or have a positive outcome, while a poor prognosis suggests that the outlook may not be very favorable.

Esther Afuape (13:03:16) (in thread): > They’rein tables 3 and 4 and the explanation is in discussion

Esther Afuape (13:03:32) (in thread): > Here - File (JPEG): e9ec6bb5-c495-44b1-ba4e-9c0c84bf5ce9

Joan C. Chukwuemeka (13:04:00) (in thread): > You may need to reconsider your group naming convention and also group 1 definition was not rightly done. > > The study requires putting on detective lenses.:nerd_face:Hoping<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovicwill grant us more insight to this once they are available:blush:

Esther Afuape (13:04:48) (in thread): > Alright > Thank you

Joan C. Chukwuemeka (13:07:00) (in thread): > the highlighted phrase means that their research revealed that the specific threshold value of microbiota abundance is a meaningful marker for predicting the outcome or prognosis of pancreaticobiliary tract cancer. This means that the level of certain microorganisms can serve as an important indicator to anticipate how patients with this type of cancer may fare in the future.

Odigiri Great Alume (13:54:49) (in thread): > @Joan C. ChukwuemekaWELL DONE:+1:but I thought we established that shannon showed some significance less than 0.05. why did you leave that out. > > > Also@Joan C. ChukwuemekaI do think that the prognosis comparison shouldn’t be curated.:thinking_face:Hhmmm. > Not too sure:cry:

Joan C. Chukwuemeka (13:56:55) (in thread): > @Odigiri Great AlumeSeehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1698770561850069?thread_ts=1698702909.878569&cid=C04RATV9VCY - Attachment: Attachment > for alpha diversity: > Alpha diversity was done for lesion type and lesion location. The Shannon index was the only measure of alpha diversity that showed a statistically significant difference between different lesion locations (p = 0.024). > However, the experiment/contrasts see in table 2 were for lesion type, which had no differences in the alpha diversity (Pielou evenness index: p = 0.902; Faith PD: p = 0.853; Chao1: p = 0.403 and Shannon index: p = 0.131) (Fig. 1C).

Odigiri Great Alume (13:58:07) (in thread): > Oh nice@Joan C. Chukwuemeka

Esther Afuape (14:02:37) (in thread): > But the prognosis was the main aim of the study…@Odigiri Great Alume

Joan C. Chukwuemeka (14:09:42) (in thread): > prognosis is a measure of diseases progression(likely outcome) from one stage to another, acute to chronic, early to advanced, etc and is measured in different ways. The condition you chose already captures that the study was on prognosis - disease progression. > Will the person’s condition move to advanced stage or not? > > However, the study still needs an in-depth second or more reads. > The sample size is still unknown for each experiment group. > More could still be uncovered:nerd_face:

Joan C. Chukwuemeka (14:18:56) (in thread): > I know some paragraphs in the study tried to talk about some microbial taxa linked to good prognosis and some to poor prognosis. But not seeing a statistical test conducted to contrasts between the 2, to know which is the reference group/group 1 > > Again, let’s just revisit the paper. > I’ll share an update, if I get any new info

Esther Afuape (14:28:14) (in thread): > This is what I’ve been referring to all day!:sob:They mentionedunivariate and/or multivariate Cox regression analysis and Cox proportional hazards model analysis. > A univariate cox regression analysis identifies individual factors related to patient survival while a multivariate cox regression analysis identifies independent prognostic factors. > I think the answer lies in finding out more about these tests and the most significant ones.

Esther Afuape (15:56:42) (in thread): > Also, I think the interpretation of the cliff’s delta is the other way. A negative value usually implies that the effect is in favor of the second group, and the first group lags behind in terms of the measured variable.@Joan C. Chukwuemeka

Chiagoziem David (18:49:31): > Hello<@U1LCB8WEA>if relative abundance and diversity was stated for an article that did a treatment on the subject and the signatures were given for before and after the treatment, which signature should be curated?

U1LCB8WEA (18:50:45) (in thread): > It sounds like the contrast is after treatment vs before treatment, assuming they reported such signatures of increased and decreased relative abundance and diversity?

Chiagoziem David (18:56:29) (in thread): > Not necessarily, they gave a contrast for both pre-treatment and after treatment. In both cases contrasting with a control group

Esther Afuape (19:45:58) (in thread): > @Joan C. ChukwuemekaI think I’ve been able to make sense of the result. In a Cox proportional hazards model, the threshold value is a point you choose to split your data into two or more groups. In supplementary table 3, clinical conditions (age, sex, ASA score, stages, and the administration of chemotherapy) were all split into 2 groups and compared. The comparisons were then assigned hazard ratios (HR). HR measures how the hazard (risk) of an event (like a medical condition) differs between the groups you created using the threshold. An HR of 1 means no difference, HR less than 1 means lower risk, and HR greater than 1 means higher risk. > In table 4, the correlation between the threshold value for relative abundance and the HR for prognosis was gotten, while considering those factors that were compared in the supplementary table. > So it’s like what’s the prognosis of bile duct lesion at a threshold value of >/= 581 for Enterococcus and is there a difference in the prognosis between male and female (sex) at that threshold value for Enterococcus. > > Here’s an excerpt that shows an instance:“In Eggerthella and Corynebacterium, the > Fisher exact test revealed that there was signifcant difference in the Sex between these two groups divided by > these threshold values (p=0.026 and p=0.046, respectively)”.I don’t think the results from this is curatable. The threshold values seem to apply only to this study and is not a standard. The clinical factors are also non-confounding and their HR doesn’t really have an effect on prognosis. > I’ll still wait for the opinions of<@UBNSEMS3S>@Levi Waldronwhen they review the article and curation

Esther Afuape (20:03:11) (in thread): > Sounds like 2 different experiments to me@Chiagoziem Davidpre-treatment vs control and after-treatment vs control.

Chiagoziem David (20:23:15) (in thread): > Abi, that’s true

Chiagoziem David (20:23:25) (in thread): > Thanks@Esther Afuape

2023-11-01

Mildred Anashie (05:19:35): > Hi<!here>This is an excerpt from the paper I’m* working on, ** > > > Observed and Chao1 are measures of species richness (number of species); the latter including a correction for unobserved species [36, 37]. In turn, Shannon and Simpson incorporate relative species abundance and thus represent Evenness or Heterogeneity [38]. “We observed that asthma samples have more species (richer) compared to control individuals (Fig. 1a; Observed and Chao1). However, measures that explicitly model Evenness (Shannon and Simpson indices) suggest that asth- matic samples are dominated by fewer species (5 of 8 cases dominated by Moraxella catarrhalis; Fig. 1a; Fig. 2) and are thus less diverse than controls”. > > *My interpretation of this is,Chao1 = IncreasedShannon = DecreasedSimpson = DecreasedDoes anyone think otherwise? And why? > > Also it’s stated that Observed and Chao1 were used to measure richness, do I still need to record Richness after recording for Chao1?

Peace Sandy (05:24:33) (in thread): > Was Richness explicitly stated as a diversity measure?

Mildred Anashie (05:27:47) (in thread): > No, just stated that Observed and Chao1 were measures of species richness (number of species)

Karen254. Kingecha (06:24:21) (in thread): > Your interpretation of the passage appears to be accurate. The passage suggests that Chao1 indicates increased species richness, while Shannon and Simpson indices suggest decreased richness and increased dominance by a specific species (Moraxella catarrhalis) in asthmatic samples compared to control individuals. This interpretation is based on the information provided in the excerpt. > Regarding your question about recording richness after using Chao1, it depends on the specific goals of your analysis. Chao1 is a measure of richness that accounts for unobserved species, which is particularly relevant when you suspect there are unobserved species in your data. If you have already used Chao1 to account for potential unobserved species, you may not need to separately record richness, as Chao1 provides an estimate of total richness, including both observed and unobserved species. > However, if you want to report both observed richness and the Chao1 estimate to provide a comprehensive view of species richness in your analysis, it can be useful to do so. It depends on the level of detail and clarity you want to convey

Chiagoziem David (07:12:13): > Hello<@UBNSEMS3S>and<@U1LCB8WEA>, there’s an article I saw on the git repo , it hasn’t been peer reviewed though, and so is not on Pubmed, should it still be curated?

Odigiri Great Alume (07:42:14) (in thread): > Well done@Esther Afuapeand@Joan C. ChukwuemekaI’m glad we are able to reach a consensus. However, we await@C. Mirzayi (please do not tag this account)and@Levi WaldronGreat work everyone

Desire Oluwarotimi (08:15:40): > Hello@C. Mirzayi (please do not tag this account)@Levi WaldronI’d like to delete an experiment. It’s a replica of an already existing one. > > It’s Signature 3, Experiment 1 of study 839.https://bugsigdb.org/Special:FormEdit/Signature/Study_839/Experiment_1/Signature_3?reload=1&returnto=Study%20839 - Attachment (BugSigDB): Special:FormEdit/Signature/Study 839/Experiment 1/Signature 3

Mildred Anashie (10:42:41) (in thread): > Thank you@Karen254. Kingechafor taking out time to do go through this…..I’m grateful

Peace Sandy (10:43:51) (in thread): > Have you been able to figure it out@Mildred Anashie

Odigiri Great Alume (11:47:22) (in thread): > If they used both then you should record both as they mean different things and are used to achieve different things like@Karen254. KingechaStated already.

Mildred Anashie (12:20:43) (in thread): > @Peace SandyYes I have

Peace Sandy (12:28:56) (in thread): > Okay

Esther Afuape (19:36:17): > Hello<@UBNSEMS3S>@Levi Waldron@Svetlana Ugarcina PerovicI’m about to curate this paperhttps://peerj.com/articles/12826/. Two different cow breeds were utilized in the study; Yak and Pian breeds. The yak breed has a scientific name ofBos grunniens (which is not available on the list of host species on BugSigDB) while Pianisn’trecognized as a breed. > What do I do? - Attachment (PeerJ): Comparison of changes in fecal microbiota of calves with and without dam > In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak :male_sign: × Pian cattle :female_sign:, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam.

2023-11-02

Joan C. Chukwuemeka (02:37:24) (in thread): > Hi@Esther AfuapeI thinkBos taurus, which is the scientific name for cow, should suffice.

Esther Afuape (03:59:38) (in thread): > Thought so too…thank you

UBNSEMS3S (09:36:56): > Hi apologies for the late notice but we will be having our weekly team meeting at 10 AM EDT today (in 24 minutes).https://us02web.zoom.us/j/2737200499

UBNSEMS3S (09:37:45) (in thread): > <@U1LCB8WEA>Any thoughts on this? Bos taurus might work but it’s not technically correct. There’s no possibility of an “other” option for the host species?

UBNSEMS3S (09:38:30) (in thread): > Yes you can curate preprints.

Chioma Onyido (09:39:50) (in thread): > Looking forward to it. Thank you for the reminder<@UBNSEMS3S>

UBNSEMS3S (09:40:08) (in thread): > Did they state that they did a statistical test somewhere? We only curate statistical differences in alpha diversity and I don’t see any evidence of statistical testing in the excerpt.

Chiagoziem David (09:41:50) (in thread): > Oh, okay.. > > > Thank you very much

Mildred Anashie (09:55:32) (in thread): > Yes<@UBNSEMS3S>they mentioned that they did > > > Althoughhere’sa link to the article, you might point out something Ididn’tnoticehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537781/pdf/12920_2015_Article_121.pdf

Aleru Divine (09:56:06) (in thread): > Thanks for the reminder<@UBNSEMS3S>

Mildred Anashie (09:56:12) (in thread): > Okay > > Thank you for the notice

U02CNMR4YEA (09:59:06): > I’m unable to join today:pensive:due to work conflict but hopefully, can view the recording. Have a great day everyone!

Peace Sandy (11:18:50): > Hi@C. Mirzayi (please do not tag this account):wave:Please is the recording for the weekly team meeting available, some of us didn’t get the information on time.I’llreally like to go through it, if it is.

Joan C. Chukwuemeka (11:24:41) (in thread): > Okay. I’m trying to resolve the signatures with _UCG (uncultured genus) suffix in the image shown. in NCBI uncultured Ruminococcaceae bacterium is under heterotypic synonym foruncultured Oscillospiraceae bacterium. > > The study recorded 2 of such Ruminococcaceae_UCG-013 and Ruminococcaceae_UCG-005. how do I capture this? > > For the other ones is it okay to go with their Uncultured/unclassified variant on NCBI?<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (PNG): image.png

Chioma Onyido (11:39:45) (in thread): > @Joan C. ChukwuemekaFor the uncultured Ruminococcaceae bacterium, I think it’s also good to check and confirm the taxon. rank with that in NCBI.I came across the same taxa during one of my curations but the rank in my paper was genus, while that in the NCBI (uncultured ruminococcaceae) was species, so I had to leave it orange.

Chioma Onyido (11:47:17): > Hello<!here>I hope we’re all doing okay and having a productive week so far. > So I can’t recall where exactly, but I saw where someone indicated that they removed “Chloroplast” from a signature because it’s not a bacteria… > However I saw a discussion where@Paulina Boadiwaa Mensahmapped Chloroplast to Cyanobacteriota, and it was verified by<@U1LCB8WEA>and<@UBNSEMS3S>So I’m not sure if this should be rightly removed from the signatures or curated as phylum Cyanobacteriota.

Chioma Onyido (11:47:35) (in thread): > Link to the discussion:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697048504747639 - Attachment: Attachment > @U1LCB8WEA asked me to post here before making edits. > Here’s a link that helped me map Chloroplasts to Cyanobacteriota: https://en.wikipedia.org/wiki/Chloroplast

Hodan Abdirisak (12:08:24): > sorry to come late, is recording the session available?

Peace Sandy (16:28:23): > I’mcurrently curating a study, and from whatI’veread, I think the study is a case control study, but this was written in the methods section. > > Methods > This is an observational pilot study, constituting part of stage 1 of a prospective study > > Which got me quite confused@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron

UBNSEMS3S (17:12:17) (in thread): > People will often misidentify their own study. If it’s a case-control from your instincts, curate it as that.

UBNSEMS3S (17:14:08) (in thread): > Heterotypic synonyms have been generally fine.

Peace Sandy (17:20:12) (in thread): > Wow…Thank You for this.

Joan C. Chukwuemeka (17:26:52) (in thread): > Okay<@UBNSEMS3S>the challenge is that the study reported two different ones, Ruminococcaceae_UCG-013 and Ruminococcaceae_UCG-005. Is it okay to useuncultured Oscillospiraceae bacteriumfor both? - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

UBNSEMS3S (17:27:20) (in thread): > Ooo now that I’m less certain of when it has the numeric designation at the end.

Joan C. Chukwuemeka (17:28:35) (in thread): > Alright then…..Guess, I’ll just leave it as it is for now:thinking_face:

UBNSEMS3S (17:29:24) (in thread): > Yeah there are going to be some that we can’t identify and that’s ok. It sucks to see them in red and on the cleanup page. I appreciate the effort though!

Joan C. Chukwuemeka (17:34:14) (in thread): > Yeah….Taxonomy is progressive…I believe it’d be sorted someday.:relaxed:Thanks.

2023-11-03

Odigiri Great Alume (02:19:15) (in thread): > @Peace SandyCase control studies are also a type of observational studies. So you are good to go with case control.:clinking_glasses:Well done

Odigiri Great Alume (02:20:59) (in thread): > Thank you@Chioma Onyido

Esther Afuape (03:48:30) (in thread): > I’ve noticed that uncultured Oscillospiraceae only works for uncultured Ruminococcaceae, and not for the ones with UCG because the numbers added to them are different most times. I think that shows thatthey’redifferent species/strains and not just uncultured Ruminococcaceae.

Peace Sandy (04:25:44) (in thread): > Thank you so much@Odigiri Great Alume:heart:

Chiagoziem David (05:08:10): > i am having troubles finding the proper ontology for ” fecal microbial transplant “<@UBNSEMS3S><@U1LCB8WEA>any pointers?

Peace Sandy (06:16:32) (in thread): > Are you using the site

Peace Sandy (06:16:49) (in thread): > I can be of help, what troubles are you having

Chiagoziem David (06:25:52) (in thread): > I can’t find the proper oncology name for the condition I am looking to curate

Peace Sandy (06:27:00) (in thread): > What’sthe condition?

Chiagoziem David (06:27:49) (in thread): > Fecal microbial transplant

Peace Sandy (06:28:50) (in thread): > Most times you might not exactly see the condition, you will have to use the closest EFO term

Peace Sandy (06:29:03) (in thread): > Let me check it out

Chiagoziem David (06:30:01) (in thread): > Yeah , but no one seems close to what it really means

Peace Sandy (06:32:40) (in thread): > Yes I noticed,the pop up option is fecal incontinence, I doubtit’srelated

Chiagoziem David (06:33:37) (in thread): > Yeah

Peace Sandy (06:33:39) (in thread): > Can I see the paper@Chiagoziem David

Fortune Nnamdi (06:34:00): > Hello:wave:I tried to work on studies marked as incomplete and this one has actually been completed by the curator. I just don’t know why it’s still marked incomplete. > > Should I go ahead and mark it complete, so that it can reviewed? > > Here is the study link:https://bugsigdb.org/Study_795 - Attachment (BugSigDB): The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children - BugSigDB > BACKGROUND: The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health.Despite this, the microbiota of healthy adults remains understudied.

Peace Sandy (06:35:47) (in thread): > Most times the initial curator might forget to click on the complete mark

Chioma Onyido (07:22:55) (in thread): > Hi@Chiagoziem Davidfrom your paper, I think the condition to use is “response to fecal transplant”, since all 3 groups had FMT, and they assessed the effects of FMT on the microbiome of the groups. > > So I searched EFO but I also couldn’t find it, however I saw “response to transplant” which is close enough, I guess:sweat_smile:

Peace Sandy (07:23:55) (in thread): > Yeah I saw it too butit’skidney transplant,which might be why he is confused

Chiagoziem David (07:25:22) (in thread): > Yeah, I think kidney transplant is quite distinct from fecal transplant

Chioma Onyido (07:27:50) (in thread): > No I don’t think kidney transplant is same as fecal transplant, > For clarity, I’m referring toresponse to transplant

Fortune Nnamdi (07:29:32) (in thread): > Oh okay,let me mark complete then. Thanks

Chiagoziem David (07:29:42) (in thread): > Oh, okay

Chiagoziem David (07:30:05) (in thread): > So what’s the closest we can use now:sweat_smile:

Chioma Onyido (07:33:39) (in thread): > That’s what I’m saying, sincewe couldn’t findresponse to fecal transplant, I thinkresponse to transplantis the closest. And it pops up just fine on BugSigDB. > See… - File (JPEG): IMG_5819

Chioma Onyido (07:34:39) (in thread): > But we should wait and hear from the mentors<@UBNSEMS3S><@U1LCB8WEA>

Joan C. Chukwuemeka (07:47:03): > Hello<!here>Here’s a note/key points I put together as regards the curation process. Hoping it’d be a helpful reference for someone:blush:https://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Esther Afuape (07:49:28) (in thread): > Awesome!Well done:hugging_face:

Fortune Nnamdi (08:20:07) (in thread): > Thanks:blush:

Fortune Nnamdi (08:40:05): > I want to go ahead and review this study. It hasn’t been curated at all:https://bugsigdb.org/Study_840I have opened the link to the paper, I saw that it’s a preprint, what’s the significance of that? - Attachment (BugSigDB): - BugSigDB > … - File (PNG): IMG_6088

Tolulope Ogunleye (08:44:52) (in thread): > Peer reviewed papers have usually gone through different expert reviews for quality before being published;@C. Mirzayi (please do not tag this account)said that preprints can be curated.

Peace Sandy (08:55:03) (in thread): > Okay

Peace Sandy (08:55:31) (in thread): > Well done@Joan C. Chukwuemeka

Peace Sandy (08:57:18) (in thread): > Incase anyone have not come across this, it’s the curation policy for bugsigdb, might be helpfulhttps://bugsigdb.org/Curation_Policy#Matched_On

Chiagoziem David (09:02:23): > Omo, the support one can get from this space is massive:heart::heart::heart:, thanks@Chioma Onyido@Peace Sandy@Esther Afuape@Joan C. Chukwuemeka

Chioma Onyido (09:02:47) (in thread): > Someone asked a similar question yesterday and<@UBNSEMS3S>answered that Preprints can be curated.

Chiagoziem David (09:02:59) (in thread): > Alrighty

Fortune Nnamdi (09:04:48) (in thread): > Oh okay…. Thank you guys

Mildred Anashie (09:10:02) (in thread): > Thank you@Joan C. Chukwuemeka

Peace Sandy (09:11:00) (in thread): > You are welcome:pray:

Chioma Onyido (09:14:40) (in thread): > Aww Always!It’sbeen a great opportunity to learn and grow together.:hugging_face:

U1LCB8WEA (09:42:32) (in thread): > Administrators can easily add new host species athttps://bugsigdb.org/Help:Admin(linked to from the help page under the description “Edit autocomplete fields”, and I just addedBos grunniens. Better to use the correct host species name. It sounds like Pian cattle areBos taurus, not a separate species. - Attachment (BugSigDB): Help:Admin

Joan C. Chukwuemeka (10:07:23) (in thread): > Thanks<@U1LCB8WEA>@Esther Afuapeyou can use the right one now.:blush:

Esther Afuape (10:08:17) (in thread): > Thank you@Levi Waldron

Esther Afuape (10:28:59) (in thread): > Any time!:heart:Collaborating helps me grow too.

Chiagoziem David (10:31:21) (in thread): > :muscle:

Fortune Nnamdi (10:35:48) (in thread): > @Chiagoziem Davidyou’re so right. > > One can literally not know but end up becoming very knowledgeable because of how supportive this space is.

Chiagoziem David (10:36:38): > Hello,<@UBNSEMS3S>and@Levi Waldronwhen curating this article:https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01452-3, i came across three groups ( CON-FMT, SD-FMT and SD-Mel FMT) from the article the control group seems to be The CON-FMT group, should i curate my experiments as : Experiment 1 ( SD - FMT Vs CON - FMT), experiment 2 (SD- MEL FMT Vs CON -FMT) and would there be a need to curate the decreased signatures twice? > > > > Also, the condition contracted against is also an issue for me, as I feel sleep is what it should be , since all groups were administered FMT…. - Attachment (BioMed Central): Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation - Microbiome > Background Sleep loss is a serious global health concern. Consequences include memory deficits and gastrointestinal dysfunction. Our previous research showed that melatonin can effectively improve cognitive impairment and intestinal microbiota disturbances caused by sleep deprivation (SD). The present study further explored the mechanism by which exogenous melatonin prevents SD-induced cognitive impairments. Here, we established fecal microbiota transplantation, Aeromonas colonization and LPS or butyrate supplementation tests to evaluate the role of the intestinal microbiota and its metabolites in melatonin in alleviating SD-induced memory impairment. Results Transplantation of the SD-gut microbiota into normal mice induced microglia overactivation and neuronal apoptosis in the hippocampus, cognitive decline, and colonic microbiota disorder, manifesting as increased levels of Aeromonas and LPS and decreased levels of Lachnospiraceae_NK4A136 and butyrate. All these events were reversed with the transplantation of SD + melatonin-gut microbiota. Colonization with Aeromonas and the addition of LPS produced an inflammatory response in the hippocampus and spatial memory impairment in mice. These changes were reversed by supplementation with melatonin, accompanied by decreased levels of Aeromonas and LPS. Butyrate administration to sleep-deprived mice restored inflammatory responses and memory impairment. In vitro, LPS supplementation caused an inflammatory response in BV2 cells, which was improved by butyrate supplementation. This ameliorative effect of butyrate was blocked by pretreatment with MCT1 inhibitor and HDAC3 agonist but was mimicked by TLR4 and p-P65 antagonists. Conclusions Gut microbes and their metabolites mediate the ameliorative effects of melatonin on SD-induced cognitive impairment. A feasible mechanism is that melatonin downregulates the levels of Aeromonas and constituent LPS and upregulates the levels of Lachnospiraceae_NK4A136 and butyrate in the colon. These changes lessen the inflammatory response and neuronal apoptosis in the hippocampus through crosstalk between the TLR4/NF-κB and MCT1/ HDAC3 signaling pathways. Video Abstract

Esther Afuape (11:50:12) (in thread): > @Levi Waldronif Pian cattle areBos taurus, I still can’t pick 2 host species. Do I just go with only* Bos grunniens*?

Chioma Onyido (12:51:34) (in thread): > Here for the answer to this too.:sweat_smile:

Esther Afuape (12:59:06): > Hello<!here>I’m curating this study on the comparison of changes in fecal microbiota of calves with and without dam. An excerpt from the paper says: > “The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome.the control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the 95 days formal experimental period” > The condition to me, is cultivation method or feeding method or something related to their nutrition but Ican’tfind anything closely related to all of these. What do you suggest?@Levi Waldron<@UBNSEMS3S>

Esther Afuape (13:10:28) (in thread): > My interpretation of the results was different:face_with_peeking_eye:. I suggested he curate it as > 1. CON-FMT (group 1) vs SD-FMT and SD-Mel-FMT > 2. SD-FMT (group 1) vs CON-FMT and SD-Mel-FMT > 3. SD-Mel-FMT vs CON-FMT and SD-FMT. > I feel this will capture the signatures for all the groups. Therewon’tbe a decrease in any of these also.

Chioma Onyido (13:13:05) (in thread): > Hmm then There would only be one signature recorded for all experiments which would beincreaseyeah?:thinking_face:

Esther Afuape (13:13:45) (in thread): > Yes. Creating a decrease will be double-entering of results

Chioma Onyido (13:14:14) (in thread): > Makes sense! I agree.

Chiagoziem David (13:18:18) (in thread): > Hmm

Chiagoziem David (13:18:43) (in thread): > So the group one would be alternating between the three groups?

Esther Afuape (13:21:16) (in thread): > I think so:thinking_face:I mean, CON-FMTisn’treally the control group itself.It’sa group from an experiment too.Let@Levi Waldronand<@UBNSEMS3S>reply.I’mnot 100% sure about my suggestion.

Chiagoziem David (13:22:28) (in thread): > Alright, Let’s wait for their response

Esther Afuape (20:40:05) (in thread): > @Joan C. ChukwuemekaRuminococcaceae UCG-005 has a taxonomy ID. I can see that the description of your signature says “genus level”, it also appears as a genus in the paperI’mcurating and I’ve also seen it as a genus in other articles from google-searching. I’d say confirm if Ruminococcaceae UCG-005 isn’t a species in the article as it’s showing on NCBI. The taxonomy ID is 3068309

Chiagoziem David (20:42:20) (in thread): > Yeah:sweat_smile::sweat_smile:, it almost drove me crazy, how could it have for 5 but not 2:sweat_smile::sweat_smile:

Chiagoziem David (20:45:40) (in thread): > Shouldn’t we also have a way where we can notify the NBCI guys to these signatures?

U1LCB8WEA (23:03:45) (in thread): > This sounds like a case with no clear right answer, but a useful consideration is, what do you communicate with an unmapped identifier it an NCBI ID. The NCBI ID allows computers to know the taxonomy, so for example knowing the genus of an uncultured bacterium will make that signature appear more similar to another signature containing known or unknown species of the same genus or even the same family,etc. the unmapped ASVs etc will be ignored in analysis,but they can be viewed by other researchers who might know something about them, or future curators whenit’sbeen added to NCBI or somehow resolved.Note there is a comment system for taxa, and note youshouldn’tseparate signatures according to taxonomic rank (all ranks can be mixed in a signature if they come from the same experiment)

U1LCB8WEA (23:04:47): > Bugsigdb.orghas been down since 9:20pm NYC time:grimacing:

2023-11-04

Chiagoziem David (02:47:11) (in thread): > Wow, backend issues?

Odigiri Great Alume (03:38:51) (in thread): > Oh I just realized. Tried logging in this morning but couldn’t

Peace Sandy (03:51:22) (in thread): > Ouch… sorry about that

Peace Sandy (03:51:35) (in thread): > Hoping it will be resolved soon

Esther Afuape (04:30:08) (in thread): > @Levi Waldron

Esther Afuape (04:31:36) (in thread): > Aha!I guessthat’swhy Icouldn’tsave a signature

Nana (05:01:23) (in thread): > Noticed too

Chioma Onyido (05:19:34) (in thread): > Oh wow, thanks for the heads-up. Hoping the technical team will have it up and running soon.

Chioma Onyido (05:23:55) (in thread): > Hi@Esther Afuape, trying to look at your paper. Can you share a link please?:slightly_smiling_face:

Esther Afuape (05:25:39) (in thread): > https://peerj.com/articles/12826/ - Attachment (PeerJ): Comparison of changes in fecal microbiota of calves with and without dam > In pastoral areas and semi-agricultural and semi-pastoral areas of Sichuan, beef cattle breeding mode is mainly dependent on nature to raise livestock. On the one hand, owing to the shortage of forage grass in spring, cows suffer from malnutrition. On the other hand, competition for milk between human and livestock further deepens the malnutrition of newborn calves, and the mortality rate even exceeds 40%, resulting in serious waste of beef cattle source resources. The objective of this study was to investigate the effect of different cultivation methods (calves with and without dam) and age on calves hindgut microbiome. Sixteen healthy calves (Yak :male_sign: × Pian cattle :female_sign:, with similar birthday 0 ± 2 d and body weight 13.1 ± 1.13 kg), were selected and randomly divided into two groups. The control group was cultivated with heifers, whereas the treatment group was cultivated without heifers and was fed milk replacer during the whole 95 days formal experimental period. Fecal samples were collected on 35, 65 and 95 days of age for high-throughput sequencing. The α-diversity was different between the two groups on day 35; however, the bacterial species richness and diversity was almost not different on day 95. Principal coordinates analysis revealed significant difference between the two groups on all the three time points, and the timepoints of day 65 and 95 were closer and separated from the timepoints of day 35 in calves with dam, whereas the timepoints of day 35 and 65 were closer and separated from day 95 in calves without dam. As time passed, the abundance of Firmicutes increased, while Proteobacteria and Actinobacteria decreased in calves with dam. But in calves without dam, the abundance of Bacteroidetes and Proteobacteria increased on day 65 and then decreased on day 95. In genus level, the relative abundance of Bacteroides decreased in calf with dam while its abundance increased first and then decreased in calf without dam but both resulted in the range of 3.5~4.5%. The relative abundance of Lactobacillus decreased, whereas Ruminococcaceae UCG-005 increased in both groups as the calf grew up. It was concluded that the richness and evenness of the microbial communities was higher in calves with dam than without dam, and a stable gut microbiome in calve with dam is established earlier than calf without dam.

Chioma Onyido (05:27:10) (in thread): > Hmmm not sure I completely understood this,:sweat_smile:to be clear, Does this mean that we can curate Ruminococcaceae UCG 005 (and similar sig) as is, regardless of the rank on NCBI?<@U1LCB8WEA>

Esther Afuape (05:28:28) (in thread): > I didn’t quite get it too:sweat_smile:@Levi Waldron

Mildred Anashie (06:11:24) (in thread): > Hopefully it gets resolved soon

U1LCB8WEA (06:25:03) (in thread): > Back up now:+1:

Chiagoziem David (06:25:25) (in thread): > Great

Chiagoziem David (06:26:20) (in thread): > Sir could you please leave a comment on the questions that were raised yesterday

Chioma Onyido (07:12:39) (in thread): > This is a tough one! > But let’s startde novocalves with dam are**** ****calves that stay under the care/ nursing their mother (dam) after birth. While thecalves without damare those that separate from their dams, for animal welfare purposes probably - Google. > > So I tried to search EFO for the best condition to use for this,cultivation method, nutrition, livestock feeding, feeding method weren’t available, the closest I saw wasGrowth conditionandGrowth condition design:thinking_face:Thoughts?:eyes:

Chioma Onyido (07:24:21) (in thread): > Also triedanimal care, animal husbandry, animal nursing, animal feed intake, laboratory livestock management, all yielded nothing.

Esther Afuape (07:26:35) (in thread): > From the definition of the two, growth condition design seems like the closest thing. Its definition includes nutrient as one of the growth conditions that can be changed for an experiment. I tried to input it for the condition now and it came up.That’ssurprising causeit’sa study design:thinking_face:

Esther Afuape (07:29:06) (in thread): > You’remore creative with coming up with terms than I am:sweat_smile:

Chioma Onyido (07:30:18) (in thread): > Oh growth condition design is a study design? Well…:sweat_smile:

Esther Afuape (07:31:28) (in thread): > From the tree view on the EFO site, it is.I’mgoing with it.It’sthe closest thing and it works

Chioma Onyido (07:34:51) (in thread): > Great, pending when the mentors confirm.:thumbsup:

Esther Afuape (07:36:05) (in thread): > Yea, thank you so much:heart:

Chioma Onyido (07:37:51) (in thread): > You’re welcome.:blush:

Hodan Abdirisak (12:44:00) (in thread): > great to resolve

Peace Sandy (16:22:59): > Can I enter two body sites and two conditions, in the studyI’mcurrently curating they is an FA group- Food Allergy , AD - Atopic Dermatitis and an ADFA group which is a combination of both groups, in this case how should the body site and condition be entered.@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron

Esther Afuape (18:12:22) (in thread): > Ibelieve you can add two conditions and body sites

U1LCB8WEA (19:12:54) (in thread): > What about something relating to nursing or breastfeeding?

U1LCB8WEA (19:33:57) (in thread): > I’mthinking that because it sounds like they are contrasting nursing to supplement feeding?

U1LCB8WEA (19:51:40) (in thread): > Have to admit I have a hard time quickly following… can I call the groups a b and c? If they did contrasts for a vs bc, b vs ac, and c vs ab, there can be signatures of increase and decrease for each of the three experiments with no duplicate entry (although there may be more overlap than if the groups were completely independent). Am I missing something?

U1LCB8WEA (19:54:51) (in thread): > This seems like@Esther Afuape‘s suggestion but whywouldn’tthere be any signatures of decrease? Just because theydidn’treport any?

Levi Waldron (22:30:10) (in thread): > You’vedescribed one of the experiments having two conditions but nothing about two body sites?I’munsure if bugsigdb supports multiple conditions,but if not you can ignore those signatures since a nonspecific outcome like that has questionable scientific value in my opinion.

2023-11-05

Chioma Onyido (03:14:40) (in thread): > Interesting… indeed breastfeeding fits best because they contrasted with supplement feeding.:sweat_smile:@Levi Waldronand there’s an EFO available forbreastfeeding duration@Esther Afuape

Odigiri Great Alume (04:17:24): > Good morning and happy weekend everyone > I will be curatinghttps://www.nature.com/articles/s41598-023-42474-7 - Attachment (Nature): Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population > Scientific Reports - Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population

Esther Afuape (04:26:06) (in thread): > Thank you!@Chioma Onyido@Levi Waldron

Peace Sandy (06:31:27) (in thread): > Wow…Thank You for the insight@Levi Waldron

Peace Sandy (06:31:34) (in thread): > Thank You@Esther Afuape

Chioma Onyido (07:11:19): > Happy Sunday<!here>:smiley:It’s been a great one month of contribution to BugSigDB on my end and I’m excited for the coming months… > > What are some of the interesting finds or taxa you’ve seen since you started curating on BugSigDB?:eyes:I’ll go first,Negativibacillus (negativ… belongs to the group of gram-negative bacteria:sweat_smile:) > Ezakiella (almost sounds like Ezekiel… ) > Elizabethkingia(was really curious about this and I when I looked it up, I found that the genus was named in honor of an American bacteriologist, Elizabeth King):sweat_smile:

Esther Afuape (07:14:35) (in thread): > Shwanella:sweat_smile:. It sounds like a native name where I’m from. Also Escherichia-Shigella. I know they’re genetically similar but never saw them paired as one in school!

Esther Afuape (07:21:21) (in thread): > I’ve mostly enjoyed the results from the papers. As a microbiologist, I always knew the significance of the microbiome but I didn’t realize how easily prone to change it is! I mean, Ididn’tthink staying indoors more during the pandemic could drastically change the gut microbiome nor the use of epidural during CS.

Chioma Onyido (07:24:08) (in thread): > Staying indoors during the pandemic changed the microbiome?:hushed:Ohh wow Interesting…

Chioma Onyido (07:25:41) (in thread): > I also came across a paper where depression changed the gut microbiome.. got me seriously thinking:sweat_smile:

Esther Afuape (07:26:16) (in thread): > In infants, it did. I wonder if adults were not so prone to such drastic changes during the pandemic:thinking_face:

Esther Afuape (07:27:19) (in thread): > Wow. Depression? Now I believe every single thing we do shapes our microbiome one way or the other.

Chioma Onyido (07:29:18) (in thread): > Yeah, it drastically reduced beneficial bacteria and increased pathogenic bacteria…I was:exploding_head:

Esther Afuape (07:50:13) (in thread): > They mentioned decreases in let’s say a vs bc, but the decreases were increases in b and c.

Odigiri Great Alume (07:56:28) (in thread): > This one I didn’t actually see it in the studies I curated, however, while doing a “detective work”:joy:finding missing NCBI ID. I got on Google to start searching for synonyms of the phyla I was interested in since I didn’t find the ID on the NCBI taxonomy browser. Lo and behold I came across this name “******Llanfairpwllgwyngyllgogerychwyrndrobwllllanty******” ( it’s a place in Wales where they got the soil bacteria Myxococcaceae) during one of my search. It’s though not the synonym for what I was looking for, it sparked curiosity and I started to read about it on wiki. > I couldn’t even pronounce the name. Got tired and let sleeping dog to lie in peace.

U1LCB8WEA (08:03:06) (in thread): > If they actually provide signatures for a vs b and a vs c, then those would be the groups?

Chiagoziem David (08:04:54) (in thread): > Okay, chioma is typing already

Chiagoziem David (08:05:02) (in thread): > Wanted to call her attention

Chioma Onyido (08:06:05) (in thread): > Hmmm…Only Increase signatures were reported for a b and c > > Does this mean that the signature should be curated more than once during curation?<@U1LCB8WEA>

Chiagoziem David (08:06:09) (in thread): > Mine was FMT , fecal microbial transplant….. > > That is really a thing:joy::wink::joy::joy:

U1LCB8WEA (08:07:00) (in thread): > what were they comparing a b and c to - increase compared to what?

U1LCB8WEA (08:07:34) (in thread): > Nosignatures shouldn’tbe entered more than once

Chioma Onyido (08:08:51) (in thread): > Here Sir, - File (JPEG): IMG_5855

U1LCB8WEA (08:08:52) (in thread): > an increase in group a compared to b is the same as a decrease in b compared to a

U1LCB8WEA (08:11:50) (in thread): > LEfSe compares 1 vs all, ie a vs bc. And it sounds like they are only reporting the “biomarker” taxa that are increased in one group compared to the rest. So three experiments,with one signature of increased for each.

Chiagoziem David (08:12:18) (in thread): > Wow , okay, this is getting clearer

Chiagoziem David (08:12:48) (in thread): > So there are no decreased signatures for the individual experiments?

U1LCB8WEA (08:13:05) (in thread): > Not in the figure above

Chioma Onyido (08:13:50) (in thread): > Sounds like@Esther Afuape’s suggestion:thinking_face:Thank you very much:pray:

Chiagoziem David (08:14:03) (in thread): > Okay, there were some mentioned in the text though, could work with that too?

U1LCB8WEA (08:14:26) (in thread): > Yes of course

Chiagoziem David (08:15:04) (in thread): > Alright, perfect, thank you very much sir

Chioma Onyido (08:17:16) (in thread): > @Odigiri Great Alumecome and learn:satisfied: - File (MPEG 4 Video): RPReplay_Final1699189350

Chiagoziem David (08:18:29) (in thread): > What!!:joy:

U1LCB8WEA (08:21:31) (in thread): > Yes, I agree with@Esther Afuape‘s solution

Chioma Onyido (08:21:47) (in thread): > @Chiagoziem DavidI thought the same when I saw it, something like “fresh feces were collected from donor mice and after dilution and centrifugation… transplanted into recipient mice”:satisfied:Science has indeed made many seemingly impossible things possible.

Odigiri Great Alume (09:21:42) (in thread): > @Chioma Onyido:joy:I’d just call it LAN

Odigiri Great Alume (09:22:58) (in thread): > @Chioma Onyidoa study that transferred feces from infant donor to mice lol

Peace Sandy (12:05:45) (in thread): > Yeah… contributing to BugSigDB has really enhanced my knowledge of microbiome… I’ve come across different taxon, this has made me to do lots of research… and it’s really interesting.

Chioma Onyido (12:12:58): > I’m working on a case-control study (type 2 diabetes vs controls) where I’ve about 7 different experiments. > In one of my experiments, gut microbiota of 2 populations-Denmark and India were contrasted, I think this be a cross-sectional study design? > If it is, > Can 2 study designs be recorded in BugSigDB?<@U1LCB8WEA><@UBNSEMS3S>https://genomemedicine.biomedcentral.com/articles/10.1186/s13073-021-00856-4 - Attachment (BioMed Central): Trans-ethnic gut microbiota signatures of type 2 diabetes in Denmark and India - Genome Medicine > Background Type 2 diabetes (T2D), a multifactorial disease influenced by host genetics and environmental factors, is the most common endocrine disease. Several studies have shown that the gut microbiota as a close-up environmental mediator influences host physiology including metabolism. The aim of the present study is to examine the compositional and functional potential of the gut microbiota across individuals from Denmark and South India with a focus on T2D. Many earlier studies have investigated the microbiome aspects of T2D, and it has also been anticipated that such microbial associations would be dependent on diet and ethnic origin. However, there has been no large scale trans-ethnic microbiome study earlier in this direction aimed at evaluating any “universal” microbiome signature of T2D. Methods 16S ribosomal RNA gene amplicon sequencing was performed on stool samples from 279 Danish and 294 Indian study participants. Any differences between the gut microbiota of both populations were explored using diversity measures and negative binomial Wald tests. Study samples were stratified to discover global and country-specific microbial signatures for T2D and treatment with the anti-hyperglycemic drug, metformin. To identify taxonomical and functional signatures of the gut microbiota for T2D and metformin treatment, we used alpha and beta diversity measures and differential abundances analysis, comparing metformin-naive T2D patients, metformin-treated T2D patients, and normoglycemic individuals. Results Overall, the gut microbial communities of Danes and Indians are compositionally very different. By analyzing the combined study materials, we identify microbial taxonomic and functional signatures for T2D and metformin treatment. T2D patients have an increased relative abundance of two operational taxonomic units (OTUs) from the Lachnospiraceae family, and a decreased abundance of Subdoligranulum and Butyricicoccus. Studying each population per se, we identified T2D-related microbial changes at the taxonomic level within the Danish population only. Alpha diversity indices show that there is no significant difference between normoglycemic individuals and metformin-naive T2D patients, whereas microbial richness is significantly decreased in metformin-treated T2D patients compared to metformin-naive T2D patients and normoglycemic individuals. Enrichment of two OTUs from Bacteroides and depletion of Faecalibacterium constitute a trans-ethnic signature of metformin treatment. Conclusions We demonstrate major compositional differences of the gut microbiota between Danish and South Indian individuals, some of which may relate to differences in ethnicity, lifestyle, and demography. By comparing metformin-naive T2D patients and normoglycemic individuals, we identify T2D-related microbiota changes in the Danish and Indian study samples. In the present trans-ethnic study, we confirm that metformin changes the taxonomic profile and functional potential of the gut microbiota. - File (JPEG): IMG_5858

Chioma Onyido (12:45:39) (in thread): > @Peace SandyI know right? Grateful for the opportunity.:grin:

Chiagoziem David (12:49:53) (in thread): > Bugsigdb has turned me, a mechanical engineer to sound like Darwin:smile::smile::smile::joy:

Chiagoziem David (12:55:02) (in thread): > Omo , let’s hear what the mentors would have to say, some curations can be “hectic” though:sweat_smile:

Peace Sandy (13:07:19) (in thread): > I doubt two study designs can be recorded, I had this same confusion a while back.

Peace Sandy (13:08:31) (in thread): > Yes@Chioma Onyido

Chioma Onyido (13:10:05) (in thread): > I remember. Hoping the mentors comment soon.:face_holding_back_tears:

U1LCB8WEA (13:29:36) (in thread): > I love this discussion!!!

Odigiri Great Alume (13:30:40) (in thread): > @Levi Waldronwe trying to have some fun “EDUTAINMENT” I guess:joy:

U1LCB8WEA (13:33:39) (in thread): > A study can only have one study design. Although it is possible to create two studies from the same publication for each of the study designs, in this case I feel that the distinction between case-control and cross-sectional observational (not case-control) is not important enough to warrant a separate study. Since it seems that the “primary” study is case-control, I would just include everything under that design. If there were a mixture of RCT and a case-control study, or longitudinal + case-control, I think it would be more important to separate those into separate studies because their epidemiological interpretation is so different.

U1LCB8WEA (13:34:11) (in thread): > It would be good to add a comment about this in the study’s Discussion page.

Peace Sandy (13:34:53) (in thread): > Wow…this has really cleared my doubt > Thank You@Levi Waldron

U1LCB8WEA (13:35:01) (in thread): > No problem!

Chioma Onyido (13:35:38) (in thread): > I would curate under same study design and add a comment as advised, thank you:blush::pray:

Chiagoziem David (13:35:38) (in thread): > Thank you very much for the clarification sire

U1LCB8WEA (13:37:15) (in thread): > And further clarification - RCTs, laboratory experiments, and longitudinal designs are so different because they can eliminate the confounding that is difficult to control for in other observational studies - RCTs and laboratory experiments by employing randomization, and longitudinal studies by comparing observations of each individual to the same individual at different points in time.

Chioma Onyido (13:37:53) (in thread): > For creating 2 studies from the same publication (if the study designs were really different), I think that was allowed in the past, I doubt if BugSigDB currently allows that, it usually flags something likeonly unique IDs allowed :thinking_face:* *

U1LCB8WEA (13:38:13) (in thread): > (confounding meaning something that can cause both the exposure/treatment and the outcome)

Odigiri Great Alume (13:38:43) (in thread): > @Levi Waldronso this is not to say that a research paper (publication) can not have two study designs right? But for the sake of curations in bigsigdb its better to use the primary study design (specifically, case control and crossectional as in@Chioma Onyidocase) right? > > Because I have read papers where they used multiple study designs to achieve different objectives.:thinking_face:

Chioma Onyido (13:41:17) (in thread): > @Odigiri Great Alumehe’s saying that if the study designs aresimilarasin my case, where case-control and cross-sectional were both used, then it can be curated withonlythe primary design used (which is case-control). But if it’s verydifferent, e.g. RCTs and case-control, then it can be curated as 2 different studies on BugSigDB.

U1LCB8WEA (13:41:27) (in thread): > @Chioma Onyidoin the past it was possible but we locked that down because it was far more common that a study was accidentally duplicated than that it really had two designs. Ithinkthere is still a tricky workaround that I forget right now, but if there’s a strong motivating case I’ll figure it out again:sweat_smile:.@Odigiri Great Alumeyes it is possible for a publication to present the results of two study designs, just unusual since it is such a broad scope. I think even in some cases where the authors use language of different study designs, it isn’t really:smile:

Esther Afuape (13:42:59) (in thread): > @Levi Waldron:face_holding_back_tears::pray:

Chiagoziem David (13:43:56) (in thread): > Yeah@Chioma OnyidoI came across that “unique iD” issue once

Odigiri Great Alume (13:44:30) (in thread): > @Levi Waldronthank you a billion

Chioma Onyido (13:45:29) (in thread): > Ohh I see.<@U1LCB8WEA>I hope to come across one soon, so that I will be taught the trick:eyes:Thank you for your time!:sweat_smile:

U1LCB8WEA (13:46:55) (in thread): > @Chioma OnyidoI would use theRuminococcaceae UCG 005species-level NCBI ID, even if the authors listed it as a genus. It’s likely that the authors don’t know what rank it is, they just saw the name returned by their taxonomic profiling software.

Esther Afuape (13:48:34) (in thread): > Thank you

U1LCB8WEA (13:48:43) (in thread): > I think researchers assume that 16S taxonomic profiling returns genus-level results, even if some ASVs or OTUs do in fact map unambiguously to a species. Since some species and genera are more genetically similar than others, both can be true (sometimes genus-level resolution, other times species-level).

Chioma Onyido (13:49:44) (in thread): > Great! Looks like we’ve some clean up to do@Esther Afuape@Odigiri Great Alume@Joan C. Chukwuemeka@Chiagoziem David:eyes:Another question, what if different numbers were reported for one genus, > E.g. lachnospiraceae UCG-001 > lachnospiraceae UCG-002 > lachnospiraceae UCG-005 > > Can all 3 be curated as uncultured lachnospiraceae bacterium?:thinking_face:

Chiagoziem David (13:50:02) (in thread): > Guys can we please not forget the second question<@U1LCB8WEA>, what should the condition be? Fecal microbial transplant is coming up on the oncology sites , whilst I still personally feel they contrast here is sleep,@Chioma Onyidoand@Peace Sandy

Chiagoziem David (13:50:13) (in thread): > @Esther Afuape

Chioma Onyido (13:53:44) (in thread): > Sinceresponse to fecal microbial transplantisn’t available, I’m thinkingresponse to transplant should suffice? It pops up on the EFO browser.:woman-shrugging: - File (JPEG): IMG_5860

U1LCB8WEA (13:54:10) (in thread): > Yeah that seems like a good compromise. It would be good to leave a comment by thatuncultured lachnospiraceae bacteriumexplaining what names were originally reported (the green text bubbles with a “+”) and perhaps mark the taxon as “follow-up needed” ? - File (PNG): image.png

Chiagoziem David (13:55:07) (in thread): > Do you think the contrast of the study is fecal transplant though

Peace Sandy (13:55:16) (in thread): > I had to recheck this thing@Chiagoziem David

Chiagoziem David (13:55:36) (in thread): > Okay….

U1LCB8WEA (13:56:18) (in thread): > Check EFO to see what kind of transplant this is referring to - it might be referring to organ transplant instead?

Chioma Onyido (13:57:53) (in thread): - File (JPEG): IMG_5861

Chioma Onyido (13:58:04) (in thread): > Though there’s EFO for liver, heart transplant etc…

Peace Sandy (13:59:11) (in thread): > Yeah,they is none for fecal microbial transplant

Chioma Onyido (13:59:20) (in thread): > @Chiagoziem Davidhmmm why do you thinkit’ssleep though?:thinking_face:I thinkit’sresponse to FMT becausethat’sthe condition contrasted in your study,

Chiagoziem David (13:59:21) (in thread): > Are we agreeing that the contrast is on FMT yet? That is my main confusion:sob::sob::sob::sob:

Esther Afuape (13:59:42) (in thread): > There’s definitely a lot of cleanup to do if we’ll be going by this:sweat_smile:. There’s also the little confusion of “uncultured” and “unclassified”. I understand that “Unclassified” bacteria have been identified but have not been placed into a specific taxonomic classification. “Uncultured” bacteria are those that have been detected in environmental samples but have not been successfully grown in a laboratory setting. > > But is it okay to use them interchangeably for unclear taxa like the UCG groups?

Chiagoziem David (14:00:19) (in thread): > Because the were all administered FMt, but some group were sleep deprived whilst others were not

Peace Sandy (14:00:21) (in thread): > But I doubt response to transplant will be suffice, judging from the meaning

Chiagoziem David (14:00:26) (in thread): > Hence SD

U1LCB8WEA (14:01:09) (in thread): > > Because the were all administered FMt, but some group were sleep deprived whilst others were not > If that’s the case, then sleep deprivation is the Condition of the experiment

U1LCB8WEA (14:02:01) (in thread): > For any experiments where FMT is the Condition, I think the best you can do for now is enter “response to transplant” and include a note about this in the Discussion.

Chiagoziem David (14:03:23) (in thread): > It flagged it as wrong though , during the review

Chiagoziem David (14:03:54) (in thread): > When I gave the condition as sleep

U1LCB8WEA (14:04:49) (in thread): > What bugsigdb URL and github ID? I can double-check

Chiagoziem David (14:05:30) (in thread): > Alright, let me drop them here

Chioma Onyido (14:05:32) (in thread): > I used this to arrive at the* response to FMT *being the condition, because they were checking for the response to FMT in all the groups after the transplant, and they found that FMT actually changed the gut microbiota.:eyes: - File (JPEG): IMG_5862

Chioma Onyido (14:05:45) (in thread): > But I see another angle from@Chiagoziem Davidand<@U1LCB8WEA>

Peace Sandy (14:06:29) (in thread): > I think FMT might be condition, the issue here is thatit’snot on EFO

Chiagoziem David (14:07:09) (in thread): > The FMT treatment was given to all the group@Chioma Onyidoand@Peace Sandy

Chiagoziem David (14:07:51) (in thread): > From their names you can even tell, CON-FMT, SD-FMT, SD +MEL - FMT

Chioma Onyido (14:10:07) (in thread): > Yea@Chiagoziem Davidyou’reright, they were all administered FMT, But the authors were studying the response to FMT in all the groups.:thinking_face:

Chioma Onyido (14:10:17) (in thread): > Hmmm

Chiagoziem David (14:10:25) (in thread): > So if it was given to all, shouldn’t the contrast be something else, although I get your point@Chioma Onyido, because FMT seems like what is actually been studied

Chiagoziem David (14:10:33) (in thread): > Omo:sweat_smile::sweat_smile:

Peace Sandy (14:10:42) (in thread): > Wow

Peace Sandy (14:11:06) (in thread): > I’llreally like to know how this study will be reviewed…it’sintriguing

Peace Sandy (14:11:37) (in thread): > I’mtrying to read through

U1LCB8WEA (14:12:26) (in thread): > Do I understand correctly from “we transplanted fecal microbiota from CON, SD, or SD + Mel groups into gut microbiota-depleted mice” that they are contrasting the effects of sleep deprivation between groups that received different FMTs? If so, then the Condition is FMT.

U1LCB8WEA (14:14:09) (in thread): > Ideallythe EFO would all these different types of FMT under an FMT class, but it doesn’t even have FMT generally, so we have to work with what we have. Ideally we could be submitting pull requests to the EFO to have terms added then go back and improve the coding of such experiments.

Chiagoziem David (14:16:18) (in thread): > Exactly<@U1LCB8WEA>, if there was a way we could collaborate with EFO it would have been perfect.

Chiagoziem David (14:16:46) (in thread): > Alright then , FMT it is

Peace Sandy (14:17:45) (in thread): > Same thing I thought of

Chiagoziem David (14:18:11) (in thread): > I am really grateful to everyone who contributed<@U1LCB8WEA>@Chioma Onyido@Peace Sandy@Esther Afuape,:raised_hands::raised_hands::pray:

Peace Sandy (14:18:18) (in thread): > @Levi WaldronThank you for clearing our doubts

Peace Sandy (14:18:36) (in thread): > You are welcome@Chiagoziem David

Chiagoziem David (14:18:40) (in thread): > Even with NCBI too

U1LCB8WEA (14:26:43) (in thread): > Whew that’s a hard question! To me the great motivation for using the NCBI taxonomy is being able to classify reported taxa as precisely as possible, but also with imprecision when needed, while still being able to communicate something about lineage. The lineage allows us to do things like compare the similarity signatures where one was produced by 16S amplicon sequencing and another by shotgun metagenomic sequencing, such as in Fig 3 of the paper (https://www.nature.com/articles/s41587-023-01872-y/figures/3). I think you’re right@Esther Afuapeabout the difference between “uncultured” and “unclassified”, and “unclassified” can be a catch-basin for a bunch of uncultured organisms (such asunclassified Oscillospiraceae). Since “unclassified Oscillospiraceae” is “no rank” whereas each bacterium under it is rank species from a known family, the terminology isn’t interchangeable. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Chiagoziem David (14:27:48) (in thread): > Hmmm

Chiagoziem David (14:28:07) (in thread): > Okay, this clears a lot

U1LCB8WEA (14:28:22) (in thread): > And the UCG groups are I think in the class of uncultured bacterium, rather than unclassified.

U1LCB8WEA (14:29:51) (in thread): > Another with an edutaining name ishttps://en.wikipedia.org/wiki/CrAssphage- with a capital “A” just to make sure you get the joke:sweat_smile: - Attachment: CrAssphage > CrAss-like phage are a bacteriophage (virus that infects bacteria) family that was discovered in 2014 by cross assembling reads in human fecal metagenomes. In silico comparative genomics and taxonomic analysis have found that crAss-like phages represent a highly abundant and diverse family of viruses. CrAss-like phage were predicted to infect bacteria of the Bacteroidota phylum and the prediction was later confirmed when the first crAss-like phage (crAss001) was isolated on a Bacteroidota host (B. intestinalis) in 2018. The presence of crAss-like phage in the human gut microbiota is not yet associated with any health condition.

Chiagoziem David (14:31:06) (in thread): > They really wanted to make sure:smile::joy:

Peace Sandy (14:32:28) (in thread): > Wow@Levi Waldron:joy::joy::joy::joy:…this is a discovery

Odigiri Great Alume (14:33:20) (in thread): > @Levi Waldron:joy:not what my “other” mind is telling me:joy:Oh lord

Chioma Onyido (14:33:25) (in thread): > Love it when they infusesciencewith humor, makes learning more enjoyable:sweat_smile:

Peace Sandy (14:33:57) (in thread): > I remember reading about bacteriophage when we did a course on virology:relaxed:

Peace Sandy (14:34:13) (in thread): > True@Chioma Onyidoand makes it easier to grab

U1LCB8WEA (14:58:59) (in thread): > It is actually possible to submit issues and even changes to the EFO, although some study would be required (by me too!) to learn how to submit an appropriate change.https://github.com/EBISPOT/efo

Chiagoziem David (14:59:36) (in thread): > Oh, okay

Chiagoziem David (14:59:44) (in thread): > This is fair

U1LCB8WEA (15:42:21) (in thread): > Here are their guidelines for contributing:https://github.com/EBISPOT/efo/blob/a6c86d912559d4e37460486f4e6a157f53e150d1/CONTRIBUTING.md- I just submitted a request for FMT:https://github.com/EBISPOT/efo/issues/2125 - Attachment: #2125 New term request for “fecal microbiota transplantation”

Peace Sandy (15:43:39) (in thread): > Oh wow…this is nice@Levi Waldron

U1LCB8WEA (15:47:45) (in thread): > Yeah! It would be better to think through any subterms we might want and potentially submit a whole branch to the ontology using their Webulous contributing instructions, but I didn’t have time:sweat_smile:

Peace Sandy (15:49:40) (in thread): > What are the basics of coming up with subterms ?

Chioma Onyido (15:49:42) (in thread): > Just viewed it, Really descriptive and detailed submission too. I’ve learnt a lot on this platform.:blush:

Esther Afuape (15:55:46) (in thread): > Got it! Thank you@Levi Waldron

U1LCB8WEA (16:00:57) (in thread): > I followed their template that appears when creating a new GitHub issue, it helped with the detail!

Peace Sandy (16:31:24): > Any ideas on how to get decreased abundance from this table, all I was able to get is increased abundance or is it meant to be only increased abundance.@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic - File (PNG): IMG_6211

Chioma Onyido (16:54:10) (in thread): > <@U1LCB8WEA>tried to use the + to add a comment as advised, It says i need permission,:sweat_smile:Also how do I mark as “follow up needed”? - File (JPEG): IMG_5868

U1LCB8WEA (16:59:52) (in thread): > Oh, I didn’t realize it required extra permissions! I’ve just given you “Reviewer” permissions so you should now be able to (and also mark studies/experiments/signatures as “reviewed”)

U1LCB8WEA (17:01:06) (in thread): > If they are comparing two species, I suppose choose the “group 1” species.

Chioma Onyido (17:02:49) (in thread): > Awesome! Works just fine now.:grin:

U1LCB8WEA (17:04:11) (in thread): > Others who now have some experience onbugsigdb.orgfeel ready for “Reviewer” permissions, please let me know.

Joan C. Chukwuemeka (18:16:26) (in thread): > This clears up a lot… Thanks a lot<@U1LCB8WEA>. I’d be grateful to also get the “Reviewer” Permission.

2023-11-06

Mildred Anashie (03:12:52): > Happy Monday<!here>It’s going to be a productive week for us all:pray:<@UBNSEMS3S>I dropped a comment on issue #97 on GitHub based on your review, I’ll like to round up with that and appreciate if you could take a look at it please:pray:<@U1LCB8WEA>could you help check it out,:blush:just incase, she’s unavailable…Thank you

Chiagoziem David (03:35:30): > hello<@UBNSEMS3S><@U1LCB8WEA>, please could i have signature 2 of experiment1 deleted for this study, thank you very much :https://bugsigdb.org/Study_804 - Attachment (BugSigDB): Gut microbiota-derived metabolites mediate the neuroprotective effect of melatonin in cognitive impairment induced by sleep deprivation - BugSigDB > Sleep loss is a serious global health concern.Consequences include memory deficits and gastrointestinal dysfunction.Our previous research showed that melatonin can effectively improve cognitive impairment and intestinal microbiota disturbances caused by sleep deprivation (SD).

Aleru Divine (05:43:20): > Happy new week everyone.Hopey’allhad a great weekend.

Nana (05:49:50): > @Aleru DivineThanks, yes

Chioma Onyido (06:02:25) (in thread): > @Peace SandyIn the feces samples, phylum Bacteroidetes was ******more abundant in AD children*******, *******less frequent in ADFA and absent from healthy controls******* (p = 0.043); *******the same was observed******* to… genera *******Stenotrophomonas and Bacteroides *****(p = 0.03 and p = 0.041, respectively). > > *This excerpt just before the table 3, > From this, I think the authors interpreted as, for example, > OTU 11: AD > ADFA > FA, C meaning…More abundant in AD, (increase) > Less frequent in ADFA (decrease) > absent from C.(Decrease) > This is how the authors deduced it,:thinking_face:ButI’mnot so sure if it should be curated.

Odigiri Great Alume (06:38:37): > Good morning@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina PerovicI dropped a comment in respect to your response on my study issues 85. > > Please I’d be grateful if you help look at it so I can make the remaining corrections > > Thank you both for always showing up when we scream for helphttps://github.com/waldronlab/BugSigDBcuration/issues/85 - Attachment: #85 Lower respiratory tract microbiome composition and community interactions in smokers > Lower respiratory tract microbiome composition and community interactions in smokers – Michael Campos et al. – Access Microbiology 2023
> DOI: 10.1099/acmi.0.000497.v3
> https://www.microbiologyresearch.org/content/journal/acmi/10.1099/acmi.0.000497.v3

Peace Sandy (07:58:52) (in thread): > Yes Dear > Just wanted to be sure if recording the decreased abundance gotten from what you said is proper. > > Although I already got increased abundance > Wish I can send a voice note so that you will properly get what I mean

USLACKBOT (08:42:15): > This message was deleted.

Nana (08:44:18): > @Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina Perovicwhen i searched for the condition on EFO found this but it did not attach EFO to the url?. Is this still correct - File (PNG): EFO.png

Chioma Onyido (09:04:50) (in thread): > Hmmm… I’m not sure about recording the decreased abundance from that deduction too.

Peace Sandy (09:07:47) (in thread): > Same Dear, I thinkit’sjust increased

Chiagoziem David (10:30:08): > hello guys , i am working on this study :https://bugsigdb.org/Study_836 - Attachment (BugSigDB): Association Between Breastmilk Microbiota and Food Allergy in Infants - BugSigDB > Regulating the composition of human breastmilk has the potential to prevent allergic > diseases early in life.The composition of breastmilk is complex, comprising varying levels > of oligosaccharides, immunoactive molecules, vitamins, metabolites, and microbes.

UBNSEMS3S (11:32:53): > Hi everyone sorry for being a bit quiet. We are working diligently behind the scenes to make our final selections for the internship. I will say you did not make it easy for us!

Peace Sandy (11:55:27) (in thread): > Well done@C. Mirzayi (please do not tag this account)…you are doing absolutely great:blush:

Chiagoziem David (12:09:30) (in thread): > :grin:, we know:sweat_smile:. Thank you:blush:

Esther Afuape (12:40:50): > @Levi Waldronmentioned how we can add a note to an experiment during curation using the talk page during one of the office hours. Ican’tseem to find my way around it now thatI’mtrying to do it:sweat_smile:. Does anyone remember?

Peace Sandy (12:44:27) (in thread): > Yes I remember

Peace Sandy (12:44:40) (in thread): > Have you been able to figure it out yet ?

Esther Afuape (12:44:50) (in thread): > No, Ihaven’t

Peace Sandy (12:45:43) (in thread): > Okay

Peace Sandy (12:46:00) (in thread): > Click on the three dot from the main page

U1LCB8WEA (12:46:02) (in thread): > Click the “…” at the top of the page and “Discussion” - File (PNG): image.png

Esther Afuape (12:46:58) (in thread): > Thank you!

U1LCB8WEA (12:50:45) (in thread): > I’m not quite sure what “did not attach EFO to the url” means, but I am able to autocomplete with this condition: - File (PNG): image.png

Nana (12:59:41) (in thread): > Well done<@UBNSEMS3S>, you are doing well

Nana (13:00:54) (in thread): > Ok..thanks@Levi Waldronplease can you check the body site question I posted before this one

Chiagoziem David (13:05:51) (in thread): > Mr macaroni@Nana:sweat_smile:

Nana (13:13:05) (in thread): > @Levi Waldronthis is what i mean by url:http://purl.obolibrary.org/obo/MONDO_0012511I thought that every OLS ontology search for EFO will have for example:http://purl.obolibrary.org/obo/EFO_12511That when looking out for condition that was not autocomplete we should search using EFO which means the url will contain EFO - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > Web site created using create-react-app

U1LCB8WEA (13:14:24) (in thread): > All of EFO should autocomplete for Condition, but we don’t have functionality for entering terms not in EFO.

U1LCB8WEA (13:14:38) (in thread): > If that’s what you’re asking?

U1LCB8WEA (13:20:19) (in thread): > Did they pool together the samples from these sites, or are they analyzed separately?

U1LCB8WEA (13:20:49) (in thread): > If they are pooled together, then you would choose the closest parent term that includes all three sites

Svetlana Ugarcina Perovic (13:21:28) (in thread): > It’s NOT AT ALL easy to do final selections! You have been doing AMAZING BugSigDB-ing!!:bouquet:**** to YOU**

U1LCB8WEA (13:21:50) (in thread): > If they are analyzed separately, then what you’re doing is correct to just find the most specific term that fits exactly or as closely as possible for each.

Nana (13:27:33) (in thread): > ok…when i typed preterm…i choose autocomplete but it has this :http://purl.obolibrary.org/obo/MONDO_0012511, is it ok to have this when you point your cursor on the condition

Nana (13:33:08) (in thread): > They were analyzed separately i believed from sending each samples to different places, but at the same time it gave birth to only one experiment and two signatures

Chloe (14:42:50) (in thread): > haaaa well done<@UBNSEMS3S>@Svetlana Ugarcina Perovicand@Levi Waldronwe are also eagering waiting for the results:innocent::blush:personally nawa days the nights are longer than before as am waiting for 20th:see_no_evil::face_with_hand_over_mouth:

Chiagoziem David (14:49:47) (in thread): > :sweat_smile:

Chiagoziem David (15:33:48) (in thread): > :pray:

Hodan Abdirisak (16:03:34) (in thread): > Well done@C. Mirzayi (please do not tag this account):+1::white_check_mark:you are doing great work we are waiting the results, I hope every one became experienced about remote working and open source contribution

Chioma Onyido (17:41:14): > Hi<!here>:wave:I’ve had a hard time interpreting this, > It’s T2D (case) contrasted with NG (normoglycemic controls), T2D had negative LDA scores, whereas NG had positive logFC scores. > I’m thinking to curate only one signature (decrease) for this experiment, which would include all the taxa (from both the negative T2D scores and positive control scores) but I’m not sure. > Need help.<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic:pray: - File (JPEG): IMG_5932

Chioma Onyido (17:50:17) (in thread): > Also the statistical analysis reported for this experiment is negative binomial regression but from the results seems to have used Lefse since they reported logFC scores, please how do I go about this ?:slightly_frowning_face:

U1LCB8WEA (17:52:14) (in thread): > Why not use the log2fc to tell direction? Opposite LD score does mean opposite direction of fold change, ie one sign is up and the other sign down

U1LCB8WEA (17:53:00) (in thread): > LEfSe produces LDA scores, regression produces logfc

U1LCB8WEA (17:53:38) (in thread): > I would just report one test or the other, even if they reported results from both

Chioma Onyido (17:54:03) (in thread): > Hmmm, that means I should ignore the “dir” column and interprete it as negative LD score (decrease) and positive LD score (increase) relative to the case group (T2D)?

U1LCB8WEA (17:54:48) (in thread): > Don’tthey correspond to the same thing?

Chioma Onyido (17:55:37) (in thread): > They should but In their dir column, the positive scores were for the controls.:sweat_smile:

U1LCB8WEA (17:57:42) (in thread): > They might have just failed to set the controls as reference group in the regression,flipping all logfc signs. Would be good to check with the text to make sure you have the directions right

Chioma Onyido (18:02:00) (in thread): > There’sonly one reference of table s3 within text,doesn’tsay much on the direction.:slightly_frowning_face: - File (JPEG): IMG_5933

Chioma Onyido (18:04:03) (in thread): > They probably forgot to set the right reference group.:woman-shrugging:I’d to go with your suggestion of curating relative to the case group, thank you for your time.<@U1LCB8WEA>:pray:

Chiagoziem David (18:18:51) (in thread): > :thinking_face:

U1LCB8WEA (18:27:23) (in thread): > Group 0 should always be the control group and group 1 the case group

Joan C. Chukwuemeka (20:24:53) (in thread): > <@U1LCB8WEA>I’m unable to leave a comment using the green text bubbles with a “+” to state names that were originally reported for the UCG taxa, as I don’t have “Reviewer” Permission.

U1LCB8WEA (20:26:30) (in thread): > @Joan C. ChukwuemekaI just gave you reviewer permissions

Joan C. Chukwuemeka (20:31:36) (in thread): > Alright, thanks

2023-11-07

Chiagoziem David (04:02:21): > hello guys, i am going through this article, i can’t seem to find any microbiome signatures from any differential abundance test, ppss: the test were carried out on plant roots. :https://www.sciencedirect.com/science/article/pii/S2590346219300033 - Attachment (sciencedirect.com): Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome > Plant-associated microbes are critical for plant growth and survival under natural environmental conditions. To date, most plant microbiome studies in…

Chioma Onyido (04:44:22) (in thread): > Hmmm…looking at it now..

Chioma Onyido (04:49:08) (in thread): > I see results reported within text, also Have you tried looking through your supplemental files? > Figure S10 for example…:eyes:

Chiagoziem David (04:50:14) (in thread): > Let me Check that..

Peace Sandy (04:51:11) (in thread): > Did you find the article on the GitHub issue link ?

Chiagoziem David (04:52:22) (in thread): > Yeah, I did pick another one though…. > > In case it’s something you are already working on

Peace Sandy (04:53:31) (in thread): > Oh…okay

Chiagoziem David (04:55:01) (in thread): > @Chioma Onyidoeven figure 5f gives the abundance information too:sweat_smile::sweat_smile::pray:

Chiagoziem David (04:55:05) (in thread): > My bad

Chiagoziem David (04:55:53) (in thread): > :sweat_smile:, I’d get back to it later, when I’m done with the new one I took up

Chioma Onyido (04:56:22) (in thread): > H, I, J too…:smiley:Glad you were able to figure it out.:+1:

Chiagoziem David (04:57:36) (in thread): > Namaste:wink:

Chiagoziem David (04:57:53) (in thread): > @Peace Sandyis it something you were already working on?

Peace Sandy (04:58:10) (in thread): > @Chiagoziem DavidNo Iwasn’t

Peace Sandy (04:58:24) (in thread): > I choose some other paper

Chiagoziem David (04:59:40) (in thread): > Aiit then , have fun Bugsigdb-ing:sweat_smile:according to@Svetlana Ugarcina Perovic

Esther Afuape (05:07:51) (in thread): > Hi@Levi Waldronmay I get the reviewer permissions too?:pray:

Chiagoziem David (05:09:32) (in thread): > me also sire:clap:

Odigiri Great Alume (05:34:20) (in thread): > @Levi Waldronplease could you grant me the reviewers permission as I need to add comments to some taxa I previously recorded as sp. Instead of spp.

Odigiri Great Alume (07:02:48): > Good day everyone > Good day@C. Mirzayi (please do not tag this account)@Levi WaldronI’d love to ask please. > > > For instance: how do I record Rastolnia_1, Rastolnia_2 and Rastolnia_3 in one signature? > As******Ralstonia spp******then add a comment stating the different Ralstonias in the paper (that is Ralstonia 1,2 and 3)? > > Also in the case of Peptostreptococcaceae_[XI][G-5], Peptostreptococcaceae_[XI][G-4] andPeptostreptococcaceae_[XI][G-9], > Do I record simply as******Peptostreptococcaceae spp ****then add comments ? > > Lastly, what if Gracilibacteria_(GN02)(G-2) appears only once in a signature. Should I record as simply******Gracilibacteria******without the subfix (GN02)(G-2) or should I record as******Gracilibacteria sp. ****to show that the species is not identified? > Or should I record it as Uncultured gracilibacteria (Candidatus gracilibacteria)? > By the way when I searched Gracilibacteria GN02 on NCBI browser. I got the candidatus gracilibacteria and below it stated that it synonym is GN02. > > Thank you everyone in anticipation for your help

Chioma Onyido (07:07:45) (in thread): > @Odigiri Great AlumeLet mepassbythe first 2 questions for our mentors.:face_with_peeking_eye:For the last part, when I don’t get the taxid for a bacteria on NCBI, I usually curate as seen in the paper,withthe subfix. > > But since the taxid forCandidatus gracillibacteria GN02, is available as the synonym on NCBI, I would curate that. > becauseCandidatusname is usually assigned to a bacteria or phylum that has not been fully characterized or classified or prob. difficult to culture… > So I would curate if the taxid is available

Aleru Divine (07:17:42) (in thread): > :sweat_smile:

Chioma Onyido (07:33:03) (in thread): > Curious about the first 2 especially because I encountered the same.:slightly_frowning_face:

Peace Sandy (07:33:25) (in thread): > Have you tried using the NCBI taxonomy platform@Odigiri Great Alume

Peace Sandy (07:36:16) (in thread): > They is something@C. Mirzayi (please do not tag this account)said about uncultured bacteria?I’mtrying to find ifit’srelated

Chioma Onyido (07:59:38) (in thread): > Please look at this… > Why am I interpreting this as different strains (1,2,3,4,5,6) in the Ralstonia genus?:thinking_face:If this is so, can this be the solution to the question on Ralstonia? - File (JPEG): IMG_5948

Peace Sandy (08:01:32) (in thread): > Shouldn’tit be entered since his main focus is Ralstonia ?@Chioma Onyido

Chioma Onyido (08:03:39) (in thread): > Yes my point exactly.

Peace Sandy (08:05:22) (in thread): > I think so

Odigiri Great Alume (08:14:04) (in thread): > @Chioma Onyidothank you. I did record as Candidatus gracilibacteria too. Thanks for helping off the scene too.:blush:

Odigiri Great Alume (08:15:56) (in thread): > @Peace SandyI did. But did not get all the ID I was seeking for

Peace Sandy (08:23:48) (in thread): > Oh…how about now@Odigiri Great Alume

Odigiri Great Alume (08:30:41) (in thread): > @Peace SandyI will wait for the mentors to clarify things out. Meanwhile, from@Esther Afuapeand@Chioma Onyidobehind the scene help. I understood quite a lot now and have effected correction where I think is right. However I just needed to collaborate the point of view of our mentors. Quality is king over quantity:joy:. > > Also thank you for always trying to help you are amazing dear.:blush:

Peace Sandy (08:31:10) (in thread): > True:sweat_smile:

Esther Afuape (08:32:52) (in thread): > Yes, I also think it’s different strains of the species forRalstoniain that screenshot@Chioma Onyidoshared.Gracillibacteriaseems sorted since the suffix appeared as a synonym.

Esther Afuape (08:36:55): > Hello:wave:@Levi WaldronMay I have reviewers permission so that I can comment on a signature?

Odigiri Great Alume (08:38:41) (in thread): > @Esther Afuape@Chioma Onyido@Peace SandyI just remembered this Excerpt from the study now. > > First column is genus level > Second is specie > Third is strain - File (JPEG): Screenshot_20231107-143716.jpg

Chioma Onyido (08:39:43) (in thread): > Ohh niceee…Ralstonia is Perfectly sorted then!:+1:Peptostreptococcaceae left now…

Odigiri Great Alume (08:40:56) (in thread): > I guess I will enter Ralstonia sp ( the ID) then comment the 1,2,3 that were specifically mentioned. > > Thanks@Chioma Onyido

Peace Sandy (08:41:20) (in thread): > @Odigiri Great Alumejust use Ralstonia sp

Chioma Onyido (08:41:35) (in thread): > @Odigiri Great AlumeWith the excerpt you just shared, Why not curate the species as listed in the red highlight? I thinkthat’smore accurate:thinking_face:

Peace Sandy (08:45:49) (in thread): > I think@Chioma Onyidois right, let me share a screenshot

Chioma Onyido (08:45:59) (in thread): > Ralstonia mannitolilytica105219Ralstonia pseudosolanacearum1310165Ralstonia syzygii28097@Odigiri Great Alume - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Peace Sandy (08:46:38) (in thread): > Try using1310165

Odigiri Great Alume (08:46:54) (in thread): > @Chioma OnyidoI did curate as******Ralstonia******* ****syzygii**** *but@C. Mirzayi (please do not tag this account)corrected me saying this….. > > “Taxa should be curated at the correct taxonomic level. Every genus in this curation has a species with it. Those species should not be curated–only the genus. For instance: Streptococcus should just be curated as that and not as Streptococcus mitis.”:thinking_face:

Odigiri Great Alume (08:48:26) (in thread): > @Peace Sandyokay, does 1310165 represent all the Ralstonia 123?:thinking_face:

Peace Sandy (08:48:35) (in thread): > Yes

Peace Sandy (08:48:45) (in thread): > Hold on, let me share a screenshot

Esther Afuape (08:48:54) (in thread): > What’sthe heading of that second column in the screenshot you shared?

Odigiri Great Alume (08:49:16) (in thread): > @Levi WaldronI will need the permit too sir.:blush:

Odigiri Great Alume (08:50:06) (in thread): > @Esther Afuapespecies

Chioma Onyido (08:50:48) (in thread): > Oh my goodness! Just when we thought we were close to the solution…:slightly_frowning_face:

Peace Sandy (08:53:00) (in thread): > I think you should use1310165 - File (PNG): ncb1

Peace Sandy (08:54:12) (in thread): > When I clicked on this taxa, I saw this - File (PNG): ncb2

Peace Sandy (08:54:32) (in thread): > Check the first line to see the strain,it’son the excerpt you shared

Chioma Onyido (08:54:37) (in thread): > But using 1310165 accoutns for just one Ralstonia which is Ralstonia 02@Peace Sandy

Peace Sandy (08:55:02) (in thread): > Check for it on the NCBI page

Chioma Onyido (08:55:35) (in thread): > Where?

Peace Sandy (08:55:59) (in thread): > Let me send the link

Peace Sandy (08:56:44) (in thread): > Check this out@Chioma Onyidohttps://www.ncbi.nlm.nih.gov/datasets/taxonomy/tree/?taxon=1310165 - Attachment (NCBI): Taxonomy Browser > An interactive browser for exploring taxonomic classifications and associated NCBI data

Esther Afuape (08:56:53) (in thread): > Ididn’tget the information<@UBNSEMS3S>was trying to pass across in the correction. The answer lies in that

Peace Sandy (08:57:20) (in thread): > Where@Esther Afuape

Odigiri Great Alume (08:57:42) (in thread): > Uhhhhm@Peace SandyI just tried it and it’s for Ralstonia 2. However@C. Mirzayi (please do not tag this account)said I cant have both the specific and generic names in the curation.

Peace Sandy (08:57:54) (in thread): > Hmmmm

Peace Sandy (08:58:17) (in thread): > I’mtrying to check something

Odigiri Great Alume (08:58:18) (in thread): > Okay@Esther Afuapeplease shoot I’m curious:blush:

Peace Sandy (09:00:26) (in thread): > If you click on the Ralstonia pseudosolancearum , you would see 97 genomes > The taxa in the excerpt you shared is there, the one with RS 476 (strain)That’swhy I thought you can use it for all

Chioma Onyido (09:00:32) (in thread): > I stilldon’tsee where from the link@Peace Sandycan you highlight it? > > I think it should be curated asRalstonia sp. 1-6, with ID 1221567, which would account for the 3 species mentioned in the paper. > This is going by the corrections of<@UBNSEMS3S>not to curate all species of one genus individually. - File (JPEG): IMG_5948

Peace Sandy (09:01:11) (in thread): > You might be right@Chioma OnyidoI just shared mine as a solution

Peace Sandy (09:01:28) (in thread): > Click on the link I shared above

Esther Afuape (09:02:43) (in thread): > No. It only represents RS 476 and not the other ones

Peace Sandy (09:03:11) (in thread): > My emphasis was on RS 476

Peace Sandy (09:04:21) (in thread): > If Ralstonia sp. 1-6 represents all, thenit’sbest practice to use it@Odigiri Great Alume

Odigiri Great Alume (09:06:25) (in thread): > Thanks to everyone for their insightful insight:blush:You guys are the best. You make this worth it. > > Now I wait for our mentors.

Esther Afuape (09:42:37): > Hello:wave:@Levi Waldron<@UBNSEMS3S>while trying to solve a curation issue alongside@Odigiri Great Alumehe mentioned that he was corrected to not curate species of the same genus individually. If the goal of curation is to capture taxa as specific as possible, why is that incorrect?https://community-bioc.slack.com/archives/C04RATV9VCY/p1699364814420979?thread_ts=1699358568.220309&channel=C04RATV9VCY&message_ts=1699364814.420979 - Attachment: Attachment > @Chioma Onyido I did curate as Ralstonia syzygii but @C. Mirzayi (please do not tag this account) corrected me saying this….. > > “Taxa should be curated at the correct taxonomic level. Every genus in this curation has a species with it. Those species should not be curated–only the genus. For instance: Streptococcus should just be curated as that and not as Streptococcus mitis.” > > :thinking_face:

Chioma Onyido (09:47:33) (in thread): > Really Curious about this too,@Esther AfuapeBecause I’ve curated individually in some of my previous curations:face_holding_back_tears:

Esther Afuape (09:47:58) (in thread): > I’mas guilty as charged too:sob:

Peace Sandy (10:21:23) (in thread): > Here for the response:sweat_smile:

Svetlana Ugarcina Perovic (11:09:35) (in thread): > You are ALL right: ” Taxa should be curated at the CORRECT taxonomic level…”

Svetlana Ugarcina Perovic (11:10:39) (in thread): > @Odigiri Great Alumeand<@UBNSEMS3S>discussed a specific study with probably particular taxonomic issue: “Every genus in THIS curation has a species with it.”

Peace Sandy (11:12:07) (in thread): > Wow…we learn everyday

Peace Sandy (11:12:23) (in thread): > Each discussion enlightens me

Svetlana Ugarcina Perovic (11:12:26) (in thread): > That’s BugSigDB-ing:wink:

Peace Sandy (11:12:40) (in thread): > True:sweat_smile:@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (11:14:24) (in thread): > I’ve been enjoying reading your discussions while seeing a true team work and learning from you - thank you!!

Esther Afuape (11:17:02) (in thread): > I think in the paper, the genera were stated and the species that appeared under them were equally stated.I’dhave thought to curate the species for the sake of accuracy?@Svetlana Ugarcina Perovic

Peace Sandy (11:18:59) (in thread): > Thank You too@Svetlana Ugarcina Perovic

Chioma Onyido (11:19:23) (in thread): > I’vealso learnt so much on this platform, always curious about new finds/ questions especially.@Svetlana Ugarcina Perovic:smile:

Odigiri Great Alume (11:21:26) (in thread): > @Svetlana Ugarcina Perovicvery true. But then I faced a challenge with some taxa. Example is the Ralstonia 1,2 and 3. > > Now I recorded Ralstonia 3 as******Ralstonia sazygii ****(generic and specific name) > Did same for every other Ralstonias. And other taxas such as*****Streptococcus mitis. > *****What I think@C. Mirzayi (please do not tag this account)meant from her statement is to curate only the genera name for each other taxa instead of both (and I lost mark for it:cry::sob:). However, I have made corrections. > > But the challenge is with taxas like Ralstonia 1,2&3. How do I curate them. > > As Ralstonia sp. Or Ralstonia spp. Then make comments on the specific Species recorded in the study.
> > That’s where our concern lies@Svetlana Ugarcina PerovicAgain it’s beautiful working with you too. > Grateful:smiling_face_with_tear:

Svetlana Ugarcina Perovic (11:23:29) (in thread): > They are all the Ralstonia genus. In this case that’s the correct taxonomic level where you can be confident.

Odigiri Great Alume (11:25:20) (in thread): > @Svetlana Ugarcina Perovicplease could you explain:cry:Do you mean Ralstonia spp or sp.

Chioma Onyido (11:27:03) (in thread): > Thing is Ralstonia spp. is not on the NCBI taxon. browser.:thinking_face:

Svetlana Ugarcina Perovic (11:27:28) (in thread): > Exactly@Chioma Onyido

Peace Sandy (11:28:06) (in thread): > Hmmmm…in this case, what should be done

Chioma Onyido (11:28:26) (in thread): > In this case, can this suffice?@Svetlana Ugarcina Perovic - File (JPEG): IMG_5948

Esther Afuape (11:29:40) (in thread): > Oh that makes sense now@Chioma OnyidoIf Ralstonia spp isn’t present but each of the species are present on NCBI!:sweat_smile:

Svetlana Ugarcina Perovic (11:30:51) (in thread): > I don’t think so@Chioma OnyidoI would stick to the confident genus level in this case.

Chioma Onyido (11:31:26) (in thread): > Which is Ralstonia sp. right?:thinking_face:@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (11:31:35) (in thread): > https://bugsigdb.org/Special:RunQuery/Taxon_filter?pfRunQueryFormName=Taxon+filter&[…]%5D=&Taxon%5BBody+site%5D=&Taxon%5BCondition%5D=&pf_free_text= - Attachment (BugSigDB): Special:RunQuery/Taxon filter

Svetlana Ugarcina Perovic (11:32:25) (in thread): > Correct.

Peace Sandy (11:33:28) (in thread): > Wow…glad this has been sorted, Thank you@Svetlana Ugarcina Perovic

Peace Sandy (11:34:09) (in thread): > Saving this link for future reference

Chioma Onyido (11:34:17) (in thread): > Finally! > Thank you so much.@Odigiri Great Alumecome and see

Esther Afuape (11:35:41) (in thread): > Thank you:hugging_face:@Svetlana Ugarcina Perovic

Esther Afuape (15:34:42) (in thread): > @Levi Waldron:face_holding_back_tears::pray:

Joan C. Chukwuemeka (17:41:34): > I noticed that this completed studyhttps://bugsigdb.org/Study_794is still listed underIncomplete pages (marked as incomplete by curator)What could be the cause?<@U1LCB8WEA><@UBNSEMS3S> - Attachment (BugSigDB): Gut microbiota display alternative profiles in patients with early-onset colorectal cancer - BugSigDB > BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) is increasing worldwide.This study aimed to explore whether there is an alternative gut microbiota profile in patients with early-onset colorectal cancer. - Attachment (BugSigDB): Special:Ask/-5B-5BState::Incomplete-5D-5D/mainlabel=/offset=0/format=ol/searchlabel=Incomplete-20pages-20(marked-20as-20incomplete-20by-20curator)

U1LCB8WEA (17:43:30) (in thread): > It takes hours to update-how long has it been completed?

Joan C. Chukwuemeka (17:50:34) (in thread): > I can’t say…. I wanted to work on it when i noticed that. > > However, looking further, I see that the one listed on the incomplete page is experiment 4 (https://bugsigdb.org/Study_794/Experiment_4/Signature_1) which is actually incomplete, however when the primary pagehttps://bugsigdb.org/Study_794is accessed it has only 3 complete experiments:thinking_face: - Attachment (BugSigDB): Study 794/Experiment 4/Signature 1 - Attachment (BugSigDB): Gut microbiota display alternative profiles in patients with early-onset colorectal cancer - BugSigDB > BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) is increasing worldwide.This study aimed to explore whether there is an alternative gut microbiota profile in patients with early-onset colorectal cancer.

Joan C. Chukwuemeka (18:03:19): > <@U1LCB8WEA>here is a video view of it. - File (MPEG 4 Video): bugsigdb study_794.mp4

Chiagoziem David (22:30:24): > Hello, whilst going through the following article, i came across some holdbacks that i’d want us to look at.<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovichttps://pubmed.ncbi.nlm.nih.gov/32804973/ - Attachment (PubMed): Learning machine approach reveals microbial signatures of diet and sex in dog - PubMed > The characterization of the microbial population of many niches of the organism, as the gastrointestinal tract, is now possible thanks to the use of high-throughput DNA sequencing technique. Several studies in the companion animals field already investigated faecal microbiome in healthy or affected …

Chiagoziem David (22:33:36): > it seems two factors were taken to consideration here. diet and sex . and group division was implemented for the two factors. i.e “S6 Table.Comparison of the mean relative abundances (RA) and coefficients of the linear discriminant analysis (LDA) using genera as input variables and considering 4 sex categories (LDA1) or 3 sex categories (LDA2). For this latter, FC and MC sex were collapsed together.” , and “S3 Table.Comparison of the mean relative abundances (RA) and coefficients of the linear discriminant analysis (LDA) using genera as input variables and considering 4 diet categories (LDA1) or 3 diet categories (LDA2). For this latter, B and H diets were collapsed together.”

Tolulope Ogunleye (22:59:50) (in thread): > This is really enlightening,I must have curated at species level in some of my previous curations:grimacing:

Chiagoziem David (23:09:20): > i intend to have different experiments done individually for both the sex and diet factors… but i want the group to give their thoughts first

2023-11-08

Peace Sandy (01:33:50) (in thread): > I went through the paper and from this excerpt I think it’s Sex and Diet - File (JPEG): IMG_6310

Mildred Anashie (01:38:46) (in thread): > Yes you are right@Chiagoziem DavidThe dogs were grouped into sex, I think using F,FC,M,MC) and they were observations for each group > > While diet was something like H,K,B and something else:woman-facepalming:Recording the different experiments wouldn’t be a wrong move in my opinion

Odigiri Great Alume (02:24:08) (in thread): > @Levi Waldron:pray::pray:

Chiagoziem David (03:52:31) (in thread): > alrighty

U1LCB8WEA (08:31:35) (in thread): > It sounds like there are at least two experiments, for diet and sex. If they contrasted multiple diet categories or sex categories, it might be more than 2 experiments - one for each contrast for which they report a signature of differential abundance.

U1LCB8WEA (08:32:36) (in thread): > So it sounds like the Incomplete pages list is correct, if it lists only an incomplete experiment?

Chiagoziem David (10:24:39) (in thread): > Yeah<@U1LCB8WEA>, it seems they contrasted for multiple sex and diet categories too.. > > Thanks for your response

Chiagoziem David (14:52:53): > Here is too quiet, how’s everyone doing:sun_with_face::sun_with_face::sunny::sunny::raised_hands::raised_hands::raised_hands::raised_hands:

Joan C. Chukwuemeka (15:18:48) (in thread): > Yes<@U1LCB8WEA>, however, I find it strange that when the main study link is accessed, there’s no experiment 4. Is that to be expected?https://community-bioc.slack.com/archives/C04RATV9VCY/p1699398199392759 - Attachment: Attachment > @U1LCB8WEA here is a video view of it.

Peace Sandy (15:30:23) (in thread): > Doing great:blush:And you ?

Chiagoziem David (15:33:58) (in thread): > Great:smiley::smile_cat:

2023-11-09

Aleru Divine (03:01:23) (in thread): > Really good David, how are you?

Chiagoziem David (03:50:55) (in thread): > Exceptional:grin:

Mildred Anashie (04:16:13): > Hello everyone, hope we are all doing great:blush:I’mcurating this articlehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9852993/And it says they used “Shallow shotgun metagenonic sequencing” and we have “Whole metagenomic sequencing” on BugSigDB which I realised are not the same thing even though I think shallow is just stating the depth (in my opinion). > Can I use WMS as the sequencing type? > > Also the samples used are Blood and Fecal samples (I think for different experiments) > How do I curate the body site?<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicI need help figuring this out - Attachment (PubMed Central (PMC)): Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes > South Asian refugees experience a high risk of obesity and diabetes yet are often underrepresented in studies on chronic diseases and their risk factors. The gut microbiota and gut permeability, as assessed through circulating lipopolysaccharide binding …

Svetlana Ugarcina Perovic (05:11:27) (in thread): > Shallow shotgun metagenomic sequencing is a type of whole metagenomic sequencing. > > “An alternative to both 16S amplicon and deep shotgun metagenomic sequencing is shallow shotgun metagenomic sequencing (SS)15.SS, defined here by depths between 2 and 5 million reads per sample, shows high concordance with DS in both taxonomic and functional gene content at a cost comparable to 16S sequencing15. Similar to DS, SS can resolve taxa to the species or even strain levels, can provide directly observed gene profiles, and has been leveraged to perform robust taxonomic and functional characterization of the microbiome in a cohort with dense longitudinal sampling16. However, the reproducibility of SS has not been explicitly compared to 16S.” See more here:https://www.nature.com/articles/s41598-023-33489-1

Svetlana Ugarcina Perovic (05:12:26) (in thread): > As for “Blood and Fecal samples (I think for different experiments)”, yes you are right, you will select in each experiment the appropriate body site.

Odigiri Great Alume (05:14:25): > Good morning everyone@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi WaldronPlease I’m working on this study and I have been able to identify a series of experiments from figure 1 and 3. I have curated for figure one Never smokers vs Current smokers. > > For figure 3: I think they compared never smokers with former smokers (0-1, 2-3,4-5,6-10, 11-62 years) after the quit smoking. > > They used heatmaps to interpret the figure, from figure 1: blue mean decrease in taxa, red means increase in taxa while yellow means there was no statistical sig diff. > > This is what I think:thinking_face:, however i would love to confirm if this is curatable and if I’m right to compare NS to each of the categories of the FS by years. > > Your contribution is appreciatedhttps://www.nature.com/articles/s41598-023-42474-7And please do help me suggest the study design used for this study too.:blush:I am thinking it’s crossesctional study design looking at the study (especially fig 1) but then looking at fig3 it’s looking like a longitudinal study:sweat_smile: - Attachment (Nature): Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population > Scientific Reports - Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population - File (JPEG): IMG_20231109_111309.jpg

Mildred Anashie (05:17:23) (in thread): > Okay….WMS it is:blush:

Chioma Onyido (05:30:29) (in thread): > Figure 3 looks curatable and looks like a longitudinal study design, to me too. Butlet’shear from the mentors.

Chioma Onyido (05:33:01) (in thread): > But assuming the mentors confirm that figure 3 should be curated, that means you’ve a case of 2 study designs for one paper- cross-sectional (fig 1) and longitudinal (fig 3), > > hmmm,<@U1LCB8WEA>once mentioned that there’s a trick around it, here for it!:sweat_smile::eyes:

Chioma Onyido (08:59:54): > Guess there’s no weekly office hour holding today?:eyes:<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Peace Sandy (09:01:02) (in thread): > I’ve been wondering too

Tolulope Ogunleye (09:02:29) (in thread): > I was also about to ask

Peace Sandy (09:10:59): > I tried joining with the link that is usually used for weekly sync and it’s saying host is not in the meeting yet. > > Please notify incase the meeting starts.

UBNSEMS3S (09:39:13): > Hi all apologies but the US just had daylight savings time so the meeting starts in 20 minutes.

UBNSEMS3S (09:39:37): > Apologies for the late notice but we will be having our weekly team meeting at 10 AM EST today (in 21 minutes).https://us02web.zoom.us/j/2737200499

Chioma Onyido (09:40:17) (in thread): > Ohh great. Thanks for the update.

Joan C. Chukwuemeka (09:40:36): > Alright… Thanks:blush:

Chioma Onyido (09:40:36) (in thread): > @Peace Sandy

UBNSEMS3S (09:41:26): > Learning today that North America and Europe are the weird ones who do daylight savings:sweat_smile: - File (PNG): image.png

Chioma Onyido (09:42:27) (in thread): > Woah Interesting.:sweat_smile:

Joan C. Chukwuemeka (09:44:00) (in thread): > Really Interesting aspects of geography:nerd_face:

Chioma Onyido (09:44:07) (in thread): > I see most parts of Africa (Nigeria inclusive) all greyed out.:sweat_smile:

Esther Afuape (09:55:07) (in thread): > Really interesting:sweat_smile:

U02CNMR4YEA (09:59:06) (in thread): > Some would say that’s the least of what makes us “the weird ones”:joy:

Peace Sandy (10:01:02): > Please join in Everyone, > > We just Startedhttps://us02web.zoom.us/j/2737200499

Peace Sandy (10:01:25) (in thread): > Wow…this makes sense

Peace Sandy (10:02:09) (in thread): > Thank You@Chioma Onyido

Peace Sandy (10:02:16) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Joan C. Chukwuemeka (10:09:41) (in thread): > It’s 10:03 am NYC time:blush:

Aleru Divine (10:10:08): > Is anyone able to join? I cant seem to join

Joan C. Chukwuemeka (10:13:32) (in thread): > Waiting to be let in

Joan C. Chukwuemeka (10:20:13): > Hoping the meeting is recorded… Still unable to join

Mildred Anashie (11:01:30) (in thread): > Hoping on this too:pray:

Chiagoziem David (11:52:09): > Couldn’t join the meeting today, hope it was recorded

Nana (13:19:36): > was not able to join, please if the meeting was recorded ?

UBNSEMS3S (13:48:57): > Meeting recording. I remembered this time. - File (MPEG 4 Video): video1010980453.mp4

Chiagoziem David (14:19:32) (in thread): > You did:joy::joy::joy::joy::joy:

Chiagoziem David (14:20:12) (in thread): > Thank you very much:joy::joy::joy:

Mildred Anashie (14:58:14) (in thread): > Thankyou:blush:

Chiagoziem David (17:18:08): > https://medium.com/@davidprincewill20/outreachy-was-the-validation-i-needed-my-bugsigdb-ing-experience-at-bioconductor-f761453257a1 - Attachment (Medium): Outreachy Was The Validation I Needed: My BugSigDB-ing experience at Bioconductor > For many months, I toyed with the idea of applying to the Outreachy internship program. My worry was probably the same as anyone else’s…

Chiagoziem David (17:18:27): > a quick read on the journey so far

Peace Sandy (17:29:23) (in thread): > Nice one:rocket:

Chiagoziem David (17:41:51) (in thread): > try to sleep@Peace Sandy:sweat_smile:

Chiagoziem David (17:43:20) (in thread): > @Peace Sandy,read that the Nigerian way:sweat_smile:

Peace Sandy (17:54:37) (in thread): > I get:sweat_smile::joy:@Chiagoziem David

2023-11-10

Svetlana Ugarcina Perovic (02:08:24) (in thread): > THIS made my day! Thank you@Chiagoziem DavidHappy Friday, ALL! :bouquet:https://twitter.com/svetlana_up/status/1722873283920466022

Peace Sandy (02:10:20) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:sparkles::confetti_ball:

Chiagoziem David (04:29:11) (in thread): > Thank you very much@Svetlana Ugarcina Perovic, happy Friday to you too:blush::tada:

Odigiri Great Alume (04:50:05) (in thread): > Hmmmmmmmm@C. Mirzayi (please do not tag this account)@Levi Waldron@Chioma Onyido@Esther AfuapeI have confusions as to what study design was used in this study. Look here they stated they used Crossectional study design.:thinking_face:And also Thier information (data) was collected by questionnaire:thinking_face: - File (JPEG): IMG_20231110_104744.jpg

Mildred Anashie (06:10:55) (in thread): > Happy Friday to you@Svetlana Ugarcina Perovic

Mildred Anashie (08:20:15) (in thread): > I’mnot sure what the study design is and Ihaven’tgone through the whole article but I thinkit’sa cross sectional study design > > The information from figure three looks to me like it was a section of the questionnaire and was analyzed based on the number of years the former smokers had stopped smoking > > For it to be longitudinal,they’llhave to collect data/samples at different points (maybe at the beginning and at the end) > > Did you come across anything like that?

Chioma Onyido (08:28:13) (in thread): > That is true@Mildred AnashieIdidn’tread the method sections and just assumed from the results that they collected data from different time points. > > Which is not the case here, since the data was gotten from a section of the questionnaire. > That means the study design should be the primary design reported in the paper which is cross-sectional.:raised_hands:

Mildred Anashie (08:37:52) (in thread): > Okay@Chioma OnyidoI’ll assume@Odigiri Great Alumehas gone through the whole article > If they stated or insinuated (might not be clearly stated) that they observed for changes over time among the former smokers…Then you both were right that the study has two study designs (which will be an interesting one:blush:) but if not, thenit’s across sectional study in my opinion > > But we could still wait for the mentors to get their opinions<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovicwe’dappreciate your insights on this:pray:

Odigiri Great Alume (09:02:00) (in thread): > Thank you both@Chioma Onyidoand@Mildred AnashieI’d go with CSS. as it’s the primary study design. However there’s nothing else that suggests a longitudinal study or case control. I mean it’s been explicitly stated that’s it’s CSS.

UBNSEMS3S (10:01:23) (in thread): > Amazing! Thank you for writing this.

Esther Afuape (14:31:15) (in thread): > Aww this was a good read, David!

Chioma Onyido (16:11:45): > Happy weekend<!here>:wave:<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina PerovicWhile reviewingbugsigdb.org/Study_809, I noticed some double entries in some of the signatures: > Expt. 3, Sig. 2 (DR vs HC) and Expt.1 Sig 2 (DM vs HC) are the same > Expt. 2 Sig. 1 (DM vs HC) and Expt. 2 Sig 2 (DR vs DM) are the same > Expt. 2 Sig. 1 (DR vs HC) and Expt. 3 Sig 1 (DR vs DM) are the same > > I think this happenedbecause of the way the curator interpreted the results. > The authors reported unique abundant taxa for HC, DR and DM, (see attached image) > > I saw somewhere<@UBNSEMS3S>said that results shouldn’t be double-entered.https://community-bioc.slack.com/archives/C04RATV9VCY/p1698164308650169My suggestion: to avoid double entries, can this be curated in a different way instead? Say, to reportonlyincreased signatures for all experiments. I.e. > DR vs HC and DM > DM vs HC and DR > that means there’ll only be one signature (increased) for each of the experiments. - Attachment: Attachment > Are compared groups always relative? For example, if the enriched taxa in group 1 were mentioned but the ones that decreased weren’t, do I only create a single signature for the enriched ones? or do I create a second signature for the group 1 using the taxa that were enriched in group 0 as decreased for group 1? > I hope I’ve not confused everyone :sweat_smile: > @UBNSEMS3S @Levi Waldron @Svetlana Ugarcina Perovic - File (JPEG): IMG_6026

Chioma Onyido (16:14:36) (in thread): > Another issue: The results from random forest analysis which identified discriminating gut microbial family biomarkerafter contrasting the groups with each other. I.e.HC-DM, HC-DR and DM-DR(see attached supp file)were not curated.**** > ****I’mnot sure but I think we curate Random forest results in BugSigDB?:thinking_face: - File (JPEG): IMG_6027

U02CNMR4YEA (17:42:04): > Happy Friday! I am curating this paperhttps://pubmed.ncbi.nlm.nih.gov/37026303/and am not quite clear what they did and whether it’s curatable. The only tables that appear to possibly have data that can be curated are Tables S2a and S2b. But I don’t know what a BH_corrected P-value represents and whether it’s truly worth capturing. Thank you in advance for any help:grinning:. [I actually just googled it an got the response that this represents a Benjamin-Hochberg correction. I am still not sure if that makes the value less reliable, however.] - Attachment (PubMed): Tear film microbiome in Sjogren’s and non-Sjogren’s aqueous deficiency dry eye - PubMed > The results of the study indicate significant changes in the phyla and genera in SS and NSS compared to healthy. Both discriminative analysis and network analysis indicated a possible association of predominant pro-inflammatory bacteria with SS and NSS.

Esther Afuape (19:19:01) (in thread): > I agree with you on not double entering results! Glad you found that thread where<@UBNSEMS3S>helped me sort out the same issue. All signatures are curated relative to group 0. Therefore, abundances in group 0 do not need to be curated as decreases in the compared groups.

U1LCB8WEA (19:26:14) (in thread): > I agree too with your solution@Chioma Onyido- go ahead and fix and mark reviewed. I think that the problems with importance scores from random forest are that they do not give an indication of direction of increase, and their relationship with the predicted outcome can be complex and non-linear.

Esther Afuape (19:33:08) (in thread): > I often see them used alongside other statistical tests,and not as a standalone test most times.

2023-11-11

Chioma Onyido (00:45:42) (in thread): > Thank you so much<@U1LCB8WEA>and@Esther Afuape:blush::pray:

Chioma Onyido (01:26:26) (in thread): > Hi<@U02CNMR4YEA>:wave:I read the through the paper and found that there are additional curatable options. > > Figure 3a and b (LogFC values for NSS vs HC and SS vs HC) > Supp. Table S3 (logFC values for each NSS vs HC and SS vs HC) and > Supp. Table S2C (NSS vs HC). - File (JPEG): IMG_6032 - File (JPEG): IMG_6033 - File (JPEG): IMG_6034

Chioma Onyido (01:30:37) (in thread): > Also, Idon’tsee anywhere within text where the threshold of BHT-corrected p value was explicitly stated buthere’san excerpt (attached screenshot) of your supp. Tables S2A-C with p < 0.01 chosen as the significance. Hmmm:thinking_face: - File (JPEG): IMG_6035

Mildred Anashie (02:12:38) (in thread): > Hi<@U02CNMR4YEA>To me, the Benjamini-Hochberg corrected P-value is an adjusted P-Value and it’s done during Multiple hypotheses testing for controlling FDR…. It makes sure we don’t mistakenly think there’s a significant result when there isn’t. It helps us trust our findings more > > And I think it’s also helpful in filling the MHT correction field on BugSigDB too:blush:So it doesn’t make the result less reliable, I’ll like corrections if I’m wrong<@U1LCB8WEA><@UBNSEMS3S>:pray:

Chiagoziem David (02:18:53) (in thread): > :grinning::+1:@Chioma Onyido

Mildred Anashie (02:24:52) (in thread): > @Chioma Onyidothe BH corrected p value was mentioned in the paper from Table S2A all through Table S2C > However I don’t know how curatable those tables are yet

Mildred Anashie (02:26:14) (in thread): > Oh sorry, I get you now > > You said within textThat’strue

Chioma Onyido (02:26:31) (in thread): > @Mildred AnashieI know the values were listed, I’m talking about the threshold. Do you get? > But I see them mention p < 0.01 for Tables S2 A-C

Mildred Anashie (02:44:40) (in thread): > Yea > > I get you@Chioma OnyidoI’ve seen that too > > That could be the threshold used since it wasn’t clearly mentioned anywhere else

Chioma Onyido (02:48:05) (in thread): > Yeahthat’swhatI’mthinking too.

Karen254. Kingecha (04:23:34) (in thread): > Good read

Chioma Onyido (05:33:44) (in thread): > I can’t seem to delete it, please help delete EXPT. 1Sig 2and Expt. 2Sig 1 and 2 :pray:**** > ****<@U1LCB8WEA>**** ****<@UBNSEMS3S>**** ****

Peace Sandy (07:01:27): > What data transformation should be used for statistical tests such as ANOVA, t-Test, linear regression,PERMANOVA, wald test, ANOSIM, random forest analysis.@Levi Waldron@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic

Esther Afuape (07:14:49) (in thread): > @Peace Sandysome of them are mentioned here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697145085673689?thread_ts=1697141457.022309&channel=C04RATV9VCY&message_ts=1697145085.673689 - Attachment: Attachment > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio -> Rare. ANCOM > > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

Peace Sandy (07:23:02) (in thread): > Hi@Esther AfuapeThank you.The ones I mentioned above are not there, I’ve seen the response.

Esther Afuape (07:36:55) (in thread): > Oh okay > Linear regression uses raw counts and ANOVA uses raw counts. > If I figure out the rest before the mentors reply, I’ll let you know.

Peace Sandy (07:45:27) (in thread): > Okay > Thank You@Esther Afuape

Joan C. Chukwuemeka (07:58:06) (in thread): > @Peace SandyT-test usually Uses Relative abundance

Esther Afuape (08:08:47) (in thread): > @Peace SandyI think linear models often use raw counts but they can also use relative abundances. Please confirm the datathey’reworking with in the papers. I did a curation once and relative abundances were used in the linear regression test carried out so I used that.

Peace Sandy (09:07:55) (in thread): > Wow…okay > Thank you so much@Esther Afuapeand@Joan C. Chukwuemeka:heart:

Peace Sandy (09:08:16) (in thread): > This was really helpful

U02CNMR4YEA (14:27:28) (in thread): > Thank you both! I appreciate your thoughtful review and suggestions. I will curate 3a and 3b. Much appreciation!

2023-11-12

Chiagoziem David (04:01:22): > Happy Sunday and happy new week guys:tada::tada:. Let’s go:muscle::muscle::muscle:

Peace Sandy (05:30:52) (in thread): > Happy Sunday:tada:

Sinmi Adesanya (05:46:12) (in thread): > Happy Sunday!

U03L1PX3D52 (11:39:07): > Hi everyone. I have tried to run this code with several different inputs within the command but I get the same error every time. Can anyone help? > > > dat <- bugsigdbr::importBugSigDB(version = 'devel', cache = FALSE) > Error in `collect()`: > ! Failed to collect lazy table. > Caused by error in `db_collect()`: > ! Arguments in `...` must be used. > ✖ Problematic argument: > • ..1 = Inf > ℹ Did you misspell an argument name? > Backtrace: > 1. bugsigdbr::importBugSigDB(version = "devel", cache = FALSE) > 11. dbplyr:::collect.tbl_sql(., Inf) > 16. dbplyr::db_collect(x$src$con, sql, n = n, warn_incomplete = warn_incomplete, ...) >

U1LCB8WEA (11:51:16) (in thread): > I couldn’t be sure about which transformation was used with these tests, but Metaphlan (and maybe other shotgun taxonomic profilers) provide relative abundances by default. An additional centered log ratio or Arcsine square-root transformation could be added to this for any of these tests, and also the ones mentioned by Chloe, but the methods would say so if they did.

U1LCB8WEA (11:52:54) (in thread): > Linear regression and ANOVA should not use raw counts (since you have to somehow account for differences in total sequencing depth, and these models do not inherently do so), but other count-based linear models do.

U1LCB8WEA (11:55:40) (in thread): > Great analysis, I think you’ve got it!

Esther Afuape (11:55:43) (in thread): > Oh wow > Could you correct this list please?@Levi WaldronANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance

U1LCB8WEA (11:57:22) (in thread): > That looks right, but any of those listed as relative abundance could also have an additional transformation applied:sweat_smile:

Esther Afuape (11:59:41) (in thread): > Ididn’tthink you could have more than one transformation for one test. How do you tell? I oftencan’ttell except relative abundanceisexplicitly mentioned in the paper

U1LCB8WEA (12:03:10) (in thread): > You would only be able to tell if the methods said - but yes, centered log-ratio or arcsine square root can be applied to relative abundances.

U1LCB8WEA (12:06:41) (in thread): > This command is working on the current Bioconductor release 3.18, so it must be something about your installation. CheckBiocManager::version()andBiocManager::valid(). Is this on your laptop? > > > library(bugsigdbr) > > dat [===================================================================| 100% > > ](- bugsigdbr::importBugSigDB(version = 'devel', cache = FALSE) > ) sessionInfo() > R version 4.3.2 (2023-10-31) > Platform: aarch64-apple-darwin20 (64-bit) > Running under: macOS Sonoma 14.1.1 > > Matrix products: default > BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib > LAPACK: /Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0 > > locale: > [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8 > > time zone: America/New_York > tzcode source: internal > > attached base packages: > [1] stats graphics grDevices utils datasets methods base > > other attached packages: > [1] bugsigdbr_1.8.1 > > loaded via a namespace (and not attached): > [1] vctrs_0.6.4 httr_1.4.7 cli_3.6.1 > [4] knitr_1.45 rlang_1.1.2 xfun_0.41 > [7] DBI_1.1.3 BiocFileCache_2.10.1 purrr_1.0.2 > [10] generics_0.1.3 glue_1.6.2 bit_4.0.5 > [13] dbplyr_2.4.0 htmltools_0.5.7 fansi_1.0.5 > [16] rmarkdown_2.25 filelock_1.0.2 tibble_3.2.1 > [19] evaluate_0.23 fastmap_1.1.1 yaml_2.3.7 > [22] lifecycle_1.0.4 memoise_2.0.1 compiler_4.3.2 > [25] dplyr_1.1.3 RSQLite_2.3.3 blob_1.2.4 > [28] pkgconfig_2.0.3 rstudioapi_0.15.0 digest_0.6.33 > [31] R6_2.5.1 tidyselect_1.2.0 utf8_1.2.4 > [34] curl_5.1.0 pillar_1.9.0 magrittr_2.0.3 > [37] withr_2.5.2 tools_4.3.2 bit64_4.0.5 > [40] cachem_1.0.8 > > BiocManager::version() > [1] '3.18' >

Esther Afuape (12:09:16) (in thread): > Thank you

Chioma Onyido (12:10:24) (in thread): > A likkle help here pleasee<@U1LCB8WEA> - File (JPEG): IMG_6037

U1LCB8WEA (12:16:21) (in thread): > Done, did I get it right?

U03L1PX3D52 (12:18:26) (in thread): > It looks like 27 packages are out of date. > > > BiocManager::version() > [1] '3.18' > > BiocManager::valid() > 'getOption("repos")' replaces Bioconductor standard repositories, see > 'help("repositories", package = "BiocManager")' for details. > Replacement repositories: > CRAN:[https://cran.rstudio.com/](https://cran.rstudio.com/)* sessionInfo() > > R version 4.3.1 (2023-06-16 ucrt) > Platform: x86_64-w64-mingw32/x64 (64-bit) > Running under: Windows 11 x64 (build 22621) > > Matrix products: default > > > locale: > [1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8 > [3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C > [5] LC_TIME=English_United States.utf8 > > time zone: America/New_York > tzcode source: internal > > attached base packages: > [1] grid stats graphics grDevices utils datasets methods base > > other attached packages: > [1] BiocManager_1.30.22 ComplexHeatmap_2.16.0 dbplyr_2.4.0 > [4] bigrquery_1.4.2 kableExtra_1.3.4 lubridate_1.9.3 > [7] forcats_1.0.0 stringr_1.5.0 dplyr_1.1.2 > [10] purrr_1.0.1 readr_2.1.4 tidyr_1.3.0 > [13] tibble_3.2.1 ggplot2_3.4.4 tidyverse_2.0.0 > [16] BugSigDBStats_0.99.2 bugsigdbr_1.9.0 bugSigSimple_0.99.5 > [19] phyloseq_1.44.0 > > loaded via a namespace (and not attached): > [1] RColorBrewer_1.1-3 rstudioapi_0.15.0 jsonlite_1.8.7 > [4] shape_1.4.6 magrittr_2.0.3 rmarkdown_2.25 > [7] GlobalOptions_0.1.2 fs_1.6.3 zlibbioc_1.46.0 > [10] vctrs_0.6.3 multtest_2.56.0 memoise_2.0.1 > [13] RCurl_1.98-1.12 webshot_0.5.5 htmltools_0.5.5 > [16] table1_1.4.3 curl_5.1.0 Rhdf5lib_1.22.1 > [19] Formula_1.2-5 rhdf5_2.44.0 plyr_1.8.9 > [22] cachem_1.0.8 gt_0.10.0 igraph_1.5.1 > [25] lifecycle_1.0.4 iterators_1.0.14 pkgconfig_2.0.3 > [28] Matrix_1.6-2 R6_2.5.1 fastmap_1.1.1 > [31] GenomeInfoDbData_1.2.11 clue_0.3-65 digest_0.6.31 > [34] colorspace_2.1-0 AnnotationDbi_1.64.1 S4Vectors_0.38.1 > [37] RSQLite_2.3.1 vegan_2.6-4 filelock_1.0.2 > [40] gtsummary_1.7.2 fansi_1.0.4 timechange_0.2.0 > [43] httr_1.4.7 mgcv_1.8-42 compiler_4.3.1 > [46] remotes_2.4.2.1 gargle_1.5.2 bit64_4.0.5 > [49] withr_2.5.2 doParallel_1.0.17 DBI_1.1.3 > [52] MASS_7.3-60 rjson_0.2.21 biomformat_1.30.0 > [55] permute_0.9-7 tools_4.3.1 ape_5.7-1 > [58] safe_3.42.0 glue_1.6.2 nlme_3.1-162 > [61] rhdf5filters_1.12.1 cluster_2.1.4 reshape2_1.4.4 > [64] ade4_1.7-22 generics_0.1.3 gtable_0.3.4 > [67] tzdb_0.4.0 data.table_1.14.8 hms_1.1.3 > [70] xml2_1.3.4 utf8_1.2.3 XVector_0.40.0 > [73] BiocGenerics_0.48.1 foreach_1.5.2 pillar_1.9.0 > [76] circlize_0.4.15 splines_4.3.1 BiocFileCache_2.10.1 > [79] lattice_0.21-8 survival_3.5-5 bit_4.0.5 > [82] SparseM_1.81 tidyselect_1.2.0 Biostrings_2.68.1 > [85] knitr_1.45 IRanges_2.34.1 svglite_2.1.1 > [88] stats4_4.3.1 xfun_0.39 Biobase_2.60.0 > [91] matrixStats_1.1.0 stringi_1.7.12 yaml_2.3.7 > [94] evaluate_0.23 codetools_0.2-19 cli_3.6.1 > [97] systemfonts_1.0.4 munsell_0.5.0 pscl_1.5.5.1 > [100] Rcpp_1.0.11 GenomeInfoDb_1.38.1 png_0.1-8 > [103] parallel_4.3.1 assertthat_0.2.1 blob_1.2.4 > [106] bitops_1.0-7 viridisLite_0.4.2 broom.helpers_1.14.0 > [109] scales_1.2.1 crayon_1.5.2 GetoptLong_1.0.5 > [112] rlang_1.1.1 KEGGREST_1.42.0 rvest_1.0.3 > > Bioconductor version '3.18' > > * 27 packages out-of-date > * 1 packages too new > > create a valid installation with > > BiocManager::install(c( > "Biobase", "Biostrings", "bugsigdbr", "ComplexHeatmap", "densvis", "digest", > "dplyr", "fansi", "htmltools", "IRanges", "multtest", "phyloseq", "purrr", > "RCurl", "rhdf5", "rhdf5filters", "Rhdf5lib", "rlang", "RSQLite", "S4Vectors", > "svglite", "systemfonts", "utf8", "vctrs", "xfun", "xml2", "XVector", > "zlibbioc" > ), update = TRUE, ask = FALSE, force = TRUE) > > more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date > > Warning message: > 27 packages out-of-date; 1 packages too new >

U03L1PX3D52 (12:19:35) (in thread): > And yes this is on my laptop RStudio.

Chioma Onyido (12:23:01) (in thread): > Yes. Thank you!:grin::raised_hands:

U03L1PX3D52 (12:23:04) (in thread): > I ran this code and downloaded all the updates. I still get the same error and the 27 packages remain out of date. > if (!require(“BiocManager”, quietly = TRUE)) > install.packages(“BiocManager”) > BiocManager::install(version = “3.18”) > BiocManager::version() > BiocManager::valid() > BiocManager::install(“remotes”, dependencies = TRUE) > BiocManager::install(“waldronlab/bugSigSimple”) > BiocManager::install(“curatedMetagenomicData”) > BiocManager::install(“waldronlab/BugSigDBStats”) > BiocManager::install(“waldronlab/bugsigdbr”)

Chioma Onyido (12:24:53) (in thread): > Saved this thread for later. Thank you:grin:

Peace Sandy (12:26:46) (in thread): > Thank You@Levi Waldron@C. Mirzayi (please do not tag this account)answered some already,I’mglad the list is complete now

Esther Afuape (12:27:49) (in thread): > I think some of it are still missing like random forest, Wald and PERMANOVA@Peace Sandy

Peace Sandy (12:28:39) (in thread): > Yeah, I think PERMANOVA is relative abundance@Esther Afuape

Peace Sandy (12:30:46) (in thread): > I saw a study that PERMANOVA has relative abundance, ButI’mnot really sure@Esther Afuape

Esther Afuape (12:31:07) (in thread): > Alright@Peace Sandy

Peace Sandy (12:31:22) (in thread): > Studies rarely record wald, just a handful

Chioma Onyido (12:33:00) (in thread): > I think<@U1LCB8WEA>mentioned yesterday that Random forest uses importance scores? But itdoesn’tgive direction of whetherthere’san increase or decrease.

Peace Sandy (12:33:44) (in thread): > Yes he did, studies with random forest are rare as well

U03L1PX3D52 (12:55:07) (in thread): > <@U1LCB8WEA>I got it working!

U02CNMR4YEA (13:45:59): > Hi Everyone! I am trying to download the curated data from GitHub using the code: BiocManager::install(“waldronlab/curatedMetagenomicData”, dependencies = TRUE, build_vignettes = TRUE) > > But I get the following error message:

U02CNMR4YEA (13:47:55): - File (PNG): image.png

Chloe (15:10:10) (in thread): > fairly good

U1LCB8WEA (15:20:00) (in thread): > Great!

U1LCB8WEA (15:22:14) (in thread): > Make sure you have a valid Bioconductor 3.18 installation withBiocManager::version()andBiocManager::valid(). Then install from Bioconductor, not GitHub:BiocManager::install("curatedMetagenomicData")

Chloe (15:41:48): > I need help on this image please…it has four experiments but am alittle confused when it comes to identifying the groups . According to the image I see only the tumor samples<@U1LCB8WEA>will be group 1 ( case group) …does this mean I can curate an experiment with only one group…??<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Levi Waldronwill be glad to hear from you please - File (JPEG): Screenshot_20231015-113216.jpg

U1LCB8WEA (17:03:15) (in thread): > There must always be two groups, otherwise there’s no comparison in the “differential” abundance. It looks like the comparison here is geographical region, not tumor vs control. ie, Kenyan vs the other three, Egyptian vs other three, European American vs other three, and African American vs other three? Here the condition would be geographical location, not cancer.

Esther Afuape (17:13:28) (in thread): > I’mworking on a study that has geographical location as its condition too. Icouldn’tfind it in the EFO

Chioma Onyido (17:13:47) (in thread): > There’sno geographical location in the EFO@Esther Afuapeand I experienced same issue.

Chioma Onyido (17:14:10) (in thread): > Tried to search for country too, couldn’t find. > But we sawpopulation.<@U1LCB8WEA>:thinking_face:

Esther Afuape (17:14:14) (in thread): > The closest thing@Chioma Onyidofound was population.

Mildred Anashie (17:59:02) (in thread): > Thank you@Esther Afuapefor this

Chiagoziem David (18:43:24) (in thread): > Think I have also come across something like this

U02CNMR4YEA (22:14:23) (in thread): > That worked! Thank you!

U1LCB8WEA (22:16:36) (in thread): > Interesting,sounds like we need a solution for geography sinceit’snot that uncommon…

U02CNMR4YEA (22:20:39) (in thread): > When I curated PMID 32106294 (which was different because it was a healthy volunteer study) I brought it to the lab meeting and it was decided to put it under “Healthy Study Participation”. Now, in retrospect, I’m thinking that isn’t really the best option for that one either because that doesn’t tell what the populations were differentiated on.:thinking_face:

U02CNMR4YEA (22:24:57) (in thread): > “country” is actually in there as an option but that won’t accurately represent what was in PMID 32106294 because they compared different regions within the same country.

2023-11-13

Peace Sandy (01:53:28) (in thread): > Hmmm…here for the solution.

Chioma Onyido (03:47:54) (in thread): > <@U02CNMR4YEA>Country doesn’t pop up when I try to fill in BugSigDB, I’m thinking maybe because it’s not an EFO term? - File (JPEG): IMG_6105 - File (JPEG): IMG_6106

USLACKBOT (05:37:21): > This message was deleted.

Peace Sandy (05:51:00) (in thread): > When entering an experiment in the lab analysis section of bugsigdb they are only 4 sequencing types allowed WMS , 16S ITS/ ITS2 and PCR, from the except you just shared I think the sequencing type is 16S targeting V1-V3. > > I can also see that they entered data from WMGS which is whole meta-genomic sequencing,Idon’tknow ifit’sthe same thing as WMS, but from the paper you just shared I think it might be 16S, butlet’swait for the mentors response.

Chioma Onyido (06:25:31) (in thread): > I agree with@Peace SandyI think WMGS is the same as WMS, both stands forwhole metagenome sequencing , just different acronyms.

Peace Sandy (06:26:00) (in thread): > True@Chioma Onyido

Chioma Onyido (06:27:12) (in thread): > But 16S and WMS were both used.:thinking_face:should she record both? Hmmmm

Peace Sandy (06:27:44) (in thread): > But for sequencing types 16S and WMS are usually used, since both are mentioned,I’mkind of unsure about the best approach

Chioma Onyido (06:35:19) (in thread): > I remember<@U1LCB8WEA>’s comment sometime ago, that researchers do this sometimes compare the signatures produced by the sequencing types. > > I would enter as separate experiments (If different results were reported for each of the sequencing type).:eyes:But If it’s the same results, I would curate as one experiment to avoid double entry.

Nana (06:49:06) (in thread): > That’s the confusion@Chioma Onyido@Peace Sandyboth sequencing platform were used but no different experiment were reported rather there were comparing performance of PICRUSt2 and Tax4Fun2

Chioma Onyido (06:50:16) (in thread): > Can you share a link@NanaLet’shave a look together.

Peace Sandy (06:52:28) (in thread): > @NanaI thinkI’vegotten a response to your question

Nana (06:54:49) (in thread): > @Peace Sandyoya answer

Peace Sandy (06:55:42) (in thread): > @NanaI just went through the recording to re-watch the last weekly sync.@C. Mirzayi (please do not tag this account)said some studies use more than one sequencing type, or they compare more than one sequencing type. > > In a case were a study used more than one sequencing type then you should curate it as different experiments. > > The question now is in the study you are currently curating, were the sequencing types used or compared.

Peace Sandy (06:57:32) (in thread): > Also I suggest you watch the last weekly sync again to get a better understanding of whatI’mtrying to say.

Nana (06:57:53) (in thread): > here:https://journals.asm.org/doi/pdf/10.1128/msystems.01003-22

Peace Sandy (06:58:31) (in thread): > Okay, I just saw your response were you said they were used. > > I think you should curate them as separate experiment if it was used, according to@C. Mirzayi (please do not tag this account)

Peace Sandy (06:58:56) (in thread): > Let me go through the paper

Nana (07:03:15) (in thread): > ok… Thanks

Chioma Onyido (07:12:19) (in thread): > In the methods section, The authors used 16S data to calc alpha diversity and construct the microbiome community types, they noted that the reason is that WMGS are less readily interpretable than 16S.@NanaIf you also read through the reviewer comments pdf, it was mentioned.

Peace Sandy (07:15:02) (in thread): > In this case I think she should just use 16S, from whatI’veread so far, I think 16S was not used along side WMGS

Chioma Onyido (07:15:38) (in thread): > Same.@Peace Sandy16S V1-V3, should be the curated.

Mildred Anashie (07:16:49) (in thread): > I don’t know if BugSigDB permits entering two sequencing types for one experiment and if you enter separately you might have double entry because i observed what they were comparing (PICRUSt2 and Tax4Fun2) was used for both 16S and WMGS from Figure 1 and from this text…I’m i wrong?:thinking_face: - File (PNG): WMS.PNG

Chioma Onyido (07:18:17) (in thread): > @Mildred Anashieread through the paper full method section and reviewers comments, you’d see more info. > > The authors generated data for both 16S and WMS, however they used only16Sdata to compare the inference methods PICURst and Taxa4fun (for reasons Idon’tfully understand yet, which was also raised as part of the reviewers comments).

Peace Sandy (07:19:11) (in thread): > Hmmm

Peace Sandy (07:20:09) (in thread): > @Mildred AnashieI think what@Chioma Onyidois saying is correct

Nana (07:21:54) (in thread): > it was 16s V1-V3, that i curated already..Thanks all

Mildred Anashie (07:31:29) (in thread): > Okay@Nana

Chiagoziem David (08:25:53): > Anyone come across a study that uses KRUSKAL-WALLIS NON PARAMETRIC TEST?

Peace Sandy (08:30:40) (in thread): > The Kruskal-Wallis test is a non-parametric statistical test used to determine if they is any statistically significant differences between groups.I’mcurrently curating a study that used it. > > Do you have any questions about it ?@Chiagoziem David

Chiagoziem David (08:31:15) (in thread): > yeah…

Chiagoziem David (08:32:31) (in thread): > its a type of Non-parametric Test, i’m trying to see something before i ask the question though

Peace Sandy (08:34:58) (in thread): > Okay

Chiagoziem David (08:59:57): > i have a question guys, in a study where alpha diversity isn’t really talked about ( beta diversity seems to be the main focus ) , should beta diversity switch to be our focus? and what does that mean for the alpha diversity indices we are supposed to curate?<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Chioma Onyido (09:02:17) (in thread): > I asked same question during the last lab meeting and<@U1LCB8WEA>gave a detailed answer on why we curate onlyalpha diversityin BugSigDB. > You can also refer to the curation policy and the last recording from the last meeting.

Chioma Onyido (09:03:02) (in thread): > If alpha diversityisn’treported in your study, I suggest you leave it blank.@Chiagoziem David

Chiagoziem David (09:06:01) (in thread): > alright, let me refer to the video. thanks@Chioma Onyido:clap:

UBNSEMS3S (10:07:24): > Hi everyone. I am out today but I’ll take a look at your questions tomorrow.

Peace Sandy (10:08:45) (in thread): > Noted

Nana (10:46:15) (in thread): > @Chiagoziem Davidonce alpha diversity is not accounted for in you article you don’t enter it. Just leave it blank

Nana (10:46:47) (in thread): > We don’t account for beta diversity in BugsigDb curation

Nana (10:47:26) (in thread): > Stamped:ok_hand:

Nana (14:06:13): > @Levi Waldronwhen i put the PMID of the paper i want to curate they saymust be unique, I don’t know why

Chioma Onyido (14:07:31) (in thread): > @NanaI thinkit’sbecauseit’salready been curated on BugSigDB.

Peace Sandy (14:07:38) (in thread): > Probably they is a paper with that ID

Nana (14:08:35) (in thread): > but it was assigned to me

Chioma Onyido (14:09:26) (in thread): > Hmmm Can you share the link? let’s see.

Tolulope Ogunleye (14:19:07) (in thread): > I have experienced this before and you might want to cross check the PMID and be sure ithasn’talready been curated

Nana (14:22:28) (in thread): > @Tolulope Ogunleyewhat did you do?

Ludwig Geistlinger (14:22:29) (in thread): > It isalwaysa good idea to check whether a certain PMID you intend to work on is already contained in BugSigDB. > > This can be simply done by putting the PMID into the search bar and see whether there are any hits. > > On the other hand, BugSigDB actually tries to prevent you from duplicating work by pointing out that the PMID should be unique, ie that it cannot create a study that would lead to duplication.

Ludwig Geistlinger (14:22:36): - File (PNG): Screenshot 2023-11-13 at 2.17.03 PM.png

Nana (14:23:52) (in thread): > @Ludwig Geistlingerok..thanks..will search henceforth

Tolulope Ogunleye (14:25:42) (in thread): > I tried to confirm that thestudy hasn’talready been curated…you can search as@Ludwig Geistlingerhas suggested

Chioma Onyido (14:26:34) (in thread): > @NanaIf you confirm thatit’salready been curated after following@Ludwig Geistlinger’s suggestions, it would be good to notify the mentors so that they can close the issue on GitHub or flag it as duplicate.

Nana (14:27:21) (in thread): > @Tolulope Ogunleye@Chioma Onyidook..I will

Peace Sandy (14:51:00) (in thread): > This was helpful > Thank You@Ludwig Geistlinger

U1LCB8WEA (21:23:58) (in thread): > Looks like you have figured this out already, thank you!

U1LCB8WEA (21:30:17): > Hi team, I was doing some analysis to prepare for a presentation tomorrow, and noticed there are a number of identical signatures in the database. Here is some reproducible R code that identifies and displays identical signatures of length >= 5 ( based on their md5sum digest. I could use your help to check on these and identify which should be deleted:slightly_smiling_face:. I suspect there are shorter signatures that need to be deleted too, but probably also more correctly identical signatures just by chance below this length. > > # BiocManager::install(c("bugsigdbr", "waldronlab/BugSigDBStats", "digest", "purrr", "dplyr")) > library(dplyr) > #> > #> Attaching package: 'dplyr' > #> The following objects are masked from 'package:stats': > #> > #> filter, lag > #> The following objects are masked from 'package:base': > #> > #> intersect, setdiff, setequal, union > bsdb <- bugsigdbr::importBugSigDB(version = "devel") > #> Using cached version from 2023-11-12 17:03:53 > sigs <- bugsigdbr::getSignatures(bsdb, > tax.id.type="taxname", > min.size = 5) > > # identify identical elements in the sigs list > purrr::map_chr(sigs, digest::digest) %>% > .[!Biobase::isUnique(.)] %>% > sort() > #> bsdb:809/1/1_Retinopathy:diabetes-mellitus-(DM)_vs_healthy-controls-(HC)_UP > #> "073ca2fec309aae2a357b6deb68c1cc6" > #> bsdb:809/2/2_Retinopathy:diabetes-retinopathy-(DR)_vs_diabetes-mellitus-(DM)_DOWN > #> "073ca2fec309aae2a357b6deb68c1cc6" > #> bsdb:443/1/1_irritable-bowel-syndrome:IBS_vs_Healthy-Control_UP > #> "28aaef70dc700d84d4d6bda6aa64477e" > #> bsdb:443/3/1_irritable-bowel-syndrome:IBS-D_vs_Health-Control_UP > #> "28aaef70dc700d84d4d6bda6aa64477e" > #> bsdb:262/1/2_atopic-asthma:nasal-brush-speciments_vs_bronchial-brush-specimens_DOWN > #> "3004eabb11c96f6100a48ffba6304302" > #> bsdb:262/3/1_atopic-asthma:induced-sputum-specimens_vs_nasal-brush-specimens_UP > #> "3004eabb11c96f6100a48ffba6304302" > #> bsdb:262/4/1_atopic-asthma:oral-wash-specimens_vs_nasal-brush-specimens_UP > #> "3004eabb11c96f6100a48ffba6304302" > #> bsdb:829/1/1_Breastfeeding-duration:Low-Total-Time-Breastfeeding_vs_Medium-Total-Time-Breastfeeding_DOWN > #> "4f2e0ba8d26ec80dcea51491c3cd8545" > #> bsdb:829/2/1_Breastfeeding-duration:High-Total-Time-Breastfeeding_vs_Medium-Total-Time-Breastfeeding_DOWN > #> "4f2e0ba8d26ec80dcea51491c3cd8545" > #> bsdb:794/1/1_colorectal-cancer:EOCRC-(Early-onset-Colorectal-cancer)-patients_vs_Healthy-controls_UP > #> "53018590674734dae9325ce808e42636" > #> bsdb:794/2/1_colorectal-cancer:EOCRC-(Early-onset-Colorectal-cancer)-patients_vs_LOCRC-(Late-onset-Colorectal-cancer)-patients_UP > #> "53018590674734dae9325ce808e42636" > #> bsdb:624/1/1_colorectal-cancer:Patients-with-CRC_vs_Healthy-Individuals_UP > #> "5c90266728439a1b5f4087c215685d62" > #> bsdb:624/3/1_colorectal-cancer:Patients-with-advanced-CRC_vs_Healthy-Individuals_UP > #> "5c90266728439a1b5f4087c215685d62" > #> bsdb:624/4/1_colorectal-cancer:After-resection_vs_Before-resection_DOWN > #> "5c90266728439a1b5f4087c215685d62" > #> bsdb:809/2/1_Retinopathy:diabetes-retinopathy-(DR)_vs_diabetes-mellitus-(DM)_UP > #> "6dea87790a2d191ce492a7a23ed5aad4" > #> bsdb:809/3/1_Retinopathy:diabetes-retinopathy-(DR)_vs_healthy-controls-(HC)_UP > #> "6dea87790a2d191ce492a7a23ed5aad4" > #> bsdb:316/3/2_premature-birth:30-day-old-Pre-term-infants_vs_30-day-old-Full-term-infants(born-after-uncomplicated-pregnancy)_DOWN > #> "7ccdbfe4a05ed473f9e735ada1e58c3a" > #> bsdb:316/4/2_premature-birth:90-day-old-Pre-term_vs_90-day-old-Full-term-infants(born-after-uncomplicated-pregnancy)_DOWN > #> "7ccdbfe4a05ed473f9e735ada1e58c3a" > #> bsdb:367/1/1_obesity:obese_vs_normal-weight_UP > #> "7eff7af0bffb227e30450e398954f089" > #> bsdb:367/2/1_obesity:overweight_vs_normal-weight_UP > #> "7eff7af0bffb227e30450e398954f089" > #> bsdb:696/4/1_Nutraceutical:colorectal-cancer-patients-perioperative-probiotics_vs_colorectal-cancer-patients-perioperative-placebo_UP > #> "824d16e25cba0eac0f044e777d760c19" > #> bsdb:696/5/1_Nutraceutical:healthy-volunteer-group_vs_colorectal-cancer-patients-perioperative-placebo_UP > #> "824d16e25cba0eac0f044e777d760c19" > #> bsdb:434/1/2_human-papilloma-virus-infection:HPV-+_vs_healthy-control_DOWN > #> "8e7556dc39fd7f200b42382236e0a578" > #> bsdb:434/2/2_cervical-glandular-intraepithelial-neoplasia:LSIL_vs_healthy-control_DOWN > #> "8e7556dc39fd7f200b42382236e0a578" > #> bsdb:434/3/2_cervical-glandular-intraepithelial-neoplasia:HSIL_vs_healthy-control_DOWN > #> "8e7556dc39fd7f200b42382236e0a578" > #> bsdb:434/4/2_cervical-cancer:cervical-cancer_vs_healthy-control_DOWN > #> "8e7556dc39fd7f200b42382236e0a578" > #> bsdb:526/1/1_endometriosis:Endometriosis/-adenomyosis-patients_vs_Endometriosis-patients_UP > #> "95746b4f08f23c0e51106aea4094f4da" > #> bsdb:526/2/1_endometriosis:Endometriosis/-adenomyosis-patients_vs_Patients-without-endometriosis_UP > #> "95746b4f08f23c0e51106aea4094f4da" > #> bsdb:279/2/2_acute-myeloid-leukemia:bacterial-infections_vs_No-bacterial-infections_DOWN > #> "9d5bbfc58f2500dd2270f365d64ed439" > #> bsdb:279/2/3_acute-myeloid-leukemia:bacterial-infections_vs_No-bacterial-infections_UP > #> "9d5bbfc58f2500dd2270f365d64ed439" > #> bsdb:794/2/2_colorectal-cancer:EOCRC-(Early-onset-Colorectal-cancer)-patients_vs_LOCRC-(Late-onset-Colorectal-cancer)-patients_DOWN > #> "a70a38ffefd64656b0ca60e9a909ccda" > #> bsdb:794/3/1_colorectal-cancer:LOCRC-(Late-onset-colorectal-cancer)_vs_Healthy-controls_UP > #> "a70a38ffefd64656b0ca60e9a909ccda" > #> bsdb:794/1/2_colorectal-cancer:EOCRC-(Early-onset-Colorectal-cancer)-patients_vs_Healthy-controls_DOWN > #> "abd1831f08b8f2fcce4caaa47667fcd0" > #> bsdb:794/3/2_colorectal-cancer:LOCRC-(Late-onset-colorectal-cancer)_vs_Healthy-controls_DOWN > #> "abd1831f08b8f2fcce4caaa47667fcd0" > #> bsdb:738/1/1_Crohn's-disease:pediatric-crohn's-disease_vs_healthy-adults_DOWN > #> "b08c6f909ac49ef7fa1f1ac141ae0f73" > #> bsdb:738/1/5_Crohn's-disease:pediatric-crohn's-disease_vs_healthy-adults_DOWN > #> "b08c6f909ac49ef7fa1f1ac141ae0f73" > #> bsdb:678/1/1_smoking-behavior:Cigarette-Smokers_vs_Nonsmokers_UP > #> "da288d7cfd25f5b1d0dd680580e4215c" > #> bsdb:678/2/1_smoking-behavior:Dokha-Smokers_vs_Nonsmokers_UP > #> "da288d7cfd25f5b1d0dd680580e4215c" > > Created on 2023-11-13 with reprex v2.0.2 - Attachment (reprex.tidyverse.org): Prepare Reproducible Example Code via the Clipboard

U1LCB8WEA (21:33:32) (in thread): > By the way, a student of ours once detected published plagiarism similarly to this! These two papers contain identical figures that were curated into BugSigDB: > > Gopalakrishnan, V. et al. Gut microbiome modulates response to anti-PD-1 immunotherapy in melanoma patients. Science 359, 97–103 (2018) > > > > Li, L. & Ye, J. Characterization of gut microbiota in patients with primary hepatocellular carcinoma received immune checkpoint inhibitors: A Chinese population-based study. Medicine 99, e21788 (2020)

Nana (21:42:27) (in thread): > @Levi Waldronyes

U1LCB8WEA (22:00:33) (in thread): > I’m happy to give someone temporary delete privileges during this cleanup. I will eventually give such privileges to anyone sticking with the project long enough, I just want you to have experience before taking on such powers:smile:

2023-11-14

Mildred Anashie (01:25:52) (in thread): > A privilege and experience I’ll love to have:blush:I have a question though, Looking at this output (which I do not really understand:smile:) the same taxas were recorded for both increase and decrease signatures for the same experiment , which shouldn’t have been so > > And what we need to do is to identify which needs to be deleted from reviewing the experiments and the study:thinking_face:Please clarify, so we shall go do some detective work:joy:

Peace Sandy (01:43:02) (in thread): > Hi@Levi WaldronI’minterested in carrying out this task

Mildred Anashie (02:18:17) (in thread): > I think I understand better what you mean@Levi WaldronI just went through study 809 on BugSigDB and I noticed Signature 1 for Experiment 1 and Signature 2 for Experiment 2 are kind of exactly the same > Which happens to be same for Experiment 2, signature 1 and Experiment 3, signature 1 > > Although Ihaven’tgone through the paper to know ifitwas reported that way in the article, but what do we do after identifying this?

Mildred Anashie (03:19:53) (in thread): > This just helped me:blush:Thank you:pray:

Odigiri Great Alume (03:57:57) (in thread): > Looking at the paper, I’d agree with@Mildred Anashiesince group 1 is already relative to group 0. It be redundant to record decrease for the experiment 2 as it be a repetition. > > However I do think I can understand why the curator will record same Signatures (increased in experiment 1) as decrease in experiment 2. I think its because Experiment 1 compared DM vs HC and whatever increases in DM should probably decrease in DR when comparing with DM. But in all I still believe that, since the paper didn’t explicitly mention that the taxas that increased in DM for experiment 1 decreased in DR in experiment 2, hence I think it shouldn’t be curated since there’s already a mention of increase for DR in DR vs DM.
> > (Hope I haven’t confused anyone:blush:) > > Also for experiment 2 signature 1 and experiment 3 signature 1 being thesame I would probably have curated just as the curator has done because they are of different experiments with different comparisons > > My thought:thinking_face:

Esther Afuape (04:18:29) (in thread): > @Levi Waldronfor study526, participants withendometriosis and adenomysishad the highest abundance of taxa when compared to the other three groups;control, adenomysis and just endometriosis. This is to say that the experiments for each of these comparisons will all have the same signatures since their group 1 is the same. > I think since experiment 1 has the signature already, the signature in experiment 2 should be deleted but this might appear like experiments 2 and 3 had no significant taxa on first glance:thinking_face:. I also added experiment 3 for the last comparison which wasn’t accounted for initially.

Odigiri Great Alume (04:21:32) (in thread): > @Levi WaldronI also noticed for study 809 the study design listed was Cross sectional study and a matched on was recorded for it. I thought matched on only works for case control:thinking_face:

Mildred Anashie (04:24:32) (in thread): > @Odigiri Great AlumeI agree with Experiment 2, signature 1 and Experiment 3, signature 1 because the group 1 is same for both experiments and what increased in the group 1 should be same

Mildred Anashie (04:31:03) (in thread): > Yes@Odigiri Great AlumeI think study 809 is a case-control study because there is an obvious control group and case groups > > Also participants were matched on age and sex in the control group (From the methods)

Odigiri Great Alume (04:34:05) (in thread): > @Mildred AnashieI think you should change it to case control then. > Well done

Mildred Anashie (04:38:14) (in thread): > Also@Odigiri Great AlumeWe should suggest deleting the decrease signature in experiment 2 because Idon’tsee the logic in whatever increases in DM should decrease in DR when itwasn’tstated that way > > What do you think?

Odigiri Great Alume (04:39:30) (in thread): > @Mildred AnashieI agree. However, I was trying to understand from the curators perspective:joy:

Chioma Onyido (04:46:00) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1699650705970979This is the thread where I tried to review this same study 809,<@U1LCB8WEA>helped delete Expt. 2 sig 1 and 2, I don’t know how it re-appeared:tired_face:I read the paper and observed that DR vs DM wasn’t statistically significant, that’s why I called attention that the signatures should be delete not the experiment because it’s possible to curate experiments without signatures. > > How it reappeared I don’t know.:woman-shrugging: - Attachment: Attachment > Happy weekend <!here> :wave::skin-tone-5: > @UBNSEMS3S @U1LCB8WEA @Svetlana Ugarcina Perovic > While reviewing bugsigdb.org/Study_809, I noticed some double entries in some of the signatures: > Expt. 3, Sig. 2 (DR vs HC) and Expt.1 Sig 2 (DM vs HC) are the same > Expt. 2 Sig. 1 (DM vs HC) and Expt. 2 Sig 2 (DR vs DM) are the same > Expt. 2 Sig. 1 (DR vs HC) and Expt. 3 Sig 1 (DR vs DM) are the same > > I think this happenedbecause of the way the curator interpreted the results. > The authors reported unique abundant taxa for HC, DR and DM, (see attached image) > > I saw somewhere @UBNSEMS3S said that results shouldn’t be double-entered. > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698164308650169 > My suggestion: to avoid double entries, can this be curated in a different way instead? Say, to report only increased signatures for all experiments. I.e. > DR vs HC and DM > DM vs HC and DR > that means there’ll only be one signature (increased) for each of the experiments.

Odigiri Great Alume (04:47:35) (in thread): > In study 262 it states that when comparing IS vs BB the relative abundance of Prevotella, Actinomyces, Cornyebacterium, and Staphylococcus was INDISTINGUISHABLE.
> > However the curator recorded the signature which in my opinion shouldn’t be recorded. - File (JPEG): IMG_20231114_104235.jpg - File (JPEG): IMG_20231114_104258.jpg

Esther Afuape (04:47:43) (in thread): > @Chioma OnyidoI was surprised it was still appearing because I know you reviewed it. I think some changesdon’ttake effect immediately

Mildred Anashie (04:48:52) (in thread): > Well done@Chioma OnyidoI guess the changehasn’tbeen effected yet > > Maybe the mentors will have to delete again

Peace Sandy (04:48:57) (in thread): > Hi@Levi WaldronI think forhttps://bugsigdb.org/Study_678Signature 1 in experiment 1 and 2 are identical - Attachment (BugSigDB): Types of tobacco consumption and the oral microbiome in the United Arab Emirates Healthy Future (UAEHFS) Pilot Study - BugSigDB > Cigarette smoking alters the oral microbiome; however, the effect of alternative tobacco products remains unclear.Middle Eastern tobacco products like dokha and shisha, are becoming globally widespread.

Chioma Onyido (04:49:14) (in thread): > Plus It was case-control before, I don’t know who changed it back:tired_face:

Odigiri Great Alume (04:49:41) (in thread): > @Chioma Onyidosorry eeeh, don’t worry,@Levi Waldronwill delete Again eh.

Mildred Anashie (04:50:19) (in thread): > Changed back to case-control > > Hopefully it stays this time:smile:

Peace Sandy (04:51:09) (in thread): > I noticed some changesdon’ttake effect immediately,it might take some days

Esther Afuape (04:58:08) (in thread): > @Levi Waldronfor study434, please deletesignature 2for experiments 1,2,3,4. The abundant taxa in the control group were curated as decreases for the other groups andthat’sredundant.

Peace Sandy (05:01:03) (in thread): > Looking at these papers since the identical signatures are in different experiments, shouldn’t it be curated@Levi WaldronI’m a little bit confused and most of the papers have been reviewed.

Esther Afuape (05:03:22) (in thread): > @Peace SandyI’m wondering the same. Should signatures that have appeared before be deleted becausethey’reappearing in another experiment?That’swhat is happening in study 526

Chioma Onyido (05:03:25) (in thread): > For Study 367, > Signature 1 and 2 for Experiments 1 and 2 are identical; Increased and decreased abundance inobese group was curated twice. Same figure (figure 3) was used to curate both, this confirms a case of double entry. > > Please delete experiment 2.<@U1LCB8WEA>bugsigdb.org/Study_367

Peace Sandy (05:03:38) (in thread): > For this experiment, I noticed Experiment 1 and 2 have identical signatureshttps://bugsigdb.org/Study_829 - Attachment (BugSigDB): Breastfeeding patterns are associated with human milk microbiome composition: The Mother-Infant Microbiomes, Behavior, and Ecology Study (MIMBES) - BugSigDB > The human milk microbiome (HMM) is hypothesized to be seeded by multiple factors, including the infant oral microbiome during breastfeeding.However, it is not known whether breastfeeding patterns (e.g., frequency or total time) impact the composition of the HMM.

Peace Sandy (05:04:06) (in thread): > Yes@Esther Afuapethese are my thoughts exactly .I’llreally like to know about it, this will be really helpful while curating more papers, in order not to make the same mistake.

Odigiri Great Alume (05:11:03) (in thread): > From the list of signatures flagged here. > Also for study 262 I think NB vs BB signatures were recorded quite correct looking at fig 3. > > For IS vs NB > the curator imputed correctly the group 1 and 0 names however switched NB to BB when recording the signatures in experiment 3 signatures 1 and 2 > > However I also believe the taxas were entered correctly for increase in IS when compared to NB > > Hence I have corrected the description from BB to NB for group 0 since th experiment compares NB vs IS and not BB vs IS > > > Lastly OW vs NB was listed too. > Here the curator I’m the experiment listed the group 1 as OW and OW for group zero and them proceeded to record signatures for NB vd OW:cry:I cross checked the signatures with fig3 and saw that it’s actually NB vs OW. Hence I changed the group 0 name to NB and affirmed that the signatures recorded here are correct too.

Chioma Onyido (05:21:13) (in thread): > Forbugsigdb.org/Study_829Which has identical experiments 1 and 2, I think I understand why the curator curated as such. > > Since medium group was used as the reference group, and since thesame taxawere identified in both Low and High total time breastfeeding, to avoid double entry, can it be curated into one experiment? Say,Experiment 1: Low and High total time breastfeeding vs Medium total time breastfeeding,:thinking_face:Then proceed to record the signature.:sweat_smile:@Esther Afuape@Peace Sandy@Odigiri Great Alume

Peace Sandy (05:22:13) (in thread): > @C. Mirzayi (please do not tag this account)has already reviewed it andit’scorrect,I think the only issue might be the experiments having the same signatures

Peace Sandy (05:23:04) (in thread): > @Chioma OnyidoI went through the curation and the fault I can find there is identical taxa in the signatures > > For the reference groups and other groups they are correct

Peace Sandy (05:23:52) (in thread): > @C. Mirzayi (please do not tag this account)said they should be four experiments from that study, judging from the paper I think she is correct

Peace Sandy (05:24:40) (in thread): > Check the figures in the paper, itcan’tbe curated as you have proposed@Chioma Onyido

Chioma Onyido (05:27:16) (in thread): > Yes I agree with the curation, the reference group was rightfully used.@Peace SandyI’msuggesting a way to avoid double entry of signatures because the same signatures were identified in both Low and High, asin restating group 1 as (decreased abundance in) ‘Low and High Total Time Breastfeeding’ > But if thatcan’tbe done maybe this study can be an exception:woman-shrugging:

Chioma Onyido (05:30:05) (in thread): > Hmmm:thinking_face:just saw your comment on Chloe’s corrections, okay then I guess this study may be exepted.

Peace Sandy (05:30:34) (in thread): > Okay

Chioma Onyido (05:46:30) (in thread): > bugsigdb.org/Study_696Expt. 4 and 5 both have same signature 1. > Both curated from same Figure 4, when I checked the figure, I found thatit’snot supposed to be so. > Does anyone want to look at this study together?:eyes::pray:

Odigiri Great Alume (05:48:03) (in thread): > @Chioma Onyidolet me look

Esther Afuape (05:51:56) (in thread): > @Chioma OnyidoI just checked it. I also don’t think experiment 5 should have been created.The control was used as group 1 when everything should have been created relative to it

Chioma Onyido (05:53:01) (in thread): > Thank you@Odigiri Great Alume@Esther AfuapeAlso noticed that was was supposed to be the increase for healthy volunteers according to Figure 4, it was curated as a decrease instead. Not sure why…?

Chioma Onyido (05:57:02) (in thread): > Signature 1 for same expt 5 isn’t accurate too. > The taxa recorded there belongs to another group (PGT). I agree@Esther Afuapeboth signatures aren’t accurate. Maybe it shouldn’t have been curated.

Chioma Onyido (06:00:58) (in thread): > From figure 4, Idon’tsee how CGT and HGT have same taxa@Odigiri Great AlumeCGT is red, HGT is green, where and how did you see the same taxa:eyes:

Odigiri Great Alume (06:01:52) (in thread): > At this point I need glasses. > > My eyes dey pain me. Sorry na green and red

Chioma Onyido (06:02:40) (in thread): - File (JPEG): IMG_6115

Esther Afuape (06:04:38) (in thread): > @Chioma Onyidoexperiment 4 seems like experiment 1 but with the incorrect signature..

Esther Afuape (06:08:04) (in thread): > I think the study should be patiently reviewed again before flagging the signatures for deletion.

Odigiri Great Alume (06:10:17) (in thread): > But@Chioma Onyidoseeing that both SIgnatures are wrong > > I agree with@Esther Afuapethat > Experiment 5 is CGT vs PGT? which is same as experiment 1 with wrong signatures > Since experiment 4 is HGT vs PGT:cry:

Odigiri Great Alume (06:10:46) (in thread): > E get as this 696 be sha. Eye don dey turn me

Esther Afuape (06:13:25) (in thread): > Yeah but the sources are different

Odigiri Great Alume (06:13:41) (in thread): > Ahaaaaaa Tor

Odigiri Great Alume (06:14:23) (in thread): > You can’t repeat Same experiment based on different source can you ?:thinking_face:

Chioma Onyido (06:15:05) (in thread): > Yes, table 3 which was used to curate expt 1 reported relative abundances (whichI’mstill trying to figure out how this was curated), > While Figure 4 was used to curate expt 4.

Mildred Anashie (06:17:44) (in thread): > Haven’tgone through the paper but if the same signatures are reported for different experiments then one should be deleted and recorded without signatures and both sources included for the other > > My opinion:woman-shrugging:

Odigiri Great Alume (06:19:40) (in thread): > @Chioma Onyidotable 3 is talking about relative abundance of each taxa withing each group. There was no comparison with outside group. You right I guess

Chioma Onyido (06:19:44) (in thread): > I think you can repeat same experiment from diff source and record the signatures (IF they are different signatures from diff statistical tests),@Odigiri Great Alumefor example if the results came from different analysis, maybe the authors were trying to compare the taxa produced between diff types of stat. test or something:woman-shrugging:Well as@Esther Afuapesuggested, maybe study 696 should be carefully reviewedde novo before flagging for deletion.

Odigiri Great Alume (06:21:30) (in thread): > @Chioma OnyidoI agree with the different analysis. However this study didn’t do different analysis sef. That table 3 shouldn’t be curated maybe. > > Entire study should be reviewed again like@Esther Afuapesuggested maybe

Chioma Onyido (06:22:30) (in thread): > YesI don’tthink they did different analysis too.:disappointed_relieved:

Odigiri Great Alume (06:25:33) (in thread): > First, the potential experiments needs to be identified then from there we can solve the signatures. But let’s wait for@C. Mirzayi (please do not tag this account)and@Levi Waldronto give a go ahead

Esther Afuape (07:57:24) (in thread): > @Levi Waldronfor experiment794, please delete experiment 1/signature 2, > experiment 2/signature 2, > experiment 3/signature 2.

Mildred Anashie (08:24:44) (in thread): > @Esther AfuapeHave you been able to identify why Experiment 1, signature 1 and Experiment 2, signature 1 have identical signatures?

Esther Afuape (08:25:13) (in thread): > For which study?

Mildred Anashie (08:26:17) (in thread): > 794

Mildred Anashie (08:28:39) (in thread): > I think, The group 1 for both Experiment 1 and Experiment 2 is the same > > That’s why the signatures are the same, going through the paper now to know why the curator recorded it that way > > If that was the comparison made in the study

Esther Afuape (08:29:03) (in thread): > They have the same group 1. Experiment 1 is EOCRC vs control while experiment 2 is EOCRC vs LOCRC . They’re different experiments so I think it’s fine for them to have the same signature 1.?

Chioma Onyido (08:30:57) (in thread): > But they were all curated form the same figure@Esther Afuape - File (JPEG): IMG_6125

Chioma Onyido (08:32:19) (in thread): > I think the descriptions should be updated as well, to properly capture the groups that were contrasted.@Mildred Anashie@Esther Afuape

U1LCB8WEA (08:32:20) (in thread): > You’re alla amazing! I don’t have time to look into these more today, but one small comment that might help. The problem isn’t exactly just that duplicate signatures exist, it’s that is they’re an indication of a likely error. Each experiment is supposed to represent a unique contrast, and it’s very unlikely that two different, unique contrasts will produce exactly the same signature, so either one signature is out of place, or an experiment has been duplicated such as experiments for groups A vs B and also B va A. And part of the delay from creation is probably that I did not turn local caching off in my program. And one more note, even Chloe Mirzayi and I make mistakes sometimes!

Peace Sandy (08:33:33) (in thread): > Wow…:sweat_smile:This is really good to know

Peace Sandy (08:35:17) (in thread): > The error, could it be from the initial curator or the paper.

Chioma Onyido (08:37:56) (in thread): > It’snot just about curating experiments based on the groups contrasted but the contrast is supposed to beunique,it is very unlikely that unique contrast will produce the same signatureshmmmm…this is anotherkeyinformation one needs to have in mind during future curations. > Much appreciated<@U1LCB8WEA>:raised_hands:

Mildred Anashie (08:38:02) (in thread): > Trying to figure that out@Peace Sandy

U1LCB8WEA (08:38:34) (in thread): > Most likely this particular error is in the curation

Peace Sandy (08:39:45) (in thread): > Wow…

Mildred Anashie (08:40:13) (in thread): > Yes<@U1LCB8WEA>Ithinkit’sfrom the curation

Peace Sandy (08:40:49) (in thread): > Thank you so much for your clarifications@Levi WaldronI’velearnt something new today and gotten a new perspective to everything afresh.

Esther Afuape (08:42:37) (in thread): > Knowing that each signature has to be unique will really help in interpreting results moving forward. Sometimes, it can be tricky to decide on what groups to contrast when the papers don’t clearly do the contrasts and only provide the results of each group. > For instance, in study 794, since experiments 1 and 2 are from the same figure, do you think each group should have only been contrasted with the control and not against each other also?@Chioma Onyido

Peace Sandy (08:43:10) (in thread): > This is true@Esther AfuapeI’mreally glad this came up and was discussed

Chioma Onyido (08:46:49) (in thread): > Hmmm tough question,@Esther AfuapeI’venoticed that most of the common errors we picked from todays review has a lot to do with how the results were presented, like you said. > > Another thing<@UBNSEMS3S>mentioned sometime was using the results reported within text as a clue too,:thinking_face:Sometimes they state the contrast properly within text, using the figures as reference. > Maybe we should try that?:sweat_smile:

Odigiri Great Alume (08:47:00) (in thread): > @Esther Afuapewith the control I think. But is it possible for the study not to state the contrast made?:thinking_face:

Odigiri Great Alume (08:47:37) (in thread): > @Chioma Onyidogood point here. > The text can be a good pointer

Esther Afuape (08:57:16) (in thread): > @Chioma Onyido@Odigiri Great Alumeplease go through the result text to see ifthere’sa contrast in it. MaybeI’mmissing something

Odigiri Great Alume (08:57:59) (in thread): > Alright ma’am@Esther Afuape

Mildred Anashie (09:04:20) (in thread): > @Esther AfuapeI think all the signatures for decrease (i.e signature 2 for all experiments) should be deleted because those were reported for the control group and I can’t find the contrast made for the LOCRC and EOCRC…..That experiment doesn’t exist in my opinion:thinking_face:

Chioma Onyido (09:06:10) (in thread): > I think they should be contrasted against control…? > Figure 3 a and b presents results for each of the groups, presentingonly increased signaturesfor all. > I think it should be curated as > EOCRC (grp 1) vs NC > LOCRC (grp 1) vs NC > > This way, the experiments will be unique with unique signatures:woman-shrugging:Also no double entries. - File (JPEG): IMG_6125

Esther Afuape (09:06:44) (in thread): > @Mildred Anashieyes, they were the ones I pointed out for deletion

Mildred Anashie (09:07:53) (in thread): > @Chioma OnyidoYou are right, Same observation

Odigiri Great Alume (09:09:01) (in thread): > @Esther Afuapelet’s not forget this is a case control study hence@Chioma Onyidois right and I think that two cases can’t or should I say shouldn’t be compared in a case control study

Chioma Onyido (09:09:07) (in thread): > Another way is to contrast against each other and curate as > NC vs LOCRC and EOCRC > EOCRC vs LOCRC and NC > LOCRC vs EOCRC and NC > > Not sure about the accuracy of this method.:thinking_face:@Esther Afuape@Mildred Anashie@Odigiri Great Alume

Chioma Onyido (09:09:46) (in thread): > @Odigiri Great AlumeI’m not sure o I don’t know if it’s right:sweat_smile:

Odigiri Great Alume (09:09:56) (in thread): > @Chioma OnyidoI don’t see that the study did these comparisons:joy:

Mildred Anashie (09:10:19) (in thread): > NC is the control group…Should we be curating for controls?:thinking_face:

Chloe (09:10:36) (in thread): > i agreeing with you@Chioma Onyido…..me too have failed to get country while filling in on Bugsigdb…@Svetlana Ugarcina Perovic@Levi Waldron@C. Mirzayi (please do not tag this account)what do we do for such a scenario…?

Chioma Onyido (09:11:07) (in thread): > Nowe’renot supposed to@Mildred AnashieI’m just thinking that means we’ll throw away all the taxa reported for control?:anguished:

Esther Afuape (09:11:24) (in thread): > Yes@Chioma OnyidoSo for study 794,experiment 2should be deleted. > Andexperiment 1/signature 2should be deletedExperiment 3/signature 2should be deleted

Esther Afuape (09:12:35) (in thread): > I reallydon’tknow how the taxa for controls should be represented. A lot of times whenthey’rereported,wedon’tget to curate them sinceit’sfor control.@Levi Waldronis there a way to go about this?

Odigiri Great Alume (09:12:47) (in thread): > @Mildred AnashieNC vs LOCRC and EOCRC > I guess what she meant is that NC will still be control then a combination of the cases EOCRC AND LOCRC will be cases:joy:Possible but the study didn’t do this I guess. But what about the rest experiment:laughing:I don’t know…@Chioma Onyidocome and explain ya sef lol

Peace Sandy (09:13:16) (in thread): > You are right@Esther AfuapeIdon’tthink we get to curate the taxa for control groups

Mildred Anashie (09:15:08) (in thread): > @Odigiri Great AlumeShe already did, what she meant was to do it that way in order not to throw away the control taxas…..Which we sadly have no business with right now:grinning:

Odigiri Great Alume (09:16:43) (in thread): > @Chioma Onyidowe must throw away the Controls:joy:no room left

Peace Sandy (09:17:35) (in thread): > :joy::joy::joy:

Chioma Onyido (09:17:42) (in thread): > I think Esther’s suggestions for deletions works. That way we end up with2 unique experiments: 1 and 3, one signature each (increased). > Makes sense to me.:smile:

Chioma Onyido (09:33:03) (in thread): > <@U1LCB8WEA>noted this geography issue. > ButI settled forpopulation**** ****in my curationinthe meantimebut I’m not sure if that’sthe closest.@Chloe

Odigiri Great Alume (09:37:03) (in thread): > Is like our mentors should just pick all of us for the internship you know:thinking_face:We make a fine team y’all. > > It’s beautiful doing this with y’all.:blush:

Mildred Anashie (09:39:42) (in thread): > Yea…Great team work actually@Odigiri Great Alume

Peace Sandy (09:41:11) (in thread): > Very amazing and collaborative community, I absolutely loved working with everyone:heart:

Joan C. Chukwuemeka (09:47:52) (in thread): > The problem isn’t exactly just that duplicate signatures exist, it’s that is they’re an indication of a likely error. *****Each experiment is supposed to represent a unique contrast, and it’s very unlikely that two different, unique contrasts will produce exactly the same signature, so either one signature is out of place, or an experiment has been duplicated such as experiments for groups A vs B and also B vs A. > *****<@U1LCB8WEA>Thanks for the clarification. > > So, If I have Experiment 1 & 2, Experiment 1 contrasts between say Low(control) and medium (case 1) While Experiment 2 is a contrast between low(control) & high(case 2). Will the Uniqueness in this context mean that signatures in both Experiments has to be unique for both decreased and/or Increased abundance?:thinking_face:Thinking an overlap of the presence of certain taxa can rightly occur?

Odigiri Great Alume (09:50:29) (in thread): > @Joan C. ChukwuemekaI think he stated that both signatures can rarrrrrely be the same if they are unique. That is E1 and E2

Odigiri Great Alume (09:50:44) (in thread): > For overlaps certainly they can be

Mildred Anashie (09:50:55) (in thread): > @Joan C. ChukwuemekaYes I believe an overlap can occur….But identical signatures all through?:thinking_face:

Joan C. Chukwuemeka (10:13:15) (in thread): > Okay… If Experiments in question had same signatures all through… it’s really unlikely as<@U1LCB8WEA>pointed out.

UBNSEMS3S (16:30:18) (in thread): > @Chioma OnyidoCondition needs to come from EFO which are terms that start with EFO or MONDO generally. I’m not sure what HANCESTRO is but that’s why it’s not working.

UBNSEMS3S (16:31:26) (in thread): > I think population is a sufficiently close option, given the limitations of the ontology.

UBNSEMS3S (16:33:30) (in thread): > Correct. We don’t curate beta diversity.

Chioma Onyido (17:27:17) (in thread): > Thank you for the clarification<@UBNSEMS3S>:blush:@Chloe@Esther Afuapehere.

2023-11-15

Chiagoziem David (02:57:30) (in thread): > Emmmm, seems I Missed a lot yesterday, I traveled from portharcourt to Ibadan(lanlate), hope the team was able to help you sort out<@U1LCB8WEA>

Odigiri Great Alume (05:37:51): > Good morning everyone@C. Mirzayi (please do not tag this account)@Levi WaldronPlease I can’t seem to Add comments to signature on a study I’m working on. For example I recorded Peptostreptococcacea_XI_G5, Peptostreptococcacea_XI_G4 and Peptostreptococcacea_XI_G5 as Uncultured peptostreptococcacea sp. (I need to add comments to show all the different strains/species under the sp.) > And I do have many other studies I have curated that I need to add comments to. > > Please I will need a reviewers permit to enablee do this. However currently@Esther Afuapeis helping really good to add some of these comments. > > Thanks:pray:

Svetlana Ugarcina Perovic (06:46:54) (in thread): > Hey@Odigiri Great Alumejust approved your reviewer status:slightly_smiling_face:Keep up the good work!

Odigiri Great Alume (06:47:45) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (07:26:24): > I went throughhttps://bugsigdb.org/Study_443and I think the way the curator recorded the results is the reason why we have identical signatures for Experiment 1, signature 1 and Experiment 3, signature 1. > > Veillonella was recorded for IBS-D whereas it was not increased for IBS-D in the paper > > Ruminococcus productus was recorded as Blautia instead of******Blautia********** **********producta ****and**** ****segmented filamentous bacteria was not recorded for IBS-D > Also I came across Gram Negative Bacteria as a taxa, I have no idea how to record the signature, can I get help with this? > Can I effect these changes?@Levi WaldronDoes anyone want to go through this, so we compare observations? > Here’s the article - Attachment (BugSigDB): Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis - BugSigDB > BACKGROUND: Dysbiosis may play a role in irritable bowel syndrome (IBS), hitherto an enigmatic disorder.We evaluated selected fecal microbes in IBS patients and healthy controls (HC). - File (PDF): shukla2015.pdf

Chioma Onyido (07:28:53) (in thread): > @Mildred Anashieon it.:crossed_fingers:

Peace Sandy (07:28:53) (in thread): > Let me go through it

Peace Sandy (07:46:25) (in thread): > Hi@Mildred AnashieFrom the paper I think Veillonela was increased for IBS-D - File (PNG): IMG_6529

Chioma Onyido (07:47:07) (in thread): > I agree that IBS-D seems to be missing some taxa in signature 2.

Peace Sandy (07:47:53) (in thread): > The description text for B, states that the taxa in that figure B is for IBS-D, and I can see Veilonella as increased

Chioma Onyido (07:48:06) (in thread): > Veillonella belongs to the IBS-C subgroup not IBS-D.:white_check_mark:

Peace Sandy (07:48:14) (in thread): > ProbablyI’llneed a third eye@Chioma Onyidowhat do you think ?

Mildred Anashie (07:48:54) (in thread): > Yea@Chioma Onyidoobservation is in line with mine

Mildred Anashie (07:49:11) (in thread): > @Peace Sandycheck results text too

Chioma Onyido (07:50:09) (in thread): > Ohh I see.@Peace Sandyobservations are from the PCA results, which seems to be correct according to the diagram she shared

Peace Sandy (07:50:10) (in thread): > Okay@Mildred Anashielet go over it

Mildred Anashie (07:50:24) (in thread): > @Chioma OnyidoI think the decreased taxas are correct > > Can you point me to where you noticed that?

Chioma Onyido (07:51:41) (in thread): > But following Table 4,Veillonella species has an # which means that it belongs to the IBS-C group according to the keys the authors used for description (image below) - File (JPEG): IMG_6144

Chioma Onyido (07:52:29) (in thread): > @Mildred Anashiecheck the image I sent,Bacteroides species has a + sign, which is for IBS-D group.

Chioma Onyido (07:53:44) (in thread): > Oopsss it belongs to the signature 1, just saw it now. Accurate.:white_check_mark:

Peace Sandy (07:55:34) (in thread): > So how was the Gram negative bacteria entered ?

Mildred Anashie (07:56:21) (in thread): > Itwasn’tentered > > > And I need help figuring out how to enter it

Peace Sandy (07:56:26) (in thread): > I can confirm for Bacteroides > And Pseudomonas aeruginosa

Peace Sandy (07:57:31) (in thread): > And then I can see segmented flagellated bacteria as well, has it been entered@Mildred Anashie

Chioma Onyido (07:57:36) (in thread): > Still trying to figure out why Expt 1 Sig 1 has same taxa with Expt 3 Sig 1.:thinking_face:

Mildred Anashie (07:58:44) (in thread): > No SFBwasn’trecorded

Mildred Anashie (07:59:55) (in thread): > @Chioma OnyidoI figured IBS-C and IBS-D are subgroups of IBS

Chioma Onyido (08:00:22) (in thread): > Wrong statistical test was entered too for expt 1. It’s supposed to be Mann-Whitney, but the curator entered Kruskall-Wallis. > See - File (JPEG): IMG_6147 - File (JPEG): IMG_6146

Peace Sandy (08:00:33) (in thread): > @Mildred Anashiethe result for IBS - D group was it only gotten from table 4

Mildred Anashie (08:01:08) (in thread): > @Chioma Onyidothat’scorrect

Peace Sandy (08:01:13) (in thread): > I noticed@Chioma Onyido

Mildred Anashie (08:01:20) (in thread): > Yes Table 4 and results text too but the curatordidn’tinclude that

Chioma Onyido (08:02:06) (in thread): > You mean the observation is correct or the statistical test?:sweat_smile:

Peace Sandy (08:02:47) (in thread): > Are we interpreting Table 3 > I thoughtit’sjust showing relative difference

Mildred Anashie (08:02:47) (in thread): > The observation

Peace Sandy (08:03:34) (in thread): > I think why the initial curator used Kruskall-Wallis is because of table 4

Peace Sandy (08:04:40) (in thread): > I noticed the statistical test thingy too

Mildred Anashie (08:04:47) (in thread): > Signatures for IBS are in Table 3 and within text while those for IBS-C ,and IBS-D are in Table 4 > > In my opinion

Peace Sandy (08:05:11) (in thread): > Oh…

Chioma Onyido (08:05:49) (in thread): > @Peace Sandyshouldn’tbe because they are different groups and different tests used.

Peace Sandy (08:06:05) (in thread): > Oh I see@Chioma Onyido

Peace Sandy (08:07:04) (in thread): > I think the initial curator mixed up somethings

Mildred Anashie (08:07:29) (in thread): > Anyone has an idea how the Gram Negative Bacteria can be recorded?@Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina Perovic

Mildred Anashie (08:09:15) (in thread): > Thank you@Chioma Onyido@Peace SandyCan we confirm my initial observations are okay including the statistical test Chioma just pointed out

Chioma Onyido (08:09:33) (in thread): > What should be done about this duplicate now?

Peace Sandy (08:10:18) (in thread): > Yes@Mildred Anashie

Mildred Anashie (08:11:40) (in thread): > You mean the signatures?

Mildred Anashie (08:13:39) (in thread): > I think editing the signature for IBS-D can solve the problem > > Removing the ones thatshouldn’tbe there and including the missing ones can solve that problem:thinking_face:

Chioma Onyido (08:15:44) (in thread): > @Mildred AnashieThe challenge with this gram negative bacteria is that they didn’t specify the exact gram negative bacteria they’re referring to, E. Coli, P. aeruginosa (to mention a few) are examples. > I doubt ifthere’sa single ID for collective gram negative bacteria on NCBI:woman-shrugging: - File (JPEG): IMG_6148

Chioma Onyido (08:16:49) (in thread): > Hmmwouldn’tit still be identical with IBS, they both have similar taxa (IBS D and IBS).@Mildred Anashie

Mildred Anashie (08:17:05) (in thread): > Yea thereisn’t@Chioma OnyidoI already checked and what you shared in the screenshot is what popped up,that’swhyI’masking for help > > Or should I record it as it is?:thinking_face:

Peace Sandy (08:17:16) (in thread): > True@Chioma Onyido@Mildred Anashiehave you figured out how the segmented flagellated bacteria can be entered too ?

Mildred Anashie (08:18:16) (in thread): > The taxas will have similarities but not identical all through, andthatshould be allowed:thinking_face:

Peace Sandy (08:20:20) (in thread): > I think so

Mildred Anashie (08:20:45) (in thread): > Yes@Peace Sandythe Segmented Flagellated Bacteria is same as Segmented Filamentous Bacteria which was used interchangeably in the article and is on NCBI as Candidatus arthromitus sp. sfb-mouse > > So I’m thinking I’ll use the ID for Candidatus arthromitus

Peace Sandy (08:21:16) (in thread): > Oh wow…nice to know

Peace Sandy (08:21:40) (in thread): > Yes, I think you should

Chioma Onyido (08:22:12) (in thread): > Yes<@UBNSEMS3S>once stated that synonyms works just fine.:+1:

Chioma Onyido (08:27:39) (in thread): > Another observation,@Mildred AnashieIm thinking maybe you could also update the descriptions for the respective signatures..?The curatordidn’t specifically state the subtypes but generalized everything as “IBS”.I’m thinking since the paper worked with diff subtypes of IBS, this is supposed to be included in the curation for easier identification during future analyses.

Chioma Onyido (08:32:45) (in thread): - File (JPEG): IMG_6151

Mildred Anashie (08:34:40) (in thread): > Thank you > > Another set of eyes is always important:blush:

Chioma Onyido (08:40:43) (in thread): > Couldn’tagree more!:smiley:

Esther Afuape (08:43:39) (in thread): > Is there anything to delete for this study?@Mildred Anashie

Mildred Anashie (08:44:55) (in thread): > In my opinion No, Just to edit > > Did you find anything?

Esther Afuape (08:47:27) (in thread): > No no, Ididn’t. I wanted to add it to the list of the ones that need deletion

Mildred Anashie (08:49:09) (in thread): > Okay > > Thought you had temporary delete privileges:grin::smile:I’llmake sure to let you know if I come across one that needs deleting

Mildred Anashie (08:49:35) (in thread): > You should add the once we figured out yesterday

Esther Afuape (08:50:32) (in thread): > Idon’t:joy:Yes,I’lladd those ones too

Chioma Onyido (08:51:57) (in thread): > I’vea short list too@Esther AfuapeI’llnotify you to merge whenI’mdone:new_moon_with_face:

Peace Sandy (08:52:12) (in thread): > @Esther AfuapeIdon’tthink all the studies detected yesterday should be deleted > They are some that still needs confirmation from the mentors

Esther Afuape (08:52:46) (in thread): > @Peace Sandydid you fix 678?

Peace Sandy (08:53:09) (in thread): > No…some are contradictory

Peace Sandy (08:53:32) (in thread): > Ididn’tfix 678…I thought someone else did

Esther Afuape (08:53:47) (in thread): > @Peace SandyI’mnot deleting anything,Ican’t!:sweat_smile:I’monly compiling the ones that need deletion for the mentors to go through them

Esther Afuape (08:54:23) (in thread): > @Chioma Onyidobest in collab:handshake::heart:

Peace Sandy (08:54:25) (in thread): > Oh Okay…I’llshare the ones I have with you too@Esther Afuape

Mildred Anashie (08:54:30) (in thread): > Was going to say that@Peace SandyI think the mentors will review before deleting

Peace Sandy (08:54:42) (in thread): > Okay@Mildred Anashie

Chioma Onyido (08:55:50) (in thread): > Yeah I think Esther’s merged list is just a compiledpre-reviewed version to make it easier for the mentors. > Great initiative BTW!:wink:@Esther Afuape

Esther Afuape (09:07:32) (in thread): > What do you guys think should be done toHttps://bugsigdb.org/Study_526? > The comparisons in the paper will have all the signatures looking similar.@Chioma Onyido@Mildred Anashie@Peace Sandy - Attachment (BugSigDB): Microbiome of the lower genital tract in Chinese women with endometriosis by 16s-rRNA sequencing technique: a pilot study - BugSigDB > Background: Endometriosis is a benign, chronic, gynecological disease which affect the women in reproductive age.The dysfunction of immune system is associated with endometriosis and the diversity of microbiota in genital tract.

Peace Sandy (09:08:14) (in thread): > Let me go through it@Esther Afuape

Mildred Anashie (09:11:03) (in thread): > Let me look at it too

Chioma Onyido (09:20:53) (in thread): > First of all, how was the curator able to interprete figure 6??:tired_face:I was only able to get results within text.

Peace Sandy (09:21:43) (in thread): > Some figures are quite complex to interpret

Chioma Onyido (09:24:42) (in thread): > Here’swhat I was able to get from the results within text, under the sub-headingMicrobiota composition of different diseases (Paragraph 5, from line 16) - File (JPEG): IMG_6152

Peace Sandy (09:24:44) (in thread): > The initial curator didn’t record any signature for Experiment 3@Esther Afuape

Mildred Anashie (09:24:53) (in thread): > I have been looking at the fig 6 too, wondering whats going on there

Esther Afuape (09:25:41) (in thread): > I just added experiment 3, the initial curatordidn’tadd it. I want to know the solution first before I add signatures to it@Peace Sandy

Peace Sandy (09:26:01) (in thread): > Oh…Okay@Esther Afuape

Peace Sandy (09:26:44) (in thread): > I noticed experiment 1 and 2 have the same signatures,I’mtrying to figure it out

Mildred Anashie (09:27:53) (in thread): > What@Chioma Onyidojust shared i observed too and its pointing us to figure 3

Esther Afuape (09:27:59) (in thread): > @Chioma Onyidothe results are from two-two comparisons so they have to be curated as such. > AMEM vs EM > AMEM vs CT > AMEM vs AM

Peace Sandy (09:29:10) (in thread): > Hmmm…I can see that from figure 6

Chioma Onyido (09:29:36) (in thread): > @Mildred Anashie@Esther Afuapethe results I shared were gotten within text, from figure 6, check the paragraph under the subheading indicated..

Peace Sandy (09:32:34) (in thread): > I can see some results in the text

Mildred Anashie (09:33:39) (in thread): > True its figure 6……I’ve read through again

Esther Afuape (09:34:52) (in thread): > You think it should have only 2 experiments of AMEM vs CT and EM, AMEM vs AM?@Chioma Onyido

Mildred Anashie (09:35:10) (in thread): > I was confused with this - File (PNG): chi.PNG

Esther Afuape (09:35:13) (in thread): > Seems to me like the results within text is the same as the one in figure 6

Peace Sandy (09:35:14) (in thread): > In the paragraph above figure 6 > > It stated that, Atopobium, Campylobacter, Ezakiella, Faecalibacterium and Escherichia / Shigella exhibited a higher abundance in the AMEM group when compared to the CT group and EM group

Peace Sandy (09:36:48) (in thread): > I think it should have > AMEM and CT > AMEM and EM > AMEM and AM@Esther Afuape

Chioma Onyido (09:36:52) (in thread): > Yes same results but interpreted more clearly, without double entry.:woman-shrugging:@Esther Afuape

Mildred Anashie (09:38:15) (in thread): > Yes…If you record AMEM vs CT and AMEM vs EM, that will give the same results because the taxas were the same when AMEM was compared with CT and EM

Chioma Onyido (09:39:11) (in thread): > @Peace SandyThe signatures increased when AMEM was compared to CT is the same for when compared to EM,that’show the curator recorded it, and this is whywe’vethe issue of double entry. > > Exactly@Mildred Anashie

Esther Afuape (09:39:16) (in thread): > @Peace Sandythat’s what I think too but the signatures will be almost the same. > What@Chioma Onyidosuggested would prevent double entries but it’s combining 2 experiments into 1..

Peace Sandy (09:39:57) (in thread): > Hmmm

Chioma Onyido (09:40:05) (in thread): > That’swhyI’msuggesting to curate as reported within text and referenceresults within textas the source,:woman-shrugging:

Chioma Onyido (09:40:13) (in thread): > That way the experiments would be unique.

Chioma Onyido (09:40:26) (in thread): > However This needs further review from the mentors.

Peace Sandy (09:40:42) (in thread): > I agree with@Chioma Onyido@Esther Afuapelet’scurate as reported within text

Peace Sandy (09:40:58) (in thread): > True@Chioma Onyidoit’sa bit tricky

Mildred Anashie (09:41:10) (in thread): > Yes we should draw their attention to this before we conclude

Esther Afuape (09:41:49) (in thread): > OkayI’llpoint that out in this list. > Thank you guys:face_holding_back_tears:

UBNSEMS3S (10:16:57) (in thread): > Taking a quick look at this and I do think there are some issues in the original curation. > > I don’t think we can curate something like “gram negative bacteria” as that doesn’t correspond to anything taxonomic. > > Pairwise comparisons as are presented in Table 4 always cause some confusion but this should be relatively straightforward. Here is what I’m seeing should be curated: > > Experiment 1 (Table 3): (currently incorrectly curated as Kruskal-Wallis though it is Mann-Whitney) IBS vs. HC (6 significant results) > Experiment 2 (Table 4): (should be curated as Mann-Whitney AND Kruskal-Wallis) IBS-C vs. HC (6 significant results) > Experiment 3 (Table 4): (should be curated as Mann-Whitney AND Kruskal-Wallis) IBS-D vs. HC (4 significant results) > Experiment 4 (Table 4): (should be curated as Mann-Whitney AND Kruskal-Wallis)IBS-U vs. HC (0 significant results) > Experiment 5 (Table 4): (should be curated as Mann-Whitney AND Kruskal-Wallis) IBS-C vs. IBS-D (3 significant results) > Experiment 6 (Table 5): Visible Abdominal distension vs. absent (5 significant results) > Experiment 7 (Table 5): Abdominal bloating vs. absent (3 significant results)

Chioma Onyido (10:18:48) (in thread): > 7 experiments! Wow!

Mildred Anashie (10:18:55) (in thread): > Interesting to note<@UBNSEMS3S>

Mildred Anashie (10:19:41) (in thread): > I actually came across the experiment 7I’llread through again to find the others

Peace Sandy (10:19:48) (in thread): > I thought so too, but I was a bit confused

Mildred Anashie (10:20:33) (in thread): > Does this mean I can edit and add the other experiments?<@UBNSEMS3S>

UBNSEMS3S (10:20:41) (in thread): > I am going to update the curation policy to include instructions on curating pairwise comparisons. It’s not something that most people are taught–even in graduate-level statistics courses–and so it can cause a lot of confusion.

UBNSEMS3S (10:20:46) (in thread): > @Mildred AnashiePlease do.

Peace Sandy (10:21:02) (in thread): > True@C. Mirzayi (please do not tag this account)

Peace Sandy (10:21:25) (in thread): > @Esther Afuapecome and see! > You can use the cue@C. Mirzayi (please do not tag this account)gave for the study you are currently working on

Mildred Anashie (10:22:19) (in thread): > Quick one<@UBNSEMS3S>So we ignore the Gram Negative Bacteria?:thinking_face:

Chioma Onyido (10:22:25) (in thread): > This will be super helpful<@UBNSEMS3S>I remember Chloe explaining pairwise comparison in the last lab meeting, I was sooo lost:sweat_smile::eyes:

Peace Sandy (10:23:09) (in thread): > I’lllike to know about this Gram negative bacteria issue ?

Chioma Onyido (10:23:14) (in thread): > same with Gram positive@Mildred Anashie

Esther Afuape (10:23:40) (in thread): > That’ll be super helpful:face_holding_back_tears:

UBNSEMS3S (10:23:44) (in thread): > @Mildred AnashieYes I would say ignore gram negative bacteria (and positive). That’s not a taxonomic classification–it’s a characteristic of the bacteria so we can’t really curate it.

Peace Sandy (10:24:14) (in thread): > Wow

Mildred Anashie (10:25:26) (in thread): > Okay<@UBNSEMS3S>I was really wondering why they had to separately report Gram -ve and Gram +ve because the we already have Gram -ve and Gram +ve organisms among the taxas reported

UBNSEMS3S (10:28:02) (in thread): > I think they combined them to do a group-level analysis rather than looking at those individual taxa since sometimes findings will be significant at a higher level. > > As a bit of trivia not directly relevant to BugSigDB, it’s important to consider the groupings in your findings as making assumptions about individuals based on groups is a common statistical fallacy:https://en.wikipedia.org/wiki/Ecological_fallacy - Attachment: Ecological fallacy > An ecological fallacy (also ecological inference fallacy or population fallacy) is a formal fallacy in the interpretation of statistical data that occurs when inferences about the nature of individuals are deduced from inferences about the group to which those individuals belong. From the conceptual standpoint of mereology, four common ecological fallacies are: > > Correlation/relation: confusion regarding relations belonging to parts versus relations belonging to wholes,Characteristics: confusion between characteristics of parts and characteristics of a whole,Extrapolation/extension: confusion from false inference of part-whole dynamics: assuming the behavior of partially unknown and/or future wholes from information which is relatively partial,Confusion between qualities not bound to individual parts, for example “atmospheres”, “moods” and “vibes”, versus properties, hæccities or identities of indivisible units.From a statistical point of view, these ideas can be unified by specifying proper statistical models to make formal inferences, using aggregate data to make unobserved relationships in individual level data.

Mildred Anashie (10:32:03) (in thread): > Okay > > This is implying they compared based on a higher classification and narrowed it down? > > And still reported for all?:thinking_face:

UBNSEMS3S (10:35:43) (in thread): > No I don’t think they narrowed it down. I think they were just interested in gram + and gram - and compared them as well as taxa as normal.

Mildred Anashie (10:38:19) (in thread): > Okay > > A bit confusing as to why they reported for a Gram + and Gram - which is a form of characterization of organisms after identifying organisms that fall within those characteristics

Mildred Anashie (10:38:54) (in thread): > Thank you for your time and responses > > Always insightful > > Let me go and do the one that concerns BugSigDB for now:blush::smile:

Mildred Anashie (11:00:23) (in thread): > I can identify just 2 significant results for Experiment 7 (Abdominal bloating vs. absent) can someone confirm thisAnd just pointing this out, Experiment 3 will have just 3 taxas recorded since we are ignoring Gram -ve bacteria - File (JPEG): IMG_5354

UBNSEMS3S (11:03:56) (in thread): > Oh yeah looks like 2

Mildred Anashie (11:06:24) (in thread): > Thank you:pray:

Chioma Onyido (11:08:15) (in thread): > But only one is curatable which is clostridium right?@Mildred AnashieSince we’re not curating gram negative? For experiment 7.

Peace Sandy (11:09:38) (in thread): > I think so

Mildred Anashie (11:09:49) (in thread): > Also<@UBNSEMS3S>you’ll have to delete the signatures recorded for Experiment 4https://bugsigdb.org/Study_443 - Attachment (BugSigDB): Fecal Microbiota in Patients with Irritable Bowel Syndrome Compared with Healthy Controls Using Real-Time Polymerase Chain Reaction: An Evidence of Dysbiosis - BugSigDB > BACKGROUND: Dysbiosis may play a role in irritable bowel syndrome (IBS), hitherto an enigmatic disorder.We evaluated selected fecal microbes in IBS patients and healthy controls (HC).

Mildred Anashie (11:10:10) (in thread): > Yes > > Sure@Chioma Onyido

UBNSEMS3S (11:15:34) (in thread): > Deleted.

UBNSEMS3S (19:57:50): > Hi everyone we will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499There was some confusion due to DST here in the US last week so if you’re unsure about when the meeting is here’s a link to find out for your time zone:https://www.timeanddate.com/worldclock/converter.html?iso=20231116T150000&p1=179

2023-11-16

Mildred Anashie (00:31:21) (in thread): > Thank you for the update:pray:

Nwajei Edgar (00:57:57) (in thread): > Noted, thanks for the update

Nana (01:24:20) (in thread): > Noted, thanks

Peace Sandy (01:33:49) (in thread): > Thank you for the update

Peace Sandy (01:38:12) (in thread): > For Nigerians the weekly sync will be by > 4:00pm Today

Chiagoziem David (02:46:31) (in thread): > Thanks<@UBNSEMS3S>, see you there

Chiagoziem David (02:49:27) (in thread): > Thanks@Peace Sandy:smile::smile:, very important:grinning:

Nana (02:52:45) (in thread): > @Peace Sandyyou are very correct

Esther Afuape (05:02:42): > Hello Everyone. From the sentence below, shannon, simpson and chao1 can be said to decreased, right? and not unchanged?“The alpha diversity indices, including ACE index, Chao1 index, Shannon diversity index, Simpson’s diversity index, and Good’s coverage index, of the gut microbiota of KS group were all lower than those of HC group, but there was no statistical significance of the gut microbiota between KS group and HC group”

Mildred Anashie (05:51:10) (in thread): > If there was no statistical significance for the diversity measures, that should be unchanged:thinking_face:

Peace Sandy (06:18:06) (in thread): > Hmmm

Peace Sandy (06:18:30) (in thread): > @Esther AfuapeI thinkit’sunchanged

Chioma Onyido (06:21:43) (in thread): > From the excerpt you shared,I’mwondering why they had 2 contradicting statements,clearly stated that alpha diversity indices were lower in the case group compared to the control, then went on to say thatthere’sno stat significance…???I’mthinking, could the “but there was no stat significance” here be referring to thegut microbiotabetween the groups not the alpha diversity…?

Chioma Onyido (06:22:47) (in thread): > @Esther Afuapeanother way wecouldget a clue is to check for the figures presenting the alpha diversity indices. Did you see any?

Peace Sandy (06:25:49) (in thread): > The statement indicates that the alpha diversity indices, including ACE index, Chao1 index, Shannon diversity index, Simpson’s diversity index, and Good’s coverage index, were lower in the gut microbiota of the KS group compared to the HC group. However, it also mentions that there was no statistical significance between the two groups.

Mildred Anashie (06:26:30) (in thread): > Uhhhmmmm@Chioma OnyidoI think an increase or decrease can be observed but with no statistical significance when the statistical analysis was conducted > > The test helps confirms the results to be significant (increased/Decreased) in my opinion > > But your suggestions on the figure is a great option, that can really help@Esther Afuape

Chioma Onyido (06:28:14) (in thread): > Ohh I see…There was a decrease in the indices but it wasnot significant. @Mildred Anashie**** ****@Peace Sandy**** ****

Esther Afuape (06:28:32) (in thread): > @Chioma Onyidothe figure for alpha diversity is in the supplementary file for the paper. Icouldn’tget the paper through the Doi and the pdf version I was able to getdoesn’thave a link to the supplemental

Chioma Onyido (06:29:10) (in thread): > If that’s the case, then it’sunchangedlike you said.@Peace Sandy@Mildred Anashie@Esther Afuape

Chioma Onyido (06:29:36) (in thread): > Is it the same meta-analysis?@Esther Afuape

Peace Sandy (06:30:34) (in thread): > Oh…never knew they was a decrease@Chioma Onyido

Esther Afuape (06:31:23) (in thread): > No..it’sa study with an incomplete review thatI’mtrying to complete@Chioma Onyido

Peace Sandy (06:31:55) (in thread): > @Esther AfuapeSee this reply by@C. Mirzayi (please do not tag this account)https://community-bioc.slack.com/archives/C04RATV9VCY/p1696973730843419

Mildred Anashie (06:32:54) (in thread): > @Peace Sandythere was a decrease > > The indices were lower in theKSgroup > Which seems to be the case group

Peace Sandy (06:33:18) (in thread): > Wow…@Mildred Anashie

Esther Afuape (06:33:42) (in thread): > @Peace Sandythe difference with<@UBNSEMS3S>reply is that itdoesn’tsay that there was no statistical difference found in the alpha diversities. It says there was a decrease but no statistical significance in the gut microbiota

Chioma Onyido (06:34:08) (in thread): > Yes there was a decrease but since it isnot significant then it isunchanged,I agree with that@Peace Sandythanks for sharing:sweat_smile:I only wanted to confirm with alpha diversity figures, maybeit’llgive us more clarifications.

Peace Sandy (06:34:12) (in thread): > Yes I just got from what@Mildred Anashiesaid

Esther Afuape (06:35:32) (in thread): > I just realized thatthere’sa “student’s t-test, p>0.05” in a bracket after the sentence.That should be the P value for the difference in the gut microbiota usingstudent’st-test, right? > Not for the alpha diversities?

Mildred Anashie (06:35:50) (in thread): > @Esther Afuapesincethere’snothing to guide us further > > My interpretation of this statement isunchanged

Chioma Onyido (06:36:28) (in thread): > @Esther AfuapeEsther at this point I think you should share the paper or the entire paragraph:confused:

Mildred Anashie (06:36:41) (in thread): > Is there a table or figure showing this?@Esther Afuape

Esther Afuape (06:36:52) (in thread): > https://sci-hub.se/http://dx.doi.org/10.1007/s00240-018-1037-y

Chioma Onyido (06:51:21) (in thread): > @Esther AfuapeThis was my thought initially, that maybe the “but there was no stat sig” was for the difference in gut microbiota not alpha diversity.The alpha diversity figure would’ve given us additional info but it’s provided in a supplemental file which can’t be accessed.:unamused::broken_heart:

Mildred Anashie (06:52:29) (in thread): > @Esther AfuapeI think this are the supplemental files - File (Word Document): 240_2018_1037_MOESM1_ESM (1).docx - File (Excel Spreadsheet): 240_2018_1037_MOESM4_ESM.xlsx

Mildred Anashie (06:53:06) (in thread): > Y’all check the word document

Peace Sandy (06:53:33) (in thread): > Let me check this out

Esther Afuape (06:55:05) (in thread): > How did you get those?!@Mildred Anashie

Chioma Onyido (06:55:18) (in thread): > Table S2 shows p values for all the alpha diversity indices and they were all above the threshold. > ThereforeNo significance!=Unchanged.:partying_face:You’reall right.

Mildred Anashie (06:55:59) (in thread): > Let’sjust say I like to find things:joy:@Esther Afuape

Esther Afuape (06:56:35) (in thread): > I need the cheat code come onnnnn:face_with_peeking_eye:@Mildred Anashie

Mildred Anashie (06:56:35) (in thread): > From the online version though on PubMed > > Just clicked the full text link and it was there when I scrolled down

Peace Sandy (06:56:37) (in thread): > Hmmm

Peace Sandy (06:57:02) (in thread): > Wow…that’sanother trick > Thank You@Mildred Anashie

Chioma Onyido (06:58:29) (in thread): > Which pubmed did you check@Mildred Anashiemaybe our pubmeds are diff:new_moon_with_face: - File (QuickTime Movie): Video Clip (2023-11-16 12:57:59)

Mildred Anashie (06:59:51) (in thread): > Absolutely the same PubMed , Click on Full text link@Chioma Onyido

Chioma Onyido (07:01:25) (in thread): > It directed me here andit’snot open access.:slightly_frowning_face: - File (QuickTime Movie): Video Clip (2023-11-16 13:00:34)

Chioma Onyido (07:03:11) (in thread): > Ohhh I’ve seen it.. > Iwasn’tpatient.:face_with_peeking_eye: - File (JPEG): IMG_6166

Peace Sandy (07:03:51) (in thread): > :joy::joy::joy:

Mildred Anashie (07:04:06) (in thread): > :sweat_smile:

Peace Sandy (07:04:15) (in thread): > I’mhappy you have figured it out@Chioma Onyido

Mildred Anashie (07:04:52) (in thread): > Patience is my other name then:sweat_smile::see_no_evil:

Chioma Onyido (07:06:37) (in thread): > Thank you for saving the day detectives@Mildred Anashie:new_moon_with_face::bouquet:@Peace Sandy@Esther AfuapeNice BugSigDB-ing everyone.:raised_hands::clap:

Esther Afuape (07:10:23) (in thread): > Thank you guys

Odigiri Great Alume (07:58:20) (in thread): > @Mildred Anashiewell-done

Odigiri Great Alume (08:09:09) (in thread): > Take home point for those who missed this conversation is that there could be a decrease Or increase in any group compared to other groups (alpha diversity, diff abundance etc) but that doesn’t mean it is statistically significant. > > Also just to add, if there were no statistical test carried out to compare the groups then don’t record. > > Good one guys@Chioma Onyido@Peace Sandy@Mildred Anashie@Esther Afuapeetc

Chiagoziem David (08:51:45) (in thread): > Thank you guys,:blush::slightly_smiling_face::blush::grin:

Chiagoziem David (08:54:12) (in thread): > Anyone has any idea what the comparison would be against here, we can infer for if it was decreased or increased statically, but I am finding it hard to know what is being compared - File (PNG): image.png

Chioma Onyido (09:00:07) (in thread): > @Chiagoziem Davidaccording to the description, I see that they were contrasting 4 diet categories, B H K and W forLDA1 results. > And 3 diet categories; B+H, K and W forLDA2**results…:thinking_face:

Chiagoziem David (09:00:53) (in thread): > Yeah, that’s there, what’s increasing or decreasing for what groups is my confusion

Peace Sandy (09:01:06) (in thread): > What is the paper contrasting for ?@Chiagoziem David

Chiagoziem David (09:01:42) (in thread): > Diet and sex

Peace Sandy (09:05:17) (in thread): > What I can see from the excerpt you shared is ? > Comparison of relative abundance of B, H, K and W using Kruskal - Wallis test

Peace Sandy (09:06:56) (in thread): > So from it I can also see that B, H, K and W are four diet categories

Chioma Onyido (09:06:58) (in thread): > Positive LDA scores are usually recorded as increase whereas negative are recorded as decrease, but we need to understand the full context of what was being compared.

Peace Sandy (09:07:11) (in thread): > True

Peace Sandy (09:07:27) (in thread): > Just what you shared might not be enough

Chioma Onyido (09:07:58) (in thread): > Care to share the paper or it’s doi?@Chiagoziem DavidLet’sall look at it together.

Chiagoziem David (09:08:07) (in thread): > This was the study I spoke about that didn’t have alpha diversity only beta diversity.. yeah@Chioma Grace, but I can’t figure out for which groups the increase or decrease is happening

Mildred Anashie (09:08:40) (in thread): > Is there a control group? > > Or is there any where Diet was contrasted against sex? > > So we can figure out the various group comparisons

Chiagoziem David (09:08:54) (in thread): > Let me share, you’d have to download the graphs though as excel sheets

Chiagoziem David (09:09:57) (in thread): > Nope there was a contrast for groups in the sex condition and also for groups in the diet condition@Mildred Anashie

Mildred Anashie (09:10:50) (in thread): > Okay….Just share the paper first

Chioma Onyido (09:12:50) (in thread): > Guys..I’mseeing something new, > They compared (genera) results obtained from 2 different stat. tests;Kruskal WallisandLDA(1 and 2).

Peace Sandy (09:13:35) (in thread): > Yes, I noticed it too

Chioma Onyido (09:13:55) (in thread): > KW has its own results > LDA 1 and 2 has its own results.

Chiagoziem David (09:13:59) (in thread): > Yeah, I didn’t even want to look at that

Peace Sandy (09:14:15) (in thread): > If we are not able to go around it before weekly sync , I suggest you bring it up during the meeting today@Chiagoziem David

Chiagoziem David (09:14:20) (in thread): > That was to confirm the tests though, from the text material

Chiagoziem David (09:14:46) (in thread): > KW was the original test carried out

Chiagoziem David (09:15:51) (in thread): > I’m trying to get my pc up, so I can share the paper

Mildred Anashie (09:17:26) (in thread): > @Chiagoziem Davidare you thinking the results we should be looking at is from LDA results since they collapsed B and H wecan’tuse LDA 1:thinking_face:

Chiagoziem David (09:18:02) (in thread): > I think we should use the KW results

Mildred Anashie (09:19:37) (in thread): > If you are suspecting LDA was a confirmatory testShouldn’twe be looking at what remained significant after the confirmatory test was done?:thinking_face:Just speculating though

Chiagoziem David (09:20:27) (in thread): > Hmmmm, That’s also true

Mildred Anashie (09:21:10) (in thread): > When you are able to share the paper > > We might get more from it

Chiagoziem David (09:22:42) (in thread): > Https://Pubmed.ncbi.nlm.nih.gov/32804973/ - Attachment (PubMed): Learning machine approach reveals microbial signatures of diet and sex in dog - PubMed > The characterization of the microbial population of many niches of the organism, as the gastrointestinal tract, is now possible thanks to the use of high-throughput DNA sequencing technique. Several studies in the companion animals field already investigated faecal microbiome in healthy or affected …

Chioma Onyido (09:33:42) (in thread): > (Unrelated…) I guess this is why they joined the groups (B and H)… - File (JPEG): IMG_6168 - File (JPEG): IMG_6169

Chioma Onyido (09:35:04) (in thread): > Wondering if this could be an example case ofecological fallacy<@UBNSEMS3S>explained yesterday…* :thinking_face: *

UBNSEMS3S (09:43:41) (in thread): > It looks to me like they didn’t present pairwise comparisons between the 4 groups making curation of this table impossible. > > Taking a quick glance at the paper and it looks like table S5 can be curated and that might be it.

Peace Sandy (09:44:27) (in thread): > Oh

Chioma Onyido (09:46:23) (in thread): > This is the results they got after using KW to confirm LDA and RF analysis. > Pairwise comparisons. Which I am not sure how to go about yet.:slightly_frowning_face:<@UBNSEMS3S>mentioned updating instructions on how to curate this soon. - File (JPEG): IMG_6170

Chiagoziem David (09:47:41) (in thread): > Hmmm, so I should work with S5 yeah?

Chiagoziem David (09:48:46) (in thread): > How do we tell what was significantly increased or decreased though

Peace Sandy (09:50:40) (in thread): > I’llreally like to know how to curate the table too@Chioma Onyido

Chiagoziem David (09:52:09) (in thread): > I think<@UBNSEMS3S>should help us out:pleading_face:

UBNSEMS3S (09:54:22) (in thread): > @Chiagoziem DavidLook at the means and the superscripts. > > For Bacteriodales, it was increased in W compared to K and increased in W compared to H-B. > > Helicobacter was increased in H-B compared to K. > > Coprococcus was increased in W compared to K. It was also increased in K compared to H-B.. Finally, it was increased in W compared to H-B.

Chiagoziem David (09:55:26) (in thread): > Alright<@UBNSEMS3S>,I’d get back to it after the office hours, thank you very much:grin::grin:

Chioma Onyido (09:59:06) (in thread): > Does this mean that for rows with thesameletters in all 3 groups (e.g.a) > **No statistical difference? And henceshouldn’tbe recorded?<@UBNSEMS3S>

UBNSEMS3S (10:00:12) (in thread): > Correct.

Chiagoziem David (10:00:53) (in thread): > Yep@Chioma Onyido

Mildred Anashie (10:00:53) (in thread): > Yea…Noticed such rows also have really low mean values

Chiagoziem David (10:02:57) (in thread): > @Chioma Onyidocan you please send the image again?

Chiagoziem David (10:03:43) (in thread): > S5

Mildred Anashie (10:04:47) (in thread): > This is S5 - File (Excel Spreadsheet): pone.0237874.s005.xlsx

Chiagoziem David (10:05:43) (in thread): > Thanks@Mildred Anashie

Chiagoziem David (10:09:50): > Anybody with access to the meeting link yet

Chioma Onyido (10:11:44) (in thread): > https://us02web.zoom.us/j/2737200499

Chiagoziem David (10:12:41) (in thread): > Thanks

Chiagoziem David (10:15:37): > I’m on hold though, can’t get in

Peace Sandy (10:17:10) (in thread): > Oh…She is currently speaking…

Peace Sandy (10:17:22) (in thread): > I think@Chioma Onyidohas alerted her

Chiagoziem David (10:17:53) (in thread): > Im in, thanks

Chioma Onyido (10:17:54) (in thread): > Chloe should let you in soon, she’s answering questions.

Mildred Anashie (11:06:16): > Quick one guys (For those that didn’t know like myself:see_no_evil:) BMI should be entered in full as Body Mass Index (that’s the EFO term) for Matched on.

Chiagoziem David (11:12:58): > Hello guys , sometimes some articles use new names of signatures that haven’t been updated in the NCBI database, but the old names are there (would auto-complete when you type them) , should we go with the old names( or synonyms) When curating?

Peace Sandy (11:31:22) (in thread): > Heard it today too:sweat_smile:Thank You@Mildred Anashie

Chioma Onyido (12:08:25) (in thread): > @Mildred Anashie:eyes: - File (JPEG): IMG_6180

Chioma Onyido (12:10:31) (in thread): > Not sure I get the question correctly, > > Could you cite an example?

UBNSEMS3S (12:15:44): > Today’s meeting recording - File (MPEG 4 Video): video1852383621.mp4

UBNSEMS3S (12:41:11) (in thread): > We should always use the NCBI taxonomy as much as possible even if that means the NCBI taxonomy has an older synonym and you’ve found a record of a newer one. > > The benefit of when we link to an NCBI ID is that even if NCBI updates that taxonomy, those changes will be reflected in BugSigDB.

Chiagoziem David (12:56:51) (in thread): > Alright, that’s what I do, just wanted to be sure I was doing the right thing<@UBNSEMS3S>, thanks for the clarification

Esther Afuape (13:12:36): > Is it okay to replaceparaprevotellaceaewith “unclassifiedparaprevotella”? <@U1LCB8WEA>. “unclassified paraprevotella” has no rank and I feel its some sort of a compromise.* *It is tagged “unfixable” in this studyhttps://bugsigdb.org/Study_47https://bugsigdb.org/Study_47

Mildred Anashie (13:23:35) (in thread): > Thankyou@Chioma OnyidoWorked blindly on that one:woman-facepalming:

Peace Sandy (13:28:54) (in thread): > Thank You:pray:

UBNSEMS3S (14:40:41) (in thread): > I’m not sure those are exactly synonyms but I’m not a microbiologist.

Odigiri Great Alume (16:36:58) (in thread): - File (JPEG): Screenshot_20231116-223549.jpg

UBNSEMS3S (16:56:16) (in thread): > I spent the last half hour or so combing the greengenes taxonomy and I think this one is just truly not defined in the NCBI taxonomy yet. Every genus associated with paraprevotellaceae is a candidate genus with no formal name.

U1LCB8WEA (17:15:11) (in thread): > I would be OK with “unclassifiedparaprevotella” and a taxon-level review noting what it was originally and that in greengenes every genus associated with paraprevotellaceae is a candidate genus with no formal name.

U1LCB8WEA (17:37:39) (in thread): > I’ve done this:https://waldronlab.slack.com/archives/C04RATV9VCY/p1699966644856079?thread_ts=1699929017.492439&cid=C04RATV9VCYandhttps://waldronlab.slack.com/archives/C04RATV9VCY/p1699956205654619?thread_ts=1699929017.492439&cid=C04RATV9VCYjust because the deletion instructions from@Esther Afuapeand@Chioma Onyidowere simple enough for me to follow:sweat_smile: - Attachment: Attachment > @Levi Waldron for experiment 794, please delete experiment 1/signature 2, > experiment 2/signature 2, > experiment 3/signature 2. - Attachment: Attachment > For Study 367, > Signature 1 and 2 for Experiments 1 and 2 are identical; Increased and decreased abundance in obese group was curated twice. Same figure (figure 3) was used to curate both, this confirms a case of double entry. > > Please delete experiment 2. @U1LCB8WEA > > bugsigdb.org/Study_367

2023-11-17

Mildred Anashie (01:52:30) (in thread): > Well done@Chioma Onyidoand@Esther Afuape<@U1LCB8WEA>for 794 > > The whole Experiment 2 needs to be deleted, this was the final conclusionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1699971084018219?thread_ts=1699929017.492439&channel=C04RATV9VCY&message_ts=1699971084.018219 - Attachment: Attachment > Yes @Chioma Onyido > So for study 794, experiment 2 should be deleted. > And experiment 1/signature 2 should be deleted > Experiment 3/signature 2 should be deleted

Mildred Anashie (01:56:43) (in thread): > Also study 809 > > Experiment 2/Signature 1 and 2 needs to be deleted > Idon’tknow if it has been effected yet, because@Chioma Onyidosaid she brought it to your notice earlier and I still observed it a few days ago

Esther Afuape (02:45:19) (in thread): > Got it!<@U1LCB8WEA>How do I use the greengenes taxonomy in future cases like you just did?<@UBNSEMS3S>

Chiagoziem David (07:36:16): > Hello guys , the article I’m curating deals with the metagenomics analysis of microbial communities during cyanobacterial blooms in a lake, the samples were gotten from the blooms, I can’t find the host species closest to “cyanobacterial blooms” and also since it’s an “algae” found in a lake, I am confused as to what body site I can use.<@UBNSEMS3S><@U1LCB8WEA>

Chiagoziem David (07:37:10): > I saw a lacrimal lake , but I don’t think it’s related

Svetlana Ugarcina Perovic (07:42:05) (in thread): > Hi@Chiagoziem Davidcould you please share with me a link to the paper?

Chiagoziem David (07:42:38) (in thread): > Alrighty, give me a moment please

Svetlana Ugarcina Perovic (07:43:33) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/162 - Attachment: #162 Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese > Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese – Sanseverino I et al. – Microb Ecol. > > https://link.springer.com/article/10.1007/s00248-021-01914-5

Svetlana Ugarcina Perovic (07:43:38) (in thread): > Ok, found it

Chiagoziem David (07:43:54) (in thread): > Oh:smile::smile:, okay

Svetlana Ugarcina Perovic (07:44:51) (in thread): > Please see the Section: Sample Collection and Processing

Chiagoziem David (07:46:01) (in thread): > On it

Svetlana Ugarcina Perovic (07:46:42) (in thread): > Think about the type of samples and is this human or environmental microbiome study?

Chiagoziem David (07:47:29) (in thread): > It’s definitely not human:smile::smile:, so it has to be an environmental microbiome study

Chioma Onyido (07:49:35) (in thread): > Yes@Mildred AnashieSometimes when a page has been deleted, it takes a while to reflect, not sure why.:thinking_face:let’sgive it some time…?

Chiagoziem David (07:50:14) (in thread): > The samples were collected from the water, but the blooms were in the collected water? Are you saying that since it wasn’t an “animal” microbiome study, the host species and body sites should be left untouched?

Svetlana Ugarcina Perovic (07:51:13) (in thread): > This is water microbiome study.

Mildred Anashie (07:52:14) (in thread): > Yes:white_check_mark:…Just confirmed for 809

Svetlana Ugarcina Perovic (07:52:46) (in thread): > <@U1LCB8WEA>how do we proceed with non-host microbiome study curation?

Chiagoziem David (07:53:44) (in thread): > Alright ma, thank you very much:blush::relaxed::pray:.. > > Is there a way it can be updated on the site if it’s a non-animal microbiome study?

Chiagoziem David (07:54:34) (in thread): > Should I wait for<@U1LCB8WEA>before I move on@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (07:55:22) (in thread): > Please note thishttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1117&lvl=3&p=has_[…]&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlockand an error in this phrase “an”animal” microbiome study, …” - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Chiagoziem David (07:57:48) (in thread): > Could you please throw more light on this ma? I don’t completely understand what you are implying

Svetlana Ugarcina Perovic (07:59:57) (in thread): > I just wanted to point out thatCyanobacteria(also called blue-green algae) are an ancient group of photosynthetic microbes not animals:slightly_smiling_face:

Chiagoziem David (08:02:06) (in thread): > Oh, yeah:grinning::grinning:, also found out that calling them “algae” is a misnomer:sweat_smile:

Svetlana Ugarcina Perovic (08:02:20) (in thread): > ok, let’s hear from@Levi Waldronhow to curate non-host/environmental microbiome studies

Chiagoziem David (08:05:18) (in thread): > Alright ma, thanks:pray:

Levi Waldron (08:15:22) (in thread): > Is there differential abundance, like a group 0 and 1? We can always make it fit, although it starts getting a little more tortured:sweat_smile:- for example we can techno enter anything we want as an allowed “host species”

Chiagoziem David (08:20:41) (in thread): > I went away from my pc<@U1LCB8WEA>, let me check though

Chiagoziem David (08:20:49) (in thread): > ,:sweat_smile:

Mildred Anashie (08:31:11): > Hi<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina PerovicCan I use Linear Regression where linear mixed-effects model was mentioned in a study?

Peace Sandy (08:31:17) (in thread): > Hmmm

U1LCB8WEA (08:32:08) (in thread): > Yes I thinkthat’sok,it’sstill a type of linear regression

Mildred Anashie (08:33:46) (in thread): > Okay…Thank you, I see ‘R package MaAsLin2’ > > This confirms it, right?

U1LCB8WEA (08:35:02) (in thread): > It is a package for linear modeling

Mildred Anashie (08:36:04) (in thread): > Okay > > Thanks:pray:

UBNSEMS3S (09:30:49) (in thread): > I would say not to worry about doing it, but if youreally wanted to check then what I do is download the entire greengene taxonomy from here:https://greengenes.secondgenome.com/?prefix=downloads/greengenes_database/gg_12_10/, open thegg_12_10_taxonomy.txt.gzfile in a text editor, and ctrl + F for the taxon.

Esther Afuape (09:31:56) (in thread): > Thank you!<@UBNSEMS3S>

Chiagoziem David (18:51:43) (in thread): > <@U1LCB8WEA>it wasn’t a case study so there was no control group (the typical generic group 0 and 1) the differentiating factor for the grouping was depth though (depth from which the water sample was gotten)

2023-11-18

Odigiri Great Alume (01:34:05): > Good morning Team. > Please who would love to help me look at study 789. > > I know we have talked about it and we concluded from the text that were ever taxas like streptococcus appeared twice as (ASV415 and ASV7 streptococcus) we record as streptococcus spp then add comments. > > It I do this for strepto, it means if have to do it for many other taxa which according to the study is represented by spp. > > The challenge is I’m going to have lots of Orange taxas in the signatures as spp isn’t in NCBI browser. > > So I’m thinking:thinking_face:is it okay if I use sp. then record the specific strains/species in the comments to reduce the orange taxas in the signatures or should I just leave them as spp and just add comments ?bugsigdb.org/study_789@Levi Waldron@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther Afuape@Mildred Anashie

Mildred Anashie (02:39:17) (in thread): > Hi@Odigiri Great AlumeMy opinion is, if you record sp. that would not properly represent all the species and I think recording spp. as you have done is okay > > Unless<@U1LCB8WEA>says it’s okay to just leave comments on the different strains > Since you’ve brought it up before I’d say we wait it out, and hear the mentors opinions, there might be a way around it

Odigiri Great Alume (02:40:52) (in thread): > Alright@Mildred Anashiethanks:+1:

Mildred Anashie (02:48:18) (in thread): > “Orange names that cannot be mapped somehow to the NCBI taxonomy should be left alone and can have comments added, but not deleted.”This is from one time<@U1LCB8WEA>was addressing the orange name issue and solving of missing NCBI ID’sSo your opinion to leave a comment is best for now

Odigiri Great Alume (02:52:12) (in thread): > Yeah I saw this however, I’m not deleting per say. It’s just a question of sp and spp. > I understand you however and I’d take your suggestion on letting@Levi Waldronthrow more light. > Thank you so much Mildred. You are amazing

Chiagoziem David (03:55:35) (in thread): > Yeah, I think it is better for the sake of more clarity to wait for the mentors to give their view

Chloe (07:55:00) (in thread): > @Odigiri Great AlumeI would suggest we leave it as spp…. > I agree with@Mildred Anashie

Chloe (08:03:04): > 1.According to this do I record age as a confounding factor for Egyptians and Sex difference as a confounding factor for EA & AA….??@Levi Waldron@Svetlana Ugarcina Perovic<@UBNSEMS3S> - File (JPEG): IMG_20231118_152642_136.jpg

Chiagoziem David (10:07:35) (in thread): > :sweat_smile:

UBNSEMS3S (11:33:08) (in thread): > Believe it or not but no this is not adjustment/controlling for confounding.

UBNSEMS3S (11:37:17) (in thread): > I know for two reasons: > 1. The language “diversity was not affected by potential confounding factors such as…” means that they looked for a statistically significant difference between the groups based on age, etc. The presence or absence of statistical significance on a variable thought to be a confounder is not the same thing as controlling for a confounder. > 2. The statistical test used–LEfSe–does not allow you to easily control for confounders. Almost always if they are controlling for confounders it will be using a regression model: linear regression, Maaslin, negative binomial regression, poisson regression, DESeq2, etc.

Chloe (14:39:10) (in thread): > :handshake:thanks for the clarity provided<@UBNSEMS3S>

Peace Sandy (15:16:39) (in thread): > Thanks for clarifying@C. Mirzayi (please do not tag this account)This cofounding can be quite confusing

U02CNMR4YEA (15:21:40): > Hi Everyone! Happy Saturday! > I am trying to look at data in bugsigdb in R. I’m following along with the videos and I’ve imported the data > bsdb <- importBugSigDB() > Upon inspection, I am able to confirm the data came in but I’m finding it strange that the same numbers of columns and rows > > [1] "data.frame" > > dim(bsdb) > [1] 2270 48 > > are showing as when Ludwig Geistlinger inspects the data in his video which I understand is from 9 month ago. Am I misunderstanding something? > > Additionally, when I try to subset the data, > Platform<- subset(bsdb, > “Sequencing platform”==“Illumina”) > and inspect, I get > > > dim(Platform) > [1] 0 48 > > I’ve tried several different subsets on “Condition”, “Body site”, “Reviewer” and all return the same number of rows- “0”. > > Thank you in advance for any help!

U02CNMR4YEA (18:19:35): > Hi all! I’m curating a study and g_Prevotella_6 is listed. Prevotella is at the genus level. I am not able to find Prevotella_6. Please advise. Thank you!:blush:

Chioma Onyido (22:44:34) (in thread): > Hi<@U02CNMR4YEA>I had the same challenge in my curation 2 weeks ago and when I brought it up during the weekly lab meeting, I was advised to curate asPrevotella sp. then add a comment that “it was originally reported as Prevotella_6”. > > Here’s a link to the recording (14:40):https://waldronlab.slack.com/files/UBNSEMS3S/F065S0JV06L/video1010980453.mp4 - File (MPEG 4 Video): video1010980453.mp4

2023-11-19

Nana (05:00:16) (in thread): > <@U02CNMR4YEA>I had the same issue but I navigated it through what was said in the meeting. Do as chioma said

U02CNMR4YEA (10:25:10) (in thread): > Thank you so much! I appreciate you both!

Nana (10:26:06) (in thread): > You are welcome

UBNSEMS3S (10:59:13) (in thread): > > > bsdb <- importBugSigDB(version="devel", cache = FALSE) > > > dim(bsdb) > [1] 3423 50 > > Try this

UBNSEMS3S (11:01:00) (in thread): > > > platform<- subset(bsdb,`Sequencing platform`=="Illumina") > > dim(platform) > [1] 2488 50 > > And this. Variable names need to be in backticks when they have a space in them, not quotation marks. Having it in quotation marks as you did was leading R to evaluate if > > “Sequencing platform” == “Illumina” > > as in R was testing if the two literal strings were the same.

Odigiri Great Alume (12:42:18) (in thread): > You are in good hands<@U02CNMR4YEA>

U02CNMR4YEA (13:05:23) (in thread): > That worked! Thank you so much!!

Chiagoziem David (13:21:37) (in thread): > Thanks for the clarity<@UBNSEMS3S>

U02CNMR4YEA (17:20:19): > Happy Sunday! I have created a subset of the bugsigdb data for my condition of interest (dry eye syndrome) and all of the studies of which I am aware are included. I am perplexed by one study, however, that is showing with the signatures as “NA” . I don’t see anything unusual regarding the curation. Below is an excerpt of the data that shows the experiments from that study with signatures as “NA”. Any thoughts on why this is happening? > > bsdb:854/1/1 Study 854 case-control 35350577 > bsdb:854/1/2 Study 854 case-control 35350577 > bsdb:854/2/1 Study 854 case-control 35350577 > bsdb:854/2/2 Study 854 case-control 35350577 > bsdb:854/3/1 Study 854 case-control 35350577 > bsdb:854/3/2 Study 854 case-control 35350577 > bsdb:855/1/NA Study 855 case-control 37026303 > bsdb:855/2/NA Study 855 case-control 37026303 > bsdb:855/3/NA Study 855 case-control 37026303

Peace Sandy (18:44:48): > I’m currently curating a study and I’m finding it difficult to correctly detect what the control or reference group is, after reading through I noticed it’s a cross observational study.In the study they aimed to directly compare microbiota between 3 different clinical presentations,these were the three groups mentioned,atopic dermatitis (eczema) , chronic urticaria (hives) and allergic rhinitis (rhinitis)@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic

Chioma Onyido (19:06:21) (in thread): > Hi@Peace Sandymind sharing the paper or a link so we can look at it?

Chioma Onyido (20:16:04) (in thread): > Ohh I think I get you, you’re saying that the authors presented results for 3 groups of skin conditions, and you’re not sure which to use as your control group for your curation. > > Hmmm… not sure about the right thing to do here as Ihaven’tcurated something similar before:thinking_face:Hopefully the mentors would give more clarity when they’re here..

2023-11-20

Chiagoziem David (01:14:50) (in thread): > When I did something like this, I compared one group against the remaining groups Ie. A against BC, b against AC and c against ab

Chiagoziem David (01:16:07) (in thread): > This was stated in my work though , maybe it applies to yours maybe not, but let’s wait for the mentors.. in the main time could you drop a link to the study

Mildred Anashie (01:30:34) (in thread): > Yea, I think you should drop the link too, what they aimed to compare is one clue but the paper could guide on what was actually contrasted in the study. > > This looks like clinical presentations for allergic reactions, they might be a group that didn’t have any of this reactions when possibly in contact with the cause of reaction:thinking_face::woman-shrugging:

Mildred Anashie (01:37:18): > Hi everyone > > I came across this study I’m completing under studies that have no experiments and I’m wondering why it was flagged with “Quality Issues”, saying Results are Suspect > > Does this mean anything?:thinking_face:Should I go on?<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic - File (JPEG): IMG_5402

Chioma Onyido (02:14:09) (in thread): > Hi@Mildred Anashieis this 340?:eyes:

Chioma Onyido (02:22:00) (in thread): > Hmmm have you read throhhh the paper? Was differential taxa reported? I’m thinking maybe there’s an issue with the paper itself, particularly the results reported… that’s why it was flagged that way…?:thinking_face:

Peace Sandy (02:32:16) (in thread): > Thank You Guys:heart:Let me share the link to the paper

Peace Sandy (02:33:28) (in thread): > Probably

Mildred Anashie (03:17:36) (in thread): > Yes@Chioma Onyidoit’s 340 > > I suspected something could be wrong,that’swhy I mentioned it here before I go ahead > > Is there something that was mentioned that I missed with 340? > > Here’s a link thoughhttps://bugsigdb.org/Study_340 - Attachment (BugSigDB): Dysbiosis in Metabolic Genes of the Gut Microbiomes of Patients with an Ileo-anal Pouch Resembles That Observed in Crohn’s Disease - BugSigDB > …

Peace Sandy (03:19:13) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7939153/ - Attachment (PubMed Central (PMC)): Differences in gut microbiota between allergic rhinitis, atopic dermatitis, and skin urticaria: A pilot study > Several forms of allergy have been clinically presented, including, among others, atopic dermatitis (eczema), urticaria (hives), and allergic rhinitis (rhinitis). As their detailed pathogenesis continues to be researched, we aimed in the current study …

Mildred Anashie (03:42:37) (in thread): > @Peace Sandy3.3 reports results for Eczema/rhinitis, Eczema/hives, Hives/rhinitis, Rhinitis/hives, Rhinitis/Eczema > > What I’m trying to figure out now is if it’ll be redundant if we report as 6 experiments with their alpha diversities all unchanged from what I see:thinking_face:

Peace Sandy (03:45:17) (in thread): > Yes@Mildred AnashieOnce I can figure out the reference groupI’mgood to go,it’squite confusing to me

Chiagoziem David (03:55:08) (in thread): - File (JPEG): Screenshot_2023-11-20-09-54-43-89_40deb401b9ffe8e1df2f1cc5ba480b12.jpg

Chiagoziem David (03:56:27) (in thread): > I think from the figure 5 we can see what signatures increased, I think the contrast Is between the three groups - File (JPEG): Screenshot_2023-11-20-09-52-31-58_2768c6f3dd71c987876b7b9730ce2453.jpg - File (JPEG): Screenshot_2023-11-20-09-51-38-07_2768c6f3dd71c987876b7b9730ce2453.jpg

Chiagoziem David (03:57:20) (in thread): > Bearing in mind that once it’s increased for one group it’s decreased for another so there won’t be need to double enter it

Chioma Onyido (04:06:36) (in thread): > Hmm…Not that I know of, maybe it had wrong expts or something, whichmust’vebeen deleted. > Just seen your recent curations on it,You’redoing great. Well done.:+1:

Mildred Anashie (04:55:57) (in thread): > Thank you ChiomaI’llhold on with further curation tillI’mgiven go ahead by<@U1LCB8WEA><@UBNSEMS3S>

Peace Sandy (05:42:55) (in thread): > Thank You guys@Chiagoziem David@Chioma Onyidoand@Mildred Anashiefor your responses so far

UBNSEMS3S (09:41:50) (in thread): > I think the issue with this one was that their statistical test revealed a huge amount of significant results that were going to take forever to curate. Looking at S1 Sheet 4 which has the linear regression results, there are 232 significant taxa.

UBNSEMS3S (09:57:21) (in thread): > Looks like it was curated fairly recently. There is a slight delay between something being curated and it showing up in the data. Try rerunning yourimportBugSigDB()line and I think they’ll be updated.

Mildred Anashie (10:06:16) (in thread): > Okay > > I observed that > Thank you

Mildred Anashie (10:07:22) (in thread): > You might have to delete the experiment I recorded already

Peace Sandy (12:21:09): > Hi@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovicthe full article of this study cannot be found online, andit’san incomplete studyhttps://bugsigdb.org/Study_811 - Attachment (BugSigDB): Failure of apicoectomy surgery and successful endodontic retreatment - BugSigDB > The optimal way to address endodontic failures is to retreat the root canal system first and only then to consider apical surgery.Unfortunately, in practice, it is often not done in this way.Patients are subjected to apical surgery, without any attempts at retreatment.

UBNSEMS3S (13:16:39) (in thread): > This study has nothing to do with microbiome. I think it was entered by mistake. I’m going to delete it.

Peace Sandy (13:19:14) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Peace Sandy (13:19:52) (in thread): > Please can you also delete this study,it’sincomplete and has no DOI or PMIDhttps://bugsigdb.org/Study_785 - Attachment (BugSigDB): - BugSigDB > …

U02CNMR4YEA (13:29:37) (in thread): > Yes, that seems to have been it. Thank you!

Mildred Anashie (13:56:11) (in thread): > Also 784 too, The PMID has been entered as study 805

UBNSEMS3S (14:18:32) (in thread): > 784 and 785 have been deleted.

Peace Sandy (14:28:44) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

2023-11-21

Chiagoziem David (11:12:49): > Congratulations guys:bouquet::bouquet:

Chiagoziem David (11:13:12): > @Chioma Onyido@Peace Sandy@Esther Afuapewell deserved

Nwajei Edgar (11:13:42): > Congratulations guys:grinning_face_with_star_eyes::grinning_face_with_star_eyes:

Sinmi Adesanya (11:13:47): > Yes! Congratulations Ladies!:heart:

Odigiri Great Alume (11:14:15): > Congratulations:tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada::tada:

Mildred Anashie (11:16:43): > Congratulations:smiling_face_with_smiling_eyes_and_hand_covering_mouth::heart:

Grace Ogundaini (11:16:56): > Congratulations!

Chloe (12:20:00): > congs:clap:

U1LCB8WEA (12:25:17) (in thread): > Take a look at the Discussion page too (https://bugsigdb.org/Talk:Study_340) - I have no recollection of this now, but I wrote on March 11 12:56 that “These experiments clearly beling to a different study.” (I guess I meant “belong”:sweat_smile:) - Attachment (BugSigDB): Talk:Study 340

Mildred Anashie (12:26:45) (in thread): > Okay > > Ididn’tsee thatI’llcheck it out

U1LCB8WEA (12:27:14) (in thread): > It looks like the offending experiments have been deleted since then, and a relevant one added, so maybe that flag can be removed

Mildred Anashie (12:27:57) (in thread): > I added the new experiment > > Are you sayingI’mon track and I can continue with that?

U1LCB8WEA (12:28:14) (in thread): > Yes:slightly_smiling_face:

Mildred Anashie (12:28:54) (in thread): > OkayI’llneed help figuring out the signatures though

U1LCB8WEA (12:29:56) (in thread): > You could do some stricter threshold to limit the 200-taxa signature:exploding_head:- or it is possible to copy/paste NCBI ID in bulk, although I imagine they don’t report NCBI IDs

Mildred Anashie (12:30:34) (in thread): > I’llappreciate if you can help look at the supplemental files to know which I could curate > > Because<@UBNSEMS3S>mentioned the 232 taxas

U1LCB8WEA (12:32:51) (in thread): > Is antibiotic use really a confounder controlled for? It looks like it is an inclusion/exclusion criterion instead, unless they also used something about antibiotics history in a multivariate regression model

Mildred Anashie (12:33:24) (in thread): > They mentioned antibiotic use was also adjusted for:thinking_face:

Mildred Anashie (12:35:01) (in thread): > Can you explain the stricter threshold limit…

Joan C. Chukwuemeka (12:35:44): > Congrats to all Selected.. All the best

U1LCB8WEA (12:36:13) (in thread): > If they described how they did that, then that’s good. Also note the closest EFO term for antibiotics use is “antimicrobial agent” - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > Web site created using create-react-app

Mildred Anashie (12:37:04) (in thread): > Thank you…I’lllook through for antibiotic use as a confounder

U1LCB8WEA (12:37:07) (in thread): > I’m not sure yet what to do about the huge signature:grimacing:

Mildred Anashie (12:39:04) (in thread): > I’ll be glad to help with curating when you figure it out > > Can I record just the experiments for now?

Peace Sandy (15:16:26): > Thank you so much everyone > I really appreciate:tada:

Tolulope Ogunleye (15:19:34): > Congratulations ladies:tada::tada::tada:@Peace Sandy@Esther Afuape@Chioma Onyidowell deserved:clap::clap::clap:.

Chioma Onyido (17:19:24) (in thread): > Thank you so much@Chiagoziem David

Chioma Onyido (17:19:58) (in thread): > Thank you so much@Tolulope Ogunleye

Chioma Onyido (17:21:03): > Thank you so much!:tada:

U1LCB8WEA (17:35:11) (in thread): > yes that’s fine@Mildred Anashie:slightly_smiling_face:

Chiagoziem David (17:36:58) (in thread): > :heart::heart:

Peace Sandy (18:14:36) (in thread): > Thank You@Tolulope Ogunleye

Hodan Abdirisak (22:43:07): > Congratulations@Chioma Onyido@Peace Sandy@Esther Afuape

2023-11-22

Esther Afuape (01:55:43): > Thank you so much guys:tada:

Peace Sandy (02:31:41) (in thread): > Thank you so much@Hodan Abdirisak

Mildred Anashie (02:55:56) (in thread): > Okay Thank you > > Is this a go ahead on the experiments?

Peace Sandy (02:59:29) (in thread): > Thank you so much@Chiagoziem David

Esther Afuape (03:00:20) (in thread): > Thank you, David

Chiagoziem David (03:59:11) (in thread): > :heart:

Chioma Onyido (04:23:53) (in thread): > Thank you@Hodan Abdirisak

Ulenyo Attah (04:37:32): > Congratulations@Chioma Onyido@Peace Sandy@Esther Afuape:partying_face::partying_face::100::100:, Omggg. You guys deserve this so much. I wish you all the very best!!:fire::face_with_hand_over_mouth:

Peace Sandy (05:56:27) (in thread): > Awwwn…I’mso grateful@Ulenyo AttahThank You:blush:

Aleru Divine (06:11:56): > Congratulations ladies:partying_face:

Chioma Onyido (06:54:22) (in thread): > Thank you@Ulenyo Attahmeans a lot.:blush:

Peace Sandy (07:55:28) (in thread): > Thank You:heart::blush:@Aleru Divine

UBNSEMS3S (09:05:55): > Hi everyone, just a reminder that we donot have a team meeting tomorrow as it is the Thanksgiving holiday here in the US. I am thankful that BugSigDB has so many amazing people working on it!

2023-11-23

Chioma Onyido (03:59:57): > Happy Thanksgiving to BugSigDB members in the US!:turkey::maple_leaf:Wishing you a day filled with joy, gratitude and good food. > To everyone else, sending good vibes your way, wherever you are.:earth_africa:

Peace Sandy (05:43:33) (in thread): > Thank You@C. Mirzayi (please do not tag this account)Happy Thanksgiving:tada:

Chiagoziem David (15:14:03) (in thread): > Our thanksgiving is on Sunday in our respective parishes:sweat_smile::sweat_smile:

Chiagoziem David (15:14:27) (in thread): > :muscle::muscle::muscle::tada:

Chioma Onyido (15:30:39) (in thread): > @Chiagoziem Davidikr!:laughing:

Chiagoziem David (15:31:25) (in thread): > :sweat_smile::sweat_smile::sweat_smile:

Mildred Anashie (16:08:26) (in thread): > @Chiagoziem David:joy:

U1LCB8WEA (21:30:45) (in thread): > Thank you!!

U1LCB8WEA (21:33:05) (in thread): > That sounds like a good plan to me@Odigiri Great Alume:thumbsup:

U1LCB8WEA (21:49:15) (in thread): > I should admit I am not an expert taxonomist andcan’tyet envision all the ways bugsigdb will be used, so these are just best guesses and I welcome others thoughts.Probably the most accurate translation for multiple sequences of unclear rank would beunclassified Streptococcus (Taxonomy ID: 2608887).AddingStreptococcus sp. might also be useful for communicating that there is a strep species present. Including the ASVs as orange taxa is fine, however ASV and OTU codes are study-specific and are never going to be mappable to the NCBI, which makes me less concerned about keeping them than some other potentially future mappable names, and to wonder whether they’re worth the clutter and that maybe for these cases comments would be better to remove these uninformative codes from our cleanup list?

U1LCB8WEA (21:49:59) (in thread): > Yes please do Mildred!

Chioma Onyido (23:36:34) (in thread): > You’rewelcome:blush:<@U1LCB8WEA>

2023-11-24

Mildred Anashie (08:35:06) (in thread): > Thank you!!!

Svetlana Ugarcina Perovic (10:54:16): > Happy Friday!

Svetlana Ugarcina Perovic (10:55:27): > Check out this opportunity for bioinformatics projects:slightly_smiling_face:https://www.cognitoforms.com/AHRI1/MentoredFellowshipInBioinformatics - File (JPEG): bioinformatics_africa.jpeg

Nwajei Edgar (10:56:26) (in thread): > Happy Friday:woman-cartwheeling::woman-cartwheeling:

Chioma Onyido (14:36:59) (in thread): > Thanks you for your thoughtfulness.@Svetlana Ugarcina PerovicEager to explore this (on it)!:blush:

Peace Sandy (21:39:29) (in thread): > Happy Friday

Peace Sandy (21:40:01) (in thread): > Thank You for sharing@Svetlana Ugarcina Perovic

2023-11-26

Chiagoziem David (03:02:47) (in thread): > Thank you very much@Svetlana Ugarcina Perovic,

2023-11-28

U01MW62UDQR (13:54:07): > Hi, we still need some help identifying duplicate studies for clean up. Please refer tohttps://waldronlab.slack.com/archives/C04RATV9VCY/p1699929017492439, which includes code to expose duplicates. I’m waiting for these to be resolved so that we can release a new version ofhttps://github.com/waldronlab/bugsigdbexports, BugSigDB’s data. > > Using cached version from 2023-11-28 18:43:07 > bsdb:262/1/2_atopic-asthma:nasal-brush-speciments_vs_bronchial-brush-specimens_DOWN > "3004eabb11c96f6100a48ffba6304302" > bsdb:262/3/1_atopic-asthma:induced-sputum-specimens_vs_nasal-brush-specimens_UP > "3004eabb11c96f6100a48ffba6304302" > bsdb:262/4/1_atopic-asthma:oral-wash-specimens_vs_nasal-brush-specimens_UP > "3004eabb11c96f6100a48ffba6304302" > bsdb:829/1/1_Breastfeeding-duration:Low-Total-Time-Breastfeeding_vs_Medium-Total-Time-Breastfeeding_DOWN > "4f2e0ba8d26ec80dcea51491c3cd8545" > bsdb:829/2/1_Breastfeeding-duration:High-Total-Time-Breastfeeding_vs_Medium-Total-Time-Breastfeeding_DOWN > "4f2e0ba8d26ec80dcea51491c3cd8545" > bsdb:279/2/2_acute-myeloid-leukemia:bacterial-infections-at-T3_vs_No-bacterial-infections-at-T3_DOWN > "9d5bbfc58f2500dd2270f365d64ed439" > bsdb:279/2/3_acute-myeloid-leukemia:bacterial-infections-at-T3_vs_No-bacterial-infections-at-T3_UP > "9d5bbfc58f2500dd2270f365d64ed439" > bsdb:678/1/1_smoking-behavior:Cigarette-Smokers_vs_Nonsmokers_UP > "da288d7cfd25f5b1d0dd680580e4215c" > bsdb:678/2/1_smoking-behavior:Dokha-Smokers_vs_Nonsmokers_UP > "da288d7cfd25f5b1d0dd680580e4215c" > bsdb:556/6/1_urinary-tract-infection:Day-5_vs_Day-1-(pre-dose)_UP > "fdf0388b4ac6d6d2f1beaf52d2fbe726" > bsdb:557/5/1_urinary-tract-infection:Day-5-(end-of-dosing-or-post-dose)_vs_Day-1-(pre-dose)_UP > "fdf0388b4ac6d6d2f1beaf52d2fbe726" >

Esther Afuape (14:18:23) (in thread): > Hello:wave:@Andres WokatyMyself and@Chioma Onyidohave been working diligently on these clean up tasks and we hope to round them up this week. We started with this list provided by@Levi Waldron(https://community-bioc.slack.com/archives/C04RATV9VCY/p1699929017492439) and we have just the ones appearing on your list left to solve! > Please, expect a feedback from us by the end of this week. - Attachment: Attachment > Hi team, I was doing some analysis to prepare for a presentation tomorrow, and noticed there are a number of identical signatures in the database. Here is some reproducible R code that identifies and displays identical signatures of length >= 5 ( based on their md5sum digest. I could use your help to check on these and identify which should be deleted :slightly_smiling_face: . I suspect there are shorter signatures that need to be deleted too, but probably also more correctly identical signatures just by chance below this length. > ```# BiocManager::install(c(“bugsigdbr”, “waldronlab/BugSigDBStats”, “digest”, “purrr”, “dplyr”)) > library(dplyr) > #> > #> Attaching package: ‘dplyr’ > #> The following objects are masked from ‘package:stats’: > #> > #> filter, lag > #> The following objects are masked from ‘package:base’: > #> > #> intersect, setdiff, setequal, union > bsdb <- bugsigdbr::importBugSigDB(version = “devel”) > #> Using cached version from 2023-11-12 17:03:53 > sigs <- bugsigdbr::getSignatures(bsdb, > tax.id.type=“taxname”, > min.size = 5) > > # identify identical elements in the sigs list > purrr::map_chr(sigs, digest::digest) %>% > .[!Biobase::isUnique(.)] %>% > sort() > #> bsdb:809/1/1_Retinopathy:diabetes-mellitus-(DM)_vs_healthy-controls-(HC)_UP > #> “073ca2fec309aae2a357b6deb68c1cc6” > #> bsdb:809/2/2_Retinopathy:diabetes-retinopathy-(DR)_vs_diabetes-mellitus-(DM)_DOWN > #> “073ca2fec309aae2a357b6deb68c1cc6” > #> bsdb:443/1/1_irritable-bowel-syndrome:IBS_vs_Healthy-Control_UP > #> “28aaef70dc700d84d4d6bda6aa64477e” > #> bsdb:443/3/1_irritable-bowel-syndrome:IBS-D_vs_Health-Control_UP > #> “28aaef70dc700d84d4d6bda6aa64477e” > #> bsdb:262/1/2_atopic-asthma:nasal-brush-speciments_vs_bronchial-brush-specimens_DOWN > #> “3004eabb11c96f6100a48ffba6304302” > #> bsdb:262/3/1_atopic-asthma:induced-sputum-specimens_vs_nasal-brush-specimens_UP > #> “3004eabb11c96f6100a48ffba6304302” > #> bsdb:262/4/1_atopic-asthma:oral-wash-specimens_vs_nasal-brush-specimens_UP > #> “3004eabb11c96f6100a48ffba6304302” > #> bsdb:829/1/1_Breastfeeding-duration:Low-Total-Time-Breastfeeding_vs_Medium-Total-Time-Breastfeeding_DOWN > #> “4f2e0ba8d26ec80dcea51491c3cd8545” > #> bsdb:829/2/1_Breastfeeding-duration:High-Total-Time-Breastfeeding_vs_Medium-Total-Time-Breastfeeding_DOWN > #> “4f2e0ba8d26ec80dcea51491c3cd8545” > #> bsdb:794/1/1_colorectal-cancer:EOCRC-(Early-onset-Colorectal-cancer)-patients_vs_Healthy-controls_UP > #> “53018590674734dae9325ce808e42636” > #> bsdb:794/2/1_colorectal-cancer:EOCRC-(Early-onset-Colorectal-cancer)-patients_vs_LOCRC-(Late-onset-Colorectal-cancer)-patients_UP > #> “53018590674734dae9325ce808e42636” > #> bsdb:624/1/1_colorectal-cancer:Patients-with-CRC_vs_Healthy-Individuals_UP > #> “5c90266728439a1b5f4087c215685d62” > #> bsdb:624/3/1_colorectal-cancer:Patients-with-advanced-CRC_vs_Healthy-Individuals_UP > #> “5c90266728439a1b5f4087c215685d62” > #> bsdb:624/4/1_colorectal-cancer:After-resection_vs_Before-resection_DOWN > #> “5c90266728439a1b5f4087c215685d62” > #> bsdb:809/2/1_Retinopathy:diabetes-retinopathy-(DR)_vs_diabetes-mellitus-(DM)_UP > #> “6dea87790a2d191ce492a7a23ed5aad4” > #> bsdb:809/3/1_Retinopathy:diabetes-retinopathy-(DR)_vs_healthy-controls-(HC)_UP > #> “6dea87790a2d191ce492a7a23ed5aad4” > #> bsdb:316/3/2_premature-birth:30-day-old-Pre-term-infants_vs_30-day-old-Full-term-infants(born-after-uncomplicated-pregnancy)_DOWN > #> “7ccdbfe4a05ed473f9e735ada1e58c3a” > #> bsdb:316/4/2_premature-birth:90-day-old-Pre-term_vs_90-day-old-Full-term-infants(born-after-uncomplicated-pregnancy)_DOWN > #> “7ccdbfe4a05ed473f9e735ada1e58c3a” > #> bsdb:367/1/1_obesity:obese_vs_normal-weight_UP > #> “7eff7af0bffb227e30450e398954f089” > #> bsdb:367/2/1_obesity:overweight_vs_normal-weight_UP > #> “7eff7af0bffb227e30450e398954f089” > #> bsdb:696/4/1_Nutraceutical:colorectal-cancer-patients-perioperative-probiotics_vs_colorectal-cancer-patients-perioperative-placebo_UP > #> “824d16e25cba0eac0f044e777d760c19” > #> bsdb:696/5/1_Nutraceutical:healthy-volunteer-group_vs_colorectal-cancer-patients-perioperative-placebo_UP > #> “824d16e25cba0eac0f044e777d760c19” > #> bsdb:434/1/2_human-papilloma-virus-infection:HPV-+_vs_healthy-control_DOWN > #> “8e7556dc39fd7f200b42382236e0a578” > #> bsdb:434/2/2_cervical-glandular-intraepithelial-neoplasia:LSIL_vs_healthy-control_DOWN > #> …

Andres Wokaty (14:19:32) (in thread): > Thanks so much for your help!

2023-11-29

UBNSEMS3S (16:49:50): > Hi everyone we will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499

2023-11-30

Peace Sandy (03:36:30) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Esther Afuape (04:51:31) (in thread): > Thank you for the reminder

Odigiri Great Alume (08:25:30) (in thread): > Alright > Thanks@C. Mirzayi (please do not tag this account)

U05T2TFALH4 (09:00:00): > Hi<@UBNSEMS3S>! For Study 760, can you please help delete signature 2 of experiment 4 and also all of experiment 5?https://bugsigdb.org/Study_760 - Attachment (BugSigDB): Postoperative Probiotics Administration Attenuates Gastrointestinal Complications and Gut Microbiota Dysbiosis Caused by Chemotherapy in Colorectal Cancer Patients - BugSigDB > The current study aims to evaluate the potential roles of taking probiotics postoperatively in attenuating the gastrointestinal complications and disturbed gut microbiota in colorectal cancer (CRC) patients undergoing chemotherapy.

Svetlana Ugarcina Perovic (09:53:15) (in thread): > Deleted.

U05T2TFALH4 (09:53:34) (in thread): > Thank you!

U02CNMR4YEA (10:03:54): > Hi All! I’m in the waiting room and not sure if the meeting has started?

Andre Nana (11:24:33): > This is the edited discussion for the psoriasis paper (https://bugsigdb.org/Talk:Study_811) : “In Figure 2 the values of Christensenella, Anaerofustis and Veillonella, are too close to the NULL value in the forrest plot, despite significant p-values. In Figure 3 the barplot of alpha diversity does not convey the same information for a p-value = 0,0001.” - Attachment (BugSigDB): Talk:Study 811 > In Figure 2 the values of Christensenella, Anaerofustis and Veillonella, are too close to the NULL value in the forrest plot, despite significant p-values. In Figure…

Andre Nana (11:31:56): > Hi<@UBNSEMS3S>, here is a list of curated papers that I think can be marked as reviewed. I included todays papers and some old curations that I presented in lab meetings as well. Thanks for your assistance.Salivary microbiome in children with Down syndrome: a case-control study - BugSigDBSalivary microbiome profiles of oral cancer patients analyzed before and after treatment - BugSigDBChanges of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy - BugSigDBVaginal microbiome of women with adenomyosis: A case-control study - BugSigDBAssociation between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor - BugSigDBThe gut microbiota profile in psoriasis: a Brazilian case-control study - BugSigDB - Attachment (BugSigDB): Salivary microbiome in children with Down syndrome: a case-control study - BugSigDB > BACKGROUND: Down syndrome (DS), a most frequently occurring genetic disorder, is associated with oral morphological abnormalities and higher incidence rates of oral diseases. - Attachment (BugSigDB): Salivary microbiome profiles of oral cancer patients analyzed before and after treatment - BugSigDB > BACKGROUND: Treating oral squamous cell carcinoma (OSCC) introduces new ecological environments in the oral cavity.This is expected to cause changes in the oral microbiome. - Attachment (BugSigDB): Changes of saliva microbiota in nasopharyngeal carcinoma patients under chemoradiation therapy - BugSigDB > OBJECTIVE: A growing body of evidence has implicated human oral microbiota in the aetiology of oral and systemic diseases.Nasopharyngeal carcinoma (NPC), an epithelial-originated malignancy, has a complex aetiology not yet fully understood. - Attachment (BugSigDB): Vaginal microbiome of women with adenomyosis: A case-control study - BugSigDB > Immune dysregulation can involve invasion and survival of endometrial glands inside the myometrium of the adenomyosis.There is limited available data concerning alterations of the bacterial microbiome in the reproductive tract of adenomyosis women. - Attachment (BugSigDB): Association between Gut Microbiota and Breast Cancer: Diet as a Potential Modulating Factor - BugSigDB > Breast cancer (BCa) has many well-known risk factors, including age, genetics, lifestyle, and diet; however, the influence of the gut microbiome on BCa remains an emerging area of investigation.This study explores the connection between the gut microbiome, dietary habits, and BCa risk.

UBNSEMS3S (12:44:29): > Meeting recording. Thank you everyone for attending. - File (MPEG 4 Video): video1927690487.mp4

Peace Sandy (15:01:19) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

2023-12-01

Chioma Onyido (05:04:07): > Hi all:wave:Happy weekend! > Still on cleaning double entry signatures, we found thatbugsigdb.org/Study_556andbugsigdb.org/Study_557were both curated from the same paper (with exactly the same content) but different PMIDs. > > Two papers: Paper 1:Microbiome recovery in adult females with uncomplicated urinary tract infections… (GSK140944)Paper 2:Correction to: Microbiome recovery in adult females with uncomplicated urinary tract… (GSK2140944). > > Apparently the second paper was published as a correction of the compound number (GSK140944 to GSK2140944) to the first paper. (With 2 diff DOIs and PMIDs, didn’t know that was possible!) > > After myself,@Esther Afuapeand@Odigiri Great Alumereviewed both studies, we confirmed that 557 seems to be more accurate than 556 (with only a few missing taxa which Esther is currently working on adding), > > We’d really appreciate help on how to proceed? Same studies, same curation, however since 557 is more updated than 556 (after review), can 556 be deleted while keep 557?<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic:pray: - Attachment (BioMed Central): Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944) - BMC Microbiology > Background With increasing concerns about the impact of frequent antibiotic usage on the human microbiome, it is important to characterize the potential for such effects in early antibiotic drug development clinical trials. In a randomised Phase 2a clinical trial study that evaluated the pharmacokinetics of repeated oral doses of gepotidacin, a first-in-chemical-class triazaacenaphthylene antibiotic with a distinct mechanism of action, in adult females with uncomplicated urinary tract infections for gepotidacin (GSK2140944) we evaluated the potential changes in microbiome composition across multiple time points and body-sites ( ClinicalTrials.gov : NCT03568942). Results Samples of gastrointestinal tract (GIT), pharyngeal cavity and vaginal microbiota were collected with consent from 22 patients at three time points relative to the gepotidacin dosing regimen; Day 1 (pre-dose), Day 5 (end of dosing) and Follow-up (Day 28 ± 3 days). Microbiota composition was determined by DNA sequencing of 16S rRNA gene variable region 4 amplicons. By Day 5, significant changes were observed in the microbiome diversity relative to pre-dose across the tested body-sites. However, by the Follow-up visit, microbiome diversity changes were reverted to compositions comparable to Day 1. The greatest range of microbiome changes by body-site were GIT followed by the pharyngeal cavity then vagina. In Follow-up visit samples we found no statistically significant occurrences of pathogenic taxa. Conclusion Our findings suggest that gepotidacin alteration of the human microbiome after 5 days of dosing is temporary and rebound to pre-dosing states is evident within the first month post-treatment. We recommend that future antibiotic drug trials include similar exploratory investigations into the duration and context of microbiome modification and recovery. Trial registration NCT03568942 . Registered 26 June 2018. - Attachment (PubMed): Correction to: Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944) - PubMed > Correction to: Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944)

Odigiri Great Alume (05:15:37) (in thread): > Well done@Chioma Onyidoand@Esther AfuapeI wonder what the mentors solutions would be as this case is quite new and strange to me too

Chioma Onyido (06:07:36) (in thread): > Ikr. Same!:thinking_face:

Esther Afuape (06:23:55): > List of studies with correctly entered double-entry signatures > 1. 829 > 2. 262 > 3. 279 > @Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U01MW62UDQR>@Chioma Onyido

Svetlana Ugarcina Perovic (06:25:56) (in thread): > This is a normal protocol when authors have an erratum – a correction of apublishedtext. In this case, there are not 2 papers; there are: > 1. a paper that is updated based on > 2. Correction reported - File (PNG): Screenshot 2023-12-01 at 12.24.28.png

Svetlana Ugarcina Perovic (06:30:52) (in thread): > In my opinion, onlybugsigdb.org/Study_557should be kept (since you recurated it correctly) BUT next is to fix the title of the paper (put the correct one: Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944)) and put the correct PMID to the paper (not to the correction).<@UBNSEMS3S>please correct me, if we have other protocol for this kind of paper corrections.

Esther Afuape (06:34:13) (in thread): > Does this mean that the correction will be reflecting in the original paper also since a second paperwasn’tcreated?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:35:16) (in thread): > Yes, please seehttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02245-8#change-history - Attachment (BioMed Central): Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944) - BMC Microbiology > Background With increasing concerns about the impact of frequent antibiotic usage on the human microbiome, it is important to characterize the potential for such effects in early antibiotic drug development clinical trials. In a randomised Phase 2a clinical trial study that evaluated the pharmacokinetics of repeated oral doses of gepotidacin, a first-in-chemical-class triazaacenaphthylene antibiotic with a distinct mechanism of action, in adult females with uncomplicated urinary tract infections for gepotidacin (GSK2140944) we evaluated the potential changes in microbiome composition across multiple time points and body-sites ( ClinicalTrials.gov : NCT03568942). Results Samples of gastrointestinal tract (GIT), pharyngeal cavity and vaginal microbiota were collected with consent from 22 patients at three time points relative to the gepotidacin dosing regimen; Day 1 (pre-dose), Day 5 (end of dosing) and Follow-up (Day 28 ± 3 days). Microbiota composition was determined by DNA sequencing of 16S rRNA gene variable region 4 amplicons. By Day 5, significant changes were observed in the microbiome diversity relative to pre-dose across the tested body-sites. However, by the Follow-up visit, microbiome diversity changes were reverted to compositions comparable to Day 1. The greatest range of microbiome changes by body-site were GIT followed by the pharyngeal cavity then vagina. In Follow-up visit samples we found no statistically significant occurrences of pathogenic taxa. Conclusion Our findings suggest that gepotidacin alteration of the human microbiome after 5 days of dosing is temporary and rebound to pre-dosing states is evident within the first month post-treatment. We recommend that future antibiotic drug trials include similar exploratory investigations into the duration and context of microbiome modification and recovery. Trial registration NCT03568942 . Registered 26 June 2018.

Chioma Onyido (06:36:56) (in thread): > I was wondering why they wouldpublishanother paper:sweat_smile:but It all makes more sense now, Thank you for your prompt response, I’ve noted your corrections and we’re implementing them asap.@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:37:38) (in thread): > Let’s check it together: > > “Following the publication of the original article [1], the authors would need to modify the typographical error in the compound number in article title, from GSK140944 (current) to GSK2140944 (correct). The correct article title is shown above.The original article has been corrected.” > > Is it corrected? - Attachment (BioMed Central): Correction to: Microbiome recovery in adult females with uncomplicated urinary tract infections in a randomised phase 2A trial of the novel antibiotic gepotidacin (GSK2140944) - BMC Microbiology > An amendment to this paper has been published and can be accessed via the original article.

Esther Afuape (06:37:57) (in thread): > Thank you@Svetlana Ugarcina Perovic. All corrections noted:white_check_mark:

Esther Afuape (06:39:16) (in thread): > Yes. The “previous article” carries the new compound name in the title

Svetlana Ugarcina Perovic (06:41:43) (in thread): > Mystery solved.Happy Friday!

Chioma Onyido (06:42:27) (in thread): > Thank you so much! Happy Friday!:smiley:

Esther Afuape (06:44:53): > Hello:wave:<@U01MW62UDQR>. Here’s an update on the duplicate signatures from myself and@Chioma Onyidoas promised. > Having reviewedstudy 262, we realized that the duplicate signatures in it were accurately entered and should be left as they are. > > Instudy 279, experiment 3/signature 1 and experiment 4/signature 1 have the same signatures and are correct as they are also.<@UBNSEMS3S>and<@U1LCB8WEA>reviewedstudy 829during the office hour yesterday, and found the signatures in it accurate as they are also. > > Following corrections from@Svetlana Ugarcina Perovic,study 556will be deleted and the PMID for 557 will be corrected. > From your list and Levi’s, I believe we have cleaned up all of the duplicate signatures.

Esther Afuape (06:45:16) (in thread): > Happy Friday!:hugging_face:

Odigiri Great Alume (08:17:31) (in thread): > Happy friyaaaaaaah:joy:

U01MW62UDQR (09:27:10) (in thread): > Wonderful. Thank you!

U1LCB8WEA (10:17:17) (in thread): > Nice work,happy Friday from British Columbia,Canada this week!

Esther Afuape (10:21:37) (in thread): > No problem!:blush:

U02CNMR4YEA (11:59:07): > Hello everyone! I hope today finds you well:blush:. I am curating PMID 32694705 and alpha diversity is discussed with indices of richness, evenness, and Shannon diversity. While richness and Shannon diversity are straight-forward, is there a way in which evenness should be entered? From what I see, Shannon diversity encompasses both richness and evenness with more weight on evenness. Thank you in advance!

Chioma Onyido (12:11:49) (in thread): > Hi<@U02CNMR4YEA>PMID32684705doesn’t look like a microbiome study..:thinking_face: - File (JPEG): IMG_6737

U02CNMR4YEA (12:13:06) (in thread): > My apologies! Typo. I fixed it:smiley:

Chioma Onyido (12:41:47) (in thread): > Thank you. > I tried to check the methods section to see if there’s a reference for the Exact evenness index but couldn’t locate one. > From my experience, the only Evenness index I am familiar with isPielou’s evenness index. > So I’m not sure what to enter here…:sweat_smile:Need your help please.<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic

U1LCB8WEA (12:54:24) (in thread): > Thanks@Chioma Onyido- as far as I’m concerned, Pielou’s evenness index would be close enough…

U02CNMR4YEA (13:05:01) (in thread): > Thank you@Chioma Onyidoand<@U1LCB8WEA>

U02CNMR4YEA (13:35:39): > Apologies for being so needy today:disappointed:but I keep reading this paper (PMID 32694705) and am on the first experiment “normal” vs “dry eye”. In the Supplement table 2, the taxon showing differential abundance are listed with p values, however, I am not able to ascertain (from the table or text) whether they are differentially increased or decreased in the study population (Dry Eye). I must just be missing it so if anyone can take a look, I’d be so grateful! TIA Here is the link to the supplemental material:https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-020-68952-w/MediaObjects/41598_2020_68952_MOESM1_ESM.pdf

Levi Waldron (13:42:23): > <!channel>I received a heartwarming testimonial from past curator@irem Kahveciand posted it with permission to a new “Testimonials” page:https://bugsigdb.org/Testimonials. I would love to have more testimonials! If you would like to say something publicly about what you have gained from your experience with BugSigDB, please go ahead and edit this page, or post here (along with your bugsigdb username) and one of the project staff will add it. - Attachment (BugSigDB): Testimonials > Curators, please add your own testimonial here, or send it to project staff! Testimonials are posted with permission from the curator….

Maria Doyle (13:55:28) (in thread): > Great testimonial and great idea to show them!

U02CNMR4YEA (14:04:57) (in thread): > I also just realized (last night) that I was thanked in the article and was so touched because I feel I am the one who owes a huge thank you to those of you who have allowed me to learn so much in working on this project. I would be happy to write a testimonial:grinning:

Chioma Onyido (14:05:39) (in thread): > It’s an inspiring read. This idea will serve as another reminder of the amazing collaborative work on BugSigDB, and a source of motivation too! > Thank you@irem Kahvecifor sharing.:blush:

Levi Waldron (15:18:47) (in thread): > There’s no direction listed in Supplemental table 2 - unless that’s given somewhere else, you won’t be able to use the results of this table on its own…

Levi Waldron (15:24:00) (in thread): > It looks like panels a & c of Figures 2-6 provide alpha diversity and differential abundance results that you can curate. I see they also give a lot of results in the Results text, but I imagine these are contained within the figures and don’t add anything.

U02CNMR4YEA (17:00:17): > Hi everyone! I wanted to share a resource that I found. Although it is called Microbiome and the Eye, there are several chapters that are focused on the gut or oral microbiome and it was published in 2023 so it’s quite recent. If you check it out, let me know what you think (chapters can be downloaded for free)https://www.sciencedirect.com/book/9780323983389/microbiome-and-the-eye - Attachment (ScienceDirect): Microbiome and the Eye > Microbiome and the Eye: What’s the connection? highlights how alterations in the gut and eye microbiomes can lead to systemic immune alterations with …

U02CNMR4YEA (19:55:04) (in thread): > Thank you! I also found it odd that the Supp tables 2 and 3 don’t have a fold-change column whereas Supp table 4 does have that column (Supp 3 and 4 are presenting the same info but for dry eye in one and for normal in the other so that especially seems strange). Figure 2c has a footnote to address the asterisks and what p-values are represented but I don’t even see any asterisks in that figure. I actually emailed the first author just to see if I can get any further information and see if something got inadvertently left out.

2023-12-02

Esther Afuape (01:38:48) (in thread): > Oh this is so heartwarming to read! I hope to write a testimonial someday too.It’shonestly been awesome working on this project:face_holding_back_tears:

Peace Sandy (06:09:00) (in thread): > Really amazing testimonial > Well done@irem Kahveci

Peace Sandy (06:09:35) (in thread): > Thank You@Mary Bearkland:tada:

U02CNMR4YEA (14:33:39): > Hi All! I’m trying to subset data by Group 0 name and keep getting a return of 0 rows. I started by creating a subset of only those PMIDs of interest and that looks good but then when trying to get just the dataframe where Group 0 name is “Control” (of which there is definitely at least one), it returns an empty dataframe. My code is as follows: Subset to include only PMID numbers of interest

included.pmid <-
  c(
    31463790,
    32931939,
    37586456,
    37762390,
    34900990,
    37803284,
    31738825,
    35350577,
    37026303,
    32717380
  )
subset.dat <-
  dat[dat$PMID %in% included.pmid,]

subset.group0<-subset(subset.dat, 'Group 0 name'== "Control")


## 2023-12-03

**Ludwig Geistlinger** (13:10:37) (in thread):
The PMIDs are identifiers not ordinary numbers so you might want to put them in quotes, ie.`included.pmid <- c("31463790", "32931939", ...)`

**Ludwig Geistlinger** (13:22:48):
Hi reviewers@Chioma Onyido@Peace Sandy@Esther Afuape@Svetlana Ugarcina Perovic: something is odd with[Study 790](https://bugsigdb.org/Study_790)and[Study 733](https://bugsigdb.org/Study_733):
* [Study 790](https://bugsigdb.org/Study_790)doesn't provide the PMID but a DOI that is associated with the PMID of[Study 733](https://bugsigdb.org/Study_733)(PMID[33996618](https://pubmed.ncbi.nlm.nih.gov/33996618/)). However, that PMID is a human study on choledocholithiasis from China, whereas Experiment 1 of[Study 790](https://bugsigdb.org/Study_790)records results from a study in cattle.
* As pointed out above[Study 733](https://bugsigdb.org/Study_733)is associated with a PMID that is a human study on choledocholithiasis (gallstones) from China, but Experiment 1 of[Study 733](https://bugsigdb.org/Study_733)records results from a study on[dermatomyositis](https://bugsigdb.org/Dermatomyositis)(a skin condition) from the US.
Could you please take a look what's going wrong? Thanks!

**Peace Sandy** (13:32:00) (in thread):
Hi@Ludwig GeistlingerI’lltake a look and get back

**Esther Afuape** (13:41:07) (in thread):
Hello@Ludwig GeistlingerI’mcurrently taking a look at this. Study 790 looks like it was created in error. Itdoesn’thave a PMID, the DOI is wrong and the experiment in it looks like that of Study 788 with PMID 32630754. The experiment is also incomplete.I’mstill taking a look at study 733

**Ludwig Geistlinger** (13:47:16) (in thread):
Thanks@Peace Sandyand@Esther Afuape. Great point, can we check whether there is any information in Experiment 1 of Study 790 that is not captured in Study 788? A good solution here would be to carry any missing information over to Study 788 and then delete both: Signature 1 and Experiment 1 of Study 790 and Study 790 itself.[Unfortunately deleting a study doesn't cause deletion of its experiment and signatures yet](https://github.com/waldronlab/BugSigDB/issues/176), so we have to delete them individually. That means first delete the signature, then the experiment, and then the study.

**Esther Afuape** (13:55:04) (in thread):
I don’t see any information in experiment 1 of Study 790 that is not captured in study 788. May I go ahead to delete the signature and experiment, and the study itself?

**U02CNMR4YEA** (14:15:52) (in thread):
Thank you@Ludwig Geistlinger! I don't think that is the issue as when I run the code to subset by PMIDs, it returns a dataframe with those studies.  It's only when I try to subset again for specific group 0 or group 1 names that it returns a null set.:thinking_face:

**Ludwig Geistlinger** (14:16:57) (in thread):
Yes pls

**Ludwig Geistlinger** (14:21:10) (in thread):
I think you wanna use backticks around Group 0 name instead:`subset(subset.dat, `Group 0 name` == "Control")`

**U02CNMR4YEA** (14:45:25) (in thread):
@Ludwig GeistlingerYES! Thank you so much!! I spent way too much time on that yesterday:upside_down_face:and I had a feeling it was going to end up being something simple yet crucial.

**Chioma Onyido** (14:49:29) (in thread):
790 and 788 seems to be solved. Thank you@Esther AfuapeLooking at 733 now.:crossed_fingers:

**Chioma Onyido** (15:54:13) (in thread):
Just found (using the ‘advanced search’ filter) that the original study this 733 (expt 1) results belong to is[bugsigdb.org/Study_747](http://bugsigdb.org/Study_747).
And 747 seems to be fully curated and reviewed too.

However, I also tried but I couldn’t find the results for 733, maybe study details were entered but it was not curated…?
If so, I think it has to be curated from scratch.@Esther Afuape@Peace SandyDo we go ahead and delete the signatures under 733 and proceed with a fresh curation?@Ludwig Geistlinger

**Ludwig Geistlinger** (16:04:20) (in thread):
Thanks@Chioma Onyido. It seems that expt 1 of Study 733 need to be carried over to Study 747 as Study733/Exp1 seems to record results from Figure 1 that are not recorded in Study 747?

**Esther Afuape** (16:05:09) (in thread):
Good work!@Chioma Onyido

**Chioma Onyido** (16:10:13) (in thread):
Ohh I just saw that now, different sources.:thinking_face:That from 747 is sourced from within text, while 733 has its own from figure 1A.

After transferring the results,
Both studies most likely need to be reviewed again for these reasons
* to give a proper description of the paragraph/ subheading the “results within text” was picked from (747)
* And also to confirm that figure 1A result was well curated (733)
Thanks for pointing that out@Ludwig GeistlingerWe’reworking on this now.

**Esther Afuape** (16:26:49) (in thread):
So do we curate the the paper with the PMID in 733? Or we delete the entire study?

**Chioma Onyido** (17:29:28) (in thread):
I thinkwe’redoing both.@Esther AfuapeCurating 733 sinceit’sa different study.
Then reviewing 747 again.

Then@Ludwig Geistlingeralso suggested transferring the results from 733 to 747, before deleting.

**Esther Afuape** (17:48:21) (in thread):
@Ludwig GeistlingerMyself and@Chioma Onyidohave gone through the paper and there’s nothing curatable in figure 1. 1A is a principal coordinate analysis. The experiment can’t be moved to 747, I think it should be deleted.

Study 747 will also be properly reviewed. The only curatable figure is 2F-H whose results are completely different from what was curated.

**Ludwig Geistlinger** (17:56:34) (in thread):
Sounds good, thanks for the update@Esther Afuape


## 2023-12-04

**Peace Sandy** (07:30:45) (in thread):
@Esther Afuapehave you reviewed study 747 
Just asking, because I was about to review it

**Esther Afuape** (07:55:28) (in thread):
@Peace Sandyno, Ihaven’t.

**Peace Sandy** (07:56:02) (in thread):
Okay

**Peace Sandy** (09:12:55) (in thread):
I’mcurrently reviewing it

**Peace Sandy** (16:06:48) (in thread):
I’vebeen reviewing study 747 and it seems to have no error, the only thing I observed is that Chao 1 was not entered

**Peace Sandy** (16:07:47) (in thread):
And I’m not sure if confounded controlled should be entered@Chioma Onyidodid you find anything different from the study

**Chioma Onyido** (20:52:23) (in thread):
From Esther’s update, Figure 2F-H has some curatable signatures which wasn’t previously curated, and an additional experiment too, where the subgroups were contrasted; ILD-MSA vs Cancer-MSA.

There seem to be more results reported within texts, too.@Peace Sandy

**Chioma Onyido** (21:00:03) (in thread):
Also I think confounders controlled for should be curated since it was mentioned in the paper…?

For MSA subgroups vs HC, they adjusted for hypertension (under figure 2 description)

For DM vs HC, they adjusted for antibiotic use@Peace Sandy
  - File (JPEG): [IMG_6835](https://community-bioc.slack.com/files/U34P8RS3B/F0686MHGATZ/img_6835.jpg)
  - File (JPEG): [IMG_6836](https://community-bioc.slack.com/files/U34P8RS3B/F069A1J3BRN/img_6836.jpg)
  - File (JPEG): [IMG_6831](https://community-bioc.slack.com/files/U34P8RS3B/F068JA15KV3/img_6831.jpg)

**U02CNMR4YEA** (23:43:13):
Hi Everyone! I am trying to find the 10 most increased signatures in Group 1 for my data.***Here is my code:***getMostFrequentTaxa(subset.final, n = 10, sig.type = "increased", direction.column ="Abundance in Group 1")***Here is the error message:***

Error in bugsigdbr::getSignatures(dat, …) : unused arguments (sig.type = “increased”, direction.column = “Abundance in Group 1”) ``` Any thoughts? Thank you in advance!

2023-12-06

UBNSEMS3S (12:04:11): > Hi everyone we will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499

2023-12-07

Peace Sandy (05:55:56) (in thread): > Thank You

UBNSEMS3S (12:18:17): > Meeting recording - File (MPEG 4 Video): video1272747270.mp4

Chioma Onyido (12:47:26) (in thread): > I just realized now that the results screen IthoughtI was sharing wasn’t showing:sweat_smile:My apologies to anyone I confused because of this, won’t happen next time. > > Thanks for the opportunity and I appreciate the constructive feedback.:100::pray:

2023-12-08

Svetlana Ugarcina Perovic (04:22:08) (in thread): > @Chioma Onyidono worries, because we could open link to the paper you talked about and follow you there in our own browser (that’s what I did). Good job!

Chioma Onyido (07:25:11) (in thread): > Phew! That’s relieving and encouraging. Thank you so much.:blush:@Svetlana Ugarcina Perovic

2023-12-09

U02CNMR4YEA (08:38:56) (in thread): > I also opened the paper and followed along:grinning:.Thank you for your presentation!

Chioma Onyido (19:21:38) (in thread): > Really good to know this, thank you for listening.:blush:<@U02CNMR4YEA>

2023-12-11

Peace Sandy (03:34:14): > Hi:wave:Everyone, is anyone currently reviewing this studyhttps://bugsigdb.org/Study_586I’mcurrently reviewing it, just wanted to be sure no one else is working on it. - Attachment (BugSigDB): Preliminary Comparison of Oral and Intestinal Human Microbiota in Patients with Colorectal Cancer: A Pilot Study - BugSigDB > In this study Next-Generation Sequencing (NGS) was used to analyze and compare human microbiota from three different compartments, i.e., saliva, feces, and cancer tissue (CT), of a selected cohort of 10 Italian patients with colorectal cancer (CRC) vs.10 healthy controls (saliva and feces).

2023-12-12

U01MW62UDQR (10:33:48) (in thread): > I’m following up to see if these issues have been resolved:slightly_smiling_face:

Esther Afuape (10:45:31) (in thread): > @Andres Wokatystudy 733 is yet to be curated butit’llbe done within the week.@Peace Sandydid you conclude the review of study 747?

Andres Wokaty (11:08:48) (in thread): > @Esther AfuapeThank you. If someone could just notify me here that everything is complete, I would appreciate it. I’m going to make new releases forhttps://github.com/waldronlab/bugsigdbexportsandhttps://github.com/waldronlab/bugsigdbr, which use BugSigDb data.

Peace Sandy (11:10:38) (in thread): > Hi@Andres WokatyI completed Study 747@Esther Afuapeis they any other study left

Esther Afuape (11:24:25) (in thread): > @Peace Sandydid you mean 747? 733 hasn’t been curated yet.It’sthe one left for this thread

Peace Sandy (11:25:46) (in thread): > Yes@Esther AfuapeI meant 747

Chioma Onyido (11:34:00) (in thread): > @Peace SandyI had thought we agreed that 747 has additional expt and signatures to be added. From figure 2F-H.

Peace Sandy (11:35:00) (in thread): > Ididn’tsee your message on timeI’lltake a look at it again, ifit’snot late

Chioma Onyido (11:37:20) (in thread): > No,I don’t thinkit’stoo late,we’dnotify@Andres Wokatyoncewe’reall done.

Peace Sandy (11:38:30) (in thread): > Alright

UBNSEMS3S (15:55:34): > Hi all, Levi and I spoke about having a weekly book club to read Hadley Wickham’sAdvanced R. This book is available freely online (https://adv-r.hadley.nz/) and a great source for anyone wanting to become a better R programmer or even just get started with R programming. > > I thought we would start the first full week of January with each book club member signing up to present a chapter. Presentations would be informal and each book club session would be about an hour. > > I’ve created a survey where you can select some times that work for you for our sessions:https://rallly.co/invite/4CKSVggeyoV7Please respond by December 22nd so we can start promoting the event. If none of these times work, feel free to suggest some alternate times. - Attachment (app.rallly.co): Advanced R Bookclub > By Guest

Andres Wokaty (18:43:45) (in thread): > Is there a guide to doing the presentation and how long should it be? I am guessing this is an overview of the key points. Thanks for organizing this.

2023-12-13

Peace Sandy (01:52:15) (in thread): > Sounds great!

Peace Sandy (05:49:01): > Hey Everyone > In the study I’m currently reviewing, n = 20 patient and control fecal samples, n = 20 patient and control saliva samples, n = 10 CT samples was obtained. Should the CT sample have an experiment on its own since itdoesn’thave a control group

Chioma Onyido (05:56:25) (in thread): > Amazing! Thank you so much.I’mLooking forward to it!:rocket:Co-asking with@Andres Wokaty, is there a template for the presentation?

Svetlana Ugarcina Perovic (06:20:54): > During today’s talk by Liao Herui (PhD Student of City University of Hong Kong) about his work on strain identification analysis (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10433603/), I remembered our discussion on why some signatures have the same species in decrease and increase reported? > > One of Liao’s slides had a nice illustration and helpful comment that I would like to share with you:******Different bacterial strains may have different biological properties due to the different genes:********for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98% [https://pubmed.ncbi.nlm.nih.gov/30837975/]** - File (JPEG): IMG_1372.jpeg

Peace Sandy (06:24:33) (in thread): > Thank You@Svetlana Ugarcina PerovicThis is really helpful

Esther Afuape (06:57:53) (in thread): > Does it have a result? If yes, What comparison is the result reporting for?

Esther Afuape (06:59:18) (in thread): > Thank you! I still came across this in the study I was reviewing yesterday.Makes more sense now

Peace Sandy (08:35:13) (in thread): > @Esther Afuapeyes it has a result, CT sample does not have any comparison

U1LCB8WEA (09:35:16) (in thread): > <@U01MW62UDQR>would you create a directory full of Slidy presentation templates athttps://github.com/waldronlab/data-science-seminar?

U1LCB8WEA (09:35:57) (in thread): > One template file per chapter

Esther Afuape (10:33:55) (in thread): > They just reported the abundance in CT without comparing it to anything?I’dsayit’snot an experiment then. An experiment has to be a comparison between 2 groups

U01MW62UDQR (14:30:33) (in thread): > I can do that.

Peace Sandy (15:17:25) (in thread): > Thank You@Esther Afuape

UBNSEMS3S (15:28:05) (in thread): > <@U01MW62UDQR>For the presentations the goal is to: > * Summarize the key information from the assigned chapter > * Go into R and show a few examples (can use the examples given in the book) > * Work collaboratively with the attendees to answer the exercises at the end of the chapter > Presentations are informal and it can include a lot of copy-and-pasting from the book. Absolutely no need to reinvent the wheel. Preparation should largely involve just reading the chapter and copying the key bits into a Slidy presentation.

UBNSEMS3S (17:13:50): > Study 262 “Bacterial biogeography of adult airways in atopic asthma” ReviewHere is my detailed review ofhttps://bugsigdb.org/Study_262which was an exceptionally challenging curation that@Chioma Onyidoreviewed last week. I wanted to present the review for everyone to see the challenges around experiment 7.Study > * Study design is case-control. I know this for two reasons: 1) a case-control study nested within an RCT is a common study design and the methods section implies that this is a nested case-control and 2) there is a disease state as a condition. As I’ve mentioned, cross-sectional observational should really only be used in situations where the condition isn’t a disease or there isn’t a clear healthy control group. > Experiments 1-6 and accompanying signatures > * Perfect. No notes. > Experiment 7 > * This experiment was incredibly confusingly described in the paper. It took me nearly 45 minutes of flipping back and forth between the supplement and the paper to fully understand what was being reported where. It is a good example of how too much extraneous information can actually hide important results. > * What was curated was a combination of Figure 4D (which is a total composition analysis using a chi-squared test and not something we typically curate) and a single sentence in the article reading: “The OTUs predominantly shared (in at least 20% of subjects) between BB-IS samples in AAs included members ofPrevotellaand a number of other genera previously reported to be associated with asthma, specificallyHaemophilus,Fusobacterium, andNeisseria[3]” > * As can be seen at the end of this sentence and from the phrase “previously reported” they are citing previous work and not presenting new findings, despite this sentence appearing in the results. Thus these three taxa should not have been curated. > * What should have actually been curated was Figure S6B which presents enriched taxa among asthmatic subjects compared to healthy controls using a ZINB (zero-inflated negative binomial regression) model. The single alpha diversity measure (Faith’s) for this experiment can be found in Figure S2A. > * I have made the changes to the curation. This curation can now be considered complete and reviewed. - Attachment (BugSigDB): Bacterial biogeography of adult airways in atopic asthma - BugSigDB > BACKGROUND: Perturbations to the composition and function of bronchial bacterial communities appear to contribute to the pathophysiology of asthma.Unraveling the nature and mechanisms of these complex associations will require large longitudinal studies, for which bronchoscopy is poorly suited.

UBNSEMS3S (17:17:21): > I will talk about this briefly tomorrow when we will be having our weekly team meeting at 10 AM EST (Thursday).https://us02web.zoom.us/j/2737200499

2023-12-14

Chioma Onyido (03:45:05) (in thread): > I was reviewing a paper yesterday and I saw ‘Bacteroides’ appearing in both decrease and increase signatures, came back to this post to remember why again and make sense of it:sweat_smile:Bookmarking this now! Thanks a bunch for sharing.:grinning:

Peace Sandy (04:26:45): > Hey everyone > Is anyone currently reviewing this study ?https://bugsigdb.org/Study_809 - Attachment (BugSigDB): Dysbiosis and Implication of the Gut Microbiota in Diabetic Retinopathy - BugSigDB > The pathogenesis of type 2 diabetes mellitus (T2DM) is commonly associated with altered gut bacteria.However, whether the microbial dysbiosis that exists in human diabetic patients with or without retinopathy is different remains largely unknown.

Chioma Onyido (04:39:39) (in thread): > Hi Peace. Yes I am.:wave:

Peace Sandy (04:40:52) (in thread): > Alright > So glad I asked:sweat_smile:Let me look for another study

Andre Nana (09:35:27) (in thread): > That would be great. I have been trying to create my own repository on GitHub. Will be the opportunity to learn these skills too.

Peace Sandy (09:51:16): > @Chioma Onyidodid you work or are you currently reviewinghttps://bugsigdb.org/Study_806 - Attachment (BugSigDB): Gut Microbial Signatures Can Discriminate Unipolar from Bipolar Depression - BugSigDB > Discriminating depressive episodes of bipolar disorder (BD) from major depressive disorder (MDD) is a major clinical challenge.

U02CNMR4YEA (09:58:39) (in thread): > Thank you for sharing that information!

Peace Sandy (09:58:45): > I’llbe working to review this studyhttps://bugsigdb.org/Study_619 - Attachment (BugSigDB): Delivery mode shapes the acquisition and structure of the initial microbiota across multiple body habitats in newborns - BugSigDB > Upon delivery, the neonate is exposed for the first time to a wide array of microbes from a variety of sources, including maternal bacteria.

Chioma Onyido (10:01:41) (in thread): > Yes@Peace SandyI reviewed 806.

Peace Sandy (10:02:28) (in thread): > Oh…it’snot marked as review

Chioma Onyido (10:10:06) (in thread): > Oops. Done.:white_check_mark:Thank you!

Svetlana Ugarcina Perovic (10:58:15) (in thread): > Sharing here link to Lactobacillus iners strains review paper:https://www.sciencedirect.com/science/article/pii/S0966842X16301810 - Attachment (sciencedirect.com): Lactobacillus iners: Friend or Foe? > The vaginal microbial community is typically characterized by abundant lactobacilli. Lactobacillus iners, a fairly recently detected species, is frequ…

2023-12-15

Svetlana Ugarcina Perovic (05:41:54): > NEXT WEEK you are welcome to join another amazing MVIFhttps://www.microbiome-vif.org/en-US/-/future-events/mvif24-1819-20-december-2023-prof-jack-gilbertAt the Atlantic#MVIFduring networking session we will be discussing how can we do better while attending an online conference. > > I’ll share some tips not only as a person behind the#MVIFglobal communication but also as an attendee who benefited a lot from online conferences! (https://www.nature.com/articles/d41586-023-02507-7)Happy Friday! - Attachment (microbiome-vif.org): MVIF.24 | 18/19 & 20 December 2023 > with Keynote talk by Prof. Jack Gilbert

Peace Sandy (05:56:33) (in thread): > @Chioma OnyidoI’ve been going through 747, The additional experiment you talked about is comparing the two sub groups which are ILD - MSA and Cancer MSA , in such case which one will be the control group

Chioma Onyido (06:12:46) (in thread): > Looking forward to it! > Happy Friday Svetlana:confetti_ball:

Esther Afuape (06:24:52) (in thread): > Thank you! > Happy Friday:confetti_ball:

Chioma Onyido (06:25:12) (in thread): > Yeah I’ve asked a similar question before,Chloe said in such cases any of them can serve as the control group, only be consistent with it.

Peace Sandy (08:35:10) (in thread): > Hi:wave:@Chioma Onyidoand@Esther AfuapeI’ve added the additional experiment to Study 747 and completed the study, help me look through to ensure accuracy

Chioma Onyido (11:29:00) (in thread): > Awesome! Thank you@Peace Sandyand Well done.:+1:

Peace Sandy (13:28:04) (in thread): > Thank You@Chioma Onyido

UBNSEMS3S (16:55:06): > Forgot to post this. Recording of yesterday’s meeting. - File (MPEG 4 Video): video1791256846.mp4

2023-12-16

Peace Sandy (05:56:38) (in thread): > Thank You

2023-12-18

Svetlana Ugarcina Perovic (04:26:59) (in thread): > Happy Monday! :woman-surfing:Could you please share with me/us here what’s challenging for you during an online conference? > > Here are my slides for MVIF discussion, if you spot that I missed something please tell me, thanks! - File (PDF): How to do better_remote conferencing.pdf

Svetlana Ugarcina Perovic (05:00:28): > What a great and important topic of the Outreachy week 3Everyone struggles!I love that they mentioned –> “Rubber duck debuggingis a method of debugging code by articulating a problem in spoken or written natural language.” Explaining code OR any other problem to a rubber duck i.e. your colleague can actually solve problems! > > To me this happens so many times, especially when I am new in the team or to the project. Usually when I can’t see direction to the solution of my current challengewithin max 30 minI’m writing to my team mate. I see that the Outreachy advised “If you’re stuck for morethan 1 to 3 hours, ask your mentor”. In my opinion, you should not wait hours to pass, feel free to ask when you feel stuck earlier than that!

Peace Sandy (05:16:50) (in thread): > Wow… this is excellent > Well done@Svetlana Ugarcina Perovic

Peace Sandy (05:18:02) (in thread): > True everyone struggles,I’malways excited when I hear people talk about their struggles. > > It shows that no one is an island and we all have struggles. > > Happy New Week@Svetlana Ugarcina PerovicThank you so much for this! > > This is really helpful:rocket:

Esther Afuape (05:56:08) (in thread): > Hello:wave:<@U01MW62UDQR>the last 2 studies have been sorted out.Everything under this thread is now solved.

Esther Afuape (05:59:37) (in thread): > I agree! Not waiting till you get overwhelmed by a problem is really the best.I’mglad this is a community that makes it very easy to seek help whenit’sneeded.

Chioma Onyido (06:24:05) (in thread): > Felt the welcoming and friendly vibe in this community from day one!I remember being stuck on my first Outreachy task and immediately reaching out by dropping a msg on the channel, and I got diff responses in less than 20minutes. All being helpful and encouraging.:sweat_smile:Sharing my challenges/ struggles (especially with tasks) has not been an issue ever since, thank you for sharing!:bouquet:

Andres Wokaty (08:34:05) (in thread): > Great job! Thanks,@Chioma Onyido@Peace Sandy@Esther Afuape

U02CNMR4YEA (09:46:52) (in thread): > Happy Monday! Any remote conference session I attend, I always want to know if the slides will be shared after the conference so I know whether I need to try to take notes on everything or just those items thataren’ton the slides.If the presenterdoesn’taddress that up front, someone almost always asks.:grinning:

Svetlana Ugarcina Perovic (09:48:20) (in thread): > <@U02CNMR4YEA>a good point, for both conferencing modes, in-person and remote!

Peace Sandy (14:05:17) (in thread): > Thank You@Andres Wokaty

UBNSEMS3S (15:24:39) (in thread): > To add on to the theme ofEveryone Struggles with my own experience. What I struggle with the most is calledproductive procrastination. I procrastinate by working on tasks that are less important or easier than important tasks. For instance, I am supposed to be working on getting one of my dissertation papers ready for Levi right now. Instead, I am working on a report for a different project. > > I was especially guilty of this during my dissertation, but I still do it a lot during my daily work. One thing that has helped me is structuring my time. Setting aside specific chunks of my week for writing, coding, and reviewing has helped. Another has been to hold myself accountable for deadlines (and sometimes setting some punishments for myself if I fail to meet them!). > > Finally I think it’s important to realize that productivity is not a static binary variable. Some days you are very productive and some days feel unproductive, even wasted. That’s ok. You’re not a machine. As long as you’re making progress, you’re not being unproductive. Setbacks and delays are part of progress, not a roadblock to progress.

Chioma Onyido (16:26:27) (in thread): > I needed to read this.:melting_face:Especially the last paragraph. Thank you for sharing:bouquet:<@UBNSEMS3S>

U02CNMR4YEA (17:58:45) (in thread): > Agree!:blush:

U02CNMR4YEA (18:02:01) (in thread): > Absolutely needed this reminder as I am slogging my way through this Monday and trying to be okay with a steady pace.Two steps forward and one step back is still forward motion:grinning:.

2023-12-19

Peace Sandy (03:45:45): > Hi Everyone > I’m trying to figure out how to get the signatures from this result. > Link to the paperhttps://pubmed.ncbi.nlm.nih.gov/32192080/ - Attachment (PubMed): Microbiome Profile of Deep Endometriosis Patients: Comparison of Vaginal Fluid, Endometrium and Lesion - PubMed > This work aimed to identify and compare the bacterial patterns present in endometriotic lesions, eutopic endometrium and vaginal fluid from endometriosis patients with those found in the vaginal fluid and eutopic endometrium of control patients. Vaginal fluid, eutopic endometrium and endometriotic l … - File (PNG): IMG_7680 - File (PNG): IMG_7679

Odigiri Great Alume (06:28:51): > @Peace Sandygood morning dear. > Take a look at figure 4. I think there are some experiments curatable there.

Peace Sandy (06:30:08) (in thread): > Yes,that’sfor relative abundance. > Ideally we are supposed to curate differential abundance > Thank you so much

Odigiri Great Alume (06:32:20) (in thread): > Sorry I sent the wrong image. Look at figure 4

Peace Sandy (06:33:34) (in thread): > Okay

Peace Sandy (06:33:53) (in thread): > Let me take a look@Odigiri Great Alume

Odigiri Great Alume (06:35:11) (in thread): > (B) Differential abundance heatmap comparing all the collection sites from case and control samples. Results are showed as the log2FC for the differentially detected genera. Most abundant genera are showed as red values considering the first sample category in the bottom legend. - File (JPEG): Screenshot_20231219-123436.jpg

Odigiri Great Alume (06:35:24) (in thread): > @Peace Sandyalright dear

Chioma Onyido (06:41:46) (in thread): > Yes I think red is for increase, while blue is for decrease.

Peace Sandy (06:43:16) (in thread): > Oh

Peace Sandy (06:43:54) (in thread): > Let me try to figure it out, yeah I saw it but I was pretty confused on how to get the correct signatures

Odigiri Great Alume (06:43:58) (in thread): > @Chioma OnyidoI think so too

Odigiri Great Alume (07:40:19): > Good afternoon team. Please I am working on study 784 and I need help with the following. > 1. I can’t seem to find group 0 sample size anywhere in the study. Atleast I saw that they said something about group 1 sample size “241 samples from 127 admitted patient”. But I can’t tell from this the specific sample sizes for each group. > 2. On alpha diversities, in one image below it says that they used shannon to measure alpha diversity while in the other image it seems they used inverse Simpson. I’m a bit confused on what exactly they used here:thinking_face:. > 3. I will appreciate if you can also look at figure three to help me confirm that’s where the correct signature is, they made reference to figure 2, however I’m in doubt. Because figure 3 seems to be the most accurate in my opinion. So please help me look. And I do think there’s only one experiment in this study. > Thank you and God bless you. > Link to paperhttp://dx.doi.org/10.1186/s13073-023-01202-6@C. Mirzayi (please do not tag this account)@Levi Waldron@Chioma Onyido@Esther Afuape@Svetlana Ugarcina Perovic - Attachment (BioMed Central): Metagenomic assessment of gut microbial communities and risk of severe COVID-19 - Genome Medicine > Background The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. Methods We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. Results Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or “long COVID,” suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Conclusions Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention. - File (JPEG): IMG_20231219_132810.jpg - File (JPEG): IMG_20231219_132830.jpg

Esther Afuape (08:21:15) (in thread): > Hi, Great!How’veyou been? > Taking a quick look at this, I can see “n=79 with severe Covid and 48 with moderate”. Are these the groupsyou’recomparing?

Odigiri Great Alume (09:47:42) (in thread): > Yes@Esther Afuapethank you

Odigiri Great Alume (09:48:19) (in thread): > @Esther AfuapeI’m fine thank you. > Thank you again

Esther Afuape (09:58:11) (in thread): > I agree with you on curating from figure 3. Ifthere’sany result you need to curate that has figure 2 as its reference,I think you can use “within text result” and point out where the result was stated within text. > For the alpha diversity, I think you should go with Inverse Simpson sinceit’sthe result reported andthere’sno result for Shannon

Esther Afuape (10:00:48) (in thread): > I’mcurious about how figure 3 should be interpreted. It seems to have only one increase?

Mildred Anashie (10:43:29) (in thread): > Hi@Odigiri Great Alume@Esther AfuapeHow have you been?Going through I thinkit’sa longitudinal study and if it is, then the sample size for group 0 and group 1 will be the sameI’llgo through the results to see if I can confirm this

Esther Afuape (10:46:42) (in thread): > @Mildred Anashiethe patients were grouped from the beginning of the study throughout the timeframe. Check that short “methods” in the abstract of the paper

Mildred Anashie (10:56:54) (in thread): > So are you saying it should be contrasted as Moderate vs Severe?

Odigiri Great Alume (11:20:25) (in thread): > @Mildred Anashieyeah the experiment contrasted severe vs moderate

2023-12-20

Levi Waldron (09:12:57): > Enjoying MVIF n.19 right now!

Svetlana Ugarcina Perovic (09:13:59): > You can still have time to register and join inhttps://hopin.com/events/microbiome-vif-n-24

Levi Waldron (09:17:38) (in thread): > I meant 24:sweat_smile:

UBNSEMS3S (20:28:55): > Hi everyone we will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499

Peace Sandy (23:08:24) (in thread): > Thank You for the reminder

2023-12-21

Svetlana Ugarcina Perovic (07:43:21): > :cat2:STUDY (not microbiome but still important one)Dr. Alexandra Zidenberg:We are looking for individuals to participate inresearchlooking athow personality might impact the bond with cats. If you have a cat, please consider participatingcc<@UBNSEMS3S>:slightly_smiling_face: - File (JPEG): cats.jpeg

UBNSEMS3S (09:33:34) (in thread): > Amazing. Filling it out right now.

UBNSEMS3S (10:51:16): > Hi all, Levi and I spoke about having a weekly book club to read Hadley Wickham’sAdvanced R. This book is available freely online (https://adv-r.hadley.nz/) and a great source for anyone wanting to become a better R programmer or even just get started with R programming. > > I thought we would start the first full week of January with each book club member signing up to present a chapter. Presentations would be informal and each book club session would be about an hour. > > I’ve created a survey where you can select some times that work for you for our sessions:https://rallly.co/invite/4CKSVggeyoV7Please respond by December 22nd so we can start promoting the event. If none of these times work, feel free to suggest some alternate times. - Attachment (app.rallly.co): Advanced R Bookclub > By Guest

Esther Afuape (10:58:40): > Hi<@UBNSEMS3S>Can you mention those days that are holidays again, please?

Chioma Onyido (11:02:36) (in thread): > I think she mentioned 26th and 27th,can’tremember other days.

UBNSEMS3S (11:04:29) (in thread): - File (PNG): image.png

U02CNMR4YEA (15:09:27): > Hi Everyone! I missed seeing you all on the meeting but had a work conflict:disappointed:. In speaking with Levi this week, he mentioned that I could request review of the articles I have curated and plan to use for my capstone. If any of you have time and wouldn’t mind reviewing these PMIDs, I would be so grateful:slightly_smiling_face:. Thank you in advance! > 31463790 > 32931939 > 37586456 > 37762390 > 34900990 > 37803284 > 31738825 > 35350577 > 37026303

Peace Sandy (15:21:35) (in thread): > Sure!

Chioma Onyido (15:25:53) (in thread): > Hi@Mary Bearklandhow’ve you been? I Noticed your absence, I hope all is resolved. Today’s meeting was exceptionally interesting,<@UBNSEMS3S>and<@U1LCB8WEA>shared some niceBugSigDBtricks on how to do an efficient review.Bookmarked your post just now.Looking forward to trying some of the new tips I learned today on your aforementioned curations.:blush:

Esther Afuape (15:30:50) (in thread): > Hi<@U02CNMR4YEA>Got you!

Peace Sandy (15:31:45): > Hey Everyone:wave:Here are some of the tips@C. Mirzayi (please do not tag this account)and@Levi Waldrongave on paper reviews during the weekly sync > These are the important points to look out for while reviewing a paper:fast_forward:Group 0 - should be correctly entered:fast_forward:Group 1:fast_forward:Condition:fast_forward:Body Site:fast_forward:Signatures:fast_forward:What is being contrasted in the paper > > The recording of the weekly sync will also be posted incase I missed any tip

UBNSEMS3S (16:03:46): > Thanks Sandy! Here is the recording. - File (MPEG 4 Video): video1358712008.mp4

U02CNMR4YEA (21:46:47) (in thread): > Thank you all!

2023-12-22

Esther Afuape (09:55:20) (in thread): > I need help with the paper for the study with PMID32931939. I can’t access it.<@U02CNMR4YEA>@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron

Chioma Onyido (12:18:11) (in thread): > Sent@Esther Afuape

U1LCB8WEA (12:27:09) (in thread): > The start of the transcript made me chuckle, “Deep God…”

Esther Afuape (12:31:12) (in thread): > Thank you:heart:@Chioma Onyido

Chioma Onyido (12:56:15): > Happy weekend all:wave:I have a few questions concerning a review I’m currently on: > In this study, they mentioned on the phylum, genus and species level for most of the (not all) microbes.@Esther Afuapeand I have had a discussion on this and she advised to curate only species for those that have their species mentioned, then to curate all the phylum and any genus that doesn’t have its species mentioned. > > As opposed to curating all the levels as the curator did (see attached images for reference). > > This is what I’m thinking of following butI’mcautious about removing taxa that have already been curated, the curator may have had valid reasons for curating all levels. > > Please I need your advise concerning this?<@U1LCB8WEA>@Svetlana Ugarcina Perovic<@UBNSEMS3S> - File (JPEG): 62651f17-e527-4684-aec5-89f2b4f1540d - File (JPEG): 70fc4a8f-96ac-4ec5-bb6c-0087ed326bda - File (JPEG): b462a6ca-95f5-45b1-b55a-6befb54b189b

2023-12-25

Odigiri Great Alume (00:15:42) (in thread): > Good morning@Chioma OnyidoI do think only the phylum (for those whose genus weren’t mentioned) and genus (for those whose phylum weren’t mentioned) should be curated. > You remember@C. Mirzayi (please do not tag this account)advised that when we havestaphylococcusaureus only Staphylococcus be curated. > So I think you should stick with genus n phylum. > > I hope I understand your question n able to remind you right. > > Merry Xmas dear

Odigiri Great Alume (00:17:20): > Merry Christmas to everyone, our mentors. It is my pleasure to have crossed paths with you all amazing people. > I love you all. > The world is for your taking. So reach out and keep taking it by the good work you all put in here and out there. > God bless you all.

Chioma Onyido (03:52:53) (in thread): > Merry Christmas Great! Merry Christmas everyone.:christmas_tree:

Chioma Onyido (03:54:49) (in thread): > Thank you Great. I do remember but I also remember you sayingit’sonly specific to your curation? When I go back to the thread from that day, I see that therewasn’ta conclusive answer that day.:weary:

Esther Afuape (10:41:33) (in thread): > Merry Christmas,Great!:tada::heart:

irem Kahveci (13:30:25) (in thread): > Merry Christmas:christmas_tree::gift::partying_face::partying_face::partying_face:

Odigiri Great Alume (13:36:13) (in thread): > Uhmmm it wasn’t specific to my curation@Chioma Onyidoremember@Svetlana Ugarcina Perovictalked about curating the taxa in their most (is it dominant or superior order). I have forgotten, but I’m quite very sure you don’t curate specific and generic names together. If you have S. Aureus. You represent as Staphylococcus. > > We can have a huddle later to talk. Maybe we can look at that thread together to remind each other.

Peace Sandy (13:48:54) (in thread): > Merry Christmas Great! > Merry Christmas Everyone:bouquet:

Odigiri Great Alume (13:53:22) (in thread): > Same to you!

Chioma Onyido (14:26:39) (in thread): > Ohhh I get it now.. hmmm:thinking_face:

Esther Afuape (14:28:19) (in thread): > Hmm S.aureus is more specific than Staphylococcus to me

Odigiri Great Alume (14:36:20) (in thread): > @Esther AfuapeI understand. Just that if we can get the thread where@Svetlana Ugarcina Perovicspoke about using correct superior order instead of both specific and generic names combined, and also where@C. Mirzayi (please do not tag this account)specifically said I should record only the genus….. I’m sure we’d come to a conclusion. > Well done dear

Svetlana Ugarcina Perovic (15:10:22) (in thread): > Hello hello, here is our discussion thread on taxonomic levels…https://community-bioc.slack.com/archives/C04RATV9VCY/p1699368157954639 - Attachment: Attachment > Hello :wave: @Levi Waldron @UBNSEMS3S while trying to solve a curation issue alongside @Odigiri Great Alume he mentioned that he was corrected to not curate species of the same genus individually. If the goal of curation is to capture taxa as specific as possible, why is that incorrect? > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1699364814420979?thread_ts=1699358568.220309&channel=C04RATV9VCY&message_ts=1699364814.420979

Svetlana Ugarcina Perovic (15:26:29) (in thread): > Signature 1 includes: > Actinomycetota > Apicomplexa > Ascomycota > Chlamydia > Chlamydia trachomatis > Chlamydiota > Enterobacter > Escherichia > Escherichia coli > Leuconostoc > Mycobacterium > Mycobacterium leprae > Plasmodium (Plasmodium) > Plasmodium ovale > Salmonella enterica > Vibrio > Leuconostoc sp. DORA_2 > > When we do the classification of the lowest taxonomic levels you will see that their higher taxonomic levels are mentioned in the text: > Phylum: Chlamydiota; Genus: Chlamydia;**** Species: Chlamydia trachomatis ****Phylum: Pseudomonadota; Genus: Escherichia;Species: Escherichia coliPhylum: Actinomycetota; Genus: Mycobacterium;Species: Mycobacterium lepraePhylum: Apicomplexa; Genus: Plasmodium;**** Species: Plasmodium ovalePhylum: Pseudomonadota; Genus: Salmonella;Species: Salmonella entericaPhylum: Bacillota; Genus: Leuconostoc;Species: Leuconostoc sp. DORA_2Phylum: Pseudomonadota;Genus: EnterobacterPhylum: Pseudomonadota;** Genus: VibrioKingdom: Fungi; Subkingdom: Dikarya;Division: AscomycotaSignature 2 includes: > Pseudomonadota > Bacillota > Enterococcus > Streptococcus > Staphylococcus > Acinetobacter > Enterococcus faecalis > Streptococcus pneumoniae > Staphylococcus aureus > Acinetobacter johnsoniiWhen we do the classification of the lowest taxonomic levels you will see that their higher taxonomic levels are mentioned in the text:Phylum: Bacillota; Genus: Enterococcus;Species: Enterococcus faecalisPhylum: Bacillota; Genus: Streptococcus;Species: Streptococcus pneumoniaePhylum: Bacillota; Genus: Staphylococcus;Species: Staphylococcus aureus Phylum: Pseudomonadota; Genus: Acinetobacter:Species: Acinetobacter johnsonii **

Svetlana Ugarcina Perovic (15:33:14) (in thread): > So, what I see here that in the text they just started to describe their signatures from above to the bottom, from phylum togenus/species (exception phylum Ascomycota, just mentioned as phylum since it’s not Bacteria****).****

Svetlana Ugarcina Perovic (15:40:56) (in thread): > Thus, IN THIS CASE/CURATION, I would report the lowest possible taxonomic level mentioned in the text.

Svetlana Ugarcina Perovic (15:44:41) (in thread): > Just as a side note: It would be very helpful when you ask questions about specific curation to leave a link to it as well.https://bugsigdb.org/Study_856 - Attachment (BugSigDB): Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye - BugSigDB > BACKGROUND: Microbiome changes on the ocular surface may cause dry eyes.

Esther Afuape (15:50:23) (in thread): > @Svetlana Ugarcina Perovicand in cases (e.g, in this case) , where the speciesisn’tmentioned,the lowest taxonomic level available should be mentioned?

Svetlana Ugarcina Perovic (15:51:35) (in thread): > yes

Esther Afuape (15:57:09) (in thread): > @Chioma OnyidoI think this still goes with our discussion

Svetlana Ugarcina Perovic (16:01:54) (in thread): > “curate only species for those that have their species mentioned, then to curate all the phylum and any genus that doesn’t have its species mentioned.” yes, in other words

Chioma Onyido (16:04:37) (in thread): > Got it! Thank you so much for your time.@Svetlana Ugarcina Perovic@Odigiri Great Alume@Esther AfuapeMeans a lot.:hugging_face:

Svetlana Ugarcina Perovic (16:23:29): > While I’m looking forward to reading your next blog post, I would like to highlight here* what I loved in your first Outreachy posts:@Esther Afuapehighlighted the importance of being kind in building a supportive scientific community,@Chioma Onyidomentioned the other two interns as an important part of her internship,@Peace Sandydescribed clearly the Outreachy steps to a reader who does not know anything about it!Thank you for such enjoyable reads!*besides my X, BlueSky and LinkedIn posts

2023-12-26

Chioma Onyido (02:50:50) (in thread): > Thank you so much for your corrections, encouraging words, sharing and continuous support.:hugging_face:My blog reach was like…:chart_with_upwards_trend::smile:

Peace Sandy (02:55:13) (in thread): > Wow…Thank you so much@Svetlana Ugarcina Perovicfor all your repost, corrections , encouragements and kindness. It really means a lot andI’mso grateful:bouquet:

Esther Afuape (03:18:13) (in thread): > Thank you for your corrections! They definitely made my blog more presentable and enjoyable. Looking forward to sharing the next one with you

Chioma Onyido (06:28:34) (in thread): > Hi<@U02CNMR4YEA>:wave:, we’ve just completed the review of all 9 studies:white_check_mark:Here’s a bullet point summary of the changes we are uncertain about and would appreciate your clarification before moving forward with implementation:STUDY 856 > 1. For experiment 2: I’m not sure where the statistical test “ANOSIM” came from, couldn’t find where that was located within text. > 2. I’m not sure where the group sample sizes of group 0 and 1: > Previous sample size: 18 and 15New sample size: 10 for each (I saw this reported in the text)STUDY 770 > 1. None observed. > STUDY 830 > 1. Additional experiments? Figure 4B (ATD vs Non-ATD) and 4C (MGD vs Non-MGD) > 2. Should the signature for expt 6 be decreased instead of increased? > because “Polarized abundance is defined as: (1) prevalence in the dry eye group islower thanthe healthy group;**** ****(2) relative abundance in the species-positive dry eye samples is significantly higher than healthy samples.

Esther Afuape (06:29:57) (in thread): > Study 759: > 1. The statistical test says Wald test but I can see DESeq2 in the methods and the description of the signatures. I’d like to confirm if this was an error. > 2. In experiment 3, I couldn’t figure out where some of the taxa were from. I didn’t see them in figure 5, I also checked the supplemental. > The taxa include Streptomyces violaceusniger in signature 1. For signature 2: Streptomyces rubiginosus.micrococcaceae, corynebacteriales and corynebacteriaceae were omitted from signature 2 according to figure 5. Was there a reason for this?

Peace Sandy (06:40:16) (in thread): > STUDY 854 > I noticed that all the phyla in each group from > From Table 3 and 4 were not entered, which was were the result was taken from. Was they any reason for this ? > > STUDY 823 > I noticed that two body sites were entered, margin of eyelid and conjunctival sac. > > The signatures for experiment 1 was taken from the relative abundance result > > Experiment two was taken from LEfSe, which did not really show any comparison. > > The experiments were not shared into the different groups such as Severe, Mild and Moderate, the numbers were available via the Table, if clicked on. > > STUDY 855:white_check_mark:- No concern

2023-12-27

UBNSEMS3S (14:53:51): > Hi everyone we will be having our weekly team meeting at 10 AM EST tomorrow (Thursday). Given that many are out this week, attendance is optional. I will be there though if anyone would like to talk.https://us02web.zoom.us/j/2737200499

2023-12-28

UBNSEMS3S (10:37:26): > It was a very brief meeting today. Here’s the recording. See you in 2024! - File (MPEG 4 Video): video1243252612.mp4

UBNSEMS3S (10:53:03) (in thread): > Starting the meeting with a prayer to a Lovecraftian horror.

Esther Afuape (11:14:02): > Hi<@UBNSEMS3S>what statistical test do I use in representing this result? Ican’ttell what exact multivariate analysis technique was used - File (JPEG): IMG_4365 - File (JPEG): IMG_4366

UBNSEMS3S (11:44:14) (in thread): > Linear regression.

Esther Afuape (11:44:30) (in thread): > Thank you

2023-12-29

U02CNMR4YEA (15:30:54) (in thread): > @Chioma Onyidothank you again for your review of the studies above. I am making my way through and would like your thoughts on the following: > STUDY 856 > 1. I agree the sample size was incorrect and very much appreciate you catching it! > 2. ANOSIM was performed (please search the term within the article as it is mentioned 3 times) but I now see that (I think) it was used for the functional groups. I am actually not sure which statistical test to put for Expt 2. Any thoughts? > STUDY 830 > 1. I added the experiments for Figures 4b and 4c but am wondering about the following: should 4d and 4e also be curated? I don’t see that they did an alpha diversity for either of these experiments- do you agree? Do you think relative abundance is the correct transformation as 4d and 4e seem to speak to relative abundance-? > 2. For decreased vs increased abundance- I am now wondering if there actually are some increased and some decreased as I think I curated based on prevalence rather than relative abundance (which would be based on the coefficient, right?). What do you think? > THANK YOU! > -

2024-01-01

Peace Sandy (02:46:40): > Happy New Year Everyone:rocket:Let’sdo more in 2024:rocket::clinking_glasses:

Chioma Onyido (05:42:02) (in thread): > 1. :white_check_mark: > 2. I’m not sure about the stat test here too. > 3. 4d and 4e have been curated in prev expt.:white_check_mark: > 4. I’mnot sure about the decreased vs increased question.:face_with_peeking_eye:

2024-01-02

UBNSEMS3S (17:28:25): > Happy New Years everyone. After the holidays and a bout of RSV, I am back to working. I look forward to another productive year of BugSigDB working with you all. > > In terms of theAdvanced R book club, I will have an update on Thursday about our first session. > > I have reached out to Ludwig about giving us all a presentation on the BugSigDB paper. I’ll let you know when I hear back from him. > > Looking forward to speaking with you all during our Thursday meeting.

2024-01-03

Peace Sandy (01:53:57) (in thread): > Happy New Year@C. Mirzayi (please do not tag this account):rocket:

irem Kahveci (05:12:19) (in thread): > :star-struck:

U02CNMR4YEA (10:49:02): > <@UBNSEMS3S>So glad you are feeling better! Happy New Year!

Chioma Onyido (15:35:20): > Happy new year everyone!:blush:I’ve just published my second blogpost- and this one is aboutBugSigDB-ing, what’s in myBugSigDB toolkit:eyes:and an easy**** ****(I hope)**** 4 step guide**on how to contribute. > > Since my first Outreachy blogpost where I wrote briefly about the Microbiome project, I’ve gotten few questions/comments from connections/ colleagues about how to contribute to the BugSigDB project, so I was inspired to write a short post about it for anyone who’s interested. > > Thank you so much<@UBNSEMS3S>and@Svetlana Ugarcina Perovicfor your guidance and inputs in making this more presentable.:bouquet:If you were contributing to BugSigDB for the first time, were these steps simple enough? Did I miss anything? Here’s the link, I’d really appreciate your comments and feedback.:blush:https://chiomaonyido.wordpress.com/2024/01/03/bugsigdb-ing-chronicles-1/ - Attachment (…tales (and tips) from a bioCurious opensource bébé…): BugSigDB-ing Chronicles 1 > The BugSigDB-ing toolkit are the tools and techniques used in BugSigDB-ing, and they include (but not limited to) the ontology and taxonomy browsers, as well as the special rules that curators/revi… - File (JPEG): IMG_7746

Esther Afuape (17:25:23) (in thread): > This is well-detailed! Well done, Chioma!:clap::fire:

UBNSEMS3S (17:26:10): > I just finished reviewing Study 541 which took me about 3 hours to figure out and correct. I had a much longer summary of the changes I made but I figured I might distill it into a few bullet points:Statistical Tests > * Correlations can only be calculated when the two variables are continuous (or at least ordinal). That means if they are comparing abundances between two groups, the statistical testcannot be correlations in normal circumstances. > * Generally we do not need to curate the results from predictive modeling (hallmarks of predictive modeling are words like: “random forests”, “discriminatory modeling,” “classifiers”, and “validation”) where the taxa were entered as predictors of a condition if a differential abundance analysis is also present. > * If you believe you need to curate a predictive model, it would be helpful to check in here first. I feel bad that multiple people working on study 541 dida ton of work that was not necessary. > Signature Sources > * Ideally a signature should come from a single source (i.e. a single table, figure, or supplement). If there is a supplement that has all the results from a figure in a raw table, it would be preferable to source from the table in most cases as there is usually more information. > * Sometimes they separate signatures for the same analysis by taxonomic level (e.g. a separate table for genus results and family results). These are a notable exception that should be combined into a single signature. > Effort vs. Reward > * Generally speaking, a curation should not take more than an hour or two unless there are an exceptional amount of experiments. If the paper has a ton of significant results (Study 541 originally had some signatures with 50+ taxa!), check in here first to see if there’s a way to narrow it down.

UBNSEMS3S (17:31:56): > And we will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499

Esther Afuape (17:53:41) (in thread): > Thank you for this. Your corrections are always so insightful because I learn new things from them. > On your second point, is this because those predictive modeling serve the same purpose as differential abundance analysis andit’d be redundant to enter the same results twice?

U02CNMR4YEA (19:46:52) (in thread): > @Chioma OnyidoI realized that you were initially correct that it should be increased as you suggested. I hope to ask about the stat test tomorrow during lab meeting:blush:. Thank you again for your help!

U02CNMR4YEA (20:27:23) (in thread): > @Esther Afuapethank you so much for your review of Study 759! I agree that the taxa is Expt 3 needed some editing. A couple of the taxa are named differently but there were some that were just wrong so thank you for catching that. > As for the DESeq2 for Expt 1 and 2, I definitely see your point. I would like to bring it up during our lab meeting, however, because I don’t completely understand this section: > DESeq2 detected differences in relative abundance for genera between groups in raw count data (significant genera defined as log2 fold change > 2 and p-adjusted values < 0.05). Pseudocounts of +1 were added to the ASV table, a statistical test with the Wald test was per > formed (adjusted p-values with false discovery rate (FDR)), and results were visualized with R package EnhancedVolcano. > > Thank you again!

2024-01-04

Chioma Onyido (02:16:02) (in thread): > Thank you Esther.:blush:

Peace Sandy (04:36:31) (in thread): > Thank you so much for your reviews, they are really insightful@C. Mirzayi (please do not tag this account)

Odigiri Great Alume (05:16:38) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Andre Nana (09:56:49): > I wanted to share the paper that I am presenting in case someone would like to take a look. It is behind paywall. - File (PDF): gut microbiome.pdf - File (PDF): Supplemental results.pdf

UBNSEMS3S (09:57:21) (in thread): > @Esther AfuapeOften they will use the results from the differential abundance analysis in the predictive model so effectively they’re double dipping. Even if they are not doing that, there are other issues we can discuss as well during today’s meeting.

Esther Afuape (09:58:14) (in thread): > Looking forward to it! Thank you

Mildred Anashie (11:14:03) (in thread): > Idon’tthink you missed anything@Chioma OnyidoWell done:clap:

Chioma Onyido (11:45:31) (in thread): > Awesome! Thank you Mildred.:blush:

UBNSEMS3S (14:57:06): > Today’s meeting recording. Thank you all for attending and asking great questions! - File (MPEG 4 Video): video1265799169.mp4

Peace Sandy (19:06:48) (in thread): > @C. Mirzayi (please do not tag this account)what if the signatures are gotten from text , in your second point you stated that ideally a signature should come from a single source (I.e single table, figure, or supplement) > > Secondly,I’mcurrently reviewing a paper, the initial curator entered separate signatures for phylum level and the different genera, is it best practice to combine the signatures to just signature 1 and 2 , instead of having four signatures for one experiment

2024-01-08

UBNSEMS3S (10:45:56): > Hi everyone MVIF is tomorrow! I highly recommend attending if you’re able to. It looks like there are some great talks this time. I’m particularly interested in the presentation about sampling wildlife microbiomes:https://www.microbiome-vif.org/As always, attendance is free–you just have to register at the link. - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Peace Sandy (12:25:17) (in thread): > Thank You@C. Mirzayi (please do not tag this account)

Odigiri Great Alume (18:00:59) (in thread): > Oh nice@C. Mirzayi (please do not tag this account)thanks

2024-01-09

Peace Sandy (05:14:03): > Hello Everyone, while reviewing studies, I usually come across Alpha diversity indices like sobs and ace , butit’snot available on BugSigDb, is they an alternative for it.

Esther Afuape (06:45:31) (in thread): > <@UBNSEMS3S>once mentioned during a meeting that you can curate ACE results as richness

Peace Sandy (08:07:13) (in thread): > Thank You@Esther AfuapeHow about sobs ?

U1LCB8WEA (08:29:34) (in thread): > I’ll be hosting the keynote session - see you there!

Chioma Onyido (10:04:34) (in thread): > Interesting talk by Dr. Wargo. > > Picked up a few things for e.g. metronidazole > and EAT YOUR FIBRE!:smile:

U1LCB8WEA (10:42:12) (in thread): > That’san important message!

Esther Afuape (14:02:02) (in thread): > Idon’tknow about that..haven’tcome across it

UBNSEMS3S (14:56:06) (in thread): > Can you show the context for “sobs”? It might be a typo for “obs” as in “taxa obseved” or perhaps “species observed” but I would have to see.

UBNSEMS3S (16:29:15): > Hi everyone! Thanks for your patience as I finalize the materials for theAdvanced Rbook club. We will be having our first session of the book club on Friday, January 19th at 11 AM EST. Please see the github repo for more info on how you can join and participate:https://github.com/waldronlab/data-science-seminarI will be presenting chapters 1 and 2 for our first session.

Peace Sandy (16:32:22) (in thread): > Thank You for the update@C. Mirzayi (please do not tag this account)

Peace Sandy (16:32:50) (in thread): > Okay

2024-01-10

Chioma Onyido (06:41:31) (in thread): > Hmmm<@UBNSEMS3S>I saw an alpha diversity result on “observed species”, and the curator curated it as richness. Is that right pls.

Esther Afuape (09:23:01): > Hello everyone > Please I need help getting this paper for study 811:https://doi.org/10.1111/lam.13630<@UBNSEMS3S><@U1LCB8WEA>

UBNSEMS3S (10:06:06) (in thread): - File (PDF): Letters Applied Microbiology - 2021 - Schade - The gut microbiota profile in psoriasis a Brazilian case‐control study.pdf

Esther Afuape (12:18:24) (in thread): > Thank you

UBNSEMS3S (17:13:11): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. It looks like no one is signed up to present so I’d love to check in with the Outreachy interns about how it’s been going briefly.

2024-01-11

Esther Afuape (03:17:15) (in thread): > <@UBNSEMS3S>could you help me with the supplemental too, please?

Peace Sandy (05:19:10) (in thread): > Hi@C. Mirzayi (please do not tag this account)It’sgoing well > I just signed up to present

UBNSEMS3S (15:45:49) (in thread): > It seems to be available at the very bottom of the DOI link you posted.

UBNSEMS3S (15:46:25): > Thanks for attending the meeting today. As always, I had fun geeking out about regression. - File (MPEG 4 Video): video1587786478.mp4

Esther Afuape (15:46:59) (in thread): > Oh! I must have missed it. Thank you

2024-01-12

Esther Afuape (08:58:37): > Hello everyone. I need help with a study I’m currently reviewing from this paper:https://sci-hub.se/http://dx.doi.org/10.1007/s11427-019-9540-yThe curatable table is table S4 in the file attached. Ican’tsee a reference adjusted P-value in the paper and this makes the result difficult to interpret.<@UBNSEMS3S><@U1LCB8WEA>

UBNSEMS3S (10:06:20) (in thread): > If they don’t state a p-value threshold, then we can assume it’s .05.

Andre Nana (12:44:20) (in thread): > Thanks<@UBNSEMS3S>. It was a good learning opportunity.

Esther Afuape (13:00:59) (in thread): > Thank you

2024-01-15

U1LCB8WEA (07:55:56): > Who could help with completing the “Study design” help page?https://bugsigdb.org/Curation_Policy#Study_DesignExamples can come from bugsigdb… - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Chioma Onyido (07:58:51) (in thread): > Hi@Levi WaldronAbsolutely I’d be more than happy to assist with this.

U1LCB8WEA (08:04:20) (in thread): > Great!Feel free to edit directly,and to ask any questions.Edits can always be rolled back sodon’tworry about making them.

U1LCB8WEA (10:08:59) (in thread): > I did a little work here just to get started and demonstrate what I had in mind. I was looking for a cross-sectional observational, not case-control study of smokinghereto add as a contrasting example to the case-control smoking example above, but the first several I looked at were all actually case-control studies incorrectly curated as cross-sectional observational, not case-control:sweat_smile:. I added clarification in the table, that in order not to be case-control, the participants in the contrast mustnotbe selected for inclusion based on whether they have the health outcome or exposure of interest. In the ones I looked at, they were all comparisons like current smokers vs never-smokers, meaning in this example that former smokers are excluded. A study where participants are included regardless of smoking status, then the analysis is of number of lifetime pack-years of smoking, would not be case-control. - Attachment (BugSigDB): Special:RunQuery/Quick filter

Chioma Onyido (11:29:16) (in thread): > Ididn’tknow that was the defining feature, I initially thoughtit’sonly if the control group is not clearly stated, > I had to go through my notes and the office-hour recording where study designs were discussed to refresh my memory.:sweat_smile:

Chioma Onyido (11:29:23) (in thread): > Thank you for the clarification and opportunity. Study design section now complete.:white_check_mark:

U1LCB8WEA (11:41:04) (in thread): > Wonderful, Chioma! I made some minor edits, and I think it will be a very useful reference now. Others still feel free to edit if anything is unclear or if we’ve gotten anything wrong:slightly_smiling_face:

2024-01-17

UBNSEMS3S (17:15:38): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499.

2024-01-18

Andre Nana (09:03:24): > Here is the paper that I will present today. May need some help, especially with the statistical analysis section. - File (PDF): doi170016supp1_prod.pdf - File (PDF): ring2017.pdf

2024-01-19

UBNSEMS3S (10:00:51): > Hi everyone the Advanced R book club will begin in one hour at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-01-22

Chioma Onyido (04:52:22): > Good morning<!here>I am aware that we don’t curate results from randomforest and the likes, I want to be sure if we don’t curate from “Ribosomal Database Project” too, description of RDP method and results attached below. Thanks<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Svetlana Ugarcina Perovic (04:58:38) (in thread): > A good question. I see there are already some curations involving RDPhttps://bugsigdb.org/w/index.php?title=_Special:Search&search=RDP&go=Go&searchToken=9cbof3j1horsdlpftwwlyl2d - Attachment (BugSigDB): Special:Search

Chioma Onyido (05:01:45) (in thread): > Great, thank you!:blush:

Chioma Onyido (05:30:49) (in thread): > @Svetlana Ugarcina Perovicis this venn diagram curatable too? > Description: Venn diagram showing the number of genera belonging to the major phyla differing significantly between BF and EU children. A total of 26 genera > are characteristic of EU children, 43 genera are in common between BF and EU children, and 25 genera are characteristic of BF children - File (PNG): image.png

Svetlana Ugarcina Perovic (05:33:52) (in thread): > Beside writing down “differing significantly” did they do a statistical test for it?

Chioma Onyido (05:36:42) (in thread): > Yes, Kruskal-wallis

Chioma Onyido (05:38:35) (in thread): > Do I curate only the taxa exclusive to BF and EU, or to also curate the taxa common to both (those in the middle of the venn diagram).

Svetlana Ugarcina Perovic (05:38:35) (in thread): > then yes

Esther Afuape (06:36:35): > Hello everyone > I’m reviewing a study on this paper:https://gut.bmj.com/content/67/8/1454.longExperiment 1 was curated from figure 5B shown below. I’m not sure if figure 5B is curatable? I’m also not sure about the statistical test used in that figure.<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic - Attachment (Gut): The oral microbiota in colorectal cancer is distinctive and predictive > Background and aims Microbiota alterations are linked with colorectal cancer (CRC) and notably higher abundance of putative oral bacteria on colonic tumours. However, it is not known if colonic mucosa-associated taxa are indeed orally derived, if such cases are a distinct subset of patients or if the oral microbiome is generally suitable for screening for CRC. > > Methods We profiled the microbiota in oral swabs, colonic mucosae and stool from individuals with CRC (99 subjects), colorectal polyps (32) or controls (103). > > Results Several oral taxa were differentially abundant in CRC compared with controls, for example, Streptococcus and Prevotella s pp. A classification model of oral swab microbiota distinguished individuals with CRC or polyps from controls (sensitivity: 53% (CRC)/67% (polyps); specificity: 96%). Combining the data from faecal microbiota and oral swab microbiota increased the sensitivity of this model to 76% (CRC)/88% (polyps). We detected similar bacterial networks in colonic microbiota and oral microbiota datasets comprising putative oral biofilm forming bacteria. While these taxa were more abundant in CRC, core networks between pathogenic, CRC-associated oral bacteria such as Peptostreptococcus , Parvimonas and Fusobacterium were also detected in healthy controls. High abundance of Lachnospiraceae was negatively associated with the colonisation of colonic tissue with oral-like bacterial networks suggesting a protective role for certain microbiota types against CRC, possibly by conferring colonisation resistance to CRC-associated oral taxa and possibly mediated through habitual diet. > > Conclusion The heterogeneity of CRC may relate to microbiota types that either predispose or provide resistance to the disease, and profiling the oral microbiome may offer an alternative screen for detecting CRC. - File (JPEG): f1c97b43-a16d-41de-b80b-2a6952cb1b7c

UBNSEMS3S (14:20:39) (in thread): > Yes it’s curatable. The test is ANCOM according to the supplemental methods.

Andre Nana (14:33:47): > Looks like Studies 837 and 836 are duplicates.

Chioma Onyido (15:41:42) (in thread): > Yes they are, just checked it. Curated differently too. Hmmm:thinking_face:

2024-01-23

Svetlana Ugarcina Perovic (03:32:56) (in thread): > Ahhh, reminder to myself:slightly_smiling_face:always checksupplementary material

Svetlana Ugarcina Perovic (04:45:57) (in thread): > https://bugsigdb.org/Study_836is reviewed by@Esther Afuape - Attachment (BugSigDB): Association Between Breastmilk Microbiota and Food Allergy in Infants - BugSigDB > Regulating the composition of human breastmilk has the potential to prevent allergic > diseases early in life.The composition of breastmilk is complex, comprising varying levels > of oligosaccharides, immunoactive molecules, vitamins, metabolites, and microbes.

Svetlana Ugarcina Perovic (04:48:25) (in thread): > @Esther Afuapecan you please take a lookhttps://bugsigdb.org/Study_837 - Attachment (BugSigDB): Association Between Breastmilk Microbiota and Food Allergy in Infants - BugSigDB > Regulating the composition of human breastmilk has the potential to prevent allergic diseases early in life.The composition of breastmilk is complex, comprising varying levels of oligosaccharides, immunoactive molecules, vitamins, metabolites, and microbes.

Svetlana Ugarcina Perovic (04:49:15) (in thread): > Thanks@Andre Nanafor the heads-up!

Esther Afuape (04:49:34) (in thread): > @Svetlana Ugarcina Perovicon it!

Esther Afuape (05:01:29) (in thread): > @Svetlana Ugarcina Perovicstudy 836 is more accurate.I’llbe deleting 837

Peace Sandy (07:54:57): > Hey Everyone:wave:What’s the closest match to Bronchoalveolar lavage (BAL) ? > > BAL - Bronchoalveolar lavage is on EFO but when I tried entering it as a body site I can’t see any results. The closest match pop up on BugSigDB is Bronchoalveolar duct junction.@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Levi Waldron

Svetlana Ugarcina Perovic (08:42:19) (in thread): > “Bronchoalveolar Lavage or BAL is a minimally invasive procedure that involves instillation of sterile normal saline into a subsegment of**** the lung**, followed by suction and collection of the instillation for analysis.”

Svetlana Ugarcina Perovic (08:42:32) (in thread): > Body site would be then Lung

Svetlana Ugarcina Perovic (08:43:43) (in thread): > Also when you check other curated studies with BALhttps://bugsigdb.org/w/index.php?title=_Special:Search&search=Bronchoalveolar+lavage+&fulltext=1&searchToken=ajaggtfppgxdtxoemtvhdzomyou can see what they recorded as Body site - Attachment (BugSigDB): Special:Search

Chioma Onyido (09:05:36) (in thread): > Hi@Svetlana Ugarcina PerovicStill on this same study, there’s results comparing BF and EU using 2 diff rep methods, venn diagram and RDP classifier, but same stat. analysis: kruskal wallis. > I’ve curated table s5 under expt. 1, do I add the venn diagram results to it? or curate separately as a new experiment?

Chioma Onyido (09:06:02) (in thread): > Table s5 and venn diagram - File (PNG): image (1).png - File (PNG): image.png

Chioma Onyido (09:06:24) (in thread): > bugsigdb.org/Study_669

Chioma Onyido (09:07:38) (in thread): > table s5 focused more on species, whereas the venn diagram focused more on genera.

Svetlana Ugarcina Perovic (09:13:19) (in thread): > Table S5 Report of the species assignment for BF and EU populations relative tothe most abundant bacterial generafound by the RDP classifier > > -> Table S5 shows species only from the most abundant bacterial genera whereas FigS2 shows all the genera

Svetlana Ugarcina Perovic (09:15:03) (in thread): > If the results are from to the same Analysis/Experiment, then they belong to the same bugsigdb Experiment record.

Chioma Onyido (09:16:57) (in thread): > Got it, thank you, so I’ll curate the genera too under same expt.

Chioma Onyido (09:17:38) (in thread): > Thank you so much.:blush:

Peace Sandy (09:51:54) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Esther Afuape (15:10:42): > Hello Everyone. I need help getting the supplementary material for this paper:https://pubmed.ncbi.nlm.nih.gov/27634868/<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA> - Attachment (PubMed): Shifts in Lachnospira and Clostridium sp. in the 3-month stool microbiome are associated with preschool age asthma - PubMed > Asthma is a chronic disease of the airways affecting one in ten children in Westernized countries. Recently, our group showed that specific bacterial genera in early life are associated with atopy and wheezing in 1-year-old children. However, little is known about the link between the early life gut …

UBNSEMS3S (15:56:01) (in thread): > I can’t access it either. I’d try emailing the corresponding author and saying that the supplementary material does not appear to be available online and ask if they’d be willing to share it.

Esther Afuape (15:56:19) (in thread): > Thank you

2024-01-24

Peace Sandy (06:27:29): > Hello Everyone:wave:Please I need help getting the paper for this study, it doesn’t have free access@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldronhttps://bugsigdb.org/Study_111 - Attachment (BugSigDB): Gut microbiota profiles in treatment-naïve children with attention deficit hyperactivity disorder - BugSigDB > BACKGROUNDS: Although increasing evidence suggests a role for the gut microbiota in neurodevelopment, the actual structure and composition of microbiota in children with attention-deficit/hyperactivity disorder (ADHD) remain unclear.

Svetlana Ugarcina Perovic (06:29:31) (in thread): > Here you go - File (PDF): 1-s2.0-S0166432817315541-main.pdf

Svetlana Ugarcina Perovic (06:30:42) (in thread): > AND:slightly_smiling_face:Supplementary material - File (Word Document): 1-s2.0-S0166432817315541-mmc1.doc

Peace Sandy (06:32:07) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:bouquet::rocket:

UBNSEMS3S (15:24:12): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. We currently have openings to present. Please feel free to signup here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-01-25

Andre Nana (11:08:55): > <@UBNSEMS3S>Here is the curation. I included the antibiotic exclusion and the richness. Thanks.

Andre Nana (13:46:09): > https://bugsigdb.org/Study_837 - Attachment (BugSigDB): Sex-specific differences in intestinal microbiota associated with cardiovascular diseases - BugSigDB > BACKGROUND: Cardiovascular diseases (CVD), including coronary heart disease (CHD), display a higher prevalence in men than women.

Andre Nana (13:47:14): > Forgot to share the link previously.

UBNSEMS3S (18:39:37): > Hi everyone the Advanced R book club tomorrow at 11 AM EST. Jackie will be presenting chapter 3: Vectors at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-01-26

Svetlana Ugarcina Perovic (03:57:48) (in thread): > I can’t make it today. Have fun!

2024-01-29

Svetlana Ugarcina Perovic (03:36:33) (in thread): > OK, we did send a kind request for supplementary material to the corresponding authors – no answer! What I usually do in this case, I give one more chance:slightly_smiling_face:andsend a kind reminder with the first author in CC.Let’s see!

2024-01-30

Peace Sandy (04:55:55): > Hello Everyone:wave:Please I need help getting the paper for this study, it doesn’t have free access@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldronhttps://bugsigdb.org/Study_149 - Attachment (BugSigDB): The gut microbiome of Mexican children affected by obesity - BugSigDB > Obesity is a metabolic disorder and global health issue.In Mexico 34.4% of children between 5 and 11 years-old are overweight or obese.Here we address this issue studying the gut microbiome in a sample of Mexican children affected by obesity.

Svetlana Ugarcina Perovic (05:49:25) (in thread): - File (PDF): 1-s2.0-S1075996418301811-main.pdf

Svetlana Ugarcina Perovic (05:50:19) (in thread): - File (PDF): 1-s2.0-S1075996418301811-mmc1.pdf

Svetlana Ugarcina Perovic (05:50:53) (in thread): > Have fun!@Peace Sandy

Peace Sandy (05:52:22) (in thread): > Thank you so much@Svetlana Ugarcina PerovicReally appreciate

2024-01-31

UBNSEMS3S (18:50:41): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. We currently have openings to present. Please feel free to signup here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-02-01

Svetlana Ugarcina Perovic (05:09:12) (in thread): > Esther and I got the supplementary material afteremailing the first author and CC-ing the corresponding authors.From my experience, the first authors are often more responsive than the corresponding (senior) authors – simply because they are happy to talk and share their work while not having a super busy schedule like their supervisors have. > > The only challenge is that usually the first author’s email address is not in the paper and sometimes is hard to get it by googling their name or searching on their lab website (I do not know why labs do not provide lab members email addresses, but yes that can happen too). The solution is to kindly ask the corresponding author to pass your greetings to the first author. In our case, it worked. :)

Svetlana Ugarcina Perovic (05:42:07) (in thread): > Of course, we mentioned why we need their supplementary material and also shared a link to their paper curation. In that way we promote our BugSigDB efforts outside of our community and make potential connections for the future activities. This all goes in line withthe Outreachy theme for this week: “Making connections”.

U1LCB8WEA (05:46:01) (in thread): > Yes! Well done Svetlana.

Esther Afuape (08:17:34) (in thread): > Thank you so much!@Svetlana Ugarcina Perovic

2024-02-02

UBNSEMS3S (10:44:09): > Hi everyone the Advanced R book club today at 11 AM EST (in 20 minutes). Tram will be presenting chapter 4: Subsetting at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

Levi Waldron (11:00:02) (in thread): > Sorry I got double-booked today:disappointed:- didn’t have this in my calendar

2024-02-05

Peace Sandy (06:18:03): > Hello Everyone:wave:Please I need help getting the paper for this study, it doesn’t have free access@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldronhttps://bugsigdb.org/Study_266 - Attachment (BugSigDB): Microbial Community of Healthy Thai Vegetarians and Non-Vegetarians, Their Core Gut Microbiota, and Pathogen Risk - BugSigDB > Pyrosequencing analysis of intestinal microflora from healthy Thai vegetarians and non-vegetarians exhibited 893 OTUs covering 189 species.

Svetlana Ugarcina Perovic (06:26:53) (in thread): > Happy Monday! - File (PDF): JMB026-10-09_FDOC_1.pdf

Peace Sandy (06:27:36) (in thread): > Happy Monday@Svetlana Ugarcina PerovicThank you so much:bouquet:

2024-02-06

Levi Waldron (11:14:58): > Here is some weirdness in R that came up during some debugging with@Peace Sandythis morning - I learned some things myself! > > # create a double vector with 100 elements, all of which are 1, > # but with a small amount of noise added to each element. > set.seed(1) > x = rep(1, 100) + rnorm(100, sd = 1e-14) > names(x) = letters[1:100] # add names to the vector > unique(x) > #> [1] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > #> [39] 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 > #> [77] 1 1 1 1 1 1 > unique(x) |> length() > #> [1] 82 > # Note that table() uses different precision than unique() - neither is > # reliable for numeric values with any imprecision > table(x) > #> x > #> 0.999999999999978 0.99999999999998 0.999999999999982 0.999999999999985 > #> 1 1 1 2 > #> 0.999999999999986 0.999999999999987 0.999999999999988 0.999999999999989 > #> 1 2 1 1 > #> 0.99999999999999 0.999999999999991 0.999999999999992 0.999999999999993 > #> 1 1 2 4 > #> 0.999999999999994 0.999999999999995 0.999999999999996 0.999999999999997 > #> 6 3 4 3 > #> 0.999999999999998 0.999999999999999 1 1.00000000000001 > #> 2 4 26 28 > #> 1.00000000000002 > #> 6 > table(x) |> length() > #> [1] 21 > > # Now let's test equality to 1. all.equal is good because it has a tolerance > # argument. However, we can't use it in logicals because it returns a character > # string if the objects are not equal, and a logical if they are. > if(all.equal(x, rep(1L, length(x)))){ > print("equal") > }else{ > print("not equal") > } > #> Error in if (all.equal(x, rep(1L, length(x)))) {: argument is not interpretable as logical > > # Can wrap it in `identical()` to return TRUE or FALSE, > if(identical(all.equal(x, rep(1L, length(x))), TRUE)){ > print("equal") > }else{ > print("not equal") > } > #> [1] "not equal" > > # but this still isn't correct because it's failing due to the names of x. > all.equal(x, rep(1, length(x))) > #> [1] "names for target but not for current" > > # So use the check.attributes = FALSE argument to ignore the names > if(identical(all.equal(x, rep(1, length(x)), check.attributes = FALSE), TRUE)){ > print("equal") > }else{ > print("not equal") > } > #> [1] "equal" > > # check when they are not equal > x[1] = 2.0 > if(identical(all.equal(x, rep(1, length(x)), check.attributes = FALSE), TRUE)){ > print("equal") > }else{ > print("not equal") > } > #> [1] "not equal" > > <sup>Created on 2024-02-06 with [reprex v2.0.2]([https://reprex.tidyverse.org](https://reprex.tidyverse.org))</sup> >

2024-02-07

UBNSEMS3S (18:20:12): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. We currently have openings to present. Please feel free to signup here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-02-08

Svetlana Ugarcina Perovic (02:30:23) (in thread): > Hello, I might be late a bit today for our meeting. My apologies.

Peace Sandy (03:47:06): > Hello Everyone:wave:Please I need help getting the paper for this study, it doesn’t have free access@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldronhttps://bugsigdb.org/Study_345 - Attachment (BugSigDB): The gut microbiome of Mexican children affected by obesity - BugSigDB > Obesity is a metabolic disorder and global health issue.In Mexico 34.4% of children between 5 and 11 years-old are overweight or obese.Here we address this issue studying the gut microbiome in a sample of Mexican children affected by obesity.

Svetlana Ugarcina Perovic (03:48:46) (in thread): > Here you go - File (PDF): 1-s2.0-S1075996418301811-main (1).pdf - File (PDF): 1-s2.0-S1075996418301811-mmc1 (1).pdf

Peace Sandy (03:55:57) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:bouquet:

UBNSEMS3S (17:32:49): > Hi everyone the Advanced R book club at 11 AM EST tomorrow. Andre will be presenting chapter 5: Control Flow at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-02-12

U03L1PX3D52 (14:46:19) (in thread): > <@UBNSEMS3S>sorry I missed the book club last week. Is there a recording posted somewhere? I did not immediately see it on the github.

2024-02-13

Svetlana Ugarcina Perovic (07:30:45): > On Thursday and Friday, here in Serbia, we have national holiday. I’ll be offline, but I’ll be checking my email if you need to reach me out.

Esther Afuape (10:13:58): > Hello everyone. > While reviewinghttps://bugsigdb.org/Study_193, I saw that there was no statistical test carried out in the paper, which is why the statistical test section of the curation was left empty by the initial curator. > Should I go ahead and delete this study? I’ve attached the supplementary material and the paper itself below.@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA> - Attachment (BugSigDB): Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods - BugSigDB > BACKGROUND: Helicobacter pylori (H.pylori) infection plays an important role in the early stage of cancer development.However, various bacteria that promote the synthesis of reactive oxygen and nitrogen species may be involved in the later stages. - File (Word Document): hel12145-sup-0001-tables1figs1 (1) - File (PDF): eun2014 (1)

UBNSEMS3S (15:32:03) (in thread): > I will have them posted today.

UBNSEMS3S (15:52:16) (in thread): > They state that the findings were “significantly” different which indicates some sort of statistical testing. I think it’s fine as is.

Esther Afuape (17:19:01) (in thread): > Thank you

2024-02-14

UBNSEMS3S (18:36:53): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. We currently have openings to present. Please feel free to signup here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTI’d love it if some people who don’t normally present were brave and volunteered! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-02-15

UBNSEMS3S (14:55:07) (in thread): > https://youtube.com/playlist?list=PLHeOp2a2kQShqgSpivMngc7TBkjVhmHow&si=RMwUTHMAHp2Xn8kW - Attachment (YouTube): Advanced R Book Club > Share your videos with friends, family, and the world

2024-02-16

UBNSEMS3S (10:35:10): > Hi everyone the Advanced R book club today at 11 AM EST (in 25 minutes). Marcel will be presenting chapter 6: Functions at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-02-19

Svetlana Ugarcina Perovic (04:23:04): > Happy Monday:tulip:https://twitter.com/svetlana_up/status/1759508725532971109 - Attachment (X (formerly Twitter)): Svetlana U. Perović (@svetlana_up) on X > @outreachy HUGE shoutout to our intern #BugSigDB team! > > Chioma @oma_bekee, Esther @folakunmiesther and Peace @PeaceSandy3 have been doing a GREAT work in curating microbiome studies https://t.co/qPQNMx5D6M > > Proud mentors: Chloe, @svetlana_up and @LeviWaldron1

2024-02-21

Odigiri Great Alume (03:30:12): > Awesome team

Odigiri Great Alume (03:30:18): > Good morning everyone

Chioma Onyido (04:15:11) (in thread): > Hi Great. Good morning!

Esther Afuape (04:23:35) (in thread): > Good morningg

U1LCB8WEA (10:29:28) (in thread): > Hi everyone!

Odigiri Great Alume (10:30:49) (in thread): > Good evening@Levi Waldron:raised_hands:

UBNSEMS3S (18:23:34): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. We currently have openings to present. Please feel free to signup here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTI’d love it if some people who don’t normally present were brave and volunteered! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-02-22

Svetlana Ugarcina Perovic (03:33:17): > Thanks@Peace Sandyfor “cleaning” the gh issues! Could you please together with@Esther Afuapeand@Chioma Onyidoreview 6 curated studies that are with “needs review”https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aopen+is%3Aissue+label%3A%22needs+review%22Thanks!

Peace Sandy (03:35:57) (in thread): > You are welcome@Svetlana Ugarcina PerovicOkay

Chioma Onyido (03:59:06) (in thread): > On it!

Esther Afuape (05:42:30) (in thread): > Got it!

Chioma Onyido (08:46:09): > Hello team.:wave:I’m currently reviewingbugsigdb.org/Study_812and I’m not sure what the data transformation for Bayesian microbial differential abundance (BMDA) is. - File (PNG): image.png

Chioma Onyido (09:08:02) (in thread): > “We then fitted the BMDA model, which is a Bayesian hierarchical framework that uses a zero-inflated negative binomial model to model the raw count data and a Gaussian mixture model with feature selection to identify differentially abundant taxa.” > > Got this excerpt from the Methods section. Could “negative binomial regression” be entered since BMDA isn’t available on BugSigDB?@Levi Waldron<@UBNSEMS3S>@Svetlana Ugarcina Perovic

UBNSEMS3S (09:58:00) (in thread): > This is just a negative binomial model with a Bayesian framework for determining taxa of interest so yeah negative binomial would be appropriate.

Chioma Onyido (09:58:27) (in thread): > Great! Thank you.:blush:

Svetlana Ugarcina Perovic (10:52:38): > @Andre Nanahere is the review on urinary microbiomehttps://journals.asm.org/doi/10.1128/mbio.00218-20

Andre Nana (10:53:28): > Ok. Thank you so much. I will take a look. Really appreciated.

Svetlana Ugarcina Perovic (10:53:38): > “Two seminal studies, by Nelson et al. (33) and Siddiqui et al. (5), used metagenomic approaches to demonstrate thatthe urine of healthy individuals is not sterileand that a UGT microbiome may exist in healthy female and male adults.”

Svetlana Ugarcina Perovic (10:54:53) (in thread): > I mentioned also this thread:arrow_up:

Andre Nana (11:00:04): > The conversation gets more and more interesting. It looks like there is still a divide between the clinical world and the purely scientific world. When I was studying medicine, it was understood that normal urine IS sterile. You still have this statement on this Johns Hopkins page - Attachment (hopkinsmedicine.org): Urinary Tract Infections > Urinary tract infections or UTIs are infections in any part of the urinary tract. They are a common health problem that affects millions of people each year. Women are especially prone to UTIs.

Andre Nana (11:00:41): > But there seem to be a paradigm shifthttps://karger.com/uin/article-abstract/94/4/445/322842/Human-Urine-Is-Not-Sterile-Shift-of-Paradigm?redirectedFrom=fulltext

Andre Nana (11:02:22): > Very interesting!

Esther Afuape (11:08:31): > I’m just as surprised! This is a new development. It was always thought that the presence of a “pathogenic” bacteria in the urine is because it moved up to the Urethra. > Really interesting…thank youuu@Svetlana Ugarcina Perovic

Esther Afuape (12:08:50): > Hello everyone > I’m reviewing study 845 at the moment and I have a question about figure 3 of the appear it was curated from. > 1. Should former smokers be curated for each year as done by the initial curator? Or should overall former smokers vs current smokers be curated from figure 1? > 2. If it should be curated from figure 3, should only the red boxes be curated or should the orange ones be included also? > NOTE: The description of figure 1 says that red means increase and blue means decrease while yellow is not significant. > > Link to paper:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10622503/<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA> - Attachment (PubMed Central (PMC)): Smoking and salivary microbiota: a cross-sectional analysis of an Italian alpine population > The oral microbiota plays an important role in the exogenous nitrate reduction pathway and is associated with heart and periodontal disease and cigarette smoking. We describe smoking-related changes in oral microbiota composition and resulting potential …

UBNSEMS3S (17:10:28): > Recording of today’s meeting - File (MPEG 4 Video): video1752147130.mp4

UBNSEMS3S (17:12:26) (in thread): > Figure 3 should not be curated. There is no way to determine if the differences between groups were statistically significant or not. Figure 1B can be curated.

Esther Afuape (17:32:19) (in thread): > Thank you so much

2024-02-23

Svetlana Ugarcina Perovic (06:56:56): > @Andre Nananext week at mvif will be a talk on urinary microbiome in menhttps://www.microbiome-vif.org/en-US/-/future-events/mvif26-2627-28-february-2024-prof-laura-s-weyrich - Attachment (microbiome-vif.org): MVIF.26 | 26/27 & 28 February 2024 > with Keynote talk by Prof. Laura S. Weyrich

Svetlana Ugarcina Perovic (06:57:36): > and other interesting topics. You are all invited:slightly_smiling_face:

Andre Nana (11:02:29) (in thread): > Great. Thanks for sharing.

2024-02-26

U1LCB8WEA (06:27:19) (in thread): > The question I still have about these is, have they really ruled out the possibility that they’re measuring environmental contamination and not what is in healthy urine while it is inside the body? Even when you use negative controls during library preparation and sequencing, it seems to me very difficult to control for contamination that occurs during sampling… Replication of the prevalent urinary microbiome by different labs, and showing that commonalities are predicted better by something other than laboratory where they were sampled (like family or history of antibiotic exposures), would add to the strength of the evidence in my mind…

U1LCB8WEA (06:30:29): > The number of unreviewed “pages” (studies + experiments + signatures) has been vastly reduced during this Outreachy period, from many thousands to 468 (https://bugsigdb.org/Help:Needs_review/Missing_review). Will we get it down to zero before then next contribution phase?:rocket::pray: - Attachment (BugSigDB): Help:Needs review/Missing review > This is a list of pages that have been marked as Complete but have not yet been reviewed….

Chioma Onyido (06:50:19) (in thread): > We’ll try our best.:100::rocket:

Esther Afuape (07:11:56) (in thread): > We’lldo our best possible

Peace Sandy (07:50:53) (in thread): > This is amazing:bouquet:Absolutely, we will try our best

Ludwig Geistlinger (08:34:07) (in thread): > This is fantastic and a great step toward improving the data quality in BugSigDB!

Svetlana Ugarcina Perovic (10:11:50) (in thread): > By suprapubic puncture, the microbiome of the bladder was identified, but the invasiveness was the highest i.e. no big group of healthy volunteers wanted to support the study and donate the samples in this way. On the other hand, yes, self-voiding methods (first catch urine, midstream urine, and clean catch urine) are less invasive but are contaminated with microbiome from the urethra and vaginal microbiome. > > Wolfe et al. tested different sampling tecniqueshttps://journals.asm.org/doi/epdf/10.1128/jcm.05852-11?src=getftr: > “For the purpose of microbiome research, the SPA (suprapubic aspirate) sampling technique appears to be the best at minimizing contamination from nonurinary sites and thus obtaining the best view of the bacteria present within the bladder. The pragmatic aspects of this collection method, however, limit its utility for most researchteams. For these teams, we recommend the use of the TUC (transurethral catheter urine) sampling method. The bacterial communities assessed via TUC and SPA in the same person were highly similar, suggesting that TUC is a sufficient approximation of SPA. While voided samples maybe currently sufficient for clinical care, special analytic approachesmay be necessary to subtract likely vulvo-vaginal contaminants aspart of subsequent microbiome analyses.”

2024-02-28

Odigiri Great Alume (07:48:32) (in thread): > Awesome work guys

UBNSEMS3S (18:50:04): > Hi everyone! We will be having our weekly team meeting at 10 AM EST tomorrow (Thursday).https://us02web.zoom.us/j/2737200499. We currently have openings to present. Please feel free to signup here:https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-02-29

Peace Sandy (09:29:47): > Hello Everyone:wave:Please I need help getting the paper for these study, it doesn’t have free access@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Levi Waldronhttps://bugsigdb.org/Study_351andhttps://bugsigdb.org/Study_260 - Attachment (BugSigDB): Overweight and Obesity in Children Are Associated with an Abundance of Firmicutes and Reduction of Bifidobacterium in Their Gastrointestinal Microbiota - BugSigDB > Background: Obesity in children continues to be a global epidemic. - Attachment (BugSigDB): The intestinal microflora in allergic Estonian and Swedish 2-year-old children - BugSigDB > BACKGROUND: The prevalence of allergic diseases seems to have increased particularly over the past 35-40 years.Furthermore, allergic disease is less common among children in the formerly socialist countries of central and Eastern Europe as compared with Western Europe.

Svetlana Ugarcina Perovic (09:46:00) (in thread): - File (PDF): 10.1089@chi.2019.0280.pdf

Svetlana Ugarcina Perovic (09:46:58) (in thread): - File (PDF): bjorksten1999.pdf

Peace Sandy (09:49:44) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

2024-03-01

UBNSEMS3S (10:01:36): > Hi everyone the Advanced R book club today at 11 AM EST (in 59 minutes). Yoon will be presenting chapter 7: Environments at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-03-03

taofeeqah bakare (11:53:17): > @taofeeqah bakare has left the channel

2024-03-04

Svetlana Ugarcina Perovic (11:00:03): > Welcome Outreachy applicants! We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started:https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion.Thank you so much for your interest and we look forward to working with you.<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (11:14:17): > Thank you > > Hello Everyone, My name is Anashie Mildred Andokie, I’m an outreachy applicant > > I’m super excited to be in this community and to contribute. > > I look forward to connecting with everybody

Scholastica Urua (11:15:05): > Hello everyone > > My name is Scholastica Urua. I am a Data Analyst, Technical Writer, and a graduate of Pharmacy. I am an Outreachy applicant looking forward to contributing to the BugSigDB project. I have a keen interest in health data analysis and human microbial studies. By participating in this project, I aim to expand my knowledge and skills while making valuable contributions > I am enthusiastic about the opportunity to collaborate with my mentors and fellow contributors and eager to make meaningful connections within the BugSigDB community. This is an exciting journey, and I’m really glad to be part of it.

Isi Irabor (11:19:38): > Hello everyone, I am Isi Irabor. I am a Project manager and UX researcher. I am an outreachy applicant and I hope to work well together with everyone and contribute meaningfully to the BugSigDBproject. I hope to gain more experience with this project and I am thankful to the mentors for this opportunity .

Scholastica Urua (11:20:28) (in thread): > Nice to meet you Anashie:+1:

Chioma Onyido (11:21:15) (in thread): > Welcome Mildred! Good to have you here.:blush:

Svetlana Ugarcina Perovic (11:22:13) (in thread): > Hello hello and welcome to the bioconductor/bugsigdb community!

Mildred Anashie (11:22:33) (in thread): > Thank you@Chioma Onyido

Chioma Onyido (11:22:36) (in thread): > Welcome Scholastica. Good to have you here! > > Kindly follow the steps here to start contributinghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Chioma Onyido (11:23:06) (in thread): > WelcomeIsi. Good to have you here!Kindly follow the steps here to start contributinghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (11:23:06) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (11:23:50) (in thread): > Welcome@Isi Irabor

Svetlana Ugarcina Perovic (11:23:55) (in thread): > Nice to e-meet you and welcome to the bioconductor/bugsigdb community!

Svetlana Ugarcina Perovic (11:24:15) (in thread): > Welcome to the bioconductor/bugsigdb community!

Isi Irabor (11:24:59) (in thread): > thank you

Nwajei Edgar (11:26:14): > Excited to be here again:joy::joy:

Svetlana Ugarcina Perovic (11:26:39) (in thread): > Welcome back!

Chioma Onyido (11:26:59) (in thread): > Welcome back Edgar! Excited to have you here again.:smiley:

Nwajei Edgar (11:27:05) (in thread): > Thank you

Nwajei Edgar (11:27:18) (in thread): > Thank you Chioma:innocent::innocent:

Scholastica Urua (11:29:17) (in thread): > Thank you Chioma and svetlana_up, it’s nice to be here.

Mildred Anashie (11:44:18) (in thread): > Welcome Edgar

Peace Sandy (11:45:16) (in thread): > Welcome

Peace Sandy (11:45:36) (in thread): > Welcome@Scholastica Urua

Peace Sandy (11:45:57) (in thread): > Welcome@Isi Irabor:partying_face:

Scholastica Urua (11:46:21) (in thread): > Welcome Edgar

Scholastica Urua (11:48:12) (in thread): > Thank you@Peace Sandy

Linda Uchenwoke (11:51:26): > Hello everyone, I’m Linda, an Outreachy applicant. I’m so excited to be able to contribute to the BugSigDBproject. Looking forward to connecting with you all!

Melodee Okigbo (11:53:16): > Hi everyone, my name is Melodee and I’m Outreachy applicant. I’m super excited to contribute to this project and learn from you all!

Melodee Okigbo (11:53:44) (in thread): > Hi Linda, nice to meet you!

Peace Sandy (11:53:59) (in thread): > Welcome !

Peace Sandy (11:54:36) (in thread): > Please see thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Peace Sandy (11:55:11) (in thread): > Welcome@Melodee Okigbo:tada:Please see the pinned message

Linda Uchenwoke (11:55:44) (in thread): > Thank you!

Melodee Okigbo (11:56:41) (in thread): > Thank you:pray:

Svetlana Ugarcina Perovic (11:56:46) (in thread): > Welcome@Linda Uchenwoke!

Svetlana Ugarcina Perovic (11:57:29) (in thread): > Hello hello! Welcome to the bugsigdb community!

Scholastica Urua (12:00:02) (in thread): > Welcome@Melodee Okigbo

Linda Uchenwoke (12:01:55) (in thread): > Thank you!@Svetlana Ugarcina Perovic

Melodee Okigbo (12:02:28) (in thread): > Thank you, happy to be here!

Victoria (Burah) Poromon (12:17:17): > Hello everyone, I’m Victoria. An outreachy applicant and I’m excited about contributing to this project.

Peace Sandy (12:19:11) (in thread): > Welcome@Victoria (Burah) PoromonGlad to have you here > > Please see the pinned message

Victoria (Burah) Poromon (12:21:35) (in thread): > Thank you:yellow_heart:

Chioma Onyido (12:24:31) (in thread): > Welcome to the bugsigdb community Victoria!:confetti_ball:

Victoria (Burah) Poromon (12:27:46) (in thread): > Thank you so much

Fausat Olasubomi Abiola (12:31:34): > Hi everyone, I’m Fausat. I’m an outreachy applicant and I’m looking forward to make contribution to this project. I’m also looking forward to work with everyone.

Scholastica Urua (12:32:34) (in thread): > Hello@Fausat Olasubomi Abiola. Welcome

Fausat Olasubomi Abiola (12:37:04) (in thread): > Thank you@Scholastica Urua

Mildred Anashie (12:37:49) (in thread): > Welcome Linda

Mildred Anashie (12:38:23) (in thread): > Welcome@Melodee Okigbo

Mildred Anashie (12:38:42) (in thread): > Welcome Victoria

Mildred Anashie (12:39:36) (in thread): > Welcome@Fausat Olasubomi Abiolaplease see the pinned messages

Victoria (Burah) Poromon (12:40:25) (in thread): > Thank you Mildred:blush:

Fausat Olasubomi Abiola (12:44:50) (in thread): > Alright, thank you@Mildred Anashie

Esther Afuape (12:53:35) (in thread): > Welcome Scholastica…glad to have you here:hugging_face:

Esther Afuape (12:53:50) (in thread): > Welcome back Edgar!:partying_face:

Esther Afuape (12:54:46) (in thread): > Glad to have you here Victoria

Victoria (Burah) Poromon (12:55:48) (in thread): > Thank you so much:blush:

Jenny (13:00:11): > good day everyone, my name is Jennifer and I am currently learning Java. > I recently got approved to join the outreachy program, I need a mentor to take me through the contribution stage of the program. > Please can anyone help me out?

Esther Afuape (13:00:29) (in thread): > Welcome Fausat@Fausat Olasubomi AbiolaGet started here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (13:01:20) (in thread): > Welcome@Jenny

Fausat Olasubomi Abiola (13:01:51) (in thread): > @Esther AfuapeOkay. Thank you.

Esther Afuape (13:03:00) (in thread): > It’s nice to have you here Jennifer! > Check this to get started:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699

Naomi Ibe (13:03:13): > Hello, Naomi here. I’m an applicant from Outreachy and this is me indicating interest to work on the microbiome project:slightly_smiling_face:

Melodee Okigbo (13:05:33) (in thread): > Hi@Naomi Ibenice to meet you, looking forward to collaborating with you!

Sneha Singh (13:06:08): > Hello Everyone! I am Sneha Singh, an outreachy applicant and im looking forward to make contributions to this interesting project. I would like to know how can I get started on Microbiome Study Curation project. Looking forward to collaborate with everyone!

Mildred Anashie (13:07:05) (in thread): > Welcome Naomi

Naomi Ibe (13:07:24) (in thread): > Thank youuu

Mildred Anashie (13:07:37) (in thread): > Welcome@Sneha Singh

Naomi Ibe (13:08:09) (in thread): > Welcome, I think we’re supposed to work with this linkhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699

Mildred Anashie (13:08:53) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Sneha Singh (13:09:18) (in thread): > Thank you!

Scholastica Urua (13:09:42) (in thread): > Welcome@Sneha Singh

Nwajei Edgar (13:13:52) (in thread): > Thank you Esther…. Its good to be here again:innocent::innocent:

Scholastica Urua (13:16:15) (in thread): > Welcome@Jenny

Nekembe Boris (13:17:45): > Hello folks, I am Boris, an Outreachy applicant. Super excited about the BugSigDB project. Looking forward to having an exceptional time with you all.

Mildred Anashie (13:19:00) (in thread): > Welcome@Nekembe Boris

Nekembe Boris (13:20:25) (in thread): > Thanks Mildred

Scholastica Urua (13:22:27) (in thread): > Welcome@Nekembe BorisWe are to started via this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Jenny (13:31:09) (in thread): > Thank you

Joan C. Chukwuemeka (13:35:30): > Good evening everyone, my name is Joan Chuks. I’m grateful for the opportunity to actively contribute to this amazing community via the Outreachy program:blush:and collaborate with others here. Hoping to make positive impact in the Microbiome Study Curation and help out where I can.:smiling_face_with_3_hearts:

Svetlana Ugarcina Perovic (13:36:11) (in thread): > Welcome@Naomi Ibe!

Svetlana Ugarcina Perovic (13:37:14) (in thread): > Thanks@Mildred Anashie!

Svetlana Ugarcina Perovic (13:37:23) (in thread): > Welcome@Sneha Singh!

Svetlana Ugarcina Perovic (13:38:18) (in thread): > Welcome back, Joan Chuks!

Scholastica Urua (13:38:40) (in thread): > Welcome@Joan C. ChukwuemekaWe are to started herehttps://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Joan C. Chukwuemeka (13:42:02) (in thread): > Welcome@Isi Irabor

Mildred Anashie (13:42:06) (in thread): > Welcome@Joan C. Chukwuemeka

Eniola Adebayo (13:42:39): > Hello everyone, my name is Eniola, an Outreachy applicant. I’m excited to be here and I am looking forward to making contributions to the BugSigDB project.

Mildred Anashie (13:43:23) (in thread): > Welcome Eniola

Nekembe Boris (13:43:34) (in thread): > Welcome@Eniola Adebayo

Mildred Anashie (13:43:48) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Eniola Adebayo (13:45:19) (in thread): > Thankyou

Nekembe Boris (13:46:10) (in thread): > @Eniola Adebayo,@Mildred Anashiejust sent you materials to start with.

Joan C. Chukwuemeka (13:55:46) (in thread): > Thank you@Svetlana Ugarcina Perovic:hugging_face:

Joan C. Chukwuemeka (13:56:16) (in thread): > Thanks@Mildred Anashie@Scholastica Urua

Joan C. Chukwuemeka (14:05:27) (in thread): > Welcome@Mildred Anashie

Scholastica Urua (14:06:52) (in thread): > Welcome@Eniola Adebayo

Juliet Ogbu (14:06:57): > Hello everyone,my name is Juliet, an outreachy applicant.I’msuper excited to be here with you all:blush:

Mildred Anashie (14:08:09) (in thread): > Welcome Juliet , Check this out to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709577828212659?thread_ts=1709577759.993659&cid=C04RATV9VCY - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (14:09:00) (in thread): > Thank You:pray:

Oluwatomisin Omojokun (14:12:04): > Hi, I’m Tomisin, an outreachy applicant. my aims is to bridge between healthcare and digital health. let’s chat

Mildred Anashie (14:13:26) (in thread): > Welcome@Oluwatomisin Omojokun

Naomi Ibe (14:13:27) (in thread): > @Svetlana Ugarcina Perovicthank you:blush:,I look forward to working with you

Nekembe Boris (14:14:25) (in thread): > @Oluwatomisin OmojokunWelcome . Get up to speed with thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (14:16:49) (in thread): > Welcome@Oluwatomisin Omojokun

Scholastica Urua (14:17:29) (in thread): > Welcome@Juliet Ogbu

Oluwatomisin Omojokun (14:17:43) (in thread): > Thanks@Scholastica Urua

Oluwatomisin Omojokun (14:18:06) (in thread): > Thanks@Mildred Anashie

Esther Afuape (14:27:04) (in thread): > Nice to have you back,Joan:bouquet:

Juliet Ogbu (14:29:27) (in thread): > Thank you:blush:

Juliet Ogbu (14:29:57) (in thread): > Thank you:blush:

Habiba Saad (14:30:49): > hello everyone, my name is habiba, i am a biotechnologist,. i am an outreachy applicant. i am excited to contribute to bugsigdb. looking forward to connect.:slightly_smiling_face:

Nekembe Boris (14:35:28) (in thread): > Welcome@Habiba Saad

Oluwaseyifunmi Taiwo (14:38:31) (in thread): > Welcome@Habiba Saad

Oluwaseyifunmi Taiwo (14:39:12): > Hello everyone. I’m Oluwaseyi Mabel. I’m an outreachy applicant from Lagos, Nigeria. Looking forward to learning from you all

Oluwaseyifunmi Taiwo (14:42:13) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699. You can read this to get started - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (14:42:40) (in thread): > Welcome@Habiba Saad

Oluwaseyifunmi Taiwo (14:42:51) (in thread): > You can also check this out toohttps://github.com/waldronlab/BugSigDBcuration/issues/94

Mildred Anashie (14:43:02) (in thread): > Welcome@Oluwaseyifunmi Taiwo

Svetlana Ugarcina Perovic (14:43:04) (in thread): > Welcome to the bugsigdb community!

Mildred Anashie (14:44:30) (in thread): > You can get started herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709579289606599?thread_ts=1709579217.672029&channel=C04RATV9VCY&message_ts=1709579289.606599 - Attachment: Attachment > Welcome Juliet , Check this out to get started https://community-bioc.slack.com/archives/C04RATV9VCY/p1709577828212659?thread_ts=1709577759.993659&cid=C04RATV9VCY

Oluwaseyifunmi Taiwo (14:44:36) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Oluwaseyifunmi Taiwo (14:45:18) (in thread): > Thank you@Mildred Anashie

Oluwaseyifunmi Taiwo (14:46:28) (in thread): > Welcome you@Oluwatomisin Omojokun

Oluwaseyifunmi Taiwo (14:47:26) (in thread): > Welcome@Nekembe Boris

Oluwaseyifunmi Taiwo (14:48:11) (in thread): > Welcome@Sneha Singh. Look forward to connecting with you

Scholastica Urua (14:48:31) (in thread): > Welcome@Habiba Saad

Oluwaseyifunmi Taiwo (14:48:58) (in thread): > Welcome@Melodee Okigbo.

Oluwaseyifunmi Taiwo (14:50:34) (in thread): > Welcome@Joan C. Chukwuemeka

Scholastica Urua (14:54:19) (in thread): > Welcome@Oluwaseyifunmi Taiwo

Bolanle Wahab (15:13:23): > Hello!:rocket:I’m excited to join this vibrant community where ideas flow freely. I’m Bolanle Wahab, an Outreachy Applicant, looking forward to connecting, learning, and sharing with all of you amazing people on the BioConductor project. Let’s make this space one filled with positivity, growth, and meaningful interactions. Cheers to new beginnings and awesome connections!

Oluwaseyifunmi Taiwo (15:14:50) (in thread): > Hi@Bolanle Wahabwelcome.

Svetlana Ugarcina Perovic (15:14:57) (in thread): > Cheers! And welcome to the bugsigdb community!

Mildred Anashie (15:15:07) (in thread): > Welcome@Bolanle Wahab

Oluwaseyifunmi Taiwo (15:15:10) (in thread): > Kindly check the pinned message to get started

Oluwaseyifunmi Taiwo (15:15:28) (in thread): > You can check this toohttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Oluwaseyifunmi Taiwo (15:16:40) (in thread): > Feel free to ask questions too. We’re all here to help:hugging_face:

Scholastica Urua (15:18:32) (in thread): > Welcome@Bolanle Wahab

Peace Daniel (15:24:35): > Hello,I’mPeace an Outreachy applicant. I look forward to learning, contributing and connecting with amazing people:purple_heart:

Svetlana Ugarcina Perovic (15:25:27) (in thread): > Hello, Peace! Welcome to the bugsigdb community.

Mildred Anashie (15:26:28) (in thread): > Welcome@Peace Daniel

Bolanle Wahab (15:26:37) (in thread): > Hi peace! Welcome:partying_face:

Mildred Anashie (15:26:53) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709577828212659?thread_ts=1709577759.993659&cid=C04RATV9VCY - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Oluwaseyifunmi Taiwo (15:27:39) (in thread): > Hi@Peace Danielwelcome

Peace Daniel (15:28:48) (in thread): > Thank you so much

Peace Daniel (15:29:10) (in thread): > Thank you

Scholastica Urua (15:54:44) (in thread): > Welcome@Peace Daniel

Oluwatosin Adesola (16:36:01): > Hello Everyone, > > I am Tosin Olatunji, an Outreachy applicant, and I am very excited to contribute to the Microbiome project > I’m really looking forward to working with the team also, and cannot wait to do awesome work together. > > P.S, you can call me Bella as well. > Thanks!

Chioma Onyido (16:41:18) (in thread): > Hi@Oluwatosin Adesola:wave:Welcome. > Hmm maybe it was a typo but this is the Microbiome Study Curation community.:slightly_smiling_face:

Mildred Anashie (16:41:22) (in thread): > Hello Bella > > Welcome

Mildred Anashie (16:42:47) (in thread): > Oops Ididn’tnotice that > > Welcome all the same@Oluwatosin Adesola

Scholastica Urua (16:47:35) (in thread): > Hello@Oluwatosin Adesola

Okache Johnpaul (16:57:38): > Hey Everyone! My name is Johnpaul, I’m a part of Outreachy’s May cohort and I look forward to contributing to the Microbiome Study, and working with you all.

Bolanle Wahab (16:59:07) (in thread): > Hi JohnPaul, Welcome:partying_face:

Scholastica Urua (16:59:39) (in thread): > Welcome@Okache JohnpaulWe are to get started via this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Adedoja Isaac (17:01:15): > Hey everyone! Isaac here, happy to be a part of the Outreachy contribution phase as a software dev. Can’t wait to collaborate, learn, and hopefully not break too many things along the way!:grin:Let’s rock this phase together!

Scholastica Urua (17:03:37) (in thread): > Welcome Adedoja. Looking forward to collaborating with you. > > Check the pinned message to get started.

Bolanle Wahab (17:06:43) (in thread): > Hey Isaac, you’re welcome:partying_face:We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started:https://github.com/waldronlab/BugSigDBcuration/issues/94.

Okache Johnpaul (17:13:07) (in thread): > Thank you,@Bolanle Wahaband@Scholastica Urua!

Chioma Onyido (17:13:48) (in thread): > Welcome Eniola. Good to have you here!

Oluwaseyifunmi Taiwo (17:21:31) (in thread): > Welcome@Adedoja Isaac.

Oluwaseyifunmi Taiwo (17:22:16) (in thread): > @Bolanle WahabI think you sent the wrong link.@Adedoja Isaachere is the right linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Oluwaseyifunmi Taiwo (17:23:34) (in thread): > Welcome@Okache Johnpaul

Oluwaseyifunmi Taiwo (17:24:25) (in thread): > Welcome@Oluwatosin Adesola

Mildred Anashie (17:34:23) (in thread): > Welcome@Adedoja Isaac

Mildred Anashie (17:36:16) (in thread): > Hello@Okache Johnpaul, Welcome

Okache Johnpaul (17:53:20) (in thread): > Thank you@Mildred Anashie,@Oluwaseyifunmi Taiwo!

Leenaa Al-Amin (18:14:38): > Hello everyone! My name is Leenaa. I’m an outreachy applicant and I’m excited to work with you all and contribute to the Bioconductor project!

Bolanle Wahab (18:16:54) (in thread): > Hi@Leenaa Al-AminYou’re welcome:partying_face:

Bolanle Wahab (18:17:13) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Bolanle Wahab (18:18:38) (in thread): > Thanks, Noted!

Oluwaseyifunmi Taiwo (19:08:12) (in thread): > Welcome@Leenaa Al-Amin

Faith Ifeoluwa Alexander (21:16:53): > Hello Everyone. My name is Faith. I am an outreachy applicant and I can’t wait to see how I can contribute to the Bioconductor Project and work with the amazing minds here!

Oluwaseyifunmi Taiwo (21:20:52) (in thread): > Welcome Faith. I’m Mabel. Look forward to connecting with you. Check this to get startedhttps://github.com/waldronlab/BugSigDBcuration/issues/94. Also check the pinned messages too and feel free to ask questions - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Scholastica Urua (21:53:41) (in thread): > Welcome@Faith Ifeoluwa Alexander

Scholastica Urua (21:56:32) (in thread): > Welcome@Leenaa Al-Amin

Desire Oluwarotimi (22:04:24): > Hello everyone! My name is Desire Oluwarotimi. I’m an Outreachy applicant. > > Feels good to be here to participate again. > > I’m looking forward to every bit of the journey.

Oluwaseyifunmi Taiwo (22:07:30) (in thread): > Welcome@Desire OluwarotimiI’m Oluwaseyi. Glad to meet you.:hugging_face::hugging_face:. Check this to get started.https://github.com/waldronlab/BugSigDBcuration/issues/94And feel free to ask questions too. Welcome once again - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Desire Oluwarotimi (22:08:37) (in thread): > Thank you very much Oluwaseyi.

Desire Oluwarotimi (22:09:25) (in thread): > Nice to have you in our midst, Faith.

Desire Oluwarotimi (22:09:54) (in thread): > Welcome@Leenaa Al-Amin

Amal Hirole (22:21:28): > Hello everyone, my name is Amal and I am from Canada. I am an Outreachy applicant for the May 2024 cohort. I look forward to making meaningful contributions to the Microbiome project.

Oluwaseyifunmi Taiwo (22:22:26) (in thread): > Welcome@Amal Hirole. I’m Oluwaseyi Mabel. Glad to meet you.:hugging_face::hugging_face:. Check this to get started.https://github.com/waldronlab/BugSigDBcuration/issues/94And feel free to ask questions too. Welcome once again - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Desire Oluwarotimi (22:25:17) (in thread): > HI Amal. Welcome here.

Sneha Singh (23:37:45) (in thread): > @Oluwaseyifunmi Taiwothank you, likewise!

Angella Namuli (23:45:27): > Hello team, my name is Angella. Iam excited to be working with you here.

2024-03-05

Scholastica Urua (00:22:32) (in thread): > Hello@Angella Namuliwelcome. > > Kindly view the issue on GitHub for instructions on how to get started.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Scholastica Urua (00:23:56) (in thread): > Welcome@Amal Hirole:tulip:

Desire Oluwarotimi (00:35:16) (in thread): > Welcome@Angella Namuli

Mildred Anashie (00:43:19) (in thread): > Welcome@Leenaa Al-Amin

Angella Namuli (00:43:50) (in thread): > Thank you dear for the head up:smiling_face_with_3_hearts::smiling_face_with_3_hearts:

Scholastica Urua (00:50:17): > Hello everyone, I’ve found the first contribution to be enlightening. If anyone has queries regarding it, I’m more than happy to assist. > > Please don’t hesitate to ask if you have any questions, as we’re all here to learn and contribute together.:hugging_face:

Desire Oluwarotimi (01:03:10) (in thread): > Yes@Scholastica UruaI think the first contribution was particularly aimed at giving first timers a soft landing into the curation project and I found it enlightening as well.

Mildred Anashie (01:05:35) (in thread): > Welcome Faith

Mildred Anashie (01:05:57) (in thread): > Welcome@Desire Oluwarotimi

Mildred Anashie (01:06:30) (in thread): > Welcome@Amal Hirole

Mildred Anashie (01:08:06) (in thread): > Welcome@Angella Namuli

Svetlana Ugarcina Perovic (01:09:40) (in thread): > Hello! Welcome to the bugsigdb community.

Svetlana Ugarcina Perovic (01:10:09) (in thread): > Hello! Welcome to the bugsigdb community.

Svetlana Ugarcina Perovic (01:10:49) (in thread): > Hello hello, welcome to the bugsigdb community!

Oluwaseyifunmi Taiwo (01:11:16) (in thread): > How did you go about the first contribution?@Desire Oluwarotimiand@Scholastica Urua

Svetlana Ugarcina Perovic (01:11:26) (in thread): > Hello! Welcome to the bugsigdb community.

Svetlana Ugarcina Perovic (01:11:45) (in thread): > Hello! Welcome to the bugsigdb community.

Svetlana Ugarcina Perovic (01:12:13) (in thread): > Welcome back, Desire!

Svetlana Ugarcina Perovic (01:12:39) (in thread): > Welcome, Amal!

Svetlana Ugarcina Perovic (01:12:56) (in thread): > Hello! Welcome to the bugsigdb community.

Saga (01:13:41): > Hello everyone,I’m sagana from India.I’m an outreachy applicant for may cohort 2024.I’m so excited to get started and I’m looking forward to make meaningful contribution :))

Svetlana Ugarcina Perovic (01:14:01) (in thread): > Hello! Welcome to the bugsigdb community.

Mildred Anashie (01:14:24) (in thread): > Hello@SagaWelcome

Mildred Anashie (01:14:46) (in thread): > Hi@Oluwaseyifunmi TaiwoHave you followed this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (01:16:42) (in thread): > This is the link to the first contribution@Oluwaseyifunmi TaiwoYou can start herehttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Roseline (01:22:30): > Hello everyone, my name is Roseline Bassey, an Outreachy applicant. I am thrilled to be here. Super excited to be contributing to the BugSigDB project. I look forward to connecting with the community.

Mildred Anashie (01:23:12) (in thread): > Welcome@Roseline

Oluwaseyifunmi Taiwo (01:23:23) (in thread): > Welcome @Rosaline I’m Oluwaseyi. Glad to meet you.:hugging_face::hugging_face:. Check this to get started.https://github.com/waldronlab/BugSigDBcuration/issues/94And feel free to ask questions too. Welcome once again - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Oluwaseyifunmi Taiwo (01:23:46) (in thread): > Welcome Saga

Mildred Anashie (01:25:44): > Hello everyone > Just in case anyone is confused on where to go to start the first contribution > > This is the link to follow for the first contributionhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcI’vebeen able to finish mine andI’mwilling to help in case of any questions

Roseline (01:25:47) (in thread): > @Mildred Anashie&@Oluwaseyifunmi TaiwoThank you.

Oluwaseyifunmi Taiwo (01:29:28) (in thread): > How did you record your first contribution? Or did you just fill in the form only?

Habibat Sakiru (01:29:48): > Hello, I’m Habibat from Nigeria. I’m an Outreachy applicant, I look forward to contributing to making meaningful contributions

Desire Oluwarotimi (01:31:26) (in thread): > Welcome@Habibat SakiruTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Oluwaseyifunmi Taiwo (01:31:47) (in thread): > Welcome Habibat. I’m Oluwaseyi Mabel

Desire Oluwarotimi (01:35:22) (in thread): > Hi@Oluwaseyifunmi TaiwoThere is a link to an article that you are expected to study and go through. Studying the article helps you to answer most of the questions for the first contribution. > > And then for questions that do not pertain to the article, you are directed on what to do by the question itself. > > Once you fill the form successfully, then it means you’ve made your first contribution.

Desire Oluwarotimi (01:35:44) (in thread): > Welcome@Roseline

Desire Oluwarotimi (01:36:09) (in thread): > Welcome@Saga

Oluwaseyifunmi Taiwo (01:36:43) (in thread): > Okay. Thank you so much

Desire Oluwarotimi (01:37:21) (in thread): > You are welcome.

Samreen Aftab (01:37:38): > Hello everyone, I’m Samreen and I’m from India. I’ve no prior experience in open source but I’m excited to learn new things and contribute to this project

Mildred Anashie (01:38:10) (in thread): > Yea@Desire Oluwarotimiis right most of the questions have been answered > > ButYou canrecord it as “you completed the mini curation/first contribution”and just include a link to the surveyWe do not need the completed survey, the mentors have a record of it

Juliet Ogbu (01:38:17) (in thread): > Welcome@Habibat Sakiruwe’reexcited to have you here:relaxed:

Mildred Anashie (01:38:38) (in thread): > Welcome@Habibat Sakiru

Mildred Anashie (01:39:04) (in thread): > Welcome@Samreen Aftab

Juliet Ogbu (01:39:27) (in thread): > Welcome@Samreen Aftab

Samreen Aftab (01:39:56) (in thread): > thank you :))

Oluwaseyifunmi Taiwo (01:40:25) (in thread): > Okay. Thank you

Desire Oluwarotimi (01:40:37) (in thread): > Welcome@Samreen AftabTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Anshuman Moharana (01:40:43): > Hello everyone, I’m Anshuman and I’m from India. I’ve some prior experience in open source and I’m excited to learn new things and contribute to this project

Desire Oluwarotimi (01:41:43) (in thread): > Hello@Anshuman MoharanaYou are welcome. > > Take a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Juliet Ogbu (01:41:45) (in thread): > Welcome@Anshuman Moharana

Anshuman Moharana (01:42:40) (in thread): > Thank you

Oluwaseyifunmi Taiwo (01:43:34) (in thread): > Welcome@Anshuman Moharana

Okache Johnpaul (01:44:37) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Mildred Anashie (01:50:45) (in thread): > Welcome@Anshuman Moharana

Blessing Laweh (01:55:29): > Hello everyone, I am Blessing Laweh from Nigeria. It’s my first time working on Open Source project so I am looking forward to working with and learning from everyone, thank you:pray:

Oluwaseyifunmi Taiwo (01:56:52) (in thread): > Welcome Blessing. Check this link to get started and don’t be shy to ask questionshttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (02:00:43) (in thread): > Welcome Blessing

Blessing Laweh (02:02:15) (in thread): > Thank you Mildred, thank you Taiwo

Bolanle Wahab (02:06:43) (in thread): > Hi@Faith Ifeoluwa AlexanderYou’rewelcome:partying_face:

Bolanle Wahab (02:07:13) (in thread): > Hi@Desire Oluwarotimiyou’rewelcome:partying_face:

Bolanle Wahab (02:08:00) (in thread): > Welcome@Amal Hirole:heart:

Scholastica Urua (02:09:25) (in thread): > Hello@Oluwaseyifunmi Taiwo, like@Mildred Anashiementioned, please follow the link. > There’s an annotated material (already explained) you’re suppose to download to use in answering most of the questions. > > I find it to be easier if you first go through the onboarding materials before attempting the first contribution. > > I hope this helps.

Bolanle Wahab (02:09:47) (in thread): > You’rewelcome@Blessing Lawehhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Desire Oluwarotimi (02:10:44) (in thread): > Welcome@Blessing Laweh

Scholastica Urua (02:10:45) (in thread): > Welcome@Blessing Laweh

Scholastica Urua (02:11:52) (in thread): > Welcome@Anshuman MoharanaExcited to e-meet you:hugging_face:

Desire Oluwarotimi (02:12:09) (in thread): > Take a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (02:12:27) (in thread): > Welcome@Samreen Aftab

Scholastica Urua (02:13:34) (in thread): > Welcome@Saga

Scholastica Urua (02:14:05) (in thread): > Welcome@Roseline

Scholastica Urua (02:18:20) (in thread): > Welcome@Habibat Sakiru

Nanlop Blessing Dafwat (02:22:25): > Hi everyone, I’m Nanlop from Nigeria. I am excited to be here. This is my first time working on Open Source, I am looking forward to learning, making connections and contributing to this project.

Mildred Anashie (02:23:24) (in thread): > Welcome@Nanlop Blessing DafwatTake a look at this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Bolanle Wahab (02:24:05) (in thread): > Hi@Nanlop Blessing DafwatYou’rewelcome:heart:Feel free to chat if you need any help.

Nanlop Blessing Dafwat (02:27:13) (in thread): > Alright, thanks@Bolanle Wahab. Nice to meet you.

Scholastica Urua (02:31:16) (in thread): > Welcome@Nanlop Blessing Dafwat

Nanlop Blessing Dafwat (02:32:31) (in thread): > Thankyou@Scholastica Urua

Habibat Sakiru (02:47:38) (in thread): > Thank you@Desire Oluwarotimi

Desire Oluwarotimi (02:56:06) (in thread): > Welcome@Nanlop Blessing Dafwat

Abiodun Oladejo (03:19:05): > Hello everyone, I am Abiodun from Nigeria, I have no prior experience in open source but I am excited to be here, learn new things and make contribuions to open source

Mildred Anashie (03:19:53) (in thread): > Welcome@Abiodun OladejoTake a look at this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Bolanle Wahab (03:22:03) (in thread): > Hi@Abiodun OladejoYou’rewelcome:partying_face:This is an open space, feel free to chat if you need any help.

Abiodun Oladejo (03:24:47) (in thread): > Thank you@Bolanle Wahab:smiling_face_with_3_hearts:

Aleru Divine (03:25:28): > Hi everyone, I’m Divine Aleru, an Outreachy applicant. I look forward to contributing and working with all of you. > > Thank you so much!

Abiodun Oladejo (03:25:57) (in thread): > Thank you@Mildred Anashie

Mildred Anashie (03:26:50) (in thread): > Welcome@Aleru Divine:blush:

Bolanle Wahab (03:27:03) (in thread): > Hey@Aleru DivineYou’rewelcome, feel free to chat if you need any help,can’twait to work with you too.

Bolanle Wahab (03:27:39) (in thread): > You can get started using this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (03:27:40) (in thread): > The mentors already shared this with us to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479

Aleru Divine (03:30:05) (in thread): > Thank you so much.

Oluwatosin Adesola (03:30:08) (in thread): > Thank you all so much!

Oluwatosin Adesola (03:30:36) (in thread): > Thanks@Chioma Onyidothis has been corrected. > Appreciate it!

Ananya Tomar (03:32:04): > Hey everyone! Ananya here , an outreachy applicant , super excited and glad to be here, hoping to learn and make valuable contributions!

Aleru Divine (03:33:13) (in thread): > Hi Ananya, welcome! > > You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Peace Daniel (03:33:19) (in thread): > Welcome Ananya

Mildred Anashie (03:33:48) (in thread): > Welcome@Ananya TomarTake a look at this to get started, alsoI’mwilling to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (03:35:09) (in thread): > Welcome@Ananya Tomar:hugging_face:

Scholastica Urua (03:35:29) (in thread): > Welcome@Aleru Divine

Esther Afuape (03:35:44) (in thread): > Welcome to BugSigDB, Roseline

Esther Afuape (03:36:15) (in thread): > Nice to have you here!@Samreen Aftab

Bolanle Wahab (03:37:15) (in thread): > Hi@Ananya Tomaryou’rewelcome,feel free to ask if you need any assistance:blush:

Scholastica Urua (03:37:45) (in thread): > Welcome@Abiodun Oladejo

Juliet Ogbu (03:37:46) (in thread): > Welcome@Blessing Laweh

Juliet Ogbu (03:38:29) (in thread): > Welcome@Nanlop Blessing Dafwat

Desire Oluwarotimi (03:38:37) (in thread): > Welcome@Abiodun Oladejo

Juliet Ogbu (03:38:48) (in thread): > Welcome@Abiodun Oladejo

Desire Oluwarotimi (03:39:06) (in thread): > Welcome@Aleru Divine

Juliet Ogbu (03:39:12) (in thread): > Welcome@Ananya Tomar

Juliet Ogbu (03:39:45) (in thread): > Welcome@Aleru Divine

Chinedu Ihedioha (03:53:21): > Hi everyone, I am Chinedu, an Outreachy Applicant from Nigeria. Super excited to be here, looking forward to learn and contribute.

Mildred Anashie (03:54:26) (in thread): > Welcome@Chinedu Ihedioha:blush:Take a look at this to get started, also I’m willing to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479

Scholastica Urua (03:56:28) (in thread): > Welcome@Chinedu Ihediohanice to e-meet you. Kindly go through the link@Mildred Anashiedropped.

Bolanle Wahab (03:57:17) (in thread): > Hi@Chinedu Ihediohayou’rewelcome.Feel free to chat if you need any help

Desire Oluwarotimi (04:05:41) (in thread): > Welcome@Chinedu Ihedioha

Zaynab Aderonke Ogunnubi (04:08:50): > Hi everyone. I’m Zaynab, a UX Researcher and Designer and and Outreachy applicant. I’m so excited to be amongst interesting mind. Looking forward to working and learning with you all.

Aleru Divine (04:09:36) (in thread): > Hi@Chinedu Ihedioha, welcome!

Mildred Anashie (04:09:41) (in thread): > Welcome@Zaynab Aderonke Ogunnubi:blush:Take a look at this to get started, also I’m willing to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (04:11:17) (in thread): > Welcome@Zaynab Aderonke OgunnubiKindly go through the link@Mildred Anashiedropped. > > Please feel free to ask any questions you may have.

abdulwasiu maryam (04:28:04): > Good day everyone, I am Maryam, an outreachy applicant, i am a microbiologist, i would be glad to contribute to this project

Aleru Divine (04:28:58) (in thread): > Hi@Zaynab Aderonke Ogunnubi, Welcome!

Mildred Anashie (04:29:14) (in thread): > Welcome@abdulwasiu maryam:blush:Take a look at this to get started, also I’m willing to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Bolanle Wahab (04:30:00) (in thread): > Hello@Zaynab Aderonke Ogunnubiyou’rewelcome:heart:

Bolanle Wahab (04:30:58) (in thread): > Hi@abdulwasiu maryamyou’re welcome. > Feel free to chat if you need any help > You can start from herehttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Scholastica Urua (04:30:58) (in thread): > Welcome@abdulwasiu maryamIt’s nice to have you here.

Abiodun Oladejo (04:37:11) (in thread): > Thank you@Scholastica Urua@Desire Oluwarotimi@Juliet Ogbu

Aleru Divine (04:38:02) (in thread): > Hi@abdulwasiu maryam, Welcome!

Melodee Okigbo (04:39:33) (in thread): > Hi@Habibat Sakirunice to meet you!

Melodee Okigbo (04:42:09) (in thread): > Hi@Samreen Aftabnice to meet you! Iwouldn’tworry too much about not having experience,we’reall here to help.:grin:Do you understand what needs to be done to complete the first contribution?

Habibat Sakiru (04:42:31) (in thread): > Nice to have you here@Melodee Okigbo

Melodee Okigbo (04:44:25) (in thread): > Hi@abdulwasiu maryam,Can’twait to learn from you, have you started on your first contribution already?

Desire Oluwarotimi (04:45:16) (in thread): > Welcome@Zaynab Aderonke Ogunnubi

Melodee Okigbo (04:45:34) (in thread): > Hey@Zaynab Aderonke Ogunnubilooking forward to collaborating with you as well!

Desire Oluwarotimi (04:45:45) (in thread): > Welcome@abdulwasiu maryam

Melodee Okigbo (04:47:11) (in thread): > Hi@Anshuman Moharana, I feel the same way too, can’twait to learn and collaborate!

Melodee Okigbo (04:48:14) (in thread): > Hello@Abiodun Oladejonice to meet you!

Svetlana Ugarcina Perovic (05:06:37) (in thread): > :tulip:Good morning, everyone! > > Take your time to go through the introduction material, and enjoy reviewing the annotated microbiome paper and doing the first contribution task. As for the second contribution task,we strongly encourage you to aim for quality over quantity.In case of any doubts, we are here to discuss it together.

Sandra Dindi (05:45:40): > Hi everyone. My name is Sandra, an Outreachy applicant. I am a technical writer with a Software development experience. Happy to be contributing to this project.

Ruth Bamgbose (05:46:15): > Hello everyone, My name is Ruth, I am an outreachy applicant. Nice to meet you all.

Mildred Anashie (05:46:30) (in thread): > Welcome@Sandra Dindi:blush:Take a look at this to get started, also I’m willing to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (05:47:06) (in thread): > Welcome@Ruth BamgboseNice to meet you too:blush:Take a look at this to get started, also I’m willing to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (05:48:14) (in thread): > Hello Sandra. Welcome > Nice to have you here

Scholastica Urua (05:49:58) (in thread): > Hello@Ruth Bamgbose. Kindly view the link Mildred dropped to get started. I’m also here to help wherever I can. > > Looking forward to contributing together:hugging_face:

Desire Oluwarotimi (05:57:38) (in thread): > Welcome@Sandra Dindi

Desire Oluwarotimi (05:57:55) (in thread): > Welcome@Ruth Bamgbose

Ruth Bamgbose (05:58:30) (in thread): > Thank you

Ruth Bamgbose (06:07:42): > Hi, If the first curation form is completed, do we start the second contribution task, or is there something we should wait for?

Bolanle Wahab (06:08:23) (in thread): > Hi@Sandra Dindiyou’rewelcome

Scholastica Urua (06:09:01) (in thread): > @Ruth Bamgboseyou can go ahead with the second contribution. > > As mentioned in the onboarding material for the second task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged“paper to curate”and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Also, remember to record your first contribution on the outreachy site. - Attachment (BugSigDB): Special:RequestAccount

Desire Oluwarotimi (06:09:21) (in thread): > Hi@Ruth BamgboseOnce the first task is completed, you can request that any of the mentors assign you to a new article on GitHub.

Mildred Anashie (06:09:23): > Found this among the pinned messages > > This should help@Ruth Bamgbose - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Desire Oluwarotimi (06:10:43) (in thread): > Weldone@Mildred Anashie:+1:

Mildred Anashie (06:14:06) (in thread): > Thank you Desire

Ruth Bamgbose (06:17:30) (in thread): > Thank you Mildred

Svetlana Ugarcina Perovic (06:21:22) (in thread): > Please seehttps://github.com/waldronlab/BugSigDBcuration/issues/96and Section**** Do I need to wait for first contribution to approved or reviewed before I start the second contribution - Attachment: #96 Outreachy Frequently Asked Questions > Hi Outreachy applicants! > > We wanted to share some answers to some frequently asked questions we received during our last contribution period. > > I asked a question on Slack but haven’t received an answer yet. Are you ignoring me? > > We are not ignoring you. We do our best to answer questions as soon as possible. Please note that I am on American Eastern time and Svetlana is on Central European Time so we may not be quick to answer questions outside normal business hours in these time zones. > > Can I make more than one second contribution? > > We ask that you only claim one article for your second contribution initially. You should focus on making that curation as perfect as possible as it will be used when we assess your performance during the contribution period. We strongly encourage you aim for quality over quantity. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, here is some ways you can help out with BugSigDB: > > • Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > • Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > • See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > I submitted my second contribution for grading. Why hasn’t it been graded yet? > > Grading takes us some time. We aim to have your contribution graded within a week. Thank you for patience! > > How do I record my contribution in the outreachy website? > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > How do I know if my first contribution is accepted or merged? > > Once you complete the survey we will have a record of it. Don’t worry! > > Should I always send a DM to mentors? > > Please ask questions in the bugsigdb channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > I have a question not covered here.** > > Communications regarding specific tasks should be done on the Slack Bioconductor channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Svetlana Ugarcina Perovic (06:22:22) (in thread): > Do I need to wait for first contribution to approved or reviewed before I start the second contributionSee herehttps://github.com/waldronlab/BugSigDBcuration/issues/96 - Attachment: #96 Outreachy Frequently Asked Questions > Hi Outreachy applicants! > > We wanted to share some answers to some frequently asked questions we received during our last contribution period. > > I asked a question on Slack but haven’t received an answer yet. Are you ignoring me? > > We are not ignoring you. We do our best to answer questions as soon as possible. Please note that I am on American Eastern time and Svetlana is on Central European Time so we may not be quick to answer questions outside normal business hours in these time zones. > > Can I make more than one second contribution? > > We ask that you only claim one article for your second contribution initially. You should focus on making that curation as perfect as possible as it will be used when we assess your performance during the contribution period. We strongly encourage you aim for quality over quantity. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, here is some ways you can help out with BugSigDB: > > • Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > • Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > • See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > I submitted my second contribution for grading. Why hasn’t it been graded yet? > > Grading takes us some time. We aim to have your contribution graded within a week. Thank you for patience! > > How do I record my contribution in the outreachy website? > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > How do I know if my first contribution is accepted or merged? > > Once you complete the survey we will have a record of it. Don’t worry! > > Should I always send a DM to mentors? > > Please ask questions in the bugsigdb channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > I have a question not covered here. > > Communications regarding specific tasks should be done on the Slack Bioconductor channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Mildred Anashie (06:24:58) (in thread): > Thank you@Svetlana Ugarcina Perovic

Ruth Bamgbose (06:25:01) (in thread): > Thank you@Svetlana Ugarcina Perovic

Barakat Akinsiku (06:46:03): > Hello everyone, my name is Barakat and I’m an outreachy applicant. I’m happy to be here and looking forward to learning and contributing to this project

Scholastica Urua (06:46:22) (in thread): > Welcome@Barakat Akinsiku:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94.

Mildred Anashie (06:46:51) (in thread): > Welcome@Barakat Akinsiku

Mildred Anashie (06:48:16) (in thread): > Follow the link to get started and also go through the onboarding materials, found that to be helpful

Barakat Akinsiku (06:53:47) (in thread): > Thank you@Scholastica Urua@Mildred Anashie

Desire Oluwarotimi (06:55:25) (in thread): > Welcome@Barakat Akinsiku

Bolanle Wahab (06:56:38) (in thread): > Hello@Barakat Akinsikuyou’rewelcome.Feel free to chat if you need any help:blush:

Aleru Divine (07:01:59) (in thread): > Welcome!@Barakat Akinsiku

Iman Ngwepe-Ntshibida (07:22:08): > Hi, I am Iman from South Africa. I am an Analytical Chemistry grad as well as a Data Scientist. I recently started learning R, excited to get to practice that skill her and to also dive into research/tech writing . Thrilled to join you all.

Scholastica Urua (07:22:29) (in thread): > Welcome@Iman Ngwepe-Ntshibida:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (07:23:27) (in thread): > Welcome@Iman Ngwepe-NtshibidaNice to e-meet you:blush:

Rahila-me (07:27:29): > Good afternoon all > > I created an account: BugSigDB > Someone, probably you from IP address 197.210.203.2, has requested an account “Rahila” with this email address on BugSigDB. > > To confirm that this > account really does belong to you on BugSigDB, open this link in your browser:https://bugsigdb.org/w/index.php?title=Special:RequestAccount&action=confirmemail&wpEmailToken=dc0b15fcaabab2d30c6cf027d711884aIf the account is > created, only you will be emailed the password. > > If this is not you, do not follow the link. > > This confirmation code will expire at 12:08, 4 > April 2024. > > However i did not get an email: when i click on > the link above I got this: > > Request account > > Invalid confirmation code. The code may have expired. > > what’s wrong - Attachment (BugSigDB): Special:RequestAccount

Bolanle Wahab (07:29:13) (in thread): > Hi@Rahila-meYou’dget the email, just be a little patient

Bolanle Wahab (07:29:34) (in thread): > Mine came almost 12hours later

Scholastica Urua (07:29:48) (in thread): > Hello@Rahila-meHave you checked your spam? I think my email went to spam when I created.

Rahila-me (07:29:56) (in thread): > ok…Thanks

Rahila-me (07:30:04) (in thread): > no, let me check

Rahila-me (07:31:02) (in thread): > is not in my spam

Scholastica Urua (07:32:31) (in thread): > Okay then. You should exercise a little patient. Hope you get it soon.

Blessing Peters (07:39:44): > Hello everyone! I’m Blessing from Nigeria, an outreachy applicant and it’s a great pleasure for me to join this community. I look forward to collaborating with you all and making a positive impact together.

Scholastica Urua (07:40:19) (in thread): > Welcome@Blessing Peters:shamrock:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Rahila-me (07:40:33) (in thread): > ok

Eniola Adebayo (07:40:33) (in thread): > Welcome

Mildred Anashie (07:40:50) (in thread): > Welcome@Blessing Peters

Desire Oluwarotimi (07:40:55) (in thread): > Welcome@Blessing Peters

Desire Oluwarotimi (07:41:13) (in thread): > Welcome@Iman Ngwepe-Ntshibida

Bolanle Wahab (07:41:16) (in thread): > Hi@Blessing Petersyou’rewelcome.Feel free to chat if you need any help:heart:

Blessing Peters (07:41:47) (in thread): > Thank you so much@Scholastica Urua

Blessing Peters (07:42:29) (in thread): > sure thing@Bolanle Wahabthank you

Muqtadirat Yussuff (07:43:21): > Hello everyone, I’m Muqtadirat, an outreachy applicant. Glad to be here and I hope to learn and make significant contributions with everyone

Scholastica Urua (07:43:50) (in thread): > Welcome@Muqtadirat Yussuff:shamrock:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Aleru Divine (07:44:16) (in thread): > Hi@Muqtadirat Yussuff, welcome:hugging_face:

Ima-obong (Aimah) (07:44:20): > Hello everyone, I am an Outreachy intern applicant, and I’m looking forward to contributing to the Bioconductor project.

Bolanle Wahab (07:44:28) (in thread): > Hello@Muqtadirat Yussuffyou’rewelcome.Feel free to chat if you need any assistance:heart:

Aleru Divine (07:44:40) (in thread): > Hi@Blessing Peters, welcome:hugging_face:

Mildred Anashie (07:44:41) (in thread): > Welcome > Nice to meet you:blush:Take a look at this to get started, also I’m willing to help where I can, feel free to ask questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (07:44:46) (in thread): > Welcome@Ima-obong (Aimah):shamrock:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Aleru Divine (07:44:59) (in thread): > Hi@Ima-obong (Aimah), welcome:hugging_face:

Amarachi Lewachi (07:45:08): > Hi everyone. My name is Amarachi. An outreachy internship applicant. I am excited to be here and I look forward to contributing on this project

Bolanle Wahab (07:45:11) (in thread): > Hello,you’rewelcome:heart:Feel free to chat if you need any help

Scholastica Urua (07:45:23) (in thread): > Welcome:shamrock:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Muqtadirat Yussuff (07:45:49) (in thread): > @Bolanle Wahabwill do, thank y’all for the warm welcome:sparkles:

Bolanle Wahab (07:45:52) (in thread): > You’rewelcome@Amarachi LewachiFeel free to ask if you need any help:heart:

Ima-obong (Aimah) (07:45:54) (in thread): > Thanks team, greatly appreciate the warm welcome

Bolanle Wahab (07:46:47) (in thread): > You’rewelcome@Iman Ngwepe-Ntshibida:heart:

Adeyemi Favour Adetayo (07:47:23): > Hola everyone, my name is Favour. An outreachy applicant. I am looking forward to contributing to the Biconductor project

Scholastica Urua (07:47:55) (in thread): > Welcome@Adeyemi Favour Adetayo:shamrock:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94.

Bolanle Wahab (07:48:40) (in thread): > Hi@Adeyemi Favour AdetayoYou’rewelcome:blush::heart:Feel free to chat if you need any help

Adeyemi Favour Adetayo (07:48:58) (in thread): > Okayyy > Thank you so much

Ima-obong (Aimah) (07:49:30) (in thread): > welcome favour

Chioma Onyido (07:52:55): > Hi<!channel>:wave:Congratulations again!:confetti_ball:And I hope you’re settling in well and have started making contributions. If you haven’t pleasestart.@Svetlana Ugarcina Perovichas done a brief introduction tho just in case you missed it,:sweat_smile:I’m Chioma and I’m a past Outreachy intern, I worked on the BugSigDB project during the last cohort alongside@Esther Afuapeand@Peace Sandy. > > I’ve had a draft on tips on the best ways to contribute/ record your contributions and the questions I’ve been receiving lately motivated me to finish it.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/I hope this helps. Don’t be afraid to ask questions, we are here for you. > All the best!:rocket: - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta…

Chioma Onyido (07:53:20) (in thread): > Welcome Favour!

levis Ngigi (07:53:56): > Thanks for this

Muqtadirat Yussuff (07:54:21) (in thread): > Thank you Chioma:sparkles:, I read a bit on this recently and some blog posts from Esther

Aleru Divine (07:54:26): > Thank you so much@Chioma Onyido:heart:

Ima-obong (Aimah) (07:54:36): > Thank you@Chioma Onyido

Naomi Ibe (07:54:40): > Hello, Outreachy applicant here, after I submit my first contribution, can I go back to edit it if I notice I made a mistake,or if I didn’t add something somewhere? > Second question, can we submit our first contribution before the first team meetings on Thursday 9am EDT? Or do you suggest we wait till after it?@Svetlana Ugarcina Perovic@Chioma Onyido

Scholastica Urua (07:54:49) (in thread): > Thank you@Chioma Onyidofor sharing. I’m sure this will really be helpful to everyone.

Isi Irabor (07:54:51): > Thank you so much

Bolanle Wahab (07:55:20) (in thread): > Thank you for this:heart:

Ukwueze Pascaline Nnenna (07:56:04): > Thank you@Chioma Onyido

Scholastica Urua (07:56:59) (in thread): > Hello@Naomi Ibe, I don’t think we can go back to edit our first contribution if you have submitted it already. Don’t know if I’m wrong about this though. > > Secondly, you can submit the first contribution before the first team meeting. However, I suggest to not submit the second contribution until the first team meeting.@Svetlana Ugarcina Perovic@Chioma Onyidomay have more to say on this.

Adedoja Isaac (07:57:11) (in thread): > Hi Chioma!:wave:Thanks for sharing these tips! It’s great to see past interns like yourself offering guidance to newcomers. We’ll definitely check out your blog post and share it with others who might find it helpful. Keep up the awesome work!

Aleru Divine (07:58:22) (in thread): > Hi@Naomi Ibe, Idon’tthinkthat’spossible.Because Qualtrics is a survey platform and onceyousubmit, there is no going back to edit.

Esther Afuape (07:58:39) (in thread): > Well done Chioma:clap:

Aleru Divine (07:58:40) (in thread): > @Svetlana Ugarcina Perovic@Chioma Onyido

Mildred Anashie (07:58:49) (in thread): > Thank you Chioma:heart:Already saved for reference

Svetlana Ugarcina Perovic (07:59:15) (in thread): > @Naomi Ibeyou can do another submission from a scratch

Naomi Ibe (07:59:39) (in thread): > @Aleru Divine@Scholastica Uruathank you

Adeyemi Favour Adetayo (07:59:52): > Thank you@Chioma Onyido

Eniola Adebayo (08:06:20): > Hi, while trying to choose a paper for my second contribution, I came across a preprint which have not been peer-reviewed. I am curious about the authenticity of such papers?:thinking_face:@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>

Chioma Onyido (08:07:32) (in thread): > Thank you everyone.:confetti_ball:

Mildred Anashie (08:08:02) (in thread): > The mentors can throw more light on authenticity but I think preprints are curated on BugSigdb

Svetlana Ugarcina Perovic (08:10:30) (in thread): > yes, we curate the bioRxiv preprints

Adenike Oladimeji-Kasumu (08:11:31): > Hello Everyone:hugging_face:I am Adenike, a 2024 Outreachy Applicant. I look forward to making contributions on the Bio conductor project.

Scholastica Urua (08:11:42) (in thread): > Welcome@Adenike Oladimeji-KasumuKindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Adenike Oladimeji-Kasumu (08:13:52) (in thread): > Thank you Scholastica. I appreciate this.

Eniola Adebayo (08:14:11) (in thread): > Great!! Thankyou@Svetlana Ugarcina Perovic@Mildred Anashie

Joan C. Chukwuemeka (08:14:17) (in thread): > @Eniola AdebayoPeer reviewed papers have usually gone through different expert reviews for quality before being published; I’d suggest you also go through bugsigdb curation policy to guide you for the second contribution

Esther Afuape (08:14:58) (in thread): > Concerning account creation: When you request for an account, check your spam/ junk folder for the email to confirm your account and another email containing your temporary password. If the confirmation email says the code has expired, go ahead and attempt to login with the temporary password provided.If you do not receive an email with your temporary password,you canrequest for an account with a different email and username.

Mildred Anashie (08:16:33): > Hi everyone > > For those who already have their accounts created and have started their second contribution > > I suggest you carefully go through the onboarding materials and read through the curation policy to guide youHere’sa linkhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Rahila-me (08:16:59): > @Esther Afuapein my case they was no temporary password

Bolanle Wahab (08:17:07) (in thread): > Hi,you’rewelcome:heart:

Eniola Adebayo (08:17:18) (in thread): > Ohhh, interesting:+1:@Joan C. Chukwuemeka

Scholastica Urua (08:17:25) (in thread): > Thank you@Mildred Anashie

Bolanle Wahab (08:17:55) (in thread): > Thank you:heart:

Rahila-me (08:18:06): > @Esther Afuape: If you do not receive an email with your temporary password, you can request for an account with a different email and username. Wont this curse a problem

Bolanle Wahab (08:18:36) (in thread): > When did you request for the account?@Rahila-me

Rahila-me (08:20:45) (in thread): > @Bolanle Wahabthis afternoon. a link was sent i clicked on it, they said it has expired

Bolanle Wahab (08:21:53) (in thread): > Okay,you’dreceive your temporary password in another mail later,don’tworry.

Adenike Oladimeji-Kasumu (08:22:54) (in thread): > Thank you Bolanle

Scholastica Urua (08:23:17) (in thread): > Hi@Rahila-me, > > Subsequently, please can you reply under your initial thread so that it can be easy to follow. In case others encounter similar problems, it will be easier to go through one thread. > > My humble suggestion:pray:.

Chioma Onyido (08:24:59) (in thread): > Hi@Rahila-meyou’resupposed to receive a temp password, but if youhaven’t, be patient the mentors@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>will attend to this soon.

Rahila-me (08:25:54) (in thread): > @Chioma Onyidook thanks, do have an idea if it will take the whole of today

Chioma Onyido (08:26:16) (in thread): > Yes please.

Joan C. Chukwuemeka (08:26:26) (in thread): > Here’s the link to the curation policyhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Chioma Onyido (08:28:27) (in thread): > If you stillhaven’treceived your temp password, I suggest you do as Esther said and go ahead and create an acc with a diff email and username, > > Don’t worry about causing a problem, send a note of the previous username you registered and the admin will delete.

Nwuguru Chidiebere (08:29:32): > Hello Everyone, > > I’m Nwuguru Chidiebere Sullivan, an entry-level healthcare data analyst. I recently got into the Summer 2024, Outreachy internship contribution phase, and hopefully will want to be part of the BugSigDB open project for this internship window. Please, can someone help get me started?:palms_up_together:. I’m actually very new to open source contribution.

Scholastica Urua (08:30:18) (in thread): > Welcome@Nwuguru Chidiebere:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (08:30:49) (in thread): > Hello@Nwuguru ChidiebereWelcome, feel free to ask questions > Willing to help

Aleru Divine (08:32:42) (in thread): > Hi@Nwuguru Chidiebere, welcome:hugging_face:

Peace Sandy (08:34:50) (in thread): > Well done Chioma:rocket:This will answer most questions

EBERE ADEKOGBE (08:43:11): > Hi everyone, I am Ebere and an Outreachy applicant, I can’t wait to start making contributions to the Bioconductor project.

Mildred Anashie (08:44:22) (in thread): > Welcome@EBERE ADEKOGBE:blush:Feel free to ask questions > Willing to help > > Follow the link to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Nekembe Boris (08:44:58) (in thread): > Great to have you@EBERE ADEKOGBE

Peace Sandy (08:46:46) (in thread): > Hi@EBERE ADEKOGBEWelcome

Victoria (Burah) Poromon (08:47:58): > Hello, Good day everyone. Hopewe’reall doing fine. I have a small question. > > Is it safe to start curating an article if you’re the first and only one who has left a comment on the GitHub page but youhaven’tbeen assigned to it yet?

Mildred Anashie (08:49:03) (in thread): > Yes I think you should,since you are the only one > > The mentors will eventually assign it to you

Peace Sandy (08:49:51) (in thread): > Have you indicated interest on the GitHub issue ?

Victoria (Burah) Poromon (08:50:58) (in thread): > Yes I have indicated interest

Ananya Tomar (08:53:23): > Hey everyone! I have chosen an article to curate, however would like some pointers on how to proceed with the curation or if there is a format to follow , any help would be greatly appreciated!

Nekembe Boris (08:54:01) (in thread): > Yes I think so. I am in the same category with you@Victoria (Burah) Poromon. I think it is done on a first come, first served basis

Mildred Anashie (08:54:03) (in thread): > The onboarding materials should guide you

Mildred Anashie (08:54:21) (in thread): > Here’sthe curation policy as wellhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Victoria (Burah) Poromon (08:54:38) (in thread): > Okay great

Chioma Onyido (08:54:45) (in thread): > Thank you Mildred.

Scholastica Urua (08:55:33) (in thread): > Welcome@EBERE ADEKOGBE

Aleru Divine (08:57:02) (in thread): > Hi@Ananya Tomar, check out the Prep Work section on this page. It contains the onboarding materials and video trainings on curation.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Scholastica Urua (08:57:41) (in thread): > The onboarding videos are really a huge help

Ananya Tomar (09:03:52) (in thread): > Thank you so much@Mildred Anashie@Scholastica Urua@Aleru Divine!

Emem Eduoku (09:04:03): > Hi Everyone. I am Emem, an outreachy applicant. I would like to know what the next step is

Mildred Anashie (09:04:47) (in thread): > Have you gone through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Ananya Tomar (09:05:09) (in thread): > Hey Emem! I think you can consult this -https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Aleru Divine (09:05:30) (in thread): > Hi@Emem EduokuI found this super helpful too.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Ananya Tomar (09:07:48) (in thread): > Furthermore, this is the link to follow for the first contribution :)https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Rahila-me (09:12:26): > @Chioma Onyido, when we talk about antibiotic exclusion is it for the diseased or HC

Rahila-me (09:14:38) (in thread): > ok..thanks

Scholastica Urua (09:14:45) (in thread): > Welcome@Emem Eduoku

Nekembe Boris (09:14:50) (in thread): > @Rahila-me, in my humble opinion, it concerns both groups

Scholastica Urua (09:16:23) (in thread): > Like@Nekembe Borissaid, I think it concerns both groups. Because both the diseased and healthy groups are suppose to be as similar as possible.

Emem Eduoku (09:17:07) (in thread): > Thanks everyone for the resources provided

Mildred Anashie (09:17:53) (in thread): > Antibiotic exclusion can differ for both groups but our concern in BugSigdb is usually the case group or diseased group@Chioma Onyido@Esther Afuapeplease throw more light:pray:

Onyeahialam Gracious (09:25:25): > Hello everyone, I’m Gracious Onyeahialam, a fellow Outreachy Applicant and I’m excited to be here to share my contributions as we all learn together.

Mildred Anashie (09:25:50) (in thread): > Welcome@Onyeahialam Gracious

Mildred Anashie (09:26:36) (in thread): > Follow link to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Onyeahialam Gracious (09:27:00) (in thread): > Thank you, Mildred. It’s my pleasure to interact with you.

Nekembe Boris (09:27:57) (in thread): > Welcome@Onyeahialam Gracious. Do not forget to equally go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349

EBERE ADEKOGBE (09:29:14) (in thread): > Thank you all for the warm welcome

EBERE ADEKOGBE (09:31:45) (in thread): > Welcome Emem glad to have you here

Aleru Divine (09:33:29) (in thread): > Hi@Onyeahialam Gracious, welcome:hugging_face:

Scholastica Urua (09:40:21) (in thread): > Welcome@Onyeahialam Gracious

Aleru Divine (09:41:04) (in thread): > I found this super helpful too. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Iman Ngwepe-Ntshibida (09:41:39) (in thread): > Thank you all:heart:

Chioma Onyido (09:51:39) (in thread): > Hmmm I am not:100:sure, especially in cases where the authors don’t delineate, they just give a general overview of exclusion criteria for both groups. > > The mentors will get to your question soon.:pray:

Bolarinwa Abosede Julianah (10:01:54): > Hello everyone. I’m Julianah. An outreachy applicant. I’m so excited to be here and I’m looking forward to contributing to the project

UBNSEMS3S (10:03:03): > Welcome everyone. My name is Chloe and I am one of the mentors here. I am mostly out on vacation this week so I’ll be quiet but starting next week you’ll be hearing from me and I’ll be running the office hours. This is my third time mentoring for Outreachy and I’m very excited to work with you all.

Mildred Anashie (10:03:57) (in thread): > Thank you<@UBNSEMS3S>Excited to be here:blush:

Bolarinwa Abosede Julianah (10:04:55) (in thread): > Hello Chloe > Nice meeting you > And looking forward to work with you

Aleru Divine (10:07:59) (in thread): > Hi Julianah, Welcome:hugging_face:

Scholastica Urua (10:08:35) (in thread): > Welcome@Bolarinwa Abosede Julianah:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Aleru Divine (10:09:56) (in thread): > I also found this super helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Mildred Anashie (10:10:00) (in thread): > Welcome@Bolarinwa Abosede Julianah

Scholastica Urua (10:10:17) (in thread): > Hello<@UBNSEMS3S>, I’m thrilled to be here. Looking forward to your mentorship.

Rahila-me (10:10:46) (in thread): > Hello<@UBNSEMS3S>nice to meet you

Bolarinwa Abosede Julianah (10:12:20) (in thread): > Thank you everyone > Thank you so much

Aleru Divine (10:12:44) (in thread): > Thank you so much<@UBNSEMS3S>

Sneha Singh (10:15:41): > Hello, I wanted to know that what should I write for slack username? The name that is displayed over here or actual username which I can find on my account settings.Since we are required to fill our slack username for first contribution.

Mildred Anashie (10:16:29) (in thread): > I think the name you are using here on slack that we can all see

Scholastica Urua (10:17:58) (in thread): > Sneha Singh is your slack username.

Oluwatomisin Omojokun (10:20:14) (in thread): > when is the submission deadline

Bolarinwa Abosede Julianah (10:20:26) (in thread): > Hello beautiful people > I have a question please

Bolarinwa Abosede Julianah (10:20:53) (in thread): > How do I go about the process of curating the file/doc?

Bolarinwa Abosede Julianah (10:21:45) (in thread): > @Aleru Divine@Mildred Anashie

Aleru Divine (10:23:12) (in thread): > Checkout the Prep Work section on this page. It contains the onboarding materials and video trainings on curation.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Aleru Divine (10:24:10) (in thread): > It looks like this - File (PNG): IMG_7698

Bolarinwa Abosede Julianah (10:24:48) (in thread): > Thank you@Aleru DivineI will read through it

Mildred Anashie (10:25:42) (in thread): > Do well to go through this as wellhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Bolarinwa Abosede Julianah (10:25:54) (in thread): > Thank you Mildred

Aleru Divine (10:28:56) (in thread): > @Oluwatomisin OmojokunI am not aware of any deadline for this submission but there is general Outreachy final applications deadline which is on April 2, 2024.@Svetlana Ugarcina Perovicis there a deadline for the first contribution?

Aleru Divine (10:29:33) (in thread): > You’reWelcome@Bolarinwa Abosede Julianah:hugging_face:

Peace Sandy (10:31:27) (in thread): > Preferably use your slack username

Esther Afuape (10:39:15) (in thread): > Inclusion and exclusion criteria apply to all the participants in a study. > When the groups have different antibiotics exclusions mentioned, you should enter both. When there’s only one mentioned, then it’s for both controls and cases.

Chioma Onyido (10:40:10) (in thread): > Thank you for clarifying Esther. > > To add, this is specific to Antibiotics exclusion criteria. > > (although not related to your question), we curatealpha diversitiesandconditionsrelative to the case/ diseased group. > > I hope it’s clearer now.

Mildred Anashie (10:41:30) (in thread): > Much clearer:blush:Thank you@Esther Afuapeand@Chioma Onyido

Desire Oluwarotimi (10:42:02) (in thread): > Welcome@Ima-obong (Aimah)

Scholastica Urua (10:42:02) (in thread): > Thank you@Esther Afuapeand@Chioma Onyido

Desire Oluwarotimi (10:42:19) (in thread): > Welcome@Amarachi Lewachi

Desire Oluwarotimi (10:42:40) (in thread): > Welcome@Adeyemi Favour Adetayo

Desire Oluwarotimi (10:43:36) (in thread): > Thank you Chioma:+1:

Desire Oluwarotimi (10:45:03) (in thread): > Welcome@Bolarinwa Abosede Julianah

Desire Oluwarotimi (10:45:30) (in thread): > Welcome@Onyeahialam Gracious

Adenike Oladimeji-Kasumu (10:51:23) (in thread): > Hello,@C. Mirzayi (please do not tag this account). I’m excited to be here as well. > I do have a question please; Asides our introduction on the Introduction channel and here#bugsigdb, do we need to personally introduce ourselves to our mentor? > You know, a part of the outline from Outreachy says to introduce ourselves to our mentor.

Barakat Akinsiku (10:52:10) (in thread): > Thank you@Bolanle Wahab@Aleru Divine

Scholastica Urua (10:53:26) (in thread): > I’ll really love to know the answer to@Adenike Oladimeji-Kasumu’s question as well.

Sneha Singh (11:01:38) (in thread): > Okay thanks:smile:

Oluwatomisin Omojokun (11:09:43) (in thread): > Thank you@Aleru Divine

UBNSEMS3S (11:20:06) (in thread): > @Adenike Oladimeji-KasumuThat’s not necessary. All the mentors for this project read this channel and so by introducing yourself here, you have introduced yourself to us.

Adenike Oladimeji-Kasumu (11:21:36) (in thread): > @C. Mirzayi (please do not tag this account)That’s taken. Thank you for responding.

Jenny (11:51:28) (in thread): > I really appreciate you Chioma for this article, I understood what I am here for

Scholastica Urua (11:51:42): > Hello everyone, please I have some questions; > > When a paper records multiple statistical tests, do I include all at once? > > Also when filling in the LDA score in the case of the attached excerpt, is it okay to input just ‘2’ or it has to be ‘>2’? > > Please I need guidance on how to go about it.<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyThanks:pray: - File (JPEG): Statistical Analysis.JPG - File (JPEG): Statistical test.JPG

Mildred Anashie (11:54:12) (in thread): > For the LDA score just 2 is fine

Joan C. Chukwuemeka (11:54:17) (in thread): > I believe the statistical test that was used to get the differential abundant organisms between the groups is the one to be curated,

Peace Sandy (11:55:43) (in thread): > Hi@Scholastica Uruaonly record statistical test used for the differential abundance. Each paper states the LDA score used, they is no specific LDA score

Scholastica Urua (11:57:41) (in thread): > Thank you all for your answers. This is helpful:pray:

Esther Afuape (12:01:46) (in thread): > To make it easier to know what statistical test to record, check the description of the figure you’re curating the result from. Sometimes, different experiments have different statistical tests carried out for their results.

Scholastica Urua (12:02:54) (in thread): > okay, thank you@Esther Afuape

Mildred Anashie (12:03:11) (in thread): > Just like what@Peace Sandyand@Joan C. Chukwuemekasaid > > Statistical test for differential abundance is what you should record for > > Also you can have multiple statistical tests used in a paper for different experiments > > They should all be recorded if you have significant results > > This might not be clear enough@Esther Afuapeplease help me give a better explanation:blush:

Svetlana Ugarcina Perovic (12:25:00) (in thread): > @Aleru Divineyou are right: there is no deadline for this submission but there is general Outreachy final applications deadline which is on April 2

Anju Maurya (12:47:08): > Hello everyone! > I am Anju Maurya. I am an aspiring Data Analytics and a College student majoring in Computer Science. I am an Outreachy applicant looking forward to contribute to the BugSigDB project. I have a keen interest in health related data and to find meaninful results. I am very excited and happy to be a part of this community and would love to learn and collaborate with all learners and mentor while making valuable contributions.

Scholastica Urua (12:47:26) (in thread): > Welcome@Anju Maurya:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Anju Maurya (12:49:18) (in thread): > Thanks !

Eniola Adebayo (12:50:59): > I need help please. I’m currently working on a longitudinal study, where they compared a case of periimplantitis after implant. All groups received the implant, both healthy and diseased subjects. The healthy group was described as the group that received implant but did not develop any disease. While the other groups received implants and developed diseases. Relative abundance results were given for both healthy group and other diseased groups. Within the healthy group (case samples), conditions were compared (healthy, mucotitis and peri-implantitis). They did same for peri-implantitis > Do I curate for healthy group or for just peri-implantitis?@Svetlana Ugarcina Perovic<@U1LCB8WEA> - File (PNG): image 1.PNG - File (PNG): image 2.PNG

Anju Maurya (12:55:30) (in thread): > Thank you@Scholastica Urua

Anju Maurya (12:56:00) (in thread): > I am really excited to be here!

Mildred Anashie (12:59:25) (in thread): > @Eniola Adebayoplease share a link to your paper > > From your description, firstly this seems like a case control study > Also you said “The healthy group was described as the group that received implants and did not develop any disease” and also referred to healthy group as (Case Samples) > This is not clear to me

Eniola Adebayo (13:04:27) (in thread): > Its a longitudinal study (from the paper). The three groups were patients who had implants, but two are the disease subject and the last is the healthy group. Here is a link to the paperhttps://www.nature.com/articles/s41522-024-00482-z#citeas - Attachment (Nature): Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases > npj Biofilms and Microbiomes - Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases

Mildred Anashie (13:04:31): > Hi@Svetlana Ugarcina Perovic<@U1LCB8WEA>@C. Mirzayi (please do not tag this account)While reading the curation policy I observed that under the MHT correction > > It says “No” should be selected if there is evidence of MHT correction and I think it should be “if there’s no evidence of MHT correction” > > I’m attaching a screenshot to that effect and a link to the curation policy I’ve been going through > > Thank you:pray:https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy… - File (JPEG): IMG_1712

Sneha Singh (13:08:58) (in thread): > Agreed

Mildred Anashie (13:17:30) (in thread): > I agree with you, It’s a longitudinal study > > Still going through the article to see if I can find anything helpful while we wait for the mentors

Eniola Adebayo (13:21:05) (in thread): > Alright. Thank you:blush:

Scholastica Urua (13:31:05) (in thread): > Nice catch@Mildred Anashie. Like you said I think it should be “if there’s no evidence of MHT correction”. > I noticed this as well, I guess it’s a typo

Scholastica Urua (13:34:32) (in thread): > @Eniola AdebayoI am going through the link as well to get a grasp of your question. Lets wait to hear what the mentors have to say.

Nana (13:40:50): > Hello good evening all, ..I am Nana. I am so happy to be here..and hopefully my contribution counts

Peace Sandy (13:42:27) (in thread): > Thank you@Mildred Anashieit will be corrected

Peace Sandy (13:42:59) (in thread): > Welcome@NanaGlad to have you here! > > Please see the pinned message

Aleru Divine (13:43:14) (in thread): > Hi Nana, welcome:hugging_face:You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (13:44:03) (in thread): > This is also very helpful.It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Scholastica Urua (13:47:04) (in thread): > Welcome@NanaNice to meet you

Eniola Adebayo (13:47:08) (in thread): > Thankyou@Scholastica Urua

Bolarinwa Abosede Julianah (13:47:51) (in thread): > Welcome@NanaNice to meet you

Eniola Adebayo (13:48:01) (in thread): > Welcome@Nana

Mildred Anashie (13:50:25) (in thread): > Welcome@NanaFeel free to ask questions, willing to help when and if I can

Habiba Saad (13:53:39): > hey there I have a question. I am curating a paper for which the body site is gut and did not specify more than that in a paper.https://pubmed.ncbi.nlm.nih.gov/38366600/. but the given options are not specifically for the gut what should I choose then? - Attachment (PubMed): Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices - PubMed > The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. …

Ojoachele Onuh (13:54:05): > Hello Everyone, I’m Ojoachele Onuh, an outreachy applicant.I’m super excited to be in this community and to contribute.I look forward to connecting with everybody

Mildred Anashie (13:54:31) (in thread): > Welcome@Ojoachele Onuhhappy to connect with you too

Scholastica Urua (13:55:11) (in thread): > Welcome@Ojoachele Onuh:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Svetlana Ugarcina Perovic (13:56:04) (in thread): > They collected fecal samples, thus the body site is “Feces”.

Scholastica Urua (13:56:35) (in thread): > There is also a list of some of the FAQs and answers that may find helpful.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Eniola Adebayo (14:01:44) (in thread): > :face_holding_back_tears:@Svetlana Ugarcina Perovic

Sneha Singh (14:01:57): > I just completed my first contribution, so I just need to paste the url of the issue#94 to add the contribution right?

Scholastica Urua (14:02:34) (in thread): > That’s right@Sneha Singh

Svetlana Ugarcina Perovic (14:02:41) (in thread): > yes

Mildred Anashie (14:04:11) (in thread): > Thank you@Scholastica Urua

Mildred Anashie (14:04:27) (in thread): > Thank you@Peace Sandy

Bolanle Wahab (14:04:34) (in thread): > Hi@Ojoachele Onuhyou’rewelcome:heart:

Mildred Anashie (14:06:56) (in thread): > Yes > But just for clarity, you are to paste the link to the first curation you just completed > Thishttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Adenike Oladimeji-Kasumu (14:12:38): > I need help. I am curating a paper on “Breast cancer patients from the Midwest region of the United States have reduced levels of short‑chain fatty acid‑producing gut bacteria”. In the First part into my Curation where some questions are asked, I need to Identify the disease fromhttps://www.ebi.ac.uk/efo/website. I have been having issues with identifying the disease@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account) - Attachment (ebi.ac.uk): The Experimental Factor Ontology < EMBL-EBI > The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets. We also add terms for external users when requested. If you are new to ontologies, there is a short introduction on the subject available and a blog post by James Malone on what ontologies are for.

Scholastica Urua (14:16:22) (in thread): > Hello Adenike, your question is a little bit unclear to me. > > Are you trying to curate the disease condition? If yes, that’ll be breast cancer in this case.

Eniola Adebayo (14:17:36) (in thread): > Search for the specific disease (e.g breast cancer) in that website and copy the EFO number

Adenike Oladimeji-Kasumu (14:17:44) (in thread): > Yes, but there are different breast cancer

Sneha Singh (14:20:08) (in thread): > Search for the disease that closely matches the one mentioned in the paper (you can search for breast cancer and then identify the one that matches closely)

Desire Oluwarotimi (14:21:17) (in thread): > There are quite a number of breast cancer options on the website but I think you really just need to select the option you think best fits the disease condition.

Bolanle Wahab (14:21:18) (in thread): > Hi@Adenike Oladimeji-Kasumuthere’sa hint attached to that question,read the article on the link you sent and choose the disease that looks most identical

Aleru Divine (14:21:29) (in thread): > Hi@Ojoachele Onuh, welcome:hugging_face:

Adenike Oladimeji-Kasumu (14:21:53) (in thread): > Thank you everyone:pray:

Desire Oluwarotimi (14:21:55) (in thread): > Welcome@Anju Maurya

Sneha Singh (14:23:39) (in thread): > @Mildred AnashieI thought we need to paste the GitHub link

Sneha Singh (14:23:58) (in thread): > Can a mentor clarify regarding the same?

Rahila-me (14:24:20) (in thread): > Welcome@Nanagood to have you here

Bolanle Wahab (14:25:40) (in thread): > @Rahila-mehey, have you received your temporary password?

Mildred Anashie (14:26:34) (in thread): > @Esther Afuape@Chioma Onyido@Peace SandyPlease help us out here

Desire Oluwarotimi (14:26:52) (in thread): > Hi@Eniola AdebayoFrom what I can see here, I think you’ll have to curate the relative abundance result (increased and decreased) for three different comparisons. > > Healthy vs Peri-implantitis > Healthy vs Mucotitis > Mucotitis vs Peri-implantits > > However, our mentors would be able to shed more light.

Rahila-me (14:27:00): > <!here>, i am happy to be here. Lets cook magic all.:smiling_face_with_3_hearts:

Svetlana Ugarcina Perovic (14:27:08) (in thread): > Please seeHow do I record my contribution in the outreachy website? https://github.com/waldronlab/BugSigDBcuration/issues/96 - Attachment: #96 Outreachy Frequently Asked Questions > Hi Outreachy applicants! > > We wanted to share some answers to some frequently asked questions we received during our last contribution period. > > I asked a question on Slack but haven’t received an answer yet. Are you ignoring me? > > We are not ignoring you. We do our best to answer questions as soon as possible. Please note that I am on American Eastern time and Svetlana is on Central European Time so we may not be quick to answer questions outside normal business hours in these time zones. > > Can I make more than one second contribution? > > We ask that you only claim one article for your second contribution initially. You should focus on making that curation as perfect as possible as it will be used when we assess your performance during the contribution period. We strongly encourage you aim for quality over quantity. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, here is some ways you can help out with BugSigDB: > > • Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > • Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > • See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > I submitted my second contribution for grading. Why hasn’t it been graded yet? > > Grading takes us some time. We aim to have your contribution graded within a week. Thank you for patience! > > How do I record my contribution in the outreachy website? > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > How do I know if my first contribution is accepted or merged? > > Once you complete the survey we will have a record of it. Don’t worry! > > Should I always send a DM to mentors? > > Please ask questions in the bugsigdb channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > I have a question not covered here. > > Communications regarding specific tasks should be done on the Slack Bioconductor channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Latifat (14:27:26): > Hello everyone. My name is Latifat. I am an Outreachy applicant. I am happy to be able to contribute to this community.

Nana (14:28:11) (in thread): > Thank you all for the warm welcome

Ojoachele Onuh (14:28:41) (in thread): > Thank you all for the warm welcome

Desire Oluwarotimi (14:28:53) (in thread): > Hi and Welcome@Rahila-meTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Desire Oluwarotimi (14:29:25) (in thread): > Hello and Welcome@LatifatTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Sneha Singh (14:30:12) (in thread): > Welcome!

Sneha Singh (14:30:47) (in thread): > Welcome!

Rahila-me (14:31:10) (in thread): > @Desire Oluwarotimithanks

Blessing Laweh (14:31:44): > @Svetlana Ugarcina PerovicHello, please I need help. I want to know if we are to pick all the projects we would like to contribute to at once or simultaneously. I am asking because I read on the Outreachy website that some mentors stop accepting applicants when the the number of applicants are getting too much for a particular project. > > I listed some projects I’d like to work on but I am staring with this first. I hope it won’t be too late to join the others I listed, thanks.

Mildred Anashie (14:31:47) (in thread): > Welcome@Latifat:blush:

Latifat (14:32:26) (in thread): > @Desire OluwarotimiThank you for the guidance. I will check it out now.

Sneha Singh (14:32:55) (in thread): > @Mildred Anashiewe need to paste the GitHub issue #94 link.

Bolanle Wahab (14:33:16) (in thread): > You’rewelcome@LatifatFeel free to chat if you need any help:blush:

Aleru Divine (14:33:56) (in thread): > Hi@Latifat, welcome:hugging_face:You can check this out.I found this super helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349

Mildred Anashie (14:34:43) (in thread): > @Desire OluwarotimiI think Blessing is talking about other communitiesshe’sinterested in joining and projectsshe’lllike to work on along side Bioconductor

Desire Oluwarotimi (14:35:49) (in thread): > Oh, I see. That was an oversight. > > Thank You Mildred.

Scholastica Urua (14:35:51) (in thread): > Welcome@Latifat

Mildred Anashie (14:35:59) (in thread): > Just clarified that either of them works though

Aleru Divine (14:36:39) (in thread): > Hey@Blessing LawehI think we are allowed to contribute to different projects at the same time.

Eniola Adebayo (14:36:53) (in thread): > Thank you@Desire Oluwarotimi, I am quite clear on the comparisons made, but as highlighted in the image-sampleswere gotten from healthy and periimplantitis. my question is do I curate samples from ‘healthy species’ too or just periimplantitis? - File (JPEG): IMG_9854

Latifat (14:37:33) (in thread): > @Aleru DivineThank you. I will check it out.

Latifat (14:37:47) (in thread): > Thank you all for the warm welcome.

Bolanle Wahab (14:38:36) (in thread): > @Blessing Lawehyoucan contribute to as much projects as you want, as long as you can handle it.

Eniola Adebayo (14:38:48) (in thread): > Yes, we can contribute to other projects

Desire Oluwarotimi (14:39:29) (in thread): > Actually, both. I’m not sure you can curate one and leave the other.

Scholastica Urua (14:40:34) (in thread): > @Blessing Lawehif you are talking about other communities, you can contribute to as many projects as possible. However, we are encouraged to chose one or two to allow you to be more focused. > > However, like you mentioned some projects stop accepting applications earlier than others.

Mildred Anashie (14:42:21) (in thread): > I think I get your question@Eniola Adebayoyou are asking if you should curate from either > > > I thinkyou’llcurate Based on the contrast made in each of the experiments you are recording for > > > And I kind of agree with Desire

Aleru Divine (14:42:50) (in thread): > You’rewelcome:hugging_face:

Blessing Laweh (14:43:18) (in thread): > Thank you@Scholastica Urua@Eniola Adebayo@Bolanle Wahab@Aleru Divine@Desire Oluwarotimi@Mildred AnashieThank you everyone for your responses.:pray:

Eniola Adebayo (14:45:04) (in thread): > Thank you everyone:pray:

Amanda Adoyi (14:48:10): > Aloha@Svetlana Ugarcina PerovicI have been told a password would be emailed to me after registering for an account on BugSigDB. How long would I have to wait for the confirmation please? Thanksss

Rahila-me (14:48:32) (in thread): > Welcome Latifat

Mildred Anashie (14:49:07) (in thread): > Depending on when you requestedyou’llget an email

Mildred Anashie (14:49:18) (in thread): > But you can check your spam folder though, it might have been sent

Scholastica Urua (14:49:24) (in thread): > Hello@Amanda Adoyiit can take up to a few hours. Just exercise a little patience.

Amanda Adoyi (14:49:51) (in thread): > Thanks plenty. I’ll be checking :)

Rahila-me (14:50:03) (in thread): > @Amanda Adoyicheck your spam, if is not there wait a little longer it will show up. mine took a little longer

Svetlana Ugarcina Perovic (14:50:24) (in thread): > Thank you all for your patience!

Nana (14:52:22) (in thread): > I think@Rahila-mehas said it all. My took longer too before showing

Latifat (14:55:30) (in thread): > Thank you

Abiola Salako (15:01:51): > Well done, Everyone. > I’m excited to be here > I look forward to a more interactive session with you all.

Scholastica Urua (15:03:01) (in thread): > Welcome@Abiola SalakoKindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX

Mildred Anashie (15:03:09) (in thread): > Welcome@Abiola Salako

Abiola Salako (15:05:35) (in thread): > Thank you@Scholastica Urua@Mildred Anashie

Desire Oluwarotimi (15:05:55) (in thread): > Welcome@Abiola SalakoI hope we have a great time learning and contributing together.

Aleru Divine (15:06:30) (in thread): > Hi@Abiola Salako, welcome

Aleru Divine (15:06:35) (in thread): > I found this super helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Abiola Salako (15:08:35) (in thread): > Thank you everyone,I’m grateful.

Amanda Adoyi (15:17:59) (in thread): > Seen it now. Thanks everyone.

Amanda Adoyi (15:19:44): > Aloha again. Just out of curiosity, what would be the Contribution URL? A link to your work on BugSigDB or a github link?

Mildred Anashie (15:20:33) (in thread): > For which of the contributions?

Amanda Adoyi (15:21:16) (in thread): > For the second contribution. As for the first was that meant to be recorded?

Scholastica Urua (15:22:29) (in thread): > The link to the form will be the URL for contribution one

Mildred Anashie (15:23:26) (in thread): > Yes you are to record the first contribution

Bolanle Wahab (15:23:49) (in thread): > Yes, it should be recorded. > And the url is the link you see on your address bar after completing your first contribution

Amanda Adoyi (15:24:00) (in thread): > When I was done with the first I was only thanked for the survey. Am I meant to copy that link? When I pasted it on a different tab it was simply the quiz all over again.

Mildred Anashie (15:24:21) (in thread): > Yes record the link that way

Mildred Anashie (15:24:59) (in thread): > As for the second contribution you record the link to the study you created/curated

Bolanle Wahab (15:25:42) (in thread): > Yes, copy it, you can use this link to record your contributionhttps://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Amanda Adoyi (15:26:33) (in thread): > So pasting it in a different tab and seeing that the form was empty is not a problem? Alright

Amanda Adoyi (15:26:43) (in thread): > Thanks plenty

Adenike Oladimeji-Kasumu (15:27:56) (in thread): > Please, after answering the questions and it says that my response have been recorded, what is the next step for me?

EBERE ADEKOGBE (15:53:46) (in thread): > Hi Chloe, Nice to meet you

Idiat Alli (15:54:51): > Hello everyone. Glad to be here

Mildred Anashie (15:55:25) (in thread): > Welcome@Idiat Alli

EBERE ADEKOGBE (15:55:48): > Welcome Idiat

Bolanle Wahab (15:56:08) (in thread): > Hi@Idiat Alliyou’rewelcome.Feel free to chat if you need any assistance

Aleru Divine (15:58:15) (in thread): > Hi@Idiat Alli, welcome:hugging_face:

EBERE ADEKOGBE (15:58:40) (in thread): > Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94.#94 Welcome Outreachy Applicants!Welcome Outreachy Applicants!Note: This task can be completed by multiple Outreachy applicants.BugSigDB ProjectBugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies,https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a me…Labelsfirst contribution, outreachy may2024Comments - Attachment (BugSigDB): Main Page > … - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Aleru Divine (15:59:55) (in thread): > Also check this out.It’ssome of the FAQs and answers to them.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Scholastica Urua (16:10:53) (in thread): > Welcome@Idiat Alli. Nice to have you here.

Nana (16:11:23): > Welcome@Idiat Alli

Desire Oluwarotimi (16:12:04) (in thread): > Welcome@Idiat Alli

Semango Nicholas (16:27:55): > hello everyone .am happy to work with all of you for the bio conductor project

Idiat Alli (16:31:32) (in thread): > Welcome@Latifat

Bolanle Wahab (16:37:36) (in thread): > You’rewelcome.Feel free to ask if you need any assistance

Bolanle Wahab (16:37:53) (in thread): > Hii!You’re welcome. Feel free to ask if you need any assistance

Semango Nicholas (16:41:34) (in thread): > thanks, how can i start contributing to the project

Bolanle Wahab (16:43:29) (in thread): > You can start by clicking this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Aleru Divine (16:44:20) (in thread): > Hi@Semango Nicholas, Welcome:hugging_face:

Muqtadirat Yussuff (17:01:50): > Hi everyone, are we expected to curate a publication within a specific time period. Perhaps if you aren’t done in 5 days for instance it gets reassigned?

Bolanle Wahab (17:08:48) (in thread): > Hi@Muqtadirat Yussuffthe contribution period lasts for 4weeks. I think we have to complete all contributions within this period

Muqtadirat Yussuff (17:11:50) (in thread): > Thank you for the response@Bolanle Wahabbut I’m not quite asking about the contribution phase, just wanted to know if a paper is reassigned if a contributior doesn’t curate within a specific time frame

Nekembe Boris (17:14:50) (in thread): > As said by@Bolanle WahabI don’t think it will. Once assigned, you to curate, submit and correct (if indicated by the mentor) before the end of the contribution phase

Bolanle Wahab (17:15:58) (in thread): > Oh, Our mentors should have a better answer to that.

U01MW62UDQR (17:18:51) (in thread): > The mentors will try to allow applicants ample time to complete an assigned contribution. They will likely try to verify that it is abandoned before reassigning, but it’s more likely that they’ll add new papers to curate before reassigning existing ones.

Muqtadirat Yussuff (17:20:51) (in thread): > <@U01MW62UDQR>Alright, that was very helpful. Thank you

Semango Nicholas (17:22:08) (in thread): > thanks

Victoria Nduka (17:46:43) (in thread): > Taddy:hugging_face::hugging_face:

Muqtadirat Yussuff (17:50:29) (in thread): > You’re everywhere:joy:@Victoria Nduka

Blessing Ene Anyebe (17:59:18): > Hello everyone, my name is Blessing. > It is lovely to be here. It has been great learning and studying how Microbiomes work. The Microbiomes curation project is invested in capturing patterns of microbial signatures and focuses on the easy use of microbial data aggregation, standardization, analysis, knowledge synthesis, etc. > > I am excited about Bugsigdb and seeing that it reminds me of the beautiful secondary school days of learning about plant and animal cells including DNA.:sweat_smile:I look forward to exploring Microbiomes, contributing, and adding value to the community as well. > > Cheers guys, it’s great to be here!:orange_heart:

Chioma Agu (18:01:58): > Hello Everyone > > my name is Chioma Agu, > > I’m excited to join the#bugsigdbproject as an Outreachy applicant. I am encouraged by the energy and activity on here and look forward to making valuable contributions, connecting and collaborating with you all.

Chioma Agu (18:12:53) (in thread): > Welcome@Blessing Ene AnyebeI totally share in the excitement! To begin making contributions, you can go through this article by a mentor@Chioma Onyidoon the best ways to contributehttps://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/Looking forward to collaborating with you - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta…

Nekembe Boris (18:21:20) (in thread): > @Blessing Ene Anyebe, the excitement is mutual. You can start by going through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Nekembe Boris (18:22:34) (in thread): > Equally, you’ll find these FAQ useful as you start your first contributionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Blessing Ene Anyebe (18:23:11) (in thread): > Thank you guys for the reception!

Nekembe Boris (18:25:28) (in thread): > Welcome@Chioma Agu:boom:. Do not hesitate to ask if you have any doubts. We are all here to contribute and help each other

Chioma Agu (18:43:03) (in thread): > you’re welcome

Chioma Agu (18:48:45) (in thread): > Thank you@Nekembe Boris:star:

Suru Olaitan (20:41:55) (in thread): > Thank you so much@Bolanle Wahab…This has helped me record my first contribution

Bolanle Wahab (21:53:19) (in thread): > You’rewelcome@Chioma Agu:heart:

Bolanle Wahab (21:53:53) (in thread): > You’rewelcome@Blessing Ene Anyebe

Olajumoke Adeoyo (22:04:06): > Hello everyone, > I’m Adeoyo Olajumoke, an Outreachy participant. I am eager to contribute meaningfully and gain valuable experience within this community.

Scholastica Urua (22:06:32) (in thread): > Welcome@Olajumoke Adeoyo:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Scholastica Urua (22:08:38) (in thread): > This is a list of some of the FAQs and answers that may be helpful.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Scholastica Urua (22:09:33) (in thread): > Welcome@Chioma Agu:hugging_face:Kindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Scholastica Urua (22:10:36) (in thread): > Welcome@Blessing Ene Anyebe

Scholastica Urua (22:16:04) (in thread): > There’s no time limit for the curation but you should try to complete it before the contribution phase is over. For the second contribution@Svetlana Ugarcina Perovicemphasised we should focus on quality over quantity. Good luck:pray:

Scholastica Urua (22:16:52) (in thread): > Welcome@Semango Nicholas. I’m happy to have you here.

Olajumoke Adeoyo (22:24:52) (in thread): > Thank you for providing this information; it will certainly help me navigate this community. I plan to pin this message for the benefit of other newcomers, I hope that’s okay with you.

Ima-obong (Aimah) (22:34:31) (in thread): > Welcome to the team@Olajumoke Adeoyo

Anshuman Moharana (23:53:04): > hello@Svetlana Ugarcina Perovic@Levi Waldron@C. Mirzayi (please do not tag this account)please help me how to choose a paper to curate

2024-03-06

Samreen Aftab (00:25:15): > can anyone help me understand what exactly we’re supposed to look for? I don’t think I understand how the website works properly - File (PNG): image.png

Desire Oluwarotimi (00:25:59) (in thread): > Welcome@Semango Nicholas

Desire Oluwarotimi (00:27:57) (in thread): > Welcome@Blessing Ene Anyebe

Desire Oluwarotimi (00:28:44) (in thread): > Welcome@Chioma Agu

Desire Oluwarotimi (00:29:25) (in thread): > Welcome@Olajumoke Adeoyo

Scholastica Urua (00:30:22) (in thread): > The mentors have already pin a similar message@Olajumoke Adeoyo

Scholastica Urua (00:36:34) (in thread): > @Anshuman Moharanaafter you’re done with the first (curation) task, you can go ahead with the second contribution. > > As mentioned in the onboarding material for the second task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Also, remember to record your first contribution on the outreachy site. - Attachment (BugSigDB): Special:RequestAccount

Desire Oluwarotimi (00:38:20) (in thread): > Hi@Samreen AftabAny article of interest has a disease condition and in the case of the article for the first contribution, it is breast cancer. > > Whenever you input the disease condition on the website provided, a number of options with regards to the disease are shown to you alongside an identifier which can be in EFO or MONDO format. You are expected to select the option that best fit the description of the disease condition by copying the EFO or MONDO identifier and providing it in that input field. > > I hope I’ve been able to help.

Scholastica Urua (00:41:24) (in thread): > @Adenike Oladimeji-Kasumuthe next step is to record your first contribution on the outreachy site. Then go ahead with the second contribution.

Samreen Aftab (00:42:35) (in thread): > Thank you@Desire Oluwarotimithat helps.

Bolanle Wahab (00:43:55) (in thread): > @Samreen Aftabyou can also check out this article as a guidehttps://chiomaonyido.wordpress.com/2024/01/03/bugsigdb-ing-chronicles-1/comment-page-1/#comments - Attachment (…tales (and tips) from a bioCurious opensource bébé…): BugSigDB-ing Chronicles 1- A 4-Step Contribution Guide > The BugSigDB-ing toolkit are the tools and techniques used in BugSigDB-ing, and they include (but not limited to) the ontology and taxonomy browsers, as well as the special rules that curators/revi…

Bolanle Wahab (00:44:43) (in thread): > You’rewelcome@Olajumoke AdeoyoFeel free to ask if you need any assistance.

Samreen Aftab (00:45:28) (in thread): > Yes@Bolanle WahabI have already checked it out. It’s very helpful :)

Bolanle Wahab (00:48:34): > Hi everyone, how would you know when a paper has been assigned to you?

Desire Oluwarotimi (00:49:41) (in thread): > Hi@Bolanle WahabThe mentors will attach an assign tag and you should see your name on the right hand side as an assignee when using a desktop view.

Amanda Adoyi (00:49:44) (in thread): > You would see on github that it has, with your image next to the paper to curate on the list.

Bolanle Wahab (00:52:11) (in thread): > Thank you

Adedoja Isaac (01:03:55): > Hello everyone, please how do we record the first contribution on the outreachy website? Which link to put

Bolanle Wahab (01:09:12) (in thread): > @Adedoja Isaacyou can click this link to record your contributionhttps://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/add/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Scholastica Urua (01:10:47) (in thread): > @Bolanle Wahabhope you’ve first requested to for the paper you are interested in to be assigned to you

Bolanle Wahab (01:11:42) (in thread): > And the url you see on your address bar after completing the first task is the linkyou’duse.

Scholastica Urua (01:12:18) (in thread): > @Adedoja Isaacthe link of the form you fill is what you should add to the contribution URL.

Bolanle Wahab (01:12:27) (in thread): > Yes I have, thanks

Adedoja Isaac (01:16:09) (in thread): > Okay, Thank you very much.@Bolanle Wahab@Scholastica Urua

Chioma Onyido (01:19:46) (in thread): > Good morning!:sunny:All pending requests for second contribution has been attended to. > If you’re yet to be assigned a paper that you’ve indicated interest in, kindly call our attention to it. > Well done!:raised_hands:

Adenike Oladimeji-Kasumu (01:35:03) (in thread): > Thank you. But, I couldn’t find how to record my first contribution. > Also, I’ve been assigned a paper to curate but how do I know the Study design of my paper? I couldn’t find it on my paper.

Roderick Momin (01:38:11) (in thread): > Hello Chioma Onyido, I have made a comment indicating interest on Issue#89 on GitHub.

Bolanle Wahab (01:43:30) (in thread): > @Chioma OnyidoI indicated interest on issue#121.

Aleru Divine (01:43:39) (in thread): > Hi@Blessing Ene Anyebe, welcome:hugging_face:

Aleru Divine (01:44:13) (in thread): > Hi@Chioma Agu, welcome:hugging_face:

Chioma Onyido (01:44:42) (in thread): > Assigned!

Aleru Divine (01:44:58) (in thread): > Hi@Olajumoke Adeoyo, welcome:hugging_face:

Rahila-me (01:47:34) (in thread): > @Anshuman Moharanaclick the link paper to curate, it will take you to github link, go through the issue then choose the one without assigned label and request for it

Nana (01:53:16) (in thread): > @Anshuman Moharanacheck on paper to curate on this link, it has answers to your question: Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started:https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @lwaldron @Chloe Mirzayi@Esther Afuape@Chioma Onyido@Peace Sandy@svetlana_up - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Scholastica Urua (01:54:21) (in thread): > Steps for recording your first contribution; > 1. Go to the outreachy website > 2. Click on the ‘Microbiome Study Curation’ > 3. Click on ‘Record Contributions and Apply to This Project’ > Hope this helps - File (JPEG): Record contribution.JPG

Nana (01:57:47) (in thread): > Noted

Scholastica Urua (01:58:12) (in thread): > @Adenike Oladimeji-KasumuYou can identify your study design by going tohttps://bugsigdb.org/Curation_Policy. Check under ‘Study Design’, you’ll find specified criteria for each design. Then compare it with your paper. - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Victoria (Burah) Poromon (02:00:55): > Good morning everyone > Hello mentors, I have a question regarding the study I am curating. > > I’m curating a study that was done in 2014, and some of the names of the bacteria in this study are now outdated according to NCBI. > > Is it advisable to input the old names on the database to match what is in the study, or to use the new names instead?

Mildred Anashie (02:02:06) (in thread): > Hi Victoria > > When you paste the names on NCBI do you find the taxas?

Victoria (Burah) Poromon (02:08:39) (in thread): > The old names or the new names?@Mildred Anashie

Mildred Anashie (02:09:29) (in thread): > The names found on your article

Desire Oluwarotimi (02:10:06) (in thread): > Hi@Victoria (Burah) PoromonI have encountered something similar. I also noticed that there are synonyms provided in those cases but I do not know if we can use the synonyms instead. > > The mentors will be able to help us out here.

Mildred Anashie (02:13:19) (in thread): > Or is it stated in the article that those names are the old names > > I think when you paste on NCBI and it pops up as a synonym, most times heterotypic synonyms (or something like that) it’s allowed to record the synonym instead > Provided you are sureit’sthe synonym@Chioma Onyido@Svetlana Ugarcina Perovic@Esther Afuape:thinking_face:

Anshuman Moharana (02:15:31) (in thread): > Thanks all for your response

Desire Oluwarotimi (02:15:58) (in thread): > I agree with@Mildred AnashieBut I don’t think the articles specify that they are old names.

Ima-obong (Aimah) (02:18:05): > For the first/mini curation task, going through the study pdf doc on the composition of the gut microbiome in breast cancer patients really gave me a surreal and nostalgic feel:smiling_face_with_3_hearts:. > With a degree in microbiology, this doc took me right back to my classes in Uni. I am getting to really love and appreciate what this project represents. > Thanks to everyone on the team who helped me find my feet here, you are doing absolutely amazing. unto the next:heart_eyes:

Desire Oluwarotimi (02:18:47) (in thread): > Weldone@Ima-obong (Aimah)

Ima-obong (Aimah) (02:19:40) (in thread): > Thank you@Desire Oluwarotimi

Chioma Onyido (02:22:49) (in thread): > Right Desire and Mildred. > The synonyms have been generally fine.@Victoria (Burah) Poromon

Victoria (Burah) Poromon (02:27:47) (in thread): > @Desire Oluwarotimiyeah, the articles do not specify because theyhaven’tbeen updated in recent times

Ima-obong (Aimah) (02:27:49): > Please for the second contribution, Can a paper be assigned to two individuals? or more like can you request an already assigned paper?

Victoria (Burah) Poromon (02:28:48) (in thread): > Thank you@Chioma Onyido

Desire Oluwarotimi (02:29:45) (in thread): > No, it can’t be assigned to two persons. > > A paper has to be peculiar to a single contributor. At least for now.

Joan C. Chukwuemeka (02:29:50): > @Ima-obong (Aimah)Two individuals are not assigned the same paper to avoid duplicate data on the BugsigDB database. You need to request for an unassigned/unrequested paper. If none is available, just let the mentors know

Ima-obong (Aimah) (02:30:36) (in thread): > thank you

Ima-obong (Aimah) (02:30:58): > Thank you Joan

Mildred Anashie (02:31:11) (in thread): > Well done@Ima-obong (Aimah)It felt the same way for me:blush:

Ima-obong (Aimah) (02:33:35) (in thread): > Thanks Mildred, good to know you enjoyed working on it:100:

Rahila-me (02:33:47) (in thread): > @Ima-obong (Aimah)no, you will have to request for anyone without the assigned tag

Ima-obong (Aimah) (02:34:19) (in thread): > Thank you Liza

Rahila-me (02:34:44) (in thread): > urw

EBERE ADEKOGBE (02:46:37) (in thread): > I felt same too

Ima-obong (Aimah) (02:50:04): > Hello@Chioma Onyido, I made a comment indicating interest on Issue#160 on GitHub. Thanks alot

Ima-obong (Aimah) (02:50:51) (in thread): > Well done Ebere

Blessing Ene Anyebe (02:51:20) (in thread): > Thank you so much guys:partying_face::partying_face:

Chioma Onyido (02:54:08) (in thread): > Hi@Ima-obong (Aimah)please look out specifically for papers labeled ‘OutreachyMay2024’ ‘second contribution’

Ima-obong (Aimah) (02:55:01) (in thread): > oh, okay thank you

Nana (02:59:59) (in thread): > Urw

Adenike Oladimeji-Kasumu (03:00:51) (in thread): > @Scholastica Uruayou’re amazing. Thank you

Michael Adekanye (03:01:26): > Hi, I just got into the slack channel. Please where can I start from in terms of contributing. Thank you

Mildred Anashie (03:02:02) (in thread): > Welcome@Michael Adekanye

Aleru Divine (03:02:16) (in thread): > Hi Michael, you can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Desire Oluwarotimi (03:02:31) (in thread): > Welcome@Michael Adekanye

Aleru Divine (03:02:39) (in thread): > I found this super helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Michael Adekanye (03:03:06) (in thread): > Thank you guys. I’ll start from here.

Ima-obong (Aimah) (03:03:22) (in thread): > Welcome Michael

Ima-obong (Aimah) (03:05:29) (in thread): > Please@Chioma Onyido, what about papers previously assigned to past interns but carries the may 2024 label, can i request for such?

Scholastica Urua (03:06:12) (in thread): > Hello@Michael Adekanyewelcome. Please go through the links@Aleru Divinedropped. > I’m happy to help wherever I can.

Chioma Onyido (03:08:04) (in thread): > If it carries the May 2024 label, that means itwasn’tcurated in the database and therefore is available. > As long asyou’resureit’spast interns, Yes you can.:thumbsup:

Mildred Anashie (03:09:54): > @Benedicta ImeldaTake a look at this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Ima-obong (Aimah) (03:10:50) (in thread): > Thanks alot. I have commented a request on it.

Benedicta Imelda (03:10:54): > Thank you

Ufomba Justina (03:10:57): > Hi good morning everyonemy name is Ufomba Justina just got into the group how can i get started please

Mildred Anashie (03:10:57): > @Benedicta Imelda - Attachment: Attachment > Hello everyone > Just in case anyone is confused on where to go to start the first contribution > > This is the link to follow for the first contribution > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > I’ve been able to finish mine and I’m willing to help in case of any questions

Mildred Anashie (03:11:37) (in thread): > Welcome@Ufomba JustinaTake a look at this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (03:11:44) (in thread): > Hi@Ufomba Justina, welcome:hugging_face:

Aleru Divine (03:12:02) (in thread): > I found this super helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Ufomba Justina (03:14:08) (in thread): > Thank you all for your quick response.

Scholastica Urua (03:19:25) (in thread): > Welcome@Ufomba Justina

Latifat (03:20:45) (in thread): > @Idiat AlliThank you

Rahila-me (03:21:14) (in thread): > Welcome@Michael Adekanye, go through the pined messages the one pinned by@Svetlana Ugarcina Perovic

Nana (03:22:02) (in thread): > Good morning and welcome@Ufomba Justina..check the pinned messages on slack

Victoria (Burah) Poromon (03:31:19): > Hello everyone, > The study I’m curating used a statistical test that is not in the database. > Please what is the best way to go about this? > > Do I leave that column blank or go ahead and type out the name of the test that was used?

Desire Oluwarotimi (03:32:35) (in thread): > What was the statistical test used?

Scholastica Urua (03:33:10) (in thread): > Hello@Victoria (Burah) Poromon, what is the name of the test? Or better still, can you provide a snapshot or link to the curated paper?

Victoria (Burah) Poromon (03:34:12) (in thread): > The name of the test is Hierarchical clustering

Bolanle Wahab (03:35:47) (in thread): > @Victoria (Burah) Poromonyou should type out the name of the test if it’s not in the database

Desire Oluwarotimi (03:36:09) (in thread): > :thinking_face:@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy

Scholastica Urua (03:37:52) (in thread): > Hierarchical clustering is not typically considered a statistical test. Hope the mentors will shed more light on this.

Bolanle Wahab (03:40:42) (in thread): > @Scholastica Uruatrue,if the studydoesn’tspecify the test,we’resupposed to leave it blank right?

Victoria (Burah) Poromon (03:42:12) (in thread): > @Scholastica Urua, yeah I thought so too and I had to start researching on it. But according to the article, this is what their result was based on.There’salso another one not on the database, “unweighted unifrac metric”. They also have results that are gotten based on this.It’sa bit confusing

Bolarinwa Abosede Julianah (03:43:34) (in thread): > Welcome@Chioma Agu

Mildred Anashie (03:43:45) (in thread): > Can you share a link to the article@Victoria (Burah) Poromon

Scholastica Urua (03:43:51) (in thread): > Yes@Bolanle Wahableave blank if the study doesn’t specify a statistical test. - File (JPEG): ST.JPG

Peace Sandy (03:44:08) (in thread): > @Victoria (Burah) Poromonis that the only statistical test mentioned

Victoria (Burah) Poromon (03:45:56) (in thread): > @Mildred Anashiesurehttps://journals.lww.com/jpgn/fulltext/2014/11000/efficacy_of_fecal_microbiota_transplantation_in_2.6.aspx# - Attachment (LWW): Efficacy of Fecal Microbiota Transplantation in 2 Children… : Journal of Pediatric Gastroenterology and Nutrition > rs old) who failed available therapeutics for RCDI, but responded remarkably well to FMT. Besides resolution of clinical features of C difficile infection (CDI), FMT administration led to marked improvement in their growth, along with increased microbiota diversity, especially proportion of Bacteroides. Our 2 cases illustrate the efficacy of FMT in children with RCDI and its positive effect on their growth and gut microbiota….

Victoria (Burah) Poromon (03:48:40) (in thread): > @Peace Sandyyes, only those 2 tests were mentioned.

Mildred Anashie (03:52:37) (in thread): > @Victoria (Burah) Poromonplease the name of the articleHaven’tbeen able to open this link

Victoria (Burah) Poromon (03:53:29) (in thread): > @Mildred AnashieEfficacy of Fecal Microbiota Transplantation in 2 Children With RecurrentClostridium difficileInfection and Its Impact on Their Growth and Gut Microbiome

Ibukun Hassan (03:54:10) (in thread): > Goodmorning Everyone > My name is Ibukun HassanI’mso excited to be here:tada:I hope to learn and contribute!

Aleru Divine (03:56:46) (in thread): > Hi@Victoria (Burah) Poromon, the study doesn’t specify a statistical test, I think it should be left blank according to the curation policy.

Victoria (Burah) Poromon (03:57:34) (in thread): > Alright, thank you.

Aleru Divine (03:58:55): > Hi@Ibukun Hassan, Welcome:hugging_face:You can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (03:59:26) (in thread): > I also found this helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Joan C. Chukwuemeka (04:01:05): > Good morning@Svetlana Ugarcina Perovic, Please I’ve made a request for Article on Issue #115 to be assigned to me for curation. Thanks.:blush:Good morning all:hugging_face:

Scholastica Urua (04:04:56) (in thread): > Welcome@Ibukun Hassan

Amarachi Lewachi (04:05:37): > Hi. Outreachy applicant here. I want to know how many times I can use the record my contribution option on the outreachy website.@Chioma Onyido@Svetlana Ugarcina Perovic

Desire Oluwarotimi (04:06:14) (in thread): > Hi@Amarachi LewachiAs many times as you make a contribution.

Scholastica Urua (04:06:50) (in thread): > Hi@Amarachi LewachiYou use it as many times as possible. Depending on how many contributions you make.

Aleru Divine (04:07:21) (in thread): > Good morning@Joan C. Chukwuemeka

Samreen Aftab (04:10:23): > is the NCBI taxonomy ID supposed to be 4-6 digits only? Since I found a taxa with a 3 digit ID, so I’m not sure if that is the ID I’m supposed to fill in - File (PNG): image.png

Roderick Momin (04:12:40): > For the second contribution from my understanding, afterAdding a Studyin BugSigDB, it needs to bereviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study, correct?

Mildred Anashie (04:13:18) (in thread): > Didn’tfind anything too@Victoria (Burah) Poromon

Bolanle Wahab (04:13:25) (in thread): > @Samreen Aftabif you found a 3 digit ID, it’s unlikely that it’s an NCBI taxonomy ID

Aleru Divine (04:14:22) (in thread): > Please confirm if it the same as seen in the photo below? - File (JPEG): IMG_7710

Scholastica Urua (04:14:43) (in thread): > It doesn’t need to be reviewed before moving forward. You can go ahead to add an experiment and signature as well.

Aleru Divine (04:15:15) (in thread): > You can go ahead and add an experiment and complete your curation.

Peace Sandy (04:15:18) (in thread): > You don’t have to wait for mentors to approve your result, click on the add experiment button above, to start a new experiment

Samreen Aftab (04:15:24) (in thread): > yes - File (PNG): image.png

Roderick Momin (04:15:47) (in thread): > I am receiving the following message when trying to do so. > > You do not have permission to edit this page, for the following reason: > The action you have requested is limited to users in the group:Users.

Aleru Divine (04:16:07) (in thread): > Then it is correct.:white_check_mark:

Peace Sandy (04:16:10) (in thread): > Good Morning

Samreen Aftab (04:16:24) (in thread): > Okay, thank you !

Roderick Momin (04:17:10) (in thread): > Never-mind, I’ve been logged out for some reason as I checked thank you for the responses.

Desire Oluwarotimi (04:17:40) (in thread): > Hi@Samreen AftabYou are right, there are some taxa ID with just 3 digits but while attempting mine, I opted for the ones between 4 and 6 so that I could tally with the specification of that question.

Victoria (Burah) Poromon (04:18:18) (in thread): > @Mildred AnashieOhit’salright, I think this is already sorted out. Thank you:yellow_heart:

Aleru Divine (04:18:50) (in thread): > :sweat_smile:it happened to me before.

Samreen Aftab (04:20:38) (in thread): > Okay thank you@Desire OluwarotimiI’ll keep that in mind

Zaynab Aderonke Ogunnubi (04:27:46): > Hi, everyone. > > Please, when recording the first contribution, what end date do we select or should we leave it open?

Mildred Anashie (04:28:22) (in thread): > The date you finished it

Aleru Divine (04:29:34) (in thread): > Hi@Zaynab Aderonke OgunnubiI think the day you submitted.

Zaynab Aderonke Ogunnubi (04:30:21) (in thread): > Thanks. That’s what I wanted to confirm.

Svetlana Ugarcina Perovic (04:38:20): > Good morning:tulip:I’m happy to seeyour supportive communication and fruitful discussion. As@Chioma Onyidohighlighted herehttps://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/Communication is Key! for successful open science/open source projects and your growth as well. > > Keep up the good work!

Aleru Divine (04:38:53) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Mildred Anashie (04:39:02) (in thread): > Thank you@Svetlana Ugarcina PerovicGood morning:sunny:

Desire Oluwarotimi (04:39:34) (in thread): > Thank you mentor@Svetlana Ugarcina Perovic:saluting_face:

Bolanle Wahab (04:40:18) (in thread): > Thank you.@Svetlana Ugarcina Perovic

Nana (04:45:44) (in thread): > Was a nice read

Zaynab Aderonke Ogunnubi (04:46:26): > Good morning@Svetlana Ugarcina Perovic. Please, I’ve made a request for the article on Issue #113 to be assigned to me for curation.

Peace Sandy (04:50:50) (in thread): > Done:white_check_mark:

Zaynab Aderonke Ogunnubi (04:51:32) (in thread): > Thank you

Esther Afuape (04:54:03) (in thread): > Hi@Samreen AftabThe length of the tax IDdoesn’tmatter. What matters is entering the correct and specific taxon

Amarachi Lewachi (04:58:13): > For the first task glanced through the article, read through my questions before heading to read the article properly to properly understand what to look out for. Remember to note the highlighted bits.

Sneha Singh (04:59:55) (in thread): > Really helpful, thank you:raised_hands:@Svetlana Ugarcina Perovic

Scholastica Urua (05:02:35) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (05:04:45) (in thread): > Really thoughtful:clap:

Barakat Akinsiku (05:06:21): > Hi everyone, good morning. Please how do we select papers to curate for our second contribution?

Svetlana Ugarcina Perovic (05:07:43) (in thread): > @Victoria (Burah) Poromonyes, you are right, this paper does not report statistical analysis and does not provide curatable results. Your effort will be recored. Please select another paper.

Peace Sandy (05:08:43) (in thread): > Hi@Barakat Akinsikuhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (05:10:16) (in thread): > Hi@Barakat AkinsikuCheck out this pageon GitHub.https://github.com/waldronlab/BugSigDBcuration/issues/94See the Second Contribution Task heading for guidelines. - File (PNG): IMG_7729

Scholastica Urua (05:10:53) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709636941179439?thread_ts=1709636862.134639&cid=C04RATV9VCY - Attachment: Attachment > @Ruth Bamgbose you can go ahead with the second contribution. > > As mentioned in the onboarding material for the second task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Also, remember to record your first contribution on the outreachy site.

Victoria (Burah) Poromon (05:11:45) (in thread): > @Svetlana Ugarcina Perovicoh, thank you. I’ll go to the GitHub page now to look for another paper.

Barakat Akinsiku (05:11:50) (in thread): > Thank you guys

Bolanle Wahab (05:12:34) (in thread): > @Barakat Akinsikuyou have to request for an account onBugSigDB.orgthen select an article from herehttps://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22And tag any of our mentors to indicate any one that interests you so they can assign it to you.

Barakat Akinsiku (05:13:42) (in thread): > Yes I have created the account@Bolanle Wahab. So I tag them here on slack?

Fausat Olasubomi Abiola (05:14:07): > I think we have to go GitHub issues tagged“paper to curate”and post a response to the issue/article we want to work on with our name and we will mark it as claimed but where I am confused is that some articles dated 2023, can someone work on those too@Svetlana Ugarcina Perovic?

Mildred Anashie (05:14:12) (in thread): > @Barakat Akinsikuyou tag them on Github > > Under the issue you intend to claim, just leave a comment

Aleru Divine (05:15:12) (in thread): > @Fausat Olasubomi AbiolaI don’t think it matters, as long as they’re listed and available, you can claim.@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:15:31) (in thread): > Tags that you follow are: > paper to curate > outreachy may2024 > second contribution

Fausat Olasubomi Abiola (05:15:34) (in thread): > @Zaynab Aderonke OgunnubiHow did you make a request,please?

Bolanle Wahab (05:16:07) (in thread): > Tag them on GitHub under the article you are interested in,I’dadvice you add your full name when tagging them

Barakat Akinsiku (05:16:40) (in thread): > Yes I’ve seen it, thanks@Mildred Anashie,@Bolanle Wahab

Fausat Olasubomi Abiola (05:16:47) (in thread): > @Aleru DivineThank you

Zaynab Aderonke Ogunnubi (05:17:09) (in thread): > Via GitHub:https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22@Fausat Olasubomi Abiola

Aleru Divine (05:17:18) (in thread): > You’rewelcome@Fausat Olasubomi Abiola

Mildred Anashie (05:17:25) (in thread): > You are welcome > > Ensure to comment on an article thathasn’tbeen assigned to anyone yet

Zaynab Aderonke Ogunnubi (05:18:13) (in thread): > Look for an article that has the “OutreachyMay2024” tag and has not been assigned to anyone. Once you find the one you want, drop a comment requesting it to be assigned to you.

Adegboye Rukayat (05:18:50): > Hello everyone, my name is Adegboye Rukayat. I am happy to be here as an Outreachy applicant. I look forward to making a phenomenal contribution.

Mildred Anashie (05:19:11) (in thread): > Welcome@Adegboye RukayatTake a look at this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Fausat Olasubomi Abiola (05:19:46) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (05:20:22) (in thread): > Hi@Adegboye Rukayatwelcome:hugging_face:I also found this helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Bolanle Wahab (05:20:40) (in thread): > Hello@Adegboye Rukayatwelcome. > Feel free to chat if you need any assistance:blush::heart:

Desire Oluwarotimi (05:20:58) (in thread): > Welcome@Adegboye Rukayat

Eniola Adebayo (05:22:00): > Good morning all:smiley:I hope our contributions are going great I came across some hurdles while curating and I was able to solve some so I thought to share. > > These links from a discussion on data transformation/ statistical test and study designs were super usefulhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697727781091049 - Attachment: Attachment > Wheww! What an interesting discussion today! :grin: > If you weren’t able to attend the meeting today, Here’s a summary of what I gathered from the office hour today: > -“Hallmarks of Study Designs”- by @UBNSEMS3S > > 1. Randomized controlled trial (RCT): participants are randomly divided into groups. The treatment group receives the intervention while control group don’t. Here, researchers randomly assign the conditions to people. > Classical example: > 50 people receive the real vaccine, 50 receive the placebo. Other examples: diet, exercise, etc. > > 2. Laboratory experiment: done using animal models, such as rats, pigs, mice, etc. > You’re not randomizing here because they’re all in the same condition. > > 3. Meta-analysis: this is a study design where researchers combine results from different studies. Meta analysis also means Pooling of results. > > 4. Prospective cohort studies: this is a study where researchers recruit a group of people based on a common characteristic (e.g. based on residence) and follow them up over time. > > Classical example #1: all patients recruited in a study who showed signs of depression in the month of October. > Classical example #2: 100 people develop some diseases of interest (cases) and some people don’t (control) > > 5. Longitudinal observational study: time series studies. There is no intervention by the researcher in this kind of study. > Data is collected at multiple time points. > > Classical example: observing COVID participants before and after the event. > > 6. Case control: when you recruit cases ( people with a disease of interest) and controls (people without) similar on some characteristics. You would sometimes see matched on: age, bmi, sex, etc. > > Classical example: Healthy control group (control) and JIA group (case) > > 7. Cross-sectional observational: Contrasting 2 geographical areas or based on some socio-demographical characteristic (for example), usually at a single time point. > > Classical example: community studies where they took 100 people from a neighborhood and contrasted with people from another neighborhood. > > Apologies if I left anything out, the recording will be posted soon. :pray::skin-tone-5:

Mildred Anashie (05:22:40) (in thread): > Thank you for sharing@Eniola Adebayo

Aleru Divine (05:23:05) (in thread): > Thanks so much for sharing@Eniola Adebayo

Bolanle Wahab (05:24:20) (in thread): > Thank you:heart:@Eniola Adebayo

Siva (05:33:25): > Hello<!channel>My name is Siva, and I’m thrilled to be here as an Outreachy applicant. I’m genuinely excited about the opportunity to contribute to the project and make a meaningful impact.

Desire Oluwarotimi (05:34:12) (in thread): > Welcome@SivaTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (05:34:51) (in thread): > Welcome@SivaNice to e-meet you

Scholastica Urua (05:34:52) (in thread): > Welcome@Siva

Adedoja Isaac (05:35:04) (in thread): > Welcome Siva

Scholastica Urua (05:35:21) (in thread): > This is a list of some of the FAQs and answers that may be helpful.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349

Blessing Laweh (05:35:29) (in thread): > Welcome@Siva

Shedrack Sunday (05:36:27): > Hello great minds!! My name is Shedrack Bamidele Sunday, I’m excited to be part of this contribution community. I look forward to enhancing the open science project at hand:clap:

Scholastica Urua (05:36:31) (in thread): > Welcome@Adegboye Rukayat

Mildred Anashie (05:36:45) (in thread): > Welcome@Shedrack Sunday

Abiola Salako (05:36:52): > Welcome @ Siva read this link as shared by@Eniola Adebayoto know what to dohttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709720520707859?thread_ts=1709720520.707859&cid=C04RATV9VCYVCY. - Attachment: Attachment > Good morning all:smiley: > > I hope our contributions are going great I came across some hurdles while curating and I was able to solve some so I thought to share. > > These links from a discussion on data transformation/ statistical test and study designs were super useful! > https://community-bioc.slack.com/archives/C04RATV9VCY/p1699808143495129?thread_ts=1699704087.950319&channel=C04RATV9VCY&message_ts=1699808143.495129 > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1697727781091049

Desire Oluwarotimi (05:37:00) (in thread): > Welcome@Shedrack SundayTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Blessing Laweh (05:37:08) (in thread): > Thank you for sharing@Eniola Adebayo:pray:

Leenaa Al-Amin (05:37:13) (in thread): > Welcome@Shedrack Sunday

Scholastica Urua (05:37:18) (in thread): > Welcome@Shedrack SundayThis is a list of some of the FAQs and answers that may be helpful.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349

Rodney Ighalo (05:37:40): > Hello, I’mRodney. I trulycan’twait to contribute to the project.Ps:I’dappreciate if I can get a guide to where the see the project and be part of it. > > Thank youu.

Nana (05:37:54) (in thread): > Welcome

Desire Oluwarotimi (05:38:07) (in thread): > Welcome@Rodney IghaloTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (05:38:13) (in thread): > Welcome@Rodney Ighalo

Scholastica Urua (05:38:19) (in thread): > This is a list of some of the FAQs and answers that may be helpful.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349

Shedrack Sunday (05:38:23) (in thread): > Thank you all:pray:

Nana (05:38:25) (in thread): > Welcome to the community

Mildred Anashie (05:38:46) (in thread): > Welcome@Rodney Ighalo

Bolanle Wahab (05:38:49) (in thread): > Hi,Welcome@Siva

Aleru Divine (05:38:51) (in thread): > Hi@Shedrack Sunday, welcome:hugging_face:

Rodney Ighalo (05:39:10) (in thread): > Thank you

Aleru Divine (05:39:17) (in thread): > Hi@Rodney Ighalo, welcome:hugging_face:

Bolanle Wahab (05:39:17) (in thread): > Hi,Welcome@Shedrack Sunday

Rodney Ighalo (05:40:58) (in thread): > Thank youu

Abiola Salako (05:41:08): > Welcome@Rodney IghaloCHECK HERE as shared by our mentor@Svetlana Ugarcina PerovicTO KNOW WHAT Nexthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699?thread_ts=1709568003.471699&cid=C04RATV9VCY - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Shedrack Sunday (05:42:35) (in thread): > Is there any difficulty you guys faced that you’ll like to share to make it seamless? I’ll appreciate it.

Rodney Ighalo (05:43:21): > @Abiola Salakothe link is redirecting me to you.I can’taccess the next step

Fausat Olasubomi Abiola (05:43:58) (in thread): > @Scholastica UruaI have requested an account fromBugSigDB.org. While I wait for approval can I go ahead and claim an article? Also, Is the account I requested from BugSigDB different from the Github account I need to create to be able to comment on the Issue I want to claim? Thanks

Shedrack Sunday (05:44:21) (in thread): > Welcome onboard. The link has been shared. Just got in too:smile:, but I’m available to navigate the space with you if you get stuck

Bolarinwa Abosede Julianah (05:44:29) (in thread): > Welcome@Rodney Ighalo

Mildred Anashie (05:45:09) (in thread): > The curation policy should guide you and make it easy for you > > Also you could always drop questions here the mentors will respond to you and everyone else can make an inputhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Scholastica Urua (05:45:21) (in thread): > Yes, you can go ahead to request an article while you wait for your account to be approved. > > And the account is different from your GitHub account. You need to create an account with GitHub if you don’t already have one to comment on the article.

Abiola Salako (05:45:25): > Okay@Rodney Ighalocheck thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699?thread_ts=1709568003.471699&cid=C04RATV9VCY - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Rodney Ighalo (05:45:26) (in thread): > Thank you@Shedrack Sunday@Bolarinwa Abosede Julianah

Fausat Olasubomi Abiola (05:45:39) (in thread): > @Scholastica UruaThanks

Sandra Dindi (05:46:19) (in thread): > Thanks for asking. I was looking for this information.

Aleru Divine (05:46:59) (in thread): > @Shedrack SundayJust take your time and go through the onboarding materials. > > If you have any specific questions you can send them here. I am more than happy to help and so are the other fellows.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Abiola Salako (05:47:27) (in thread): > Thank you@Svetlana Ugarcina PerovicI look forward to a more collaborative experience.

Rodney Ighalo (05:47:39): > @Abiola SalakoThank you

Abiola Salako (05:48:11): > You’re welcome@Rodney Ighalo.

Shedrack Sunday (05:48:32) (in thread): > Alright. Thank you@Mildred Anashieand@Aleru Divine. I’ll do well to reach out if I face any hurdle. I appreciate:pray:

Aleru Divine (05:57:20) (in thread): > You’rewelcome@Shedrack Sunday

Rahila-me (06:01:24): > Welcome@Rodney Ighalohope you are done with the first curation?

Michael Adekanye (06:02:48) (in thread): > The task in the first contribution is to fill in the form after going thru the annotated pdf and see how to do extraction,right?

Collins Carshy (06:03:47): > Hello team, I am so excited to be here to contribute to the project. I can’t wait to collaborate with you all by exchanging knowledge and sharing ideas.@Abiola Salakothank you for sending me the channel link. That was so helpful

Abiola Salako (06:05:04) (in thread): > @Collins CarshyYOU’RE WELCOME

Mildred Anashie (06:05:51): > @Faith Ifeoluwa AlexanderThis is the link for your first contributionhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Joan C. Chukwuemeka (06:06:46) (in thread): > Good morning@Aleru Divine

Faith Ifeoluwa Alexander (06:06:51): > Okay. Thank you@Mildred Anashie. I will check it out.

Mildred Anashie (06:07:14) (in thread): > Since you have watched the videos follow the steps and answer the questions > > Also this link will guide you when you start making your second contributionhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Scholastica Urua (06:07:41) (in thread): > Welcome@Collins CarshyKindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Faith Ifeoluwa Alexander (06:07:55) (in thread): > I didn’t understand the videos.

Mildred Anashie (06:09:24) (in thread): > I think you should just start with the first contribution > > Also you can ask specific questions > Willing to help

Rahila-me (06:10:17) (in thread): > @Michael Adekanyeyes, it will guide you on how to answer the questions

Faith Ifeoluwa Alexander (06:11:22) (in thread): > Okay. Thank you. Let me go through the document first then.

Aleru Divine (06:11:27) (in thread): > Hi@Collins Carshy, welcome:hugging_face:Also check this out. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Aleru Divine (06:14:51): > Hi@Rodney Ighalo, how is it going?

Adegboye Rukayat (06:15:41) (in thread): > Thank you all

Rodney Ighalo (06:15:44): > Stillshaky but I’m sure I’ll find my way around.@Aleru Divine

Aleru Divine (06:16:38) (in thread): > Alright@Rodney Ighalo:+1:Happy to help if you feel stuck or something:hugging_face:

Faith Ifeoluwa Alexander (06:16:46) (in thread): > Pls, the document is a lot. Where do I start from.?

Collins Carshy (06:17:44) (in thread): > @Scholastica Uruaand@Aleru Divinethank you guys. I’m diving into the task and in case of anything I will not hesitate to reach out for guidance

Mildred Anashie (06:18:57) (in thread): > Start with the first contributionhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Aleru Divine (06:19:01) (in thread): > Alright@Collins Carshy.I’llbe happy to help in anyway I can:hugging_face:

Faith Ifeoluwa Alexander (06:19:50) (in thread): > It’s like you don’t understand what I am trying to say. Am I meant to read through the whole document?

Scholastica Urua (06:19:51) (in thread): > Good luck with your curation@Collins Carshy

Mildred Anashie (06:19:58) (in thread): > I can also advise you go through the onboarding materials againI’msureyou’llunderstand

Faith Ifeoluwa Alexander (06:20:24) (in thread): > I did and I was confused that was why I asked for help.

Mildred Anashie (06:21:02) (in thread): > This link has the onboarding materialshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (06:21:21) (in thread): > After going through the videosYou’dunderstand the project

Mildred Anashie (06:22:08) (in thread): > Then you start with the first contribution > > And yesit’sadvisable to go through the whole document (if you mean the curation policy)

Faith Ifeoluwa Alexander (06:22:33) (in thread): > I have gone through the videos and it sounded like Greek to me & that was why I asked for help.

Faith Ifeoluwa Alexander (06:23:37) (in thread): > I am just frustrated & we have not even started work yet.

Aleru Divine (06:23:38) (in thread): > Hi@Siva, welcome:hugging_face:If you have any questions regarding your first contribution or anything in general,do not hesitate to ask.I’mdone with my first contribution and will be happy to help in anyway I can:hugging_face:

Mildred Anashie (06:24:22) (in thread): > Happy to get on a huddle with you in the next one hour > > If that’s okay

Faith Ifeoluwa Alexander (06:25:06) (in thread): > Next one hour, you mean from now?

Leenaa Al-Amin (06:26:22): > hello! for my second contribution, after adding the study, its indicated that it needs review. Do I go ahead to add a new experiment regardless? - File (PNG): Screenshot (19).png

Mildred Anashie (06:26:46) (in thread): > Please go on to add an experiment

Bolanle Wahab (06:27:06) (in thread): > Yes

Aleru Divine (06:27:11) (in thread): > @Leenaa Al-AminYes please, go ahead and add a new experiment and complete your curation.

Leenaa Al-Amin (06:27:28) (in thread): > Alright, just wanted to be sure. Thank you!

Bolanle Wahab (06:27:29) (in thread): > You’rewelcome:heart:

Mildred Anashie (06:28:37) (in thread): > Yes

Scholastica Urua (06:30:09) (in thread): > @Leenaa Al-AminYes, you should. > > However, I noticed from this picture that your citation is not complete. I experienced it at first but I edited it by also adding the PMID and the rest were automatically populated.

Nwajei Edgar (06:33:44) (in thread): > Welcome

Leenaa Al-Amin (06:46:15) (in thread): > I’ve done as you suggested and it has been populated. Thank you so much!@Scholastica Urua

Scholastica Urua (06:47:49) (in thread): > You’re welcome@Leenaa Al-Amin

Amarachi Lewachi (06:55:39): > Hi everyone. So after the first curation task using the form provided is there anything else to be done before proceeding to the second contribution?

Bolanle Wahab (06:57:16) (in thread): > @Amarachi Lewachiyou should Record your contribution on Outreachy before proceeding to the second contribution

Aleru Divine (06:58:15) (in thread): > @Amarachi LewachiNot really, but first; > > Record your first contribution. > > Request an account with bugsigdb > > Claim an article on GitHub > > Proceed to curate after it has been assigned to you.

Mildred Anashie (06:58:22) (in thread): > Record your first contribution > Then comment on a GitHub issue for an article to be assigned to you

Sandra Dindi (07:03:22) (in thread): > Where do I find the PMID@Scholastica Urua

Mildred Anashie (07:04:47) (in thread): > Paste your articles DOI on pubmed@Sandra Dindi

Sandra Dindi (07:05:51) (in thread): > Noted. Thanks@Mildred Anashie

Adedoja Isaac (07:07:57): > @Rodney IghaloHaving trouble with the initial tasks of this contribution phase? Here’s a little guide: > > 1. Identify Microbial Signatures: Look for findings of bacterial taxa that differed between one condition and another. >
> 2. Document Signatures: Record the species, genera, orders, and families of bacteria showing significant differences between conditions. > > 3. Follow Article Structure: Extract microbial signatures from relevant sections of the research article. > > 4. Specify Disease: Identify the disease being studied for accurate documentation. > > 5. Add the identified microbial signatures to BugSigDB for future reference and analysis and then attempt the task. > > This is how I was able to attempt mine.

Scholastica Urua (07:08:03) (in thread): > Just what Mildred said@Sandra Dindi. If you need anymore assistance I’ll be happy to provide wherever I can.

Aleru Divine (07:10:54) (in thread): > Nicelydone@Adedoja IsaacThank you so much for sharing:heart:

Blessing Ene Anyebe (07:15:05) (in thread): > Hi guys, when you say the link, you mean the link to the initial form question after it has been filled yes? > CC:@Adedoja Isaachttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc

Sandra Dindi (07:15:14) (in thread): > Thanks@Scholastica Urua@Mildred AnashieThis is the result I’m getting. - File (PNG): Screenshot 2024-03-06 151356.png

Mildred Anashie (07:15:57) (in thread): > Try pasting the name of the article

Scholastica Urua (07:16:34) (in thread): > Can you drop the link to your article?@Sandra Dindi

Tanya Dwivedi (07:16:43): > Hi Everyone, My name is Tanya, l am genuinely excited about this opportunity and look forward to making valuable contribution to this project , please I just joined how can I get started in terms of contributing ,Thank you

Samreen Aftab (07:17:06): > Hello everyone, can anyone guide me on how to record my contribution after I’m done with the first task?

Sandra Dindi (07:17:08) (in thread): > Here’s the link :https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01657-0 - Attachment (BioMed Central): PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation - Microbiome > Background The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples. Results The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes. Conclusions Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract

Scholastica Urua (07:17:11) (in thread): > Welcome@Tanya Dwivedi:hugging_face:Kindly view the issue on GitHub for instructions on how to get started > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Mildred Anashie (07:17:19) (in thread): > Yea > > We could check it for you

Sandra Dindi (07:17:33) (in thread): > Thank you

Desire Oluwarotimi (07:18:13) (in thread): > Welcome@Tanya Dwivedi

Blessing Ene Anyebe (07:18:16) (in thread): > Hello Tanya, check this article to get a soft landing:sweat_smile:https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well Blessing.:orange_heart: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Adedoja Isaac (07:18:26) (in thread): > Yes,@Blessing Ene AnyebeThis link

Blessing Ene Anyebe (07:18:43) (in thread): > Thank you

Mildred Anashie (07:19:06) (in thread): > 37805557@Sandra Dindithis is the PMID

Desire Oluwarotimi (07:19:11) (in thread): > This is going to be helpful. Weldone@Adedoja Isaac

Michael Adekanye (07:19:30) (in thread): > This will help Samreen.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349?thread_ts=1696436306.217349&cid=C04RATV9VCY - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Sandra Dindi (07:19:36) (in thread): > Thanks@Mildred Anashie

Adenike Oladimeji-Kasumu (07:19:45) (in thread): > In trying to record my first contribution, I do not know how to get the link to my contribution and how do I write the description?

Mildred Anashie (07:19:55) (in thread): > I used the name of the article to search instead

Adenike Oladimeji-Kasumu (07:19:55) (in thread): > Please help@Svetlana Ugarcina Perovic

Sandra Dindi (07:20:40) (in thread): > Ah! Noted. I’ll keep that in mind. Thank you@Mildred Anashie

Aleru Divine (07:21:52) (in thread): > @Sandra Dindiin case of next time, search your article on google or directly on NIH.Andyou’llsee the PMID and DOI. - File (JPEG): IMG_7731 - File (JPEG): IMG_7730

Scholastica Urua (07:22:03) (in thread): > Nice one@Mildred Anashie

Mildred Anashie (07:22:14) (in thread): > Welcome@Tanya Dwivedi

Tanya Dwivedi (07:22:54) (in thread): > Thankyou@Scholastica Urua@Blessing Ene Anyebe@Desire Oluwarotimi

Scholastica Urua (07:23:37) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709708061930569?thread_ts=1709665958.322809&cid=C04RATV9VCY - Attachment: Attachment > Steps for recording your first contribution; > 1. Go to the outreachy website > 2. Click on the ‘Microbiome Study Curation’ > 3. Click on ‘Record Contributions and Apply to This Project’ > Hope this helps

Sandra Dindi (07:24:03) (in thread): > Thanks for the tip@Aleru Divine

Desire Oluwarotimi (07:24:18) (in thread): > This should help.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709723151610279 - Attachment: Attachment > @Faith Ifeoluwa Alexander >
> This is the link for your first contribution > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc

Scholastica Urua (07:24:40) (in thread): > Copy the link you click to fill the form initially.

Adenike Oladimeji-Kasumu (07:26:14) (in thread): > Thank you. How about the description?

Bolanle Wahab (07:26:59) (in thread): > You’re welcome@Tanya Dwivedi

Blessing Ene Anyebe (07:27:41) (in thread): > You’re welcome@Tanya Dwivedi

Aleru Divine (07:29:08) (in thread): > In addition, to what@Scholastica Uruaand@Michael Adekanyehas said. > > Justinclude a link to the surveyfor the CONTRIBUTION URL - File (JPEG): IMG_7735

Michael Adekanye (07:29:59): > Just coming in here? Please follow this - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (07:30:04) (in thread): > You’rewelcome@Sandra Dindi

Michael Adekanye (07:30:58) (in thread): > Don’t forget to do this. I just finished mine.

Samreen Aftab (07:31:47) (in thread): > Thank you everyone, this helps a lot :)

Scholastica Urua (07:32:03) (in thread): > @Adenike Oladimeji-KasumuYou can include a little description of what the first contribution is about.

Amarachi Lewachi (07:35:08) (in thread): > Thank you@Adedoja Isaac

Adenike Oladimeji-Kasumu (07:35:46) (in thread): > Okay. Thank you.

Bolanle Wahab (07:36:34) (in thread): > @Adenike Oladimeji-Kasumubasically describe what the article is about, the topic,purpose, analysis,discussions and findings.

Michael Adekanye (07:36:38) (in thread): > You don’t have to click apply now, right? I mean in the record contribution page. And do I have to finish the second task before office hours tomorrow?

Mildred Anashie (07:37:28) (in thread): > @Michael Adekanyeyou don’t have to finish the second contribution before tomorrow > > It’s advisable to be thorough > The mentors preach quality

Aleru Divine (07:38:40) (in thread): > Yeah youdon’t. Take your time to finish your second contribution as quality matters more than quantity@Michael Adekanye

Samreen Aftab (07:44:00) (in thread): > @Aleru Divine@Mildred Anashieso we’re supposed to complete the two tasks in the contribution period right?

Mildred Anashie (07:45:32) (in thread): > Yes you are to complete the first contribution > > It says the second is optional (althoughit’sadvisable to do that also)

Michael Adekanye (07:45:39) (in thread): > Yes,Samreen

Michael Adekanye (07:46:50) (in thread): > Really!?

Aleru Divine (07:47:45) (in thread): > @Samreen Aftabyes complete the first contribution task, but the second contribution task is totally optional.

Muqtadirat Yussuff (07:50:41): > Hi everyone, I’m curating a paper and I realized the host specie is not in the dropdown. It says to contact the team in order to add it, do I do that here or meet up with the mentor?

Mildred Anashie (07:52:08) (in thread): > What’s the host specie in your paper? > > Just tag the mentors to the question here and I think you should drop a link to the paper for cross checking

Svetlana Ugarcina Perovic (07:53:14) (in thread): > The host species should be recorded in Latin.

Amanda Adoyi (07:53:15): > Hello:slightly_smiling_face:Is it advisable to share supplementary reading material that one may consider helpful to someone else on this platform or is that not allowed?

Mildred Anashie (07:55:09) (in thread): > @Amanda Adoyiit’sallowed to ask questions when you feel stuck and Idon’tthinkit’san issue sharing your supplementary materials with someone else on the platform

Svetlana Ugarcina Perovic (07:55:56) (in thread): > @Muqtadirat Yussuffthe host species of your assigned paper is on the list.

Aleru Divine (07:56:26) (in thread): > It’sopen source so yes it is allowed:hugging_face:

Amanda Adoyi (07:56:32) (in thread): > I meant in general chat rooms like this one. I observe more general conversation is encouraged instead of private chats.

Amanda Adoyi (07:56:50) (in thread): > Thank you:slightly_smiling_face:

Scholastica Urua (07:57:46) (in thread): > If the supplementary material will be helpful, I think it’s okay to share

Mildred Anashie (07:58:09) (in thread): > Yea > > Like Divine said,it’sopen source > More general conversations are advisable

Muqtadirat Yussuff (07:58:32) (in thread): > @Svetlana Ugarcina PerovicOh, I did try “Premnas biaculeatus” multiple times and it did not show up. I’m trying to input for the Maroon Clownfish but I’ll refresh my tab and recheck. Thank you

Svetlana Ugarcina Perovic (08:00:02) (in thread): - File (PNG): Screenshot 2024-03-06 at 13.59.29.png

Svetlana Ugarcina Perovic (08:00:11) (in thread): > the very last

Muqtadirat Yussuff (08:00:20) (in thread): > Now it shows, sorry about that

Svetlana Ugarcina Perovic (08:01:09) (in thread): > Now I deserve a tea break:teapot:

Suru Olaitan (08:13:54) (in thread): > Thank you for the detailed guideline@Svetlana Ugarcina PerovicI look forward to a wonderful collaborative journey with this community:tada:

Amanda Adoyi (08:15:47): > Aloha:slightly_smiling_face:So on adding a study, I saw from the video guides that the next page should be populated with relevant data after you have added the correct doi, but this is not the case for me. Just a page with the doi and study design shows up. Is this normal?

Mildred Anashie (08:16:16) (in thread): > Paste the PMID instead

Mildred Anashie (08:16:34) (in thread): > It will auto populate when you do that

Amanda Adoyi (08:16:43) (in thread): > Okay. Will do and thanks

Aleru Divine (08:16:53) (in thread): > @Amanda AdoyiAdd the PMID and it will automatically populate.

Mildred Anashie (08:16:57) (in thread): > You can paste the name of the study on PUBMED to get the PMID

Suru Olaitan (08:20:02): > Hiii EveryoneIt’sgreat to be here once again, I just completed my first contribution and I appreciate the support and guide available on this platform > It really helped me have a soft landing. > > I want to make my second contribution but I am not so familiar with the few available projects on gitbhub. > Would it be a good idea to wait for more projects to be uploaded or just make do with what is available???

Aleru Divine (08:21:04) (in thread): > Congratulations on completing your first contribution@Suru Olaitan:partying_face::partying_face:I would suggest you pick one of the available articles, ask questions when it becomes difficult, I am available to help with anything you need and the mentors@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy@Esther Afuapeare here too to answer any questions you might have. > > But we learn by trying and there’s no assurance that you’ll be familiar with the projects that’ll be uploaded in the future. > > So pick one and get started:heart:

Suru Olaitan (08:21:24) (in thread): > Thank you:pray:@Aleru Divine

Blessing Ene Anyebe (08:21:30) (in thread): > I thinkit’sbetter to pick one and start learning about it. > Congratulations@Suru Olaitan:orange_heart::partying_face:

Mildred Anashie (08:21:56) (in thread): > The mentors should be able to help with this@Chioma Onyido@Esther Afuape@Peace Sandy@Svetlana Ugarcina Perovic

Suru Olaitan (08:22:54) (in thread): > Thank you,@Mildred Anashie

Blessing Ene Anyebe (08:25:06) (in thread): > If you Check the video resources provided via the GitHub urlyou’llget a good understanding of how curation works andit’llpoint you in the right direction. > > SoI’lladvise you take time to read through the available papers, pick one, and then research well, learn about it and contribute.

Suru Olaitan (08:27:59) (in thread): > Appreciate the detailed responses:heart:

Blessing Ene Anyebe (08:28:37) (in thread): > You can reach out to me for assistance as well.

Blessing Ene Anyebe (08:28:43) (in thread): > You’rewelcome:orange_heart:

Scholastica Urua (08:30:13) (in thread): > @Aleru Divinehas said it all. Its better to pick one of the available articles and ask questions when you encounter difficulty than to wait.

Suru Olaitan (08:31:44) (in thread): > Really appreciate > I’ll definitely reach out should I encounter any difficulty@Blessing Ene Anyebe

Scholastica Urua (08:31:57) (in thread): > @Amanda Adoyiyou can input both the Doi and PMID and the rest rest will auto populate.

Adenike Oladimeji-Kasumu (08:32:55): > Hello everyone, > Kindly check the attached photo. Does this mean that I have to redo my First contribution? And Can you please state whatever you think I might not have gotten right?:pray:@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)and my fellows - File (JPEG): IMG_20240306_143008_245.jpg

Amarachi Lewachi (08:33:10) (in thread): > Congratulations. I suggest you watch the videos attached to the introductory document as well as it helped me navigate the site. Do not forget to request for an account with BugSigDB

Mildred Anashie (08:33:41) (in thread): > It looks like youdidn’tupdate the date when you were recording

Amanda Adoyi (08:34:05) (in thread): > @Svetlana Ugarcina PerovicI’m sorry to interrupt your tea break but I believe I have the same problem.

Aleru Divine (08:34:23) (in thread): > You need to update the “Date contribution was accepted or merged”. > > Not redo, you’ve done nothing wrong.@Adenike Oladimeji-Kasumu

Scholastica Urua (08:34:24) (in thread): > Hello@Adenike Oladimeji-Kasumuthis does not mean you have to redo your first contribution. > You can however, edit it anytime to add merge date, which can be the date you submitted.

Amarachi Lewachi (08:35:54) (in thread): > You need to add the date contributed or merged. You do not need to redo the contribution. Click the edit button and add the appropriate column.

Adenike Oladimeji-Kasumu (08:36:43) (in thread): > Yes, I only included Date Contribution was started. > I didn’t include Date Contribution was accepted or merged. This is because I don’t know if it has been accepted. Is there a way to find out? > I submitted it yesterday.

Mildred Anashie (08:37:39) (in thread): > I think the mentors already have a record of it soit’saccepted

Scholastica Urua (08:37:48) (in thread): > As far as you’ve submitted, you can include that date as your merge date.

Nana (08:38:19): > @Melodee Okigboweldone

Muqtadirat Yussuff (08:38:55) (in thread): > The form was submitted so in this case that should count as accepted as I don’t think we would be getting any other confirmation

Esther Afuape (08:39:08) (in thread): > Please add the date you finished as the merge date as@Scholastica Uruasaid

Amanda Adoyi (08:39:18): > I seem to have got a ton of questions today…em… I realise that my host species of interest is not on the dropdown. I have reloaded the page but nothing starts with a ‘ph’

Adenike Oladimeji-Kasumu (08:39:26) (in thread): > Done. Thank you all. > It now shows merged.

Aleru Divine (08:40:37) (in thread): > What is the host species?

Amanda Adoyi (08:41:03) (in thread): > It’s a Koala

Melodee Okigbo (08:41:23): > Hi everyone:relaxed:, I just finished my first contribution and I must say it was quite tedious especially because I have a limited microbiology background, but it was definitely worth it! I have learnt sooo much and can’t wait to learn more from you all. > > Do you have any useful tips for the second contribution, aside from watching the videos of course? One thing I’ve realized is that thorough research is key when it comes to this project! Are there any resources you have found helpful for the second task?

Blessing Ene Anyebe (08:41:58) (in thread): > Congratulations@Melodee OkigboIt really exciting!:partying_face:

Leenaa Al-Amin (08:42:39) (in thread): > Congratulations !

Aleru Divine (08:43:03) (in thread): > @Svetlana Ugarcina Perovic

Melodee Okigbo (08:43:35) (in thread): > Thank you!@Blessing Ene Anyebe@Michael LeeIt really is!

Melodee Okigbo (08:44:08) (in thread): > Thank you!

Ananya Tomar (08:44:15): > hey everyone! while submitting the first contribution do i need to attach my link for the survey or just the link would work?

Aleru Divine (08:45:06) (in thread): > Hey@Ananya Tomar, attach the link to the survey.Ithink it’sgeneral.

Esther Afuape (08:45:17) (in thread): > Hi@Suru Olaitanplease watch the videos in the onboarding materials (https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699) to see how to curate a study and add a signature to bugSigDB. You can also go to therandom page onBugSigDB.orgto see previously curated studies. It’ll help to highlight the details in the paper as you study it so that it’s easier for you to pick them out to curate.Also, go through the curation policy!We added some new papers today and we’re still adding more. I suggest you pick one that interests you. Hope this helps - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Ananya Tomar (08:45:25) (in thread): > alright thank you!

Scholastica Urua (08:46:04) (in thread): > @Amanda Adoyiyou can ask as many questions as possible. I’m sure everyone is more than happy to help and we are all learning as well. > > The scientific name for a koala is Phascolarctos cinereus although I can’t seem to find it on the list.<@UBNSEMS3S>@Svetlana Ugarcina Perovic

Mildred Anashie (08:46:41) (in thread): > The curation policy for a start

Esther Afuape (08:47:21) (in thread): > What’sthe host species?@Amanda Adoyi

Amanda Adoyi (08:47:37) (in thread): > @Scholastica UruaThanks for the go ahead. Lolz. How do I proceed then? I would really love to continue with this Study. It’s pretty fascinating so I’m hoping I wouldn’t have to change.

Amanda Adoyi (08:47:58) (in thread): > It’s a Koala.

Esther Afuape (08:48:12) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709732717638569?thread_ts=1709731202.283519&channel=C04RATV9VCY&message_ts=1709732717.638569 - Attachment: Attachment > Hi @Suru Olaitan please watch the videos in the onboarding materials (https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699) to see how to curate a study and add a signature to bugSigDB. You can also go to the random page on BugSigDB.org to see previously curated studies. It’ll help to highlight the details in the paper as you study it so that it’s easier for you to pick them out to curate. We added some new papers today and we’re still adding more. I suggest you pick one that interests you. Hope this helps

Muqtadirat Yussuff (08:48:39) (in thread): > @Esther AfuapeMost likely* Phascolarctos cinereus *

Amanda Adoyi (08:49:17) (in thread): > @Muqtadirat YussuffYes. That is it and it is not on the list.

Aleru Divine (08:49:31) (in thread): > Congratulations@Melodee OkigboHere’sthe curation policy@Mildred Anashiejust mentionedhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Scholastica Urua (08:49:32) (in thread): > Just the survey link would work. Like Aleru said, its a general link for everyone

Aleru Divine (08:49:57) (in thread): > You’rewelcome:hugging_face:

Scholastica Urua (08:51:43) (in thread): > Congratulations@Melodee Okigbofor completing your first contribution. Good luck with the second contribution:pray:.

Esther Afuape (08:52:52) (in thread): > Please leave that space blank and go ahead with the curation.I’lllet you know when the specie has been added

Amanda Adoyi (08:53:33) (in thread): > Alright. I’ll be waiting then. Thanks.

Scholastica Urua (08:55:06) (in thread): > I think you should continue with the curation while waiting for response from the mentors. You can always edit an entry even after moving to the next page.

Amanda Adoyi (08:55:28) (in thread): > Alright. Thank you.

Melodee Okigbo (08:57:53) (in thread): > Thank you so much@Esther Afuape@Aleru Divine, I’ll definitely check it out:pray:

Melodee Okigbo (08:59:09) (in thread): > Thank you!@Scholastica UruaAnd same to you too!:relaxed:

Svetlana Ugarcina Perovic (09:03:12) (in thread): > @Amanda AdoyiPhascolarctos cinereus added.

Amanda Adoyi (09:03:43) (in thread): > Thank you so much :)

Svetlana Ugarcina Perovic (09:03:45) (in thread): > Phascolarctos cinereus added. Thank you for your patience!

Amanda Adoyi (09:04:08) (in thread): > Really grateful for that :)

Suru Olaitan (09:07:05) (in thread): > @Aleru DivinePlease, after completing the survey, are we suppose to submit the link somewhere,asides from recording the contribution on the outreachy website?

Aleru Divine (09:08:12) (in thread): > @Suru Olaitanno,we’reonly to submit the link when recording our contribution on the Outreachy website

Suru Olaitan (09:08:29) (in thread): > Thank you@Esther Afuape:heart:

Svetlana Ugarcina Perovic (09:11:51) (in thread): > Beside communication there is also one more important skill –to be patient :teapot:**** ****If you are stuck, we will get back to you as soon as possible. In the meantime, you can help others with their challenges. Once again thank you for your patience!:cupcake:

Tanya Dwivedi (09:14:16) (in thread): > Thank you everyone for warm welcome

Samreen Aftab (09:17:27): > Hello everyone, should I put today’s date here or should I leave this blank? - File (PNG): image.png

Desire Oluwarotimi (09:17:48) (in thread): > Add today’s date.

Scholastica Urua (09:17:54) (in thread): > Put today’s date

Aleru Divine (09:17:56) (in thread): > Todays date is fine@Samreen Aftab

Blessing Ene Anyebe (09:18:10) (in thread): > Today’s date

Aleru Divine (09:19:30): > Hi everyone, I have a question. > > My topic is “Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study” > > There is no specific disease condition in my article as the study aims to investigate microbiome features associated with the performance measures in each group. > > So in this case, what do I do?@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido

Svetlana Ugarcina Perovic (09:21:03) (in thread): > You could choose “health study participation”

Aleru Divine (09:21:50) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

EBERE ADEKOGBE (09:24:45): > Hi everyone, I have finished with my first contribution, I picked a topic which is “Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome” for my second contribution, and asked if i could go ahead with it tagging@Svetlana Ugarcina Perovicand@Chioma Onyido, but i didn’t receive a response. I cant even find the topic on the GitHub repository any more. I really don’t know what to do. please help!

Peace Sandy (09:25:33) (in thread): > Hi@EBERE ADEKOGBEPlease be patient > > We will look into it

Svetlana Ugarcina Perovic (09:25:45) (in thread): > It’s herehttps://github.com/waldronlab/BugSigDBcuration/issues/161 - Attachment: #161 Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome > Host-Associated Quantitative Abundance Profiling Reveals the Microbial Load Variation of Root Microbiome – Guo X et al– Plant Commun. > > https://www.sciencedirect.com/science/article/pii/S2590346219300033

EBERE ADEKOGBE (09:26:37) (in thread): > Thank you! , so grateful

Svetlana Ugarcina Perovic (09:26:41) (in thread): > Please choose another paper. Thank you! - File (PNG): Screenshot 2024-03-06 at 15.26.17.png

EBERE ADEKOGBE (09:27:26) (in thread): > Alright. Thank you

Scholastica Urua (09:30:20) (in thread): > Thanks for the answer@Svetlana Ugarcina Perovic.:pray:Was also curious how to go about it.

Desire Oluwarotimi (09:34:20) (in thread): > Hi@Aleru DivineI have a similar study as you do but whenever I input “healthy study participation” in the condition input field, it disappears. > > How did you go about yours?

Svetlana Ugarcina Perovic (09:35:16) (in thread): > https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0010130?lang=en - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Aleru Divine (09:35:28) (in thread): > It’s HEALTH STUDY PARTICIPATION. > > check if you spelt health or healthy@Desire Oluwarotimi

Svetlana Ugarcina Perovic (09:35:50) (in thread): > You can always check your term in OLS and fix typos :)

Adenike Oladimeji-Kasumu (09:36:13): > What could be the reason why the information on my paper is not automatically populating when I create a study? Even after filling the appropriate gaps.

Desire Oluwarotimi (09:36:24) (in thread): > Yeah, it was a typo error. > > Thank you@Aleru Divine@Svetlana Ugarcina Perovic

Mildred Anashie (09:36:41) (in thread): > You’vepasted the PMID?

Aleru Divine (09:36:56) (in thread): > Did you input the PMID?@Adenike Oladimeji-Kasumu

Aleru Divine (09:37:30) (in thread): > You’rewelcome:hugging_face:

Desire Oluwarotimi (09:37:37) (in thread): > Hi@Adenike Oladimeji-KasumuInput PMID and make sure it’s set to auto.

Adenike Oladimeji-Kasumu (09:37:44) (in thread): > Yes, i pasted it on Doi as my paper containsDoi.org

Adenike Oladimeji-Kasumu (09:38:00) (in thread): > it is set to auto

Mildred Anashie (09:38:42) (in thread): > Paste the PMID not just the doi

Aleru Divine (09:39:06) (in thread): > Can you send a screenshot please.There’sPMID and PMCID, make sure to input the PMID.

Desire Oluwarotimi (09:39:10) (in thread): > Not doi but PMID > > Copy the title of your article and paste in the pubmed website. You’d be able to fetch the PMID.https://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Mildred Anashie (09:39:17) (in thread): > You can type the name of the paper on PUBMED and get PMID

Ikeh Darlington Ikeh (09:39:29): > Hello Team#bugsigdb, I am new here and still trying to find a way to make my first contribution. Any tip is highly appreciated.

Desire Oluwarotimi (09:40:20) (in thread): > Welcome@Ikeh Darlington IkehTake a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (09:40:22) (in thread): > Hi@Ikeh Darlington Ikeh, welcome:hugging_face:I also found this helpful. It’s a list of some of the FAQs and answers.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Adenike Oladimeji-Kasumu (09:41:41) (in thread): > @Desire OluwarotimiThat was helpful. It has poulated the information. Thank you everyone.

Muqtadirat Yussuff (09:43:55) (in thread): > Hey@Ikeh Darlington Ikeh, after going through resources sent by the fellow contributors, ensure you record your first contribution on Outreachy. You do not need a merged date and can fill that section with the date you submitted the form for your first curation. > > If you need more help keep asking and there’s bound to be a reply.

Esther Nelson (09:48:31) (in thread): > Welcome@Peace Daniel

Esther Nelson (09:51:37) (in thread): > Chioma, thanks for this gold. It really helped calm me from fretting and now, I’m getting started.

Scholastica Urua (09:52:17) (in thread): > Welcome@Ikeh Darlington Ikeh

Suru Olaitan (10:01:26) (in thread): > Thank youuu

Desire Oluwarotimi (10:02:54) (in thread): > I’m glad I could help. You are welcome.

Esther Nelson (10:07:16) (in thread): > Welcome@Ikeh Darlington Ikeh, a lot has been mentioned, however, I found this guide to be very useful in getting started:https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/I wish you all the best and look forward to learning greatly from you. - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta…

Mildred Anashie (10:14:14) (in thread): > Welcome@Ikeh Darlington IkehFeel free to ask questions, willing to help when I can

Mildred Anashie (10:19:27): > Hello everyone@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyThis is a table from the studyI’mcurating,I’mnot sure which LDA score to use because it was lefse test that was used and there was no mention of LDA within the paper, asides this supplemental table > Confused on what to record for LDA as each taxa has either 4 or 5 - File (JPEG): IMG_1741

Aleru Divine (10:24:58): > Hi everyone, > > Quick question, just to be sure. > > Can we have multiple statistical tests? > > My study mentions about 4 statistical tests.@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido

Mildred Anashie (10:25:58) (in thread): > Yes > > I think different experiments can have different statistical test > So multiple statistical test is possible

Svetlana Ugarcina Perovic (10:26:24) (in thread): > The default LDA value is 2.00 in LefSe. For p value they stated: “Pvalues < 0.05 were considered statistically significant.”

Desire Oluwarotimi (10:27:17): > Hi everyone. > > I’m a bit conflicted and I need help determining the study design of my article. > > It involved participants from different ethnicity (Chinese, Malay and Indian) but the article didn’t state they shared different geographical areas at the time of the study which is making me rule out Cross-sectional observational. > > At the same time, I could say longitudinal observational because it was a time series (Day 1, 7 and 14) but the participants were given a course of omeprazole for seven days which is also making rule it out.@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Mildred Anashie (10:27:23) (in thread): > Okay that means I should I record LDA as 2 for all experiments

Esther Afuape (10:27:43) (in thread): > Yes, you can have multiple statistical tests. However, be sure that the test is for differential abundance, and not for p-value. You should check the description of the figure or table you’re curating the result from to be certain of the test being carried out for that comparison/experiment

Aleru Divine (10:29:35) (in thread): > Thank you so much:blush:@Mildred Anashie@Esther Afuape

Mildred Anashie (10:33:11) (in thread): > Excerpt from the paper or the link might help@Desire Oluwarotimi

Desire Oluwarotimi (10:35:17) (in thread): > Here is the link.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6875812/ - Attachment (PubMed Central (PMC)): Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore > The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome. PPIs are commonly used for the treatment of acid-related disorders. We hypothesised that PPI therapy …

Svetlana Ugarcina Perovic (10:42:18) (in thread): > This might helphttps://bugsigdb.org/Curation_Policy#Study_Design - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Bolanle Wahab (10:43:36) (in thread): > @Desire OluwarotimiI think it is Longitudinal design because regardless of their difference in ethnicity, you’re still observing changes over time

Ibukun Hassan (10:48:27) (in thread): > PlsI’mlost:disappointed:

Desire Oluwarotimi (10:48:35) (in thread): > @Bolanle WahabI get your point but a longitudinal study is supposed to happen without interference. They were given Omeprazole.

Svetlana Ugarcina Perovic (10:50:53) (in thread): > Check carefully out examples herehttps://bugsigdb.org/Curation_Policy#Study_Design@Desire Oluwarotimi

Desire Oluwarotimi (10:51:42) (in thread): > I will go through it again. > > Thank You@Svetlana Ugarcina Perovic

Mildred Anashie (10:52:18) (in thread): > It seems to be a prospective cohort to me > > Longitudinal should have Mention of pre and post treatments in my opinion:thinking_face:I’llread further to confirm my statement

Scholastica Urua (10:53:00) (in thread): > Hi@Ibukun Hassanwhat seems to be the problem?

Aleru Divine (10:54:42) (in thread): > Hi@Ibukun Hassanhave you gone through this on GitHub?https://github.com/waldronlab/BugSigDBcuration/issues/94If not, go through it, this is a guideline on how to curate, examples of completed curations and how to make your first contribution.

Bolanle Wahab (10:55:35) (in thread): > If your study had a control group,Ithink i’d stick to longitudinal,if not,it’sprobably another study design.

Leenaa Al-Amin (10:56:51) (in thread): > I believe its a prospective cohort

Aleru Divine (10:56:54) (in thread): > @Ibukun HassanTo make your first contribution, > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Aleru Divine (11:06:53): > Is anyone having trouble finding their way to the first or second contribution task? > > I’m here to assist. > > Please don’t hesitate to ask if you have any questions. > > Goodluck in your contributions:hugging_face:

Bolanle Wahab (11:11:02) (in thread): > True, could be this too since they observed the effect of Omeprazole

Desire Oluwarotimi (11:11:06) (in thread): > @Mildred AnashieAfter going through the study design policy again, I’m beginning to gear towards your idea. > > That’s because over time in prospective cohort, some participants can develop conditions of interest. Something similar to this was mentioned in the article where they speculated the possibility of developing Irritable Bowel Syndrome with the use of PPI. > > But there’s a lot of if and if not.

Mildred Anashie (11:13:40) (in thread): > Yea@Desire Oluwarotimi. a lot of if and if not.:joy:I still think it is a prospective cohort study > The only confusion here to me, is that the participants should share the same characteristics (does the ethnic group classify this)? > > Also the short duration of the study with no follow up or results for after treatment is making me rule out longitudinal:thinking_face:

Rahila-me (11:15:23): > Hello lovely people, Are you done with your first contribution and does not know how to record on the outreachy website? feel free to jump on a huddle with me so i can show you, how to navigate your way.

Desire Oluwarotimi (11:16:09) (in thread): > The joint characteristic is that they all had to be healthy. Two were excluded because of this reason so they weren’t actually treating any ailment.@Mildred Anashie

Leenaa Al-Amin (11:16:33) (in thread): > The characteristic that they share is that they are all healthy individuals from the three major asian ethnic groups

Bolanle Wahab (11:17:18) (in thread): > @Mildred Anashieare you saying longitudinal designs can be used for short duration observations?

Leenaa Al-Amin (11:17:38) (in thread): > yes two were excluded because of this reason@Desire Oluwarotimi

Mildred Anashie (11:21:11) (in thread): > @Bolanle WahabI’m saying Longitudinal designs can be used for short durations but there should always be a follow up giving room for before and after results (Pre and Post) > > My opinion though

Mildred Anashie (11:21:52) (in thread): > Dear mentors@Chioma Onyido@Peace Sandy@Esther AfuapePlease can you help us figure this out:pray:

Barakat Akinsiku (11:24:28): > Hi, please did anyone else have this issue where after inputing doi, the next page doesn’t populate with relevant data? I tried pasting the study title on pubmed and it doesn’t show up either. I think this may be due to the paper being a protected study published on sciencedirect. Did anyone else have this challenge and if so, how were you able to solve it? the link to the study below:https://www.sciencedirect.com/science/article/abs/pii/S0044848623000224?via%3Dihubhttps://doi.org/10.1016/j.aquaculture.2023.739249

Mildred Anashie (11:25:15) (in thread): > Hi@Barakat Akinsikupaste your study on PUBMED > When you use the PMID it will populate automatically

Bolanle Wahab (11:25:53) (in thread): > At this point,please mentors?:joy:

Barakat Akinsiku (11:26:44) (in thread): > I already did that, it didn’t work

Anju Maurya (11:27:24): > @Svetlana Ugarcina Perovic@Chioma OnyidoMa’am! Could you please let me know where we can find information about the online lab meeting?

Desire Oluwarotimi (11:27:24) (in thread): > This should help.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709735950567729?thread_ts=1709735773.104749&cid=C04RATV9VCY - Attachment: Attachment > Not doi but PMID > > Copy the title of your article and paste in the pubmed website. You’d be able to fetch the PMID. > > https://pubmed.ncbi.nlm.nih.gov/

Mildred Anashie (11:28:25) (in thread): > The link will be posted here by tomorrow although it’s mentioned on the GitHub issuehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Esther Nelson (11:29:20) (in thread): > Yes, I think it’s this as mentioned in the github issue: Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at:https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here:https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Mildred Anashie (11:29:48) (in thread): > @Barakat Akinsikuyoucouldn’tget the PMID or the PMIDdidn’tautomatically populate?

Anju Maurya (11:30:25) (in thread): > Thank you so much!

Barakat Akinsiku (11:31:06) (in thread): > @Mildred Anashiethis is the result from searching on pubmed - File (PNG): s.png

Desire Oluwarotimi (11:32:07) (in thread): > Hmmmm:thinking_face:

Scholastica Urua (11:32:21) (in thread): > @Barakat AkinsikuI’m going through the link to check if I can find the PMID

Aleru Divine (11:32:44) (in thread): > Icouldn’tfind the PMID either.@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma OnyidoPlease help:pray::pray:

Ibukun Hassan (11:35:14) (in thread): > Alright > Thank you so much > I will go through again.

Scholastica Urua (11:37:38) (in thread): > Office hours are held at 9 AM EDT (eastern daylight time) every Thursday. Find out the time in your local time zone here.

Mildred Anashie (11:39:52) (in thread): > Same hereCouldn’tfind it, maybethere’sa trick to it:smile:@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Barakat Akinsiku (11:42:10) (in thread): > Yeah, exactly@Mildred Anashie. Thanks@Scholastica UruaWe’ll figure it out@Aleru Divine@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyidoplease help out here

Rahila-me (11:43:47) (in thread): > You can use google time converter to check it out on your own time zone

Scholastica Urua (11:48:26) (in thread): > Haven’t been able to find the PMID@Barakat Akinsiku. Wish I could be of more help.

Chioma Onyido (11:55:37) (in thread): > Hi@Barakat AkinsikuOne of the reasons why some studies don’t come with PMID is because it’s not published in a journal t that’s indexed by PubMed or for very recent publications too. > > Can you try using the ‘manual’ option instead to enter the Doi and other details.

Nana (11:56:18) (in thread): > 9 am EDT is 3pm in Lagos Nigeria

Svetlana Ugarcina Perovic (12:01:05) (in thread): > During curation we use PMID preferably.You can instead enter a DOI or URL to identify the source: note those other identifiers are only needed if there is not a PMID, otherwise PMID alone is enough.

Barakat Akinsiku (12:02:05) (in thread): > Okay, thanks@Chioma Onyidocc@Aleru Divine

Barakat Akinsiku (12:02:20) (in thread): > Noted. Thank you@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (12:07:04): > Hello, I’m having another issue:woman-bowing:The topic of my Paper is “Microbial communities associated with honey bees in Brazil and in the United States”. The Body sites where samples are collected are corbicular pollen, beebread, hive debris, and intestinal contents. I could not find a term for the body site. Also, i want to ask if it is okay to use ‘Microbiome’ as the condition term.@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido

Svetlana Ugarcina Perovic (12:07:06) (in thread): > I’ll post tomorrow morning our online meeting link.See you tomorrow at 9 AM EDT (eastern daylight time)! > > Find out the time in your local time zone here:https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179

Suru Olaitan (12:09:09) (in thread): > Thank you@Svetlana Ugarcina Perovic

Peace Sandy (12:09:59) (in thread): > Did you check the EFO site

Faith Ifeoluwa Alexander (12:11:01) (in thread): > I just finished my first contribution but I am confused on how to record it on Outreachy.

Faith Ifeoluwa Alexander (12:11:17) (in thread): > I don’t know if it has been accepted and merged.

Faith Ifeoluwa Alexander (12:14:59): > Hello everyone. I just finished my first contribution but I am stuck on how to record it on the Outreachy website. How do I know if my contribution has been accepted and merged?

Scholastica Urua (12:16:05) (in thread): > Hi@Faith Ifeoluwa Alexanderas far as you have submitted your first contribution, you can record the submission date as the merge date.

Adenike Oladimeji-Kasumu (12:16:28) (in thread): > Do you mean here:www.ebi.ac.uk? I checked here and did not find any.

Svetlana Ugarcina Perovic (12:18:21) (in thread): > https://www.ebi.ac.uk/ols4 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Aleru Divine (12:18:49) (in thread): > @Faith Ifeoluwa Alexanderjust go ahead and record your contribution and use the day you submitted as the day it was merged.

Peace Sandy (12:19:09) (in thread): > Check the one@Svetlana Ugarcina Perovicposted

Nana (12:20:20) (in thread): > @Faith Ifeoluwa Alexanderthis will help..the images below - File (JPEG): Screenshot_2024-03-06-13-29-11-66_abb9c8060a0a12c5ac89e934e52a2f4f.jpg - File (JPEG): Screenshot_2024-03-06-13-29-31-70_abb9c8060a0a12c5ac89e934e52a2f4f.jpg

Nana (12:20:44) (in thread): > Remember to paste your link

Adenike Oladimeji-Kasumu (12:24:43) (in thread): > Thank you@Svetlana Ugarcina Perovicand@Peace SandyI’ll check now

Suru Olaitan (12:24:43) (in thread): > Yes, very important > The link to the survey in your browser

Faith Ifeoluwa Alexander (12:24:55) (in thread): > Okay. Thank you so much. I appreciate your kindness and help.

Temitayo Ogidan (12:25:05): > Pleased to meet you all,I’mcurrently going through the chats to understand better.I’mnew to open source:see_no_evil:

Anju Maurya (12:26:23): > @Temitayo OgidanHey Temitayo!

Scholastica Urua (12:26:49) (in thread): > Welcome@Temitayo Ogidanpleased to meet you too. Going through the chats/pinned messages will give you a soft landing.:+1:

Rahila-me (12:26:54): > @Temitayo Ogidanwelcome, start from here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (12:26:56) (in thread): > Pleased to meet you@Temitayo Ogidan

Aleru Divine (12:27:24) (in thread): > Pleased to meet you too@Temitayo Ogidan:hugging_face:

Temitayo Ogidan (12:27:42): > Thank you@Rahila-me

Rahila-me (12:27:50): > urw

Scholastica Urua (12:27:58) (in thread): > Do well to ask questions wherever you encounter difficulty. I’ll be happy to help.

Anju Maurya (12:28:07): > > @Temitayo OgidanYou can check out it! Kindly view the issue on GitHub for instructions on how to get started. > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94.#94 Welcome Outreachy Applicants!Welcome Outreachy Applicants!Note: This task can be completed by multiple Outreachy applicants.BugSigDB ProjectBugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies,https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a me…Labelsfirst contribution, outreachy may2024 - Attachment (BugSigDB): Main Page > … - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Suru Olaitan (12:28:21) (in thread): > Hello@Temitayo OgidanYou’re welcome:tada:Get ready to make your first contribution!Here’show to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699Should you encounter any difficulties, I am here to help!:sparkles: - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Temitayo Ogidan (12:29:09) (in thread): > Thank you everyoneI’mso glad to be getting so much support

EBERE ADEKOGBE (13:04:02): > Hi,@Svetlana Ugarcina Perovic,@Chioma Onyidohttps://github.com/waldronlab/BugSigDBcuration/issues/urlThis link leads to nowhere. The article is empty. Kindly help me look into it. Thank you

Amanda Adoyi (13:08:07): > @Svetlana Ugarcina PerovicHi:slightly_smiling_face:In the alpha diversity portion when adding a study we are told to determine if the Shannon index is decreased, increased or unchanged. What of a situation where your Shannon values are varied; perhaps over about four different areas of a cycle where it goes up and down? How do you determine if it increases or decreases there?

Aleru Divine (13:09:46) (in thread): > Hi@EBERE ADEKOGBE, this is what I got. - File (PNG): IMG_7738

EBERE ADEKOGBE (13:11:01) (in thread): > Thank you but i have been assigned a task and the link is not opening

Aleru Divine (13:12:35): > @Precious Orakwehave you gone through this on GitHub?https://github.com/waldronlab/BugSigDBcuration/issues/94If not, go through it, this is a guideline on how to curate, examples of completed curations and how to make your first contribution. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Aleru Divine (13:14:08) (in thread): > Could be bad service, because it opened on my end.Just keep trying

Mildred Anashie (13:14:09) (in thread): > @EBERE ADEKOGBEhave you tried again?

EBERE ADEKOGBE (13:14:46) (in thread): > yes I have

Mildred Anashie (13:14:49) (in thread): > Yea@Aleru Divineis right > > It opened from my end too

Aleru Divine (13:14:55) (in thread): > @EBERE ADEKOGBEtry thishttps://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22

eneje promise (13:15:35): > Good evening everyone, my name is Eneje Promise. I an outreachy intern Applicant, I haven’t worked in an open source project I will be happy if am guided on what and what to do. I promise to learn fast

Aleru Divine (13:17:55) (in thread): > Hi@eneje promiseYou can go through this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699

EBERE ADEKOGBE (13:18:39) (in thread): > I thought the link is an article which will lead us to a PDF file?

Aleru Divine (13:19:04) (in thread): > @eneje promiseHere’sa quick guide tomake your first contribution, > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design)3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM.Link to curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Mildred Anashie (13:19:08) (in thread): > Most papers will state if the alpha diversity was significant or not and if it was lower or higher > > If it’s higher (increase) > Lower (Decrease) > Not significant (unchanged)@Chioma Onyidoplease correct me ifI’mwrong

EBERE ADEKOGBE (13:20:27) (in thread): > I am not talking about the GitHub itself, am referring to the link that is the Topic I am to work on, the PDF file is not opening

Mildred Anashie (13:20:48) (in thread): > Welcome@eneje promiseI’m sureyou’dfind this easy to navigate > Feel free to ask questions, willing to help

Aleru Divine (13:20:58) (in thread): > @EBERE ADEKOGBENo,itis the BugSigDB curation repository on GitHub.

Aleru Divine (13:21:31) (in thread): > Can you share the link here? You shared the link to GitHub.

Mildred Anashie (13:22:32) (in thread): > If you have commented on an issue on the GitHub repository and it has been assigned to you > > you can just click on it and you’d find the DOI that’ll redirect you to the PDF > > If not you should use the link you shared to find an article thathasn’tbeen assigned to anyone and click on it and leave a comment that you wish to claim this articleit’llbe assigned to you

Rahila-me (13:23:53) (in thread): > welcome promise feel free to reach out if stucked

Scholastica Urua (13:24:05) (in thread): > Welcome@eneje promise

EBERE ADEKOGBE (13:24:46) (in thread): > It is not leading me to the PDF file

Mildred Anashie (13:25:57) (in thread): > Do you have an issue assigned to you already?

EBERE ADEKOGBE (13:26:49) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709748661999349?thread_ts=1709748242.323029&cid=C04RATV9VCY - Attachment: Attachment > Thank you but i have been assigned a task and the link is not opening

Bolanle Wahab (13:26:51) (in thread): > You’rewelcome@eneje promisefeel free to chat if you need any help:heart:

Aleru Divine (13:27:21) (in thread): > Can you send the link to the article you were assigned?

EBERE ADEKOGBE (13:27:31) (in thread): > I have been assigned that issue, but the link is not opening to the PDF File

Muqtadirat Yussuff (13:27:51) (in thread): > Amanda’s paper might have multiple experiments with varying alpha diversity for each but yes@Mildred Anashiethe significance tends to be stated. I’d also like to co ask how the alpha diversity status would be determined in such scenario.

Mildred Anashie (13:28:17) (in thread): > Please drop the link like@Aleru Divinesuggested

EBERE ADEKOGBE (13:28:57) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/url

Abiola Salako (13:29:05) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (13:30:29) (in thread): > @Muqtadirat Yussuffthe different alpha diversities will be stated in the paper with their resultsIt’sadvisable to read the text very well you’d definitely pick the ones relevant to the study

Abiola Salako (13:31:14) (in thread): > Welcome@eneje promise

Aleru Divine (13:31:45) (in thread): > I don’t think this is the right link. Please check again.It’staking me to the main BugSigDB page - File (PNG): IMG_7740

Suru Olaitan (13:32:00): > Good Evening Everyone > Please, There are no issues to select on the github page at the moment, so I am unable to proceed to my second contribution. Do I wait for more upload or reach out to our mentor?

Mildred Anashie (13:33:37) (in thread): > Did you get a mail that the study has been assigned to you? > If youcan’tremember the name of the study you can check the mail and You click on “issue” and find the name of the one you claimed

Aleru Divine (13:33:47) (in thread): > Hey@Suru Olaitan, just be patient, the mentors will surely upload new issues.@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido

Suru Olaitan (13:34:21) (in thread): > Thank you,@Aleru Divine

Peace Sandy (13:34:26) (in thread): > Hi@Suru OlaitanMore issues will be added soon

Mildred Anashie (13:35:12) (in thread): > Ifit’sokay by you, drop your GitHub name so I can check if I can get the link for you > > Idon’tknow if this is allowed though

EBERE ADEKOGBE (13:36:05) (in thread): - File (PNG): Screenshot 2024-03-06 193243.png

Abiola Salako (13:37:13): > Good evening everyone, please how do I find the next task after the first contribution? Thank you as I look forward to your responses.

Mildred Anashie (13:37:59) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (13:38:11) (in thread): > @EBERE ADEKOGBEHere’sthe link to the articlehttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03042-1

Mildred Anashie (13:38:24) (in thread): > Comment on an issue herehttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

EBERE ADEKOGBE (13:39:50) (in thread): > Thank you!

Abiola Salako (13:40:01) (in thread): > Thank you@Mildred Anashiehave completed my first contribution

Aleru Divine (13:40:39) (in thread): > You’rewelcome. Happy to help:hugging_face:

Mildred Anashie (13:40:42) (in thread): > It’salso the link to where you can find your second

Mildred Anashie (13:41:22) (in thread): > You need to request for an account > Then claim an issue and start the second contribution

Abiola Salako (13:42:02) (in thread): > Yes, Sis. I’ve seen it. How do I claim an issue please?

Nekembe Boris (13:42:34) (in thread): > Go to the Github pagehttps://github.com/waldronlab/BugSigDBcuration/issues/94. Select an issue tagged“paper to curate”and asked that it be assigned to you by the mentor. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Abiola Salako (13:43:17) (in thread): > Thank you@Nekembe Boris

Mildred Anashie (13:43:25) (in thread): > Drop a comment on an issue thathasn’tbeen assigned to anyone

Abiola Salako (13:44:23) (in thread): > Thank you@Mildred Anashie. I appreciate it.

Nekembe Boris (13:44:44) (in thread): > As said by@Mildred Anashie, ensure that there is no tag labeled “assigned” on the Github issue

Aleru Divine (13:45:17) (in thread): > @Abiola Salakothere are no more issues available right now for claim. > > But when it is, you can just go to to the issue/topic that interests you. > > Request to curate the article (also add your name in the comment) and it will be assigned to you. > > Then proceed to curate in BugSigDB.

Abiola Salako (13:45:24) (in thread): > @Nekembe BorisThank you.

Abiola Salako (13:46:01) (in thread): > @Aleru DivineThank you .

Aleru Divine (13:46:17) (in thread): > You’rewelcome:hugging_face:

Mildred Anashie (13:46:33) (in thread): > Well done@Aleru Divine

Nekembe Boris (13:46:52) (in thread): > We are here for each other@Abiola Salako

Aleru Divine (13:47:26) (in thread): > That’sright@Nekembe Boris:hugging_face:

Chioma Onyido (13:51:20) (in thread): > Thank you@Mildred Anashieand@Aleru Divinefor helping out with this.:raised_hands:

Mildred Anashie (13:55:13) (in thread): > One of the reasons we are here:grin:

eneje promise (14:10:51): > Good everyone, i ahve read through the processes involved. Can i install R in my VS code or i need to install it seperately?

Scholastica Urua (14:14:05) (in thread): > Hello@eneje promiseinstalling R is not a requirement for the contribution phase

Elsie Dickson (14:16:20) (in thread): > Hi@eneje promiseit is not a requirement at the moment, however you need to check the first contribution and complete it.

Ima-obong (Aimah) (14:16:54): > Hello please for my assigned paper, after adding the PMID, i got this hint : > “must be unique > ⧼A valid PMID containing only integers is expected. Please omit leading zeroes.⧽ > (If you get the message”must be unique”, this study already exists in BugSigDB and should not be added.)” > > please what can i do next. Thanks alot

Ima-obong (Aimah) (14:18:46) (in thread): > Hello, just go ahead to answer the questions on the curated form for your first contribution.

Desire Oluwarotimi (14:20:13) (in thread): > Hi@Ima-obong (Aimah)Be sure that the PMID includes just integers. If it remains the same after that, then the article most likely already exist and you might need the help of our mentors.

Nekembe Boris (14:20:29) (in thread): > Hi@Ima-obong (Aimah), The PMID is supposed to consist of just numbers

Ima-obong (Aimah) (14:21:26) (in thread): > * Yes, this is it “34766210”

UBNSEMS3S (14:22:04) (in thread): > Looks like someone started on that curation but never finished it. You can finish it here:https://bugsigdb.org/Study_860 - Attachment (BugSigDB): Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese - BugSigDB > Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments.Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health.

Ima-obong (Aimah) (14:23:04) (in thread): > oh thanks<@UBNSEMS3S>

Mildred Anashie (14:23:19) (in thread): > Hmmmmmm > > When it says must be uniqueit’spossible that study already exist

Hamidat Mohammed (14:23:32): > Good Evening everyone. My name is Mohammed Hamidat. I am an outreachy intern Applicant. This is my first open source project and I am very excited to be here and ready to make meaningful contributions

UBNSEMS3S (14:23:37) (in thread): > As others have mentioned, R is not a requirement for the contribution phase. If you want to learn how to use R for fun; however, then yes you can install it via VS code.

Ima-obong (Aimah) (14:24:20) (in thread): > Thanks Mildred

Desire Oluwarotimi (14:24:56) (in thread): > Hi@Hamidat Mohammed. You are welcome > > Take a look at this to get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (14:25:18) (in thread): > Good evening@Hamidat Mohammedwelcome

Hamidat Mohammed (14:25:40) (in thread): > Thank you so much

Scholastica Urua (14:26:02) (in thread): > This is a list of some of the FAQs and answers that may be helpful.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Amanda Adoyi (14:27:10) (in thread): > Thank you@Mildred Anashiedoing just that :)

UBNSEMS3S (14:28:23) (in thread): > Welcome!

Nana (14:31:40) (in thread): > @Hamidat Mohammedwelcome. After creating your first curation endeavor to record it on outreachy website. These images will guide you - File (JPEG): Screenshot_2024-03-06-13-29-11-66_abb9c8060a0a12c5ac89e934e52a2f4f.jpg - File (JPEG): Screenshot_2024-03-06-13-29-31-70_abb9c8060a0a12c5ac89e934e52a2f4f.jpg

Blessing Ene Anyebe (14:32:42) (in thread): > You’rewelcome@Hamidat Mohammed:orange_heart:

Ima-obong (Aimah) (14:33:47) (in thread): > <@UBNSEMS3S>the Experiment1 already has the name of the previous curatoron it, should I go ahead to maybe add another experiment and will the changes be updated to mine?@Chioma Onyido

UBNSEMS3S (14:34:40) (in thread): > You can just edit the existing experiment. We know that that curator never finished it and we will of course give you full credit for completing the curation that they did not.

Mildred Anashie (14:35:56) (in thread): > Excited to have you here too@Hamidat MohammedYou are welcome

Ima-obong (Aimah) (14:36:17) (in thread): > Thank you very much<@UBNSEMS3S>, really appreciate your help

Hamidat Mohammed (14:38:15) (in thread): > Thank you everyone:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Chioma Agu (14:39:25) (in thread): > Welcome@Hamidat Mohammed:sparkles:

Abiola Salako (14:40:28) (in thread): > Welcome@Hamidat Mohammed

Abiola Salako (14:41:37): > How do I know if I get assigned to a paper?

Mildred Anashie (14:42:26) (in thread): > Once you comment andit’sjust your comment thereI’msureit’llbe assigned to you

Aleru Divine (14:42:59) (in thread): > Hi@Hamidat Mohammed, welcome:hugging_face:

Mildred Anashie (14:43:00) (in thread): > You can just keep checking it > > I got a mail though

Aleru Divine (14:43:33) (in thread): > Hi@Abiola Salakoyou’llget an email.I got an email.

Nana (14:44:12) (in thread): > Have you requested for it

Ima-obong (Aimah) (14:44:21) (in thread): > you’ll get an email

Desire Oluwarotimi (14:44:42) (in thread): > This should help.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709704181863569?thread_ts=1709704114.665069&cid=C04RATV9VCY - Attachment: Attachment > Hi @Bolanle Wahab > > The mentors will attach an assign tag and you should see your name on the right hand side as an assignee when using a desktop view.

Nana (14:44:51) (in thread): > If so you will see assigned attached to it and you will get an email notification

Abiola Salako (14:45:32) (in thread): > Thank you@Mildred Anashie@Aleru Divine@Ima-obong (Aimah)@Desire Oluwarotimi

Abiola Salako (14:45:53) (in thread): > Thank you@Nana

Ima-obong (Aimah) (15:01:41): > Hello, I have a little situation, the host specie and body site (Anatomical site where microbial samples were extracted from) of my study paper is water, and I could not find a term for the body site in the list.

Mildred Anashie (15:12:33) (in thread): > Do not have an appropriate answer for this > > Let me tag the mentors to this@Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account)

Adenike Oladimeji-Kasumu (15:15:25) (in thread): > @Svetlana Ugarcina PerovicCould you please explain how I can find the body sites and the condition term. I have entered the list of sample extraction sites from my Paper onhttps://www.ebi.ac.uk/ols4and searched, but I did not find anything. - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Svetlana Ugarcina Perovic (15:16:10) (in thread): > @Ima-obong (Aimah)please share a link to the paper to check it out.

Svetlana Ugarcina Perovic (15:17:42) (in thread): > Is it this onehttps://bugsigdb.org/Study_860? - Attachment (BugSigDB): Metagenomics Analysis to Investigate the Microbial Communities and Their Functional Profile During Cyanobacterial Blooms in Lake Varese - BugSigDB > Toxic cyanobacterial blooms represent a natural phenomenon caused by a mass proliferation of photosynthetic prokaryotic microorganisms in water environments.Bloom events have been increasingly reported worldwide and their occurrence can pose serious threats to aquatic organisms and human health.

Ima-obong (Aimah) (15:17:43) (in thread): > Alright@Svetlana Ugarcina Perovichttps://link.springer.com/article/10.1007/s00248-021-01914-5

Ima-obong (Aimah) (15:18:13) (in thread): > yes it is

Svetlana Ugarcina Perovic (15:22:32) (in thread): > <@UBNSEMS3S>this is an environmental study with water samples, how should we recorded it; just to skip body site and make a note about water samples?

UBNSEMS3S (15:29:00) (in thread): > Yeah I suppose that’s the best solution. We haven’t curated many environmental studies at all.

C. Mirzayi (please do not tag this account) (15:30:06) (in thread): > It looks like the ontology lookup service might be having issues right now. What is the body site for your study?

Adenike Oladimeji-Kasumu (15:30:50) (in thread): > The topic of my Paper is “Microbial communities associated with honey bees in Brazil and in the United States”. The Body sites where samples are collected are corbicular pollen, beebread, hive debris, and intestinal contents. I could not find a term for the body site. Also, i want to ask if it is okay to use ‘Microbiome’ as the condition term.

Ima-obong (Aimah) (15:33:53) (in thread): > That means I can continue with the other questions, but Will I be able to save the current page if the body site field is empty?

Svetlana Ugarcina Perovic (15:34:30) (in thread): > Yes.

Ima-obong (Aimah) (15:34:54) (in thread): > Alight, Thank You.

C. Mirzayi (please do not tag this account) (15:36:28) (in thread): > If they’re contrasting Brazilian bees vs. the US, then the condition would be geographic location. I’d leave body site blank for now.

Adenike Oladimeji-Kasumu (15:37:15) (in thread): > Alright. Thank you@C. Mirzayi (please do not tag this account)

Adenike Oladimeji-Kasumu (15:41:15) (in thread): > @C. Mirzayi (please do not tag this account)Sorry to bother you, but there is no option for ‘Geographic location’ in the condition terms. can I use ‘Restricted to specific Location’ instead?

Sandra Dindi (15:46:05): > Hello. I’m stuck at creating signatures. Looking at other other studies, I see most signatures are recorded as Figures. So do I pick one figure in my study and compare the result using two signatures? The video does not elaborate. Apologies if I’m not using the correct terms, I’m new to Microbiology. - File (PNG): Screenshot 2024-03-06 234033.png

Mildred Anashie (15:47:46) (in thread): > In creating signatures you create only results (taxas) that are significant based on the experiment you are recording

Desire Oluwarotimi (15:48:51) (in thread): > No, you can’t pick any figure to just curate. You have to know which of the figures relates to the experiment you are dealing with.

Mildred Anashie (15:49:43) (in thread): > Also the taxas that are differentially abundant should be focused on

Sandra Dindi (15:50:18) (in thread): > Makes sense. Thanks guys@Desire Oluwarotimi@Mildred Anashie

Scholastica Urua (15:51:08) (in thread): > The result of the signatures does not necessarily need to be recorded as figures. I’ve seen some curation where the signature ‘source’ is a paragraph or line etc.

Mildred Anashie (15:51:54) (in thread): > Just to add based on your question > > Signatures are not just recorded as figures, you can get signatures from within text too > > Just indicate the source as either Figure or Result text or both (Figure ** and Result Text)

Aleru Divine (15:54:22) (in thread): > I agree with@Scholastica Uruaand@Mildred Anashie. Mine is a table. > > So basically whatever has the relevant information on the differential abundance should be used whether a figure or table or text.

Chioma Onyido (16:35:51) (in thread): > Have you tried ‘Country’?

eneje promise (16:44:24): > hello everyone, pls I am trying to install the biocondutor package and it’s asking if I would like to use a personal library yes or No. which one should I choose?

Scholastica Urua (16:50:34) (in thread): > Hello@eneje promiseI don’t know the answer to this. A mentor will be able to provide an answer for you, just exercise patient.

Bolanle Wahab (16:52:34) (in thread): > @eneje promiseI’mnot sure what you mean by bioconductor package

Blessing Ene Anyebe (16:53:51) (in thread): > Hello@eneje promisecan you share more about what you are trying to achieve?

Abiola Salako (16:54:14): > hello everyone, I got a message while trying to add a study on the main page that I do not have the permission to edit the page. what shall I do, please? - File (PNG): image.png

Ima-obong (Aimah) (16:56:58) (in thread): > You need to logIn to your account first

Nekembe Boris (16:57:44) (in thread): > @Abiola Salako, was the paper assigned to you by a mentor?

Abiola Salako (16:58:02) (in thread): > Yes, THANK YOU@Ima-obong (Aimah)

Abiola Salako (16:58:36) (in thread): > @Nekembe BorisYES. THANK YOU. IT HAS BEEN RESOLVED

Mildred Anashie (16:59:02) (in thread): > You should have permission once you login like@Ima-obong (Aimah)said

Ima-obong (Aimah) (17:02:48) (in thread): > Hello please@svetlana_upthe previous paper I was assigned which was already halfway worked on by a past curator has completely different experimental procedures carried out in it which is highly distinct from the questions that we need to respond to… > > it uses different tests and methods and I’m stuck because the questions do not tally with the answers I’m to give from the paper.. > Please can I be assigned a new paper? . Thanks alot

Elsie Dickson (17:13:12): > Hello, please after the first mini-curation can I record my progress on the outreachy website?

Ruth Bamgbose (17:20:09) (in thread): > Yes you can

Elsie Dickson (17:26:11) (in thread): > Thank you so much@Ruth Bamgbose. I do have a follow up question though. There is a provision to include a link. Do I include the link to the page that says my survey has been completed after submitting the mini-curation?

Mildred Anashie (17:27:14) (in thread): > Include the link to the survey or the GitHub linkthat’stalking about the first contribution

Mildred Anashie (17:30:17): > @Elsie DicksonThis should help - Attachment: Attachment > Please see How do I record my contribution in the outreachy website? https://github.com/waldronlab/BugSigDBcuration/issues/96

Ruth Bamgbose (17:33:40) (in thread): > Yes, the link to the survey

Mildred Anashie (17:33:51): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy<@UBNSEMS3S>This is an excerpt from the paperI’mworking on “We found no significant enrichment of bacterial taxa in ‘culture-positive’ specimens when compared to the enrollment specimens of asymptomatic volunteers” > > > My question is should I still record this as an experiment, even though the results were not significant? > > Thank you for your help and responses so far:blush:

Naomi Ibe (17:43:31): > Please I need more clarity on bullet point 2, I don’t exactly understand what I should do when I find taxa with missing IDs plus how should I check for them too? > For bullet point 3, that asks to check the “Help” page on the website, are Outreachy applicants allowed to pick anything they’d like to work on right there on the site? - File (PNG): Screenshot_20240306-233942.png

Mildred Anashie (17:52:12): > For bullet point 2: You can follow the link andyou’dfind the pages with missing NCBI ID you can resolve but with the mentors confirmation and consent > > For Bullet point 3:it’sjust simply saying you can help out (contribute as well) in other ways too > > But the mentors can explain with more informed responses:blush:They might not be available immediately butI’msurethey’llrespond@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy

Elsie Dickson (17:52:14) (in thread): > Thank you, I appreciate your help.

Elsie Dickson (17:53:04) (in thread): > Thank you.@Mildred Anashie

Aleru Divine (17:54:37) (in thread): > @Naomi IbeFor bullet point 2, when you find a taxa with missing ncbi ID’s, you can search the name of the taxon on the taxonomy browser, get the taxonomy ID and record it. > > Link to taxonomy browser:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgiBugSigDB will recognize the ID and output the correct name > > See example image below. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (JPEG): IMG_7710

Naomi Ibe (17:56:37) (in thread): > Okay thanks alot:blush:

Naomi Ibe (17:57:19) (in thread): > Alrighty then, gracias:blush:

Aleru Divine (17:58:10) (in thread): > Then enter the Taxonomy ID as shown below. - File (JPEG): IMG_7742

Aleru Divine (18:02:48) (in thread): > For bullet point 3, that is just another way you can contribute to BugSigDB. > > > I will advice you ask the mentors before you work on anything on the help page.@Naomi IbeI hope I was able to help clarify this somehow:hugging_face:

UBNSEMS3S (18:05:23) (in thread): > I would just not record if it there are no significant results.

Mildred Anashie (18:06:27) (in thread): > Okay then > > Thank you:pray:

UBNSEMS3S (18:06:56) (in thread): > Look at “TODO for reviewers” on this page for additional options to help out:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Help:Contents > …

Muqtadirat Yussuff (18:11:06) (in thread): > Hi@eneje promiseI can’t give a definite response to your question but did you watch the YouTube video on importing BugSigDB data? I recall seeing “bugsigdbr” as the library. > > Here’s the link and I hope it provides some help:Importing BugSigDB data in R - Attachment (YouTube): Importing BugSigDB data in R

eneje promise (18:12:48) (in thread): > @Scholastica Urua@Bolanle Wahab@Blessing Ene AnyebeBioconductor is an open source software or tools in R used to make data analysis, visualization and statistics of data modelled on it. With this software we can manipulate or collaborate with data contained BugSigDB

Mildred Anashie (18:14:44): > Hello<@UBNSEMS3S>I have this organism found this way on the paper I’m curating ‘’Subdoligranulum spp.’’ but its this way on NCBI ‘’Subdoligranulum sp.’ can i go ahead to record it this way? > > Thank you:pray:

Joan C. Chukwuemeka (18:25:10): > Hello everyone, let’s remember our office hour on Thursday, 7 Mar 2024,:blush:Time: > 09:00 AM EST, > 14:00 (2:00PM) UTC, > 15:00 (3:00PM) WAT, > 17:00 (5:00PM) EAT, > 19:30 (7:30PM) IST; > For time zone not stated, you can check -https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Peace Daniel (18:25:20): > Hello > > I’m trying to find missing NCBI ID’s and I found this one on a google search and in some research articles but there’s no ID search result in NCBI or Uniprot. How do I proceed please > Ps:https://bugsigdb.org/Study_806/Experiment_2/Signature_1 - Attachment (BugSigDB): Study 806/Experiment 2/Signature 1 > Source: Supplementary file: Figure. S4a. Description: Discriminative OTUs observed in the pairwise comparisons between major depressive disorder (MDD) and healthy…

Peace Daniel (18:25:52) (in thread): > Thanks Joan:clap:

Mildred Anashie (18:26:24) (in thread): > Thank you@Joan C. Chukwuemeka

Joan C. Chukwuemeka (18:31:14) (in thread): > @Mildred AnashieSubdoligranulum spp.is plural (that is, refers tomultiple specieswithin the genus Subdoligranulum. It’s a broader term encompassing all known species in the genus) whileSubdoligranulum sp. is the singular, (refers to aspecific, unidentified specieswithin the genus Subdoligranulum.) > > I think it can be used as it is:thinking_face:… or perhaps try to see it the classified it further to the species level in the paper.

UBNSEMS3S (18:32:13) (in thread): > Some taxa will not have NCBI ids.

UBNSEMS3S (18:32:57) (in thread): > Yeah I think that’s close enough to curate.

Mildred Anashie (18:33:07) (in thread): > Itwasn’tfurther classified@Joan C. Chukwuemeka

Mildred Anashie (18:33:24) (in thread): > Okay > > Thank you<@UBNSEMS3S>:blush:

Peace Daniel (18:34:50) (in thread): > Am I to leave it as it is?

Mildred Anashie (18:35:07) (in thread): > @Peace DanielI think there are some taxas that should be left unresolved since there have probably not been classified and documented on NCBI

Mildred Anashie (18:35:57) (in thread): > You should leave it as it is

Peace Daniel (18:36:05) (in thread): > Alright,thanks

UBNSEMS3S (18:39:52) (in thread): > Correct leave them as-is.

Peace Daniel (18:52:03): > I added an NCBI ID, do I need to wait for a review first or can I record this as a contribution ?

Eniola Adebayo (18:54:03) (in thread): > Yes, I think it’s okay to record. But let our mentors confirm this.

Aleru Divine (19:01:58) (in thread): > You can record as a contribution and when it is reviewed by the mentors, you update the “Date contribution was accepted or merged”.

Joan C. Chukwuemeka (19:02:37): > In the study i’m curating (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8250416/), Supragingival biofilm samples were collected from patients who underwent allo-HSCT.(Supragingival biofilm samples refer to the collection of plaque ******from the teeth above the gum line.******* This plaque is a sticky film composed of bacteria, food debris, and salivary components.)****Body site - Supragingival dental plaque******Samples were collected with sterile swabs at three phases during allo-HSCT: before the conditioning regimen (preconditioning), at aplasia and at engraftment.In the context of the research, supragingival biofilm samples were collected at different stages of a stem cell transplant process to analyze the dental biofilm microbiota (DBM), which is the community of microorganisms living in the dental plaque. By studying these samples, researchers aimed to understand how the composition of this bacterial community changes throughout the transplant and whether these changes are associated with a potential complication called acute graft-versus-host disease (aGVHD).Condition- acute graft-versus-host disease (aGVHD).The researchers noted that,Differentially abundant genera across transplantation phases were identified using ANCOM.******ANCOM W represents the proportion of null hypotheses rejected when subtesting the differential abundance of a genus normalized by the abundance of each one of the genera in the dataset.********W > 0.7 was considered as statistically significant.*********Statistical test - ANCOM*** - Attachment (PubMed Central (PMC)): Dental Biofilm Microbiota Dysbiosis Is Associated With the Risk of Acute Graft-Versus-Host Disease After Allogeneic Hematopoietic Stem Cell Transplantation > Acute graft-versus-host disease (aGVHD) is one of the major causes of death after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Recently, aGVHD onset was linked to intestinal microbiota (IM) dysbiosis. However, other bacterial-rich gastrointestinal …

Peace Daniel (19:03:56) (in thread): > @Aleru Divinesounds good

Peace Daniel (19:04:00) (in thread): > Thank you both

Joan C. Chukwuemeka (19:04:59) (in thread): > However, the figure (figure 1C) which shows the differentially abundant genera via the ANCOM test, shows forpreconditioning (before treatment)andEngraftment (after treatment), but not forAplasia (during treatment). The supplementary material doesn’t capture such for Aplasia too > > Now, I’m having dual thoughts on what Experiements to create: > > A.One Experiment:Preconditioning (control) vs Engraftment > > OR > > BTwo Experiments::thinking_face:1. Preconditioning vs Aplasia(control) > 2. Aplasia (control) vs Engraftment > > Tho I’m looking more to go for my first thought of one Experiment..:thinking_face:<@UBNSEMS3S><@U1LCB8WEA>Please which do you think is more appropriate?

Joan C. Chukwuemeka (19:05:34): - File (JPEG): IMG-20240307-WA0000.jpg

Joan C. Chukwuemeka (19:06:17) (in thread): > https://community-bioc.slack.com/files/U05UTDTUHMH/F06NP8C8W5P/img-20240307-wa0000.jpg - File (JPEG): IMG-20240307-WA0000.jpg

Mildred Anashie (19:15:52) (in thread): > @Joan C. ChukwuemekaI can confirm your observation although I didn’t look at the supplemental figures /tables > > If you go with go with your B thought would you have appropriate results? > > More like increase and decrease based on the contrast:thinking_face:Just a way to brainstorm with you though

Eniola Adebayo (19:17:49) (in thread): > You can have more than one experiment. So I think you can curate the three.:thinking_face:

Muqtadirat Yussuff (19:30:41): > Hi everyone, I was editing an incomplete signature form I created. I saved and realized a signature 3 form was created instead of signature 2 being edited. I tried deleting but it’s an admin privilege. What do I do asides bringing it up here?

Mildred Anashie (19:32:34) (in thread): > Just request for it to be deleted as you already have > > The mentors will delete it, we do not have permission to do that > > Also be patient, it will be attended to:blush:

Muqtadirat Yussuff (19:35:26) (in thread): > Will do, thank you

Abiola Salako (20:04:08) (in thread): > Kindly make it known to our mentor@Esther Afuape

Peace Daniel (20:06:18) (in thread): > :eyes::eyes:mentor??:face_with_hand_over_mouth::man_dancing:

Abiola Salako (20:10:56) (in thread): > @Joan C. ChukwuemekaI would suggest you do the grouping as it was being grouped in your article.

Praise Agbetuyi (20:22:14): > Hello everyone!@Svetlana Ugarcina PerovicThank you for the concise and easily comprehensible introduction to the project and the tasks ahead.

Scholastica Urua (22:03:57) (in thread): > Nice one@Aleru Divine, this is a really helpful tip.:pray:

Scholastica Urua (22:06:31) (in thread): > Thank you for the reminder@Joan C. Chukwuemeka. For those of us in Nigeria that’ll be 3 PM today.

Scholastica Urua (22:13:18) (in thread): > We do not have permission to delete. Just exercise a little patience, I’m sure a mentor will get to it.

Scholastica Urua (22:14:06) (in thread): > Welcome@Praise Agbetuyi, nice to have you here.

Adegboye Rukayat (23:04:18) (in thread): > @Rahila-meplease how do you record your first contribution.

Adegboye Rukayat (23:19:07): > Please I need help, I did and finished my first contribution yesterday, just for me to record my contribution on the Outreachy website now and I couldn’t/ didn’t know how to get contribution URL. Anyone that can help me please. I am new to open source.

Adegboye Rukayat (23:20:10): > Do I have to redo the survey again?

Scholastica Urua (23:25:52) (in thread): > Hello@Adegboye Rukayatyou do not need to redo your first contribution. As far as you filled the first curation form appropriately with your name, email, GitHub and slack address the mentors have what they need. > > What you need to do is copy a link to the form and paste as your contribution URL (https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc). > > I hope this is helpful. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Adegboye Rukayat (23:48:51) (in thread): > Thank you, it is helpful

2024-03-07

Mildred Anashie (00:31:11) (in thread): > I agree with you@Praise AgbetuyiThank you to our mentors for making it quite easy to understand the project and being responsive as well:blush:<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape:pray:

Ifeyinwa Ohondu (00:36:23): > Hi@Svetlana Ugarcina Perovic@Peace SandyI’ve concluded my first contribution and would like to do second but there are no available issues to choose from. kindly advise.

Mildred Anashie (00:37:47) (in thread): > Hi@Ifeyinwa OhonduI think the issue has been raised and the mentors are awareI’msurethey’lladd more issues, just be patient with them

Blessing Ene Anyebe (00:41:14) (in thread): > Thank you for sharing@Joan C. Chukwuemeka:orange_heart:

Aleru Divine (00:45:12) (in thread): > Hi@Praise Agbetuyi, welcome:hugging_face:

Aleru Divine (00:45:48) (in thread): > Nicely done@Scholastica Urua:white_check_mark:

Aleru Divine (00:48:03) (in thread): > Hi@Ifeyinwa Ohondu, I agree with@Mildred Anashie, the mentors will add some more issues soon.They are already aware.

Aleru Divine (00:48:26) (in thread): > Thank you@Scholastica Urua

Faith Ifeoluwa Alexander (00:48:43): > Hello, Good Morning everyone. If you are new here, you are free to reach out to me to help with your first contribution. I will be glad to help.

Faith Ifeoluwa Alexander (00:49:18) (in thread): > How would we know when new issues are added?

Aleru Divine (00:50:44) (in thread): > Good morning@Faith Ifeoluwa Alexander

Aleru Divine (00:51:32) (in thread): > @Faith Ifeoluwa AlexanderI think we will be informed here when new issues are added.

Faith Ifeoluwa Alexander (00:51:40) (in thread): > Good morning@Aleru Divine, hope your night was restful?

Scholastica Urua (00:51:57) (in thread): > @Faith Ifeoluwa Alexanderthe new issues will appear on the GitHub issue page

Faith Ifeoluwa Alexander (00:52:11) (in thread): > Okay. Thanks@Aleru Divine.

Aleru Divine (00:52:47) (in thread): > Yes it was, I hope yours was too.

Faith Ifeoluwa Alexander (00:54:27) (in thread): > Yes, it was. Thank you.

Faith Ifeoluwa Alexander (00:56:17) (in thread): > Okay.@Adegboye Rukayat. Go to the project page for BugSigDB on the outreachy website and click on the link to record your contributions.

Elsie Dickson (01:10:09) (in thread): > Hi there@Ifeyinwa Ohonduat the moment, I can see two or more new issues and they have not been assigned to anyone yet. You may want to check them out and leave a comment asking to be assigned to one of them. This link will take you to the issues page on Github directlyhttps://github.com/waldronlab/BugSigDBcuration/issues

Naomi Ibe (01:14:51) (in thread): > @Aleru Divinethank you very much

Faith Ifeoluwa Alexander (01:18:11) (in thread): > Hi@Svetlana Ugarcina Perovic, is it Okay to apply for multiple papers to increase my chances to getting assigned to one?

Joan C. Chukwuemeka (01:22:00) (in thread): > Thanks everyone for your insights.@Eniola AdebayoExperiments are defined by contrasts that are made: Hence in this case, although samples were collected in three stages, the current contrast I can see for differentially abundant genera is between Preconditioning (before treatment) and Engraftment (after treatment).
> My question is for a second look at article, perhaps if the stage not captured can be used as control… > I think I’d be going for my first thought of curating one Experiment -Preconditioning (Control) vs Engraftment (Group 1)@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI’d appreciate our input on this please. > Hope I’m on the right track?:pray:

Abiola Salako (01:31:49) (in thread): > Good Morning@Faith Ifeoluwa Alexander.

Faith Ifeoluwa Alexander (01:31:49) (in thread): > I have asked to be assigned to one. However, can I apply to be assigned to more than one paper to increase my chances of being assigned?@Elsie Dickson

Okache Johnpaul (01:33:03): > Hey Everyone, good morning. I’d like to confirm the time for office hours please?

Mildred Anashie (01:33:43) (in thread): > Hi@Okache Johnpaulthe time is 9am EDT@Svetlana Ugarcina Perovicsaid the link will be posted today

Mildred Anashie (01:34:45): > @Okache Johnpaulsee this post - Attachment: Attachment > Hello everyone, let’s remember our office hour on Thursday, 7 Mar 2024, :blush: > Time: > 09:00 AM EST, > 14:00 (2:00PM) UTC, > 15:00 (3:00PM) WAT, > 17:00 (5:00PM) EAT, > 19:30 (7:30PM) IST; > For time zone not stated, you can check -https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179

Aleru Divine (01:34:59) (in thread): > Hi@Okache Johnpaul, here’s is the time for office hours.@Joan C. Chukwuemekahelp with conversion to different time zoneshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709767510011139 - Attachment: Attachment > Hello everyone, let’s remember our office hour on Thursday, 7 Mar 2024, :blush: > Time: > 09:00 AM EST, > 14:00 (2:00PM) UTC, > 15:00 (3:00PM) WAT, > 17:00 (5:00PM) EAT, > 19:30 (7:30PM) IST; > For time zone not stated, you can check -https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179

Scholastica Urua (01:35:47) (in thread): > That’s 3 PM if you are in Nigeria@Okache Johnpaul

Faith Ifeoluwa Alexander (01:36:23) (in thread): > Good morning@Abiola Salako

Okache Johnpaul (01:37:15) (in thread): > Awesome. Thank you very much@Mildred Anashie,@Aleru Divineand@Scholastica Urua!

Aleru Divine (01:38:35) (in thread): > @Faith Ifeoluwa Alexanderyou can only curate one paper at a time.When you are done curating and it is reviewed, you can ask to be assigned another one.

Aleru Divine (01:39:25) (in thread): > You’rewelcome@Naomi Ibe:hugging_face:Good morning:sunny:

Faith Ifeoluwa Alexander (01:42:17) (in thread): > Okay@Aleru Divine. I asked because I saw two other people asking to be assigned on the paper I asked to be assigned to. So I was thinking if I applied on another paper, maybe my chances will improve.

Mildred Anashie (01:44:51) (in thread): > No@Faith Ifeoluwa Alexanderpick a paper thathasn’tbeen assigned to anyone and if there are other comments thereit’llpossibly be assigned to the first

Mildred Anashie (01:45:17) (in thread): > Look for one and be first to comment on it > > ThenI’mpositiveyou’dbe assigned to it

Abiola Salako (01:46:11) (in thread): > @Mildred Anashieyou’re right. She should look for the one that hasn’t been assigned to anyone yet.

Faith Ifeoluwa Alexander (01:47:24) (in thread): > I have seen a couple of papers that have not been assigned yet but people have commented on it before me.

Desire Oluwarotimi (01:48:41): > Good morning everyone. > > Yesterday’s discussion on the platform was enlightening and I got to learn a lot. I’m looking forward to what today has in store. > > Let’s get it guys.:sunglasses:

Eniola Adebayo (01:49:41): > Good morning@Desire OluwarotimiToday is going to be another great day

Aleru Divine (01:49:43) (in thread): > Good morning@Desire OluwarotimiLet’sgooo!!!:sunny:

Sandra Dindi (01:50:05): > Morning guys. I have finished my second contribution. Where do I submit? Thank you.

Mildred Anashie (01:50:24) (in thread): > Good morning@Desire OluwarotimiDefinitely enlightening:hugging_face:

Desire Oluwarotimi (01:50:37) (in thread): > @Aleru DivineThat’s the energy.:laughing:

Desire Oluwarotimi (01:50:51) (in thread): > Yeah@Mildred Anashie

Desire Oluwarotimi (01:51:29) (in thread): > Hi@Sandra DindiYou can simply indicate on the GitHub issue you worked on saying you are done. Do well to tag the mentors as well.

Mildred Anashie (01:51:44) (in thread): > Comment on the issue and drop the link to the study on BugSigdb along side the comment on GitHub

Scholastica Urua (01:51:52) (in thread): > I think you’re suppose to tag the mentors so they can review it. And also record it on outreachy as your second contribution

Desire Oluwarotimi (01:51:59) (in thread): > Yes, it is.

Aleru Divine (01:52:25) (in thread): > Good morning@Sandra Dindi, leave a comment on GitHub that you have completed the curation and it will be reviewed.You can add your second contribution on the outreachy website too using the link to the study you curated.

Eniola Adebayo (01:52:25) (in thread): > Record your contribution on Outreachy

Sandra Dindi (01:52:42) (in thread): > Thanks for the help guys.:pray:

Elsie Dickson (01:54:15) (in thread): > @Faith Ifeoluwa AlexanderI do not think so, the person who commented on it first will most likely be assigned to curate it. If that is the case I am sure there will be other papers to curate and you can ask to be assigned to one as soon as it is available.

Aleru Divine (01:54:25) (in thread): > @Faith Ifeoluwa AlexanderI thinkIt’llbe assigned to the first person that indicated interest.

Faith Ifeoluwa Alexander (01:55:09) (in thread): > Okay. I will be on the lookout then. Thank you.

Faith Ifeoluwa Alexander (02:12:36): > @ADAEZE SIMONThis is the introduction you need to start with your first contribution. > > However, you can let me know if you need further clarification. - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

ADAEZE SIMON (02:17:02) (in thread): > Thank you

Ifeyinwa Ohondu (02:36:16) (in thread): > Thanks@Elsie Dickson

Ifeyinwa Ohondu (02:36:28) (in thread): > Thanks everyone for the responses

Okache Johnpaul (02:42:22) (in thread): > Thank you@Joan C. Chukwuemeka!

Chioma Agu (02:49:02): > Good morning everyone. > Yesterday, I finished my first contribution and I must say when I had challenges, it was much easier to scale through because there was a solution to it right on the chat. Thank you to everyone who has been contributing solutions and everyone asking questions too! A supportive community for real! > > looking forward to the office hours today:star:

Blessing Ene Anyebe (02:49:55) (in thread): > Congratulations Chioma!You’reabsolutely correct! > > Looking for office hours as well!:partying_face:

Desire Oluwarotimi (02:50:20) (in thread): > Weldone@Chioma AguI’m glad you are getting along.

Aleru Divine (02:51:47) (in thread): > Congratulations on completing your first contribution@Chioma Agu:partying_face:I’m glad you were able to find a solution to the challenge you faced through the chats:hugging_face:Community support is one of the amazing things I love about open source.:blush::heart:

Eniola Adebayo (02:51:48) (in thread): > Congratulations. I agree, the chats are so helpful.Well done everyone:thumbsup:

Scholastica Urua (02:54:46) (in thread): > Well done@Chioma Agu:+1:Thank you everyone, the chats here have also helped me a lot:pray:

Aleru Divine (02:56:43) (in thread): > Nicely done@Faith Ifeoluwa Alexander:white_check_mark:

Chioma Agu (03:03:26) (in thread): > Thanks guys!:sparkles::sparkles:

Rahila-me (03:13:49) (in thread): > YOu are welcome

Chimdimma Nwachukwu (03:19:38): > @Faith Ifeoluwa Alexanderhi, I am extremely new. Please help. I feel a bit nervous already.

Rahila-me (03:21:28): > @Chimdimma Nwachukwucalm down, no need for that you can start from here.https://github.com/waldronlab/BugSigDBcuration/issues/94. click the link all you needed is there. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Bolanle Wahab (03:22:01) (in thread): > @Chimdimma Nwachukwuhey,you’rewelcome,this is a safe space andeveryone’swilling to help with whatever you need I assure you, all you have to do is ask:heart:

Nekembe Boris (03:22:03) (in thread): > Do not be@Chimdimma Nwachukwu. We are all here to help. Just ask any questions

Desire Oluwarotimi (03:22:24) (in thread): > Hi@Chimdimma NwachukwuWhile this can be daunting at first, there’s really no need to fret because you’ll get a hang of things as you go on. > > By the way, asking questions will help you greatly. Everyone here is kind enough to assist when they can.

Desire Oluwarotimi (03:23:13) (in thread): > You might want to check this out too.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Nana (03:23:26) (in thread): > @Chimdimma Nwachukwufeel free to reach me for more clarification

Chimdimma Nwachukwu (03:23:29) (in thread): > Thank you so much@Rahila-me

Blessing Ene Anyebe (03:24:00) (in thread): > Hello@Chimdimma Nwachukwuyou’revery welcome.:orange_heart:It is okay to feel overwhelmed but rest assured that we are all here to help and be helped as well.You’vegot this!:hugging_face:

Aleru Divine (03:26:14) (in thread): > Welcome@Chimdimma Nwachukwu:hugging_face:It’sokay to be nervous but I assure you that this is a very supportive community.We are all here to contribute, learn and help each other.I also found this helpful. It’s a list of some of the FAQs and answers to get started with for your first contributionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Chioma Agu (03:26:48) (in thread): > Hello, Welcome@Chimdimma NwachukwuIt’sokay to feel that way at first but youdon’tneed to feel nervous. > You will get all the help you need here > > Here are some FAQs you could go through to give you some understandinghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349

Aleru Divine (03:28:42) (in thread): > @Chimdimma NwachukwuHere’s a quick guide to make your first contribution, > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > Link to curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcBe sure to ask questions when it gets challenging - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Svetlana Ugarcina Perovic (03:37:09): > Good morning:umbrella_with_rain_drops:from rainy Novi Sad (Serbia) > > Today we will have ourteam weekly meeting where we will introduce ourselves, you will have a chance to introduce yourself, bring up your project doubts and/or share with others how you solved some of your issues in the project.To join the video meeting, click this link: https://meet.google.com/uit-bzbe-tcySee you at 9 AM EDT (eastern daylight time)! > Find out the time in your local time zone here:https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179(edited)

Esther Afuape (03:37:17) (in thread): > Please provide a link to the study and what should be deleted@Muqtadirat Yussuff

Blessing Ene Anyebe (03:37:40) (in thread): > Thank you@Svetlana Ugarcina PerovicLooking forward to it.

Scholastica Urua (03:37:41) (in thread): > Thanks@Svetlana Ugarcina PerovicLooking forward to meet everyone.:hugging_face:

Aleru Divine (03:39:01) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Peace Daniel (03:41:45) (in thread): > Looking forward to it

Nwajei Edgar (03:43:06) (in thread): > Good morning:innocent::innocent:

Nana (03:44:11) (in thread): > Noted

Esther Afuape (03:46:50) (in thread): > Hi@Joan C. Chukwuemekayes, you’re right to curate one experiment for the only comparison carried out. Only comparisons carried out should be curated as experiments

Raihanat Adewuyi (04:00:15) (in thread): > Looking forward to it. > Thanks@Svetlana Ugarcina Perovic

Desire Oluwarotimi (04:02:20) (in thread): > Thank you.@Svetlana Ugarcina Perovic

Blessing Ene Anyebe (04:02:42): > Hello everyone, this may not be a very specific question but for better understanding, can you share how you went about the second contribution? > What are the first steps you took and how did you go about it? > Thank you so much.

eneje promise (04:03:39) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (04:03:47) (in thread): > Hi@Blessing Ene AnyebeThis should help youhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Ifenna Muonagolum (04:04:07): > Hello everyone, I am new here. Can someone direct me on what is required of me to do?

Mildred Anashie (04:04:08) (in thread): > Also the onboarding videos are helpful too

Blessing Ene Anyebe (04:04:59) (in thread): > Hello@Ifenna Muonagolumyou’re welcome to the community. Check this article to get a soft landing.https://chiomaonyido.wordpress.com/2024/03/05/from-learner-to-contributor-strategies-for-making-the-most-out-of-your-outreachy-contribution-stage/To get started on the project see this repohttps://github.com/waldronlab/BugSigDBcuration/issues/94I hope it helps, don’t hesitate to reach out! Good luck as well. - Attachment (…tales (and tips) from a bioCurious opensource bébé…): From Learner to Contributor: Strategies for Making the Most out of Your Outreachy Contribution Stage > I shared some tried-and-true tips and advice for future contributors looking to make their mark in their respective open-source communities. The post emphasizes starting contributions early, mainta… - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Blessing Ene Anyebe (04:06:20) (in thread): > Yes the onboarding videos are helpful. Thank you@Mildred AnashieThe add a study video helps us well for the second contribution task.

Mildred Anashie (04:06:28) (in thread): > You can start by going through the article and identifying what should be curated based on what BugSigdb requires > > Then you record them following the steps provided from the onboarding videos

Blessing Ene Anyebe (04:07:19) (in thread): > I think whatI’masking is from a personal POV, how did you tackle yours, what did you do first. > > But thank you so much.

Mildred Anashie (04:07:32) (in thread): > Hello@Ifenna MuonagolumWelcome

Scholastica Urua (04:08:19) (in thread): > Hello@Ifenna Muonagolumwelcome > You can also check out the pinned messages. They’re very helpful.

Blessing Ene Anyebe (04:08:22) (in thread): > Plus I don’t know if we are allowed to share that:sweat_smile:

Aleru Divine (04:08:23) (in thread): > Hey@Blessing Ene Anyebe, > > Just like@Mildred Anashiepointed out, the curation policy and the onboarding videos were very helpful to me too. > > Then I noted the things that I would need to curate and I kept it in mind as I read through the article that was assigned to me. That way I knew exactly the important information to look out for.

Mildred Anashie (04:08:32) (in thread): > Okay I understand you

Peace Daniel (04:08:41) (in thread): > Welcome@Ifenna MuonagolumDo let us know if you still need help after reading the article:blush:

Svetlana Ugarcina Perovic (04:08:51) (in thread): > @Blessing Ene Anyebeexcellent question! Looking forward to read the answers here.

Blessing Ene Anyebe (04:09:21) (in thread): > Wow thank you so much@Svetlana Ugarcina Perovic:sweat_smile:

Desire Oluwarotimi (04:09:32) (in thread): > Welcome@Ifenna Muonagolum

Mildred Anashie (04:09:42) (in thread): > @Blessing Ene Anyebeyea I think we are allowed to help each other and ask questions too:blush:

Nana (04:09:52): > @Ifenna Muonagolumwelcome. Check out the pinned messages

Peace Daniel (04:10:47) (in thread): > I agree with@Aleru DivineTaking a note of whatyou’rerequired tocurate is important, you can also try highlighting the document when reading through so youdon’tmiss important points

Mildred Anashie (04:11:28) (in thread): > Reading the article thoroughly helped me bearing in mind whatI’mlooking out for, the contrasts made and identify the significant signatures

eneje promise (04:11:29): > Hello everyone, I have read through the first task extensively. I want to know if I am supposed to point out the key points I think the author didn’t point out or didn’t structure? Or I should just summarize the key points and structure it the way I think it should be.

Svetlana Ugarcina Perovic (04:12:08) (in thread): > @Faith Ifeoluwa Alexanderchoose paper of your interest, we will be adding more soon.

Peace Daniel (04:12:36) (in thread): > Hello promise, you’re supposed to respond to a survey

Aleru Divine (04:12:39) (in thread): > @Blessing Ene AnyebeI also checked out some completed curations and their respective articles.That was really helpful because they gave me more insights on how to curate mine.Goodluck with your second contribution:hugging_face:

eneje promise (04:12:52) (in thread): > Welcome@Ifenna Muonagolum

Mildred Anashie (04:12:59) (in thread): > I’mnot sure I understand you > > But you are supposed to answer the survey questions

Scholastica Urua (04:13:24) (in thread): > @eneje promiseThe first task involves filling a survey form.

Peace Daniel (04:13:47) (in thread): > Let me get the link to the survey for you@eneje promise

Svetlana Ugarcina Perovic (04:14:07) (in thread): > Ok@Ima-obong (Aimah)I already assigned to you other paper. No worries, keep up the good work!

eneje promise (04:14:09) (in thread): > @Peace Danielcan I have the link to the survey?

Desire Oluwarotimi (04:14:29) (in thread): > Here’s my little input. > > Like others have mentioned, make sure to go through the provided materials. I also think the style of approach to curating might differ from person to person. > > In my case, I go through the article and then try to later highlight the answers to each input field for curation. That way I can easily pinpoint at other times.

Aleru Divine (04:14:30) (in thread): > Hi@Ifenna Muonagolum, welcome:hugging_face:

Blessing Ene Anyebe (04:14:37) (in thread): > Thank you@Aleru Divine@Peace Danielit’s great you hear from your POV. Thank you for sharing.

Peace Daniel (04:15:15) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Aleru Divine (04:16:06) (in thread): > @eneje promiseyou are supposed to fill the survey after going through the annotated article.That is the first contribution.Here is the link:https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

eneje promise (04:16:26) (in thread): > @Peace Danielok because from the one I used they asked us to summarize the key points from the article that talked about the things that causes breast cancer

Peace Daniel (04:16:39) (in thread): > @eneje promisethere’san article in the link, read it carefully and answer the survey questions. > Feel free to ask ifyou’restill confused

Peace Daniel (04:16:40) (in thread): > @eneje promisethere’san article in the link, read it carefully and answer the survey questions. > Feel free to ask ifyou’restill confused

dehbeie donatus (04:17:12) (in thread): > Just to be sure, that’s 4pm Nigeria time right?

Blessing Ene Anyebe (04:17:37) (in thread): > Its 3PM for us in Nigeria

Blessing Ene Anyebe (04:17:52) (in thread): > @dehbeie donatus

Peace Daniel (04:17:57) (in thread): > Please read the instructions again, Ididn’tnote any summary requests or you can just point me to it

Aleru Divine (04:18:11) (in thread): > You’rewelcome@Blessing Ene Anyebe:hugging_face:

Aleru Divine (04:21:08): > Incase anyone is confused regardingtime for office hours.@Joan C. Chukwuemekahelpedwith conversion to different time zoneshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709767510011139 - Attachment: Attachment > Hello everyone, let’s remember our office hour on Thursday, 7 Mar 2024, :blush: > Time: > 09:00 AM EST, > 14:00 (2:00PM) UTC, > 15:00 (3:00PM) WAT, > 17:00 (5:00PM) EAT, > 19:30 (7:30PM) IST; > For time zone not stated, you can check -https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179

Hamidat Mohammed (04:21:23): > Good morning everyone. Please I am finding it difficult to understand the second contribution

Peace Daniel (04:22:06) (in thread): > Good morning,can you share what your difficulty is?

Blessing Ene Anyebe (04:22:18) (in thread): > Hi@Hamidat MohammedI think you will find this useful as wellhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709802162577809 - Attachment: Attachment > Hello everyone, this may not be a very specific question but for better understanding, can you share how you went about the second contribution? > What are the first steps you took and how did you go about it? > Thank you so much.

Aleru Divine (04:22:47) (in thread): > Hi@Hamidat Mohammed, please what exactly are you finding difficult so we can know how best to help.

Blessing Ene Anyebe (04:23:05) (in thread): > Plus it really helps to read/study and comprehend the available resources.

Hamidat Mohammed (04:23:45) (in thread): > I am confused what am is supposed to do first please?

Scholastica Urua (04:23:53) (in thread): > Hello@Blessing Ene AnyebeThis is a summarized steps I made up for the second curation; > > 1. First go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly. > > 2. Check out already curated papers > > (I found it very helpful to do 1 and 2 simultaneously. That way you’ll easily understand what the curation policy is talking about) > > 3. Watch the onboarding videos especially “a step-by-stepwalk-throughof how to add a new study through the curation interface of BugSigDB” > > 4. After being assigned a paper, go through the paper and highlight informations to be curated. > > In addition, I find searching (Ctrl + f) for specific information to be very helpful. Like specifically searching for the word ‘match’ or ‘antibiotic’ to identify matched-on or antibiotics exclusion criteria respectively. - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy… - Attachment (YouTube): Adding a study to bugsigdb.org

Aleru Divine (04:23:57) (in thread): > I agree with@Blessing Ene Anyebebe sure to go through the resources and watch the video tutorials.

Aleru Divine (04:24:27) (in thread): > @Hamidat Mohammedhave you been assigned an issue?

Hamidat Mohammed (04:24:35) (in thread): > NoI haven’t

dehbeie donatus (04:25:22) (in thread): > Thank you@Blessing Ene Anyebe

Mildred Anashie (04:26:25) (in thread): > Thank you@Aleru DivineAlso the link to use to join whenIt’stime has already been postedby one of our mentors@Svetlana Ugarcina PerovicThis is the linkhttps://meet.google.com/uit-bzbe-tcy - Attachment (meet.google.com): Meet > Real-time meetings by Google. Using your browser, share your video, desktop, and presentations with teammates and customers.

Aleru Divine (04:26:53) (in thread): > @Hamidat MohammedOkay, first off, you need to request to claim an issue(when it is available) and it will be assigned to you. > > While you wait, you can go through the curation policy and onboarding materials.

Mildred Anashie (04:27:01) (in thread): > @Hamidat Mohammedplease request for an issue to be assigned to you

Hamidat Mohammed (04:27:49) (in thread): > No issue is available

Mildred Anashie (04:27:52) (in thread): > Just to add to what@Aleru Divinesaid > > You can also go through other curated papers that have been reviewed on BugSigdb to help you familiarize with how to go about yours

Mildred Anashie (04:28:22) (in thread): > The mentors will upload more > > They are aware, just be patient

dehbeie donatus (04:28:33) (in thread): > Looking forward to it@Svetlana Ugarcina Perovic

Hamidat Mohammed (04:28:33) (in thread): > Okay thank you everyone

Aleru Divine (04:28:34) (in thread): > @Hamidat MohammedYes that’s true, the mentors will upload more issues soon. > > You can see the Curation policy here:https://community-bioc.slack.com/files/U05UTDTUHMH/F06133YQJHH/curation_policy_-_bugsigdb.pdf - File (PDF): Curation Policy - BugSigDB.pdf

Blessing Ene Anyebe (04:29:04) (in thread): > What you did with the first contribution was also a curation but in that you were curating what had already been curated and pointing out important details you should note about curations. > > With these understanding in working on your second contribution you already have ideas on major things to look out for when curating. > > I hope this helps when you are assigned an issue. > > So read the curation policy as@Aleru Divineshared. This will certainly help make the terms easier to understand and walk through.

Hamidat Mohammed (04:30:47) (in thread): > Thank you so much

Mildred Anashie (04:30:52) (in thread): > This is detailed@Scholastica UruaWell done

Blessing Ene Anyebe (04:31:48) (in thread): > Yes, love it@Scholastica Uruathanks for sharing!

Muqtadirat Yussuff (04:32:21) (in thread): > @Esther AfuapeSignature 3 please and thank youFeeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut - Attachment (BugSigDB): Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut - BugSigDB > Diet is a major determinant of intestinal microbiome composition.While studies have evaluated microbiome responses to diet variation, less is understood about how the act of feeding influences the microbiome, independent of diet type.

Aleru Divine (04:33:05) (in thread): > I agree, well done@Scholastica Urua

Esther Afuape (04:34:23) (in thread): > Signature 3 deleted:white_check_mark:

Muqtadirat Yussuff (04:35:52) (in thread): > Thank you so much

Abiola Salako (04:36:15) (in thread): > You’re welcome@Ifenna Muonagolum

Desire Oluwarotimi (04:36:55) (in thread): > Weldone@Scholastica Urua

Scholastica Urua (04:37:05) (in thread): > @Hamidat MohammedIn addition to what@Blessing Ene Anyebesaid, this may also be helpful:point_down:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709803433606669?thread_ts=1709802162.577809&cid=C04RATV9VCY - Attachment: Attachment > Hello @Blessing Ene Anyebe > This is a summarized steps I made up for the second curation; > > 1. First go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly. > > 2. Check out already curated papers > > (I found it very helpful to do 1 and 2 simultaneously. That way you’ll easily understand what the curation policy is talking about) > > 3. Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study through the curation interface of BugSigDB” > > 4. After being assigned a paper, go through the paper and highlight informations to be curated. > > In addition, I find searching (Ctrl + f) for specific information to be very helpful. Like specifically searching for the word ‘match’ or ‘antibiotic’ to identify matched-on or antibiotics exclusion criteria respectively.

Mildred Anashie (04:39:23): > Hello everyone > > Figured this will be helpful seeing as some of the questions asked here have already been answered by the mentors previously > > PS: This was created by one of our co-mentors@Chioma Onyidobut I thinkit’sopen access and more questions can be added for response by the mentors (This is also me seeking permission to share this instead of recreating another) > > Also can this be pinned for easy access?https://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/edit - File (Google Docs): Questions for BugSigDB Mentors

Muqtadirat Yussuff (04:39:39) (in thread): > @Hamidat MohammedTo add to what everyone has said, do not rush, if you feel stuck or conflicted go through already curated papers, compare with yours and if it’s not enough bring your questions here. > > Mentors and participants would be available to assist you. Happy reading:sparkles:

Hamidat Mohammed (04:40:55) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Muqtadirat Yussuff (04:41:11) (in thread): > Thank you for providing this, it answers a few questions I was about to ask

Ruth Bamgbose (04:41:26) (in thread): > Thank you, this would be really helpful

Blessing Peters (04:41:33) (in thread): > Thank you for this.

Aleru Divine (04:41:43) (in thread): > Thanks for sharing@Mildred Anashie:pray:

Desire Oluwarotimi (04:42:04) (in thread): > Thank you.

Blessing Ene Anyebe (04:42:15) (in thread): > Yes, this is so helpful! Thank you for sharing@Mildred Anashie

Scholastica Urua (04:43:15) (in thread): > Thanks for sharing@Mildred Anashie:pray:

Hamidat Mohammed (04:46:14) (in thread): > Please can I get the link to where I can find already curated papers.

Blessing Ene Anyebe (04:47:20) (in thread): > https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Blessing Ene Anyebe (04:47:47) (in thread): > Check this resource

Scholastica Urua (04:48:35) (in thread): > In the curation policy link, under the ‘Study Design’ section, each study design has an already curated examples.

Hamidat Mohammed (04:48:38) (in thread): > Thank you

Mildred Anashie (04:49:14) (in thread): > If you have requested for an account and it has been approved you can find studies on BugSigdb > > Butyou’llhave to search though

Abiola Salako (04:49:58) (in thread): > Thanks for sharing@Mildred Anashie

Muqtadirat Yussuff (04:50:02) (in thread): > You can also use the “Random Page” feature if you’re not searching for a specific topic

Adejoke Ogunyinka (04:51:02) (in thread): > Thank you for sharing

Aleru Divine (04:53:09) (in thread): > You can find studies herehttps://bugsigdb.org/Main_PageGo to Random page and a random study will pop up - Attachment (BugSigDB): Main Page > … - File (JPEG): IMG_7746 - File (JPEG): IMG_7745

NWAKAEGO VINCENT (04:53:46): > thank you@Suru Olaitanfor your assistance

Adenike Oladimeji-Kasumu (04:55:18) (in thread): > @Chioma OnyidoYes, but there is no option for country

Abiola Salako (05:02:01): > Well done, everyone. Please what do I do if the paper I’m working on gets stuck on “Needs Review” to which I’m yet to add any signatures?

Aleru Divine (05:03:08) (in thread): > @Abiola Salakoyou can proceed to add the signatures and complete your curation. The mentors are responsible for reviewing.

Nitya Singhal (05:03:17): > Is the paper named “Breast cancer patients from the Midwest region of the United States have reduced levels of short‑chain fatty acid‑producing gut bacteria.” allotted to me?

Scholastica Urua (05:03:47) (in thread): > @Abiola SalakoAfter curation, your paper will be automatically tagged “Needs Review”. You can go ahead to add experiment by clicking ‘Add Experiment’ or add a signature by clicking ‘Add Signature’

Desire Oluwarotimi (05:03:57) (in thread): > @Abiola SalakoIt probably means it’s up for review already but you can still make any changes you want.

Mildred Anashie (05:04:01) (in thread): > Yea proceed to add experiment and signatures

Amanda Adoyi (05:04:14): > @Svetlana Ugarcina Perovic@Chioma OnyidoAloha people. Hope your day is going great? I’ve got a question about semantics here. For instance the term “neonatal mortality” refers to death within the first 28 days of life. Imagine your paper uses that exact phrasing but refers to early death which may have occurred even within six months of life. Do you just go ahead and add “neonatal death” as your condition knowing that when a reviewer clicks on it they’ll probably understand it differently from what you intended?

Nitya Singhal (05:04:38): > How will I know if a paper is allotted to me? Kindly help me with this.

Mildred Anashie (05:04:53) (in thread): > You’dget a mail

Desire Oluwarotimi (05:04:59) (in thread): > Hi@Nitya SinghalNo, it isn’t. > It is just the paper you need to study to be able to attempt the first task.

Abiola Salako (05:05:12) (in thread): > Alright. Thanks, everyone.

Nitya Singhal (05:05:16) (in thread): > How will that happen? Do we need to fill a form for that?

Mildred Anashie (05:05:51) (in thread): > But if you are the only one that has dropped a comment on an issue > > You can go ahead and start curating,it’ll be assigned to you

Desire Oluwarotimi (05:06:00) (in thread): > You have to first make a request to get assigned to a paper.

Aleru Divine (05:06:07) (in thread): > @Nitya Singhal, that paper is general.It is the first contribution.It is in the second contribution that we get assigned different papers for curation.

Nitya Singhal (05:06:14) (in thread): > May I know what exactly task 1 expects us to do by the word “mini-curation”?

Mildred Anashie (05:06:22) (in thread): > No youdon’tneed to fill a form > > Drop a comment on an issue thathasn’tbeen assigned to anyone yet on GitHub

Muqtadirat Yussuff (05:07:08) (in thread): > Here’s the github link for issues, you’d get a mail once you’ve been assignedhttps://github.com/waldronlab/BugSigDBcuration/issues

Desire Oluwarotimi (05:07:20) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709704181863569?thread_ts=1709704114.665069&cid=C04RATV9VCY - Attachment: Attachment > Hi @Bolanle Wahab > > The mentors will attach an assign tag and you should see your name on the right hand side as an assignee when using a desktop view.

Aleru Divine (05:07:59) (in thread): > @Nitya SinghalRequest to claim an issue on GitHubhttps://github.com/waldronlab/BugSigDBcuration/issuesThenyou’llget a mail when you have been assigned.

Desire Oluwarotimi (05:08:07) (in thread): > You are expected to simply answer a survey.

Scholastica Urua (05:08:37) (in thread): > @Nitya Singhalin addition to what others have said, you have to go to the GitHub issue page (the link@Aleru Divinedropped) and drop a comment on the paper your are interested to curate. > A mentor will add an ‘assigned’ tag to let you know you’ve been assigned to the paper. You may also get a mail alerting to it.

Desire Oluwarotimi (05:09:39) (in thread): > Take a look at this.@Nitya Singhalhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709619944874449 - Attachment: Attachment > Hello everyone > Just in case anyone is confused on where to go to start the first contribution > > This is the link to follow for the first contribution > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > I’ve been able to finish mine and I’m willing to help in case of any questions

Mildred Anashie (05:10:06) (in thread): > Most times you might not find the term used on BugSigdbthat’swhyit’sadvised to search for the closest EFO term and input > > Also if the paper used the term I thinkyou’dhave to record according to how it is stated in the paper > I hope i understand your question

Nitya Singhal (05:10:43) (in thread): > Thank you so much, ma’am. Grateful for the help.

Chioma Onyido (05:11:21) (in thread): > Mildred is right. In bugsigdb, we curateConditionas what distinguishes the case group from the control group. If the paper says ‘neonatal mortality’, then enter as neonatal mortality or the closest ontology term you can find.

Amanda Adoyi (05:12:10) (in thread): > Alright. Since that’s the closest term I’ll stick to it. Thanks :)

Mildred Anashie (05:12:35) (in thread): > To add to what others have said > > You should download the annotated paper for the mini curation, go through the paper and start answering the survey questions

Amanda Adoyi (05:12:36) (in thread): > @Mildred AnashieYes you understood my question. Thank you

Aleru Divine (05:12:42) (in thread): > @Amanda AdoyiIt’s important to use the right terms to describe what the condition in your paper. > > But in this case neonatal death is the closest term.

Chimdimma Nwachukwu (05:13:27) (in thread): > Must you make a contribution before a paper gets assigned to you?

Amanda Adoyi (05:13:48) (in thread): > @Aleru Divineneonatal mortality is the actual term. neonatal death is the closest term I can find.

Aleru Divine (05:14:25) (in thread): > @Chimdimma Nwachukwuyou are required to complete the first contribution (mini curation) task before you can request for an issue to be assigned to you.

Chimdimma Nwachukwu (05:14:54) (in thread): > @Aleru Divinethank you

Aleru Divine (05:15:37) (in thread): > Sorry! My mistake:woman-facepalming:

Amanda Adoyi (05:16:09) (in thread): > Lolz. That’s okay. I get what you mean.

Aleru Divine (05:16:30) (in thread): > Thanks:blush:

Aleru Divine (05:17:08) (in thread): > You’rewelcome@Chimdimma Nwachukwu

Scholastica Urua (05:20:13) (in thread): > @Nitya Singhallike others have said, you are required to fill the form with the answers. The “Breast cancer patients from the Midwest region of the United States have reduced levels of short‑chain fatty acid‑producing gut bacteria” is one of the paper you use in answering the questions on the form. The paper has been heavily annotated (by highlighting the answers) already. > > The form also include a link to Bugsigdb and a curated paper for use in answering subsequent questions. > > I deduce that the mini-curation (task 1) is to assess your attention to details by being able to pick out answers already provided for you. > > Good luck:100:.

Abiola Salako (05:20:38) (in thread): > @Nitya Singhalput into cognizance the highlighted parts of the paper. Good luck.

Chimdimma Nwachukwu (05:20:54): > Hi everyone. Please is there a sample or template on how the curated article for task 1 should look like?

Blessing Ene Anyebe (05:21:29) (in thread): > This is onehttps://bugsigdb.org/Study_457 - Attachment (BugSigDB): Alteration of salivary microbiome in periodontitis with or without type-2 diabetes mellitus and metformin treatment - BugSigDB > We aimed to explore the effects of type-2 diabetes mellitus (T2DM) and hypoglycemic therapy on the salivary microbiome in periodontitis patients and identify the potential salivary micro-biomarker for the early warning of T2DM.

Aleru Divine (05:21:57) (in thread): > @Chimdimma Nwachukwuno thereisn’t.Just complete the survey.

Desire Oluwarotimi (05:22:03) (in thread): > Hi@Chimdimma NwachukwuI don’t think there’s a template for the first task. It’s just a survey

Chimdimma Nwachukwu (05:22:24) (in thread): > So I will just answer questions?

Blessing Ene Anyebe (05:22:33) (in thread): > Oh yes, the sample I shared if for task 2.

Desire Oluwarotimi (05:22:39) (in thread): > Yeah

Aleru Divine (05:22:45) (in thread): > Yes@Chimdimma Nwachukwuthat’scorrect.

Blessing Ene Anyebe (05:23:08) (in thread): > Yes just answer the form questions and your response will be recorded.

Eniola Adebayo (05:23:33): > Hello, I have a question. > If the significant threshold for the Lefse analysis under the methodology section is p<0.05, but the study added other significant differences of 0.1 and 0.01 to the results. > Should I curate signatures for just pvalue<0.05 or should I add others?@Svetlana Ugarcina Perovic

Chimdimma Nwachukwu (05:23:53) (in thread): > After reading, I will answer questions and submit. Then wait for the grade before proceeding to task 2 right?

Desire Oluwarotimi (05:25:02) (in thread): > @Eniola AdebayoI think you should use the significance threshold for LeFse analysis if that was the test used to determine differential abundance.

Aleru Divine (05:25:18) (in thread): > @Chimdimma Nwachukwuno need to wait for the grade. Just proceed to request for an issue. > > Although there aren’t any available at the moment.

Blessing Ene Anyebe (05:25:57) (in thread): > There is no seen grading for task 1. Yes after reading answer the questions and then proceed to your second contribution. > > Which is picking an issue on GitHub.

Amanda Adoyi (05:26:52) (in thread): > Just a pointer incase you didn’t see it… You should not add “<” to your value. Just the threshold, Example “0.05” would suffice.

Chimdimma Nwachukwu (05:26:53) (in thread): > Thank you so much everyone. You are that best. > But how long does it take to have available issues?

Scholastica Urua (05:26:57) (in thread): > I think you should use p<0.05 since it was specifically mentioned for the LeFse analysis provided that was the statistical test used.

Blessing Ene Anyebe (05:27:22) (in thread): > For now just wait for updates from the mentors

Blessing Ene Anyebe (05:27:44) (in thread): > I know it will be shared once more issues are made available.

Eniola Adebayo (05:28:38) (in thread): > Thankyoueveryone:pray:

Aleru Divine (05:29:14) (in thread): > @Eniola Adebayouse the significance threshold for the differential abundance testing done in your paper.In this case it is LEfSe and it is p<0.05

Chimdimma Nwachukwu (05:29:24) (in thread): > Thank you very much:pray:

Suru Olaitan (05:31:09) (in thread): > @Chimdimma NwachukwuYou can check now, some were just uploaded

Suru Olaitan (05:31:49) (in thread): > Thank you@Svetlana Ugarcina PerovicLook forward to it

Mildred Anashie (05:38:07): > @Suru Olaitanjust confirmed that more articles have been uploaded in GitHub for those who haven’t been assigned an issue yet - Attachment: Attachment > @Chimdimma Nwachukwu You can check now, some were just uploaded

Aleru Divine (05:39:59) (in thread): > @Hamidat Mohammed

eneje promise (05:40:11) (in thread): > @Aleru Divinepls where did you find what you are working on because I am lost.

Abiola Salako (05:41:20) (in thread): > @eneje promise

Mildred Anashie (05:42:17) (in thread): > @eneje promiseare you asking about the second contribution?

Abiola Salako (05:43:31) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues

Mildred Anashie (05:43:46) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issuesCheck for issues on this link

Aleru Divine (05:46:26) (in thread): > @eneje promiseis it to find your study on BugSigDB?

Muqtadirat Yussuff (05:51:21): > Hi everyone, again. For papers we weren’t assigned on github but found through the help section such as incomplete pages, do we also have to inform the mentors to review if we populate some data?

Aleru Divine (05:53:06) (in thread): > @Muqtadirat Yussuffyes it is important to inform them before and after you populate data on incomplete pages.So they can be aware and review it.

Desire Oluwarotimi (05:54:32) (in thread): > @Muqtadirat YussuffYou can simply put it on here for the mentors to be aware of what you are working on and do the same when you are done for review but it’s important that you complete your second task before attempting such.

Nitya Singhal (05:54:42) (in thread): > Thank you@Mildred Anashie@Scholastica Urua@Abiodun Oladejofor the guidance.

Muqtadirat Yussuff (05:55:25) (in thread): > Understood, thank you

Nitya Singhal (05:57:49): > Can anyone please advice me about the expectations in curating a paper

Mildred Anashie (05:58:46): > @Nitya Singhalyou can go through other curated papers

Mildred Anashie (05:59:21): > You can also go through the curation policyhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Aleru Divine (05:59:41) (in thread): > I’ll advice you to watch the tutorial videos included the resources, and go through some already completed citations.

Joan C. Chukwuemeka (05:59:58) (in thread): > @Muqtadirat YussuffIt’s advisable that you post a study that you see under incomplete pages here first, to be sure that it’s not a curation that some one is currently working on.

Desire Oluwarotimi (06:00:36) (in thread): > @Nitya SinghalOne major advise I’m trying to work with is “Quality over Quantity”. > > However going through the videos and all other provided materials is an important way of getting started.

Aleru Divine (06:02:29) (in thread): > @Nitya SinghalThe curation policy was very helpful to me too. > > Then I noted the things that I would need to curate and I kept it in mind as I read through the article that was assigned to me. That way I knew exactly the important information to look out for. > > Link to curation policy:https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Muqtadirat Yussuff (06:06:07): > Hello@Peace Sandy, I found this incomplete page through the help section and would like to be given the go ahead to curate if there are no blockers. Thank youhttps://bugsigdb.org/Study_761 - Attachment (BugSigDB): The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study - BugSigDB > The oral microbiome, like the fecal microbiome, may be related to breast cancer risk.Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana.

Eniola Adebayo (06:06:20) (in thread): > I would like to delete an experiment I curated that included a significant threshold of 0.1@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuapebugsigdb.org/Study_877

Mildred Anashie (06:08:44) (in thread): > It looks like you started curating already > > I think you are advised to finish your second contribution before you start others but@Peace Sandycan throw more light and possibly grant permission

Emmanuel Doreen (06:11:04): > I think it would be good to have a separate channel for discussions and tasks.It’sstressful going over the top to look for tasks. Am I just the only one that feels this way?

Muqtadirat Yussuff (06:11:04) (in thread): > Yes I started curating before I realized I should have asked, my bad. Although I am done with my second contribution and have asked for a review on github.

Mildred Anashie (06:11:51) (in thread): > Here on slack or on GitHub?

Mildred Anashie (06:12:39) (in thread): > The task (issues) are uploaded on GitHub and other things you can do can be found on BugSigdb under the help page

Mildred Anashie (06:13:17) (in thread): > OkayThat’sokay > Well done

Emmanuel Doreen (06:13:51) (in thread): > Thank you

Joan C. Chukwuemeka (06:13:51) (in thread): > @Emmanuel DoreenTasks are on Github while discussions are here on Slack. > for task:https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Emmanuel Doreen (06:15:43) (in thread): > Very straight forward. Thank you

Joan C. Chukwuemeka (06:17:13) (in thread): > You’re welcome:blush:

Scholastica Urua (06:17:20) (in thread): > @Nitya SinghalThe second contribution is also graded based on this; - File (PNG): Screenshot_20240307-121658.png

Scholastica Urua (06:17:47) (in thread): > Check this link for more details;https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

idiaru Angela (06:22:37) (in thread): > Thank you@Svetlana Ugarcina Peroviclooking foward to it

Oluwatoyosi Victoria Olanrewaju (06:25:46) (in thread): > Hi@Joan C. Chukwuemekacan you please confirm what platform the meeting will hold, if there’s a link to join kindly share:relaxed:

Mildred Anashie (06:26:43) (in thread): > It will hold on Zoom@Oluwatoyosi Victoria Olanrewaju

Blessing Ene Anyebe (06:27:00) (in thread): > @Oluwatoyosi Victoria Olanrewajuhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709800629808009 - Attachment: Attachment > Good morning :umbrella_with_rain_drops: from rainy Novi Sad (Serbia) > > Today we will have our team weekly meeting where we will introduce ourselves, you will have a chance to introduce yourself, bring up your project doubts and/or share with others how you solved some of your issues in the project. > > To join the video meeting, click this link: https://meet.google.com/uit-bzbe-tcy > > See you at 9 AM EDT (eastern daylight time)! > Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 (edited)

Blessing Ene Anyebe (06:27:10) (in thread): > see the link to the call here

Mildred Anashie (06:27:11): > @Oluwatoyosi Victoria Olanrewaju - Attachment: Attachment > Thank you @Aleru Divine > > Also the link to use to join when It’s time has already been posted by one of our mentors @Svetlana Ugarcina Perovic > > This is the link https://meet.google.com/uit-bzbe-tcy

Oluwatoyosi Victoria Olanrewaju (06:27:25) (in thread): > Thank you ladies:heart:

Joan C. Chukwuemeka (06:29:20) (in thread): > @Oluwatoyosi Victoria Olanrewajuthe responses above are correct. Hope that helps:slightly_smiling_face:

Temitayo Ogidan (06:29:48) (in thread): > @Svetlana Ugarcina Perovic@Suru OlaitanI’ve just made my first contribution, I submitted a fully completed mini-curation via the link provided. Moving on to the next contribution.

Mildred Anashie (06:30:58) (in thread): > Well done@Temitayo Ogidan

Aleru Divine (06:31:14) (in thread): > Congratulations on completing your first contribution@Temitayo Ogidan:partying_face::hugging_face:

Mildred Anashie (06:31:30) (in thread): > Hopefully an issue have been assigned to you > > If not please request for one to be assigned

Nitya Singhal (06:34:12): > I didn’t get the mail even after being assigned with a paper to curate on github.

Mildred Anashie (06:34:47) (in thread): > You wouldIt’sprobably delayed

Mildred Anashie (06:35:27) (in thread): > But sinceyou’vebeen assigned and you can confirm that > > I think it should be just fine going ahead to continue curation:blush:

Blessing Ene Anyebe (06:37:17) (in thread): > I don’t think you should worry about that. The mail you’ll get is usually a GitHub notification. Since you have confirmed you’ve been assigned a task. You can get started! > Good luck @Nitya Singhal

Oluwatoyosi Victoria Olanrewaju (06:37:49): > I’m done with my first contribution but there are no unassigned paper for me to curate to make a second contribution on github:pensive:

Mildred Anashie (06:38:29) (in thread): > Let me tag the mentors to this

Mildred Anashie (06:38:49) (in thread): > @Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther Afuape

Temitayo Ogidan (06:41:02) (in thread): > Me too:cry:

Esther Afuape (06:41:46) (in thread): > We’readding papers, you guys are just really fast in claiming them!:sweat_smile:Please be patient,we’readding more

Scholastica Urua (06:42:22) (in thread): > @Oluwatoyosi Victoria Olanrewajuand@Temitayo Ogidanplease exercise a little patient, I’m sure the mentors will get to it shortly.

Oluwatoyosi Victoria Olanrewaju (06:42:22) (in thread): > Oh thank you!@Esther Afuape:laughing:

Aleru Divine (06:42:41) (in thread): > Congratulations on completing the first contribution@Oluwatoyosi Victoria Olanrewajuand@Temitayo OgidanI believe more issues will be added soon enough:hugging_face:

idiaru Angela (06:43:17) (in thread): > Thank you!:weary:@Esther Afuape

Scholastica Urua (06:44:10) (in thread): > Just like others said, since you can confirm on the Github issue page that you have been assigned then it yours to start working on.

Aleru Divine (06:44:11) (in thread): > I agree with@Blessing Ene Anyebeas long asyou’veconfirmed that you have been assigned.Don’tworry about the mail and go ahead with curation.But you can check your spam folder just to be sure.:hugging_face:

Temitayo Ogidan (06:45:15) (in thread): > @Mildred Anashiethere are no unassigned paper for me to curate to make a second contribution on github

Mildred Anashie (06:45:45) (in thread): > Okay > > The mentors are adding more > > Please be patient

Scholastica Urua (06:51:09) (in thread): > Oh, didn’t know we are suppose to inform mentors before working on new articles. > > I was working on an article I found on “Pages with missing NCBI ID” although I didn’t alert the mentors before doing that. How will it be reviewed?@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Eniola Adebayo (07:06:36) (in thread): > :face_holding_back_tears:@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (07:22:51) (in thread): > Thanks@Esther AfuapeFor the Experimental Factor Ontology (EFO) condition being studied - There’re 2 possible onesA. response to allogeneic hematopoietic stem cell transplant(EFO:0007044), defined as any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an allogeneic hematopoietic stem cell transplant)B. acute graft vs. host disease (Graft-versus-host disease (GVHD) (EFO:0004599****),****defined asa common complication following an allogeneic tissue transplant. It is commonly associated with stem cell or bone marrow transplant but the term also applies to other forms of tissue graft. > * Option Adescribes theresponseto the treatment (allo-HSCT), which is a broad category encompassing various potential outcomes. > * Option B, specifically focuses on thedisease stateof interest, which isacute graft-versus-host disease (aGVHD). > > > On one hand, it seems like option B. However, the study is investigatinghow changes in the dental biofilm microbiota (DBM) are associated with the risk of developing aGVHD ******after the transplant (allo-HSCT). **** > (after the transplant (allo-HSCT) = Engraftment) > > I recall, that<@U1LCB8WEA>once said that “******condition is based on what is being contrasted not what is shared by both groups.”******And I’m thinking it should be OptionA. ******response to allogeneic hematopoietic stem cell transplant, ****Since the contrast carried out were between the stages of transplant (pre and post). Hope I’m right in this line of thought?:thinking_face:@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Peace Sandy@Chioma Onyido

Nekembe Boris (07:36:24): > Hey Team. Please I need some help. The paper I am working on does not have a PMID. It is not PUBMED. But it does have a DOI. I don’t know what to do.

Mildred Anashie (07:36:55) (in thread): > You might have to manually enter it

Aleru Divine (07:37:01) (in thread): > Hi@Nekembe Borisyou can manually populate the data.

Mildred Anashie (07:37:26) (in thread): > Also you can share with us to check with youI’mtalking of the PMID

Nekembe Boris (07:37:52) (in thread): > I have already done so. I just want to know if i can leave it blank

Mildred Anashie (07:38:37) (in thread): > Okay > > You can leave the PMID section blank and enter others

Nekembe Boris (07:38:42) (in thread): > Here is the linkhttps://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients - Attachment (Authorea): Oral lesion and microbiome diversity in COVID-19 hospitalized patients. > Introduction: The oral cavity is an important site for the entry and multiplication of respiratory viruses, and the immune system and oral microbiome act as antiviral barriers. Data regarding oral microbiome and COVID-19 is scarce. Therefore, a prospe

Aleru Divine (07:38:42) (in thread): > Yes you can leave the PMID blank.

Nekembe Boris (07:39:32) (in thread): > Ok. Thank you@Aleru Divine. Much appreciated.

Scholastica Urua (07:41:30) (in thread): > I think one of the mentors mentioned earlier that if the paper is not on PUBMED then its not going to have a PMID.

Nekembe Boris (07:44:03) (in thread): > OK@Scholastica Urua. If that’s the case, then it’s all good. Thank you..

Blessing Ene Anyebe (08:00:48): > Hello guys, its an hour to the office hour meeting! super excited:partying_face:

Peace Daniel (08:01:27) (in thread): > Thanks for the reminder

Svetlana Ugarcina Perovic (08:01:45) (in thread): > @Eniola Adebayoyou have to specify which experiment/signature

Blessing Ene Anyebe (08:01:52) (in thread): > You’re most welcome Peace!

Blessing Ene Anyebe (08:02:06) (in thread): > here is more details to the meetinghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709800629808009 - Attachment: Attachment > Good morning :umbrella_with_rain_drops: from rainy Novi Sad (Serbia) > > Today we will have our team weekly meeting where we will introduce ourselves, you will have a chance to introduce yourself, bring up your project doubts and/or share with others how you solved some of your issues in the project. > > To join the video meeting, click this link: https://meet.google.com/uit-bzbe-tcy > > See you at 9 AM EDT (eastern daylight time)! > Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 (edited)

Adenike Oladimeji-Kasumu (08:02:45): > Hi Everyone. Please help! Is it possible to edit my saved signature in my study and how can i do that?

Eniola Adebayo (08:03:44) (in thread): > Experiment 1. Deleting all the signatures@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (08:04:47) (in thread): > there is 1 signature under experiment 1, and it’s deleted now

Aleru Divine (08:04:56) (in thread): > Hi@Adenike Oladimeji-Kasumuyes it is, look for the edit button on the top of your signature. - File (JPEG): IMG_7754

Faith Ifeoluwa Alexander (08:05:36) (in thread): > Okay, it’s not only@Svetlana Ugarcina Perovicthat is adding papers???

Faith Ifeoluwa Alexander (08:06:33) (in thread): > Let me quickly go and claim one of the new ones then.

Mildred Anashie (08:06:40) (in thread): > No@Faith Ifeoluwa Alexander

Mildred Anashie (08:07:04) (in thread): > Other mentors are doing that also

Faith Ifeoluwa Alexander (08:07:23) (in thread): > I thought@Svetlana Ugarcina Perovicwas the only one adding papers.

Mildred Anashie (08:08:20) (in thread): > @Aleru Divinealready said > > > You can always edit your signatures and experiment

Svetlana Ugarcina Perovic (08:08:36) (in thread): > No,@Svetlana Ugarcina Perovicis not the only one in#bugsigdbmentoring team:wink:

Eniola Adebayo (08:09:19) (in thread): > Thankyou. Iwant to delete the whole of experiment 1@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (08:09:58) (in thread): > When i click on edit, it takes me just to the study part. Not the signature

Mildred Anashie (08:10:29) (in thread): > There’salso an edit button at the top of the signature section click on that

Mildred Anashie (08:11:26) (in thread): > If you want to edit signature you click on the edit button at the top of the signature section you intend to edit > For the experiment, you do same and for the study design you do same

Aleru Divine (08:12:02) (in thread): > Go to the signature section and click on edit.There’salso an edit button at the experiment.Every section is editable.

Adenike Oladimeji-Kasumu (08:12:58) (in thread): > Seen. Thank you all for the help

Suru Olaitan (08:12:58): > There are new issues uploaded now > Do well to check

Scholastica Urua (08:13:32) (in thread): > Thanks for the update@Suru Olaitan

Blessing Ene Anyebe (08:13:33) (in thread): > @Oluwatoyosi Victoria Olanrewaju

Blessing Ene Anyebe (08:13:42) (in thread): > You can check now

Andre Nana (08:13:42) (in thread): > Hi@Muqtadirat Yussuff. Thank you for your initiative. I started the paper and was about to finish it sometime this week-end when I have more free time. But I can share some useful materials for you. I think the curable material will ne Table 2 of the NIHMS1811919-supplement-supinfo2 (1) file. - File (PDF): INTLJO~1.PDF - File (PDF): NIHMS1811919-supplement-supinfo.pdf - File (Binary): NIHMS1~2.XLS

Blessing Ene Anyebe (08:13:51) (in thread): > Thank you@Suru Olaitan

Svetlana Ugarcina Perovic (08:14:31): > A KIND REMINDER: > > Please when claiming an article for curation, post a response to the issuewith your nameand we will mark it as claimed. Please only claim one article for curation until you have completed the 1st curation. > > Available articles are ONLY the ones with tags: > outreachy may2024 > second contribution > paper to curate

Mildred Anashie (08:16:57) (in thread): > You are welcome@Adenike Oladimeji-Kasumu

Adegboye Rukayat (08:17:59): > Please I am yet to be assigned a paper to curate since yesterday. I have asked for papers to be assigned to me on github but unfortunately I am not always the first person to ask and presently all papers have be assigned.@Svetlana Ugarcina Peroviccan you please help me out

Scholastica Urua (08:18:30) (in thread): > Some new papers have been added recently. Have you checked now?

Mildred Anashie (08:18:49) (in thread): > Be patient > Also I think you should check now someone just confirmed new issues have been uploaded

Faith Ifeoluwa Alexander (08:18:50) (in thread): > They are not tagged outreachy o

Faith Ifeoluwa Alexander (08:19:20) (in thread): > The new issues are not tagged as outreachy issues.

Adegboye Rukayat (08:21:03) (in thread): > @Svetlana Ugarcina Perovicplease I need some clarity, the first step is to be assigned a paper then the assignee will claim it before curating right?

Scholastica Urua (08:21:21) (in thread): > I just checked, all the open outreachy papers have been assigned. Please exercise a little patience as the mentors will get to it.

Faith Ifeoluwa Alexander (08:21:48) (in thread): > Yay!!!:dancer:I just got assigned. Finally!!!

Adegboye Rukayat (08:21:53) (in thread): > Thank you all.

Mildred Anashie (08:22:26) (in thread): > I’msure the mentors are currently working on that

Faith Ifeoluwa Alexander (08:22:45) (in thread): > @Svetlana Ugarcina Perovicis tagging & assigning the new issues now.@Adegboye Rukayatsome are still unclaimed. Go there now.

Mildred Anashie (08:22:59) (in thread): > Congratulations@Faith Ifeoluwa AlexanderGood luck:four_leaf_clover:

Faith Ifeoluwa Alexander (08:23:26) (in thread): > Thanks@Mildred Anashie.

Muqtadirat Yussuff (08:23:59) (in thread): > @Andre NanaI’ll go through the materials, thank you and I do apologize for working on a curation in progress

Adegboye Rukayat (08:27:46) (in thread): > @Faith Ifeoluwa Alexanderit has all been assigned.

Nitya Singhal (08:28:20) (in thread): > can you please attach the link of some curated papers for help.

Nitya Singhal (08:29:06) (in thread): > @Aleru Divinewhere can I find the tutorials and citations. Can you please attach the link here?

Mildred Anashie (08:29:14) (in thread): > Check again@Adegboye RukayatI can see one or two without comments

Nitya Singhal (08:29:30) (in thread): > Where can I find the curated papers?

Roderick Momin (08:29:37): > I am having some issues accessing thesupplementary materialsfor mysecond curation. Would someone kindly try accessing them from their end?

Mildred Anashie (08:30:04) (in thread): > On BugSigdb

Mildred Anashie (08:30:14) (in thread): > Let try to see if I can share a link

Joan C. Chukwuemeka (08:30:19) (in thread): > @Roderick MominKindly share your article link

Joan C. Chukwuemeka (08:31:15) (in thread): > Is this the article: - File (PNG): image.png

Aleru Divine (08:31:20) (in thread): > @Nitya Singhalcheck the Prep Work section in this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Mildred Anashie (08:31:40) (in thread): > https://bugsigdb.org/Special:RandomInCategory/Studies - Attachment (BugSigDB): Nasopharyngeal Microbiome Signature in COVID-19 Positive Patients: Can We Definitively Get a Role to Fusobacterium periodonticum? - BugSigDB > Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the pandemic Coronavirus Disease 2019 (COVID-19).This virus is highly transmissible among individuals through both droplets and aerosol leading to determine severe pneumonia.

Anju Maurya (08:31:43): > In how many days, can we get access to the BugSigDB account while the account is requested?

Roderick Momin (08:31:44) (in thread): > @Joan C. ChukwuemekaIt is provided in the text. You can click on the “supplementary materials” on my provided text.

Roderick Momin (08:31:53) (in thread): > Yes, that is the article.

Joan C. Chukwuemeka (08:32:12) (in thread): > Okay, on it..

Adenike Oladimeji-Kasumu (08:32:21) (in thread): > @Adegboye RukayatYes, that’s right. Once it is assigned to you, you can start curating.

Aleru Divine (08:32:34) (in thread): > @Anju MauryaIt took about 4 minutes for me after I confirmed my email.

Mildred Anashie (08:33:10) (in thread): > The link leads to a particular study but once you open BugSigdb you click on Random page a reviewed study will pop up

Mildred Anashie (08:33:45) (in thread): > And i believe you’d get a different study for everytime you click

Praise Agbetuyi (08:33:54): > @Svetlana Ugarcina PerovicI am done with my first contribution, and I would like to start the second contribution. Do I need to wait for my account to be approved before I can start that?

Peace Sandy (08:34:00) (in thread): > “If you have done your 1st and 2nd contributions and you want to contribute more, you could do tasks under the “TODO for reviewers” or “NCBI cleanup” in the help page on bugsigdb - just post here before making other edits to the wiki.”

Adenike Oladimeji-Kasumu (08:34:08) (in thread): > @Anju MauryaYou should get your account soon. Check your mail.

Peace Sandy (08:34:35) (in thread): > Yes

Mildred Anashie (08:35:18) (in thread): > Yes you do > > You can only curate on BugSigdb with an approved account

Peace Sandy (08:35:23) (in thread): > @Muqtadirat Yussuff”If you have done your 1st and 2nd contributions and you want to contribute more, you could do tasks under the “TODO for reviewers” or “NCBI cleanup” in the help page on bugsigdb - just post here before making other edits to the wiki.”

Mildred Anashie (08:35:44) (in thread): > But while you wait you can familiarize yourself with other studies and the curation policy

Adenike Oladimeji-Kasumu (08:35:56) (in thread): > Thank you@Peace Sandyas i was going to ask

Mildred Anashie (08:36:00) (in thread): > I could share a link if you donot have it already

Peace Sandy (08:36:29) (in thread): > You are welcome@Adenike Oladimeji-Kasumu

Adegboye Rukayat (08:37:13) (in thread): > Thank you@Adenike Oladimeji-Kasumu

Adenike Oladimeji-Kasumu (08:38:20): > Please who knows whether there is an with my signatures? The quality control and Links. And if yes, what are the issues? - File (JPEG): IMG_20240307_143631_865.jpg - File (JPEG): IMG_20240307_143640_358.jpg

Mildred Anashie (08:39:02) (in thread): > The quality control and links is normal

Mildred Anashie (08:39:58) (in thread): > But the first image has unresolved signaturesthat’swhy they appear in orange > > Check for signatures on NCBI taxonomy site and upload the NCBI ID insteadthatshould resolve it

Aleru Divine (08:40:25) (in thread): > Thank you so much@Peace SandyI wanted to ask too

Faith Ifeoluwa Alexander (08:40:26) (in thread): > It is true. Just go ahead if you have been assigned. GitHub has the record of you being assigned already.

Adenike Oladimeji-Kasumu (08:40:46) (in thread): > Alright. Thank you

Scholastica Urua (08:41:10) (in thread): > Thank you@Peace SandyI already carried out 2 tasks under the “Pages with missing NCBI ID” before now so I’ll drop the links.:pray:

Roderick Momin (08:41:50) (in thread): > @Joan C. ChukwuemekaThank you, please let me know of your results.

Faith Ifeoluwa Alexander (08:42:48) (in thread): > Go to issue #226 now!!!!!!@Adegboye Rukayat

Iman Ngwepe-Ntshibida (08:44:26): > Hi Team, how do add in our first contribution on Outreachy, i.e what URL do we put in the “Contribution URL” section and after task 1 how do we move forward. I already have the account made and approved.

Anju Maurya (08:44:40) (in thread): > Thanks buddy ! I was a little bit confuse.

Faith Ifeoluwa Alexander (08:45:02) (in thread): > Sorry issue #205 is tagged outreach paper and it isn’t assigned yet. Issue #226 isn’t tagged yet.@Adegboye Rukayat

Mildred Anashie (08:45:08) (in thread): > There’ssomething complied by someone to that effect I can search for it for you

Leenaa Al-Amin (08:45:48): > In the study I’m curating, patients included were initially separated into two categories based on clinical outcome: recovered and mortality . Recovered patients were further divided into three sub-phenotypes: mild , moderate, and severe. Should I to enter these as separate experiments?@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Scholastica Urua (08:46:04): > Hello@Svetlana Ugarcina Perovic,@Peace Sandy,@Chioma Onyido,@Esther Afuapeand everyone, I found these tasks under the “Pages with missing NCBI ID” and worked.https://bugsigdb.org/Study_373/Experiment_1/Signature_2https://bugsigdb.org/Study_300/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 373/Experiment 1/Signature 2 > Source: Figure 3, Table S2 Description: Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level. Abundance… - Attachment (BugSigDB): Study 300/Experiment 1/Signature 2 > Source: Figure 1C Description: Phylum analysis of altered microbiota in mice after antibiotic water feeding compared to mice fed with regular water Abundance in…

Peace Sandy (08:47:06) (in thread): > Great

Muqtadirat Yussuff (08:47:27) (in thread): > @Peace SandyNoted, thank you for the response.

Esther Afuape (08:48:15) (in thread): > What changes did you make?@Scholastica Urua

Mildred Anashie (08:49:19) (in thread): > @Roderick MominI think the supplementary materials for your study are attached to the study because when i click on the link provided within text it leads me back to the studies pdf

Mildred Anashie (08:49:47) (in thread): > https://www.sciencedirect.com/science/article/am/pii/S0020751919300074This is the pdf

Adenike Oladimeji-Kasumu (08:50:14) (in thread): > @Mildred Anashie… I’m on the NCBI taxonomy site. Can you kindly teach me how to get the NCBI ID of my organisms?:pray:I’m only seeing PMID number.

Mildred Anashie (08:50:43) (in thread): > Please share a screenshot of the page you are on

Scholastica Urua (08:50:51) (in thread): > @Leenaa Al-AminI think you are suppose to curate them as different experiments but if the study observed no significant difference in the dissimilarity of bacterial structures among patient subgroups then you may curate it as one.@Svetlana Ugarcina Perovicis this accurate?

Joan C. Chukwuemeka (08:51:40) (in thread): > @Roderick Mominit leads back to the paper like@Mildred Anashiepointed out, not sure why though.:thinking_face:perhaps@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA>@Chioma Onyido@Peace Sandy@Esther Afuapecould help out further

Nitya Singhal (08:52:31) (in thread): > ok thank you ma’am.

Bolanle Wahab (08:53:57) (in thread): > @Leenaa Al-AminIt depends on the comparisons you plan to conduct, If you know the differences between these subgroups are significant and warrant separate experiments then entering them as separate experiments would be the right thing but if the interest was primarily comparing recovered patients to those who experienced mortality, can keep them all in the same experiment and use the sub phenotypes as variables within that experiment.

Praise Agbetuyi (08:55:00): > Hi, Everyone, Office meeting hour in 5 minutes!! Here is for more details.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709800629808009

Bolanle Wahab (08:55:09): > Hi everyone,can someone please resend the link to the office meeting?

Raihanat Adewuyi (08:55:18) (in thread): > Please after the answering the survey question.. What else are am I to do@Scholastica Urua

Mildred Anashie (08:55:23) (in thread): > Thank you:blush:

Anju Maurya (08:55:46): > https://meet.google.com/uit-bzbe-tcy - Attachment (meet.google.com): Meet > Real-time meetings by Google. Using your browser, share your video, desktop, and presentations with teammates and customers.

Anju Maurya (08:55:54): > Meeting link

Desire Oluwarotimi (08:55:57) (in thread): > Here@Bolanle Wahabhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709800629808009 - Attachment: Attachment > Good morning :umbrella_with_rain_drops: from rainy Novi Sad (Serbia) > > Today we will have our team weekly meeting where we will introduce ourselves, you will have a chance to introduce yourself, bring up your project doubts and/or share with others how you solved some of your issues in the project. > > To join the video meeting, click this link: https://meet.google.com/uit-bzbe-tcy > > See you at 9 AM EDT (eastern daylight time)! > Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 (edited)

Mildred Anashie (08:56:14) (in thread): > You record it as a contribution on Outreachy

Bolanle Wahab (08:56:23) (in thread): > Thank you

Mildred Anashie (08:57:09) (in thread): > Request for an account if youhaven’tand also select a study on GitHub, comment on it with your name and ask to claim it for curation

Mildred Anashie (08:57:36) (in thread): > Alsoyou’dhave to wait for your account to be approved before you can start the second contribution

Idiat Alli (08:58:00) (in thread): > Thanks

Nitya Singhal (08:58:07) (in thread): > Thank you so much

Praise Agbetuyi (08:58:27) (in thread): > Thank you for the clarity,@Svetlana Ugarcina PerovicI would like to ask if I can claim a paper while waiting for my account to be approved?

Scholastica Urua (08:58:42) (in thread): > @Esther Afuapeonhttps://bugsigdb.org/Study_373/Experiment_1/Signature_2, I updated ‘Lachnoclostridium lactaris’ to ‘1965569’. > While onhttps://bugsigdb.org/Study_300/Experiment_1/Signature_2I updated ‘TM7’ to ‘443342’. > I don’t know if I’m conveying my message properly:pray:

Temitayo Ogidan (09:43:13): > @Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther AfuapeWas issue #222 removed? I was previously assigned to it, but I’m unable to locate it now.

Esther Afuape (09:44:00) (in thread): > Yes it was removed. My bad!Ithas been curated already, I mistakenly added the paper again. Please pick another paper:pray:

Temitayo Ogidan (09:47:20) (in thread): > okay Esther, but there are no unassigned papers for me to pick at the moment

Esther Afuape (09:48:15) (in thread): > There are papers available > Check again

U1LCB8WEA (09:48:50) (in thread): > I agree! Note you can use the group 1 definition to clarify exactly how the condition was defined in your paper.

Amanda Adoyi (09:55:05) (in thread): > <@U1LCB8WEA>Alright. I’ll do that:slightly_smiling_face:

Peace Sandy (09:57:40) (in thread): > Please record your contributions@Scholastica Urua

Scholastica Urua (09:58:45) (in thread): > Okay, will do that > Thanks@Peace Sandy

Scholastica Urua (10:02:42): > Hello everyone > > These are some of the tips mentioned by the mentors during the office hours. Hope this helps! > > 1. Initially, highlight the important parts of a paper to facilitate easier curation later on. Utilize tools such as Adobe for this purpose. > > 2. Some papers may feature multiple statistical tests. However, it’s crucial to discern between them, as one test might be conducted for the p-value while another for differential abundance. (Data transformation for common statistical tests was mentioned here.) > > 3. When p-values and LDA scores are not specified in a paper, the default values are typically considered to be 0.05 for the p-value and 2 for the LDA score. > > 4. Always remember to check for supplementary materials during curation. These materials may be located at the beginning or end of the paper. > > 5. Consider creating a talk page to provide guidance for other curators or reviewers. > > > 6. Prioritize quality over quantity when conducting curation. Take the necessary time to ensure a thorough and high-quality curation process. > > 7. An experiment involves a comparison between two specific elements, not the entirety of the project conducted in the lab. > > 8a. Condition - This is relative to the case group, which refers to the disease or condition present in the patient population but absent in the healthy population. > > 8b. Condition - When the patient population is further subgrouped, a second experiment is usually required. However, in this case, the condition will pertain to specific diseases present in the subgroup.

Muqtadirat Yussuff (10:02:44): > Hi everyone, the meeting was quite insightful and here some tips I noted down. Please comment if there’s any misinformation and I’ll edit. Happy curating everyone! > 1. Experiments in BugSigDB are comparisons. > 2. Conditions are contrasts, basically what’s in group A and what’s not in group B. > 3. Well populated curations are preferred over more but less quality curations. > 4. If your paper has multi stage tests i.e the increase and decrease in abundance isn’t clearly stated and you’re unsure how to record the significance, you can put in the notes section indicating the paper isn’t curateable. > 5. If the significance threshold of your paper is omitted, it’s appropriate to use the default value. For example the default value for p value is 0.05 > 6. If there is no alpha diversity in your paper you can curate the paper but omit the signature page. > 7. BugSigDB is currently interested in alpha diversity and not beta diversity which can be found in some papers so do not record for beta.

Peace Daniel (10:03:08): > Thank you so much@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy

Okache Johnpaul (10:03:58): > Thank you@Svetlana Ugarcina Perovic,@Chioma Onyido@Peace Sandy@Esther Afuape!

Ima-obong (Aimah) (10:04:05) (in thread): > Thank youuu@Muqtadirat Yussuff..I find this really helpful as I missed about 15mins of the call

Mildred Anashie (10:04:40): > Hello everyone > > What an interesting section:blush::blush:I see many of us took notes, I’ll still share mine > > In case we missed anyone > > How to make your curation easy > 1. Know what you are looking out for > 2. Highlight the points you are looking out for on Adobe Acrobat then you start your curation > 3. Ensure not to mix the statistical test for the p value and that for the differential abundance (you can know by checking the description of the figure you are curating) > 4. Check a pinned thread on the BugSigdb channel it has information on Data transformation (Data transformation is usually mentioned in the methods part of the study) > 5. Always check the supplemental for other information and results > 6. Sample sizes might not be stated in the study, you can create a talk page stating that the study didn’t explicitly state the sample size( you can do that by clicking on discussion at the top of the screen, there’s a three dot icon that can lead you there) > 7. Before you resolve a missing NCBI ensure to confirm it has not been resolved before you go ahead with that > 8. Do not forget to check the supplementary materials for your study > 9. Focus on the quality of your curation than quantity (your curation should be accurate instead of you curating a lot studies) > 10. Experiments are comparisons done in the paper for BugSigdb e.g IDB Vs Healthy controls. You curate for the comparisons made and not the entire lab work done in the paper > 11. Condition is curated it relative to the case in the study. If there are sub types in the paper you curate the condition as the sub types > 12. When curating check NCBI for the taxas there will always be record of the synonyms on NCBI (You are allowed to record the heterotypic synonyms on BugSigdb) > 13. Report the significant differences recorded in the paper > 14. Pay attention to details and ensure to divide sub groups and identify all the groups > 15. If you can’t find the PMID or the DOI input the link you can find and also curate that section manually

Scholastica Urua (10:04:44): > Thank you@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther Afuape

Mildred Anashie (10:05:36): > Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy

Svetlana Ugarcina Perovic (10:05:43): > THANK you all for a great meeting today!

Muqtadirat Yussuff (10:06:04) (in thread): > You’re welcome, I’m sure there’ll be more tips coming in so you’ll be filled with information. I’m glad you found this helpful:sparkles:

Desire Oluwarotimi (10:06:17): > Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeThe meeting was definitely insightful.

Svetlana Ugarcina Perovic (10:06:17): > Can I post it on X, LinkedIn and Bluesky? - File (PNG): Screenshot 2024-03-07 at 15.10.34.png - File (PNG): Screenshot 2024-03-07 at 15.14.58.png - File (PNG): Screenshot 2024-03-07 at 15.47.06.png

NWAKAEGO VINCENT (10:06:24) (in thread): > thank you for hosting us

Praise Agbetuyi (10:06:30) (in thread): > Thank you,@Muqtadirat Yussuff.

Abiola Salako (10:06:33): > Good of you@Muqtadirat Yussuff.Thank you so much@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther Afuape.

Mildred Anashie (10:06:44) (in thread): > Yes:hugging_face:

Muqtadirat Yussuff (10:06:46) (in thread): > Yes ma’am:sparkles:

Suru Olaitan (10:07:19) (in thread): > Thank you so much@Svetlana Ugarcina PerovicI hope that your throat feels better soon..Do take care

Blessing Ene Anyebe (10:07:43): > Thank you so much for the meeting.@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther AfuapeKudos to everyone sharing minutes notes!:orange_heart::partying_face:

Chioma Agu (10:07:43): > Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Muqtadirat Yussuff (10:07:43) (in thread): > Thank you too and enjoy your tea. Do take care:sparkles:

Adegboye Rukayat (10:07:55) (in thread): > Thank you@Faith Ifeoluwa Alexander@Mildred AnashieI am the first person to comment on issue 206. waiting for@Svetlana Ugarcina Perovicto assign it to me. Thank you so much

Ima-obong (Aimah) (10:07:58) (in thread): > Thank you@Scholastica Urua, I missed point 3.

Mildred Anashie (10:08:52) (in thread): > You are welcome > > Happy you are getting a paper assigned to you

Blessing Ene Anyebe (10:09:05) (in thread): > Yes you can!:sweat_smile::orange_heart:

Amanda Adoyi (10:09:34) (in thread): > Yes please. I want to be a known “Bioinformician…”?:woman-shrugging:Someone help me with the correct term…

Muqtadirat Yussuff (10:10:11) (in thread): > @Amanda AdoyiBioinformatician

Amanda Adoyi (10:10:34) (in thread): > Lolz. Thanks and thanks

Ruth Bamgbose (10:11:24): > Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Ima-obong (Aimah) (10:12:18): > Thank you team and mentors@Chioma Onyido,@Svetlana Ugarcina Perovic,@Peace Sandy..I have a more robust understanding now.

Aleru Divine (10:12:21): > I just completed my second contribution:partying_face:Thank you so much for the wonderful session@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido:hugging_face::heart:

Suru Olaitan (10:12:23) (in thread): > Yes ma’am!:blush:

Adegboye Rukayat (10:12:26) (in thread): > In the meantime, can you walk me through how you claim the paper? Do you just write your name in the comment after being assigned the paper?@Svetlana Ugarcina Perovicsaid claiming the paper, you should respond to it with your name. Is it by commenting your name in the comment section

Blessing Ene Anyebe (10:12:49) (in thread): > Yaaayy congratulations:raised_hands::partying_face:

Aleru Divine (10:12:54) (in thread): > Yes sure:hugging_face:

Blessing Ene Anyebe (10:13:21) (in thread): > Was nice seeing you on the call:orange_heart:

Praise Agbetuyi (10:13:26) (in thread): > Yes, please. It was so nice hearing your voice and that of other contributors. Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandyand@Esther Afuape. The session helped calm the tiny little tension building up in my head. Thank you for the clarity.

Scholastica Urua (10:13:27) (in thread): > Yes, you can

Desire Oluwarotimi (10:13:34): > I’d love to share what I thought was quite vital that was mentioned in the meeting by@Peace SandyIt is that we focus more on quality than quantity. It is preferred that your contributions are accurate than having multiple inaccurate or far from accurate contributions. > > Thank You.

Scholastica Urua (10:14:02) (in thread): > You are welcome@Ima-obong (Aimah)

NWAKAEGO VINCENT (10:14:56): > thank you for that insightful session@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic

NWAKAEGO VINCENT (10:15:52) (in thread): > yes you can

NWAKAEGO VINCENT (10:17:45): > i just completed my first task. thank you@Suru Olaitan

Faith Ifeoluwa Alexander (10:18:01): > I had another meeting to attend so I couldn’t finish up with the meeting. How was it friends?

Praise Agbetuyi (10:18:16): > My take-home from the session. 1. Quality is more appreciated than quantity. 2. Be sure to check the Supplementary material, there may be relevant information that will help your curation 3. Be free to ask questions and communicate on the channel; it’s open source and everyone here is really supportive.

Barakat Akinsiku (10:18:23) (in thread): > @Roderick Mominhave you been able to resolve this? I can’t access the supplementary materials for my paper either and I think it’s because the paper has restricted access similar to yourshttps://www.sciencedirect.com/science/article/abs/pii/S0044848623000224

Peace Daniel (10:18:34): > Hello@Peace Sandy@Chioma OnyidoI added NCBI ID’s to the following, would love a review pleasehttps://bugsigdb.org/Study_876/Experiment_1/Signature_2Added NCBI ID’s to signature 2 under “Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices/Experiment 1/Signature 2”. > > NCBI ID’s I added to signatures include: Anaerotignum faecicola, Bacteroidaceae bacterium, Brachyspira pilosicoli, Campylobacteraceae bacterium, Lacrimispora amygdalina and Prevotellamassilia timonensishttps://bugsigdb.org/Study_876/Experiment_1/Signature_1Added NCBI ID’s to signature 1 under “Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices/Experiment 1/Signature 1” > > NCBI ID added include: Clostridia bacterium, Methanomassiliicoccales archaeon and Blautia massiliensis (ex Durand et al. 2017) - Attachment (BugSigDB): Study 876/Experiment 1/Signature 2 > Source: figure 4 (c) Description: Species-level taxonomic biomarkers identified using LEfSe58 to associate with behaviors having ( 0–3) sexual partners. Only taxonomically… - Attachment (BugSigDB): Study 876/Experiment 1/Signature 1 > Source: figure 4 (c) Description: Species-level taxonomic biomarkers were identified using LEfSe58 to associate with behaviors having >3 sexual partners. Only taxonomically…

Peace Daniel (10:19:30) (in thread): > It was great,I’dsend some links to the notes that was taken by others

Svetlana Ugarcina Perovic (10:19:37) (in thread): > WELL said! Can I post it on X, LinkedIn and BlueSky? Do you have there your account registered so i could tag you?

Esther Afuape (10:19:58) (in thread): > Hi Peace. Please specify the exact changes you made

Peace Daniel (10:20:24) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709823762913479 - Attachment: Attachment > Hello everyone > > These are some of the tips mentioned by the mentors during the office hours. Hope this helps! > > 1. Initially, highlight the important parts of a paper to facilitate easier curation later on. Utilize tools such as Adobe for this purpose. > > 2. Some papers may feature multiple statistical tests. However, it’s crucial to discern between them, as one test might be conducted for the p-value while another for differential abundance. (Data transformation for common statistical tests was mentioned here.) > > 3. When p-values and LDA scores are not specified in a paper, the default values are typically considered to be 0.05 for the p-value and 2 for the LDA score. > > 4. Always remember to check for supplementary materials during curation. These materials may be located at the beginning or end of the paper. > > 5. Consider creating a talk page to provide guidance for other curators or reviewers. > > > 6. Prioritize quality over quantity when conducting curation. Take the necessary time to ensure a thorough and high-quality curation process. > > 7. An experiment involves a comparison between two specific elements, not the entirety of the project conducted in the lab. > > 8a. Condition - This is relative to the case group, which refers to the disease or condition present in the patient population but absent in the healthy population. > > 8b. Condition - When the patient population is further subgrouped, a second experiment is usually required. However, in this case, the condition will pertain to specific diseases present in the subgroup.

Suru Olaitan (10:20:25) (in thread): > Yayyyyy…Congratulations on your first contribution@NWAKAEGO VINCENTDon’tforget to record your contribution on the outreachy website and also be on the look out for new issues upload so you can move on to carry out your 2nd contribution > > Should you need guidance,I’llbe more than glad to help

Praise Agbetuyi (10:20:26): > It was really nice. The mentor and co-mentors gave clarity to some questions. You can check thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709823880846889 - Attachment: Attachment > Hello everyone > > What an interesting section :blush: :blush: > I see many of us took notes, I’ll still share mine > > In case we missed anyone > > How to make your curation easy > > 1. Know what you are looking out for > 2. Highlight the points you are looking out for on Adobe Acrobat then you start your curation > 3. Ensure not to mix the statistical test for the p value and that for the differential abundance (you can know by checking the description of the figure you are curating) > 4. Check a pinned thread on the BugSigdb channel it has information on Data transformation (Data transformation is usually mentioned in the methods part of the study) > 5. Always check the supplemental for other information and results > 6. Sample sizes might not be stated in the study, you can create a talk page stating that the study didn’t explicitly state the sample size( you can do that by clicking on discussion at the top of the screen, there’s a three dot icon that can lead you there) > 7. Before you resolve a missing NCBI ensure to confirm it has not been resolved before you go ahead with that > 8. Do not forget to check the supplementary materials for your study > 9. Focus on the quality of your curation than quantity (your curation should be accurate instead of you curating a lot studies) > 10. Experiments are comparisons done in the paper for BugSigdb e.g IDB Vs Healthy controls. You curate for the comparisons made and not the entire lab work done in the paper > 11. Condition is curated it relative to the case in the study. If there are sub types in the paper you curate the condition as the sub types > 12. When curating check NCBI for the taxas there will always be record of the synonyms on NCBI (You are allowed to record the heterotypic synonyms on BugSigdb) > 13. Report the significant differences recorded in the paper > 14. Pay attention to details and ensure to divide sub groups and identify all the groups > 15. If you can’t find the PMID or the DOI input the link you can find and also curate that section manually

Peace Daniel (10:21:29) (in thread): > I added the NCBI ID’s to the signatures I listed here

Peace Daniel (10:21:45) (in thread): > Initially they were missing IDs

Praise Agbetuyi (10:22:51) (in thread): > Thank you. Yes, you can. I am on X and LinkedIn but not on BlueSky

Esther Afuape (10:23:57) (in thread): > Okay > Got it:white_check_mark:

Eniola Adebayo (10:24:19) (in thread): > Yes:star-struck:

Praise Agbetuyi (10:25:39) (in thread): > https://twitter.com/Praise_Agbetuyifor X andPraise Agbetuyi-tayoon linkedIn

Amanda Adoyi (10:26:32): > The first thing that was said in the meeting about multi-stage cycle research work where it’s difficult to measure decrease or increase in quantities was pick a stage with significant change as a reference.@Svetlana Ugarcina Perovicthen proceeded to say I should determine if it may be not be possible to curate the paper. I am holding on to the former for now because because it frankly is an awesome read. Is anyone here having a paper with similar content or the same problem?

Muqtadirat Yussuff (10:30:15) (in thread): > Not just you, my paper had different feeding times for the subject but I picked the feeding time that had the most significant change. It might not be the exact scenario as yours but I was conflicted on this too

Amanda Adoyi (10:31:33) (in thread): > This has kept me up. But you’re right about the significant change. I’m sticking to that and would perhaps leave a comment on it.

Ima-obong (Aimah) (10:32:54) (in thread): > Thank you so much@Svetlana Ugarcina Perovic.. I have claimed the paper.

Ruth Bamgbose (10:33:22): > I have a question, so a sub-experiment in my study stated the use of Generalized Linear Models, I don’t know If this should be recorded as Linear regression in the statistical test? or both linear and logistic.

Mildred Anashie (10:33:40) (in thread): > @Adegboye Rukayatyes please > > Just leave a comment on the issue

Mildred Anashie (10:34:57) (in thread): > Here for the answer:thinking_face:<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape

Svetlana Ugarcina Perovic (10:35:21) (in thread): > https://twitter.com/svetlana_up/status/1765762512287330795

Raihanat Adewuyi (10:35:58) (in thread): > @Mildred AnashieSo my account has been approved but there is no more paper.. > Can a paper that has been assigned be reassigned to another person

Mildred Anashie (10:37:46) (in thread): > I’m not sure it can be reassigned if someone is already working on it > > But you can comment on a new issue once more are uploaded > > The mentors will definitely be working on it and during the just concluded meeting we were asked to be patient as they upload more papers

Scholastica Urua (10:40:02): > Hello everyone, > > Unfortunately, I didn’t get the opportunity to ask my question during the office hour, so here it goes. For the second contribution, I have curatedhttps://bugsigdb.org/Study_875. I have gone through the paper several times but I’m not sure if I missed something. I am unsure if it’s supposed to have more than one experiment. > > The patient group in this study was further subgrouped by the severity of mild, moderate, severe and very severe acne. However, the results showed that no significant difference was observed among patient subgroups with different severity levels. Therefore, I curated it as one experiment. > > Please, I could use a second set of eyes to review this. - Attachment (BugSigDB): Patients with Acne Vulgaris Have a Distinct Gut Microbiota in Comparison with Healthy Controls - BugSigDB > Acne vulgaris has been postulated to have a gastrointestinal mechanism; however, little is known about gut microbiota dysfunction in this condition.The aim of this cross-sectional study was to investigate whether the gut microbiota is altered in acne.

Amanda Adoyi (10:44:45): > Aloha again:slightly_smiling_face:How do you list taxa in the NCBI portion when it is labelled “Others”? Should we ignore the unidentified microbes?

Raihanat Adewuyi (10:45:57) (in thread): > Alright > Thanks@Mildred Anashie

Peace Sandy (10:46:38) (in thread): > If it was stated in the paper thatit’sunidentified > > Please ignore

Aleru Divine (10:46:45) (in thread): > @Amanda AdoyiI think we should ignore it.

Eniola Adebayo (10:50:09) (in thread): > If the study did not include alpha diversity and there are no significant difference between the subgroups like you said, Idon’tthink you need to curate the experiment.@Svetlana Ugarcina Perovicplease help confirm:pray:

Amanda Adoyi (10:51:17) (in thread): > Thank you. And on that topic@Peace Sandyplease would like to know if we are to list all taxon irrespective of level…I realise I only listed family level taxons even though there was genus level groupings there…I feel like I’m repeating meself.

Barakat Akinsiku (10:56:53) (in thread): > Hi@Scholastica UruaI agree with Eniola. If there was no significant difference in the subgroups you can go with one experiment but let’s wait for more expert opinion

Aleru Divine (10:58:43) (in thread): > @Amanda AdoyiI thinkwe’reto list all taxa levels.

Rahila-me (10:59:03): > @Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyYou all made the meeting lovely with all the insights. Thank you all. Had a great time

Nana (11:00:18): > <!here>my take on the meeting was to prioritize quality over quantity. Thank you peace and to you all for your time

Scholastica Urua (11:01:23) (in thread): > @Amanda AdoyiI think you should because the curation policy says to curate all taxa no matter of their taxonomic levels.

Amanda Adoyi (11:01:53) (in thread): > As long as it shows up in the text…alright then. Thanks.

Roderick Momin (11:03:31) (in thread): > @Barakat AkinsikuAs of now, no.

NWAKAEGO VINCENT (11:06:12) (in thread): > how do i record my contribution on outreachy website

Barakat Akinsiku (11:08:15) (in thread): > I see. Let’s ask our mentors for help.@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuapeplease help out here

Esther Afuape (11:09:38) (in thread): > @Peace Danielplease mention the exact taxa you changed and the IDs you replaced them with

Esther Afuape (11:17:55): > Hello <!channel>**** > *******Thank you for putting your efforts in NCBI cleanup issues!******* > > ****Pease notify us of the changes you’re about to make before you actually make them:if you think you have solved a NCBI ID issue, please drop it here on the channel first and let us cross check before you change anything.Some times, taxa are best left in orange and do not need to be changed!

Joan C. Chukwuemeka (11:19:18): > I wish I could get clarification on this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709814171516569?thread_ts=1709769757.884109&cid=C04RATV9VCY - Attachment: Attachment > Thanks @Esther Afuape > > For the Experimental Factor Ontology (EFO) condition being studied - There’re 2 possible ones > > A. response to allogeneic hematopoietic stem cell transplant (EFO:0007044), defined as any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an allogeneic hematopoietic stem cell transplant) > > **B. acute graft vs. host disease (Graft-versus-host disease (GVHD) (*EFO:0004599),* defined as a common complication following an allogeneic tissue transplant. It is commonly associated with stem cell or bone marrow transplant but the term also applies to other forms of tissue graft. > > • Option A describes the response to the treatment (allo-HSCT), which is a broad category encompassing various potential outcomes. > • Option B, specifically focuses on the disease state of interest, which is acute graft-versus-host disease (aGVHD). > > On one hand, it seems like option B. However, the study is investigating how changes in the dental biofilm microbiota (DBM) are associated with the risk of developing aGVHD after the transplant (allo-HSCT). > (after the transplant (allo-HSCT) = Engraftment) > > I recall, that @U1LCB8WEA once said that “condition is based on what is being contrasted not what is shared by both groups.” > > And I’m thinking it should be Option A. response to allogeneic hematopoietic stem cell transplant, Since the contrast carried out were between the stages of transplant (pre and post). Hope I’m right in this line of thought? :thinking_face: > > @Svetlana Ugarcina Perovic @UBNSEMS3S @Peace Sandy @Chioma Onyido

Abiola Salako (11:19:40): > Noted@Esther Afuape

Esther Afuape (11:22:59) (in thread): > @Amanda Adoyiif you have the lowest level of hierarchy present (I.e species), you should curate that instead. This is because it is the most specific.

Esther Afuape (11:23:23) (in thread): > Curate the lowest hierarchy present

Scholastica Urua (11:23:27) (in thread): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyI found this curation with unmapped NCBI taxonomy ID;https://bugsigdb.org/Study_400/Experiment_1/Signature_2. Can I go ahead with the correction? (edited) - Attachment (BugSigDB): Study 400/Experiment 1/Signature 2 > Source: Figure 2a, Text (Association between gut metabolites and microbiota for rhinitis and asthma) Description: Differential expression of genera of bacteria…

Mildred Anashie (11:25:23) (in thread): > Noted@Esther Afuape

Esther Afuape (11:27:16) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698177815616049?thread_ts=1698080347.724249&channel=C04RATV9VCY&message_ts=1698177815.616049 - Attachment: Attachment > Please only curate the lowest taxonomic rank. That is to say in this case for the first row do not curate Bacteroidetes, bacteroidia, or bacteroidales–instead curate S24-7 which is a family better known as muribaculaceae (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2005473&lvl=3&lin=f&keep=1&srchmode=1&unlock)

Peace Daniel (11:27:41) (in thread): > Alright, so (Anaerotignum faecicola, Bacteroidaceae bacterium, Brachyspira pilosicoli, Campylobacteraceae bacterium, Lacrimispora amygdalina and Prevotellamassilia timonensisClostridia bacterium, Methanomassiliicoccales archaeon and Blautia massiliensis)were all without links to the NCBI ID, I searched and added these IDs (235814122124675258422681792532571852370204493919066671737424)

Peace Daniel (11:28:16) (in thread): > Ididn’tchange the names, I just added the IDs as they were not linked, Idon’tknow if you understand me now

Amanda Adoyi (11:28:19) (in thread): > @Esther AfuapeBut like what@Scholastica Uruasaid…I also did read that all taxonomic levels should be curated. What should be done then?

Esther Afuape (11:29:01) (in thread): > I agree with you@Joan C. Chukwuemekago with option A.

Esther Afuape (11:30:08) (in thread): > You have to mention the specific taxon/taxa and the ID you found so that we can compare both

Esther Afuape (11:30:42) (in thread): > Please share a link to the paper

idiaru Angela (11:31:41) (in thread): > Thank you@Scholastica Urua

Scholastica Urua (11:32:25) (in thread): > okay

Svetlana Ugarcina Perovic (11:32:28) (in thread): > @Barakat Akinsikuhere you go - File (Zip): ScienceDirect_files_07Mar2024_16-31-28.335.zip

Joan C. Chukwuemeka (11:34:29) (in thread): > Thanks again@Esther Afuapemuch appreciated:blush:

idiaru Angela (11:35:05) (in thread): > Very insightful > A few people have shared very succinct minutes of the meeting already

Amanda Adoyi (11:35:06) (in thread): > My paper?

Amanda Adoyi (11:35:10) (in thread): > Sure

Svetlana Ugarcina Perovic (11:35:36) (in thread): > Now I’m looking forhttps://www.sciencedirect.com/science/article/pii/S0020751919300074@Joan C. Chukwuemeka

Barakat Akinsiku (11:35:45) (in thread): > Thank you!@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (11:37:26) (in thread): > @Joan C. Chukwuemekaare you assigned to this paperhttps://github.com/waldronlab/BugSigDBcuration/issues/89?

idiaru Angela (11:38:04) (in thread): > I think it should be linear regression > I stand corrected though

Mildred Anashie (11:38:29) (in thread): > Issue 89 is for@Roderick Momin

Svetlana Ugarcina Perovic (11:38:37) (in thread): > exactly

Joan C. Chukwuemeka (11:38:50) (in thread): > No, it’s for@Roderick Momin. Was trying to help find the supplementary material

Svetlana Ugarcina Perovic (11:38:59) (in thread): > ahh, I see:smile:

EBERE ADEKOGBE (11:41:00) (in thread): > The answer to your question is NO.@eneje promise

Suru Olaitan (11:43:36) (in thread): > https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/Here@NWAKAEGO VINCENT - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Svetlana Ugarcina Perovic (11:44:00) (in thread): > @Roderick Mominyou should contact the corresponding author of this paperrobert.li@ars.usda.govfor supplementary material since it’s not available online.

Scholastica Urua (11:52:31) (in thread): > @Esther AfuapePlease, I am encountering some challenges while attempting to access the full (PDF) article of some previously curated studies in order to compare taxa with unmapped NCBI IDs. I keep being prompted to make a purchase. How should I proceed? - File (JPEG): Purchase.JPG

Chioma Onyido (11:53:25) (in thread): > Sharing the link will help.:slightly_smiling_face:

Scholastica Urua (11:55:14) (in thread): > This is one of such links;https://bugsigdb.org/Study_408/Experiment_2/Signature_2 - Attachment (BugSigDB): Study 408/Experiment 2/Signature 2 > Source: Figure 1b Description: Differentially abundant OTUs Identified by Deseq2 analysis at 1 year Abundance in Group 1: decreased abundance in asthma at 1 year…

Esther Afuape (11:57:40) (in thread): > @Scholastica Uruaplease leave Lachnoclostridium lactaris as it is. The aim of NCBI clean up is to get the ID for that exact taxa, a synonym or something very similar to it. Lachnoclostridium sp. An169 is not a good fit. Same for TM7…well done!:bouquet:

Mildred Anashie (11:57:58): > Hi Everyone > > I’m curating this study ‘’Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states’’ and I have identified four experiments with significant results. The Contrast made is in the images attached. > My question is, The Last two experiments were not mentioned explicitly within text and I am not sure which of them should be Group 0 and Group 1. > I was thinking following the presentation of results (Corresponds with text where Culture positive is Group 1) > For Experiment 3 i should have > Group 0-Asymptomatic > Group 1-Insignificant and 4
> Group 0-Asymptomatic > Group 1-No growth. > > I’m really concerned about the last as the description for No growth is simply organisms with No Bacterial or Fungal growth. > Having significant results for increase and Decrease for the group doesn’t seem right by me So I’m wondering if i should flip the arrangement? Using Asymptomatic as Group 1? > But it also says Asymptomatic patients had no clinical evidence of the condition UTI > > Please I need help figuring this out@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy - File (PNG): Cohort Description….PNG - File (PNG): Figure 3.PNG

Chioma Onyido (12:01:53) (in thread): > Here - File (PDF): Article.pdf

Temi (12:02:48) (in thread): > I had something similar for my article since the auto in bugsigdb did not provide linear model option I picked linear regression for mine, I don’t know if that’s right tho please help us clarify@Svetlana Ugarcina Perovic@Esther Afuape

Aleru Divine (12:03:30): > Hello@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma OnyidoI found this page with missing NCBI IDhttps://bugsigdb.org/Study_217/Experiment_2/Signature_1Although it is just one taxon with missing NCBI ID > > It is Clostridium cluster XIVa also known as Clostridium coccoides group > > Can I go ahead to replace it with the correct ID? > > The correct Taxonomy ID is 1532 and the correct name is Blautia coccoides. > > Clostridium coccoides is a basionym of Blautia coccoides. > > Thank you! - Attachment (BugSigDB): Study 217/Experiment 2/Signature 1 > Source: Figure 1 Description: Relative contribution of phylum-like bacterial groups to the total HITChip signals of infants at 6 and 18 months of age Abundance…

Scholastica Urua (12:20:35): > Hello@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma OnyidoI found this page with a missing NCBI ID:https://bugsigdb.org/Study_408/Experiment_2/Signature_2. It contains a taxon labeled ‘RF32’ without an NCBI ID. Upon conducting a search, I discovered it may correspond to ‘Streptococcaceae bacterium RF32’ with the Taxonomy ID: 423432, ranked as a species. > Please confirm if this information is accurate, and if I can proceed with the edit. Thank you!

Scholastica Urua (12:21:54) (in thread): > Thank you@Chioma OnyidoPlease I’d like to know what I can do differently because I also experienced same with other articles as well.

Scholastica Urua (12:31:41) (in thread): > @Esther AfuapeUpon conducting further research onhttps://bugsigdb.org/Study_400/Experiment_1/Signature_2, I was unable to identify the NCBI ID of the taxon ‘SMB53’. Please I will now proceed to check other ones. Thank you:pray: - Attachment (BugSigDB): Study 400/Experiment 1/Signature 2 > Source: Figure 2a, Text (Association between gut metabolites and microbiota for rhinitis and asthma) Description: Differential expression of genera of bacteria…

Esther Afuape (12:32:28) (in thread): > If you checked the discussion page,it’sbeen noted under the unresolved list.

Scholastica Urua (12:33:23) (in thread): > Yes, I noticed. Thank you for pointing that out.

Esther Afuape (12:33:53) (in thread): > Where did you see Clostridium cluster IVa to be the same as coccoides?

Mildred Anashie (12:38:54): > Hello@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma OnyidoI found this pages with a similar missing NCBI ID******Clostridium sensu stricto 1******https://bugsigdb.org/Study_237Experiment 1 signature 1 and Experiment 3 signature 2https://bugsigdb.org/Study_767/Experiment_2/Signature_1Experiment 2 Signature 1https://bugsigdb.org/Study_518/Experiment_1/Signature_1Experiment 1 signature 1https://bugsigdb.org/Study_717/Experiment_4/Signature_1Experiment 4 Signature 1 > > Found this linkhttps://www.midasfieldguide.org/guide/fieldguide/genus/clostridium_sensu_stricto_1that shows the NCBI ID for the taxa as 1485 which is same as the ID for Clostridium > Found an information on google that seems to support this in my opinion, please help cross check this information and let me know if I can update it > Thank you! - Attachment (BugSigDB): Intestinal microbiota in patients with chronic hepatitis C with and without cirrhosis compared with healthy controls - BugSigDB > BACKGROUND & AIMS: The importance of the intestinal microbiota for the onset and clinical course of many diseases, including liver diseases like non-alcoholic steatohepatitis and cirrhosis, is increasingly recognized. - Attachment (BugSigDB): Study 767/Experiment 2/Signature 1 > Source: Supplementary Table S2D and Supplementary Table S2B Description: Differentially Abundant Genus level Taxa Between mild cognitive impairment (MCI) and Non… - Attachment (BugSigDB): Study 518/Experiment 1/Signature 1 > Source: Figure 3 Description: Patients with endometriosis demonstrated a significantly higher abundance of the following taxa compared to control patients. There… - Attachment (BugSigDB): Study 717/Experiment 4/Signature 1 > Source: Table S8 (B) in supplementary results. Description: Differential abundance comparison results for disease phenotype (TD vs PIGD; within the PD patient group… - File (PNG): Clostriduim senso.PNG

Aleru Divine (12:38:58) (in thread): > I found it in this article in BMChttps://jasbsci.biomedcentral.com/articles/10.1186/s40104-019-0402-1#:~:text=Clostridium%20cluster%20XIVa%2C%20also%20known,species%20%5B5%2C%2012%5D. - Attachment (BioMed Central): Clostridium species as probiotics: potentials and challenges - Journal of Animal Science and Biotechnology > Clostridium species, as a predominant cluster of commensal bacteria in our gut, exert lots of salutary effects on our intestinal homeostasis. Up to now, Clostridium species have been reported to attenuate inflammation and allergic diseases effectively owing to their distinctive biological activities. Their cellular components and metabolites, like butyrate, secondary bile acids and indolepropionic acid, play a probiotic role primarily through energizing intestinal epithelial cells, strengthening intestinal barrier and interacting with immune system. In turn, our diets and physical state of body can shape unique pattern of Clostridium species in gut. In view of their salutary performances, Clostridium species have a huge potential as probiotics. However, there are still some nonnegligible risks and challenges in approaching application of them. Given this, this review summarized the researches involved in benefits and potential risks of Clostridium species to our health, in order to develop Clostridium species as novel probiotics for human health and animal production. - File (JPEG): IMG_7757

USLACKBOT (12:48:40): > This message was deleted.

Desire Oluwarotimi (12:50:48) (in thread): > @Mildred AnashieThis is quite tricky. > > Could it be that if you use Asymptomatic as group 1, you get to have only increased abundance signatures of asymptomatic but not decreased for that experiment?

Aleru Divine (12:51:57) (in thread): > @Blessing Ene AnyebeI’dsuggest to find the closest related term.

Aleru Divine (12:52:16) (in thread): > But yeah, better wait for the mentors:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Blessing Ene Anyebe (12:52:53) (in thread): > I tried that generalization and didn’t get much luck. I also searched the ENVO ontology.

Desire Oluwarotimi (12:53:10) (in thread): > Yeah, I agree with@Aleru Divineabout waiting for the mentors.

Blessing Ene Anyebe (12:53:17) (in thread): > Thank you guys

Joan C. Chukwuemeka (12:57:39) (in thread): > What’s the condition@Blessing Ene Anyebe? And could share your article link too?

Blessing Ene Anyebe (12:59:14) (in thread): > The condition is a ’Microbial composition and transmission” > > This is my article:https://www.nature.com/articles/s41598-019-43280-wWhat do you think?@Joan C. Chukwuemeka - Attachment (Nature): Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota > Scientific Reports - Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota

Joan C. Chukwuemeka (13:06:25) (in thread): > @Mildred AnashieWhat I see first is specimen categorization. Now question is were any of these categories contrasted with another? That I think will determine your experiment. It’s a bit like mine, samples were collected at 3 stages of transplant, but contrast was done for only pre- and post- transplant. > > Secondly, I don’t see the direction of abundance (either increased/decreased) from the table/text:thinking_face:

Joan C. Chukwuemeka (13:08:11) (in thread): > Okay, let me check through…

Blessing Ene Anyebe (13:08:38) (in thread): > Thank you:orange_heart:

Mildred Anashie (13:18:04) (in thread): > @Desire OluwarotimiI would have subdoligranulum spp as increased for asymptomatic and cutibacterium as decreased sinceit’senriched in No Growth

Mildred Anashie (13:20:57) (in thread): > @Joan C. Chukwuemekayes. The figure shows the contrast made and I mentioned that text explains the first and second but not the third and fourth > > As for the increased and decreased signature > > The bolded text under each shows increase and decrease in my opinion because for the two I could find in text that was confirmed

Isoken Ibizugbe (13:22:33): > Hello guys I had network issues while taking the survey anddidn’tanswer some prior questions because of that, but Ididn’tknow I got to the end of the survey. How can I go back or should I take another one?

Mildred Anashie (13:23:49) (in thread): > Yes > > I think you can take it again@Svetlana Ugarcina Perovicconfirmed this

Isoken Ibizugbe (13:24:32) (in thread): > Ok thanks

Akinbode Mariam (13:27:03): > Hello everyone! My name is Mariam, and I’m new here. I’m still checking out the pinned messages for guidance. Also, can I get a link to the onboarding video to start with?

Mildred Anashie (13:28:00) (in thread): > Welcome@Akinbode Mariam

Mildred Anashie (13:28:06) (in thread): > The videos can be found under prep workhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (13:28:07) (in thread): > Hi@Akinbode Mariamwelcome:hugging_face:Here is the link to the videoshttps://m.youtube.com/playlist?list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq - Attachment (YouTube): BugSigDB HOWTO videos > Videos describing the functionality and purpose of BugSigDB.org

Akinbode Mariam (13:28:51) (in thread): > Thank you so much

Aleru Divine (13:29:16) (in thread): > @Akinbode MariamBut it’s advisable for you to go through this firsthttps://github.com/waldronlab/BugSigDBcuration/issues/94

Aleru Divine (13:30:01) (in thread): > @Isoken IbizugbeYup.Retake the survey

Scholastica Urua (13:34:52) (in thread): > You can retake the test

Scholastica Urua (13:35:22) (in thread): > Welcome@Akinbode Mariam

Isoken Ibizugbe (13:37:01) (in thread): > How do I record it on outreachy

Mildred Anashie (13:37:55) (in thread): > Use the link to the survey > > You can write “I carried out a mini curation”

Adenike Oladimeji-Kasumu (13:38:26) (in thread): > You are welcome@Akinbode Mariam

Aleru Divine (13:38:59) (in thread): > Go to “record contributions” use the link of the survey as the “contribution URL” and the day you completed the survey as the merge date.

Adenike Oladimeji-Kasumu (13:39:46) (in thread): > Thank you@Mildred AnashieThe issues have been resolved as i will be curating a new paper.

Mildred Anashie (13:40:30) (in thread): > Okay:thumbsup:

Mildred Anashie (13:40:32) (in thread): > Well done

Scholastica Urua (13:41:13) (in thread): > Just to add to what@Aleru Divinesaid, this is where you will click to record contribution under the Microbiome Study Project - File (JPEG): record.JPG

Isoken Ibizugbe (13:42:14) (in thread): > Thanks

Aleru Divine (13:42:41) (in thread): > You’rewelcome:hugging_face:

Desire Oluwarotimi (13:44:36) (in thread): > Welcome@Akinbode Mariam

Desire Oluwarotimi (13:48:35) (in thread): > @Mildred AnashieSo do you think that will be wrong?

Sneha Singh (13:57:55): > Can anyone help me with finding doi and URI forhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8507064/ - Attachment (PubMed Central (PMC)): Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease > The gut microbiota can affect human metabolism, immunity, and other biologic pathways through the complex gut-kidney axis (GKA), and in turn participate in the occurrence and development of kidney disease. In this study, 39 patients with stage 4-5 chronic …

Joan C. Chukwuemeka (14:01:30) (in thread): > @Sneha Singh - File (PNG): image.png

Sneha Singh (14:04:13) (in thread): > @Joan C. ChukwuemekaI was asking about doi:sweat_smile:

Aleru Divine (14:04:53) (in thread): > @Sneha SinghIcouldn’tfind the doi yet,I’mstill checking tho

Joan C. Chukwuemeka (14:04:59) (in thread): > once you input pmid on Bugsigdb, it should populate that too?

Sneha Singh (14:06:23) (in thread): > No its not doing that

Joan C. Chukwuemeka (14:06:49) (in thread): > oh, really?..hmmm:thinking_face:

Mildred Anashie (14:13:42) (in thread): > I’mnot sure the DOI is available,couldn’tfind it > > Did other fields auto populate?

Desire Oluwarotimi (14:15:07) (in thread): > Yes@Mildred AnashieI don’t think so too. Been on it for the past few minutes.

Sneha Singh (14:16:45) (in thread): > It’snot available even after auto populate, so I guessI’llleave it like this. Thank you everyone:smile:

Mildred Anashie (14:16:59) (in thread): > Yes > > I was going to say so

Mildred Anashie (14:17:36) (in thread): > During the meeting@Svetlana Ugarcina Perovicpointed out that some fields could be left blank > I think this case applies

Aleru Divine (14:17:46) (in thread): > Yeah just leave it blank.:sweat_smile:

Sneha Singh (14:18:40) (in thread): > Yes will do, thank you everyone

Abiola Salako (14:21:17) (in thread): > @Sneha Singh, I have checked. Couldn’t find it as well.@Esther AfuapeWhat is she to do, please? Thank you.

idiaru Angela (14:26:32) (in thread): > Welcome@Akinbode Mariam

Svetlana Ugarcina Perovic (14:40:44) (in thread): > Please note that we arecurating microbial sequencing results, not culturing results.

Mildred Anashie (14:49:20) (in thread): > This results are the LEfSe results for the differential abundance between the groupsShouldn’tit be curatable?:thinking_face:

Joan C. Chukwuemeka (14:50:44) (in thread): > @Blessing Ene Anyebeyet to get a solution. I’d revert if i do.

Svetlana Ugarcina Perovic (15:01:13) (in thread): > bugsigdb is about collecting data fromculture-independent studiesbased on 16S rRNA gene sequencing and shotgun sequencing approaches (please seehttps://www.nature.com/articles/s41587-023-01872-y) > > LEfSe analysis can be done on different features, such as organisms, clades, operational taxonomic units, genes, or functions. > > Here in the Microbiome Study Curation project we are interested in identifying replicated patterns from 16S rRNA gene sequencing and shotgun sequencing approaches.

Svetlana Ugarcina Perovic (15:05:18) (in thread): > This study above mentioned involves shotgun metagenomic sequencing and urine standard culturing. We are curating only sequencing results.

Mildred Anashie (15:05:25) (in thread): > I’ll take a look at this article now

Leenaa Al-Amin (15:22:55) (in thread): > The study is “Increased Abundance ofAchromobacter xylosoxidansandBacillus cereusin Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome”https://journals.asm.org/doi/10.1128/spectrum.02311-21. There was an enhanced presence of bacterial transcripts in severe and mortality patient’s nasopharynx compared with mild/moderate groups however Achromobacter xylosoxidans and Bacillus cereus is only has a significant presence in the case of mortality. So do I just compare the severe cases with the moderate case? Also the study doesn’t mention a decrease in transcriptional intensity or abundance of specific bacterial species - File (PNG): Screenshot (23).png - File (PNG): Screenshot (24).png

Mojisayo Awolesi (15:47:48): > Hello everyone, I’m a bit confused and I’d appreciate some guidance. > Are we to make a summary of the Human Microbiome analysis as stated in the attached screenshot? - File (PNG): IMG_8799

Flourish Ralph (15:48:41) (in thread): > Hi@Aleru DivineI just joined, can you explain to me the next step to take?There’sa lot of information here all at once

Mildred Anashie (15:48:58) (in thread): > Pleasewhere’sthis from?:thinking_face:

Mildred Anashie (15:49:29) (in thread): > The reading materials?

Mildred Anashie (15:50:06) (in thread): > Welcome@Flourish Ralph

Aleru Divine (15:50:44) (in thread): > @Flourish Ralphgo through this to get startedhttps://github.com/waldronlab/BugSigDBcuration/issues/94There’sa lot of info here and resources included.Also a guide on how to make your first contribution. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Mojisayo Awolesi (15:51:12) (in thread): > Yes, it was from a link I got from the reading materials

Mildred Anashie (15:51:52) (in thread): > You are to go through it to understand the project

Mildred Anashie (15:52:06) (in thread): > Have you done your first contribution?

Aleru Divine (15:52:21) (in thread): > @Flourish Ralphplease take your time, read the resources, watch the video in the Prep work section and proceed to make your first contribution.There is a guide on how to do that there too.You can ask any questions and Iand other fellow contributors will be more than happy to help:hugging_face:

Flourish Ralph (15:52:38) (in thread): > Thank you

Mildred Anashie (15:52:48) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcThis is the link to follow if youhaven’t - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Mojisayo Awolesi (15:52:52) (in thread): > Oh okay > I thought I was to do that first before contributing

Mildred Anashie (15:53:32) (in thread): > You are to do your first contribution after studying the materials

Aleru Divine (15:53:41) (in thread): > No youdon’tneed to make any summary, this is just to get you familiar with the human microbiome.

Mildred Anashie (15:54:07) (in thread): > The materials prepare you for contributing (in my opinion)

eneje promise (15:54:38): > @everyone kindly assist me to explain because I don’t understand how to go about it Many microbiome papers do not have enough space to include all the tables and figures and so will include a supplemental document, pdf, or spreadsheet with additional information. Did the published paper have a supplement? If so, paste the URL for the supplement below (it should begin with “https://doi.org”). If not, write “NA” instead.

Odigiri Great Alume (15:55:01) (in thread): > @Svetlana Ugarcina Perovicthank you for always responding promptly. Please could you help elaborate more. I’m a bit confused. Does shotgun and 16s Rna have different methods or ways of experiment curation?:thinking_face:More light will be appreciated ma’am

Mojisayo Awolesi (15:55:26) (in thread): > I appreciate the guidance you have both offered@Aleru Divine@Mildred Anashie

Mildred Anashie (15:55:41) (in thread): > If this is regarding the first contribution > > You can ctrl+f and then search supplement > > If there’s a supplemental material you would find it

Mildred Anashie (15:57:14) (in thread): > But you’d need to download the annotated pdf

Aleru Divine (16:00:18) (in thread): > You’rewelcome@Flourish Ralph

eneje promise (16:00:21): > “@Mildred Anashieyes I have downloaded it

Aleru Divine (16:04:04): > @eneje promisesearch the keyword “supplement” > > Most of the time, the supplementary info is located before or after the references.So you would look towards the end of the article.

Svetlana Ugarcina Perovic (16:04:52) (in thread): > @Odigiri Great Alumeno, they do not. I just wanted to highlight that the above discussed paper has both culture and sequencing based methods involved, and in bugsigdb curation we are curating only sequencing results. Hope I was more clear now.

Svetlana Ugarcina Perovic (16:12:10) (in thread): > Ok, I found a nice example herehttps://www.sciencedirect.com/science/article/pii/S2666517421000432 - File (PNG): Screenshot 2024-03-07 at 22.11.33.png

Ima-obong (Aimah) (16:13:11): > Hello..please when one is done with curating the paper, how do they submit and what is the next step. > > Also, do I record this second task as a contribution on outreachy immediately? > > Thank you

Bolanle Wahab (16:14:05) (in thread): > @Leenaa Al-Aminyes i think you just compare the severe cases with the moderate cases and focus on the presence or absence of the two bacterial species since there was no mention of the decrease in transcriptional intensity or abundance of them.

Bolanle Wahab (16:16:34) (in thread): > @Ima-obong (Aimah)yes , record your second contribution.

Aleru Divine (16:17:49) (in thread): > @Ima-obong (Aimah)to submit, simplycomment on the issue on GitHub notifying the mentors that you have finished curating.Also add a link to the study there.

Svetlana Ugarcina Perovic (16:18:09) (in thread): > We can study microbial communities i.e. microbiomes using: > * culture-dependent methods: include a culturing step ranging from traditional culturing to various combinations of improved culturing techniques, leading to isolation and counting CFUs (colony forming units) and screening of isolates. > * culture-independent sequencing methods rely on DNA extraction followed by 16S rRNA gene sequencing or shotgun sequencing. > In bugsigdb curation we are curating only sequencing results of microbiome studies.

Aleru Divine (16:19:18) (in thread): > And yes, you can record your second contribution.The “contribution URL” is the link to the study you finished curating.For the merge date, you have to wait until the mentors review your curation, then you can update that.

Ima-obong (Aimah) (16:21:16) (in thread): > I really appreciate your responses@Aleru Divineand@Bolanle Wahabthank you

eneje promise (16:24:14) (in thread): > @Mildred Anashieplease there’s supplement in the downloaded article, how do I convert the link to be in the same format as stated in the question

eneje promise (16:27:11) (in thread): > how do i make it to be in this format “https://doi.org”

Blessing Ene Anyebe (16:28:37) (in thread): > Thank you@Joan C. ChukwuemekaLikewise. > > I look forward to it!

Ima-obong (Aimah) (16:33:50) (in thread): > Please@Aleru Divinewhen you say “URL to the the study” is it the study assigned on GitHub or the URL to my completed curation that begins with bugsigdb?

Mildred Anashie (16:34:36) (in thread): > Thank you for this enlightenment to the study:pray:From my understanding of the study the culture method was done and subsequently they performed the sequencing based methods (you already pointed out) which differentially abundant results were presented > > This sequenced based method used the groups from the culture results which led them to define the groups by diagnostic categories:thinking_face:And I focused on the contrasts made from my observation and the differential abundant results > > Please am I mixing it all up?:woman-facepalming:

Adenike Oladimeji-Kasumu (16:35:00): > Hello@Chioma Onyidoand everyone, please I am having a hard time in figuring out the Alpha diversity for Shannon, Simpson and the rest from my paper. Here is the statement from my paper: “The profiles of PD patients’ and controls’ fecal microbiota differed significantly, and the alpha and beta diversity differed in the two studied groups. The alpha-diversity indices, including Shannon’s (p-value < 0.007), Simpson’s (p-value: 0.003), and Fisher’s (p-value < 0.001), were significantly different between PD patients and controls. In PD patients, significantly higher bacterial diversity was observed than in the controls. The richness based on observed OTUs (p-value < 0.002), ACE (p-value < 0.001), and Chao1 (p-value < 0.003) indices were significantly higher in PD patients than in control.” Can you please help to determine which is increasing and which is decreasing or unchanged. Thank you.

Mildred Anashie (16:36:20) (in thread): > If I remember correctly the DOI is already highlighted in the paper

Victoria (Burah) Poromon (16:40:05) (in thread): > Can you link the article?

Flourish Ralph (16:43:05) (in thread): > From the resource you sent, I can see 2 contributions. Does this mean we’re meant to fulfill just these 2 contributions for Bioconductor?

Mildred Anashie (16:43:33) (in thread): > You can also search this > > I believe you would find it too or just look at the foot of the pages (hopefullyI’mdescribing it correctly)

Ima-obong (Aimah) (16:44:22) (in thread): > I believe the alpha values are the ones stated above: Shannon’s, Simpson’s…I will say the beta values are not explicitly stated

Scholastica Urua (16:44:28) (in thread): > @Adenike Oladimeji-KasumuAttaching a link to the paper will be better. > > Although I’m still familiarizing myself on paper curation, from this excerpt both Fisher’s and Chao1 are increased. I think the same goes for Shannon’s and Simpson’s. > > The mentors will give a more accurate response.

Mildred Anashie (16:45:14) (in thread): > https://bugsigdb.org/Study_717Something that looks like this (but specific to the study you curated)You can open the studyyou curatedand copy the link

eneje promise (16:45:49) (in thread): > https://cunysph.az1.qualtrics.com/CP/File.php?F=F_09C6LErMWXUBOVU

eneje promise (16:46:19) (in thread): > This is the link am seeing not withdoi.ng

Ima-obong (Aimah) (16:46:58) (in thread): > Awesome…thank you@Mildred Anashie

Scholastica Urua (16:48:04) (in thread): > @Ima-obong (Aimah)it’s the URL to your completed curation. Similar to what@Mildred Anashiehighlighted.

Svetlana Ugarcina Perovic (16:48:11) (in thread): > I will take a look again at this paper in the morning, thank you for your patience.

NWAKAEGO VINCENT (16:48:37) (in thread): > There is no url for the first task should i leave it blank? also i have been assigned a paper to curate

Mildred Anashie (16:49:10) (in thread): > From what I see here > > PD vs Control > Shannon, Simpson = increased > Richness is also increased > > You can attach a link to the paper for this to be confirmed:white_check_mark:

Odigiri Great Alume (16:49:27) (in thread): > @Svetlana Ugarcina Perovicthank you for the clarification. However, having gone through the study I understand that’s Urine samples were collected from UTI patients and then cultured. After culturing they grouped the specimens into cohorts based on the result post culture:petri_dish:. > culture Positive > Insignificant > Asymptomatic > No growth > And contaminated. > > Furthermore the differential abundance of these cohorts were then compared with one another. I see 4 experiments hereGroup 0. Group 1 > **No growth vs Culture positive > Insignificant vs Culture positive > Assymptomatic vs Insignificant > Asymptomatic vs no growth > > These experiments are represented in figure 3. And all the experiments appeared to be conducted using the shotgun metagenomic sequencing

Adenike Oladimeji-Kasumu (16:51:03) (in thread): > https://pubmed.ncbi.nlm.nih.gov/34884399/this the the link to the paper - Attachment (PubMed): Differences in the Composition of Gut Microbiota between Patients with Parkinson’s Disease and Healthy Controls: A Cohort Study - PubMed > Gut microbiome and colonic inflammation can be associated with the predisposition and progression of Parkinson’s disease (PD). The presented study aimed to compare gastrointestinal microbiota composition between patients diagnosed with PD and treated only with Levodopa to healthy controls. In this p …

Adenike Oladimeji-Kasumu (16:52:02) (in thread): > @Mildred AnashieI thought so too, but I am not too sure.

Scholastica Urua (16:53:01) (in thread): > Hi@NWAKAEGO VINCENTthe URL ishttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Ima-obong (Aimah) (16:53:13) (in thread): > The URL is the link to that your submitted task…the form itself ..just copy it from your browser

eneje promise (16:53:37): > Hello everyone. I am still finding hard to convert the searched supplement from annotion pdf article to be in this formathttps://doi.org

Mildred Anashie (16:53:50) (in thread): > @Flourish RalphNot specific to just the two even though the second is optional > There are still other things you can do if you are done with the two included in the resource you are talking about

Svetlana Ugarcina Perovic (16:54:33) (in thread): > And Suppl. material.

Mildred Anashie (16:54:48) (in thread): > The DOI is within text of the downloaded annotated article

Scholastica Urua (16:55:04) (in thread): > You can go ahead to start your second contribution since you’ve been assigned a paper.

Aleru Divine (16:55:10) (in thread): > @Adenike Oladimeji-Kasumuthis excerpt states that “In PD patients, significantly higher bacterial diversity was observed than in the controls. The richness based on observed OTUs (p-value < 0.002), ACE (p-value < 0.001), and Chao1 (p-value < 0.003) indices were significantly higher in PD patients than in control.”So Shannon, Simpson and Fisher increased in PD compared to controls.Also the Richness and Chao1increased in PD compared to controls.

Svetlana Ugarcina Perovic (16:55:46) (in thread): > At first I did not catch the grouping part, thanks@Odigiri Great Alume

Scholastica Urua (16:57:10) (in thread): > @eneje promiseplease provide a full link to your paper.

Mildred Anashie (16:57:36) (in thread): > @eneje promiseplease share a screenshot of the first page of the article

Mildred Anashie (16:57:47) (in thread): > I’lltry to point it out to you

Svetlana Ugarcina Perovic (16:57:50) (in thread): > especially because urinary microbiome papers do have often combination of both approaches.

Aleru Divine (17:00:19) (in thread): > Thanks@Mildred Anashie:hugging_face:

Emem Eduoku (17:00:36): > Hi everyone. How do I make my first contribution. I read I’m supposed to curate a study but can’t find the link.

Mildred Anashie (17:01:50) (in thread): > My observations are correct > > For richness and Chao1 Increased > Shannon, Simpson and Fischer increased

Aleru Divine (17:01:59) (in thread): > @eneje promiseThis is for the first contribution correct?

Mildred Anashie (17:02:28) (in thread): > Yes it is@Aleru Divine

Emem Eduoku (17:02:32): > Where can I find the link to the first task anyone?

Aleru Divine (17:02:51) (in thread): > Yes you were@Mildred Anashie:clap::clap:weldone

Aleru Divine (17:04:37) (in thread): > Okay.@eneje promiseI didn’tneed to convert.It came in that format.Paste the URL for the supplement.It is in the right format already.

Ananya Tomar (17:05:06) (in thread): > Hey Emem!

Ananya Tomar (17:05:17) (in thread): > This is the link to follow for the first contributionhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Scholastica Urua (17:05:21) (in thread): > Hello@Emem Eduokuplease go through thehttps://github.com/waldronlab/BugSigDBcuration/issues/94. you’ll get both the link to the first curation and other useful information as well. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/ - File (JPEG): first curation.JPG

Adenike Oladimeji-Kasumu (17:05:49) (in thread): > Those were my observations too. So, I am on track. Thank you so much y’all

Aleru Divine (17:06:02) (in thread): > Hi@Emem Eduokuthis is the link to the task.You will find the link to the annotated article here.https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Naomi Ibe (17:06:56): > Hello so I’d like to work on missing NCBI IDs, I picked this articlehttps://bugsigdb.org/Study_844/Experiment_5/Signature_1and I’d like to add the id to this microorganism “Christensenellaceae_R7”, Tax id 990719 with name “Christensenellaceae”, may I proceed to edit? - Attachment (BugSigDB): Study 844/Experiment 5/Signature 1 > Source: Supplemental. Table S3A Description: Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian…

Aleru Divine (17:07:04) (in thread): > Yes yes:clap::clap:weldone@Adenike Oladimeji-Kasumu

Ananya Tomar (17:08:06): > hey guys! is the doi supposed to populate or is there another step to follow? - File (PNG): image.png

Odigiri Great Alume (17:08:07) (in thread): > You are welcome ma.@Svetlana Ugarcina Perovic

Aleru Divine (17:08:56) (in thread): > @Ananya Tomarthe PMID is supposed to automatically populate the page with the data and not the doi.Try with the PMID

Emem Eduoku (17:09:08) (in thread): > Thank you@Scholastica Urua@Aleru Divine

Mildred Anashie (17:09:10) (in thread): > @Svetlana Ugarcina Perovichttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-021-01204-9 - Attachment (BioMed Central): Substantial overlap between symptomatic and asymptomatic genitourinary microbiota states - Microbiome > Background The lack of a definition of urinary microbiome health convolutes diagnosis of urinary tract infections (UTIs), especially when non-traditional uropathogens or paucity of bacteria are recovered from symptomatic patients in routine standard-of-care urine tests. Here, we used shotgun metagenomic sequencing to characterize the microbial composition of asymptomatic volunteers in a set of 30 longitudinally collected urine specimens. Using permutation tests, we established a range of asymptomatic microbiota states, and use these to contextualize the microbiota of 122 urine specimens collected from patients with suspected UTIs diagnostically categorized by standard-of-care urinalysis within that range. Finally, we used a standard-of-care culture protocol to evaluate the efficiency of culture-based recovery of the urinary microbiota. Results The majority of genitourinary microbiota in individals suspected to have UTI overlapped with the spectrum of asymptomatic microbiota states. Longitudinal characterization of the genitourinary microbiome in urine specimens collected from asymptomatic volunteers revealed fluctuations of microbial functions and taxonomy over time. White blood cell counts from urinalysis suggested that urine specimens categorized as ‘insignificant’, ‘contaminated’, or ‘no-growth’ by conventional culture methods frequently showed signs of urinary tract inflammation, but this inflammation is not associated with genitourinary microbiota dysbiosis. Comparison of directly sequenced urine specimens with standard-of-care culturing confirmed that culture-based diagnosis biases genitourinary microbiota recovery towards the traditional uropathogens Escherichia coli and Klebsiella pneumoniae. Conclusion Here, we utilize shotgun metagenomic sequencing to establish a baseline of asymptomatic genitourinary microbiota states. Using this baseline we establish substantial overlap between symptomatic and asymptomatic genitourinary microbiota states. Our results establish that bacterial presence alone does not explain the onset of clinical symptoms. Video Abstract

Scholastica Urua (17:09:14) (in thread): > Try adding the PMID as well

Aleru Divine (17:09:33) (in thread): > You’rewelcome@Emem Eduoku

idiaru Angela (17:09:40) (in thread): > You are to read an annotated article of which the link has been provided, then complete a survey after downloading and reading the article. Hope this helps

Ananya Tomar (17:09:45) (in thread): > alright , the doi is specified in the onboarding videos thus the misunderstanding i presume

Ananya Tomar (17:09:55) (in thread): > thank youu@Aleru Divine@Scholastica Urua

Aleru Divine (17:10:22) (in thread): > You’rewelcome@Ananya Tomar:hugging_face:

Mildred Anashie (17:10:25) (in thread): > Thank you so much@Odigiri Great Alumefor clearly stating this out

Svetlana Ugarcina Perovic (17:13:32) (in thread): > “No growth” on the plate does not mean that there is no microbiome in urine. Does this help?

Svetlana Ugarcina Perovic (17:15:47) (in thread): > It means that specific culturing conditions did not support detection of potential bacterial/fungal growth.

Emem Eduoku (17:16:52) (in thread): > Do I have to sign up on BugSigDB site for this task or just filling my details for the curating task is enough?

Aleru Divine (17:18:23) (in thread): > Just your details are enough for the first task@Emem Eduokubut for the second contribution, you’ll need to request an account in BugSigDB.

Emem Eduoku (17:19:00) (in thread): > Alright

Ananya Tomar (17:22:37): > @Svetlana Ugarcina Perovic@Peace SandyI have found the host species for an article missing in the dropdown menu, is there a way I could contribute towards its addition?

Svetlana Ugarcina Perovic (17:23:23) (in thread): > Please send me which one and link to the paper. Thanks.

Ananya Tomar (17:24:24) (in thread): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01596-w#Sec1Host Species -Macaca assamensis - Attachment (BioMed Central): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - Microbiome > Background During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. Results In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. Conclusions In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract

Svetlana Ugarcina Perovic (17:26:30) (in thread): > Macaca assamensis is on the list.

Mildred Anashie (17:27:13) (in thread): > This helps a lot > > It clarifies my confusion > Thank you so much for patiently putting me throughI’mreally grateful:face_holding_back_tears:@Svetlana Ugarcina Perovic

Ananya Tomar (17:27:27) (in thread): > oh alright , wasn’t turning up , I’ll check again , thank you!

Odigiri Great Alume (17:27:32) (in thread): > Thank you so much@Svetlana Ugarcina PerovicAlways to the rescue:muscle:

Svetlana Ugarcina Perovic (17:27:46) (in thread): - File (PNG): Screenshot 2024-03-07 at 23.27.24.png

Mildred Anashie (17:27:58) (in thread): > Thank you@Odigiri Great Alume:pray:

Svetlana Ugarcina Perovic (17:28:35) (in thread): > oh my, thank YOU for this discussion

Svetlana Ugarcina Perovic (17:29:29) (in thread): > I had in parallel 3 papers open for reviewing and could not catch the reason of your doubt

Svetlana Ugarcina Perovic (17:30:07) (in thread): > but yes, I see now why is so confusing

Svetlana Ugarcina Perovic (17:31:51) (in thread): > Have a good rest and see you tomorrow!

Mildred Anashie (17:34:07) (in thread): > Oh myIt’stotally understandable > Just appreciating all your efforts in responding to us all at almost the same time > > Thank you and see you tomorrow:blush:

Flourish Ralph (18:01:19) (in thread): > Okay, but those 2 MUST be done before moving on to other contributions,right?

eneje promise (18:09:40) (in thread): > https://cunysph.az1.qualtrics.com/CP/File.php?F=F_09C6LErMWXUBOVU

Oluwatomisin Omojokun (18:16:10): > Hello, i have completed the first article, did anyone get any link that will be uploaded on the Outreachy platform. Thanks

Bolanle Wahab (18:19:03) (in thread): > @Oluwatomisin Omojokundo you mean the article for your second contribution or the first contribution task?

Mildred Anashie (18:26:38) (in thread): > I underlined with black what you are meant to use@eneje promise - File (JPEG): IMG_2081

Mildred Anashie (18:27:22) (in thread): > Yes@Flourish Ralph

Mildred Anashie (18:30:48) (in thread): > If it’s for your first contribution upload thishttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcFor the second > > Something that looks like thishttps://bugsigdb.org/Study_717(but specific to the study you curated) > You can open the study you curated and copy the link - Attachment (BugSigDB): Gut microbiota in Parkinson’s disease: Temporal stability and relations to disease progression - BugSigDB > BACKGROUND: Several publications have described differences in cross-sectional comparisons of gut microbiota between patients with Parkinson’s disease and control subjects, with considerable variability of the reported differentially abundant taxa.

Flourish Ralph (18:38:01) (in thread): > Please do we have to write the description as well? That is when adding the contribution.

Flourish Ralph (18:40:03) (in thread): > @Mildred Anashiedoes this mean we are making 2 contributions now? That is after finishing the ‘first contribution task’ on the repo?

Mildred Anashie (18:54:09) (in thread): > Yes@Flourish Ralph

Mildred Anashie (18:59:00) (in thread): > For the second contribution you’d > * Request for an account if you haven’t and wait for your account to be approved before you can start the second contribution > * Select a study on GitHub and comment on it with your name and ask to claim it for curation (There are available studies now)

Flourish Ralph (19:02:18) (in thread): > Thank you

Mildred Anashie (19:13:04): > @Akinbode MariamUse this link to start your first contributionhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Akinbode Mariam (19:14:24) (in thread): > Okay thanks

Mildred Anashie (19:15:07) (in thread): > When you are done, you record on OutreachyFor the second contribution you’d > * Request for an account if you haven’t and wait for your account to be approved before you can start the second contribution > * Select a study on GitHub and comment on it with your name and ask to claim it for curation (There are available studies now)

Emem Eduoku (19:58:35): > I’m happy to announce that I have finished my first task and I must confess I loved it. I think I’m in love with this project after going through the documentations. > > It’s a huge help to researchers and students who have to comb the Internet trying to gather information on the many studies on microbiome. I wish I knew about BugSigDB while writing my undergraduate thesis. Could have saved me a lot of stress. > > Looking forward to my second curation.

Bolanle Wahab (20:10:49) (in thread): > Weldone@Emem Eduoku:thumbsup:

Akinbode Mariam (20:40:05) (in thread): > Same here! loved it also now that it says my record has been recorded what next ?

Akinbode Mariam (20:41:23) (in thread): > I just finished my first task Thank you so much for your help,@Mildred Anashie

Akinbode Mariam (20:44:24) (in thread): > How do i request for an account ?

Nitya Singhal (20:46:24) (in thread): > Indeed, this project is very interesting. The best part is we are able to add value to the world and contribute to assisting researchers in their work. I absolutely love the concept@Svetlana Ugarcina Perovic

Nitya Singhal (20:49:58) (in thread): > Thank you so much@Scholastica UruaAmazing insights. Will keep them in mind:smile:

Nitya Singhal (20:56:14): > Can someone please explain the concept of Groups? How do we bifurcate them into 0, 1, 2 and so on?

Nitya Singhal (20:59:45) (in thread): > In my paperhttps://www.nature.com/articles/s41531-023-00554-5, are the three groups ET,PD and HC? - Attachment (Nature): Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease > npj Parkinson’s Disease - Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease

Abiola Salako (21:05:50) (in thread): > Well done@Emem Eduoku

Abiola Salako (21:07:57) (in thread): > Well done@Akinbode Mariam

Abiola Salako (21:09:56) (in thread): > @Flourish RalphYes, you are to write the description

Akinbode Mariam (21:23:30) (in thread): > Thank you@Abiola Salako

Akinbode Mariam (21:24:51) (in thread): > @Mildred AnashieI already requested an account, so I will wait till I am approved before starting the next phase. cant wait:smiling_face_with_3_hearts:

Scholastica Urua (22:29:13) (in thread): > Hello@Nitya Singhalyes, your paper has 3 groups; ET (Patients with Essential Tremor), PD (Patients with Parkinson’s disease) and HC (Healthy Control). I’m still going through the paper.

Scholastica Urua (22:30:17) (in thread): > Well done@Emem Eduoku, I’m glad you were able to find your way.

Scholastica Urua (22:32:09) (in thread): > Well done@Oluwatomisin Omojokun, good luck with your second contribution:+1:.

Scholastica Urua (22:39:55) (in thread): > @Flourish Ralphin addition to@Mildred Anashieresponse, you can make as many contributions as possible but you have to first finish the first contribution which is a compulsory task. Then move on to the second contribution, although this is not compulsory it is advisable to do it. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > > Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > > Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_IDSee other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsHope this is helpful. - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Scholastica Urua (22:47:30) (in thread): > While going through the article, I noticed that ET was compared to HC and ET was again compared to PD. This will form 2 different experiments. Don’t know if@Chioma Onyido@Peace Sandy@Esther Afuapehave more to say on this.

Desire Oluwarotimi (23:06:06) (in thread): > Hi@Nitya SinghalTo answer your first question, the concept of groups is simply just the experiment comparisons made in your paper. And like@Chioma Onyidosaid in yesterday’s office hour, an example could be IBD vs healthy controls. > > Concerning placing them into groups 1 and 0, most times you really just have to look through your paper to lay hands on that. In your article (under the discussion), they mentioned the groups and they are comparing; > ET vs HC > ET vs PD > PD vs HC > > To confirm this, Fig 2 in your article also gave off the same information with regards to group splitting. > > I hope this helps.

Scholastica Urua (23:49:31) (in thread): > Nice one@Desire Oluwarotimi. This is well detailed.

2024-03-08

Okache Johnpaul (00:31:44) (in thread): > Good job@Desire Oluwarotimi!

Scholastica Urua (00:35:10): > Hello everyone, how is the contribution phase progressing? The first week is slowly coming to an end, and it has been wonderful collaborating with everyone here. > I’ve noticed that there have been over a dozen questions asked, and I’ve been able to identify a few that are recurring. Please feel free to add other questions and answers under this thread. I hope this helps someone! > > Q1. I couldn’t find how to record my first contribution. > A: Steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > Q2. When recording the first contribution, what is the ‘merged date’? > A: The merged date refers to the date you submitted your contribution. > > Q3. What URL are we submitting for the first contribution? > A: The link to the curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcwill serve as your Contribution URL. > > Q4. After I submit my first contribution, can I go back to edit it if I notice I made a mistake, or if I didn’t add something somewhere? > A: Unfortunately, you cannot edit a submitted contribution but you can make another submission from scratch. > > Q5. Are we making 2 contributions? > A: While you can make as many contributions as possible, the first contribution is compulsory. After completing the first contribution, you may proceed to the second. Although the second contribution is not mandatory, it is advisable to complete it. Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsQ6. For the second contribution, after Adding a Study in BugSigDB, does it need to be reviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study? > A: You do not need to wait for mentors to review. You can click on the ‘Add Experiment’ button to add an experiment. > > Q7. I want to know how many times I can use the record my contribution option on the Outreachy website. > A: You can use the ‘Record My Contribution’ option as many times as needed, depending on how many contributions you make. > > Q8. How to I get assigned a paper for my second curation? > A: Find an unassigned paper you’ll like to curate viahttps://github.com/waldronlab/BugSigDBcuration/issues, then ask for it to be assigned to you by commenting on it. Mentors will assign it to you if you are the first to request for it. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Desire Oluwarotimi (00:36:53) (in thread): > Weldone@Scholastica Urua

Scholastica Urua (00:43:58) (in thread): > Thank you@Desire Oluwarotimi

Roderick Momin (00:45:53) (in thread): > @Svetlana Ugarcina PerovicUnderstood, thank you.

Nitya Singhal (00:58:00) (in thread): > Yes yes I remember@Chioma Onyidotalking about groups in yesterday’s meeting but it was a bit unclear to me. Thank you for making things absolutely clear.@Desire Oluwarotimi:blush:

Ruth Bamgbose (00:59:11) (in thread): > So basically you would have 3 experiments,and remember when assigning the grouping, that group 1 is the conditionyou’retesting for. For instance; group 0 = HC, and group 1 = ET and so on.

Desire Oluwarotimi (01:06:17): > Good morning mentors and fellow contributors.:smile:I have enjoyed the ride so far, thanks to you all.:hugging_face:I’m looking forward to doing more together with you all again today. Let’s get it.:sunglasses:

Nitya Singhal (01:11:42) (in thread): > ok, i got you@Ruth Bamgbose

Adedoja Isaac (01:15:38): > Hello everyone, Thanks for your your assistance so far. I’m kind of stuck. My curation is not a case control study. So, for forms like Group 0 (control (unexposed) group for case-control studies) and others, do I leave that particular space blank?

idiaru Angela (01:18:53) (in thread): > This is really helpful. Thank you@Scholastica Urua

Scholastica Urua (01:19:45) (in thread): > Hello@Adedoja Isaacaccording to the ‘Curation Policy’ some study may not have control and exposed groups. In some cases, there are groups with low vs. high severity of a disease, use group 0 for low severity and group 1 for high severity cases.

Desire Oluwarotimi (01:21:19) (in thread): > Hi@Adedoja IsaacBecause your study isn’t a case-control study doesn’t mean that there wouldn’t be experimental comparisons (group 0 and 1). > > Please check again or you could as well share so we go through it together.

Scholastica Urua (01:21:23) (in thread): > This is a link to the curation policy;https://bugsigdb.org/Curation_Policy. > Read the ‘Contrast’ section for further clarity. - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Ruth Bamgbose (01:24:21) (in thread): > Well done@Emem Eduoku

Ruth Bamgbose (01:26:20) (in thread): > @Akinbode Mariamyou add the link to your outreachy contribution and also check this outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709636941179439?thread_ts=1709636862.134639&channel=C04RATV9VCY&message_ts=1709636941.179439 - Attachment: Attachment > @Ruth Bamgbose you can go ahead with the second contribution. > > As mentioned in the onboarding material for the second task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Also, remember to record your first contribution on the outreachy site.

Adedoja Isaac (01:27:01) (in thread): > Thank you very much@Scholastica Urua@Desire Oluwarotimi. Understood

Adedoja Isaac (01:29:18) (in thread): > https://journals.asm.org/doi/10.1128/mbio.03519-22@Desire Oluwarotimi

Adedoja Isaac (01:29:57) (in thread): > Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis is what I’m working on

Desire Oluwarotimi (01:44:34) (in thread): > Hi@Adedoja IsaacLike I mentioned earlier, there are groups which means you can’t leave the space blank. Your article divided the patients into mild, moderate, severe and critical groups. > > By the way, your article also has supplementary materials. I didn’t go through them but you should because they will contain important information. > > I hope this helps.

Aleru Divine (01:45:58) (in thread): > Thanks for sharing this@Scholastica Urua

Adedoja Isaac (01:48:28) (in thread): > Thank you for the assistance@Desire Oluwarotimi, I understand what you mean perfectly now.

Roderick Momin (02:04:36): > If anyone is interested in cross-curating/cross-checking their second contributions with me before final submission please DM me.

Aleru Divine (02:09:04) (in thread): > Good morning@Desire Oluwarotimi:hugging_face:

Mildred Anashie (02:18:55) (in thread): > Good morning@Desire OluwarotimiTruly this has been really enjoyable:blush:

Praise Agbetuyi (02:20:36) (in thread): > Thank you for sharing. Well done,@Scholastica Urua

Desire Oluwarotimi (02:20:53) (in thread): > Good morning@Aleru Divine

Desire Oluwarotimi (02:21:28) (in thread): > Good morning@Mildred AnashieIt truly has.:smile:

Desire Oluwarotimi (02:22:15) (in thread): > By the way@Mildred AnashieI think I might have been able to decipher the exact study design for my article.

Desire Oluwarotimi (02:22:42) (in thread): > I’ll put my explanation under that thread and you can share your opinion. > > You too.@Aleru Divine

Amanda Adoyi (02:23:08): > Aloha my people. Hope you slept well and your day is going great. I would like to point out something about typos. I have spotted one in my paper. It was on phylum-level taxons. In the material I found “Plantomycetes”. However on searching around the internet I found “Planctomycetes” I thought I was in the wrong. If you do come across such, you could check the taxonomy browser and look around the web:slightly_smiling_face:

Mildred Anashie (02:24:34) (in thread): > Yes@Flourish RalphYou need to briefly describe what you did when recording your contribution on outreachy > > For e.g The first contribution was a mini-curation task > You can simply say, “ I carried out a mini-curation” > PS: you can add more details if you want

Mildred Anashie (02:25:21) (in thread): > Okay > > Please do, identifying study designs are a bit tricky:smiley:

Aleru Divine (02:26:34) (in thread): > Good morning@Amanda Adoyithank you for sharing. > > I agree with you, typos occur from time to time and you did the right thing by going further to check.:hugging_face::hugging_face:

Aleru Divine (02:27:17) (in thread): > Alright@Desire Oluwarotimi:sweat_smile:

Aleru Divine (02:28:38) (in thread): > Could you tag me to the thread again please@Desire Oluwarotimi

Mildred Anashie (02:28:41) (in thread): > @Amanda AdoyiI think cases like that occur, researching on it to cross check is important > > And I think using the discussion page of the study might be important for those reviewing > > Let me tag the mentors to confirm this statement:blush:@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape

Desire Oluwarotimi (02:28:58) (in thread): > Hi guys, I think I might have been able to get the exact study design for my article so I decided to share my explanation. > > I assume I was wrong by saying there was interference with the use of Omeprazole in the study but the study which was to understand the human gut microbiome profile couldn’t have happened without the use of Proton Pump Inhibitors (PPI). > > This means that Omeprazole wasn’t an interference but an actual part of the study thus making the study a longitudinal observational study (time series).@Svetlana Ugarcina Perovic@Mildred Anashie@Bolanle Wahab@Leenaa Al-Amin@Aleru Divine

Naomi Ibe (02:29:01): > Hello so I’d like to work on missing NCBI IDs, I picked this articlehttps://bugsigdb.org/Study_844/Experiment_5/Signature_1and I’d like to add the id to this microorganism “Christensenellaceae_R7”, Tax id 990719 with name “Christensenellaceae”, may I proceed to edit? - Attachment (BugSigDB): Study 844/Experiment 5/Signature 1 > Source: Supplemental. Table S3A Description: Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian…

Muqtadirat Yussuff (02:29:24) (in thread): > Good morning everyone, hey@Desire OluwarotimiI admit, so far this has been fun and the community is pretty warm. I hope to keep learning more from you guys

Mildred Anashie (02:29:38) (in thread): > @Aleru DivineI think once he drops a comment on the thread we’d be notified

Desire Oluwarotimi (02:29:51) (in thread): > I have tagged you both@Mildred Anashie@Aleru Divine

Flourish Ralph (02:30:23) (in thread): > @Abiola Salako@Mildred Anashiethank you guys

Desire Oluwarotimi (02:30:49) (in thread): > Here.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709882938283769?thread_ts=1709738837.701009&cid=C04RATV9VCY - Attachment: Attachment > Hi guys, I thought I might have been able to get the exact study design for my article so I decided to share my explanation. > > I assume I was wrong by saying there was interference with the use of Omeprazole in the study but the study which was to understand the human gut microbiome profile couldn’t have happened without the use of Proton Pump Inhibitors (PPI). > > This means that Omeprazole wasn’t an interference but an actual part of the study thus making the study a longitudinal observational study (time series). > > @Svetlana Ugarcina Perovic @Mildred Anashie @Bolanle Wahab @Leenaa Al-Amin @Aleru Divine

Mildred Anashie (02:36:08) (in thread): > This is really interesting@Desire OluwarotimiI’ll have to agree with you because I believe you have thoroughly gone through the paper and this explanation makes a whole lot of sense > > Plus the study has characteristics of a longitudinal study, I was confused with the before and after treatment I saw and still didn’t notice results for the post intervention > I believe it doesn’t rule out the fact that it was done regardless, which still makes it part of the study

Blessing Ene Anyebe (02:37:15) (in thread): > Ha yes thank you for pointing this out and further doing your research@Amanda Adoyi

Desire Oluwarotimi (02:37:55) (in thread): > Yeah@Mildred AnashieThank you.:saluting_face:

Praise Agbetuyi (02:38:26) (in thread): > Well done,@Emem Eduokuon the completion of your first curation. I look forward to completing mine.

Mildred Anashie (02:38:56) (in thread): > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy

Leenaa Al-Amin (02:39:40) (in thread): > Ok so that means I’ll have only 1 signature indicating the abundance of the species Achromobacter xylosoxidans and Bacillus cereus in the mortality right? No need for mention of the other species found in the mortality group although not as abundant as Achromobacter xylosoxidans and Bacillus cereus? Also patients of each sub-phenotype were administered antibiotics during their hospital stay, do I note that down@Bolanle Wahab@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy

Leenaa Al-Amin (02:39:49) (in thread): > Good morning

Esther Afuape (02:40:08) (in thread): > Hi@Mildred Anashieplease check the discussion page for clostridium sensu stricto.It’son the list and explained.

Desire Oluwarotimi (02:40:46) (in thread): > Good morning@Muqtadirat YussuffI hope to learn from you too.:+1:

Praise Agbetuyi (02:44:26): > Good morning, House. Happy International Women’s Day! Please, I need help with this. My paper is not open-access, and I have not been able to download it. doi: 10.1016/j.parkreldis.2021.12.012.

Blessing Ene Anyebe (02:44:56): > Happy internationalwomen’sday:orange_heart::tada:

Mildred Anashie (02:45:44) (in thread): > Seen@Esther AfuapeThank you, Shared what I found to know if I just had a discovery:joy:I’llskip it then

idiaru Angela (02:46:12): > Happy international women’s Day everyone:heart_hands::partying_face::gift_heart:. You all are so welcoming and wonderful

Leenaa Al-Amin (02:46:33) (in thread): > Good morning. Try entering the doi intohttps://sci-hub.se/ - Attachment (sci-hub.se): Sci-Hub: making uncommon knowledge common > Sci-Hub website. Get free access to academic journals. Download research papers for free from ScienceDirect, IEEE, Wiley, Springer, Nature and others

Amanda Adoyi (02:47:16) (in thread): > Yea It is. Thanks

Mildred Anashie (02:47:48) (in thread): > Yes > > Thank you@Leenaa Al-Amin@Praise AgbetuyiSci-hub usually helps

Aleru Divine (02:48:39) (in thread): > Brilliant@Desire OluwarotimiI agree with you > > Omeprazole was not interfering with the study but rather was a deliberate intervention administered to participants as part of the study protocol. Therefore, it was an integral component of the study rather than an interference. > > So it is a time series / longitudinal observational study > > Brilliant:clap:

Aleru Divine (02:50:12) (in thread): > Thanks@Leenaa Al-Amin:heart:

Scholastica Urua (02:50:59) (in thread): > Thanks@Leenaa Al-Amin, I actually find this helpful

Desire Oluwarotimi (02:51:44) (in thread): > Yes@Aleru DivineThank you for your input.:saluting_face:

Ima-obong (Aimah) (03:00:34): > Good morning and Happy international women’s Day to my ladies… > > Just to be sure I’m not missing out on anything, please after submitting your second task(paper curation) what is next? > > And I also see some people working on some papers that are not on GitHub, please how did you find this other papers…thank you everyone.

Mildred Anashie (03:01:48) (in thread): > You can check out this linkhttps://bugsigdb.org/Help:Contents#TODO_for_reviewers - Attachment (BugSigDB): Help:Contents > …

Desire Oluwarotimi (03:02:15) (in thread): > Hi@Ima-obong (Aimah)After your second task, you can pick up other todos using the Mildred has shared.

Rahila-me (03:02:29) (in thread): > Go to Bugsiddb documentation and click onhttps://bugsigdb.org/Help:Contents#TODO_for_reviewers

Mildred Anashie (03:02:59) (in thread): > I don’t know about the other papers people are working on though > > It was probably found under this help page > > Possibly tagged as incomplete or studies without experiments

Rahila-me (03:03:29): > Happy international women’s day, my ladies.:dancer:

Ima-obong (Aimah) (03:03:56) (in thread): > @Mildred Anashieit was the help contents I was referring…the very link you shared…thank you

Aleru Divine (03:04:04) (in thread): > @Ima-obong (Aimah)) In addition to the link Mildred sent, here’s what you should look out for to work on - File (JPEG): IMG_7765

Ima-obong (Aimah) (03:04:48) (in thread): > Thank you@Aleru Divine,@Rahila-me@Desire Oluwarotimi

Bolanle Wahab (03:06:46) (in thread): > @Leenaa Al-Aminyes, since the focus of your study is mainly those two. > And you should probably note that the patients were administered antibiotics if it had an effect on them.

Leenaa Al-Amin (03:11:41) (in thread): > I have reason to believe it did because the species found abundant in the mortality group were reported to be antibiotic resistant. Where do I note it down, under the Antibiotic Exclusion Criteria?

Nwajei Edgar (03:12:08): > Happy international women’s day everyone:innocent::innocent:

Muqtadirat Yussuff (03:13:58) (in thread): > @Desire OluwarotimiI went through the method and I agree with you. > > To me “time series” emphasizes the collection of data over multiple time points to observe changes over time, while “longitudinal observational” refers to the observational nature of the study where participants are followed over time without any intervention beyond what is naturally occurring or deliberately introduced by the researchers which also aligns with what@Aleru Divinenoted in regards to the interference of Omeprazole > > In this case, the intervention with omeprazole makes it more than purely observational, but the focus on following participants over time still aligns with the longitudinal aspect of the study design. > > You came to a really nice conclusion:clap:

Suru Olaitan (03:14:02): > Good Morning Everyone > Please, I have a question > > There are 3 groups in my article, We have: > > First Degree Relatives (Those that might have the disease because they are genetically related to someone who has) > > Adult Celiac Disease (Those that actually have it) > > Controls (They have hepatitis B) and other health issues > > What basis do I use to determine my group 0 and 1? > > Here’s a link to my article for more contexthttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.00164/full?utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field&journalName=Frontiers_in_Microbiology&id=419818 - Attachment (Frontiers): Frontiers | Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls

Mildred Anashie (03:15:17) (in thread): > The Group 1 consists of those with the condition (cases)

Aleru Divine (03:15:51) (in thread): > @Suru OlaitanI’d suggest you go with two experiments. > 1. First degree relatives(1) vs controls (0) > 2. First degree relatives(1) vs Adult Celiac Disease(0) > But let me look at the article.

Barakat Akinsiku (03:16:25): > Happy International Women’s Day everyone:partying_face::partying_face::dancer:Thank you for all you do

Suru Olaitan (03:16:58) (in thread): > Alright, Thank you

Bolanle Wahab (03:21:25) (in thread): > @Suru Olaitani think your > Group 0 should be your Controls ( those with hep B and other health issues) > > Group 1 should be First degree Relatives and Adult Celiac Disease .

Suru Olaitan (03:22:38) (in thread): > Do you suggest that I break it down into 2 experiments like@Aleru Divinesuggested?

Mildred Anashie (03:23:55) (in thread): > You might have more than two@Suru OlaitanBut What you shared shows possibility 2 different experiments as Divine pointed out

Victoria (Burah) Poromon (03:23:58): > Good morning everyone, and happy IWD:yellow_heart::yellow_heart:I have an observation and a question. > > I was going through the curation policy for NCBI and came across a minor grammatical error. - File (JPEG): IMG_7505

Muqtadirat Yussuff (03:24:24) (in thread): > @Suru OlaitanI would also suggest you go with two experiments

Scholastica Urua (03:24:27) (in thread): > In addition to what@Aleru Divinesaid, you may also have a third experiment; ‘First degree relative vs Adult Celiac Disease’ if the comparison was done in the study. Just my thoughts though.

Suru Olaitan (03:24:33) (in thread): > Thought as much…

Suru Olaitan (03:25:55) (in thread): > Quite a number of comparisons were done in the studyThat’swhy I am a bit confused

Bolanle Wahab (03:26:01) (in thread): > Yes.You’renoting both recovered and mortality group right?

Muqtadirat Yussuff (03:26:01) (in thread): > Great observation, I think the co-mentors should be able to edit@Peace Sandy@Esther Afuape

Aleru Divine (03:26:30) (in thread): > @Suru OlaitanI am reading the discussion and here is an excerpt > > “The aim of the present study was to investigate differences in the duodenal and fecal microbiota of pre-diseased state i.e., FDRs subjects compared to diseased state i.e., CeD and DC.“ > > So FDR(1) vs CeD(0) > And > FDR(1) vs DC (0)

Mildred Anashie (03:26:39) (in thread): > Let me go through it as well

Victoria (Burah) Poromon (03:28:09) (in thread): > AndI’lllike to know what this quality control message means. > And what to do about it. Do I remove that particular signature or leave it. > Ps:It’slisted on my paper. - File (JPEG): 7304693b-a8a2-4be7-b37c-b1d8fe605b2f

Muqtadirat Yussuff (03:28:39) (in thread): > Note the ones that had significant results in respect to this particular paper which also align with BigSigDB interest such as alpha diversity and not beta. Some papers do like to reference data from other studies but I would go through your paper before I give further suggestions.

Suru Olaitan (03:31:05) (in thread): > Okay > I’ll wait for you to go through it as well > So I can be clear on what to do > > I sincerely appreciate all the help I’m getting

Muqtadirat Yussuff (03:33:23) (in thread): > I don’t think you can remove it, here’s a link to understand why there are quality flags on BugSigDBhttps://bugsigdb.org/Help:Quality_control - Attachment (BugSigDB): Help:Quality control

Aleru Divine (03:33:29) (in thread): > @Suru OlaitanI thinkit’sstill 2 experiments but between > > FDR(1) vs CeD(0) > > And > > FDR(1) vs DC(0)

Suru Olaitan (03:34:44) (in thread): > Okay@Aleru DivineI really do appreciate you taking out time to read through and help me:heart:

Aleru Divine (03:35:16) (in thread): > You’rewelcome@Suru OlaitanI enjoyed doing that actually:hugging_face:

Bolanle Wahab (03:35:18) (in thread): > @Aleru Divineis it possible to have more that one set of experiments,I mean Group 0s and 1s but in two separate sets of experiments?

Mildred Anashie (03:35:23) (in thread): > I see that two samples were collected “duodenal and Faecal” > > Pairwise comparison was done for all three groups for both samples from your table 1 > > Still going through it though but I suspect 4-6 experiments

Victoria (Burah) Poromon (03:37:26) (in thread): > @Muqtadirat Yussuffthank you so much

Aleru Divine (03:38:45) (in thread): > @Bolanle Wahabyes it is very possible to have multiple experiments in a study, for example, my second contribution had 2 sets of experiments.Because my case group was further divided into 2. > > In my case it was athletes(strength and endurance) vs non-athletes.I had to record each case differently against the control.Strength athletes(1) vs non-athletes(0) > Endurance athletes(1) vs non-athletes(0)

Leenaa Al-Amin (03:39:49): > hello everyone. In relation of the data transformation used in the study I’m curating, I checked the data transformation thread that’s pinned and saw transformations typically associated with various statistical tests. Is it ok to put down a particular transformation based on the statistical test employed even if the data transformation is not clearly stated in the study.

Victoria (Burah) Poromon (03:41:25) (in thread): > But my question is if that particular taxon should be removed or kept. Not the quality control flag

Svetlana Ugarcina Perovic (03:42:11): > Good morning:bouquet:and I wish you HAPPY March 8, HAPPY Friday and HAPPY first week of outreachy contribution successfully completed! > > Tip: After finishing your microbiome study curation on bugsigdb and before claiming it for review, ask your outreachy colleague(s) to review it together one more time. Do not forget to tag your colleague(s) in the the GitHub issue. > > You are doing amazingly well! Today, enjoy in your team work. > > TogetherEveryoneAchievesMore > > NOTE: you can team up in as large of groups as you wish:blush:Please do not edit your colleague’s curation; it’s up to them how they will apply your review suggestions/remarks. A reviewer’s task in science is to give a constructive and critical feedback (not to edit someone’s work). - File (GIF): image_processing20200308-4098-1vg7deu.gif

Mildred Anashie (03:42:32) (in thread): > I believe it is > > Most studies do not explicitly state it > Reason why the mentors tried to help us with further information (In my opinion)

Bolanle Wahab (03:42:42) (in thread): > @Aleru DivineOkay then, it’s possible@Suru Olaitan‘s study can have two experiments > Comparison of Gut Microbiome in First-Degree Relatives (FDRs) of Celiac Disease (CeD) Patients and Controls > * Group 0: FDRs of CeD patients > * Group 1: Controls (individuals without CeD or FDR status) > Comparison of Gut Microbiome in CeD Patients and Controls > * Group 0: CeD patients > * Group 1: Controls (individuals without CeD or FDR status)

Ima-obong (Aimah) (03:43:12) (in thread): > Thank you for the tip.

Blessing Ene Anyebe (03:43:54) (in thread): > Happy internationalwomen’sday@Svetlana Ugarcina PerovicThank you for the tip!:orange_heart:

Mildred Anashie (03:44:12) (in thread): > Please keep the signature@Victoria (Burah) PoromonIf you cross check other curated worksyou’dobserve the same thing

Ima-obong (Aimah) (03:44:15) (in thread): > Yes I think you can, even though it wasn’t stated in the study

Victoria (Burah) Poromon (03:44:24) (in thread): > Is it okay to still do this after claiming it for review?@Svetlana Ugarcina Perovic

Aleru Divine (03:44:31) (in thread): > Yes I think it is okay@Leenaa Al-Amin

Rahila-me (03:44:45) (in thread): > Happy international women’s day to you too@Svetlana Ugarcina Perovic<@UBNSEMS3S>and to you all amazing women out there

Svetlana Ugarcina Perovic (03:45:46) (in thread): > @Victoria (Burah) Poromonyes

Aleru Divine (03:45:47) (in thread): > Thank you@Svetlana Ugarcina Perovic.Is it okay to do this even if I have submitted?

Svetlana Ugarcina Perovic (03:45:57) (in thread): > @Aleru Divineyes

Aleru Divine (03:46:20) (in thread): > Okay, thanks:blush:@Svetlana Ugarcina Perovic

Suru Olaitan (03:46:39) (in thread): > Thank you so much@Bolanle WahabI do appreciate:heart:

Scholastica Urua (03:48:13) (in thread): > Thanks you@Svetlana Ugarcina Perovic

Amanda Adoyi (03:51:12): > Say hello if you’d like a review of my work and vice versa. Could really use the fresh set of eyes…aye. I keep going through my work I think I’m dizzy now.

Aleru Divine (03:51:44) (in thread): > Hello@Amanda Adoyi

Scholastica Urua (03:52:08) (in thread): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyido

Suru Olaitan (03:53:08) (in thread): > Just a quick one > Can you help me confirm that my body site is Small Intestine and Fecal? > > Is that correct, please?

Bolanle Wahab (03:53:15) (in thread): > You’rewelcome@Suru Olaitan

Amanda Adoyi (03:54:43) (in thread): > Thanks@Aleru DivineReally appreciate it. I’ll dm you briefly

Bolanle Wahab (03:54:56) (in thread): > Yes,you’recorrect.

Aleru Divine (03:55:21) (in thread): > You’recorrect@Suru Olaitan

Suru Olaitan (03:55:57) (in thread): > Thank you so much:pray:

Muqtadirat Yussuff (03:57:47) (in thread): > @Victoria (Burah) Poromonoh no, keep it. I’ve seen a number of curated papers with quality flags

Desire Oluwarotimi (03:57:58) (in thread): > Is a group of 3 allowed?:smile:@Aleru Divine@Amanda Adoyi

Mildred Anashie (03:58:57) (in thread): > Duodenal diagnosis groups > > DC vs FDR > CeD vs DC > CeD vs FDR > >
> Faecal diagnosis groups > > FDR vs DC > CeD vs FDR > CeD vs DC > > You’d find results within text and in Figure 3 for duodenal and Figure 5 for Faecal > > My observations, can someone help me confirm this > > NB: The body site for the first groups will be Small intestine and the second groups will be Feaces@Suru Olaitan

Muqtadirat Yussuff (04:01:46) (in thread): > Hey@Aleru Divinecan I tag you on my issue for a review?

Praise Agbetuyi (04:01:47) (in thread): > Thank you@Leenaa Al-Amin

Aleru Divine (04:02:19) (in thread): > Yes@Muqtadirat Yussuffit’llbe my pleasure:hugging_face:

Amanda Adoyi (04:03:10) (in thread): > Lolz. Should we ask@Svetlana Ugarcina Perovic?

Mildred Anashie (04:03:57) (in thread): > Late to the party:sweat_smile:Hello though

Muqtadirat Yussuff (04:04:12) (in thread): > @Aleru DivineThank you so much, what’s your GitHub username?

Praise Agbetuyi (04:04:55) (in thread): > I tried SciHub but they don’t have the paper.

Aleru Divine (04:05:49) (in thread): > @Muqtadirat Yussuffit’sAleruDivine

Leenaa Al-Amin (04:06:25) (in thread): > Hello@Mildred Anashie. I have a question regarding the 11th point you noted regarding curating the condition as the subtypes. I’m working on a study focused on the Role of Co-Infections in Disease Severity and Outcome. The patients were first divided according to outcome: recovered and mortality and the recovered group further divided into mild, moderate and severe. The patients were administered antibiotics and only the mortality group had an abundance of bacteria that’s antibiotic resistant. I plan to create two signatures, one with the bacteria found to be abundant in the mortalty group and one for the bacteria found to be abundant in the recovered. Now here’s my question regarding the point, am I to curate the condition as the subtypes of recovered or am i just confusing myself. Here’s the link to the study for more contexthttps://journals.asm.org/doi/10.1128/spectrum.02311-21

Mildred Anashie (04:06:53) (in thread): > Thank you for the tip@Svetlana Ugarcina PerovicHappy International Women’s day:sparkles:Willing to collaborate with anyone to review each others work:blush:

Desire Oluwarotimi (04:07:47) (in thread): > Let’s have it. > > I don’t think there’s any issue.

Ruth Bamgbose (04:08:24) (in thread): > You should ask the mentors, mine was also not open access but the pdf was provided.

Aleru Divine (04:09:19): > Hello everyone, if you’d like me to review your work and you review mine please reach out. > > I’ve completed my second contribution and I’m open to collaboration:hugging_face::heart:My GitHub is @AleruDivine

Amanda Adoyi (04:09:53) (in thread): > Awesome

Desire Oluwarotimi (04:09:56) (in thread): > Hey Hey Hey:sunglasses:

Svetlana Ugarcina Perovic (04:10:03) (in thread): > This is a wonderful proposal!

Desire Oluwarotimi (04:10:14) (in thread): > Let’s have it.@Aleru Divine

Scholastica Urua (04:10:46) (in thread): > Hi@Amanda Adoyidrop a link to your curation

Leenaa Al-Amin (04:11:07) (in thread): > Yes

Scholastica Urua (04:11:34) (in thread): > Drop a link to your curation@Aleru Divine

Aleru Divine (04:11:47) (in thread): > Hi@Desire OluwarotimiWhat is your GitHub?

Aleru Divine (04:11:57) (in thread): > So I can tag you

Ima-obong (Aimah) (04:12:14): > Hello Everyone, I’m done with my second contribution and I’m open to collaboration. If you’re free and would love to review my work while I review yours please say hi and drop your GitHub username so I can tag you..thank you.

Aleru Divine (04:12:44) (in thread): > @Svetlana Ugarcina Peroviccan multiple people review my curation? I already have someone reviewing it.

Blessing Ene Anyebe (04:13:23) (in thread): > Hi@Aleru Divinelet’sdo it?

Desire Oluwarotimi (04:14:35) (in thread): > @RotimiDesire

U1LCB8WEA (04:17:23) (in thread): > I think you should team up in as large of groups as you wish! Love seeing the collaboration.

Blessing Ene Anyebe (04:18:29): > I am not done with my second contribution but I would love if anyone can review my progress while I also do same? > > Is this okay@Svetlana Ugarcina PerovicIf yes, who would be up for this?

Aleru Divine (04:18:36) (in thread): > Send me your GitHub@Scholastica Uruaand@Blessing Ene AnyebeMine is @AleruDivine

Amanda Adoyi (04:19:00) (in thread): > @Levi WaldronThanks:slightly_smiling_face:That’s the go ahead everyone. Let’s do this. We could drop our links here or what do you suggest is better?

Blessing Ene Anyebe (04:19:06) (in thread): > @kwennb this is mine@Aleru Divine

Aleru Divine (04:19:23) (in thread): > Thanks:blush:

Blessing Ene Anyebe (04:20:38) (in thread): > Thank youuu

Svetlana Ugarcina Perovic (04:21:51) (in thread): > it’s ok, but afterwards do not forget to tag your colleague in your gh issue

Scholastica Urua (04:21:59) (in thread): > @Scholarpat is my GitHub user

Desire Oluwarotimi (04:22:25) (in thread): > Not an issue. > > Share your project@Blessing Ene Anyebe

Ima-obong (Aimah) (04:23:52) (in thread): > Hello, I’d love to make a review

Aleru Divine (04:24:03) (in thread): > Please tag me to your studies:pray:

Mildred Anashie (04:25:38) (in thread): > Hi@Ima-obong (Aimah)Let’sdo it

Ima-obong (Aimah) (04:26:09) (in thread): > Thank you@Mildred Anashie

Abiola Salako (04:26:33): > @Svetlana Ugarcina PerovicAlright. Thank you for the support.

Barakat Akinsiku (04:26:47) (in thread): > Hi@Ima-obong (Aimah)@BarakatAA I’m not done but can review as you review my progress. The same too@Mildred Anashie

Scholastica Urua (04:27:30) (in thread): > Hello@Ima-obong (Aimah)mine is @Scholarpat.

Blessing Ene Anyebe (04:28:33) (in thread): > Thanks guys. how do we go about it? A call?

Blessing Ene Anyebe (04:28:35) (in thread): > https://www.nature.com/articles/s41598-019-43280-w - Attachment (Nature): Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota > Scientific Reports - Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota

Muqtadirat Yussuff (04:28:39) (in thread): > I went through the paper and I’m in line with@Bolanle Wahab’s suggestion

Scholastica Urua (04:28:55) (in thread): > @Aleru Divine@Desire OluwarotimiI’ve just tagged you both to my curation. Thank you as I look forward to your comments.

Ima-obong (Aimah) (04:30:22) (in thread): > Alright…thank you…will be tagging y’all on GitHub now

Mildred Anashie (04:30:43) (in thread): > @MyleeeA

Ima-obong (Aimah) (04:30:55) (in thread): > Here is my username, I’m free to review yours as well @imalovee

Mildred Anashie (04:31:01) (in thread): > Sure@Barakat Akinsiku

Mildred Anashie (04:33:41): > Hello everyone > > I already have a few persons reviewing my work butI’mopen to more@Levi Waldronand@Svetlana Ugarcina Perovicsaid we could team up in as large of groups as possible:blush:

Aleru Divine (04:35:09) (in thread): > @Mildred Anashiehere’smy GitHub @AleruDivineI’dlike to review it and you review mine > > Please send me your GitHub:hugging_face:Thank you!

Mildred Anashie (04:35:54) (in thread): > Thank you@Aleru DivineMine is @MyleeeA

Esther Afuape (04:35:59) (in thread): > Hi@Scholastica UruaI checked the paper and what was reportedwasn’ta specie. It seems like an order.That’swhyI’munsure about this as a good match

Scholastica Urua (04:37:08) (in thread): > Thank you@Esther Afuapefor your response. I’ll hold off on that then.

Aleru Divine (04:37:58) (in thread): > Thanks@Mildred Anashie

Scholastica Urua (04:38:14) (in thread): > Hi@Mildred Anashiemy username is @Scholarpat. You can tag me as well while I do same.

Emem Eduoku (04:42:05) (in thread): > Thank you@Praise AgbetuyiDo let us know when you complete it

Emem Eduoku (04:43:00) (in thread): > @Ruth BamgboseHow do i add the link of my first curation to my outreachy contribution?

Amanda Adoyi (04:44:06): > Ps…I think I just figured that you could edit someone else’s work. Is that well known or am I late to the realization? If that’s so please be careful when peer reviewing. If I’m wrong let me know. Also…If I’m reviewing yours don’t be scared that I may have done something to it judging by this statement because I didn’t.

Mildred Anashie (04:44:15) (in thread): > Noted@Scholastica UruaThank you

Mildred Anashie (04:45:09) (in thread): > Yes you can edit someoneelse’swork

Amanda Adoyi (04:45:49) (in thread): > hm… Good to know

Mildred Anashie (04:46:08) (in thread): > I’mnot sure we should do that while reviewing though, letting the person know your observations seems okay to me@Svetlana Ugarcina Perovicplease throw more light on this:pray:

Ima-obong (Aimah) (04:48:17) (in thread): > I think the best approach to be followed is to read, note your observations, and share them with the individual whose work we’re reviewing and they’ll decide if they want to make the changes

Scholastica Urua (04:50:33) (in thread): > I agree with@Ima-obong (Aimah)You can also post it here to get more options.:pray:

Amanda Adoyi (04:50:45) (in thread): > Yep. That’s correct everyone. Just a heads up for someone who may not know or may have clumsy fingers on the keyboard at the wrong time.

Emem Eduoku (04:51:00): > Hi everyone. So yesterday I completed the first task on the Annotated Shrode PDF. Is that counting as first contribution? If yes, how do I record that contribution on Outreachy? I’m seeing something about adding the link but dont know how to find that. Can anyone guide me clearly on how to go about it?

Scholastica Urua (04:52:14) (in thread): > Hi@Emem Eduokuthis should answer your question.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709876110262569 - Attachment: Attachment > Hello everyone, how is the contribution phase progressing? The first week is slowly coming to an end, and it has been wonderful collaborating with everyone here. > I’ve noticed that there have been over a dozen questions asked, and I’ve been able to identify a few that are recurring. Please feel free to add other questions and answers under this thread. I hope this helps someone! > > Q1. I couldn’t find how to record my first contribution. > A: Steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > Q2. When recording the first contribution, what is the ‘merged date’? > A: The merged date refers to the date you submitted your contribution. > > Q3. What URL are we submitting for the first contribution? > A: The link to the curation form: [https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc](https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc) will serve as your Contribution URL. > > Q4. After I submit my first contribution, can I go back to edit it if I notice I made a mistake, or if I didn’t add something somewhere? > A: Unfortunately, you cannot edit a submitted contribution but you can make another submission from scratch. > > Q5. Are we making 2 contributions? > A: While you can make as many contributions as possible, the first contribution is compulsory. After completing the first contribution, you may proceed to the second. Although the second contribution is not mandatory, it is advisable to complete it. Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > - See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > Q6. For the second contribution, after Adding a Study in BugSigDB, does it need to be reviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study? > A: You do not need to wait for mentors to review. You can click on the ‘Add Experiment’ button to add an experiment. > > Q7. I want to know how many times I can use the record my contribution option on the Outreachy website. > A: You can use the ‘Record My Contribution’ option as many times as needed, depending on how many contributions you make.

Ima-obong (Aimah) (04:52:15) (in thread): > Yes it does

Mildred Anashie (04:52:34): > @Emem Eduokuplease see this - Attachment: Attachment > Hello everyone, how is the contribution phase progressing? The first week is slowly coming to an end, and it has been wonderful collaborating with everyone here. > I’ve noticed that there have been over a dozen questions asked, and I’ve been able to identify a few that are recurring. Please feel free to add other questions and answers under this thread. I hope this helps someone! > > Q1. I couldn’t find how to record my first contribution. > A: Steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > Q2. When recording the first contribution, what is the ‘merged date’? > A: The merged date refers to the date you submitted your contribution. > > Q3. What URL are we submitting for the first contribution? > A: The link to the curation form: [https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc](https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc) will serve as your Contribution URL. > > Q4. After I submit my first contribution, can I go back to edit it if I notice I made a mistake, or if I didn’t add something somewhere? > A: Unfortunately, you cannot edit a submitted contribution but you can make another submission from scratch. > > Q5. Are we making 2 contributions? > A: While you can make as many contributions as possible, the first contribution is compulsory. After completing the first contribution, you may proceed to the second. Although the second contribution is not mandatory, it is advisable to complete it. Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > - See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > Q6. For the second contribution, after Adding a Study in BugSigDB, does it need to be reviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study? > A: You do not need to wait for mentors to review. You can click on the ‘Add Experiment’ button to add an experiment. > > Q7. I want to know how many times I can use the record my contribution option on the Outreachy website. > A: You can use the ‘Record My Contribution’ option as many times as needed, depending on how many contributions you make.

Victoria (Burah) Poromon (04:52:46) (in thread): > Okay great. Thank you

Ima-obong (Aimah) (04:53:01) (in thread): > Go ahead and record it as your first contribution.. weldone sis:clap:

Victoria (Burah) Poromon (04:53:26) (in thread): > Thank you@Mildred Anashie,@Muqtadirat Yussuff

Scholastica Urua (04:53:34) (in thread): > Please let me know if you need further clarification

Ima-obong (Aimah) (04:53:57) (in thread): > And the link to be included in your recording is the link of the form your just submitted as your first task

Aleru Divine (04:55:25) (in thread): > Hi@Emem EduokuGo to “record contributions” use the link of the survey as the “contribution URL” and the day you completed the survey as the merge date.

Victoria (Burah) Poromon (04:56:06): > @Svetlana Ugarcina PerovicIs it okay for multiple people to review your curation? If not, pleasewhat’sthe maximum number of persons that can review it?

Aleru Divine (04:56:35) (in thread): > @Victoria (Burah) Poromonyes it’s okay,there’sno limit.:hugging_face:

Mildred Anashie (04:56:37) (in thread): > It’sokay@Victoria (Burah) Poromon

Ima-obong (Aimah) (04:57:00) (in thread): > @Barakat Akinsikuplease tag me on your GitHub paper thank you…

Emem Eduoku (04:58:30) (in thread): > The problem is getting the link to be be included. This is the form i filled to start my contribution. where do i get the link to submit? - File (PNG): Screenshot 2024-03-08 at 10.55.23.png

Barakat Akinsiku (04:58:33) (in thread): > Hi@Aleru DivineI am not done yet but you can review my progress while I review your work. Here’s my github @BarakatAA

Emem Eduoku (04:58:35) (in thread): > The problem is getting the link to be be included. This is the form i filled to start my contribution. where do i get the link to submit? - File (PNG): Screenshot 2024-03-08 at 10.55.23.png

Barakat Akinsiku (04:59:28) (in thread): > I’ve done that@Ima-obong (Aimah)thank you

Emem Eduoku (04:59:47) (in thread): > @Ima-obong (Aimah)there was no link on the form

Emem Eduoku (05:01:33) (in thread): > @Aleru DivineDo you mean i should just copy the link that was used to open to site above and that is the link of my first contribution? Isnt it the same link for everyone? I thought theres a link to show what we contributed

Scholastica Urua (05:01:45) (in thread): > Hi@Emem Eduokueveryone is including the same link for the first curation

Aleru Divine (05:02:01) (in thread): > Yes@Emem Eduoku

Victoria (Burah) Poromon (05:02:24) (in thread): > Okay okay:blush:thank you

Mojisayo Awolesi (05:02:25): > Good morning, > Was the office hours session was recorded yesterday? > I’d like to do some playbacks.

Svetlana Ugarcina Perovic (05:03:14) (in thread): > Unfortunately not, but the next ones will be recorded and shared here.

Emem Eduoku (05:03:59) (in thread): > Alright.

Abiola Salako (05:04:55): > Hello everyone, I’m open to review your work with you and would like that you help with mine as I’m through with my Second contribution. Kindly avail me with your study-link or probably tag me @ Abiola-Salako on GitHub. Thank you.

Mojisayo Awolesi (05:04:58) (in thread): > Alright, thank you.

Bolanle Wahab (05:06:24): > @Mojisayo Awolesithis should help - Attachment: Attachment > Hello everyone > > These are some of the tips mentioned by the mentors during the office hours. Hope this helps! > > 1. Initially, highlight the important parts of a paper to facilitate easier curation later on. Utilize tools such as Adobe for this purpose. > > 2. Some papers may feature multiple statistical tests. However, it’s crucial to discern between them, as one test might be conducted for the p-value while another for differential abundance. (Data transformation for common statistical tests was mentioned here.) > > 3. When p-values and LDA scores are not specified in a paper, the default values are typically considered to be 0.05 for the p-value and 2 for the LDA score. > > 4. Always remember to check for supplementary materials during curation. These materials may be located at the beginning or end of the paper. > > 5. Consider creating a talk page to provide guidance for other curators or reviewers. > > > 6. Prioritize quality over quantity when conducting curation. Take the necessary time to ensure a thorough and high-quality curation process. > > 7. An experiment involves a comparison between two specific elements, not the entirety of the project conducted in the lab. > > 8a. Condition - This is relative to the case group, which refers to the disease or condition present in the patient population but absent in the healthy population. > > 8b. Condition - When the patient population is further subgrouped, a second experiment is usually required. However, in this case, the condition will pertain to specific diseases present in the subgroup.

Mojisayo Awolesi (05:07:12): > I appreciate this@Bolanle Wahab

idiaru Angela (05:07:23) (in thread): > You can also look at the notes that others madehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709823762913479?thread_ts=1709823762.913479&cid=C04RATV9VCY - Attachment: Attachment > Hello everyone > > These are some of the tips mentioned by the mentors during the office hours. Hope this helps! > > 1. Initially, highlight the important parts of a paper to facilitate easier curation later on. Utilize tools such as Adobe for this purpose. > > 2. Some papers may feature multiple statistical tests. However, it’s crucial to discern between them, as one test might be conducted for the p-value while another for differential abundance. (Data transformation for common statistical tests was mentioned here.) > > 3. When p-values and LDA scores are not specified in a paper, the default values are typically considered to be 0.05 for the p-value and 2 for the LDA score. > > 4. Always remember to check for supplementary materials during curation. These materials may be located at the beginning or end of the paper. > > 5. Consider creating a talk page to provide guidance for other curators or reviewers. > > > 6. Prioritize quality over quantity when conducting curation. Take the necessary time to ensure a thorough and high-quality curation process. > > 7. An experiment involves a comparison between two specific elements, not the entirety of the project conducted in the lab. > > 8a. Condition - This is relative to the case group, which refers to the disease or condition present in the patient population but absent in the healthy population. > > 8b. Condition - When the patient population is further subgrouped, a second experiment is usually required. However, in this case, the condition will pertain to specific diseases present in the subgroup.

Adenike Oladimeji-Kasumu (05:07:59) (in thread): > Good day,@Abiola SalakoPlease I would like you and anyone else who is will to review my second curation. Here is the link;https://bugsigdb.org/Study_909 - Attachment (BugSigDB): Differences in the Composition of Gut Microbiota between Patients with Parkinson’s Disease and Healthy Controls: A Cohort Study - BugSigDB > Gut microbiome and colonic inflammation can be associated with the predisposition and progression of Parkinson’s disease (PD).The presented study aimed to compare gastrointestinal microbiota composition between patients diagnosed with PD and treated only with Levodopa to healthy controls.

Abiola Salako (05:09:17) (in thread): > @Ima-obong (Aimah)here is mine@Abiola Salako

Suru Olaitan (05:09:51) (in thread): > Thank you@Muqtadirat Yussuff:pray:

Ima-obong (Aimah) (05:15:25) (in thread): > Hello Abiola, weldone.. currently working on a review, will take up yours when I’m done with the current one …tag me on your GitHub @imalovee

Svetlana Ugarcina Perovic (05:16:04) (in thread): > Please do not edit your colleague’s curation; it’s up to them how they will apply your review suggestions/remarks. A reviewer’s task in science is to give a constructive and critical feedback (not to edit someone’s work).

Ima-obong (Aimah) (05:19:23) (in thread): > Thank you@Abiola Salako

Mojisayo Awolesi (05:19:51) (in thread): > @Adenike Oladimeji-KasumuPlease check your private chat

Abiola Salako (05:22:59) (in thread): > Alright@Adenike Oladimeji-Kasumuwill go through it and revert, thank you.

Abiola Salako (05:23:58) (in thread): > Thank you@Ima-obong (Aimah)

Adenike Oladimeji-Kasumu (05:24:55) (in thread): > @Abiola SalakoI appreciate that. I will also try to tag you and@Ima-obong (Aimah)along side 1 0r 2 mentors on Github to help review my work. Thank you.

Mildred Anashie (05:25:10) (in thread): > 1st point you’ve made is they were recovering and dying from something before they were further divided into disease severity (mild, moderate, severe) which I think was just used as contrasts > > What was mentioned as what they were recovering from or dying from might be the condition here > > But let me look at the link you shared

Abiola Salako (05:26:23) (in thread): > @Mojisayo AwolesiIf you want me to review your work you can drop your study-link. thank you.

Emem Eduoku (05:27:22) (in thread): > Thanks everyone. I have been able to record my first contribution on Outreachy site

Scholastica Urua (05:28:34) (in thread): > You’re welcome@Emem Eduoku

Mildred Anashie (05:36:15) (in thread): > Yea@Mojisayo AwolesiNotes were shared here you can go through the chatsyou’dfind them

Adenike Oladimeji-Kasumu (05:38:24) (in thread): > @Abiola Salako, could you please explain how I can tag you on GitHub? Your name is not showing, just the mentors. Thank you.

Abiola Salako (05:39:09) (in thread): > @Adenike Oladimeji-Kasumu@ Abiola-Salako

Adenike Oladimeji-Kasumu (05:40:45) (in thread): > It’s not coming up - File (JPEG): IMG_20240308_114018_243.jpg

Mojisayo Awolesi (05:43:20) (in thread): > Oh yes I have, thank you@Mildred Anashie

Abiola Salako (05:43:50) (in thread): > Please go on to click on the comment it will pop up. Thank you.

Adenike Oladimeji-Kasumu (05:44:12) (in thread): > Oh… Alright > Thank you

Amanda Adoyi (06:11:40): > I’ve learnt a lot from this community and I’ve also had to look around the internet for added material that could help me with better curations. Found this because it explained some concepts in a way that I consider easy to read. Check it out if you’re interested. - File (PDF): microbiome research guide.pdf

Blessing Ene Anyebe (06:12:50) (in thread): > This is awesome, thank you for sharing.@Amanda Adoyi

Scholastica Urua (06:13:47) (in thread): > Thank you for sharing@Amanda Adoyi:pray:

Adenike Oladimeji-Kasumu (06:19:01) (in thread): > Wow! This is going to help. Thank you@Amanda Adoyi

NWAKAEGO VINCENT (06:19:23) (in thread): > thank you@Ima-obong (Aimah)@Scholastica Urua

Aleru Divine (06:20:18) (in thread): > Thank you so much for this resource@Amanda Adoyi

NWAKAEGO VINCENT (06:21:17) (in thread): > thanks for sharing@Amanda Adoyi

Ima-obong (Aimah) (06:21:55) (in thread): > Congratulations:clap:.. you’re welcome

USLACKBOT (06:31:29): > This message was deleted.

Leenaa Al-Amin (06:31:54) (in thread): > what they’re recovering and dying from id COVID-19

Adenike Oladimeji-Kasumu (06:33:49) (in thread): > :smile:A mistake, please ignore. I’ve take down the message,

idiaru Angela (06:35:06) (in thread): > Thank you for sharing@Amanda Adoyi

Idiat Alli (06:37:54) (in thread): > Thank you

Bolanle Wahab (06:40:12): > Hi everyone > My study is based of administering prebiotics to my subject, this diet had effect on the gut health and several other parameters of the subject.My question now is when I defined the diagnostic criteria for the group 1 test, is it okay that I defined each of these parameters separately or the entire group 1 test should have one definition?

Eniola Adebayo (06:41:46) (in thread): > Thank you@Amanda Adoyi

Adenike Oladimeji-Kasumu (06:42:29): > Hello everyone, I have been able to put together some of the curation process for those who are just joining. As I wait for my second curation to be reviewed by other curators, I was able to put down the processes that helped me. Its in the next message, Kindly do well to check through if I omitted or made any wrong statements. Thank you.

Adenike Oladimeji-Kasumu (06:42:58): > Welcome! If you just joined. > Here is a summary I compiled on how to make your contributions. > 1. Join the BugSigDB channel on the Slack platform and introduce yourself on the channel. > Now all the information flying around here might seem overwhelming at times, do not worry. Take a deep breath as everyone on the channel is willing to help. Our mentors including@Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account)are also working to support us. You’ve got this. > 2.https://github.com/waldronlab/BugSigDBcuration/issues/94Check out this link for information to get started. Take your time to go through every link in the Prep work and watch all videos, All information will come in handy. > Go through the BugSigDB pagehttps://bugsigdb.org/Main_PageNow click on the link to the First Curation Form (https://bugsigdb.org/Main_Page.) > > On your Browser, open this linkhttps://github.com/jointo create a github account. Do not worry if you have never used GitHub before. Its not that hard. Just follow every step on the page. > > Review the article tagged**** Annotated Shrode article pdf. ****Download and read through. Do not worry if you do not understand all the information. Do well to focus on the highlighted parts of the documents. Every answer to the survey question will come from these highlighted parts. > > Now enter your Name (the one you used to register on Outreachy), your email address, your username on GitHub and your username on Slack the channel. Then Click on the next button. Go ahead to answer the survey questions. > Request for an account here.https://bugsigdb.org/Special:RequestAccountIf you have troubles Identifying the disease fromhttps://www.ebi.ac.uk/efo/website, be calm. Look for the closest disease to the one you are curating and use that. > You have already begun. No need to fret now! That was your First contribution. > After submitting your First contribution, it is time to record it. > Go to the Outreachy main pagewww.outreachy.org, make sure you are logged in. Click on Applicants, then click on current projects. Click on Click on the ‘Microbiome Study Curation’, Click on ‘Record Contributions and Apply to This Project’. > This is the link to fill for link to your contributionhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc. Include the date when you made your contribution and the date you submitted. Then add a description of your contribution (describe what the article is about, the topic, purpose, analysis, discussions, and findings.) and Record.Now to the Second Contribution:Note: Our mentor has advised that for this second contribution task, you arestrongly encouragedyou to aim for quality over quantity.https://github.com/waldronlab/BugSigDBcuration/issues/94See the Second Contribution heading. > Click on ”Paper to Curate” and check through all available articles, especially the ones that are yet to have the ‘assigned’ tags on them. Click on your choice Article and request that it be assigned to you. A mentor will give you a feedback soon enough. > After it is assigned to you, download the PDF file of your article and red through. > Go to the BugSigDB main pagehttps://bugsigdb.org/Main_Page, make sure you log in. Then select ‘Add a study’ from the top Bar. > Enter the Study Design, you can find which design your Article falls under here:Curation Policy - BugSigDBUnder Citation, Select Auto mode, Enter the PMID and the Doi. You will find the PMID herehttps://pubmed.ncbi.nlm.nih.gov/when you copy and paste the tittle of your Article on the search bar. The Doi is available on your Article, Most times on the top part. Now, scroll down to From Data and select Complete. Then save page. > The information on your Article should automatically populate on the next page. > Click on ‘Add a new Experiment’ > > Fill in all the gaps from the information in your Article > > Make sure on each page, you select complete and save > > Now, click on ‘Add Signature’. The onboarding videos will help a lot especiallyhttps://www.youtube.com/watch?v=yfpnwxefLFcYou can now select ‘complete’ and ‘save page’ > > I advise that you allow other curators to review your work then proceed to Record your contribution on the BugSigDB main page. The link for your curation will be the link for that study that you finished Curating. For the merged date, you will have that when a mentor has reviewed your work, then you can update your contribution. > > #Note# It is emphasized that you Choose Quality over Quantity in our Contribution. - Attachment (BugSigDB): Main Page > … - Attachment (BugSigDB): Special:RequestAccount - Attachment (ebi.ac.uk): The Experimental Factor Ontology < EMBL-EBI > The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets. We also add terms for external users when requested. If you are new to ontologies, there is a short introduction on the subject available and a blog post by James Malone on what ontologies are for.

Amanda Adoyi (06:45:13) (in thread): > You’re welcome:slightly_smiling_face:Happy to.

Ikeh Darlington Ikeh (06:46:43) (in thread): > Thanks@Scholastica Urua, in a situation where the sequencing platform is not mentioned in the article or in any reference, should we leave it blank?

Mildred Anashie (06:48:13) (in thread): > Ihaven’tgone through the paper yet:pray:but.I will now, so I stop speculating

Emem Eduoku (06:48:19): > For my second contribution, I just need to look for a issue that is yet to be assigned on the github issue repo right? How do i get assigned the issue?

Mildred Anashie (06:48:41) (in thread): > Yes@Emem Eduoku

Mildred Anashie (06:48:57) (in thread): > Ask it be assigned to you by leaving a comment

Leenaa Al-Amin (06:48:57) (in thread): > Alright thank you so much

Scholastica Urua (06:49:08) (in thread): > When you find an unassigned issue, you comment on it. Mentors will assign it to you if you are the first to request for it.

Adenike Oladimeji-Kasumu (06:51:44) (in thread): > @Emem EduokuWhile you wait for it to be assigned, you can download the document and start going through it.

Desire Oluwarotimi (06:55:58) (in thread): > Hi@Bolanle WahabI’m not quite sure I understand what you are talking about.

NWAKAEGO VINCENT (06:57:22): > when i opened the main page for my second contribution, it says i don’t have permission to edit the file. i created my account yesterday how do i know if it was approved@Adenike Oladimeji-Kasumu

Mildred Anashie (06:58:41) (in thread): > Try to Login with your account

Mildred Anashie (06:59:09) (in thread): > Did you get a mail though?You can check your spam folder

Idiat Alli (06:59:57) (in thread): > @Adenike Oladimeji-Kasumuthis is very useful, thank you:blush:

Mildred Anashie (07:00:10) (in thread): > In my opinion it’s SARS-CoV-2 infection

Adenike Oladimeji-Kasumu (07:00:58) (in thread): > Yes, as@Mildred Anashiehas said, check your mail

Bolanle Wahab (07:01:19) (in thread): > I’m asking if I can separate my group 1 definition into each of the parameters that were affected in my study? > OrI’msupposed to have just one definition

Adenike Oladimeji-Kasumu (07:01:41) (in thread): > You are welcome@Idiat Alli

Mojisayo Awolesi (07:02:34): > Hello everyone, > So I’m having issues downloading the pdf file for the study I was assignedstudy. > I’m asked to make a subscription before downloading the full issue. > > What can I do? - Attachment (PubMed): Dysbiosis of gut microbiota in a selected population of Parkinson’s patients - PubMed > PD showed a distinctive microbiota composition. Functional predictions suggest changes in pathways favoring a pro-inflammatory environment in the gastrointestinal tract, and a reduction in the biosynthesis of amino acids acting as precursors of physiological transmitters.

Okache Johnpaul (07:02:37): > Hey everyone! I’m a little unsure as to what experiments to curate as my topic isn’t a typical one that has a diseased condition vs Healthy. Mine’s more of a dietary comparison. Here it is, I’d appreciate any helpful inputs please. Thank you very much.https://www.nature.com/articles/s41591-023-02761-2#Sec8 - Attachment (Nature): Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans > Nature Medicine - In a post hoc multiomics analysis of a trial comparing a plant-based, low-fat diet to an animal-based, ketogenic diet, the diets have differential effects on peripheral immune…

Desire Oluwarotimi (07:05:06) (in thread): > I think that at every point in time for different experiments, you might have different group 1s but you are supposed to essentially use the definition or inference of those groups as it was given in your paper. > > I hope this helps.

Mildred Anashie (07:06:29) (in thread): > This is the PDF - File (PDF): pietrucci2019

Bolanle Wahab (07:07:01) (in thread): > Thank you@Desire Oluwarotimi

eneje promise (07:07:26) (in thread): > Oh I saw it thank you

Mildred Anashie (07:08:19) (in thread): > You are welcome@eneje promise

Mojisayo Awolesi (07:15:40) (in thread): > Thank you@Mildred Anashie

Desire Oluwarotimi (07:17:03) (in thread): > Hi@Okache JohnpaulI think mentioning the groups in your article will be of help. The groups you have are 5 (they were paired based on diet and sex). > > For diet, you have: > Baseline > Ketogenic > Vegan > > For Sex, you have: > Male > Female. > > I hope this helps.

Joan C. Chukwuemeka (07:18:54): > Good day all,@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace SandyIn the study I’m curating, the number of observed amplicon sequence variants (ASVs) was stated to be decreased, and the study stated that ASVs serve as a proxy for species richness. > Will it be right to record species richness as decreased under alpha diversity, despite the study not specifically mentioning “richness”, rather ASVs was stated?

Mildred Anashie (07:24:51) (in thread): > ASV stands for Amplicon sequence variant andIt’s another method (more detailed actually) used to identify and characterize microbes.There are mostly used as labels in identifying microbes in most studies (This is what I know about ASVs > > We could be describing different ASVs though > > Interesting what you found, here for the answer:blush:

Okache Johnpaul (07:26:00) (in thread): > Thank you for adding that@Desire Oluwarotimi!

Mildred Anashie (07:26:12) (in thread): > Thank you@Desire OluwarotimiI got caught up with something else looking at this > > I hope this helps@Okache Johnpaul

Okache Johnpaul (07:27:58) (in thread): > If you have more input,@Mildred Anashie,I welcome it please. I’m trying to be as clear on this as I can get.

Joan C. Chukwuemeka (07:29:39) (in thread): - File (PNG): image.png - File (PNG): image.png

Idiat Alli (07:30:24) (in thread): > Please how do I get the condition from my article

Idiat Alli (07:30:44) (in thread): > All what I input were not in the drop down

Scholastica Urua (07:30:45) (in thread): > Interesting, didn’t know these about ASVs.

Adenike Oladimeji-Kasumu (07:32:26) (in thread): > The Article usually contain what condition you are curating. Can you drop the link of your Article so I can take a look?@Idiat Alli

Idiat Alli (07:32:50): > Hello everyone, Please how do I get the condition from my article

Adenike Oladimeji-Kasumu (07:33:59) (in thread): > The condition is usually in the Article. Cn you drop the Link to your Article so we can take a look at it?

Idiat Alli (07:36:52) (in thread): > https://www.mdpi.com/1422-0067/24/17/13329Thank you - Attachment (MDPI): Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals > This study aimed to investigate alterations in the gut microbiota of patients with depression compared to those in the gut microbiota of healthy individuals based on enterotypes as a classification framework. Fecal bacteria FASTA/Q samples from 333 Chinese participants, including 107 healthy individuals (Healthy group) and 226 individuals suffering from depression (DP group), were analyzed. The participants were classified into three enterotypes: Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). An α-diversity analysis revealed no significant differences in microbial diversity between the Healthy and DP groups across all enterotypes. However, there were substantial differences in the gut microbial composition for β-diversity, particularly within ET-L and ET-B. The DP group within ET-B exhibited a higher abundance of Proteobacteria, while a linear discriminant analysis (LDA) of the DP group showed an increased relative abundance of specific genera, such as Mediterraneibacter, Blautia, Bifidobacterium, and Clostridium. Within ET-L, Bifidobacterium, Blautia, Clostridium, Collinsella, and Corynebacterium were significantly higher in the DP group in the LDA and ANOVA-like differential expression-2 (ALDEx2) analyses. At the species level of ET-L, Blautia luti, Blautia provencensis, Blautia glucerasea, Clostridium innocuum, Clostridium porci, and Clostridium leptum were the primary bacteria in the DP group identified using the machine learning approach. A network analysis revealed a more tightly interconnected microbial community within ET-L than within ET-B. This suggests a potentially stronger functional relationship among the gut microbiota in ET-L. The metabolic pathways related to glucose metabolism, tryptophan and tyrosine metabolism, neurotransmitter metabolism, and immune-related functions showed strong negative associations with depression, particularly within ET-L. These findings provide insights into the gut–brain axis and its role in the pathogenesis of depression, thus contributing to our understanding of the underlying mechanisms in Asian individuals. Further research is warranted to explain the mechanistic links between gut microbiota and depression and to explore their potential for use in precision medicine interventions.

Adenike Oladimeji-Kasumu (07:39:28) (in thread): > Did you check for ‘Depression’?

Idiat Alli (07:39:34) (in thread): > https://www.mdpi.com/1422-0067/24/17/13329

Idiat Alli (07:40:47) (in thread): > Use the username and password that was sent in the most recent mail

Mildred Anashie (07:41:18) (in thread): > Sure i would share if i find something i consider helpful

Ruth Bamgbose (07:42:42) (in thread): > Hello@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)please I still need advice on this

Desire Oluwarotimi (07:43:28): > Is there still anyone who wants to go through each other’s work? > > I’m down for that.

Adenike Oladimeji-Kasumu (07:44:34) (in thread): > Yes@Idiat Allithat one

Adenike Oladimeji-Kasumu (07:45:09) (in thread): > Yes please@Desire Oluwarotimi

Emem Eduoku (07:45:41) (in thread): > @Idiat AlliThe condition is the usually the disease state that the study is cntered around. In you case, from your article, it is depression.

Ruth Bamgbose (07:46:03) (in thread): > From your article it seams the condition is depression as the gut microbiota is campared between members with depression and healthy members

Adenike Oladimeji-Kasumu (07:46:12) (in thread): > I can tag you on GitHub with my link. What is your username?

Idiat Alli (07:46:38) (in thread): > @Emem Eduoku,it didnt accept it.typed it several times

Emem Eduoku (07:48:05): > I am yet to be assigned an issue for my second contribution. If there is any one who needs help reviewing their curation I can assist.

Desire Oluwarotimi (07:48:25) (in thread): > @RotimiDesire

Idiat Alli (07:49:33) (in thread): > It wants me to pick from the drop down - File (JPEG): IMG_20240308_134825.jpg

Emem Eduoku (07:49:55) (in thread): > Thanks everyone.@Adenike Oladimeji-Kasumui think this is smart.@Scholastica Uruaif i can only see my request to be assigned in the comment that means i am the first to request for it right?

Adenike Oladimeji-Kasumu (07:50:44) (in thread): > @Emem EduokuKindly drop your GitHub handle and i will tag you to my Curation. Thank you.

Emem Eduoku (07:51:18) (in thread): > @Idiat Alliuse the dropdown menu to scroll throught the option. you should see an option that has only depression come up

Adenike Oladimeji-Kasumu (07:52:06) (in thread): > Done.@Desire Oluwarotimi

Idiat Alli (07:52:41) (in thread): > Yes I did@Adenike Oladimeji-Kasumu

Scholastica Urua (07:54:18) (in thread): > Yes@Emem Eduoku. That means it’ll be eventually assigned to you. You can start familiarizing yourself with the paper at the mean time.

Leenaa Al-Amin (07:55:05) (in thread): > alright thank you, also I am having a bit of an issue in terms of signature addition, based on Figure 3h,i,j , do I count the fact that there is more of an abundance of those species in the recovered group as a decrease for the mortality group. I’d really appreciate your input

Idiat Alli (07:55:14) (in thread): > I have done that severally, these are all the options@Emem Eduoku

Adenike Oladimeji-Kasumu (07:55:44) (in thread): > Yes,@Idiat AlliPlease do as@Emem Eduokuhas said. You could also read through your article if a type of Depression was specified.

Idiat Alli (07:57:00) (in thread): > Thank you@Adenike Oladimeji-Kasumu@Emem EduokuI have chosen depressive disorder

Emem Eduoku (07:57:06) (in thread): > Then the depression there is probably an aliase. Did you see Depressive disorder in the option@Idiat Alli

Adenike Oladimeji-Kasumu (07:57:42) (in thread): > @Idiat AlliYou are on track. Welldone

Idiat Alli (07:58:56) (in thread): > Thank you@Adenike Oladimeji-Kasumu

Emem Eduoku (07:59:25) (in thread): > my username is Codegirlemem

Mildred Anashie (08:02:22) (in thread): > Ermmmmmm:thinking_face:My interpretation of this is in line with yours as I’m looking at Observed ASVs to be Observed species (microbes) > > Found this when I conducted further research “Species richness refers to the number of different species present in a community. ASVs, being unique sequence variants derived from high-throughput sequencing data, can be used as a proxy for species richness.”

Emem Eduoku (08:04:02): > If you are finding it hard to get the condition of the research you are curating, check for other aliases. Aliases are other names by which the condition can be known as. Be sure the condition you choose has the disease condition in your paper as an aliase before adding it.

Ima-obong (Aimah) (08:06:39) (in thread): > You’re absolutely correct

Joan C. Chukwuemeka (08:07:00) (in thread): > Okay, Thanks@Mildred Anashie. I’d want to know if the Mentors thinks otherwise before I go ahead though. Documentation for BugSigDB is special and sometimes different from the norm:blush:.@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace Sandy

Aleru Divine (08:07:16): > @Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoI would like to delete the following signatures in my study. > 1. Signature 2 in Experiment 1 > 2. Signature 2 in Experiment 2 > Here is the link to my study:https://bugsigdb.org/Study_873Thank you! - Attachment (BugSigDB): Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study - BugSigDB > The influence of human gut microbiota on health and disease is now commonly appreciated.Therefore, it is not surprising that microbiome research has found interest in the sports community, hoping to improve health and optimize performance.

Benedicta Imelda (08:10:58) (in thread): > Hi

Benedicta Imelda (08:11:19) (in thread): > My username is oziomaekeh

Adenike Oladimeji-Kasumu (08:13:51) (in thread): > @Benedicta ImeldaThank you. I’ll tag you and also be in your DM.

Adenike Oladimeji-Kasumu (08:18:06) (in thread): > Hi@Aleru Divineyou can click ‘Delete’ above the Experiment you want to delete on your study and it will be deleted.

Aleru Divine (08:25:32) (in thread): > @Adenike Oladimeji-Kasumuit appears I don’t have the permission to delete a page

Adenike Oladimeji-Kasumu (08:27:47) (in thread): > Oh… Really? I thought we could that.

Aleru Divine (08:28:40) (in thread): > I suppose only the mentors can@Adenike Oladimeji-Kasumu

Mildred Anashie (08:29:29) (in thread): > @Adenike Oladimeji-KasumuOnly the Mentors have permission to do that, like Divine pointed out

Mildred Anashie (08:30:04) (in thread): > Okay > > Let me look at the Fig 3

Adenike Oladimeji-Kasumu (08:31:02) (in thread): > Okay@Aleru Divineand@Mildred Anashie.@Svetlana Ugarcina Perovic,@Chioma Onyidowould be able to help then. > Well done.

Esther Afuape (08:33:25) (in thread): > Deleted:white_check_mark:

Esther Afuape (08:35:25) (in thread): > You can curate that as a decrease for richness.You’reright. ACE index is also curated for richness in case you come across that

Scholastica Urua (08:36:47) (in thread): > Noted@Esther Afuape

Joan C. Chukwuemeka (08:42:19) (in thread): > Thanks a lot@Esther Afuape

Joan C. Chukwuemeka (08:43:06): > @Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeBased on the below excerpt and Image from my study, is figure 1B curatable? I was initially focused on figure 1C due to the statement in bold. But currently looking at curating from figure 1b based on comparison of the changes from preconditioning to engraftment?:thinking_face:******For a more quantitative assessment of DBM changes during************allo-HSCT, we compared genera abundances at preconditioning************and engraftment using the ANCOM test (Figure 1C)*******. The most > statistically significant differences in abundance were observed > for Enterococcus, Lactobacillus, and Mycoplasma,*confirming the > expansion of these potentially pathogenic genera in DBM during > allo-HSCT. We also observed statistically significant (although > less pronounced in terms of relative abundance change) > decreases in commensal genera (Figure 1C). - File (PNG): image.png - File (PNG): image.png

EBERE ADEKOGBE (08:47:07) (in thread): > It does not usually give the exact name on the paper. It uses an alias sometimes

Leenaa Al-Amin (08:51:04) (in thread): > thank you:pray:

EBERE ADEKOGBE (08:52:01) (in thread): > login in with the email you used in creating the account. From the Bugsigdb site

Ruth Bamgbose (08:54:57) (in thread): > They were divided into two groups with both male and female, and each group on a different diet. I think your main experiment is between ketogenic diet and vegan diet, then you have ketogenic vs baseline and vegan vs baseline(For these two you have to note if there was a significance)

Ruth Bamgbose (08:55:13) (in thread): > Hope this helps

Michael Adekanye (09:01:27) (in thread): > Please what’s a talk group? Or what does it look like?

Scholastica Urua (09:03:01) (in thread): > Yes@Ikeh Darlington Ikeh

Aleru Divine (09:03:24) (in thread): > Thank you so much@Esther Afuape

Okache Johnpaul (09:07:46) (in thread): > This is perfect@Ruth Bamgbose! Thank you sooo much!:sparkles:

Michael Adekanye (09:08:55): > Do we have to wait to be assigned to start working on an unassigned paper?

Nana (09:09:39) (in thread): > Have you requested for one on GitHub

Michael Adekanye (09:10:02) (in thread): > Yes I have.

Muqtadirat Yussuff (09:10:15) (in thread): > From the github issues? Yes but if you find one from the help section on BugSigDB inform the mentors before working on it

Scholastica Urua (09:11:32) (in thread): > @Chioma Onyidomentioned it yesterday during office hour.@Michael AdekanyeFrom my understanding, a talk page is a feature that allows curators/reviewers to discuss data or share insights within a curation. When you are actively carrying out a curation and there’s something unique that you may want to point out to someone reviewing your work in future, you can create a talk page and add such description. > > I have not created one before so my knowledge about it may be limited.@Chioma Onyidocan you please elaborate further.:pray:

Joan C. Chukwuemeka (09:13:32) (in thread): > @Michael AdekanyeIf you are the first person to comment on the issue to request for the article, you can start reading through for curation. you’d however need an account to be crated for you by the mentors before you can record/curate it on BugSigDB

Scholastica Urua (09:14:14) (in thread): > @Michael AdekanyeFor your second contribution, you have to first request for a paper to be assigned to you then wait for it to be approved. Then you can start curating.

Nana (09:14:40) (in thread): > Yes wait when it has been assigned to you then you start your curation

Victoria (Burah) Poromon (09:17:45) (in thread): > Right. But I think you can start curating ifyou’resureyou’rethe first to request for that particular paper. Because the mentors will eventually assign it to you.

Michael Adekanye (09:17:56) (in thread): > Thank you guys.

Michael Adekanye (09:19:27) (in thread): > I’m not the first on the ones I have seen so far@Victoria (Burah) Poromonbut I asked to be assigned anyways.

Victoria (Burah) Poromon (09:19:58) (in thread): > Oh I think you should wait then

Muqtadirat Yussuff (09:21:27) (in thread): > @Michael AdekanyeYou should wait and perhaps go through the help section on BugSigDB, you’d find tasks you can help with. However you need to inform the mentors here before making changes

Victoria (Burah) Poromon (09:21:40) (in thread): > Or find another paper and if youcan’tfind one. You should reach out to the mentors.@Michael Adekanye

Akinbode Mariam (09:23:38) (in thread): > Yea i think you should wait, because i noticed the first person that commented was already assigned a paper so i still commented regardless. ill just start reading on the paper till i am assigned one

Joan C. Chukwuemeka (09:23:48): > <!here>Here’s some info I put together that would be helpful while you curate.https://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Mildred Anashie (09:25:21) (in thread): > If you look at the text under fig 3 it explains figure 3 E-J or so and also shows the comparisons done

Mildred Anashie (09:26:53) (in thread): > I think Fig 8 also shows the organisms that was increased in the groups, just look at it and read in between lines (the text) you’d pick the increased signatures and decreased signatures

Michael Adekanye (09:27:48) (in thread): > @Akinbode MariamThank you

Ruth Bamgbose (09:34:59) (in thread): > You’rewelcome

U01MW62UDQR (09:47:28) (in thread): > Please check if the paper the one you’re looking for. - File (PDF): 1-s2.0-S1353802021004673-main.pdf

Emem Eduoku (10:13:21): > Hello everyone. This resourcehttps://bugsigdb.org/Curation_Policygives a step by step explanation of every information that is needed in curating a study. You can go through it as a guide while working on an assigned issue - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Samreen Aftab (10:15:40) (in thread): > Thank you! I was overwhelmed on how to get started on the second task, but your text came right on time! :)

Mojisayo Awolesi (10:18:00): > Hi everyone, I just completed my second contribution. > I’d appreciate your reviews.Contribution - Attachment (BugSigDB): Dysbiosis of gut microbiota in a selected population of Parkinson’s patients - BugSigDB > INTRODUCTION: In recent years the hypothesis that gut microbiota associates with Parkinson’s disease (PD) has gained importance, although it has not been possible to define a specific microbiota composition as a predictive biomarker of this disease.

Emem Eduoku (10:18:09) (in thread): > you are welcome. I’m also about to start my second task and i found this in their help section. There is a lot of resources to guide us there so check it out. Also try to watch the videos listed in the help section to

Scholastica Urua (10:22:17) (in thread): > Hello@Mojisayo Awolesicongratulations on completing your second curation. I’m currently going through other curations but will get to this as soon as possible.:pray:

Ruth Bamgbose (10:23:21): > Hello everyone,are covariates also cofounders controlled for?

Samreen Aftab (10:24:35): > Can someone tell me what URI is? I can’t find the URI for my paper.

Mildred Anashie (10:28:50) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696874309029659@Ruth BamgbosePlease see this - Attachment: Attachment > Can covariates be filled in for confounders controlled for? @Levi Waldron

Aleru Divine (10:29:13) (in thread): > URL is a link. So URL for your paper is the link of your paper.

Samreen Aftab (10:30:57) (in thread): > And the citation mode should be auto or manual?@Aleru Divine

Aleru Divine (10:32:12) (in thread): > It could be either.If your paper has a PMID, just enter the PMID and everything automatically populates if you select Auto.

Ruth Bamgbose (10:32:39) (in thread): > Thanks@Mildred Anashie

Scholastica Urua (10:36:18): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandyand everyone > > I found this study among the ‘Incomplete pages (marked as incomplete by curator)’https://bugsigdb.org/Study_599with the study design ‘Retrospective Cohort Study’. However, Retrospective Cohort Study is not on the list of study design in BugsigDB. On research I noticed its quite similar to Prospective Cohort (Observational) Study. My question is how should this be curated on BugSigDB? - Attachment (BugSigDB): Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study - BugSigDB > BACKGROUND: The relationship between intestinal obstruction due to colorectal cancer (CRC) and the gut microbiota remains largely unknown.The aim of this study was to investigate the potential association between alterations in gut microbiota and CRC in the presence of intestinal obstruction.

Mildred Anashie (10:39:18) (in thread): > @Suru Olaitanplease properly look at the paper again > > What I observed is correct and clearly spelt out

Adenike Oladimeji-Kasumu (10:40:48) (in thread): > @Samreen Aftab, most times, the Paper carries only the Doi link. To get the PMID, copy your topic and paste on the search bar ofhttps://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

U1LCB8WEA (10:41:00): > Is there an Advanced R book club scheduled for today? I know the organizer<@UBNSEMS3S>is on vacation this week.

Scholastica Urua (10:41:08) (in thread): > @Mildred Anashielet me also take a look at the paper.

Odigiri Great Alume (10:41:56) (in thread): > Hello everyone, going through the study, I understand that > 1. Two sample sites were involved i.e. feces and duodenum (Small intestine) > 2. The study groups are CeD, FDR & DC > 3. The study aimed to investigate if these groups have site-specific dissimilarities, and that the experiments were carried out based on the sampling sites. > 4. Figure 3 has 3 experiments with results explained in the text For Duodenum site (small intestine) > Group 0. Group 1. > DC. VS. CeD > DC. VS. FDR > FDR. VS. CeD > > 5. Figure 5 also has 3 experiments with results explained in the text For feces site. > Group 0. Group 1. > DC. VS. CeD > DC. VS. FDR > FDR. VS. CeD > > > Which is a total of six experiments with curatable signatures for “Differential abundance”@Chioma Onyido@Esther Afuape@Svetlana Ugarcina PerovicPlease help with this please, as I don’t seem to agree with the logic of just two experiments when the paper says otherwise. > > Thanks:pray:

U1LCB8WEA (10:44:13) (in thread): > You can use prospective cohort study, since the differences are only practical in terms of data collection, but their analysis and interpretation should be (at least mostly, I think!) the same.

U1LCB8WEA (10:44:52) (in thread): > A “retrospective” cohort seems to me a pretty rare thing to cook up, finding a cohort after the fact.

Mildred Anashie (10:45:00) (in thread): > Thank you@Odigiri Great AlumeMy observations as well

Joan C. Chukwuemeka (10:45:27) (in thread): > Please I do need help with this@Svetlana Ugarcina Perovic@Esther Afuape<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy

Scholastica Urua (10:46:16) (in thread): > Thank you for your response<@U1LCB8WEA>:pray:Please do I have permission to edit the curation?

Esther Afuape (10:46:58) (in thread): > Figure 1B is not curatable

Joan C. Chukwuemeka (10:48:40) (in thread): > Okay then. Thanks@Esther Afuape

U1LCB8WEA (10:49:04) (in thread): > Ok with me! For nowit’sgood that you check in here before editing existing data.

Scholastica Urua (10:50:19) (in thread): > @Mildred Anashieand@Odigiri Great Alumeboth your observations are similar. Scanning through the paper (although I haven’t gone through it in detail) I agree with your observations.

Scholastica Urua (10:51:13) (in thread): > Okay, thanks Levi

Esther Afuape (10:52:25) (in thread): > Hi Levi! > Idon’tthink so. There was no mention of it yesterday.

U1LCB8WEA (10:53:25) (in thread): > thank you Esther!

Michael Adekanye (10:54:39) (in thread): > I have been assigned one.

Victoria (Burah) Poromon (10:57:04): > Hi everyone, > If there’s anyone available to review my work? I’ll be happy to review theirs too:blush:

NWAKAEGO VINCENT (10:57:19) (in thread): > happy international women’s day@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (10:59:45) (in thread): > Nice to Know@Michael AdekanyeFeel free to reach out if you need help

Muqtadirat Yussuff (11:31:55): > Hi everyone@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape, I would love some insights on this > > For my second curation signature I recorded Streptococcus as decreasing in abundance. I initially recorded as increasing but there were conflicting texts which are: > > “Like Photobacterium, the majority of these bacteria were also detected at low abundance in the food and barely detectable in prefeeding samples but spiked in representation immediately postfeeding (at 1230 h). Many of these taxa were members of the phylum Firmicutes, including diverse genera of lactic acid bacteria (LAB) (order Lactobacillales) such as Lactobacillus, Vagococcus, Leuconostoc, and Streptococcus (see Table S2 in the supplemental material).” > > and > > “A smaller number of significantly varying ESVs showed the opposite trend, decreasing in representation after feeding. These included ESVs of the Firmicutes genus Streptococcus and unclassified members of the gammaproteobacterial order Alteromonadales (Table S2)” > > So would you say it increase, decreased or both? > > Here’s the link to the paper and thank youhttps://journals.asm.org/doi/10.1128/aem.02479-18

Flourish Ralph (11:39:23) (in thread): > @Aleru DivineI’lllike to review your work and have you review mine as well

Flourish Ralph (11:40:59) (in thread): > Hi@Amanda AdoyiI’lllike to review your work and have you review mine ifit’sfine by you

Ruth Bamgbose (11:41:50) (in thread): > Hey, I would love to review your work. Tag me @keamybams on github

Victoria (Burah) Poromon (11:42:33) (in thread): > Okay okay:blush:Right away

Flourish Ralph (11:43:29) (in thread): > Hi hi, you can tag me too @flourishralph on GitHub.I’lllike you to review my work as well

Victoria (Burah) Poromon (11:46:23) (in thread): > @Buraah on GitHub

Peace Sandy (11:47:59) (in thread): > @Emem EduokuHave you been assigned a paper now ?

Leenaa Al-Amin (11:58:02) (in thread): > ok thank you:pray:

Aleru Divine (11:58:03) (in thread): > Sure thing@Flourish Ralph

Michael Adekanye (12:00:22) (in thread): > Thanks

Emem Eduoku (12:04:21) (in thread): > @Peace Sandyyes I have

Emem Eduoku (12:08:16): > I would like to know at what level of the microbiome taxa we are documenting Signatures for. Is it at the Phyllum, Class or Genus level or do we document for all taxa levels that shows significant differential abundance

Mildred Anashie (12:08:57): > Up to Genus-species level

Joan C. Chukwuemeka (12:11:01): > @Emem EduokuThis is from the curation policyhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy… - File (PNG): image.png

Flourish Ralph (12:12:04) (in thread): > I’lltag you to my GitHub, mine is @flourishralph

Bolanle Wahab (12:16:51) (in thread): > @Emem Eduokuwe’resupposed to document all taxa levels

Joan C. Chukwuemeka (12:21:01) (in thread): > Hi@Blessing Ene AnyebeI think “animal reproductive system cell” is the closest EFO condition i can see for now

Druscilla Nakanwagi (12:25:26): > Hello everyone, I am not sure which link I should submit to record a first contribution

Emem Eduoku (12:26:14) (in thread): > Thanks for this

Joan C. Chukwuemeka (12:26:15) (in thread): > Hi@Druscilla NakanwagiYou can submit the survey link.

Scholastica Urua (12:26:34) (in thread): > Hello@Druscilla Nakanwagithis is the linkhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Joan C. Chukwuemeka (12:26:43) (in thread): > Mentors have the record of our individual responses

EBERE ADEKOGBE (12:27:19): > Hello everyone, if you’d like me to review your work and you review mine please reach out. > > I’ve completed my second contribution and I’m open to collaboration and reviews:hugging_face::heart:My GitHub is @Ebere330

Joan C. Chukwuemeka (12:27:21) (in thread): > You’re Welcome:blush:

Druscilla Nakanwagi (12:27:22) (in thread): > So I submit the link with the page that shows that I have completed the survey?

EBERE ADEKOGBE (12:28:14) (in thread): > Yes you can submit with that

Druscilla Nakanwagi (12:28:44) (in thread): > Thank you everyone

EBERE ADEKOGBE (12:29:10) (in thread): > You are welcome

Druscilla Nakanwagi (12:33:38) (in thread): > What of the description? What do we talk about?

EBERE ADEKOGBE (12:36:49) (in thread): > description based on what?

Druscilla Nakanwagi (12:37:13) (in thread): > The description part of filling in a contribution

Scholastica Urua (12:38:59) (in thread): > @Druscilla Nakanwagifor the description part, you can write up a little description of what the first curation is about.

Druscilla Nakanwagi (12:39:24) (in thread): > Okay thanks

Amanda Adoyi (12:49:45) (in thread): > Of course@Flourish RalphWould love that

Amanda Adoyi (12:52:56) (in thread): > Thought the curation guide said all taxa…

Adenike Oladimeji-Kasumu (12:56:59) (in thread): > I was not too sure about whether it’s only the Taxa name or if it was referring to Genus-species level. From the picture I sent, does it mean I have to change my signature to their Genus-species level?@Mildred Anashie - File (JPEG): IMG_20240308_185540.jpg

Mildred Anashie (12:59:47) (in thread): > No@Adenike Oladimeji-KasumuYou curate based on what is reported in the paper > > I meant up to Genus-specie level

Mildred Anashie (13:00:06) (in thread): > Thank you@Amanda Adoyi

Amanda Adoyi (13:01:37) (in thread): > Someone help explain the first and third points please…under NCBI I mean - File (PNG): Screenshot (124).png

Adenike Oladimeji-Kasumu (13:03:52) (in thread): > @Mildred Anashiethe thing is I have a figure that shows the taxa of interest and I have another that shows the Bacteria species level. See attached pictures… But I decided to use the Taxa. > > Kindly help me check through please - File (JPEG): IMG_20240308_190252.jpg - File (JPEG): IMG_20240308_190321.jpg

Mildred Anashie (13:06:25) (in thread): > Recording the species would be more appropriate in my opinion@Adenike Oladimeji-Kasumu

Adenike Oladimeji-Kasumu (13:06:26) (in thread): > @Amanda AdoyiI guessed it meant to use what you have on the paper. What I’m not understanding is what do I use when I have the Genus (Taxa name) and also the species on my paper.

Mildred Anashie (13:12:17) (in thread): > All taxa mentioned in the paper, whether they are at the kingdom, phylum, class, order, family, genus, species, or any other taxonomic level should be recorded for point 1.

Mildred Anashie (13:12:36) (in thread): > Can I see Figure 5 clearly?

Samreen Aftab (13:14:08): > Hello, how can I properly determine the body site?

Adenike Oladimeji-Kasumu (13:14:08) (in thread): - File (JPEG): IMG_20240308_191331.jpg

Joan C. Chukwuemeka (13:14:56) (in thread): > @Samreen AftabIts the anatomical site where microbial samples were extracted from according to theUber Anatomy Ontology - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Mildred Anashie (13:15:04) (in thread): > @Adenike Oladimeji-Kasumunot all results should be curated > > I see Figure 6 is talking about the abundant bacterial species which is curatable > > Not sure about figure 5

Joan C. Chukwuemeka (13:15:35) (in thread): > You can also share your study link so I guide you further

Mildred Anashie (13:15:43) (in thread): > With the foot note please or share the paper

Adenike Oladimeji-Kasumu (13:16:14) (in thread): > Thats me not Amanda:smile:yeah… I think you are right. I’m checking other papers now

Mildred Anashie (13:16:53) (in thread): > My apologies > > I mixed the names:pray:

Amanda Adoyi (13:16:55) (in thread): > @Adenike Oladimeji-KasumuI get you totally. That part has kept me up tbh. I decided to go ahead and record everything I found as long as there was relative abundance comparisons between the groups of interest irrespective of taxonomy level.

Samreen Aftab (13:17:05) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10640746/pdf/12866_2023_Article_3084.pdfthis is my study link. The bacteria is taken from the gut, so what should be the body site?

Adenike Oladimeji-Kasumu (13:17:38) (in thread): > Here@Mildred Anashie - File (JPEG): IMG_20240308_191625.jpg - File (JPEG): IMG_20240308_191702.jpg

Mildred Anashie (13:20:05) (in thread): > I’m not sure this should be curated (Figure 5) > > Let me tag the mentors to help us out with this and give their opinions@Esther Afuape@Chioma Onyido@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (13:20:40) (in thread): > Thank you

Adegboye Rukayat (13:21:23): > Hi everyone, I am presently on my second contribution, in the paper only Beta diversity analysis was used. should I still go ahead to add a signature since I have nothing to fill for Alpha diversity? Thank you

Samreen Aftab (13:21:23) (in thread): > Oh it’ll be feces I assume. My bad

Joan C. Chukwuemeka (13:21:39) (in thread): > Below Excerpt is from the study. > Body site would be feces - File (PNG): image.png

Aleru Divine (13:21:50) (in thread): > @Samreen Aftabthe body site is feces

Samreen Aftab (13:21:56) (in thread): > Yeah, thank you so much

Amanda Adoyi (13:22:36) (in thread): > Maybe… If you look at the figure or table or sentence and you notice that the taxa are stated relative to how abundant they are in each of the groups you’re considering…then that should be curated.

Aleru Divine (13:23:17) (in thread): > @Adegboye RukayatIfthat’sthe case then go ahead and add the signature.Can you share a link to the paper please?

Joan C. Chukwuemeka (13:23:21) (in thread): > Can you share the article link? Perhaps I can help

Adenike Oladimeji-Kasumu (13:24:10) (in thread): > I am re reading to get it right:smile:

Adegboye Rukayat (13:24:22) (in thread): > https://doi.org/10.1128/msystems.01191-21Thank you

Mildred Anashie (13:26:57) (in thread): > We are not to record beta diversity on BugSigdb > > So if alpha diversitywasn’tmentioned it should be left blank > > But I agree with others, we can go through the study with you

Joan C. Chukwuemeka (13:27:19) (in thread): > Alright,@Adegboye Rukayat > * If there is no alpha diversity test conducted, leave the sections blank. This is based on the curation policy. - File (PNG): image.png

Adegboye Rukayat (13:29:38) (in thread): > Thank you so much@Aleru Divine@Joan C. Chukwuemeka@Mildred Anashie

Mildred Anashie (13:36:08) (in thread): > I see specie richness mentioned (Chao1) which is one of the alpha diversity indices > Check figure 2:smirk:

Samreen Aftab (13:36:22): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10640746/pdf/12866_2023_Article_3084.pdfIf I’m not wrong, for this paper, I should create two experiments -one for HC vs CD, and another for HC vs UC. Please correct me if I’m wrong

Mildred Anashie (13:38:57) (in thread): > Showing a significant result between Jejunum and IleumDon’tknow if those are the groups in your study

Adegboye Rukayat (13:42:56) (in thread): > Yes, but the author clearly states that beta diversity analysis was performed. “To determine whether the treatments affected the proximal small intestinal or ileal microbiota compositions, β-diversity analyses using distance-based redundancy analysis (dbRDA) with UniFrac distance constraining for treatment was performed.”

Aleru Divine (13:46:47) (in thread): > @Samreen Aftabyou’recorrect:+1:

Scholastica Urua (13:50:28) (in thread): > You’re right@Samreen Aftab

Emem Eduoku (13:51:01) (in thread): > Yes. Both CD and UC are types of IBD and the ain was to diagnose then using the differential abundance in comparison with the HC

Emem Eduoku (13:52:26) (in thread): > The body site is simply the type of sample used in the study. Could be feces, blood, saliva etc

Joan C. Chukwuemeka (13:52:51) (in thread): > Oh…On a second look, I see what@Mildred Anashieis referring to. Also in data analysis, Richness and diversity was stated. See below snapshots from the study@Adegboye RukayatIf the contrasts here are part of your experiments, you’ll need a deep study to know if it increased or decreased, cos they said is was different. - File (PNG): image.png - File (PNG): image.png

Amanda Adoyi (13:58:57): > Ciao people:slightly_smiling_face:If you would like to assist with figuring out taxa with missing NCBI ids, would you need permission to do so? Think I saw this answered here sometime but can’t find it now.

Adegboye Rukayat (13:59:23) (in thread): > @Joan C. Chukwuemekawhere it is a little bit confusing is that it is written that b Beta diversity analyses was performed just below the highlighted image you sent. What do you think I do

Raihanat Adewuyi (13:59:33) (in thread): > Yes you are right..@Samreen Aftab

Mildred Anashie (14:01:01) (in thread): > Hi Amanda > > You can go ahead and try to figure it out then post here for permission and perusal by the mentors before you update > > Alsoit’sadvisable to look at the discussion pageit’llguide you on the ones that have been noted as “can’tbe resolved” or one comment or the other has been made about them

Amanda Adoyi (14:01:41) (in thread): > Alright. Thanks

Mildred Anashie (14:02:16) (in thread): > Your focus is not on Beta diversity@Adegboye Rukayatbut alpha diversity > > > I think you should not pay attention to the Beta diversity being mentioned

Mildred Anashie (14:03:50) (in thread): > Studies conduct both Beta and Alpha diversity but BugSigdb focuses on Alpha diversityIcan’tstate categorically why though:blush:

Raihanat Adewuyi (14:04:15) (in thread): > @Victoria (Burah) Poromonplease tag me too. To review > GitHub @Oyizaadewuyi

Abiola Salako (14:07:38) (in thread): > @Mildred AnashieThanks for your response. > O,

Mildred Anashie (14:10:30) (in thread): > You are welcome@Abiola SalakoI tried solving one taxa yesterday and it took a lot of time > I didn’t check the discussion page, posted it here and one of our mentors@Esther Afuapepointed me to the discussion page and I realized that it was on the discussion page as unresolved (With reasons) > > So that tip is one I’ll always remember:sweat_smile:

Abiola Salako (14:19:30) (in thread): > Thanks for sharing.

Sandra Dindi (14:38:21): > Hello guys. If the mentor adds the label ’ Needs review’ to my assignment on GitHub. Does it mean I need to review the study again? or it’s yet to be reviewed? Thanks

Mildred Anashie (14:38:46) (in thread): > Yet to be reviewed by the mentors

Sandra Dindi (14:39:22) (in thread): > Okay. Thanks. I had started sweating:joy:

Aleru Divine (14:40:14) (in thread): > @Sandra Dindiit means they will review your curation and provide feedback soon. > > You don’t have to do anything.Just wait for feedback.

Mildred Anashie (14:41:13) (in thread): > I can only imagine@Sandra DindiNo need to panic:grin:It is exactly what Divine just said

Flourish Ralph (14:49:42) (in thread): > Okayyy, please tag me on GitHub @flourishralph

Samreen Aftab (15:01:19) (in thread): > @Emem Eduokushould I create another experiment for CD vs UC?

Abiola Salako (15:07:40) (in thread): > Well done@EBERE ADEKOGBE

EBERE ADEKOGBE (15:08:52) (in thread): > Thank you@Abiola Salako

Samreen Aftab (15:08:59): > There is no other mention of MHT in my paper except this. Does this mean that MHT was used? - File (PNG): image.png

Mildred Anashie (15:12:51) (in thread): > I think FDR adjusted could mean yes to MHT > > > Does it mention”Bonferroni-adjusted p-values”?

Scholastica Urua (15:15:29) (in thread): > Hello@Samreen Aftabif MHT was mentioned in your paper, it means it was used. > > FDR stands for False Discovery Rate which is another indication of MHT.

Samreen Aftab (15:19:35) (in thread): > @Mildred AnashieNo it doesn’t

Scholastica Urua (15:20:54) (in thread): > @Samreen Aftabthis is an excerpt from the mini-curation; > > ’Due to the large number of statistical tests conducted, sometimes researchers correct their p-values for how many tests they conducted. This is called a multiple hypothesis test correction. You can often find this if they refer to “q,” “q-value,” “Benjamini-Hochberg procedure,” “false discovery rate,” “adjusted p-value,” or “MHT-corrected p-value”

Mildred Anashie (15:20:54) (in thread): > Okay……FDR is enough though

Welile Dlamini (15:37:12): > Hello team just arrived What should I do how do I start and where

Svetlana Ugarcina Perovic (15:40:11) (in thread): > Welcome! Please check out this welcoming message with all the information to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Scholastica Urua (15:42:43) (in thread): > Hello@Welile Dlaminiwelcome to the community:hugging_face:

Mildred Anashie (15:44:33) (in thread): > Hello@Welile DlaminiWelcome:hugging_face:You can view the pinned messages too

Abiola Salako (15:45:03) (in thread): > @Welile DlaminiWelcome

Samreen Aftab (15:51:36): > since the instruction is asking for only the highest taxonomic rank, so only these (marked in red) should be applicable for increased abundance right? (CD vs HC) > figures C and D are of the genus and species levels. E is for phylum - File (PNG): image.png

Peace Daniel (15:58:52) (in thread): > Welcome:woman-raising-hand:@Welile Dlamini

Emem Eduoku (15:59:05) (in thread): > Was there an experiment for CD vs UC or they just compared CD and UC based on their microbiome differential abundance with HC

Mildred Anashie (15:59:23) (in thread): > I do not agree with > > > ButI’llsuggest you read text to know ifyou’llget better information on how the taxas were reported

Emem Eduoku (16:01:44) (in thread): > You have to account for all taxa levels that were involved. Atleast that’s what I read from the curation guide

Ima-obong (Aimah) (16:02:12) (in thread): > Welcome@Welile Dlamini

Emem Eduoku (16:02:58) (in thread): > https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Aishat Ijiyode (16:07:02): > Hello everyone, my name is Aishat. I’m an outreachy applicant, I am excited to contribute to this project and connect with you all

Scholastica Urua (16:08:42) (in thread): > Welcome@Aishat IjiyodeKindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Peace Daniel (16:16:09) (in thread): > Welcome:woman-raising-hand:

idiaru Angela (16:33:58) (in thread): > Welcome! Aishat

Naomi Ibe (16:34:00): > My laptop currently has issues, is it possible to do the second curation task on my phone? > Plus I’d like to work on missing NCBI IDs, I picked this articlehttps://bugsigdb.org/Study_844/Experiment_5/Signature_1and I’d like to add the id to this microorganism “Christensenellaceae_R7”, Tax id 990719 with name “Christensenellaceae”, may I proceed to edit?@Svetlana Ugarcina Perovic@Chioma Onyido - Attachment (BugSigDB): Study 844/Experiment 5/Signature 1 > Source: Supplemental. Table S3A Description: Differential abundant taxa between type 2 diabetes (T2D) VS normoglycemic controls (NG) in the combined Danish-Indian…

Svetlana Ugarcina Perovic (16:36:52) (in thread): > We curatedifferential alpha diversity to record microbial signatures on how microbial communities vary under different conditions. BugSigDB is focused on comparisons between two GROUPS of samples and there’s no differential beta diversity. For example, for beta diversity, the most frequently used is Bray-Curtis index - a measure of the similarity of two SAMPLES. It can range between 0 and 1, where 0 means the two SAMPLES have the same composition (that is they share all the species), and 1 means the two SAMPLES do not share any species. > > Another thing that I would like to highlight is actually in Esther’s blog nicely explained: “Another struggle of mine was telling apart relative abundance and differential abundance results. Relative abundance gives you an idea of the proportion of a microbein a single samplewhiledifferential abundance compares the abundance levels between different samples or conditions.I’m glad this is one thing I no longer struggle with.”https://kunmiwrites.wordpress.com/2023/12/29/everyone-struggles-week-3-of-outreachy/Have a good rest and nice weekend! See you on Monday.

Abiola Salako (16:45:50) (in thread): > Welcome Aishat

Emem Eduoku (16:46:27) (in thread): > Thanks@Svetlana Ugarcina Perovic@Mildred AnashieI’d like to know, if we have genuses or families which were mentioned as substantially reduced in the H1 group but did not achieve statistical significance, they don’t need to be included under the decreased signature right?

Abiola Salako (16:48:45) (in thread): > Thanks for the clarification@Svetlana Ugarcina Perovic

Emem Eduoku (16:49:38): > I’d like to know, if we have genuses or families which were mentioned as substantially reduced in the H1 group but did not achieve statistical significance, they don’t need to be included under the decreased signature right?

Svetlana Ugarcina Perovic (16:51:21) (in thread): > @Emem Eduokuas for taxa. we only recordstatistically significant differences in alpha diversity.

Svetlana Ugarcina Perovic (16:52:50) (in thread): > Right, we only recordstatistically significant differences in alpha diversity.

Glorious Katushabe (16:52:56): > Hello everyone, how can I can do 2nd contribution since all papers to curate seemed to be assigned? are there new papers to curate? I need guidance to be able to move forward.

Abiola Salako (16:54:22) (in thread): > Thank you for sharing@Eniola Adebayo

Desire Oluwarotimi (16:57:02) (in thread): > Hi@Glorious KatushabeIt actually seems to be that all the available papers have been assigned at the moment but be patient. The mentors are definitely aware and they’ll add more papers.

Emem Eduoku (16:58:38) (in thread): > Ok. Thank you

Mildred Anashie (16:59:22) (in thread): > yes@Emem EduokuJust as@Svetlana Ugarcina Perovicstated only statistically significant results are recorded

Glorious Katushabe (16:59:56) (in thread): > Thank you@Desire Oluwarotimilet me be Patient.

Emem Eduoku (17:04:32) (in thread): > While waiting to be assigned ypu could help others review their curated papers

Svetlana Ugarcina Perovic (17:05:02) (in thread): > @Glorious Katushabejust added one

Emem Eduoku (18:01:11): > Hi guys. From the image below, these are the cofounders accounted for in the study right? - File (JPEG): Screenshot_20240308-235806_WPS Office.jpg

Aishat Ijiyode (19:48:11) (in thread): > Thank you so much. I really appreciate this

Blessing Peters (20:42:23): > Hello Everyone! So the information on the paper I’m curating doesn’t automatically populate on the next page like in the adding a study video. is that normal, I wonder if I’m doing the right thing.

Nitya Singhal (21:15:39): > Good morning from India. I wanted to know if I have judged my paper “cross-sectional observation, not case-control,” right?https://www.nature.com/articles/s41531-023-00554-5 - Attachment (Nature): Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease > npj Parkinson’s Disease - Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease

Nitya Singhal (21:47:14) (in thread): > Yes, it’s happening with me, too.

Scholastica Urua (22:27:45) (in thread): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (22:31:45) (in thread): > Hello@Blessing Petersand@Nitya Singhalyou can also fill in the PMID part and it will populate others.

Desire Oluwarotimi (22:32:40) (in thread): > Hi Guys@Blessing Peters@Nitya SinghalUsing your article’s PMID should automatically populate the other details for you but just in case that’s not available, there’s also an option to manually input the details. > > I hope this helps.

Joan C. Chukwuemeka (22:32:44) (in thread): > @Samreen AftabThe Images seems to show relative abundances across the taxa levels, and not differential abundance which is what is curated in Bugsigdb > > You can check this out.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709933812055619?thread_ts=1709922083.850489&cid=C04RATV9VCY - Attachment: Attachment > We curate differential alpha diversity to record microbial signatures on how microbial communities vary under different conditions. BugSigDB is focused on comparisons between two GROUPS of samples and there’s no differential beta diversity. For example, for beta diversity, the most frequently used is Bray-Curtis index - a measure of the similarity of two SAMPLES. It can range between 0 and 1, where 0 means the two SAMPLES have the same composition (that is they share all the species), and 1 means the two SAMPLES do not share any species. > > Another thing that I would like to highlight is actually in Esther’s blog nicely explained: “Another struggle of mine was telling apart relative abundance and differential abundance results. Relative abundance gives you an idea of the proportion of a microbe in a single sample while differential abundance compares the abundance levels between different samples or conditions. I’m glad this is one thing I no longer struggle with.” https://kunmiwrites.wordpress.com/2023/12/29/everyone-struggles-week-3-of-outreachy/ > > Have a good rest and nice weekend! See you on Monday.

Scholastica Urua (22:33:57) (in thread): > Another option is manually adding the details like@Desire Oluwarotimimentioned.

Scholastica Urua (22:47:30) (in thread): > Hello@Emem EduokuI can’t accurately tell from the image alone if they are confounders. But let’s brainstorm together… > > We know that confounders are variables other than the ones being studied that could potentially influence the outcome of the research. That is, from my understanding, those variables that can interfere with the disease of interest and maybe give a distorted result. > > For example, if effects of a particular diet on the gut microbiome is studied, factors like age, sex, medication use, and underlying health conditions of the population could be classified as confounders since they may ultimately interfere with the result if not properly controlled.

Scholastica Urua (23:09:10): > Hello everyone > For those without papers to curate for the second contribution, new unassigned paper has been added. Please do well to check it out.

Scholastica Urua (23:46:37) (in thread): > On further research, these may indeed be confounders in the study of the intestinal microbiota in Parkinson’s disease (PD) patients. As these variables could potentially influence the composition of the intestinal microbiota and thereby confound the results if not properly controlled for in the analysis.@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic:pray:

Desire Oluwarotimi (23:50:15) (in thread): > @Scholastica UruaYes, I don’t think one can easily tell from the image provided.@Emem EduokuYou could share the link to your paper and let’s go through it.

Nitya Singhal (23:53:44) (in thread): > where can we find it’s PMID@Scholastica Urua?

Nitya Singhal (23:54:12) (in thread): > Kindly help me out@Svetlana Ugarcina Perovic@Scholastica Urua

Desire Oluwarotimi (23:54:51) (in thread): > Hi@Nitya SinghalTake a look at this.https://bugsigdb.org/Curation_Policy#Study_Design - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Desire Oluwarotimi (23:57:35) (in thread): > @Nitya SinghalHere.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709735950567729?thread_ts=1709735773.104749&cid=C04RATV9VCY - Attachment: Attachment > Not doi but PMID > > Copy the title of your article and paste in the pubmed website. You’d be able to fetch the PMID. > > https://pubmed.ncbi.nlm.nih.gov/

2024-03-09

Nitya Singhal (00:03:08) (in thread): > Yes yes even I googled it and reached to the website of PubMed, searched by the title of my paper and found the PMID. Thanks for the help@Desire Oluwarotimi..

Nitya Singhal (00:04:06) (in thread): > I did, but I am confused between “case-control” and “cross-sectional observation, not case-control”

Nitya Singhal (00:18:22) (in thread): > Can anyone help me with this?@Scholastica Urua

Scholastica Urua (00:19:56): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI foundhttps://bugsigdb.org/Study_862under ‘Studies that have no Experiments’, can I go ahead to curate it? > Also, please can I get access to the pdf file? I haven’t been able to download it. Thanks - Attachment (BugSigDB): The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study - BugSigDB > BACKGROUND: Infection is a key component of bronchiectasis pathophysiology.Characterisation of the microbiome offers a higher degree of sensitivity and resolution than does traditional culture methods.

Desire Oluwarotimi (00:20:16) (in thread): > @Nitya SinghalI’ll take a look at it now and let you know what I think.

Scholastica Urua (00:22:03) (in thread): > Hi@Nitya SinghalI’ll also take a look at it and let you know what I think.:pray:

Desire Oluwarotimi (00:25:46) (in thread): > I think you are right be saying it cross-sectional observational. > > Here is an excerpt from your paper: “The three groups also had similar percentages of smoking, alcohol, coffee and tea consumption.” > > And that’s an important feature of cross-sectional observational which is comparison of participants based on the observation of their exposures. > > I hope this helps.

Evelyn Mary Attah (00:27:43): > Hello@Scholastica Urua, Do I apply to be assigned a paper to curate or I can go ahead and curate? Kindly enlighten me on this please. thank you

Desire Oluwarotimi (00:31:55) (in thread): > Hi@Evelyn Mary AttahYes, you need to apply to be assigned a paper before you can curate. You can apply by leaving a comment on the GitHub issue you want to work on. Simply tag the mentors, state your name and imply that you want to be assigned > > But while you wait to be assigned, you can help others in reviewing their curations.

Nitya Singhal (00:32:28) (in thread): > Hey@Evelyn Mary Attahyou have to checkout for the papers with the label ” papers to curate” on github and comment over there to get that paper assigned to you.

Nitya Singhal (00:33:35) (in thread): > But before that, you need to do the first contribution which is available on the below link.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Evelyn Mary Attah (00:35:23) (in thread): > Thank you so much@Desire Oluwarotimi@Nitya Singhal

Samreen Aftab (00:37:35): > Good day everyone. > If I’m getting the signatures from a specific paragraph, and not from a table/figure, then what should I mention the source as?

Desire Oluwarotimi (00:39:14) (in thread): > Hi@Samreen AftabYou can simply indicate the source as “Text”.

Nitya Singhal (00:40:37) (in thread): > yes thanks@Desire Oluwarotimi

Nitya Singhal (00:43:00): > In my paperhttps://www.nature.com/articles/s41531-023-00554-5, there are three groups ET,PD and HC but in an experiment we can only have 2 groups so does that mean I would have to make 3 experiments where.. ET vs HC, ET vs PD and HC vs PD? - Attachment (Nature): Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease > npj Parkinson’s Disease - Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease

Samreen Aftab (00:43:42) (in thread): > @Emem Eduokuthere is data in my paper for differential abundance of CD vs UC, but what should be the group 0 and group 1 for that experiment then?

Desire Oluwarotimi (00:47:02) (in thread): > @Nitya SinghalYes, you would have 3 experiments but the way your article arranged them are: > > HC vs ET > HC vs PD > ET vs PD > > You can check Table 1 to confirm the grouping comparisons and so, I’d suggest you stick to that. > > I hope this helps.

Ima-obong (Aimah) (00:52:22) (in thread): > Sure.. you’re to curate three experiments and check your results section of the paper to be sure varying results for the three experiments were explicitly stated.

Ima-obong (Aimah) (00:53:22) (in thread): > Good morning, I agree with@Desire Oluwarotimi

Aleru Divine (00:55:02) (in thread): > That’scorrect@Nitya Singhalconfirm as@Desire Oluwarotimihas suggested

Scholastica Urua (00:56:18) (in thread): > I have conflicting opinions on this. > > At first glance, I think the study could be classified as a case-control study design. Here’s why: > - There’s the selection of Cases and Controls > - The study compares individuals with essential tremor (ET) and de novo Parkinson’s disease (PD) to healthy controls (HC). > - It assesses the presence or absence of a particular condition (ET or PD) by comparing them to a control group (HC). > - It examines exposure variables (fecal SCFA levels) in relation to the presence of the disease (ET or PD) and compares them with healthy controls. > > Upon further consideration, the study could indeed be classified as an observational cross-sectional study like@Desire Oluwarotimi. Here’s why I think so: > - Data is collected at a single point in time from individuals with essential tremor (ET), de novo Parkinson’s disease (PD), and healthy controls (HC). > - Comparison of different individuals at a point in time, based on observation of their exposure or health outcome of interest is a feature of observational cross-sectional study. > - I also found this excerpt in the paper indicating a cross-sectional study design; - File (JPEG): cross.JPG

Aleru Divine (01:02:08) (in thread): > @Samreen AftabI believe any one can serve as a group 0 or 1.

Samreen Aftab (01:03:09): > Can I mention the NCBI taxon identifier like this? - File (PNG): image.png

Aleru Divine (01:04:12) (in thread): > Yes@Samreen Aftabit will automatically replace it with the correct name when you save.

Ima-obong (Aimah) (01:04:22) (in thread): > Yes you can

Mildred Anashie (01:11:30) (in thread): > I also can not tell from the image but to add to what has been said@Emem Eduokuyou could Ctrl+F and search the paper for words like Confounders, controlled for, adjusted for it could lead you directly to what you are searching for > > But then not all study designs control for confounders, Some can adjust for covariates ( Andcovariates are additional variables that are not your main variables of interest (exposure and outcome)but often have a direct effect on the outcome and need to be controlled for to assess the relationship between the independent variable(s) and the outcome accurately. > So you can also search for ‘covariates’ but you have tobe sure they are covariates and not the exposure or outcome of interest before you enter them as confounders

Desire Oluwarotimi (01:13:13) (in thread): > @Scholastica UruaThank you for further clarifying that. I didn’t even see the part of the article that said it is cross-sectional.

Scholastica Urua (01:14:01) (in thread): > This has prompted me to delve deeper into the paper I’m curating;https://bugsigdb.org/Study_875. Initially, I opted for a cross-sectional study design based on the information provided in the paper. But the study also involved comparing healthy controls with individuals with the disease of interest. > > I would appreciate insights from everyone regarding whether a study can be both case-control and cross-sectional designs. If so, how should such a study be documented on BugSigDB?:thinking_face:@Svetlana Ugarcina Perovic<@UBNSEMS3S>:pray: - Attachment (BugSigDB): Patients with Acne Vulgaris Have a Distinct Gut Microbiota in Comparison with Healthy Controls - BugSigDB > Acne vulgaris has been postulated to have a gastrointestinal mechanism; however, little is known about gut microbiota dysfunction in this condition.The aim of this cross-sectional study was to investigate whether the gut microbiota is altered in acne.

Scholastica Urua (01:15:59) (in thread): > Yes, it will be updated automatically like@Aleru Divinesaid.

Nitya Singhal (01:16:37) (in thread): > This is what happened to me, too. When I referred to the paper and definition mentioned in the Curation Policy, I signified that this paper should come under the “case-control” category. Still, some instances in the paper showed that it could lie under a “cross-sectional” study design. What would be the better one? I guess it would be cross-sectional. > Please give your opinions@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido

Scholastica Urua (01:17:13) (in thread): > Yes, I agree with@Desire Oluwarotimi

Scholastica Urua (01:18:58) (in thread): > In addition to what@Desire Oluwarotimisaid, you can also include the ‘line/paragraph’ of the source. I’ve seen it done in some curation.

Mildred Anashie (01:21:01) (in thread): > I agree with@Scholastica Uruafirst point > > It is a case control study in my opinion because we have an obvious disease condition and a clear healthy control group.

Aleru Divine (01:23:52): > Good morning and a happy weekend to everyone:heart::sparkles:

Desire Oluwarotimi (01:24:00) (in thread): > @Mildred AnashieThis is something similar to the discussion we had a few days ago, I can’t provide a more concrete explanation to back up my point than I have but I’ll try to go through the article again to pick up one or two. But I still strongly believe it’s cross-sectional observational.

Scholastica Urua (01:24:07) (in thread): > @Evelyn Mary Attah,@Nitya Singhaland@Desire Oluwarotimihave said it all. > > Why I dropped this here (which may have prompted your question) is because I found it under ‘Studies that have no Experiments’, The mentors previously mentioned to ask for a go ahead before you edit a previous work.

Desire Oluwarotimi (01:25:31) (in thread): > Good morning@Aleru Divine

Muqtadirat Yussuff (01:25:51) (in thread): > Hello:wave:, I did not get response to this

Ima-obong (Aimah) (01:26:39) (in thread): > Happy weekend@Aleru Divine

Scholastica Urua (01:27:05) (in thread): > Good morning@Aleru Divine, enjoy the weekend:confetti_ball:

Nitya Singhal (01:38:59) (in thread): > My only strong point is that it is mentioned in the paper itself as a “cross-sectional” study.

Scholastica Urua (01:42:28) (in thread): > Its a confusing one for me too.

Nitya Singhal (01:44:32) (in thread): > Will the entire green-highlighted portion be included in the Antibiotic exclusion? - File (PNG): image.png

Scholastica Urua (01:45:12) (in thread): > Nice to know you were able to find your way@Nitya Singhal:+1:@Blessing Petershave you been able to populate yours?

Desire Oluwarotimi (01:46:10) (in thread): > @Nitya SinghalNot necessarily. I mean you could but this is quite a lot a text so I’d say the exclusion period is just fine.

Bolanle Wahab (01:49:12) (in thread): > Good morning@Aleru Divine,Thanks and you too:heart:

Mildred Anashie (01:49:31) (in thread): > I still think it’s case-control > I think something that can happen is, most papers might state a particular thing but actually did something else > > > Because like I said we have an obvious healthy control group with an obvious disease condition > > Also the participants were matched on age, sex and BMI (Typical to case-control)

Joy Gold (01:54:28): > Hello everyone I am Joy from Nigeria and I am happy to be here

Aleru Divine (01:55:39) (in thread): > Hi@Joy Gold, welcome:hugging_face:

Desire Oluwarotimi (01:55:40) (in thread): > @Mildred AnashieI don’t think matching factors is enough to decide the study because they could be matched on the factors you mentioned and still be cross-sectional. Also there was an analysis of their exposures.

Anju Maurya (01:55:42): > @Joy GoldHey Joy!

Anju Maurya (01:55:55): > Welcome to the community.

Anju Maurya (01:56:06): > You can start from here:

Anju Maurya (01:56:08): > Welcome Outreachy applicants!We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started:https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion.Thank you so much for your interest and we look forward to working with you.<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic#94 Welcome Outreachy Applicants!Welcome Outreachy Applicants!Note: This task can be completed by multiple Outreachy applicants.BugSigDB ProjectBugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies,https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a me…Labelsfirst contribution, outreachy may2024Comments8 - Attachment (BugSigDB): Main Page > … - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Desire Oluwarotimi (01:56:35) (in thread): > Hey@Joy Gold. Welcome.

Ima-obong (Aimah) (01:56:37) (in thread): > Welcome@Joy Goldplease check out this link and follow the introductions to begin your contributions.https://community-bioc.slack.com/archives/C04RATV9VCY/p1709568003471699 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (01:58:27) (in thread): > Please point me to where they were analyzed based on exposures > > I was actually looking for andI’mnot sure I found it:pray:

Mildred Anashie (02:00:05) (in thread): > Good morning to you@Aleru DivineHappy weekend everyone:heart_eyes:

Mildred Anashie (02:00:49) (in thread): > Hi@Joy GoldWelcome:hugging_face:

Desire Oluwarotimi (02:03:53) (in thread): > Check “Demographics and clinical characteristics of subjects” under result. They mentioned smoking, alcohol, coffee and tea consumption.@Mildred Anashie

Scholastica Urua (02:05:31) (in thread): > @Nitya SinghalI think just stating one month will be find.

Ima-obong (Aimah) (02:09:25) (in thread): > No..just state the period which is one month.

Scholastica Urua (02:10:37) (in thread): > Hello@Joy Goldnice to e-meet you.

Ruth Bamgbose (02:20:46) (in thread): > I believe your study is a cross-sectional observation, although we have a control group, data is collected from participants who represent a particular group at a single point. They collect data from those with the condition and those without but they do not manipulate variables, and the study was not to determine the association between the exposure variables(fecal SCFA levels) and how it affects the outcome of the disease (ET, PD), it was simply to note the fecal SCFA levels in the different groups, and it’s association with clinical severity and gut microbiota.

Scholastica Urua (02:22:48) (in thread): > Hi@Mildred AnashieTalking about papers stating a particular thing but actually doing something else, aren’t we just suppose to curate what is in the paper

Ruth Bamgbose (02:27:38) (in thread): > Hi Welcome

Leenaa Al-Amin (02:39:26) (in thread): > Good morning@Aleru Divine

Mildred Anashie (02:41:17) (in thread): > Even though I have gone through the paper and found only where it was mentioned that the participants shared the same characteristics such as alcohol,smoking status and tea which appeared to me as just stating the participants characteristics@Desire OluwarotimiI stand to be corrected but I still have the same opinion regarding the study design@Scholastica UruaYes we are to record what is found in the paper but if you have conflicting opinions on what is in the paper and what you think was done you can check in with the mentors > > I should tag the mentors to this at this point (my opinion might be wrong):woman-shrugging:@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Esther Afuape@Peace Sandy@Chioma OnyidoPlease help out with this:pray:

Bolanle Wahab (02:43:25) (in thread): > Hi@Joy Goldwelcome:heart:

Samreen Aftab (02:46:01): > Hello everyone! I’m happy to inform you that I’ve completed my second contribution for the paperhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10640746/pdf/12866_2023_Article_3084.pdf, and it was indeed a fun and learning experience for me, considering that the last time I studied biology was in high school.https://bugsigdb.org/Study_926Here is the link, any reviews would be appreciated :) > Also I would like to add a small question here. I’ve included experiments for HC vs CD, HC vs UC, CD vs UC. Do I need to add additional experiments for Chron’s disease/UC- mild vs moderate. > Thank you, and a good day to everyone - Attachment (BugSigDB): Diagnosis of Crohn’s disease and ulcerative colitis using the microbiome - BugSigDB > BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota.

Aleru Divine (02:48:39) (in thread): > Congratulations@Samreen Aftab,I’llhelp review as soon as I am done with the ones I am already reviewing.Here is my GitHub: @AleruDivine

Desire Oluwarotimi (02:49:36) (in thread): > Our mentors will be help us out then.

Samreen Aftab (02:50:18) (in thread): > Thank you@Aleru DivineShould I mark it complete now, or should I wait?

Bolanle Wahab (02:51:15) (in thread): > @Muqtadirat YussuffIt seems some taxa of Streptococcus increased in representation immediately after postfeeding, while others decreased in representation after feeding so I think you can say the abundance of Streptococcus increased and decreased depending on the specific taxa within the genus.

Aleru Divine (02:51:52) (in thread): > @Samreen Aftabdo you mean on BugSigDB? If so, yes.Thenit’llbe marked as “needs review”

Muqtadirat Yussuff (02:56:25) (in thread): > They weren’t specific but I’d go through again just in case I missed it. Thank you@Bolanle Wahab

Bolanle Wahab (03:00:05) (in thread): > @Muqtadirat YussuffI’dalso go through it again just to be sure.

Mildred Anashie (03:01:02) (in thread): > Well done@Samreen Aftab:clap:I’ll cross check the paper to see if you need to add the experiment > > But if the experiment was done and we have significant results then it’s a yes

Ima-obong (Aimah) (03:01:19) (in thread): > Congratulations@Samreen Aftabwill look it up as soon as I’m done..

Scholastica Urua (03:01:49) (in thread): > Well done@Samreen Aftab

Ima-obong (Aimah) (03:02:21) (in thread): > And also, it’s good to check if that particular experiment’ result was significantly stated before adding it cause that’s what matters.

Flourish Ralph (03:03:04) (in thread): > Happy weekend everyone:hugging_face:

Scholastica Urua (03:03:23) (in thread): > For your question, if the study was further subgroup to by mild and moderate and the result shows significant abundance then yes.

Latifat (03:06:28): > Hello everyone. I’m new to Microbiome studies therefore I’m still struggling with my first contribution. I am struggling with identifying the disease of interest in the study. I identified the condition being studied as ‘short-chain fatty acid-producing gut bacteria’ then I searched on the database provided but it shows ‘No result’. > > Also, I have been unable to identify the differentially abundant taxa in the study. > > I will really appreciate any advice. Thank you.

Leenaa Al-Amin (03:14:10) (in thread): > Congratulations!@Samreen AftabI’ll help review. If you don’t mind, could you review mine as well:)https://journals.asm.org/doi/10.1128/spectrum.02311-21and here’s the link to the curationhttps://bugsigdb.org/Study_891 - Attachment (BugSigDB): Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome - BugSigDB > The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis.This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs.

Desire Oluwarotimi (03:14:12) (in thread): > Hello@LatifatThe condition of the first task you are talking about is “breast cancer” and not “short-chain fatty acid-producing gut bacteria” > > Also, identifying abundant taxa is simply just about pairing experimental groups and pointing out the increased and decreased signatures. You’ll mostly always get hold of this information somewhere in your article.

Leenaa Al-Amin (03:15:36) (in thread): > Also if anyone here wouldn’t mind helping review mine:point_up_2:I’d really appreciate it!

Joan C. Chukwuemeka (03:15:53) (in thread): > Good morning@Muqtadirat Yussuff, I did a surface scan of the article, and I think it requires deep reading to pick out curatable information. It also has supplemental materials that should be studied as well… > > I’d see what insights I can draw and share with you.:blush:

Ima-obong (Aimah) (03:18:38) (in thread): > @Leenaa Al-Amin… we’ll check it out shortly.. Congratulations

Joan C. Chukwuemeka (03:20:21) (in thread): > Hi@LatifatWelcome to the community. You can check the study materials first and curation policy on Bugsigdb before carrying out the task.. It’ll go a long way to equip and help you familiarise with what the microbiome curation is all about.

Latifat (03:21:06) (in thread): > Thank you very much for the response.

Ima-obong (Aimah) (03:21:10) (in thread): > Hello@Latifat, like@Desire Oluwarotimisaid, the study of interest is breast cancer

Muqtadirat Yussuff (03:21:47) (in thread): > Good morning@Joan C. Chukwuemeka, your input would be really appreciated, thank you for helping with this

Aleru Divine (03:21:57) (in thread): > Hi@Latifatto identify a differentially abundant taxa in the study (look for one of the figures reporting significantly increased/decreased bacteria in the compared groups).

Flourish Ralph (03:22:32) (in thread): > @Latifathere’sthe link to the curation policyhttps://bugsigdb.org/Curation_Policy#Study_Design - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Latifat (03:22:34) (in thread): > @Desire OluwarotimiThank you.

Ima-obong (Aimah) (03:22:45) (in thread): > Also check this curation policy, it will help you understand the task better.https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Joan C. Chukwuemeka (03:23:40) (in thread): > The heading with “prep work” has resources that will equip you. Rooting for you:wink: - File (JPEG): Screenshot_2024-03-09-09-21-27-277_com.android.chrome.jpg

Mildred Anashie (03:24:25) (in thread): > You can also go through the pinned messagesit’llhelp@Latifat

Latifat (03:26:13) (in thread): > Thank you all for the assistance. I will check out all the guidance. I appreciate.

Muqtadirat Yussuff (03:26:19) (in thread): > Hi@Leenaa Al-AminI would review yours and get back to you today. You can also tag me on the issue at GitHub@Muqtadirat Yussuff

Samreen Aftab (03:33:03) (in thread): > sure@Leenaa Al-AminI’ll review yours:slightly_smiling_face:

Flourish Ralph (03:33:51): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeThis is my study for the second contribution task, is it possible to add a laboratory experiment study design (for the mouse models) apart from having the study design for the human subjects? - File (JPEG): IMG_2808

Ruth Bamgbose (03:34:58): > Hello everyone, who is available to review my work andI’llreview theirs?

Desire Oluwarotimi (03:36:31) (in thread): > Hi guys. Let’s take a look at this together. > > I have gone through it and I have the same question as to whether it is possible to have two study designs for one particular paper.

Ima-obong (Aimah) (03:37:49) (in thread): > Seems quite tricky cause this actually has two types of study in it..both the case control and the lab experiment…but what I don’t know is if both study design can be listed at once or separately…

Ima-obong (Aimah) (03:38:24) (in thread): > I think the mentors will have a more detailed insight on this

Amarachi Lewachi (03:55:21) (in thread): > Hi everyone. My PMID brought the message “must be unique” which indicates not to add it as it is already in BugSigDB. Do I just leave that spot blank?@Svetlana Ugarcina Perovic@Chioma Onyido@Aleru Divine

Samreen Aftab (03:56:59) (in thread): > @Ruth BamgboseHello, here is my workhttps://bugsigdb.org/Study_926https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10640746/pdf/12866_2023_Article_3084.pdflink down your work so that I can review it :) - Attachment (BugSigDB): Diagnosis of Crohn’s disease and ulcerative colitis using the microbiome - BugSigDB > BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota.

Evelyn Mary Attah (03:57:03) (in thread): > Hello@Nitya Singhal, is the first contribution like a quiz, survey or am to write an article? kindly assist

Muqtadirat Yussuff (04:03:57) (in thread): > Where’s the link to the paper please?

Evelyn Mary Attah (04:05:26) (in thread): > @Scholastica Uruathank you very much

idiaru Angela (04:06:54) (in thread): > It is a survey that you are to complete using the annotated article that is provided. Download the article, read it, then you can use it to answer the survey@Evelyn Mary Attah

Flourish Ralph (04:07:53) (in thread): > Here it ishttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7029363/ - Attachment (PubMed Central (PMC)): A Pilot Microbiota Study in Parkinson’s Disease Patients versus Control Subjects, and Effects of FTY720 and FTY720-Mitoxy Therapies in Parkinsonian and Multiple System Atrophy Mouse Models > Parkinson’s disease (PD) and multiple system atrophy (MSA) patients often suffer from gastrointestinal (GI) dysfunction and GI dysbiosis (microbial imbalance). GI dysfunction also occurs in mouse models of PD and MSA.To assess gut dysfunction …

Evelyn Mary Attah (04:08:22) (in thread): > @idiaru Angelathank you very much, have done that, wanted to be sure i’m doing the right thing

Leenaa Al-Amin (04:10:42) (in thread): > I’ll help review, please link your work. Here’s mine:)https://journals.asm.org/doi/10.1128/spectrum.02311-21and here’s the link to the curationhttps://bugsigdb.org/Study_891BugSigDBIncreased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome - BugSigDBThe modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis.This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthrough

idiaru Angela (04:15:02) (in thread): > You’re welcome. Don’t forget to record the contribution on the outreachy website.

Muqtadirat Yussuff (04:25:19) (in thread): > Hmm, I would go with one study design but multiple experiments for different objectives. The primary objective of the study is human subject

Svetlana Ugarcina Perovic (04:35:29) (in thread): > @Amarachi Lewachiit’s herehttps://bugsigdb.org/Study_933as an already open study; please continue curating it on this pagehttps://bugsigdb.org/Study_933. - Attachment (BugSigDB): Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis - BugSigDB > …

Flourish Ralph (04:45:58) (in thread): > Thank you for this@Muqtadirat Yussuff

Amanda Adoyi (04:52:51): > Aloha and ciao and halo:slightly_smiling_face:I notice some contributors in github comments under their issues signaling for@Svetlana Ugarcina Perovicto see their Studies for review. Is this necessary to do or not a requirement before being reviewed@Svetlana Ugarcina Perovic?

Mildred Anashie (04:53:54) (in thread): > It’simportant to inform the mentors that your study is ready for review as the second contribution is being scored

Amanda Adoyi (04:54:14) (in thread): > Alryty

Mildred Anashie (04:54:48) (in thread): > Also drop the link to the study you curated along side the comment

Amanda Adoyi (04:55:10) (in thread): > Alryt. Thanks

Amanda Adoyi (04:59:39): > When I look through previous curations, some of them site signature sources as “text” without specifications on page number or heading. Who knows if that’s accepted? Seeing it in previous curations, one would assume that it’s okay.

Muqtadirat Yussuff (05:00:39) (in thread): > I have the same question because I didn’t cite the exact text location but in the canvas section, it was written “text” is an appropriate source

Aleru Divine (05:00:51) (in thread): > @Amanda AdoyiI believe it is.Also is there a way to specify text? If there is, then you can add it in the discussions page.

Emem Eduoku (05:01:34) (in thread): > Thanks@Mildred Anashie@Desire Oluwarotimi@Scholastica Urua

Mildred Anashie (05:02:05) (in thread): > I’m interested in knowing if it’s necessary > > Although like you pointed out other curators have been doing it that way > Maybe putting it as “Results text” should be more specific

Aleru Divine (05:02:07) (in thread): > @Amanda Adoyihere’swhat I did > > Hi @mentor > > I have finished the curation. This article is ready for review. > > Link to curation: > > Thank you so much!:sweat_smile:Hope this helps

Amanda Adoyi (05:02:46) (in thread): > Yea@Aleru Divineyou did say this. Just looking at opinions on the issue.

Amanda Adoyi (05:05:07) (in thread): > Lolz.@Aleru DivineIt does. I’ll do that then.

Blessing Peters (05:06:15) (in thread): > @Scholastica UruaYes I have, Thank you for your help.

Nana (05:06:22): > @Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyGood morning please I have a question > 1. Are they sequencing platform used If is WMS? Meantioned as the Sequencing type > 2. Does over representation means increase in taxa mentioned to be present

Blessing Peters (05:07:09) (in thread): > @Desire OluwarotimiThank you for your help. I used the PMID.

Peace Sandy (05:09:44) (in thread): > @Nanawhat sequencing platform was mentioned in the study

Nana (05:10:58) (in thread): > None

Nana (05:11:19) (in thread): > Should I send you the link

Peace Sandy (05:11:52) (in thread): > Yes

Nana (05:11:55) (in thread): > Ok

Ima-obong (Aimah) (05:12:55) (in thread): > Yes@Nanayou can also share the link here.. though in my paper, 16Sr wasn’t the sequencing type but illumina was stated as the sequencing platform

Nana (05:15:20) (in thread): > @Peace Sandyhere:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.780568/full - Attachment (Frontiers): Frontiers | Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Nana (05:18:21): > @Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyI have a conflicting test, bonfereoni was mentioned meaning MHT: yes then LEfSe and lda at 3 was mentioned please what should I choose as my statistical test..here is an image for better clarification - File (JPEG): Screenshot_2024-03-09-11-11-42-39_99c04817c0de5652397fc8b56c3b3817.jpg - File (JPEG): Screenshot_2024-03-09-11-11-37-42_99c04817c0de5652397fc8b56c3b3817.jpg

Peace Sandy (05:19:14) (in thread): > The one used for the differential abundance

Nana (05:20:14): > @Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandycan this be entered as confounder and log 10 as Data transformation..image - File (JPEG): Screenshot_2024-03-09-11-11-46-96_99c04817c0de5652397fc8b56c3b3817.jpg - File (JPEG): Screenshot_2024-03-09-11-10-37-37_99c04817c0de5652397fc8b56c3b3817.jpg

Ruth Bamgbose (05:20:46) (in thread): > Hi here’s the link to my workhttps://github.com/waldronlab/BugSigDBcuration/issues/124https://bugsigdb.org/Study_881 - Attachment (BugSigDB): Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls - BugSigDB > Posttraumatic stress disorder (PTSD) imposes a significant burden on patients and communities. - Attachment: #124 Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls > Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls – Stefanie Malan-Muller et al. – European Neuropsychopharmacology 2022 > > https://www.sciencedirect.com/science/article/abs/pii/S0924977X21016539 > > NOTE: This paper is without open access, here is downloaded pdf: Exploring-the-relationship-between-the-gut-microbiome-and-m_2022_European-Ne 2.pdf

Mildred Anashie (05:21:29) (in thread): > I see LEfSe was used for the differential abundance from the image shared

Nana (05:21:38) (in thread): > The one used for differential abundance is LEfSe but the MHT was mentioned and from curation policy it says if MHT is mentioned then you rule out LEfSe and lda

Mildred Anashie (05:23:11) (in thread): > @Nanait should be LEfse as the test > > I also encountered the Same in my paper and the mentors asked me during the last office hour to use the actual test mentioned and also enter yes for MHT since it was stated so in the paper

Nana (05:24:28) (in thread): > Ok@Mildred Anashie:ok_hand::ok_hand:

Ima-obong (Aimah) (05:25:21) (in thread): > @Mildred Anashieis right, you’ll still enter yes for MHT even though the test used was LEfse, so far MHT was explicitly stated…saw that too in my paper.

Ima-obong (Aimah) (05:26:51) (in thread): > I see age(gestational) and diet can be mentioned as confounders..

Mildred Anashie (05:28:54) (in thread): > For the data transformation it should be Relative abundance (That’s what the second image says) > > And also since your statistical test is LEfSe it backs it up > > If you check the pinned messagesyou’dsee where Data transformation was discussed

Preethi grace Manthena (05:43:02): > Hii everyone, I’m Preethi grace from Electronic and communication Engineering, I’m here to contribute to Bioconductor Success. I’m happy and curious to work with u all..

Scholastica Urua (05:43:45) (in thread): > Welcome@Preethi grace ManthenaKindly view the issue on GitHub for instructions on how to get started. > > Please feel free to share any questions you may have. I’m happy to help wherever I can.https://github.com/waldronlab/BugSigDBcuration/issues/94. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Ima-obong (Aimah) (05:44:42) (in thread): > You’re welcome@Preethi grace Manthenaplease go through the link@Scholastica Uruashared for info on how to begin..have fun

Scholastica Urua (05:50:05) (in thread): > I also think ‘Text’ alone can be sited as the source. But if it’s possible to clearly specify where, you should also do that to easily guide someone checking your work.

Amanda Adoyi (05:52:08) (in thread): > @Scholastica Uruayep. Would also help to always check discussions on any page. Helpful info may be found there.

Desire Oluwarotimi (05:52:09) (in thread): > Welcome@Preethi grace Manthena

Preethi grace Manthena (05:53:00) (in thread): > Thank you@Ima-obong (Aimah)

Scholastica Urua (05:55:02) (in thread): > Okay@Esther Afuape, thank you

Muqtadirat Yussuff (05:56:15) (in thread): > Hi@Preethi grace Manthenaand welcome to the community:wave:

Nitya Singhal (05:59:16) (in thread): > ok thank you@Desire Oluwarotimi@Scholastica Urua@Ima-obong (Aimah)

Scholastica Urua (06:05:05) (in thread): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Anju Maurya (06:22:06) (in thread): > Welcome@Preethi grace Manthena!

Aleru Divine (06:28:34) (in thread): > Hi@Preethi grace Manthena, welcome:hugging_face::hugging_face:

Mildred Anashie (06:37:20) (in thread): > Hi@Preethi grace ManthenaYou are Welcome:blush:

Aleru Divine (06:37:49) (in thread): > @Nana, there are a few confounding factors there.Antibiotics, diet, gestational age. > > Could you please share the paper so I go through it and see ifI’mright.Thanks!

Success Ologunsua (07:12:03): > Hi everyone, my name is Success and I am very interested in the Microbiome Study Curation project. As a microbiology graduate turned software developer, I’m excited about a project that combines these two fields and hope to make meaningful contributions.

Mildred Anashie (07:12:33): > Welcome > > Please check the pinned messages

Mildred Anashie (07:12:51): > Go through this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Bolanle Wahab (07:14:48) (in thread): > You’rewelcome:heart:@Success Ologunsua

Scholastica Urua (07:15:01) (in thread): > Hello@Success Ologunsuawelcome to the community

idiaru Angela (07:20:04) (in thread): > Hi@Success Ologunsuayou’re welcome!

Aleru Divine (07:23:32) (in thread): > Hi@Success Ologunsua, welcome:hugging_face:

Samreen Aftab (07:27:20): > How can I contribute more while I’m waiting for my second contribution to get reviewed?

Scholastica Urua (07:28:32) (in thread): > Hello@Samreen AftabWhile waiting for grading, here is some ways you can help out with BugSigDB: > * Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > * Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > * See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Aleru Divine (07:29:15) (in thread): > Here@Samreen Aftabhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697144958544289 - Attachment: Attachment > Someone asked what you can do while waiting for your second contribution to be graded. Here are some suggestions: > 1. double-check your contribution for accuracy and completeness, which is what it will be scored for. > 2. check out the <https://bugsigdb.org/Help:Contents#TODO_for_reviewers|TODO for reviewers> - we’d love to have help! > 3. resolve some of the <https://bugsigdb.org/Help:Contents#NCBI_cleanup|NCBI cleanup> - I find this surprisingly fun, like detective work :sweat_smile: > When you first get started reviewing, it’s best if you post proposed changes here to check that you’re on the right track. Actually it’s OK to make edits to the wiki, just post here and we can always roll back changes if needed, and mark a study as reviewed if it seems like you’ve reviewed it sufficiently.

Samreen Aftab (07:29:54) (in thread): > Thank you guys:heart:

Nana (07:38:56) (in thread): > Ok.thank you

Success Ologunsua (07:40:07) (in thread): > Thank you everyone:heart:

Nana (07:40:11) (in thread): > Ok

Nana (07:40:16) (in thread): > Thanks guys

Scholastica Urua (07:40:37): > Hello everyone, I have been going through this paper (a prospective observational study) and trying to identify the groups and how many experiments are involved. > > In the study, 49 patients provided more than one sample when clinically stable and were included in the longitudinal analysis. 64 patients provided both stable and exacerbation samples. > > Please I’ll like your suggestions. > > Link:https://bugsigdb.org/Study_862 - Attachment (BugSigDB): The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study - BugSigDB > BACKGROUND: Infection is a key component of bronchiectasis pathophysiology.Characterisation of the microbiome offers a higher degree of sensitivity and resolution than does traditional culture methods.

Oluwatomisin Omojokun (07:40:42) (in thread): > welcome@Success Ologunsua

Nana (07:41:21) (in thread): > @Aleru Divinehere:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.780568/full - Attachment (Frontiers): Frontiers | Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Aleru Divine (07:41:32) (in thread): > @Scholastica UruaCould you share the paper please

Aleru Divine (07:42:02) (in thread): > Thanks@NanaI’llcheck it out now

Mildred Anashie (07:43:00) (in thread): > Share link to the paper please

Nana (07:43:23) (in thread): > @Peace Sandyany luck..sent the link since > Does also over representation means increase in taxa mentioned to be present

Scholastica Urua (07:44:08) (in thread): > This is the paper. Thanks - File (PDF): S2213260020305579.pdf

Nana (07:44:58) (in thread): > Urw

Aleru Divine (07:49:22) (in thread): > Thanks@Scholastica UruaI’llcheck it out

Scholastica Urua (07:50:03) (in thread): > Thank you@Aleru Divine, looking forward to your response.

Aleru Divine (07:57:20) (in thread): > @Nanafrom this excerpt, > > “Altogether, the arguments listed above raised our interest to first uncover the microbiota of Tunisian newborns and then to assess the impact of DM on the composition of early gut bacteria by minimizing confounding factors. A shotgun metagenomic approach was applied to better capture the microbial resolution in the ECS and VD newborns.” > > It looks like the confounding factor they minimized(or we can say controlled) for was Caesarian Section(CS).Because they wrote this: > > “Altogether, the arguments listed above raised our interest to first uncover the microbiota of Tunisian newborns and then to assess the impact of DM on the composition of early gut bacteria by minimizing confounding factors. A shotgun metagenomic approach was applied to better capture the microbial resolution in the ECS and VD newborns.”

Desire Oluwarotimi (08:08:47) (in thread): > Welcome@Success Ologunsua

Mildred Anashie (08:08:48) (in thread): > Please share the link to this study > > I want to look at the additional materials

Scholastica Urua (08:11:33) (in thread): > Just added the link@Mildred Anashie. Sorry I omitted that before.

Emem Eduoku (08:14:20): > Hi everyone. I’m confused about the number of experiments I should have. > > So the first comparison was done between the control group and the PD group. But later in the paper it was stated the PD group were further divided into the mild and severe group and the differential abundance in microbial composition in both groups were compared to control group. > > Do I record three experiments of HC vs PD, HC vs MPD and HC vs SPD? > > See image and link below for more clarity - File (JPEG): Screenshot_20240309-135706_WPS Office.jpg - File (JPEG): Screenshot_20240309-135717_WPS Office.jpg - File (PDF): Download.article.pdf

Scholastica Urua (08:15:57) (in thread): > I have a lot of questions concerning this study. The location was Scotland which is not available on the list. Some of the confounders are also not highlighting during curation. > > Please what are we suppose to do in this case?@Esther Afuape@Chioma Onyido@Peace Sandy

Blessing Ene Anyebe (08:16:47) (in thread): > Congratulations Samreen

Nana (08:23:15) (in thread): > @Aleru Divinebut confounding can only be found in methods as stated by the policy

Nana (08:23:43) (in thread): > Do you think this is a longitudinal study

Aleru Divine (08:27:21) (in thread): > @Nanathis was found in the introduction, so maybeI’mwrong.

Nana (08:29:20) (in thread): > @Aleru Divinedo you think it’s longitudinal study?

Aleru Divine (08:29:47) (in thread): > Yes it is, it was also stated in the discussion.

idiaru Angela (08:30:52) (in thread): > I don’t think it requires 3 experiments since the difference in MPD and SPD were not talked about using diversity but the percentage of occurrence@Emem Eduoku

Aleru Divine (08:30:56) (in thread): > And to back this up, “The neonatal meconium from VD and ECS newborns was collected during the first 24 h (Day 0) at the regional hospital of Zaghouan and at the Aziza Othmana hospital, located in Zaghouan and Tunis, respectively. The collection was renewed for 2 weeks (Day 15) and 1 month (Day 30) after birth. The samples were transported in ice bags to the laboratory and then stored at −80°C until DNA extraction.” > > Data was collected at different time points.

Mildred Anashie (08:36:54) (in thread): > Ican’tfind the additional materials > > Do you have them?

Nana (08:38:19) (in thread): > Ok…just wanted to be sure .thanks

Scholastica Urua (08:38:39) (in thread): > The paper did not mention any supplementary data. Or am I missing something:thinking_face:

Mildred Anashie (08:43:02) (in thread): > The paper kept referring to Appendices with page numbers

Mildred Anashie (08:43:16) (in thread): > I’msuspectingthere’san additional material

Scholastica Urua (08:47:20) (in thread): > Yes, you are right. I noticed that too but when I searched for supplementary materials nothing came up.

Aleru Divine (08:50:49) (in thread): > I am so confused, I couldn’t figure anything out either@Scholastica Urua

Mildred Anashie (08:52:03) (in thread): > I’llkeep trying > > Anyone who can help, should please help with the additional materials > There might be some leads there

Scholastica Urua (08:53:38) (in thread): > Thank you@Aleru Divineand@Mildred AnashieI’ll let you know what I find.

Modinat Ganiyu (09:04:22): > Good day everyone. Please for clarity I want to state the steps taken to be sure I’m doing the right thing. > * I followed this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 > * watch videos under ‘prep work’ > * Under first contribution, clicked on ‘go to the first curation form’ > * It took me to a new page and I entered my name, email, and Github username > * clicked on an arrow which indicate next page > * Here I followed all instructions to answer these questions > * I kept clicking on the arrow to lead me to the next page but the last arrow took me to a page saying ‘your contribution has been recorded’ > At this point I’m not sure of what to do because I know I didn’t take the step to record contribution (I haven’t done that). Please can you put me through - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Mildred Anashie (09:05:55) (in thread): > Hi > > I supposeitmeant recorded on the side of the mentors for BugSigdb

Mildred Anashie (09:06:13) (in thread): > You’dstill have to record it on outreachy

Scholastica Urua (09:06:27) (in thread): > Hello@Modinat Ganiyusince you answered the questions in the form, it means you have carried out a first contribution.

Scholastica Urua (09:07:10) (in thread): > All you need to do now is record it on outreachy site as your first contribution

Adedoja Isaac (09:07:10) (in thread): > You’re done with the first contribution

Aleru Divine (09:07:34) (in thread): > Hi@Modinat GaniyuYou need to record your first contribution now thatyou’redoneGo to “record contributions”on the outreachy website(bioconductor project page)use the link of the survey as the “contribution URL” and the day you completed the survey(today)as the merge date.

Mildred Anashie (09:08:36) (in thread): > Paste this link to record on outreachyhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Scholastica Urua (09:10:00) (in thread): > @Modinat GaniyuHope this helps to answer some of your questions;https://community-bioc.slack.com/archives/C04RATV9VCY/p1709876110262569 - Attachment: Attachment > Hello everyone, how is the contribution phase progressing? The first week is slowly coming to an end, and it has been wonderful collaborating with everyone here. > I’ve noticed that there have been over a dozen questions asked, and I’ve been able to identify a few that are recurring. Please feel free to add other questions and answers under this thread. I hope this helps someone! > > Q1. I couldn’t find how to record my first contribution. > A: Steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > Q2. When recording the first contribution, what is the ‘merged date’? > A: The merged date refers to the date you submitted your contribution. > > Q3. What URL are we submitting for the first contribution? > A: The link to the curation form: [https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc](https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc) will serve as your Contribution URL. > > Q4. After I submit my first contribution, can I go back to edit it if I notice I made a mistake, or if I didn’t add something somewhere? > A: Unfortunately, you cannot edit a submitted contribution but you can make another submission from scratch. > > Q5. Are we making 2 contributions? > A: While you can make as many contributions as possible, the first contribution is compulsory. After completing the first contribution, you may proceed to the second. Although the second contribution is not mandatory, it is advisable to complete it. Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > - See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > Q6. For the second contribution, after Adding a Study in BugSigDB, does it need to be reviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study? > A: You do not need to wait for mentors to review. You can click on the ‘Add Experiment’ button to add an experiment. > > Q7. I want to know how many times I can use the record my contribution option on the Outreachy website. > A: You can use the ‘Record My Contribution’ option as many times as needed, depending on how many contributions you make. > > Q8. How to I get assigned a paper for my second curation? > A: Find an unassigned paper you’ll like to curate via https://github.com/waldronlab/BugSigDBcuration/issues, then ask for it to be assigned to you by commenting on it. Mentors will assign it to you if you are the first to request for it.

Bolanle Wahab (09:10:32) (in thread): > @Scholastica UruaI think for the first group (patients that provided more than one sample when stable), you can consider each patient as a separate experiment, with the samples taken at different time points that is Sept 11, 2012, to Dec 21, 2015, Jan 8, 2019 according to the article. > > For the second group (patients that provided both stable and exacerbation samples), each patient can also be taken as a separate experiment, with samples taken during stable periods compared to samples taken during exacerbation. > But this is going to lead to alot of experiments,Idon’tknow if this suggestion is feasible.

Scholastica Urua (09:11:51) (in thread): > Thank you@Bolanle Wahab, I’ll look into it

Bolanle Wahab (09:18:14): > Hi everyone, please what would be the likely condition for a study where there’s no disease per se but they observed the effect of a diet supplemented with prebiotics on the subject?

Emem Eduoku (09:29:52) (in thread): > I’d say Diet supplemented with Prebiotics is the condition. There is a control group who don’t get the prebiotic supplemented diet right?

Emem Eduoku (09:30:25) (in thread): > The condition should be what is being compared. What is in one group that the reference group don’t have?

Emem Eduoku (09:32:00) (in thread): > So just one experiment with the HC and PD will suffice?@idiaru Angela

Emem Eduoku (09:34:28) (in thread): > But if you check further down the circled sentence it states the relative abundance between the MPD, SPD and HC group with two signatures highlighted.@Svetlana Ugarcina Perovic?what do you think

Barakat Akinsiku (09:36:14) (in thread): > Yeah@Bolanle Wahabwas their like a digestive issue because I know prebiotics usually aid digestion. There would be a reason the diet is being supplemented and that would be the condition

Scholastica Urua (09:36:21) (in thread): > ‘Diet’ can be a condition. I’m not sure about the supplementation with prebiotics though.

Modinat Ganiyu (09:36:42) (in thread): > Thank you so much everyone! Your responses was really helpful:heart:

Bolanle Wahab (09:36:59) (in thread): > @Emem Eduokuyes, there’s a control groupThere’sno term for ’diet supplemented with prebiotics,I have tried that

Adedoja Isaac (09:37:04) (in thread): > Condition could be Mild digestive issues, occasional bloating, elevated cholesterol or constipation… Depends on aspect of health the study is focusing on.

idiaru Angela (09:38:20) (in thread): > @Emem EduokuI think one would since we’re not curating for beta diversity but let us wait for our mentors opinion

Modinat Ganiyu (09:38:51): > I have made my first contribution! Thank you so much everyone for being helpful:heart:. Unto the next step

Bolanle Wahab (09:38:53) (in thread): > @Barakat Akinsikunot atall, they simply just explored the gut health of the subject

Aleru Divine (09:39:34) (in thread): > Yoo hoo:confetti_ball::partying_face::partying_face::partying_face::clap::clap:congrats@Modinat Ganiyu

Nana (09:39:50): > @Modinat Ganiyunext level is to go and request for a paper on GitHub and wait until assigned to you then you start curation

Bolanle Wahab (09:39:59) (in thread): > @Scholastica Uruayou’reright butI’vebeen reluctant cause itdoesn’treally explain the condition

idiaru Angela (09:40:04) (in thread): > Congratulations@Modinat Ganiyu

Nana (09:40:55): > @Chioma Onyidodo we record observed in alpha diversity.

Modinat Ganiyu (09:41:24) (in thread): > Please how do I go about that@NanaKindly explain pls

Bolanle Wahab (09:42:11) (in thread): > @Adedoja Isaachttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548677/This is the article, itwasn’tspecific about any condition, you can check just to be sure,thanks - Attachment (PubMed Central (PMC)): Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics > The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited. The aims of this study were to investigate associations between variation in taxonomical …

Adedoja Isaac (09:47:35) (in thread): > Okay@Bolanle Wahab. I will read through the study

Aleru Divine (09:48:46) (in thread): > @Nanawe’re to record increased, decreased or unchanged. > > I don’t know if I got to question right. > > Do you mean Observed OTUs? > > Then yes, it’s the same as Richness.

Desire Oluwarotimi (09:54:32) (in thread): > Hi@NanaYes, you are to record all information on alpha diversity (increased, decreased or unchanged) but not beta diversity.

Adenike Oladimeji-Kasumu (09:55:27) (in thread): > @Nana, yes, all observations in regards to Alpha diversity are to be recorded.

Barakat Akinsiku (09:57:39) (in thread): > @Bolanle WahabI see what you mean. Maybe like Scholastica said ‘diet’ may be the best bet. Let’s see if there’ll be a better suggestion

NWAKAEGO VINCENT (10:10:44): > what is the next line of action to carry out i just finished my second task

Adedoja Isaac (10:11:36) (in thread): > @Bolanle WahabYou’re right, while the fish weren’t necessarily diseased, they also weren’t in a neutral state regarding their gut health. The most accurate condition in this study should be “Diet” like@Scholastica Uruasaid.

Modinat Ganiyu (10:13:22) (in thread): > Congratulations@NWAKAEGO VINCENT

Bolanle Wahab (10:13:30) (in thread): > @Adedoja Isaac@Scholastica Urua@Barakat Akinsikuthank you

Nana (10:14:13): > @NWAKAEGO VINCENTgo to bugsigdb documentation and help and read you will see what to work on while you wait

Modinat Ganiyu (10:15:02) (in thread): > Welcome@Success Ologunsua. Go through this link to get startedhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

NWAKAEGO VINCENT (10:16:09): > thank you@Nana, do i need to submit it for review?

Scholastica Urua (10:16:19) (in thread): > Hi@NWAKAEGO VINCENTafter finishing your second task, you wait for the mentors to review and grade it. You can comment on the GitHub issue to let the mentors know you want your work to be reviewed. > > While waiting for grading, here is some ways you can help out with BugSigDB: > * Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > * Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > * See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents

Emem Eduoku (10:16:42) (in thread): > Hopefully there can be some clarity to this

Adenike Oladimeji-Kasumu (10:17:10): > Hello everyone. Please@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI need your help to delete Signatures 1 and 2 in my curation. Here is the link:https://bugsigdb.org/Study_909. I need to re-enter the signatures. Thank you. - Attachment (BugSigDB): Differences in the Composition of Gut Microbiota between Patients with Parkinson’s Disease and Healthy Controls: A Cohort Study - BugSigDB > Gut microbiome and colonic inflammation can be associated with the predisposition and progression of Parkinson’s disease (PD).The presented study aimed to compare gastrointestinal microbiota composition between patients diagnosed with PD and treated only with Levodopa to healthy controls.

Nana (10:18:30) (in thread): > No

Ikeh Darlington Ikeh (10:22:46) (in thread): > Hi Latifat and welcome, also check the videos from BugSigDB on how to add a study.https://www.youtube.com/watch?v=yfpnwxefLFc&t=2s - Attachment (YouTube): Adding a study to bugsigdb.org

Nana (10:26:28) (in thread): > @Chioma Onyido@Aleru Divine@Desire Oluwarotimihere is the trick : Please which is correct from the image here are > My first thought Day 0 has higher Shannon evenness and Simpson diversity indices. Day 15 and Day 30, there was a significant decrease in these indices. Observed and Faith increased across in Day 0, 15 and 30 > OR > My second thought Day 0 has decrease Shannon evenness and Simpson diversity indices. Day 15 and Day 30, there was a significant decrease in these indices too. Observed and Faith increased across in Day 0, 15 and 30 - File (JPEG): Screenshot_2024-03-09-16-24-05-57_99c04817c0de5652397fc8b56c3b3817.jpg

Adenike Oladimeji-Kasumu (10:29:22) (in thread): > Also,@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeand everyone, Kindly help check Page 10 of my Paper,https://pubmed.ncbi.nlm.nih.gov/34884399/The Bacteria species were noted for PD with known disease vs control and for PD without known disease vs Control. My issue is how to Curate for the abundance (increase and decrease) of the Signatures. And to ask, this figure 6 implies that I will have two experiments in my Curation. Right? - Attachment (PubMed): Differences in the Composition of Gut Microbiota between Patients with Parkinson’s Disease and Healthy Controls: A Cohort Study - PubMed > Gut microbiome and colonic inflammation can be associated with the predisposition and progression of Parkinson’s disease (PD). The presented study aimed to compare gastrointestinal microbiota composition between patients diagnosed with PD and treated only with Levodopa to healthy controls. In this p …

Desire Oluwarotimi (10:35:02) (in thread): > @Adenike Oladimeji-KasumuIf what you want to do is re-enter the signatures, there might not be the need to delete them instead you could just edit.

Ikeh Darlington Ikeh (10:35:45): > Hello Team, in my article, sequencing type and platform were not specified, should I leave it blank?

Adenike Oladimeji-Kasumu (10:37:18) (in thread): > Oh… Good. I didn’t think of that. Thank you@Desire Oluwarotimi

Aleru Divine (10:38:00) (in thread): > @NanaReally tricky.ButI think the second interpretation aligns more closely with what you highlighted .The Shannon evenness and Simpson diversity indices decrease over time (from Day 0 to Day 15 and Day 30)

Adenike Oladimeji-Kasumu (10:38:19) (in thread): > I still need help with my second issue though before I can proceed.

Desire Oluwarotimi (10:39:39) (in thread): > @NanaI think Day 0 had a higher alpha diversity but as the days went by, the alpha diversity decreased. > > However sharing Figure 1A might shed more light.

Scholastica Urua (10:39:46) (in thread): > I think if you should leave blank if not specified

Mildred Anashie (10:41:12) (in thread): > Hi@Nanasome papers present Observed as specie richness > > Might be the case here

Bolanle Wahab (10:41:19) (in thread): > @Ikeh Darlington Ikehyou should probably leave it blank but you could send your article just to be sure.

Desire Oluwarotimi (10:41:38) (in thread): > @Ikeh Darlington IkehIf it really isn’t specified, then I think you should.

Nana (10:41:50) (in thread): > Ok. This link will take you to GitHub hope you have an account already:https://github.com/waldronlab/BugSigDBcuration/issues?page=2&q=is%3Aissue+is%3Aopen

Nana (10:42:55) (in thread): > Then look for a paper that has march 2024 paper to curate and request for it. Do not request the paper someone else indicated interest in. Then the mentor will assign the paper to you

Nana (10:47:13) (in thread): > @Desire Oluwarotimiimage as requested - File (JPEG): Screenshot_2024-03-09-16-46-43-28_99c04817c0de5652397fc8b56c3b3817.jpg

Ikeh Darlington Ikeh (10:50:18) (in thread): > Ok, here’s a link to the articlehttps://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-021-01589-0also please help me confirm if this table in the screenshot below provides data for either “cofounders controlled for” or “matched on” as there is no statement in the article that infers for this fields. - Attachment (BioMed Central): Evaluation of fecal microbiota transplantation in Parkinson’s disease patients with constipation - Microbial Cell Factories > Parkinson’s disease (PD) is a neurodegenerative disorder and 70–80% of PD patients suffer from gastrointestinal dysfunction such as constipation. We aimed to assess the efficacy and safety of fecal microbiota transplantation (FMT) for treating PD related to gastrointestinal dysfunction. We conducted a prospective, single- study. Eleven patients with PD received FMT. Fecal samples were collected before and after FMT and subjected to 16S ribosomal DNA (rDNA) gene sequencing. Hoehn-Yahr (H-Y) grade, Unified Parkinson’s Disease Rating Scale (UPDRS) score, and the Non-Motion Symptom Questionnaire (NMSS) were used to assess improvements in motor and non-motor symptoms. PAC-QOL score and Wexner constipation score were used to assess the patient’s constipation symptoms. All patients were tested by the small intestine breath hydrogen test, performed before and after FMT. Community richness (chao) and microbial structure in before-FMT PD patients were significantly different from the after-FMT. We observed an increased abundance of Blautia and Prevotella in PD patients after FMT, while the abundance of Bacteroidetes decreased dramatically. After FMT, the H-Y grade, UPDRS, and NMSS of PD patients decreased significantly. Through the lactulose H2 breath test, the intestinal bacterial overgrowth (SIBO) in PD patients returned to normal. The PAC-QOL score and Wexner constipation score in after-FMT patients decreased significantly. Our study profiles specific characteristics and microbial dysbiosis in the gut of PD patients. FMT might be a therapeutic potential for reconstructing the gut microbiota of PD patients and improving their motor and non-motor symptoms. - File (PNG): image.png

idiaru Angela (10:52:07) (in thread): > But you need to inform the mentors before making any changes or edits@NWAKAEGO VINCENT

idiaru Angela (10:53:16) (in thread): > @Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther Afuape

Desire Oluwarotimi (10:55:34) (in thread): > @Adenike Oladimeji-KasumuI couldn’t find anything like the groups you listed above. PD with known disease and PD without known disease. > > The only thing I saw was PD patients and Healthy controls indicating a single experiment. > > You can further point it out if you think I’m missing something.

Okache Johnpaul (10:55:42) (in thread): > This clears up my confusion! Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (10:56:52) (in thread): > I think this should be interpreted as richness@Nana

Adenike Oladimeji-Kasumu (11:00:29) (in thread): > Oh… Good. I didn’t think of that. Thank you@Desire OluwarotimiThere are actually two groups. Check figure 6. PD with known diseases e.g diabetes and the likes and then PD without known diseases. It’s in the introduction also.

Nana (11:01:13) (in thread): > @Mildred Anashiedid you open the image

Nana (11:02:32) (in thread): > @Desire Oluwarotimimy paper mentioned alpha diversity twice separately here is the image which do I record now - File (JPEG): Screenshot_2024-03-09-17-01-34-37_99c04817c0de5652397fc8b56c3b3817.jpg - File (JPEG): Screenshot_2024-03-09-17-01-27-17_99c04817c0de5652397fc8b56c3b3817.jpg

Desire Oluwarotimi (11:05:34) (in thread): > @NanaI’m not sure the details you are looking for can be found in that image. > > Check in between texts in your article. You should lay hands on something.

Mildred Anashie (11:07:29) (in thread): > Yes@NanaI opened the image and I see that the article referred to Observed as specie richness > > You could share a link to the paper though

Bolanle Wahab (11:10:14) (in thread): > @Ikeh Darlington Ikehthe sequencing type is 16S rDNA, you can find it here. > The platform wasn’t specified but it’s most likely illumina cause 16S commonly uses that, but you could leave it blank. - File (JPEG): IMG_9581

Muqtadirat Yussuff (11:12:19) (in thread): > Like@Bolanle Wahabsaid, it is 16S and for the platform, you can search for the keyword “Illumina” just to be sure if not leave it blank

Ikeh Darlington Ikeh (11:15:03) (in thread): > Thank you@Bolanle WahabOfcourse, I saw the Sequencing type to be 16S rDNA. But I meant the sequencing type 6S variable region (lower bound) and (upper bound) were not specified. If to leave it blank.

Bolanle Wahab (11:17:18) (in thread): > @Ikeh Darlington Ikehoh, your questiondidn’tsay variable but yeah, it says to leave it blank on the form if not needed.

Muqtadirat Yussuff (11:18:27) (in thread): > Does your paper mention the base pair range? You can use that to figure out the V region

Ima-obong (Aimah) (11:18:53) (in thread): > Yes..if the V- region is not stated, please leave it blank

Ikeh Darlington Ikeh (11:18:56) (in thread): > Yeah, my bad. Thank you so much@Bolanle Wahaband@Muqtadirat Yussuff

Ikeh Darlington Ikeh (11:20:06) (in thread): > base pair range? Don’t think i saw anything like that@Ima-obong (Aimah)let me recheck and confirm

Ikeh Darlington Ikeh (11:24:09) (in thread): > @Ima-obong (Aimah)No, it didn’t mention base pair range anywhere in the paper

Ima-obong (Aimah) (11:25:23) (in thread): > Alright then.. leaving it bank is a safe option.

Ikeh Darlington Ikeh (11:29:55) (in thread): > Thanks everyone. I appreciate your contributions; they are very useful.

Ikeh Darlington Ikeh (11:30:19): > Hi can anyone help me confirm if this table in the screenshot below provides data for either “cofounders controlled for” or “matched on” as there is no statement in the article that infers for this fields. > > link to article belowhttps://microbialcellfactories.biomedcentral.com/articles/10.1186/s12934-021-01589-0 - File (PNG): image.png

Aleru Divine (11:35:13) (in thread): > Hi@Ikeh Darlington Ikehit doesn’t provide data for either one of them. If there was no statement then it means there was no confounder controlled for and there was no “matched on” criteria.

Ikeh Darlington Ikeh (11:37:26) (in thread): > @Aleru DivineThank you.

Aleru Divine (11:37:44) (in thread): > You’rewelcome:hugging_face:

Adedoja Isaac (11:41:13) (in thread): > @Adenike Oladimeji-KasumuBased on the image in your study, which appears to be Figure 6, the key difference between Panel A and Panel B lies in the health status of the Parkinson’s disease (PD) patients being compared with the healthy control group. Here’s a breakdown: > > Panel A: > > PD Patients: This panel focuses on PD patients who also have other diagnosed diseases like hypertension or diabetes (written as “comorbidities” in the legend). > > And to the focus: It analyzes the differences in gut microbiota composition between PD patients with comorbidities and healthy controls. > > Panel B: > > PD Patients: This panel focuses on PD patients diagnosed only with PD, with no other known diseases. > > The focus too: Analyses the differences in gut microbiota composition between PD patients without comorbidities and healthy controls.

Barakat Akinsiku (11:41:22): > Hi everyone, please I’m trying to confirm if it’s okay to create 3 experiments from this data? No alpha diversity is specified but there are enriched OTU’s found across 3 separate contrasted groups: healthy vs Sg-affected, healthy vs Kidney with calcification and healthy vs sick( where sick is composed of both sg-affected and kidney with calcification) - File (PNG): s.png - File (PNG): s1.png - File (PNG): s2.png - File (PNG): s5.png

Nana (11:47:39) (in thread): > Ok

Mojisayo Awolesi (11:51:52): > Hello everyone, > So I’m done with my second contribution, here’s thelink, I’d appreciate your reviews. > Is there anything else I should be doing after completing my curation? - Attachment (BugSigDB): Dysbiosis of gut microbiota in a selected population of Parkinson’s patients - BugSigDB > INTRODUCTION: In recent years the hypothesis that gut microbiota associates with Parkinson’s disease (PD) has gained importance, although it has not been possible to define a specific microbiota composition as a predictive biomarker of this disease.

Amanda Adoyi (11:52:49) (in thread): > While there isn’t any such statement in the table, you should probably take the time to carefully comb through the text incase it was inferred but you probably missed it.

Grace Paul (11:55:10): > Hello everyone, in the case where alpha diversity was mentioned to have no significant alterations but the values were not given…do I just leave that section untouch? Or what do I do?

Desire Oluwarotimi (11:55:53) (in thread): > Hi@Adenike Oladimeji-KasumuPlease pay attention to the explanation@Adedoja Isaacgave. > > I was wrong. My apologies.

Adenike Oladimeji-Kasumu (11:56:50) (in thread): > Thank you@Adedoja IsaacYes, I got that. So does that mean I am recording 2 experiments? > Also, how do I identify the abundance (decrease and increase) in the PD patients for my signatures according to Figure 6? > Kindly help.

Desire Oluwarotimi (11:59:52) (in thread): > Hi@Grace PaulI think that would mean that it was unchanged.

Grace Paul (12:03:19) (in thread): > So am I to mark every section I.e Pielou, Shannon, Chao1, Simpson, inverse Simpson, Richness and Faith as unchanged?

Nana (12:04:53) (in thread): > You can’t request a paper some else is working on, and that is exactly what you did, it won’t be assigned to you

Nana (12:05:25) (in thread): > Use unchanged

Nana (12:06:33) (in thread): > @Peace Sandyabout the sequencing platform I didn’t hear from you again

Nitya Singhal (12:06:50) (in thread): > Kindly help@Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account)

Scholastica Urua (12:12:15) (in thread): > Hi@Grace Paulif all the diversities were mentioned i.e Pielou, Shannon, Chao1, Simpson, inverse Simpson, Richness and Faith to be ‘not significant’ then you can mark all as unchanged. If not, just mark the ones that were mentioned in the paper.

Grace Paul (12:14:00) (in thread): > That’s the thing. None was mentioned in the paper.

Grace Paul (12:15:17) (in thread): > I ve checked the supplementary material in the future where it was mentioned but didn’t find any. I’m about to download the pdf containing the entire supplementary materials, hopefully I find at least one

Scholastica Urua (12:18:09) (in thread): > In my opinion if non was mentioned, you can leave it blank.

Amanda Adoyi (12:19:04) (in thread): > @Grace PaulYou did mention that alpha diversity was left unchanged. Shannon and Simspon values are measures of that quantity so I’m not sure none was mentioned.

Nitya Singhal (12:23:39): > I read about Alpha Diversity on Google, but I wonder if my study has any Alpha Diversity. Could you help me with this?https://www.nature.com/articles/s41531-023-00554-5#citeas - Attachment (Nature): Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease > npj Parkinson’s Disease - Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease

Mariam Hammed Gambina (12:27:37): > Hello all, I am having a little challenge on this part of the project in the first survey. > How do I go about this below. > Using this site, search for a differentially abundant bacteria from the study. Find the identifier for the result that best matches the name of the bacteria and enter the information below. (Hint: From the search results look carefully for the one that most closely matches the taxa in the study) > > Taxa name (firmicutes) > NCBI taxanomy ID (4 -6) > RANK OF BACTERIA (GENUS)

Grace Paul (12:30:56) (in thread): > Okay thanks everyone….i found a chao1 plot in the supplementary pdf. So I think chao1 is the only one I should mark as unchanged because no other can be found anywhere else.

idiaru Angela (12:31:23) (in thread): > You are to check the annotated article for a bacteria that was said to be differentially abundant > (The table is an easy way to check for this) then follow the link to the site and search for the bacteria. > Then from the information on the site you’d input the > Taxa name > The taxonomy ID > Then the rank > All three information can be found on the site

Grace Paul (12:34:29) (in thread): > You need to look out for anywhere (Pielou, Shannon, Chao1, Simpson, inverse Simpson, Richness and Faith) is mentioned

Adedoja Isaac (12:36:51) (in thread): > Check the article for the bacterias and find the one that is very abundant in the study. Then use NCBI Taxonomyhttps://www.ncbi.nlm.nih.gov/taxonomyto check for those details. > > You’d see it at the top of the page after the search

Ikeh Darlington Ikeh (12:39:26): > Hi please I need a little clarification. From the screenshot below, am I supposed to input increased or decreased in the “alpa diversity” and “abundance in group 1” fields? Reason for confusion here is it states, > > “Significant differences in the diversity indexes were observed, not only between the pre-FMT and 12 weeks after FMT (P < 0.01; Fig. 2a, b) but also between pre-FMT and HCs (P < 0.01; Fig. 2a, b). The species diversity and the pattern of the richness of preFMT PD patients weresignificantly decreasedcompared to 12 weeks after FMT and HCs (P<0.05)” > > I am comparing Group 0 (Healthy Control) and Group 1(preFMT) - File (PNG): image.png

Mildred Anashie (12:47:04) (in thread): > Richness is decreased from the excerpt

Mildred Anashie (12:47:54) (in thread): > I actuallyhaven’tcome across any in this paper@Nitya SinghalbutI’llkeep checking

Adedoja Isaac (12:48:06) (in thread): > Hi@Nitya SinghalThe study likely doesn’t directly analyze alpha diversity of the gut microbiota in essential tremor (ET) patients. > > Alpha diversity measures the richness (number of species) and evenness (abundance distribution) of bacteria, Shannon, pielou and others… within a single sample. This study focuses on the levels of specific Short-Chain Fatty Acids (SCFAs) produced by gut bacteria, not the overall diversity of the bacterial community itself. > > And like@Grace Paulsaid, if you use the Ctrl + F to look for those terms, you can further confirm.

Mildred Anashie (12:52:27) (in thread): > @Adedoja IsaacThe footnote of that figure explains it > > Red bar plots indicates increase in the control group which means decrease for the PD group and Blue bar plots shows increased signatures for the PD group (whichI’mguessing is your group 1)

Aleru Divine (12:52:42) (in thread): > @Ikeh Darlington IkehSignificant differences were observed in the diversity indexes between PD patients (before and after FMT). > > The species diversity and richness of gut microbiota in PD patients before FMT were significantly lower compared to both 12 weeks after FMT and healthy controls. > > It decreased.

Adedoja Isaac (12:58:08) (in thread): > The text states that the “species diversity” and “richness” of pre-FMT PD patients (Group 1) were significantly decreased compared to healthy controls (Group 0). This indicates lower alpha diversity in Group 1.

Mildred Anashie (12:58:58) (in thread): > Hi@Barakat AkinsikuYes there are three groups but itdoesn’tnecessarily translate to 3 experiments unless you have statistically significant results for the contrasts you are proposing

Ruth Bamgbose (13:09:39): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeplease I need to delete signature 3 & 4 of experiment 2 on my study. Thank youhttps://bugsigdb.org/Study_881 - Attachment (BugSigDB): Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls - BugSigDB > Posttraumatic stress disorder (PTSD) imposes a significant burden on patients and communities.

Adenike Oladimeji-Kasumu (13:12:25) (in thread): > @Mildred AnashieYes. The footnote gave an explanation. Are you saying, I should not be curating any Decreased abundance since it only shows increase? > Because that’s what I think I just need to be sure. That is I will be adding only one signature. Right?

Barakat Akinsiku (13:12:29) (in thread): > Thank you@Mildred AnashieSo should I curate as one and have three signatures for the three different groups? Please look through the article to see if one experiment is the way to go or three - File (PDF): Pavloudi.et.al (1).pdf

Mildred Anashie (13:18:25) (in thread): > No > > I’m saying the red bar plots are the decreased signatures and the blue increased signatures > > You will be having both increase and decrease signatures

Adedoja Isaac (13:18:50) (in thread): > Okay

Adedoja Isaac (13:19:33) (in thread): > Yes,@Mildred Anashie. You’re right > Was also mentioned in the study material

Adenike Oladimeji-Kasumu (13:21:49) (in thread): > @Mildred AnashieThe red Bar plot represents the Healthy Controls while the the Blue Bar plot represents the PD patients. > Or is there something I’m not understanding? Please help me explain

Adenike Oladimeji-Kasumu (13:23:56) (in thread): - File (JPEG): Screenshot_20240309-192243.jpg

Samreen Aftab (13:26:22): > Hello everyone, if my paper has no mention of LDA score, should I put the standard value or should I leave it blank?

Mildred Anashie (13:27:28) (in thread): > Okay so you know your > Group 0 = Healthy controls > Group 1 = PD patients > > And this is so for both experiments except the PD also has with other diseases and without other diseases > > So the blue bar plots are increased in the PD group and the Red increased in the HC group > > The signatures that are increased in the HC group is translating to a decrease in the PD group and we only record increase and decrease for Group 1 so we have to record the increased signatures for group 1 and the ones that were not increased in Group 1(Increased in Group 0) > > Isaac has pointed out thatit’s withintext, I think you should read within results text to confirm this

Aleru Divine (13:28:04) (in thread): > Did LEfSe test for the differential abundance? If yes then put the default value which is 2.

Eniola Adebayo (13:28:35) (in thread): > Use the standard LDA score which is 2 for a LEFSE analysis. I asked this question in the last office hour.@Samreen Aftab

Samreen Aftab (13:30:11) (in thread): > @Aleru Divinenope, no mention of LEfse test either

Aleru Divine (13:30:35) (in thread): > Then it’s okay to leave it blank.@Samreen Aftab

Chioma Onyido (13:31:02) (in thread): > Please go ahead, and you can share with a peer to help you review when you’re done curating.

Adenike Oladimeji-Kasumu (13:31:47) (in thread): > Alright. Thank you. I will read the material again. > I appreciate you both@Mildred Anashieand@Adedoja Isaac

Scholastica Urua (13:32:01) (in thread): > If there’s no mention of LeFse, then you can leave it blank@Samreen Aftab

Scholastica Urua (13:32:38) (in thread): > Thank you@Chioma Onyido

Chioma Onyido (13:33:02) (in thread): > Have you been able to download it now?

Samreen Aftab (13:33:27) (in thread): > @Aleru Divinecan you review my paper please?

Aleru Divine (13:34:01) (in thread): > Yes please tag me @AleruDivine

Scholastica Urua (13:35:15) (in thread): > Yes, I’ve been able to download the PDF but the article keeps making reference to a supplementary data which I can’t find.

Chioma Onyido (13:40:07) (in thread): - File (PDF): Supplementary File.pdf

Aleru Divine (13:41:02) (in thread): > @Samreen Aftabseen.Would review in a minute

Chioma Onyido (13:41:30) (in thread): > Done.:white_check_mark:

Ruth Bamgbose (13:45:07) (in thread): > @Chioma OnyidoThank you so much.

Samreen Aftab (13:45:37) (in thread): > @Aleru Divineokay, thank you!

Scholastica Urua (13:46:21) (in thread): > Thank you so much for this:pray:

Evelyn Mary Attah (13:49:31): > Hello@Nitya Singhal, the name of the disease on the article am curating is not coming up for me to enter the condition for my form. Do you have any suggestions on how to go about this?

Samreen Aftab (13:53:58) (in thread): > Can you share your article please?

Scholastica Urua (13:57:51) (in thread): > Hello@Chioma Onyidoplease kindly confirm that the supplementary file is for the article above. The article is focused on ‘The sputum microbiome and clinical outcomes in patients with bronchiectasis’. This seems to be different from the supplementary file. > Looking forward to your response.

Scholastica Urua (13:59:24) (in thread): > Hello@Evelyn Mary Attahyou can always use this link;https://www.ebi.ac.uk/ols4/ontologies/efoto find a term. - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Mildred Anashie (14:01:13) (in thread): > Okay@Barakat AkinsikuI’llgo through it as well

Temi (14:03:23) (in thread): > Hihere’sthe link to my workhttps://bugsigdb.org/Study_894 - Attachment (BugSigDB): Hair Microbiome Diversity within and across Primate Species - BugSigDB > Primate hair and skin are substrates upon which social interactions occur and are host-pathogen interfaces.While human hair and skin microbiomes display body site specificity and immunological significance, little is known about the nonhuman primate (NHP) hair microbiome.

Chioma Onyido (14:06:50) (in thread): > Hi@Naomi IbeThank you for working on this. Before you proceed, I’m curious, is there a specific reason why you think they’re the same? If so, please share sources.

Abiola Salako (14:13:09) (in thread): > Yes, Leave it blank if no Lefse was mentioned,@Samreen Aftab

Chioma Onyido (14:15:52) (in thread): > You’re right, that’s not the right supp file for this study. > I don’t see anywhere making ref to a supp file within this article’s text. Or could you point me to it?

Chioma Onyido (14:16:27) (in thread): > Looks to me like all curatable details are there,

Abiola Salako (14:22:07) (in thread): > Yes, You can, it updates itself automatically after saving the page@Samreen Aftab

Abiola Salako (14:23:05) (in thread): > @Aleru DivineThank you

Peace Sandy (14:23:24) (in thread): > @Adenike Oladimeji-Kasumushould I still delete signatures 1 and 2

Adenike Oladimeji-Kasumu (14:24:32) (in thread): > @Peace SandyPlease leave it for now since I’ve been told that I can edit it instead. I will let you know if I still want to delete them. > I appreciate your response.

Abiola Salako (14:24:38) (in thread): > @Muqtadirat Yussuffhave you been able to resolve this?

Abiola Salako (14:25:01) (in thread): > Welcome@Joy Gold

Abiola Salako (14:26:53) (in thread): > @Leenaa Al-Aminyou can tag me to your work on Github @ Abiola-Salako

Isoken Ibizugbe (14:28:14) (in thread): > Probably network problems, it did same for me when I had unstable internet connection

Mildred Anashie (14:28:33) (in thread): > Hi@Evelyn Mary AttahType the condition in the site Scholastica shared and search for the closest term and enter it on BugSigdb

Abiola Salako (14:29:00) (in thread): > @Latifathave you been able to find your way around it yet?

Abiola Salako (14:35:09) (in thread): > @Amanda, don’t forget to have at least a Co-Contributor review before finally tagging@Svetlana Ugarcina Perovicfor review.

Abiola Salako (14:36:53) (in thread): > @Esther Afuapekindly help with this. Thank you.

Abiola Salako (14:38:41) (in thread): > You’re welcome@Preethi grace Manthena:saluting_face:

Abiola Salako (14:39:25) (in thread): > Welcome@Success Ologunsua

Amanda Adoyi (14:39:50) (in thread): > @Abiola Salakoyea. Def not forgetting that.

Abiola Salako (14:40:57) (in thread): > You’re welcome@Samreen Aftab

Abiola Salako (14:44:14) (in thread): > @NanaWere you able to resolve this?

Isoken Ibizugbe (14:44:16): > Can someone please help me review my workhttps://bugsigdb.org/Study_934 - Attachment (BugSigDB): Gut microbiota are related to Parkinson’s disease and clinical phenotype - BugSigDB > In the course of Parkinson’s disease (PD), the enteric nervous system (ENS) and parasympathetic nerves are amongst the structures earliest and most frequently affected by alpha-synuclein pathology.

Adenike Oladimeji-Kasumu (14:48:50) (in thread): > @Isoken IbizugbeI’ll check through your work and let you know my observations. Our other colleagues have helped a lot with reviewing mine so I can also help others:hugging_face:

Isoken Ibizugbe (14:49:29) (in thread): > Thanks, I’d appreciate that

Abiola Salako (14:50:26) (in thread): > Yes@Mojisayo AwolesiHi@NWAKAEGO VINCENTafter finishing your second task, you wait for the mentors to review and grade it. You can comment on the GitHub issue to let the mentors know you want your work to be reviewed. > > While waiting for grading, here is some ways you can help out with BugSigDB: > * Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > * Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > * See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Abiola Salako (14:53:47) (in thread): > Well done@Adenike Oladimeji-Kasumu@Isoken Ibizugbeyou can tag me your issue on GitHub @Abiola - Salako

Isoken Ibizugbe (14:54:15) (in thread): > Ok I will

Abiola Salako (14:54:33) (in thread): > Well done@Amanda Adoyi

Amanda Adoyi (14:55:47) (in thread): > Thanks :)

Desire Oluwarotimi (15:02:23): > How has it been going guys? > > Is there anyone who still wants a review??

Scholastica Urua (15:08:42) (in thread): > There’s a recurring reference to an appendix which can’t be found on the main article. - File (PNG): Screenshot_20240309-203747.png

Amanda Adoyi (15:17:55): > Just a thought that came to me…I think that if you think it matters and you are reviewing a person’s work you should probably take your time and do a quality review of it that could help you both; perhaps focus less on making too many reviews for the sake of it instead of actually really reading the Study and curation. Buonanotte…maybe.

Ruth Bamgbose (15:19:55) (in thread): > Hi, I would love a reviewhttps://github.com/waldronlab/BugSigDBcuration/issues/124.Thanks.I can also review yours too if you want - Attachment: #124 Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls > Exploring the relationship between the gut microbiome and mental health outcomes in a posttraumatic stress disorder cohort relative to trauma-exposed controls – Stefanie Malan-Muller et al. – European Neuropsychopharmacology 2022 > > https://www.sciencedirect.com/science/article/abs/pii/S0924977X21016539 > > NOTE: This paper is without open access, here is downloaded pdf: Exploring-the-relationship-between-the-gut-microbiome-and-m_2022_European-Ne 2.pdf

idiaru Angela (15:20:20) (in thread): > I definitely agree with you > A quality review is definitely much better

Desire Oluwarotimi (15:23:05) (in thread): > Hi@Ruth BamgboseSure, let’s hop on it.

Blessing Ene Anyebe (15:24:45) (in thread): > You are on point.That’swhyit’sbetter not to gather so much projects to review. (With this approachyou’llbe focused on giving at leastacontribution to someone -instead of giving a lot.) > > I really agree-it also reinforces the mantra ofquality over quantity.

Modinat Ganiyu (15:55:30): > Hello! Please do you know if I can start the second contribution after commenting under the issue on github while@Svetlana Ugarcina Perovichasn’t assigned it to me just yet?

Mildred Anashie (15:56:06) (in thread): > Hi@Modinat Ganiyuyou can

Blessing Ene Anyebe (15:56:18) (in thread): > I think you can start your research while you wait approval

Amanda Adoyi (15:56:44) (in thread): > I think it’s advisable to have the go ahead and be assigned. Nonetheless you can peruse the paper. Some really interesting stuff here.

Blessing Ene Anyebe (15:56:45) (in thread): > So yes get started, as long as you confirmthat it hasn’tbeen assigned to someone else

Mildred Anashie (15:56:54) (in thread): > It will be assigned to you if you are the first person to comment > It will eventually be assigned to you

Modinat Ganiyu (15:59:30) (in thread): > Thanks for your responses but it has already been assigned to few people

Muqtadirat Yussuff (16:01:41) (in thread): > @Abiola Salakonot really, can I get your thoughts on it?

Muqtadirat Yussuff (16:02:15) (in thread): > Then do not curate

Modinat Ganiyu (16:02:21) (in thread): > Oh! Does that mean I can’t work on a project that has already been assigned to someone?

Muqtadirat Yussuff (16:03:08) (in thread): > Look for an open issue or go through the help section on BugSigDB for tasks you can do. However before you make changes in the database inform the mentors to receive a go ahead

Muqtadirat Yussuff (16:03:30) (in thread): > @Modinat Ganiyuyes, you can’t work on papers that have been assigned

Modinat Ganiyu (16:25:32) (in thread): > Thank you all for your responses

Modinat Ganiyu (16:33:21): > Please I need help. I don’t seem to see papers that aren’t assigned to anyone on github. All issue has the assign tag. Please how can I get one

Mildred Anashie (16:41:01) (in thread): > Let me check it out > > But ifit’sthe case that all the papers are assigned we’d have to inform the mentors to upload more

eneje promise (16:45:55): > Hello everyone, how do I get a second task to contribute to?

Mildred Anashie (16:46:38) (in thread): > Are you asking about a second contribution?

Modinat Ganiyu (16:47:48) (in thread): > please help me, thanks

Mildred Anashie (16:53:08) (in thread): > You are right, i didn’t come across any unassigned issues….We could tag the mentors to inform them@Esther Afuape@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy

eneje promise (16:53:15) (in thread): > @Mildred Anashieyes

Mildred Anashie (16:54:32) (in thread): > You are to comment on an issue on GitHub and asked it be assigned to you > > You start working on it onceit’sassigned

Mildred Anashie (16:55:09) (in thread): > But they are no available issuescurrently,you would have to be patient till the mentors upload more

Modinat Ganiyu (16:58:00) (in thread): > Thank you so much@Mildred Anashie

Abiola Salako (17:00:20) (in thread): > @Muqtadirat YussuffBased on the excerpts you provided, it seems that there are conflicting findings regarding the abundance of Streptococcus bacteria after feeding. While one text suggests an increase in representation immediately after postfeeding, another text mentions a decrease in representation after feeding. Therefore, it appears that both trends are observed in different parts of the study. So what do we do?@Esther Afuape, what do you think, please?

Modinat Ganiyu (17:02:30): > @Svetlana Ugarcina PerovicPlease upload more issues, all issues I see are been assigned and I’m yet to claim one. Thank you!

Peace Daniel (17:03:38) (in thread): > I’msure they will,you have to be patient

Peace Daniel (17:03:43) (in thread): > Plusit’sa weekend

eneje promise (17:15:58): > @Svetlana Ugarcina Perovickindly upload more issues, as all issues have been assigned. Thank you

Aishat Ijiyode (17:23:26) (in thread): > @Ajayi Mercysee this to help you get started

Mariam Hammed Gambina (17:59:14): > I just finished my first issue and I am ready for the second one.@Svetlana Ugarcina Perovic, I have requested an issue already.

Aishat Ijiyode (20:47:43): > How do I request for an issue please?

Amanda Adoyi (21:00:09) (in thread): > You head to the github repo and look at the issues that are tagged “paper to curate” with no “assigned” next to them, then open one of those and in the comment section, tag@Svetlana Ugarcina Perovic, requesting to be assigned to it.

Aishat Ijiyode (21:04:19) (in thread): > Okay I understand now, thank you. I thought it meant requesting for an issue when there’s no unassigned issue

Amanda Adoyi (21:06:35) (in thread): > If you can’t find any unassigned issues, you could bring that to the attention of@Svetlana Ugarcina Perovicor@Chioma Onyidoor@Peace Sandyor@Esther Afuapehere, on Slack.

Aishat Ijiyode (21:06:53) (in thread): > I have done my first contribution, is there a way to see it after submission? I tried to go through the curated form but it’s showing blank like I want to start again > I was wondering which link would be attached when submitting my contribution on Outreachy’s page

Amanda Adoyi (21:09:47) (in thread): > If you have finished and receive the “thank you for the survey” message or something like that, then I believe that means you’re done. You shouldn’t repeat it, you’ve submitted. Just make sure that when done you copy that link you found after you finished on the browser and paste it as the link to your first contribution in your Outreachy records.

Amanda Adoyi (21:13:16) (in thread): > If you paste the link on another browser tab it shows up as an empty form; don’t panic, your records are received…just use it.

Aishat Ijiyode (21:18:40) (in thread): > I don’t think I still have the link:disappointed_relieved:I’ll try to reopen all my closed tabs

Aishat Ijiyode (21:23:48) (in thread): > I can’t find the page again, but I got to the thank you for taking the survey page. I really hope it doesn’t affect

Amanda Adoyi (21:40:42) (in thread): > No not at all. You can get the link from comments here. Lemme get ithttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

USLACKBOT (21:52:28): > This message was deleted.

Scholastica Urua (22:00:31) (in thread): > Hi@Aishat Ijiyodehope you’ve been able to find your way?@Amanda Adoyihas been kind enough to drop the link.:+1:In addition to what has been said, I just want to point out that it’s the same link you click to fill the form. Everybody is filling out the same link. > > Don’t worry when the link brings up an empty form again because the mentors already have what they need since you already submitted.

Scholastica Urua (22:03:28) (in thread): > @Esther Afuapementioned earlier that you have to include the specific taxon/taxa and the ID you found so that the mentors can compare both.

Amanda Adoyi (22:04:56) (in thread): > Oh… thanks

Abiola Salako (22:32:20) (in thread): > You’re right @Amadi and it’s better to focus on just a section of the work so you don’t feel too overwhelmed by the whole thing.

Abiola Salako (22:36:10) (in thread): > Well done@Mariam Hammed Gambina

Abiola Salako (22:37:42) (in thread): > @eneje promise, more issues will get uploaded just be patient and remember it’s a weekend.

Muqtadirat Yussuff (23:50:06) (in thread): > @Abiola SalakoYeah that was my observation but I did settle for decreasing. Hopefully the mentors would give their insights@Peace Sandy

2024-03-10

Muqtadirat Yussuff (00:07:53): > Hi everyone, does this indicate confounders? I feel like I’ve been going back and forth on it. - File (JPEG): Screenshot_20240310-060458.jpg

Desire Oluwarotimi (00:11:10) (in thread): > Hi@Muqtadirat YussuffI don’t think anything in the image you’ve sent indicates confounders.

Muqtadirat Yussuff (00:12:11) (in thread): > Hi@Desire Oluwarotimifor you, what’s a definite indicator of confounders? I thought confounders are variables that are adjusted for?

Desire Oluwarotimi (00:33:56) (in thread): > Hmmmm. That’s a strong point. > > Can you share a link to the paper please?@Muqtadirat YussuffThat’ll help.

Samreen Aftab (00:40:41): > Hello everyone, do I need to wait for my second contribution to be reviewed before I can request another issue on github?

Muqtadirat Yussuff (00:42:59) (in thread): > Here’s the link, thank you. Although the image I initially shared is from the supplemental material, table 2. It can be found at the bottom of the paper’s linkhttps://onlinelibrary.wiley.com/doi/full/10.1002/ijc.34145

Desire Oluwarotimi (00:50:20) (in thread): > @Muqtadirat YussuffYes, you are right. > > The confounding factors are shared in the notes attached to table 2 and 3. There are about 8 or 9 of them

Desire Oluwarotimi (00:50:43) (in thread): > Thank you@Muqtadirat Yussuff

Muqtadirat Yussuff (00:52:28) (in thread): > @Desire OluwarotimiI’m not sure why I’m getting thanked:joy:but thank you so much for you time, that was really helpful

Desire Oluwarotimi (00:54:36) (in thread): > :joy:I said thank you because I could have easily missed that but your first response set things straight. So yeah, thank you.:+1:

Amanda Adoyi (01:04:58) (in thread): > I believe so. Reviewing another should likely not be the priority though. Use the time to help review work of co-collaborators or find NCBI taxonomy ids and ensure your contribution is as perfect as you can make it.

Mildred Anashie (01:16:51) (in thread): > Yes@Muqtadirat Yussuffage and others are Confounders controlled for in your study > > Confounders can be variables adjusted for > > I believe when they use the language “adjusted for” it is almost always using a model and the statistical test should be for e.g logistics regression model like your paper states > > Also I think some statistical tests and study designs make it difficult to control for confounders > My understanding of the term Confounders, adjusted for and the rest:smile:

Mildred Anashie (01:19:56) (in thread): > Well done Mariam > > From a few hours ago I believe there was no available issue you could request for > Please ensure the one you requested forhasn’tbeen assigned to anyone

Muqtadirat Yussuff (01:24:37) (in thread): > @Mildred AnashieThank you for your input, I actually did learn a bit more so thank you

Scholastica Urua (01:26:07) (in thread): > Yes@Samreen Aftab, your second contribution needs to be reviewed before requesting for another one. There are other was you can contribute to BugSigDB while you wait just like@Amanda Adoyimentioned.

Scholastica Urua (01:30:47) (in thread): > While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Leenaa Al-Amin (01:42:49) (in thread): > @Abiola Salakook i will

Modinat Ganiyu (01:46:01) (in thread): > Congratulations@Mariam Hammed GambinaMildred is right. I also checked but couldn’t find one unassigned issue. Please be sure the claimed one is unassigned

Ifeyinwa Ohondu (01:49:33): > Hi guys. i have a question about the signatures - are we entering both the genus and the species? Also what do we do when the taxa is not found on NCBI? And also when multiple IDs are shown? Example: A search for Erysipelatoclostridium shows multiple results and Ruminicoccus gnavus group doesn’t bring up any results.

Millicent Adzepa (01:56:36): > Hello Good morning everyone, please I need help with my account request, > I requested an account to start my second task, after filling the forms I waited for 2 hours without any confirmation link in my email, so I figured that I might have missed a letter in my email, then decided to request a new one which i got the confirmation within few minutes, clicked on the linked and it was successful. > I tried logging in and could not, so I requested for reset of password . then the attached email was sent. Please how do I go about it. @@Svetlana Ugarcina PerovicThank you - File (JPEG): WhatsApp Image 2024-03-09 at 9.26.33 PM.jpeg

Leenaa Al-Amin (03:01:44) (in thread): > Please could you review mine as well@Desire Oluwarotimihttps://journals.asm.org/doi/10.1128/spectrum.02311-21and here’s the link to the curationhttps://bugsigdb.org/Study_891 - Attachment (BugSigDB): Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome - BugSigDB > The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis.This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs.

Modinat Ganiyu (03:02:58) (in thread): > @Aishat Ijiyodedon’t feel bad. We are here to help each other out. It’s always like that at first but as we move on, we will begin to get a hang of it.@Amanda Adoyiand@Scholastica Uruahas been very helpful. And if you still encounter any challenge don’t hesitate to ask. But for now, I hope you’ve been able to record your first contribution?

Scholastica Urua (03:03:58) (in thread): > Hi Millicent, I don’t know much about this but from this email it seems your first account was approved.

Barakat Akinsiku (03:05:28) (in thread): > Hi Millicent, since you’ve already responded to the email, wait a while and then try logging in again to see if the account is now accessible

Scholastica Urua (03:05:31) (in thread): > The mentors will get back to you on this. It’s the weekend so you have to exercise some patience. > I hope it gets resolved soon:pray:.

Millicent Adzepa (03:07:13) (in thread): > yes, but I did not receive any email regarding the first account, probably because i might have missed a letter when inputting the email address@Scholastica Urua

Millicent Adzepa (03:07:52) (in thread): > okay, thank you very much@Scholastica Urua,@Barakat Akinsiku

Modinat Ganiyu (03:11:43) (in thread): > Hi Millicent, I’ll suggest you wait for their response since you replied to this mail, hopefully they will reply and attach the link to get through your account.

Mildred Anashie (03:40:45) (in thread): > HiIfeyinwa > > When you search for a particular taxon and another name pops up it’s advisable to click on the first it might be the synonym to what you are searching for and synonyms are just fine on BugSigdb (In my opinion) > > In the case ofErysipelatoclostridiumyou should use Thomasclavelia it says it’s the homotypic synonym > > See attached image - File (PNG): IMG_2161

Mildred Anashie (03:41:52) (in thread): > Maybeyou’llhave to leaveRuminicoccus gnavusthat way for now

Amanda Adoyi (03:49:26) (in thread): > I’ve learnt that while homotypic synonyms definitely refer to the same taxon on the same level ( like how one person may be named jude and kevin) heterotypic synonyms should be investigated a little more online…as they usually refer to different levels and may not be interchangeable sometimes. Just research wello.

Precious Orakwe (03:54:31): > Good morning team, my name is precious, my initial application was approved by outreachy. I am so excited to contribute to the bioconductor community. > Please can anyone help and tell me what to do or where to start contributing. Thanks@Svetlana Ugarcina Perovic

Mildred Anashie (03:57:32) (in thread): > Yea@Amanda AdoyiHeterotypic synonyms should be researched more on

Mildred Anashie (03:58:45) (in thread): > Welcome@Precious OrakweTake a look at this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709575733408479?thread_ts=1709575568.383219&channel=C04RATV9VCY&message_ts=1709575733.408479 - Attachment: Attachment > Welcome Outreachy applicants! > > We’re so excited to have you here for the contribution period. Please see this issue on GitHub for instructions on getting started: https://github.com/waldronlab/BugSigDBcuration/issues/94. > If you have any questions, please post them in this channel so that all applicants can participate in and benefit from the discussion. > > Thank you so much for your interest and we look forward to working with you. > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (04:08:21) (in thread): > Hi@Precious Orakwe, welcome:hugging_face:

Samreen Aftab (04:16:14): > Hello everyone, so@Aleru Divinehelped review my article and I have a question regarding the sample size of the study I’m curating. > Here should I consider the number of patients excluded and deduct it from the sample size, or should I leave the sample size as it is? > Thank you. - File (PNG): image.png - File (PNG): image.png

Barakat Akinsiku (04:16:52) (in thread): > Welcome@Precious OrakweThe above resources shared by Mildred are a good guide

Scholastica Urua (04:16:59) (in thread): > Welcome to the community@Precious Orakwe. > You can also check out pinned messages for some guidance.

Precious Orakwe (04:18:29) (in thread): > Thanks@Mildred Anashie@Barakat Akinsiku@Scholastica Urua

Mildred Anashie (04:18:34) (in thread): > In my opinion the final sample that was used for the experiments > > You already found out they excluded some

Scholastica Urua (04:19:06) (in thread): > Hi Samreen, since the study mentioned the numbers excluded then you should exclude them. You should curate only those that were finally used in the study.

Samreen Aftab (04:19:43) (in thread): > Okay but since the table I referred to used the original sample size, that is why I was confused

Mildred Anashie (04:41:03) (in thread): > You are welcome@Muqtadirat Yussuff:blush:

Muqtadirat Yussuff (04:59:30) (in thread): > Hi@Precious Orakwe, welcome to the community and if you do get stuck, do not hesitate to ask. The community is really friendly, I hope you have fun learning

Abiola Salako (05:00:35) (in thread): > @Muqtadirat YussuffAlright.

Ikeh Darlington Ikeh (05:12:22) (in thread): > Since they were excluded, meaning their samples were not used in the statistical analysis, hence, has no effect on the signatures. So you should use 173-(82+4+18)=69, as your sample size for the patients with CD. > > This is my opinion though. I wish a mentor can help out here.

Ikeh Darlington Ikeh (05:18:10): > @Scholastica Urua@Samreen AftabPlease can you help me review my curation? Here’s the linkhttps://bugsigdb.org/Study_918 - Attachment (BugSigDB): Evaluation of fecal microbiota transplantation in Parkinson’s disease patients with constipation - BugSigDB > Parkinson’s disease (PD) is a neurodegenerative disorder and 70-80% of PD patients suffer from gastrointestinal dysfunction such as constipation.We aimed to assess the efficacy and safety of fecal microbiota transplantation (FMT) for treating PD related to gastrointestinal dysfunction.

Mariam Hammed Gambina (05:22:06) (in thread): > Hi Millicent I have a similar issue, but mine is password related. I have been waiting for the password to be sent to my email. I don’t know how long it takes to receive the password after account creation onBugsigDB.org.

Mariam Hammed Gambina (05:22:09): > I have been waiting for the password to be sent to my email. I don’t know how long it takes to receive the password after account creation onBugsigDB.org.

Mildred Anashie (05:22:43) (in thread): > Hi MariamYou’dhave to be patient sinceit’sweekend

Mariam Hammed Gambina (05:23:25) (in thread): > Yea, I thought of that too. Thanks

Peace Daniel (05:25:05) (in thread): > You can also check your spam mails and any other inbox.

Precious Orakwe (05:27:10) (in thread): > yes@Muqtadirat Yussuffthank you

Mariam Hammed Gambina (05:47:47) (in thread): > I have done that also.

Mariam Hammed Gambina (06:00:42) (in thread): > Thanks all, I checked all of them as well and couldn’t find an unassigned issue. My guess is that multiple people can be assigned an issue. Let’s see what the mentors have to say about that by Monday.

Mariam Hammed Gambina (06:01:14) (in thread): > Thanks for this guys.

Abiola Salako (06:03:54) (in thread): > @Mariam Hammed GambinaNo, only one person gets assigned to a paper. More papers to curate shall be uploaded soon. Just be patient and remember that it’s a weekend.

Abiola Salako (06:14:22) (in thread): > @Mildred AnashieYour insights are usually helpful

Aleru Divine (06:15:19): > Good morning everyone,@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoI found this incomplete study without experiments and signatures andI’dlike to complete it.Here is the linkhttps://bugsigdb.org/Study_861Can I go ahead? - Attachment (BugSigDB): Resilience of the respiratory microbiome in controlled adult RSV challenge study - BugSigDB > This study of healthy adults revealed no major changes in the bacterial community of the respiratory tracts following RSV inoculation, suggesting that the adult respiratory microbial community is resilient to viral perturbations https://bit.

Abiola Salako (06:20:07) (in thread): > Hi@Precious Orakweyou’re welcome

Esther Afuape (06:29:31) (in thread): > Yes please

Mildred Anashie (06:35:00) (in thread): > Thank you:pray:@Abiola SalakoWe are all learning:blush:

Aleru Divine (06:38:17) (in thread): > Thank you so much@Esther Afuape

Leenaa Al-Amin (06:53:57): > hello everyone,@Aleru Divinereviewed my curation and she suggested comparing the recovered sub groups mild, moderate and severe each to the mortality group rather than the recovered group as a whole. However I’m a bit skeptical about that because in figures 3e-3j, the graphs of the differentially abundant species in the mild group is comparing it to the moderate rather than the mortality and the graph of the differentially abundant species in the severe group is comparing it to moderate/mortality. Another angle would be comparing each subgroup by severity i.e, mild vs moderate, moderate vs severe, severe vs mortality but the challenge with that is that I would not be able to account for the differentially abundant species in mortality because in the graphs, its being compared to the mild and moderate subgroups. The way comparisons are being made in figures 3e-h are just very confusing. So I compared the recovered group as a whole because all the differentially abundant species in each subgroup of recovered were decreased in mortality and the abundant species in mortality is decreased in the recovered group. Please what are your thoughts? This is my study:https://journals.asm.org/doi/10.1128/spectrum.02311-21and this is my curation:https://bugsigdb.org/Study_891 - Attachment (BugSigDB): Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome - BugSigDB > The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis.This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. - File (PNG): Screenshot (23).png - File (PNG): Screenshot (25).png

Desire Oluwarotimi (07:22:18) (in thread): > Sure thing@Leenaa Al-Amin

Samreen Aftab (07:26:17) (in thread): > Hello@Ikeh Darlington IkehI will look into it.

Evelyn Mary Attah (07:32:41): > Hello@Nitya Singhal@Scholastica Urua@Desire Oluwarotimi, can you kindly review my article? The link =https://bugsigdb.org/Study_941, Thank you very much. - Attachment (BugSigDB): Characteristics of gut microbiota in patients with asthenozoospermia: a Chinese pilot study - BugSigDB

Habiba Saad (07:54:03) (in thread): > heres a link for PMIDhttps://pubmed.ncbi.nlm.nih.gov/38225541/ - Attachment (PubMed): Characteristics of gut microbiota in patients with asthenozoospermia: a Chinese pilot study - PubMed > It appears that gut microbiota composition in AS patients significantly differed from that in healthy men, and the development of AS might be associated with intestinal flora dysbiosis.

Barakat Akinsiku (08:07:00) (in thread): > Hi@Desire OluwarotimiPlease review my work and I can help review yours toohttps://bugsigdb.org/Study_817

Samreen Aftab (08:07:09): > Hello, based on this table, can I say that the subjects are matched on age and bmi? - File (PNG): image.png

Scholastica Urua (08:11:38): > Good day everyone, how’s the Sunday going? > > I would appreciate your assistance in reviewing this curation:https://bugsigdb.org/Study_862I stumbled upon it in the section labeled ‘Studies that have no Experiments.’ The curation appears to be quite lengthy, and I’m uncertain if I’ve included the right information, particularly regarding the number of experiments and groups. > > For the study design, I opted for a Prospective Cohort. However, within the study, a longitudinal cohort study was conducted. > > Regarding the location of subjects, they were situated in Scotland. However, since I couldn’t locate Scotland among the list of locations, I selected UK as the location instead. > > Also some of the confounders are not listed in BugSigDB. > > I would greatly appreciate your feedback on this. Thank you:pray: - Attachment (BugSigDB): The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study - BugSigDB > BACKGROUND: Infection is a key component of bronchiectasis pathophysiology.Characterisation of the microbiome offers a higher degree of sensitivity and resolution than does traditional culture methods.

Habiba Saad (08:33:39) (in thread): > shannon in unchanged, richness is lower, and chao 1 is lower. according to what i studied in this study.

Habiba Saad (08:42:55) (in thread): > hey@Scholastica Uruai think the doi is not correct. can you again check it?

Mildred Anashie (08:43:47) (in thread): > Okay@Scholastica UruaI can get on it onceI’mdone with the studiesI’mcurrently reviewing

Chioma Onyido (08:48:36) (in thread): > I’m unable to access it too, seems it wasn’t attached to the pdf. > Another way is to try sending an email to the corresponding author (email address is attached in the image) requesting for access to the supplementary file. - File (PNG): image.png

Scholastica Urua (08:53:11) (in thread): > @Habiba Saadthank you for that observation. I have corrected it.

Habiba Saad (08:56:31) (in thread): > in case you have a pdf, kindly share.

Peace Daniel (09:01:39) (in thread): > Was there no mention of matched-on factors in your article?

Scholastica Urua (09:03:08) (in thread): > Here’s the pdf file. - File (PDF): S2213260020305579.pdf

Scholastica Urua (09:03:40) (in thread): > Hello@Evelyn Mary AttahI’ll get on it once I’m done with the one I’m currently working on and let you know my observations.

Samreen Aftab (09:13:07) (in thread): > The matched-on keyword wasn’t there@Peace Daniel

Mildred Anashie (09:14:57) (in thread): > Hi@Leenaa Al-AminI am also of the opinion that you shouldn’t have compared Mortality to recovered because i didn’t come across that experiment > > I rather think it to be curated as > > Mild vs Moderate > Mild vs Severe > Moderate vs Severe > Mild vs Mortality > Severe vs Mortality > Moderate vs Mortality > > But I’m still trying to identify the signatures that were increased and decreased for the comparisons I’m proposing

Muqtadirat Yussuff (09:17:52): > Hey everyone, how are all doing? > > I would like some assistance with reviews in regards to a curation:https://bugsigdb.org/Study_761Any bit of input would be really appreciated, thank you. > > Also, if anyone needs a review on theirs, you can let me know. > > Link to the research paper:The oral microbiome and breast cancer and non-malignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study - Attachment (BugSigDB): The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study - BugSigDB > The oral microbiome, like the fecal microbiome, may be related to breast cancer risk.Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana. - Attachment (PubMed Central (PMC)): The oral microbiome and breast cancer and non-malignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study > The oral microbiome, like the fecal microbiome, may be related to breast cancer risk. Therefore, we investigated whether the oral microbiome was associated with breast cancer and non-malignant breast disease, and its relationship with the fecal microbiome …

Muqtadirat Yussuff (09:22:01) (in thread): > Hi@Scholastica UruaI’ll get on it soon

Scholastica Urua (09:22:44) (in thread): > Thank you Chioma

Scholastica Urua (09:27:19): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoI found this incomplete study without experiments and signatures and I’d love to complete it. > Link:https://bugsigdb.org/Study_333Can I go ahead? - Attachment (BugSigDB): Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study - BugSigDB > OBJECTIVE: To investigate factors related to bifidobacterial colonization in early infancy, with a focus on maternal antimicrobial use at delivery.STUDY DESIGN: A cross-sectional pilot study was performed.

Peace Daniel (09:41:23) (in thread): > Please share a link to your article

Amanda Adoyi (09:41:53): > Happy Sunday people:slightly_smiling_face:In a situation where a confounder controlled for in your text is not on the list of permissible values, what do you do? > I can see that list can be edited but em…obviously that has to be a bad idea without permission. However it is important I think that I add this confounder because it was included.@Svetlana Ugarcina Perovic@Esther Afuape

Samreen Aftab (09:44:05) (in thread): > @Peace Danielherehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10640746/pdf/12866_2023_Article_3084.pdf

Scholastica Urua (09:48:43) (in thread): > Hi Amanda, I had this issue too with the paper I just curated. Looking forward to replies from mentors.

Amanda Adoyi (09:49:11) (in thread): > Alryty. We wait then.

Flourish Ralph (09:57:57) (in thread): > @Mariam Hammed GambinaI thinkit’sbecauseit’sthe weekend,it should be approved by tomorrow (Monday) sinceit’sa working day

Muqtadirat Yussuff (10:01:45) (in thread): > I’ve seen curated papers where the confounders aren’t among the permissible values, it ends up being tagged/flagged. You can either input or wait, I suggest waiting for the mentors

Modinat Ganiyu (10:18:04) (in thread): > Well done@Scholastica UruaPls I want to ask where I can find incomplete study so I can work on because I’ve not been able to get an issue to work on as my second contribution. Also can I record it as a contribution when I’m done?

Desire Oluwarotimi (10:19:32) (in thread): > Hi@Leenaa Al-AminI think@Aleru Divinesuggested the correct thing to do and@Mildred Anashiefurther consolidated her point by stating out those groups for you. > > But I have a bit of difficulty identifying the abundance signatures as well. I’ll continue to look through.

Desire Oluwarotimi (10:20:25) (in thread): > Hi@Leenaa Al-Aminhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710080372279219?thread_ts=1710068037.599959&cid=C04RATV9VCY - Attachment: Attachment > Hi @Leenaa Al-Amin > > I think @Aleru Divine suggested the correct thing to do and @Mildred Anashie further consolidated her point by stating out those groups for you. > > But I have a bit of difficulty identifying the abundance signatures as well. I’ll continue to look through.

Desire Oluwarotimi (10:20:41) (in thread): > Sure thing@Barakat Akinsiku

Desire Oluwarotimi (10:30:40) (in thread): > @Barakat AkinsikuI can’t access your article. Can you share it?

Scholastica Urua (10:31:46) (in thread): > Hi@Modinat Ganiyu, > > So sorry I’m not able to give an accurate answer to your question about completing and recording incomplete studies as your second contribution.@Esther Afuape@Chioma Onyido@Peace SandyThe mentors will add more papers soon. We have to exercise patience (also note that its the weekend). > > (For the links to find incomplete studies:point_down:) > Once your second contribution has been completed some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Modinat Ganiyu (10:41:14) (in thread): > Okay, thank you for your honest feedback, its highly appreciated. > Yes, of course its weekend and I know activities on weekends and during week days are incomparable. I’m also certain that our mentors will upload more soon, I just wanted to know if I can do something else apart from the initial paper to curate but since we aren’t sure, I’ll just follow the due process. Thank you once again

Peace Daniel (10:43:23) (in thread): > I’llgo through it and give an honest review on your question

Esther Afuape (10:43:27) (in thread): > Hi guys > Please enter them like that

Muqtadirat Yussuff (10:44:38) (in thread): > Hi@Esther Afuape, thank you for your response

Scholastica Urua (10:45:09) (in thread): > Thank you Esther

Amanda Adoyi (10:46:35) (in thread): > @Esther AfuapeThose warning symbols sort of put me on alert when I open the page. Lolz. Thanks

Esther Afuape (10:47:20) (in thread): > Idon’tlike seeing them either:sweat_smile:

Abiola Salako (10:49:27) (in thread): > Thank you@Esther Afuape

Barakat Akinsiku (11:14:56) (in thread): > Here it is, thanks - File (PDF): Pavloudi.et.al (1).pdf

Desire Oluwarotimi (11:17:25) (in thread): > Hi@Evelyn Mary AttahHere is the details of what I could find. > > Antibiotics exclusion should be 6 months. > 16S variable region should be V3-V4. > Alongside age and sex, I think they were also matched on weight, height and body mass index. > Simpson shouldn’t be a part of your alpha diversity instead Faith should be. It’s decreased. > There wasn’t multiple hypothesis testing. > Your increased and decreased signatures could be more. Check Fig 6b. > > That’s it from me. Please check throughly also in case I missed something.

Desire Oluwarotimi (11:19:17) (in thread): > Thank you.

Evelyn Mary Attah (11:26:13) (in thread): > @Desire OluwarotimiThank you very much

Bolanle Wahab (11:27:34): > Hi everyone > Can we curate a signature from Supplemetary materials as the source?

Mildred Anashie (11:28:56) (in thread): > Hi@Bolanle WahabYes you can > I believethat’swhy we are advised to always check for additional/supplemental materials so wedon’tleave any information out

Eniola Adebayo (11:29:02) (in thread): > Yes you can

Bolanle Wahab (11:29:21) (in thread): > Thank you

Leenaa Al-Amin (11:38:11) (in thread): > Hello@Mildred Anashie@Desire Oluwarotimi@Aleru Divinebased on your suggestions, this is what the signatures would be > mild vs moderate - decrease in Actinomyces meyer, Halomonas sp. > mild vs mortality - increase in Achromobacter xylosidans > moderate vs severe - increase in Leptotrichia buccalis > moderate vs mortality - increase in Bacillus cereus, decrease in Veillonella parvula > severe vs mortality - decrease in Leptotrichia bucallis > > The abundant signatures are in the screenshot below:point_down: - File (PNG): Screenshot (27).png

Aleru Divine (11:41:23) (in thread): > Thanks@Esther Afuape:sweat_smile:

Eniola Adebayo (11:43:22): > Good day everyone. The significant threshold was not specified for the study in the methodology, but three p values (0.01, 0.001, 0.0001) was used to show significance in the results. Should I curate everything and use 0.01 as the significant threshold?@Svetlana Ugarcina Perovic@Esther Afuape

Mildred Anashie (11:45:59) (in thread): > I think you should use 0.01 since it was mentioned in the study

Eniola Adebayo (11:47:31) (in thread): > There was no specific threshold in the method. The three p values were used in the results@Mildred Anashie

Mildred Anashie (11:52:42) (in thread): > Did they do Bonferroni correction?

Eniola Adebayo (11:53:13) (in thread): > Yes

Aleru Divine (11:53:20): > Good evening everyone,@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyI have completed the curation of the incomplete study.It is now ready for review > > Here is the link:https://bugsigdb.org/Study_861 - Attachment (BugSigDB): Resilience of the respiratory microbiome in controlled adult RSV challenge study - BugSigDB > This study of healthy adults revealed no major changes in the bacterial community of the respiratory tracts following RSV inoculation, suggesting that the adult respiratory microbial community is resilient to viral perturbations https://bit.

Mildred Anashie (11:53:44) (in thread): > Adjusted p value was what?

Mildred Anashie (11:58:51) (in thread): > I’m of two opinions you either use 0.01 (No specific reason) > > Or you use the conventional 0.05 > > We can wait for the Mentors to get their opinions

Eniola Adebayo (11:59:04) (in thread): > The adjusted p value was not explicitly stated but they carried out Bonferroni correction. BugSigDB.org/study_944

Esther Afuape (12:00:30) (in thread): > If P value is not explicitly stated, default is .05

Eniola Adebayo (12:01:05) (in thread): > Thank you. If I use 0.05 I won’t be able to add any signature. So that means I can curate the significanttaxa that are less than 0.05

Esther Afuape (12:02:23) (in thread): > Why? All the p values showing significance are less than 0.05

Esther Afuape (12:02:55) (in thread): > The significant results are meant to be less than 0.05 (p<0.05)

Eniola Adebayo (12:03:13) (in thread): > Yessss…. Thank you

Desire Oluwarotimi (12:04:37) (in thread): > Hi@Leenaa Al-AminWhile checking your article earlier, I had a suspicion that the code used under each of the subgroups in Fig 3d should direct us to taxas but I couldn’t find them so I didn’t mention. However, after going through@Barakat Akinsikupaper, they did something similar but dedicated a table to indicate the taxa for each code which your paper didn’t do unless I couldn’t find it. > > I strongly believe the taxa could still be more than what you’ve provided but I can’t seem to find my way around it at all.

Joan C. Chukwuemeka (12:07:20) (in thread): > @Samreen AftabIf it wasn’t stated, then there’s likely no matching. Here’s info on “matched on” from the curation policy/guide > * Matching typically only occurs in a case control study. > * Matching occurs when they select controls similar to cases and match them on certain characteristics such as race, age, health status, gender, etc. > * It will often be phrased along the lines of “Cases were matched to controls on race, age, and gender” or “Age, gender, and race-matched study population”. > * Ctrl+F for the word “match” is generally an easy way to look for matching. > * Use the drop down to select the matched on terms. Don’t use abbreviated terms in the field.

Hamza Haji (12:16:25): > Hello everyone. My name is Hamza, a medical doctor from Kenya in the outreachy program. I have already made my first contribution by mostly following the instructions in the prep documents and the discussions here by@Scholastica Urua.
> > I am very interested in curating microbiome studies involving the pathobiology of cervical cancer, especially those made on African populations since the disease is on the rise here. I have not yet started my second contribution because most of the research papers are already assigned. This is an amazing project. I can’t wait to continue contributing to open science and being up to date on the latest research.@Esther Afuape@Svetlana Ugarcina Perovic

Peace Daniel (12:16:46) (in thread): > Sorry for the delay, I had to read through everything. There was no mention of matching

Leenaa Al-Amin (12:17:22) (in thread): > I have gone through my study over and over and there’s no information about any more differentially abundant Taxa. Please can you share with me the link to her paper and curation so I can look through what she did@Desire Oluwarotimi

Peace Daniel (12:18:17) (in thread): > Welcome Hamza, looking forward to more contributions from you

Aleru Divine (12:18:34) (in thread): > Well done:clap:@Hamza Haji

Aleru Divine (12:19:31): > Hello again everyone,:sweat_smile:@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoI found this incomplete study (experiment is marked as incomplete) and there are no signatures. > > I’d like to complete the curation > > Here is the linkhttps://bugsigdb.org/Study_585Can I go ahead?

Scholastica Urua (12:20:03) (in thread): > Welcome@Hamza Haji:wave:Looking forward to collaborating with you.

Mildred Anashie (12:20:22) (in thread): > Welcome@Hamza Haji

Desire Oluwarotimi (12:20:51) (in thread): > Check Fig 6 and Table 2https://community-bioc.slack.com/archives/C04RATV9VCY/p1710083696379929?thread_ts=1710014543.820869&cid=C04RATV9VCY - Attachment: Attachment > Here it is, thanks

Bolanle Wahab (12:21:58) (in thread): > Welcome@Hamza Haji

Ima-obong (Aimah) (12:31:22) (in thread): > Welcome@Hamza Haji

Aleru Divine (12:45:57) (in thread): > I’llgo through this again@Muqtadirat Yussuff

Muqtadirat Yussuff (12:47:50) (in thread): > Thank you so much@Aleru Divine

Hamza Haji (12:48:26) (in thread): > Thank you@Peace Daniel

Hamza Haji (12:50:40) (in thread): > Thank you@Mildred Anashie@Bolanle Wahab@Ima-obong (Aimah)@Scholastica Urua@Aleru DivineHope to collaborate with you soon.

Peace Daniel (12:53:44): > Hello@Esther Afuape@Chioma OnyidoI noticed there are duplicate studies on BugSigdb, can I work on merging the details to one?

Muqtadirat Yussuff (12:56:30) (in thread): > Hi@Peace Daniel, I think you should specify the studies in question just in case

Peace Daniel (13:03:37) (in thread): > There are lots of studies, I want to be sureit’sokay to work on it first before specifying whichI’dlove to work on

Amanda Adoyi (13:05:17): > Aloha people. Hope your evening is great. If you’re up for a review you could say hi to me. Thanks

Aleru Divine (13:07:02) (in thread): > Likewise@Hamza Haji

Mildred Anashie (13:07:15) (in thread): > I thinkit’sokay to work on themYou’dchoose the one you are interested in and merge then ask the mentors to review and possibly delete the other > > This is my opinion

Peace Daniel (13:13:24) (in thread): > Yo@Mildred AnashieI noticed a study had two different study design and one had two experiments while the other had just one.

Adegboye Rukayat (13:14:11) (in thread): > Well-done@Aleru Divine

Adegboye Rukayat (13:14:18): > Hi everyone, please how can I get more paper to work on. I am new to open source and I have done the two contributions. How can I contribute more by and who can help me review my curation to know if I am doing it right. Thank you

Mildred Anashie (13:15:27) (in thread): > You can check this outhttps://bugsigdb.org/Help:Contents#TODO_for_reviewers - Attachment (BugSigDB): Help:Contents > …

Aleru Divine (13:15:42) (in thread): > Hi@Adegboye Rukayatyou can check this out and find other ways to contributehttps://bugsigdb.org/Help:Cleanup#Links_to_lists_of_pages - Attachment (BugSigDB): Help:Cleanup

Peace Daniel (13:16:38): > Hi@Chioma Onyido@Peace Sandy@Esther AfuapeCan a study design be both case-control and a laboratory experiment? > A link to my articlehttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6 - Attachment (BioMed Central): A metagenomic study of the gut microbiome in Behcet’s disease - Microbiome > Background Behcet’s disease (BD) is a recalcitrant, multisystemic inflammatory disease that can lead to irreversible blindness. Microbial agents have been considered to contribute to the pathogenesis of this disease, but the underlying mechanisms remain unclear. In this study, we investigated the association of gut microbiome composition with BD as well as its possible roles in the development of this disease. Methods Fecal and saliva samples were collected from 32 active BD patients and 74 healthy controls. DNA extracted from fecal samples was subjected to metagenomic analysis, whereas DNA extracted from saliva samples was subjected to 16S rRNA gene sequencing analysis. The results were used to compare the composition and biological function of the microbiome between patients and healthy controls. Lastly, transplantation of pooled fecal samples from active BD patients into B10RIII mice undergoing experimental autoimmune uveitis (EAU) was performed to determine the causal relationship between the gut microbiome and BD. Results Fecal samples from active BD patients were shown to be enriched in Bilophila spp., a sulfate-reducing bacteria (SRB) and several opportunistic pathogens (e.g., Parabacteroides spp. and Paraprevotella spp.) along with a lower level of butyrate-producing bacteria (BPB) Clostridium spp. and methanogens (Methanoculleus spp. Methanomethylophilus spp.). Analysis of microbial functions revealed that capsular polysaccharide transport system, oxidation-reduction process, type III, and type IV secretion systems were also increased in active BD patients. Network analysis showed that the BD-enriched SRB and opportunistic pathogens were positively correlated with each other, but they were negatively associated with the BPB and methanogens. Animal experiments revealed that fecal microbiota transplantation with feces from BD patients significantly exacerbated EAU activity and increased the production of inflammatory cytokines including IL-17 and IFN-γ. Conclusions Our findings revealed that BD is associated with considerable gut microbiome changes, which is corroborated by a mouse study of fecal microbiota transplants. A model explaining the association of the gut microbiome composition with BD pathogenesis is proposed.

Amarachi Lewachi (13:18:09): > Hi Everyone. I just completed my second contribution and would appreciate reviews.https://bugsigdb.org/Study_933/Experiment_1 - Attachment (BugSigDB): Study 933/Experiment 1 > …

Mildred Anashie (13:18:44) (in thread): > I think you can have more than one study design, if that’s what is done in the article:thinking_face:

Amarachi Lewachi (13:19:04) (in thread): > https://bugsigdb.org/Study_933/Experiment_1. Hi Amanda Kindly review this. - Attachment (BugSigDB): Study 933/Experiment 1 > …

Aleru Divine (13:19:10) (in thread): > Thank you@Adegboye Rukayat

Amanda Adoyi (13:19:59) (in thread): > Awesome. Yes I will:slightly_smiling_face:

Adegboye Rukayat (13:20:16) (in thread): > Thank you so much@Aleru Divine@Mildred Anashie

Joan C. Chukwuemeka (13:20:34): > Good evening all, > I just noticed this study,https://bugsigdb.org/Study_936has no info at all, Did someone just create it newly and trying to input details? or can I alert the mentors to delete it?:thinking_face: - Attachment (BugSigDB): - BugSigDB > … - File (PNG): image.png

Amanda Adoyi (13:21:54): > Tip: If you listen to lofi while you curate, the names just start looking normal for some reason. Take the tip how you will:woman-shrugging:

Peace Daniel (13:23:41) (in thread): > What is lofi?

Mildred Anashie (13:23:53) (in thread): > :sweat_smile:I should try it > Thanks for the tip

Amanda Adoyi (13:25:32) (in thread): > @Peace Daniel******excited dance**** It’s a kind of em…music. Seriously though helps me through hard and/or confusing activities. Lolz

Joan C. Chukwuemeka (13:25:52): > Hey again:relaxed:If you are done with your 2nd contribution, I want to suggest you go and do a recheck to ensure you saved all experiments and signature input as complete, so that it shows “needs review” and not “Incomplete”. While searching for incomplete experiments, I noticed that some persons may have missed this detail. > > Well done guys:hugging_face:

Muqtadirat Yussuff (13:26:43) (in thread): > What’s your lofi playlist?:joy:

Amanda Adoyi (13:27:32) (in thread): > Lolzzz. I go on youtube and download hours worth. I’ll take this over panadol.

Aleru Divine (13:27:58) (in thread): > On the other hand Idon’teven want to hear a single sound:sob::sob::sob:

Peace Daniel (13:28:30) (in thread): > Just searched online, seems relaxing…I listen to Beethoven when I need to relax but Ihaven’tbeen feeling like hearing any other sound:sob:@Amanda Adoyi

Nana (13:28:53): > @Joan C. ChukwuemekaSome people did not miss it, just that they are still entering data. That’s the main reason march 2024 cohort should not review any curation that has march 2024 tagged to it. People are still working on their studies.

Amanda Adoyi (13:29:00) (in thread): > @Aleru DivineSeriously and honestly everyone is different.

Nana (13:29:31): > And as soon as one saves their work it enters in needs help

Amanda Adoyi (13:29:58) (in thread): > @Peace DanielAbeg o. Take a break. Listen to Beethoven and relax small. It’ll get clearer when you return.

Muqtadirat Yussuff (13:30:27) (in thread): > @Peace Danielsweett, I actually use classical music for studies. Once in a while, lofi

Amanda Adoyi (13:31:31) (in thread): > Think I listen to lofi more these days. Classical music suffered in my secondary school days aye…:sweat_smile:

Mildred Anashie (13:32:21) (in thread): > Check this out@Peace Danielmight be similar to yours, I see two study designs and its a study that has been reviewed

Mildred Anashie (13:32:23) (in thread): > https://bugsigdb.org/Study_16 - Attachment (BugSigDB): Melatonin prevents obesity through modulation of gut microbiota in mice - BugSigDB > Excess weight and obesity are severe public health threats worldwide.Recent evidence demonstrates that gut microbiota dysbiosis contributes to obesity and its comorbidities.

Muqtadirat Yussuff (13:32:26) (in thread): > I used to use metal:face_palm::joy:

Peace Daniel (13:32:36) (in thread): > @Muqtadirat Yussuffclassical music is my go to

Joan C. Chukwuemeka (13:33:07) (in thread): > @NanaYea, I was referring to those who may have missed it. Just a nudge and heads up you know:slightly_smiling_face:. > > I’m also not editing any curation from our present cohort.:right-facing_fist:

Joan C. Chukwuemeka (13:33:49): > @Scholastica Uruayour curation forhttps://bugsigdb.org/Study_862The genus Rothia is actually available on NCBI.Rothia1)Taxonomy ID: 32207. - Attachment (BugSigDB): The sputum microbiome and clinical outcomes in patients with bronchiectasis: a prospective observational study - BugSigDB > BACKGROUND: Infection is a key component of bronchiectasis pathophysiology.Characterisation of the microbiome offers a higher degree of sensitivity and resolution than does traditional culture methods. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (PNG): image.png

Peace Daniel (13:36:02) (in thread): > Thank you so much Anashie, reading through

Amanda Adoyi (13:36:24) (in thread): > @NanaThank you plenty. Why didn’t you say this last night? Lolz. I had made that mistake in the early hours of the morning. When I saw that the paper needed review and was fairly recent, was pretty sure someone was working on it.

Peace Daniel (13:37:34) (in thread): > You can cross check on Uniprot and also confirm the rank

Leenaa Al-Amin (13:39:40) (in thread): > I’ve seen what you were reffering to. I don’t really think it’s similar to mine though, the codes in her work are OTUs that were enriched in each group whereas my study didn’t employ the use of OTUs but rather figure 3d is the distribution of top 30 bacterial species in sub-groups, from which the 6 species found to be differentially abundant in the various subgroups were obtained. I don’t believe the codes above the figure are of any significance in identifying the abundant taxas@Desire Oluwarotimi

Desire Oluwarotimi (13:42:30) (in thread): > Okay then

Nana (13:46:27) (in thread): > @Joan C. Chukwuemekaok..I get..but for some they should not make such a mistake on someone’s curation

Nana (13:48:47) (in thread): > @Amanda Adoyiurw, it is talk that brings talk. You can go and revert your changes so the original curator will continue. Or not to worry the person will revert back

Amanda Adoyi (13:49:36) (in thread): > No no. I realized it on time. Happy for that.

Joan C. Chukwuemeka (13:53:43): > Good evening@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyido<@U1LCB8WEA>I noticed that a studyhttps://bugsigdb.org/Study_794/Experiment_4/Signature_2under pages with incomplete experiments, but the main study pagehttps://bugsigdb.org/Study_794only has Experiment 1 and 3? How can this be resolved:thinking_face:? - Attachment (BugSigDB): Study 794/Experiment 4/Signature 2 > Source: Table 2 Description: kruskal-wallis test on the abundance of bacteria in the three groups at different levels to verify the results of LEfSe analysis Abundance… - Attachment (BugSigDB): Gut microbiota display alternative profiles in patients with early-onset colorectal cancer - BugSigDB > BACKGROUND: The incidence of early-onset colorectal cancer (EOCRC) is increasing worldwide.This study aimed to explore whether there is an alternative gut microbiota profile in patients with early-onset colorectal cancer.

Scholastica Urua (14:01:04) (in thread): > Thank you@Joan C. Chukwuemekafor the observation. I recheck and make corrections.

Joan C. Chukwuemeka (14:01:58) (in thread): > You’re welcome:+1:

Joan C. Chukwuemeka (14:05:29): > Hello all, > I found this study:https://bugsigdb.org/Study_714underIncomplete pages (marked as incomplete by curator). > I’d be working to complete it.:hugging_face: - Attachment (BugSigDB): Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells - BugSigDB > Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in metabolic fuel utilization that elevates circulating ketone bodies; however, the consequences of these compounds for host-microbiome interactions remain unknown. - Attachment (BugSigDB): Special:Ask/-5B-5BState::Incomplete-5D-5D/mainlabel=/offset=0/format=ol/searchlabel=Incomplete-20pages-20(marked-20as-20incomplete-20by-20curator)

Joan C. Chukwuemeka (14:10:23) (in thread): > Good evening@Peace Sandy, I noticed you worked on reviewing this study. > Is there anything I should know before attempting to complete it?

Nana (14:35:22) (in thread): > Ok

Aleru Divine (14:39:05) (in thread): > I was surprised when I found my study there:sob:

Amanda Adoyi (14:58:22): > I am of the strong suspicion that the missing NCBI taxonomy ID in the paper below is 95818 for the taxon “TM7” in the paper . In research papers it appears TM7 is an older name for (and a large part of ) Saccharibacteria and the prefix “Candidatus” seems to indicate that the taxonomic status is not officially recognized. Please let me know if that is wrong perhaps so I don’t proceed. Else…may I?@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyThanks :)https://bugsigdb.org/Study_300/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 300/Experiment 1/Signature 2 > Source: Figure 1C Description: Phylum analysis of altered microbiota in mice after antibiotic water feeding compared to mice fed with regular water Abundance in…

idiaru Angela (15:21:46): > Hi everyone, > I’d like to know If a curation can have more than one location of subjects > I.e different countries

Amanda Adoyi (15:23:41) (in thread): > That’s not usually the case from what I’ve seen… Where were the subjects recruited from?

idiaru Angela (15:26:53) (in thread): > From the highlighted parts you can see United States, Germany , and China mentioned@Amanda Adoyi - File (JPEG): 1710098737693.jpeg

Desire Oluwarotimi (15:28:31) (in thread): > Like@Amanda Adoyihas said, it’s not usually the case but I don’t think it’s impossible.

Amanda Adoyi (15:31:36) (in thread): > @idiaru AngelaIn my opinion, since we are allowed to submit more than one country and it is clearly stated that the different cohorts came from those different countries, then you could add them all. However……..It is better to bring this to the attention of the mentors before making that move.

idiaru Angela (15:32:31) (in thread): > Thank you@Amanda Adoyi@Desire Oluwarotimi

Eniola Adebayo (15:47:22) (in thread): > It’spossiblehttps://bugsigdb.org/Curation_Policy#Study_Design - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

idiaru Angela (15:48:17) (in thread): > Thank you@Eniola Adebayo

Chioma Onyido (15:49:00) (in thread): > https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID#changed_TM7_to_Candidatus_saccharibacteria - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Peace Sandy (15:50:21) (in thread): > @idiaru AngelaYes it can

Precious Orakwe (15:52:24) (in thread): > Please what am I suppose to do here, help please - File (PNG): Screenshot_20240310-204927.png

Chioma Onyido (15:52:37) (in thread): > This study has been reviewed. Perhaps during review, expt. 4 was deleted. Sometimes, when an experiment is deleted in bugsigdb, it takes some time to reflect. I guess that’s why you still see it under that category.

Peace Sandy (15:53:31) (in thread): > Yes you can

Amanda Adoyi (15:54:20) (in thread): > Aye… thank you

Aleru Divine (15:54:54) (in thread): > Thank you so much@Peace Sandy

Chioma Onyido (16:00:24) (in thread): > Yes please.

idiaru Angela (16:00:59) (in thread): > Thank you@Peace Sandy

Ikeh Darlington Ikeh (16:02:26) (in thread): > List all the locations where samples used for analysis were collected.

Precious Orakwe (16:04:04) (in thread): > Please help me, what am I suppose to do here - File (PNG): Screenshot_20240310-205444.png - File (PNG): Screenshot_20240310-205604.png

Mildred Anashie (16:05:25) (in thread): > Hi@Chioma Onyido@Esther Afuape@Peace SandyI went through this study with@Peace DanielandI’malso of the opinionthatit has two study designs > As they collected samples from BD patients and healthy controls and carried out the experiment > > > Also they induced the BD patients samples and healthy control samples into mice and carried out a laboratory experiment > > I initially had the thought that it was done to come up with treatments but there are results reported for it with taxasIt’sa little confusing

Mildred Anashie (16:08:34) (in thread): > Hi@Precious OrakweIn the Annotated article you need to copy a taxa and paste on the NCBI taxonomy website, get the NCBI ID and input along side the Taxa name and the bacteria rank > > You can get the taxas in either the increased or decreased figures in the article

Mildred Anashie (16:10:00) (in thread): > I believe the instruction says any taxon found there

Scholastica Urua (16:10:53) (in thread): > Thank you Chioma

Precious Orakwe (16:11:33) (in thread): > Please, what’s taxa

Scholastica Urua (16:12:13) (in thread): > I noticed while adding experiment 1 it loaded up experiment 2. Is there a reason for this please?@Chioma Onyido

Mildred Anashie (16:13:56) (in thread): > In biology and ecology, “taxa” is the plural form of “taxon,” which refers to a group of organisms classified together on the basis of shared characteristics. Taxa can range from very broad categories, such as kingdoms or phyla, to very specific ones, such as species or genera. The classification system helps scientists organize and understand the diversity of life on Earth. > > From Chatgpt:smile:I hope this helps

Mildred Anashie (16:17:28) (in thread): > Interestingly this is also from chatgpt > > BugSigDB, or Bacterial Signature DataBase, is a resource used in microbiome research to identify and study bacterial signatures associated with specific conditions or phenotypes. In BugSigDB, “taxa” refers to taxonomic groups of bacteria, typically identified at various levels such as phylum, class, order, family, genus, or species. These taxonomic groups help researchers understand the composition and diversity of bacterial communities within different environments or conditions.

Success Ologunsua (16:24:20): > Hi folks, are we allowed to suggest papers for curation seeing that the ones on github have already been assigned and there’s nothing for some of us to work on?

Mildred Anashie (16:25:07) (in thread): > I’m not sure about this > > I thinkit’sbetter to wait on the mentors to upload more

Muqtadirat Yussuff (16:26:04) (in thread): > Suggest? Do you mean asking to curate incomplete pages? If not you should wait, more papers would be uploaded

Success Ologunsua (16:27:15) (in thread): > Alright, I’ll wait then

Aleru Divine (16:28:56) (in thread): > @Success OlogunsuaIdon’tthink we are,we’rejust to curate the ones added by the mentors.

Abiola Salako (16:29:30) (in thread): > @idiaru AngelaYes, it very possible to have more than one location.

Abiola Salako (16:31:00) (in thread): > @Success Ologunsuajust wait till more papers are uploaded.

Eniola Adebayo (16:32:48): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Chioma OnyidoI identified a study under pages with missing ID, and according to internet sources TG5 belong to Order Synergistales. Please confirm, can I go ahead an correct this to unclassified Synergistales with the Tax ID:1151719https://bugsigdb.org/Study_157/Experiment_2/Signature_2 - Attachment (BugSigDB): Study 157/Experiment 2/Signature 2 > Source: Table 3 Description: Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group Abundance in Group 1: decreased…

Ikeh Darlington Ikeh (16:33:27) (in thread): > Can’twait for more papers to be uploaded.This is fun and enlightening at the same time.

Eniola Adebayo (16:49:21) (in thread): > I agree. I have learnt so much in such a little time@Ikeh Darlington Ikeh

Peace Daniel (16:51:07) (in thread): > @Chioma Onyido:woman-raising-hand:

Muqtadirat Yussuff (16:51:24): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyI found a paper with missing NCBI taxonomy IDParabacteroides goldsteiniii and Clostridium bolteae, I looked it up and I believe the first is a typographical error forParabacteroides goldsteinii with an ID of “328812” and the second isEnterocloster bolteae with an ID of “208479” asClostridium bolteae was it’s old name. May I proceed with the edit? > > Here’s the link to the signature on BugSigDB:https://bugsigdb.org/Study_929/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 929/Experiment 1/Signature 2 > Source: Figure 5 Description: Bacteroides strains implicated in PUFA metabolism are escalated in AD microbial recolonised GF mice Abundance in Group 1: decreased…

Ima-obong (Aimah) (17:01:08): > Hello, Is it possible for the decreased microbiomes for group 1 to not be stated in a paper even though the increased microbiomes have been stated both for the “control” and “case” group? > > Like in both groups, it’s only increased microbiomes that was mentioned and non for decrease > > And since we’re to enter the signatures for just group 1 for both increase and decrease, what can I do ….do I record signatures for only increase in group 1?

Eniola Adebayo (17:06:15) (in thread): > I think you should focus on the listed significant taxa only, whether it’s stated to be increased or decreased@Ima-obong (Aimah)

Ima-obong (Aimah) (17:07:54) (in thread): > Okay@Eniola Adebayo..so that means I’ll input just one signatures -increase.. right?

Aleru Divine (17:08:03) (in thread): > @Ima-obong (Aimah)Yes it’s possible.In this case you could record the increased microbiome for control as decreased(signature 2)

Ima-obong (Aimah) (17:09:27) (in thread): > Ohh.. okay@Aleru Divine..I had taught of doing that but wasn’t so sure cause I’ll have to set it to group 1 instead of group 0..was really confusing

Ima-obong (Aimah) (17:11:47) (in thread): > Thanks for your assistance@Eniola Adebayoand@Aleru Divine..I deeply appreciate it

Aleru Divine (17:13:45) (in thread): > You’rewelcome

Ima-obong (Aimah) (17:14:38) (in thread): > Just to be sure please..@Chioma Onyido,@Peace SandyShould I proceed with adding the increased signatures for the control group as decreased for group 1? Or I should only have one signatures which is increased microbiomes for group 1. > > Thanks for your assistance.

Mildred Anashie (17:19:57) (in thread): > @Ima-obong (Aimah)I agree with Divine. The increased signatures in the Control group are decreased in the case group…But you could wait for go ahead from the mentors though

Ima-obong (Aimah) (17:21:11) (in thread): > Thank you@Mildred Anashie..

Joan C. Chukwuemeka (17:31:05) (in thread): > Alright

Nana (17:45:55) (in thread): > Once you complete the entire thing it leaves there. That’s just the good part - File (PNG): 12970644657304163713.png

Abiola Salako (17:47:38) (in thread): > @Ima-obong (Aimah)you can go on to add the Increased microbiomes for the control and do the reverse( decreased ) for the case group. Let’s see what@Peace Sandywould likely say.

Mildred Anashie (17:48:00): > Hello@Chioma Onyido@Svetlana Ugarcina Perovic@Esther Afuape@Peace SandyI found this studies under incomplete pages.I found thathttps://bugsigdb.org/Study_872already exist ashttps://bugsigdb.org/Study_873. Alsohttps://bugsigdb.org/Study_783exists with an incomplete experiment and happens to share the same DOI ashttps://bugsigdb.org/Study_873.I suggest 872 be deleted and I’m not sure what should be done about 783Also I’ll like to complete this studyhttps://bugsigdb.org/Study_908found under incomplete pages, Thank you:pray: - Attachment (BugSigDB): - BugSigDB > … - Attachment (BugSigDB): Microbiome features associated with performance measures in athletic and non-athletic individuals: A case-control study - BugSigDB > The influence of human gut microbiota on health and disease is now commonly appreciated.Therefore, it is not surprising that microbiome research has found interest in the sports community, hoping to improve health and optimize performance. - Attachment (BugSigDB): - BugSigDB > … - Attachment (BugSigDB): Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease - BugSigDB > The gut microbiota can affect human metabolism, immunity, and other biologic pathways through the complex gut-kidney axis (GKA), and in turn participate in the occurrence and development of kidney disease.

Joan C. Chukwuemeka (17:54:00): > @Mildred Anashiedo confirm that study 908 is not for someone Still trying to curate their assigned paper.

Peace Daniel (17:56:56) (in thread): > It seems it belongs to Aleru Divine

Mildred Anashie (17:58:10) (in thread): > Divine’s study is 873

Mildred Anashie (17:58:52) (in thread): > I’m asking that 872 be deletedIt’sthe same PMID with 873

Mildred Anashie (18:00:07) (in thread): > 908 doesn’t seem to exist among the issues posted on GitHub > > Someone else can help me confirm
> “Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease”

Mildred Anashie (18:01:01) (in thread): > I will > > Thanks

Ifeyinwa Ohondu (18:01:30) (in thread): > Yes, you can have different locations. This was mentioned in the video tutorial for adding a study.

Peace Daniel (18:04:06) (in thread): > And 783, looks like the same article but a different result…wonder who worked on it:thinking_face:

Mildred Anashie (18:05:02) (in thread): > Yea > > My point exactly > Plus Ican’tfind the actual article and I don’t know the name

Ima-obong (Aimah) (18:05:23) (in thread): > @Abiola Salako..I will.. thanks

Peace Daniel (18:06:29) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/192It’sassigned to sneha - Attachment: #192 Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease > Differences in gut microbiota structure in patients with stages 4-5 chronic kidney disease - Wu et al- Am J Transl
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8507064/

Peace Daniel (18:08:51) (in thread): > 783 was curated last year butI don’tknow how to find the article either

Ima-obong (Aimah) (18:16:53): > Hello@Chioma Onyido,@Peace Sandy,@Esther Afuape@Svetlana Ugarcina PerovicI found this paper with a missing NCBI ID;******Lachnoclostridium******* *******lactaris*******. > > I looked it up on the site and no result was found for it, then I checked Google and read through some papers on Google and found that just two has a record ofLachnoclostridium*********lactaris******but recorded it to be in the family of******Lachnospiraceae,******which of course is listed in the NCBI site, but still doesn’t have******Lachnoclostridium lactaris******as it’s family member.. > > I want to assume that there must have been a change of name for******Lachnoclostridium************lactaris******and it’s not been updated on the NCBI..cause three papers made mention of it… > > Well I’m not certain if I should go ahead and add this observation to the “Discussion page” > > Thank you for your assistance.https://bugsigdb.org/Study_373/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 373/Experiment 1/Signature 2 > Source: Figure 3, Table S2 Description: Composition of fecal pools used as inocula according to dominant taxa classified at the phylum or species level. Abundance…

Naomi Ibe (18:39:43) (in thread): > @Chioma Onyidoso I checked google and found this articlehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7889099/the last paragraph before the “figure 2” illustration ,contains this paragraph “…Genera belonging to Christensenellaceae (Christensenellaceae R7 group), Porphyromonadaceae (Parabacteroides),…….” And that’s how I drew my own conclusion, I may be wrong tho. - Attachment (PubMed Central (PMC)): Elevated gut microbiome abundance of Christensenellaceae, Porphyromonadaceae and Rikenellaceae is associated with reduced visceral adipose tissue and healthier metabolic profile in Italian elderly > Aging is accompanied by physiological changes affecting body composition and functionality, including accumulation of fat mass at the expense of muscle mass, with effects upon morbidity and quality of life. The gut microbiome has recently emerged as a …

Mildred Anashie (18:42:23) (in thread): > Thank you@Peace Daniel

Mildred Anashie (18:44:01) (in thread): > Did you check the discussion page andLachnoclostridium lactariswasn’tmentioned?

Welile Dlamini (20:32:41): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoI found this incomplete study can I go ahead and complete ithttps://bugsigdb.org/Study_945/Experiment_1/Signature_1 - Attachment (BugSigDB): Study 945/Experiment 1/Signature 1 > Source: Fig. 1. and Result Text Description: Differences in the gut microbiome between subjects clinically diagnosed with mild cognitive impairment (MCI) versus…

Desire Oluwarotimi (22:28:00) (in thread): > Hi@Welile DlaminiThis is going to be a study that one of us is still most likely working on for the contribution phase.

Scholastica Urua (22:50:59): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyidoand everyone. Hope we had a nice weekend. > > I found this incomplete study without experiments and signatures and I’d love to complete it. > Link:https://bugsigdb.org/Study_333@Chioma Onyidogave me the go ahead to complete but I’m having some challenges. While entering the first experiment its load up as ‘experiment 2’. Please how do I proceed? - Attachment (BugSigDB): Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study - BugSigDB > OBJECTIVE: To investigate factors related to bifidobacterial colonization in early infancy, with a focus on maternal antimicrobial use at delivery.STUDY DESIGN: A cross-sectional pilot study was performed. - File (JPEG): Experiment 2.JPG

Muqtadirat Yussuff (23:49:50) (in thread): > @Welile DlaminiHi, please check the dates as 2024/03 curations are still in progress regardless of their incomplete/needs review status. > > I can also see you’ve made some changes, that’s someone’s work. Kindly find another

2024-03-11

Leenaa Al-Amin (00:04:07): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeplease I need to delete signature 2 of experiment 1 in my study. Thank youhttps://bugsigdb.org/Study_891 - Attachment (BugSigDB): Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome - BugSigDB > The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis.This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs.

Hamza Haji (00:57:18): > Good morning everyone. There’s something that I wanted clarification on. When looking to make a second contribution and all the issues are already assigned, does on look through the catalogue of studies in the Bugsigdb and look for incomplete projects? How does one know if a study is assigned to someone else and is working on it? Lastly, is there any other contribution we came make as we wait for the mentor and co-mentors to open new issues on GitHub? I am open to contributing however I can.@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy

Desire Oluwarotimi (01:07:54) (in thread): > Hi@Hamza HajiSince all issues have been assigned at the moment, you can definitely look through the catalogue of studies for something to work on but you’ll have to ask permission here before you can begin any edit. The mentors will surely add more papers when they can and then you can request to be assigned to one of them when they do. > > On the GitHub issues, when an article has been assigned to a curator, you’ll see an assigned tag on that issue as well as the individual profile picture towards the right hand side indicating that the paper is no longer up for grabs. > > I think I’ve answered your third question with my first paragraph. > > However, I’d love to advise that you avoid study 850 and above when looking to make contributions pending the time mentors will put up more papers. This is because they’ll most likely be a curation someone from this summer cohort is working on for the contribution phase. > > I hope this helps.

Scholastica Urua (01:13:09) (in thread): > Hello@Hamza Hajiwhen you open an incomplete study, the one withCurated date:2024/03/.. is most likely being worked on by a current applicant. > > Other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsBefore making any edits please seek permission from the mentors like@Desire Oluwarotimimentioned. - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Hamza Haji (01:26:23) (in thread): > Thank you@Desire Oluwarotimi@Scholastica Urua

Blessing Ene Anyebe (01:29:57): > Good day everyone! Happy new week and hope you had a good weekend. > It the start of a fresh week and another week on this amazing journey, I pray we all have an awesome week and add value to everything around us. > > Cheers!:orange_heart::clinking_glasses:

Scholastica Urua (01:33:24) (in thread): > Good morning Blessing:boom:

Desire Oluwarotimi (01:34:12) (in thread): > Good morning@Blessing Ene AnyebeLet’s get it this week.:sunglasses:

Blessing Ene Anyebe (01:35:34) (in thread): > Good morning@Scholastica Urua:partying_face:

Blessing Ene Anyebe (01:35:59) (in thread): > Let’s get it!:rocket:@Desire Oluwarotimi

Desire Oluwarotimi (01:39:22): > Good morning everyone.@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI found an incomplete study. Although it says it has been reviewed already, it doesn’t have any experiment at all. So, I’d like to work on it. > > Here is the link.https://bugsigdb.org/Study_784Can I go ahead? - Attachment (BugSigDB): Metagenomic assessment of gut microbial communities and risk of severe COVID-19 - BugSigDB > BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections.However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

Bolanle Wahab (01:48:21) (in thread): > Good morning@Blessing Ene AnyebeHappy new week to you too!:heart:

Abiola Salako (01:57:54): > Good morning everyone, > > Wishing you all a wonderful day ahead! Just a friendly reminder: it’s essential to understand the details of the curation policy to be a great curator. > > If you haven’t read it before, now is a perfect time. > > Check out the link below: > > Curration Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Ima-obong (Aimah) (01:59:01) (in thread): > Yes I did@Mildred Anashie…it wasn’t mentioned.

Blessing Ene Anyebe (02:02:40) (in thread): > Thank you so much@Bolanle Wahab:orange_heart:

Ima-obong (Aimah) (02:03:42) (in thread): > Good morning@Blessing Ene Anyebe.. happy new week to you too

Ima-obong (Aimah) (02:04:36) (in thread): > Happy new week@Abiola Salako

Ima-obong (Aimah) (02:09:25) (in thread): > Hello, if your curation has not yet been reviewed, you can click on “edit” on the signatures page and delete the one you want and save the page..the changes will be reverted.

Blessing Ene Anyebe (02:11:46) (in thread): > Yaayyy happy new week@Ima-obong (Aimah):orange_heart:

Aleru Divine (02:13:26) (in thread): > @Hamza HajiThe mentors will soon add new issues I believe

Amanda Adoyi (02:14:11) (in thread): > @Ima-obong (Aimah)like you said, Likely has not been updated on the ncbi taxonomy database. I also checked on that and found no known synonyms…So…probably can’t be corrected in the curation at this time….maybe

Ima-obong (Aimah) (02:42:17): > Hello everyone..asides form the main paper curation, when we find missing NCBI IDs or work on incomplete studies on the help page ..do we also record these on outreachy as contributions? > > And also, if you’re done with your second contribution which is the main curation, can you ask to be assigned a new paper on GitHub, or we’re only restricted to one paper and then focus on missing NCBI IDs?? > > Thank you.

Aleru Divine (02:44:14) (in thread): > @Ima-obong (Aimah)You can record it on outreachy, > > You can ask to be assigned a new one once your last one is reviewed and you have gotten feedback(and maybe completed it) > > So for now, I suggest to do the tasks on the help page while we wait for the reviews.

Desire Oluwarotimi (02:44:26) (in thread): > Hi@Ima-obong (Aimah)You can record all contributions you make on Outreachy. > > I’m not sure you can ask to be assigned a new paper while your second curation is still under review.

Eniola Adebayo (02:46:16) (in thread): > Record all your contributions. > > You can request for another study for curation (if available) after the first one (when you are done)

Adedoja Isaac (02:48:02): > Hello everyone, thanks for your contribution and assistance so far. I need help:grin:I’m working on a study that investigates the relationship between bacterial communities and COVID-19 severity. In previous experiments, I observed distinct bacterial profiles in mild, moderate, severe, and critical COVID-19 groups. > > However, in the latest experiment, the study compared the entire bacterial community from all COVID-19 severity groups (mild, moderate, severe, and critical) to a healthy control group. This design differs from our previous approach, where we compared bacteria specific to each severity group. > > Given this new approach, I’m unsure how to interpret the bacterial signature data. Here’s what I understand so far: > 1. Since all COVID-19 groups (including mild) are compared to the healthy controls, we might expect lower bacterial abundance in the mild group compared to healthy controls. > 2. Conversely, bacteria associated with severe, and critical cases might show higher abundance in the COVID-19 group compared to healthy controls. > 3. Additionally, the bacteria identified in the mild COVID-19 group might still be present in the healthy control group. > My question is: How should I interpret and record the bacterial signature data considering these points? And I’d love to know if I’m missing something too > > NB: The previous experiment identified bacterial “guilds” with specific abundance patterns across severity groups (e.g., Guild 1 enriched in mild/moderate and Guild 2 in severe/critical) according to the attached picture illustration. > > I would appreciate any insights or suggestions the community might have on this. Attached are some references and the link to the study.https://journals.asm.org/doi/10.1128/mbio.03519-22#fig7Please help me:pray: - File (JPEG): Screenshot_20240311-073033.jpg - File (GIF): mbio.03519-22-f007.gif

Ima-obong (Aimah) (02:50:32) (in thread): > Thanks everyone..I appreciate your responses.

Aleru Divine (02:50:56) (in thread): > Good morning@Blessing Ene Anyebeand cheers everyone:clinking_glasses:

Joan C. Chukwuemeka (02:58:56) (in thread): > Good morning@Adedoja Isaac. Trust you’re doing fine… I’m yet to go through the article, however, to know what to curate as an Experiment, check for the contrasts that were made

Aleru Divine (02:59:21) (in thread): > @Adedoja IsaacAs you’ve mentioned, the paper compared the the entire bacterial community from COVID-19 severity groups to the healthy control. > > I suggest you curate just what the paper compared which is COVID-19 severity groups vs controls. > > I will go through the paper and share more insights.

Joan C. Chukwuemeka (03:02:14): > Good morning all, Trust we had a great weekend. Wishing us a wonderful microbiome Curation week. > For our new entrants, check the pinned messages and feel free to reach out once you need help. > Happy BugSigDBing:grinning:

Blessing Ene Anyebe (03:03:05) (in thread): > Cheers@Aleru Divine:orange_heart:

Bolanle Wahab (03:03:26) (in thread): > @Adedoja IsaacI think you can record the specific taxa that shows significant differences in abundance between the COVID-19 groups and healthy controls. > And also note any taxa that was present or absent consistently in all the groups and record them as well

Adedoja Isaac (03:10:11) (in thread): > Thank you very much.@Joan C. Chukwuemeka@Aleru Divine@Bolanle WahabI will check again and note them one by one

Desire Oluwarotimi (03:12:23) (in thread): > Hi@Adedoja IsaacAt first glance at the article, I couldn’t find a control group like you mentioned as I think the study was trying to point out differential abundance among the patient groups instead. > > Also, they merged severe and critical groups together for the study because of the few number of both groups leaving you with just 3 groups. > > Mild, Moderate, Severe/Critical. > > By the way, there’s still a few important things to uncover from the paper. I’m still trying to wrap my head around the guilds thing.

Scholastica Urua (03:12:48) (in thread): > Hi Evelyn, sorry it took me a while to get to it. After going through it, I agree with all Desire said.

Adedoja Isaac (03:13:50) (in thread): > @Desire OluwarotimiSee this - File (JPEG): Screenshot_20240311-073033.jpg

Mildred Anashie (03:13:54) (in thread): > @Adedoja IsaacThe image you shared and from the article Fig 5,6,7 shows Beta Diversity results > > And I think itshouldn’tbe curated

Desire Oluwarotimi (03:20:54) (in thread): > @Adedoja IsaacI’m not sure that counts because it has to do with beta diversity. > Check Fig 7 alongside the image you shared to confirm.

Adedoja Isaac (03:22:06) (in thread): > Thank you@Desire Oluwarotimi@Mildred Anashie

Desire Oluwarotimi (03:23:04) (in thread): > Sure thing@Adedoja IsaacSo, this all leaves you with the 3 groups I mentioned earlier.

Hamza Haji (03:23:59) (in thread): > Thank you@Aleru Divine. I will definitely be checking the repository regularly.

Mildred Anashie (03:26:40) (in thread): > Good morning@Joan C. ChukwuemekaHappy BugSigdbing everyone:bouquet::heart:

Desire Oluwarotimi (03:28:33) (in thread): > Good morning@Joan C. ChukwuemekaHappy BugSigDBing indeed.:joy::bouquet:

Mildred Anashie (03:28:36) (in thread): > Yea@Ima-obong (Aimah)Youshouldrecord all your contributions and as@Eniola Adebayosaid when you are done you can request for another one if available

Aleru Divine (03:32:01) (in thread): > @Adedoja IsaacI agree with@Desire Oluwarotimi, > Severe and critical groups were combined due to limited sample size > > I noticed there are 2 control groups. > > Pneumonia controls and Healthy controls.

Rahila-me (03:41:38): > <!here>, Good morning all,Attention! Attention!! Attention!!Just a little observation I want to point out, please if you are done with your second curation and you go to help clean up on BugsigDb please when you open a work and it has March 2024 as its date of curation please leave it alone and look for another probably 2023 down. > Reason, I don’t know how BugsigDb Algorithm works but once a curator curates anything and save it , it automatically keeps your work on Needs clean_up even when your are still working on that study util you are done.

Aleru Divine (03:42:50) (in thread): > Thanks for this info@Rahila-me

Blessing Ene Anyebe (03:43:45) (in thread): > Super helpful, thank you for sharing@Rahila-me

Peace Sandy (03:44:32) (in thread): > Have you tried reloading

Ima-obong (Aimah) (03:48:06) (in thread): > Thank you for this ..

Ima-obong (Aimah) (03:48:33) (in thread): > Wishing you a great week too

Idiat Alli (03:48:39) (in thread): > Okay, thank you@Rahila-me

Scholastica Urua (03:49:07) (in thread): > Yes, I have tried that

Scholastica Urua (03:50:28) (in thread): > Can the ‘Experiment 2’ be deleted so I can re-enter it? Will that work?@Peace Sandy

Welile Dlamini (03:52:04) (in thread): > Okay noted thank you

Rahila-me (03:52:05) (in thread): > My lovely curators una welcome

Hamza Haji (03:52:53) (in thread): > Thank you@Rahila-me

Peace Sandy (03:55:25) (in thread): > Okay, give me some minutes to look at it

Mildred Anashie (03:55:28) (in thread): > @Aleru Divineare you suggesting the Covid 19 vs controls should be recorded?@Adedoja IsaacI noticed another experiment but still checking to see if I’ll find significant results for it > > Covid 19 patients @baseline and Covid Patients@ Day 7

Scholastica Urua (03:57:36) (in thread): > Thank you Peace:pray:

Adedoja Isaac (04:10:52) (in thread): > Thank you@Rahila-me

Aleru Divine (04:22:04) (in thread): > @Mildred AnashieI was thinking > > COVID vs healthy controls > COVID vs pneumonia controls > All severity vs healthy controls > > But then the article says that the guild was used in classifying COVID-19 patients with various levels of severity and to differentiateCOVID-19 patients from pneumonia control and healthy individuals was validated in four independent data sets.So I don’t know if the way to go will beCOVID vs healthy controlsCOVID vs pneumonia controlsAnd > > Mild vs moderate > Mild vs severe/critical > Moderate vs severe/critical. > > This is a mere speculation as it is still unclear to me > > For some reason unknown to me, I can’t open the supplemental materials.

Nana (04:26:14) (in thread): > Noted, well said

Nana (04:26:29): > @Peace Sandygood morning

Nana (04:26:44): > You never got back to me again?

Nwajei Edgar (04:28:54) (in thread): > Thank you

Nana (04:30:41) (in thread): > Morning to you too:two_hearts::two_hearts:

Muqtadirat Yussuff (04:30:42) (in thread): > I also can’t access the supplementary materials but I agree with@Aleru Divine, > > COVID vs healthy and COVID vs pneumonia. > > The study also states there were significant differences between mild, moderate and severe so that would be accounted for. > > Probably not as experiments but signatures within the experiments. So two experiments with three signatures each?

Bolanle Wahab (04:31:14): > Good morning everyone,this is a link to a supplementary material for my study, am I supposed to record everything here or just the ones in the actual article?https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548677/bin/42523_2023_269_MOESM3_ESM.xlsx

Muqtadirat Yussuff (04:34:06) (in thread): > Hi everyone, I’m back. How are we all doing? > > If there’s anyone up for reviews, please indicate as I would like some insights on this. Thank you

Peace Daniel (04:35:17) (in thread): > Hey, do you need help with this?

Aleru Divine (04:35:41) (in thread): > @Bolanle Wahabdo they give information that is different from the one in the article? > > Can you share your article please.

Muqtadirat Yussuff (04:35:59) (in thread): > @Peace DanielYes please

Peace Daniel (04:36:04) (in thread): > Good morning,Icouldn’topen this. Can you share a link to the study so I can source this material?

idiaru Angela (04:36:45) (in thread): > Hey@Muqtadirat YussuffI’m up for a review

Peace Daniel (04:37:08) (in thread): > It’sa supplementary material, it contains more information about the test thatcouldn’tbe added in the research article@Aleru Divine

Bolanle Wahab (04:37:18) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10548677/ - Attachment (PubMed Central (PMC)): Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics > The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited. The aims of this study were to investigate associations between variation in taxonomical …

Muqtadirat Yussuff (04:37:21) (in thread): > If the information correlates to/supplements the required data from the paper then yes, record what you need

Bolanle Wahab (04:37:56) (in thread): > @Aleru Divineno, it just listed all the taxa

Muqtadirat Yussuff (04:39:06) (in thread): > @idiaru Angelathank you so much, please provide feedbacks when you’re through and if you want me to review yours, I’m available

Adedoja Isaac (04:40:01) (in thread): > Thank you@Aleru Divine@Muqtadirat Yussuff

Peace Daniel (04:44:38) (in thread): > @Bolanle WahabI just checked the file and I understand why you asked, I’ll need some time to assess

Peace Daniel (04:45:23) (in thread): > Alright, will give it a look

Mildred Anashie (04:46:44) (in thread): > Okay@Aleru DivineIf the experiment you are proposing yielded significant results then it should be recorded > > My opinion is that those figures showing that also shows Beta diversity which is not usually recorded on BugSigdb

Bolanle Wahab (04:56:15) (in thread): > Thank you

Idiat Alli (05:02:50): > Hello everyone, I am done with my second task. You can help review my curated article and I am up to peer review yours too. Thank you in anticipation.https://github.com/waldronlab/BugSigDBcuration/issues/194 - Attachment: #194 Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals > Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals - Park et al - International Journal of Molecular Sciences
> https://www.mdpi.com/1422-0067/24/17/13329

Muqtadirat Yussuff (05:03:55) (in thread): > Hi@Idiat Alli, I’m up for peer reviews

Idiat Alli (05:06:04) (in thread): > Thank you.

Muqtadirat Yussuff (05:07:02) (in thread): > I’ll tag you in my thread, thank you too

Muqtadirat Yussuff (05:07:27) (in thread): > @Idiat AlliHere’s the paper in question, thank you

Bolanle Wahab (05:08:03) (in thread): > About this, it mentions 32 different taxa in genus level, but the supplementary article has over 32, how do I go about it?

Mildred Anashie (05:09:58) (in thread): > Hi@Bolanle WahabMy opinion is that you curate what’s in the article, the article narrowed down their results > > The only supplemental material I find with taxa information is Table S2 and that list looks over 100 andI’mnot sure you should curate thatit’sway too long

Muqtadirat Yussuff (05:10:47) (in thread): > Good morning mentors, how were your weekends?. I did not get a response so just checking in again@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther Afuape

Bolanle Wahab (05:12:07) (in thread): > @Mildred Anashieit says there were 32 others so I should just use the ones mentioned in the article?

Mildred Anashie (05:12:45) (in thread): > Please what page says there were 32 others? > > Point me to it

Muqtadirat Yussuff (05:12:58) (in thread): > @Idiat AlliPlease add the BugSigDB link too, thanks

Bolanle Wahab (05:14:52) (in thread): > @Mildred Anashiehere - File (JPEG): IMG_9603

Mildred Anashie (05:16:10) (in thread): > And there is no ref to where the taxas were mentioned:thinking_face:

Svetlana Ugarcina Perovic (05:16:54): > Good morning:tulip:we are happy to seeyour GREAT team work.Today we will be adding new papers for curation. Also, we will go through your still open questions. > Thank you for your patience! > > One question for you:slightly_smiling_face:What was your biggest curation challenge last week, and how did you solve it? Please leave the comment below.

Bolanle Wahab (05:19:17) (in thread): > @Mildred AnashieYes, do you think it would be advisable to record those 3 thatwere pointed out?

Muqtadirat Yussuff (05:19:31) (in thread): > Good morning@Svetlana Ugarcina Perovic, my biggest curation challenge was documenting signatures which might seem basic but for some reason I could not wrap my head around it. > > I solved it by reading curated papers and some help from@Aleru Divine, also thanks again Aleru. However to be honest, I still feel unsure about how to document them:sweat_smile:

Ima-obong (Aimah) (05:20:58): > Hello@Chioma Onyido,@Peace Sandy,@Svetlana Ugarcina Perovic… > > I found this paper under the “studies that have no experiment section” > > Is there a way you can help me check if it’s a paper that’s currently being worked on as there’s no date on the “study section” but it’s marked incomplete.. > > I’d love to work on it if it’s an old one..thank you > Here is the link.https://bugsigdb.org/Study_872 - Attachment (BugSigDB): - BugSigDB > …

Blessing Ene Anyebe (05:21:57): > Hello everyone, so I have a question. Is it possible for there to be an abundance signature when comparing two groups, rather than observing an increase or decrease in abundance relative to a specific group?

Mildred Anashie (05:23:28) (in thread): > Good morning@Svetlana Ugarcina Perovic:coffee:I’m excited for the team work I’ve experienced so far, it’s very encouraging:heart:My biggest curation issue was identifying experiments found within studies I was reviewing for my colleagues > > Mine seemed so easy to curate but going through other articles and identifying those experiments was a bit challenging > I solved it by reading the articles up to three times and trying not to miss a word > Also discussed the article with my colleagues and they had more insights and better understanding of the article which made the brainstorming and review much easy:bouquet::hugging_face:

Desire Oluwarotimi (05:24:23) (in thread): > Good morning@Svetlana Ugarcina PerovicMy biggest challenge from last week had to be the number of experiments in my paper. They were about 7 of them. > > Things got a bit tricky at some point when I had to make do with just the information given from the text of the paper because there wasn’t any data shown with the usual tables and diagrams. > > It took a bit of patience plus reading over and over again to be able to get things done. It was a great one regardless.:smile:

Blessing Ene Anyebe (05:24:42) (in thread): > They are no truer words@Muqtadirat YussuffMy challenge was also related to signatures. I came to better understand it by figuring that they were distinct patterns to look out for in understanding the changes that occurs within groups. > > Happy new week@Svetlana Ugarcina PerovicIt nice to hear from you.

Mildred Anashie (05:25:40) (in thread): > If I understand you, you are asking if it’s possible to have only increased signatureIf that’sthe case then yes it is, you can have just increased signatures for an experiment

Aleru Divine (05:26:29) (in thread): > Good morning@Svetlana Ugarcina Perovic:sunny:I am delighted to be a part of this community. The teamwork so far has been an incredibly enriching experience. > > My biggest curation challenge from last week was thinking whether it was okay to add 10 different experiments (since the case groups took two different exercise tests; (1) a repeated 30-s all-out Wingate test (WT) and (2) the Bruce Treadmill Test (BT), and all participants collected fresh stool samples before and after each exercise intervention.) or just 2 experiments(Sub-case 1 vs control and sub-case 2 vs control) > > I finally decided to go with 10 because the paper recorded 5 different time points: > W1 - The same day after the Wingate test (Strength and endurance athletes). > W2 - In the morning after the Wingate test on an empty stomach (Strength and endurance athletes). > B0 - In the morning before the Bruce Treadmill Test (Strength and endurance athletes). > B1 - The same day after the Bruce Treadmill Test (Strength and endurance athletes). > B2 - In the morning after the Bruce Treadmill Test on an empty stomach (Strength and endurance athletes > > I’d also like to say a big thank you to@Desire Oluwarotimi. His insights were very helpful in this decision:heart:

Desire Oluwarotimi (05:27:22) (in thread): > @Blessing Ene AnyebeI think the increase and decrease are exactly what make up the abundance. > > For example, you can see something like Colihomins was increased in 0 when paired with 1.

Aishat Ijiyode (05:29:45): > Hello everyone, happy new week. Hope you all had a good weekend

Ima-obong (Aimah) (05:29:47) (in thread): > Yes it’s possible…I had only increased signatures for both groups in my paper..the decreased wasn’t stated

Aleru Divine (05:30:00) (in thread): > @Blessing Ene AnyebeYes, it is

Mildred Anashie (05:30:06) (in thread): > Yes > > I think so,it’swhat was mentioned you can record > The other onesweren’tmentioned

Bolanle Wahab (05:30:42) (in thread): > @Blessing Ene Anyebeyes, it possible.

Aleru Divine (05:31:08) (in thread): > I agree with this too@Mildred Anashie@Bolanle Wahab

Mildred Anashie (05:32:40) (in thread): > Are you implying something like this@Blessing Ene Anyebe“Lactobacillus was found to be abundant in CN and MC (In this case CN and MC are the groups being contrasted)”

Aishat Ijiyode (05:33:50): > I hope our mentors will open new articles for us to work on soon@Svetlana Ugarcina Perovicor@Chioma Onyido@Peace Sandy@Esther AfuapeI’m still looking forward to making my second contribution

Blessing Ene Anyebe (05:34:29) (in thread): > So I agree with everyone that says it is possible but here is why. If you have a counterwhy opinion or more insights, I will appreciate it. > > In some cases, the abundance signature may simply indicate a difference in the composition or distribution of certain elements between the two groups, without implying a specific direction of change relative to the reference group. > > With this in mind how would it be recorded in the abundance group section of “adding a signature” - since it does not progress to neither a decrease or increase.

Blessing Laweh (05:34:52): > Happy New week BugSig buddies. I wish everyone the best of this New week and Ramadan Kareem to the Muslim Bug Buddies. May all of your prayers be answered in this holy month:pray::purple_heart:

Aleru Divine (05:35:35) (in thread): > @Aishat Ijiyodehere’swhat one of the mentors said, so I am positive more issues will be added today. Just be on the lookout:hugging_face:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710148614247319 - Attachment: Attachment > Good morning :tulip: > > we are happy to see your GREAT team work. > Today we will be adding new papers for curation. Also, we will go through your still open questions. > Thank you for your patience! > > One question for you :slightly_smiling_face: What was your biggest curation challenge last week, and how did you solve it? Please leave the comment below.

Idiat Alli (05:35:48) (in thread): > https://bugsigdb.org/Study_921@Muqtadirat Yussuff - Attachment (BugSigDB): Gut Microbiota Alterations and Their Functional Differences in Depression According to Enterotypes in Asian Individuals - BugSigDB > This study aimed to investigate alterations in the gut microbiota of patients with depression compared to those in the gut microbiota of healthy individuals based on enterotypes as a classification framework.

Mildred Anashie (05:35:48) (in thread): > They already started adding and assigning articles, noticed one was added and assigned an hour agoI’lladvise you keep checking

Isoken Ibizugbe (05:36:34) (in thread): > Good morning@Svetlana Ugarcina Perovicmy biggest curation challenge was the taxon name as some are heteronyms. I researched more on them before I made a decision to include them.

Bolanle Wahab (05:37:09) (in thread): > Good morning@Svetlana Ugarcina PerovicMy biggest challenge was deciding if I should record 3 separate experiments or merge them into 1 because the results from my study was marginal and there were no significant differences in the results even though they were carried out at different time points,I’malso still struggling to record the signatures causethey weren’tvery specific in the article. > But overallI’mgrateful to everyone that has helped me in one way or another, thank you:heart:

Blessing Ene Anyebe (05:37:18) (in thread): > @Mildred AnashieI am taking my reference from Figure 1 of my study let me add the link here:https://www.nature.com/articles/s41598-019-43280-w/figures/1

Bolanle Wahab (05:38:56) (in thread): > @Svetlana Ugarcina Perovicsaid they would today:partying_face:

Desire Oluwarotimi (05:39:10) (in thread): > @Blessing Ene AnyebeThat was why I said increase and decrease are a part of abundance. > > Take a look at the example@Mildred Anashiesent. In that case, you might need to refer to a table or read further in the text to be sure whether it’s an increase or decrease. > > Or am I missing something??

Ima-obong (Aimah) (05:40:01) (in thread): > Good morning@Svetlana Ugarcina Perovicmy challenge was majorly with the signatures.. > In my paper, it was only increased signatures that was accounted for in both groups 1 and control group…there were no decreased microbiomes… > > Well, I had asked here on the channel what to do about it, If I can only curate 1 signature for just the increased microbiomes… > > I was told I could curate for two signatures, the first for the increased microbiomes in group1 and for the second one; I was to use the increased microbiomes in the control group as the decrease microbiomes for group 1. > > I had gone ahead with the advice I was given here But I had also tagged the mentors on this if I could go ahead with that but I’m yet to get a reply

Bolanle Wahab (05:40:02) (in thread): > Okay, Thank you@Mildred Anashie@Aleru Divine

Desire Oluwarotimi (05:42:35) (in thread): > If I’m right, I think you might be talking about the description of that figure. > > I don’t think that has done enough justice to those taxas by the way. I believe the explanation will be more explicit somewhere in the paper.

Isoken Ibizugbe (05:43:34): > Good morning, everyone. I’ve observed that some applicants are waiting for issues to be assigned after someone else has commented on them. It’s best to go for another issue or patiently wait if none are currently provided on GitHub. Although it was during the weekend, I think this information is also useful for the new week.

Blessing Ene Anyebe (05:45:06) (in thread): > Yes you are right@Desire Oluwarotimi

Blessing Ene Anyebe (05:45:30) (in thread): > the figure doesn’t do enough justice

Ima-obong (Aimah) (05:45:37) (in thread): > Hello@Chioma Onyido,@Svetlana Ugarcina Perovic,@Peace Sandy..please can I go ahead with the suggested option?

Eniola Adebayo (05:45:41) (in thread): > Good morning@Svetlana Ugarcina PerovicMy biggest challenge so far was identifying the test used for the analysis of the microbiota as the paper did not specify which was used and other analysis were carried out. > I solved it by reading the curation policy and other materials on the different analyses used and I was able to differentiate the different analyses and whatit’sused for.

Mildred Anashie (05:47:04) (in thread): > The text below further shows which taxa was increased in which group > > For just a few though,doesn’tmention all

Hamza Haji (05:48:31) (in thread): > Hello@Svetlana Ugarcina PerovicMy biggest challenge was actually getting started with the curation process. I had read the documentation but was overwhelmed by the amount of attention to detail needed. I eventually decided to take 3 hours with breaks between them, got started and did my best. I have enjoyed every bit of the curation process. I hope to start my second contribution soon as I have seen new articles have been posted on the GitHub repository page. I am excited to be part of the team.

Oluwatomisin Omojokun (05:53:37) (in thread): > After your second contribution, you can make as many contributions as possible although this is not compulsory it is advisable to do it. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > > Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > > Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_IDSee other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsHope this is helpful.BugSigDBCategory:Pages with missing NCBI IDSep 4th, 2021 - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Scholastica Urua (05:59:13) (in thread): > Good morning@Svetlana Ugarcina Perovic, > > The past week was equally challenging and rewarding. I encountered some hurdles, but I also learned a lot of new and exciting information about BugSigDB and curation as a whole. > > Identifying and documenting increasing and decreasing signatures was particularly challenging for me. I tackled this by reviewing previously curated studies and interacting with fellow applicants. Although it’s still somewhat confusing, my understanding improves day by day. > > I also faced difficulty in identifying study designs in some papers, including the second contribution. I noticed that more than one study design was mentioned in the paper. I’m still unclear on how to navigate such situations.

Oluwatomisin Omojokun (06:05:31): > Hello, > > while awaiting an article to be assigned to you. kindly provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > > Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_IDSee other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsHope this is helpful.BugSigDBCategory:Pages with missing NCBI IDSep 4th, 2021

Adedoja Isaac (06:07:48) (in thread): > Good morning@Svetlana Ugarcina PerovicMy biggest curation challenge last week was determining the specific methods used in a study investigating the gut microbiome of COVID-19 patients. > > The provided excerpt mentioned metagenomic sequencing but I was unable to quickly identify details about specific aspects like: > > Sequencing platform (Illumina, Ion Torrent, etc.) > Data transformation (relative abundance, CLR/ALR) > Statistical tests for differential abundance > MHT correction methods > Estimator for species richness/evenness > > To overcome these challenges, I took the following steps: > 1. Searched for the original research article: I looked for the full publication by the authors mentioned in the excerpt to see if the methods section provided detailed information about the techniques used. > 2. Consulted online resources: I explored resources like the LEfSe website and general microbiome research protocols to gain a broader understanding of common methods used in this field. > While I couldn’t definitively determine the specific methods used in every case, these steps helped me: > 1. Identify possible approaches commonly used in similar studies. > 2. Understand the limitations of the information available from the excerpt. > 3. Formulate questions to ask the community for clarification on specific methods. > By following these steps, I was able to gain a deeper understanding of the research methods used in microbiome studies and identify areas where I needed further information.

Blessing Ene Anyebe (06:08:10) (in thread): > Do you mean this text@Mildred Anashie”The Faith PD and Shannon index value of the immature hen group were signifcantly lower than those of mature hens and showed large individual variance (Fig. 1b,c). In the 2D PCoA plot, the immature hen group was separated from the mature hen groups belonging to two diferent chicken breeds (Fig. 1d)”

Mildred Anashie (06:08:53) (in thread): > The one talking about fig 1a

Oluwatomisin Omojokun (06:08:55) (in thread): > Good morning@Svetlana Ugarcina Perovic, i will like to add some article to the issues in the github, if that is allowed. Thank you

Blessing Ene Anyebe (06:09:19) (in thread): > Alright, thank you

Amanda Adoyi (06:10:52): > Happy Monday people. I have checked that this is not on the Discussion page of the Taxonomy Id clean up. I found “RF32”. It wasn’t found on the NCBI database but I did find a reference to it on uniprot with the id423432, except…this id is for “Streptococcaceae bacterium RF32” and I think the strains of interest in the Study are Lachnospira and Clostridium. The problem now is I can’t go any further because I don’t have access to the pdf. It isn’t open access. I would like to dig a little deeper. How do I get access? This is the curation:@Svetlana Ugarcina Perovic@Esther Afuapehttps://bugsigdb.org/Study_408/Experiment_2/Signature_2 - Attachment (BugSigDB): Study 408/Experiment 2/Signature 2 > Source: Figure 1b Description: Differentially abundant OTUs Identified by Deseq2 analysis at 1 year Abundance in Group 1: decreased abundance in asthma at 1 year…

Victoria (Burah) Poromon (06:14:03) (in thread): > Good morning@Svetlana Ugarcina PerovicMy biggest curation challenge was identifying my decreasing microbiome’s. > My study used coloured bars that were a bit difficult to differentiate, about 3 to 4 bars had almost the same colour. > > I solved this by curating only the microbiome’s that were significant.

Nana (06:15:08): > @Chioma Onyido@Svetlana Ugarcina Perovicplease i have this image how do i enter the name of the taxa in my signature and how do i type it to be able to finding it in NCBI, some name appers twice with little diffrence i have used a marker to highlight the most confusing part - File (JPEG): Screenshot_2024-03-11-10-41-53-51_99c04817c0de5652397fc8b56c3b3817.jpg

Oluwatomisin Omojokun (06:18:53) (in thread): > Hello@Svetlana Ugarcina Perovic. I had a challenge curating the article that was assigned to me. The study documented both the families and the genera of the microbiome were analyzed. I was able to curate it using the families rather than the genera microbiome.

Oluwatomisin Omojokun (06:22:05) (in thread): > Hello@Svetlana Ugarcina Perovic. I had a challenge curating the article that was assigned to me. The study documented both the families and the genera of the microbiome were analyzed. I was able to curate it using the families rather than the genera microbiome.

idiaru Angela (06:22:33) (in thread): > Good morning@Svetlana Ugarcina PerovicI’m glad to be a part of this community. I’m also learning quite a lot:sweat_smile:My biggest challenge from this past week was identifying the kind of study design and country the paper i was curating worked on. I solved it by looking at past papers and asking questions on the forum > Thank you to all those that gave those helpful replies:heart_hands:. > I also encountered challenges in identifying the differential abundance in the species but reading the paper multiple times definitely gave me more clarity.

Mildred Anashie (06:22:57) (in thread): > For the Bifidobacterium > I think you should type it that way > Bifidobacterium dentuim and search for the NCBI ID

Aleru Divine (06:23:45) (in thread): > For the ones that you highlighted, I would suggest you type the first names eg(Bifidobacterium_pseudocatenulatum) in the NCBI input box.

Nana (06:25:48) (in thread): > In the paper s stands for stain.

Peace Daniel (06:31:19) (in thread): > Hello@Svetlana Ugarcina PerovicMy biggest challenge has been identifying experiments, I’ve overcome this by doing more research, open discussions with peers and reading more articles. Also, I’ve been able to work on seclusion, I’ve learnt more about team work and accepting the opinions of others. > > Shoutout to@Mildred Anashie@Muqtadirat Yussuff@Amanda Adoyi@Bolanle Wahab:purple_heart::heart:

Abiola Salako (06:33:14) (in thread): > Thank you@Rahila-me

NWAKAEGO VINCENT (06:35:10): > i have made my first and second contribution on the biconductor project , do i record the contribution together on outreachy

Peace Daniel (06:35:36) (in thread): > Take a look at thishttps://www.uniprot.org/uniprotkb?query=s_Bifidobacterium_dentium

Peace Daniel (06:36:18) (in thread): > Is it stain or strain? Cuz I saw something about a strain in this link I sent you@Nana

Scholastica Urua (06:36:25) (in thread): > Hello@NWAKAEGO VINCENT, record them as 2 separate contributions on outreachy.

Abiola Salako (06:36:31) (in thread): > @Bolanle WahabYes. you report those 3 that were mentioned.

Mildred Anashie (06:37:24) (in thread): > Iwas going to say same too > > S might be a strain or characteristic of the organism:woman-shrugging:

Abiola Salako (06:37:53) (in thread): > @Muqtadirat YussuffI’m available for review, please

idiaru Angela (06:38:04) (in thread): > @Emem Eduokuhave you been able to finish the curation

Mildred Anashie (06:38:33) (in thread): > Hello@NWAKAEGO VINCENTWell done, please record them separately

Abiola Salako (06:38:39) (in thread): > alright@Idiat Alli

Scholastica Urua (06:38:53) (in thread): > I think the ‘s’ stands for specie. The same way the ‘g’ is for genus.

Aleru Divine (06:39:05) (in thread): > @NWAKAEGO VINCENTRecord each separately as they require different start and merge dates and different contribution URLsRecord all contributions separately

Mildred Anashie (06:39:31) (in thread): > That’sanother point@Scholastica Urua

Scholastica Urua (06:40:23) (in thread): > ‘c’ - class > ‘o’ - order and so on. > > I think they specify the different taxonomy levels.

Precious Orakwe (06:42:19) (in thread): > Please how am I going to get this - File (PNG): Screenshot_20240311-114010.png - File (PNG): Screenshot_20240311-113950.png

Ima-obong (Aimah) (06:43:11) (in thread): > Congratulations@NWAKAEGO VINCENT..record them separately and the required URL will be the links of both contributions you submitted

Mildred Anashie (06:44:10) (in thread): > It is all within the article > Did you download the article?

Scholastica Urua (06:44:25) (in thread): > Let’s say you want to enter s_Bifidobacterium_dentuim (g_Bifidobacterium) as a signature, you’ll enter the species ‘Bifidobacterium dentuim’ since that is the smallest taxonomy level mentioned and as such more specific. This is just my thoughts, I’ll have to do more research to be sure.

Precious Orakwe (06:46:48) (in thread): > Yes, I did, but am not seeing anything like EFO there

Peace Daniel (06:49:28) (in thread): > Or species like@Scholastica Uruasaid

Bolanle Wahab (06:53:03) (in thread): > @Abiola SalakoThank you

Peace Sandy (06:53:30) (in thread): > Hi@NWAKAEGO VINCENTPlease record every contribution you make on Outreachy

Mildred Anashie (06:57:21) (in thread): > The condition in the article is Breast cancer > > You follow the link provided by the question(Experimental Factor Ontology EFO) and type the condition thenyou’llcome across the MONDO or EFO identifierYou’llhave to copy the closest term and paste, I usually go for the first in most cases

Adenike Oladimeji-Kasumu (06:59:11) (in thread): > Good morning@Svetlana Ugarcina PerovicMy biggest challenge last week was curating the signatures from my Paper. I was not able to differentiate between the increased abundance and decrease Abundance. > Getting a solution was not difficult as I posted my problem on the channel and my colleagues helped me in figuring it out. > Getting reviews from my colleagues for me is a great deal. Their help does a lot.

Peace Daniel (07:02:45) (in thread): > @Bolanle Wahabfrom your article, I thank you should record for mycoplasma and the other 3 depending on what your comparisons are.They’remostly recorded in your article with a reference to the 32 others.

NWAKAEGO VINCENT (07:06:06) (in thread): > THANK YOU@Peace Sandy

NWAKAEGO VINCENT (07:08:08): > How do i retreive the link to the first task since i didn’t copy the link before submitting the task?

Aleru Divine (07:08:52) (in thread): > @NWAKAEGO VINCENTjust submit the link to the survey.That’sokay too.

Mojisayo Awolesi (07:08:57): > Can we record the second contribution on Outreachy while still waiting for review?

Mildred Anashie (07:09:24) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Adenike Oladimeji-Kasumu (07:09:40) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc

Adenike Oladimeji-Kasumu (07:09:45) (in thread): > Here is the linkhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc

Aleru Divine (07:09:47) (in thread): > @Mojisayo Awolesiyes we can, butyou’llhave to leave the “merge date” blank for now until it is reviewed.

Mildred Anashie (07:09:56) (in thread): > Yes you can > > > But you would hold on with the merge date

Mojisayo Awolesi (07:10:24) (in thread): > Thank you

NWAKAEGO VINCENT (07:14:27) (in thread): > thank you ladies

Scholastica Urua (07:14:50) (in thread): > Yes, we can. You can still make edits on your curation even after recording it on Outreachy.

Ruth Bamgbose (07:16:30) (in thread): > Hello@Svetlana Ugarcina PerovicMy biggest challenge last week was figuring out what statistical tests I’m supposed to curate as my paper had many, but I was able to solve this by reading the note on this page and having getting review from a colleague. I also had read the paper over and over again, read through curated papers on the website to really understand. My brain feels heavy from all the information I’ve collected and the microbiome names:sweat_smile:. But I’m enjoying it so much.

Bolanle Wahab (07:16:45): > Hi, here’s a link to my studyhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC3564958/and the curation linkhttps://bugsigdb.org/Study_912, I’d like your reviews, Thank you - Attachment (PubMed Central (PMC)): Structure, Function and Diversity of the Healthy Human Microbiome > Studies of the human microbiome have revealed that even healthy individuals differ remarkably in the microbes that occupy habitats such as the gut, skin, and vagina. Much of this diversity remains unexplained, although diet, environment, host genetics, … - Attachment (BugSigDB): Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics - BugSigDB > BACKGROUND: The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited.

Precious Orakwe (07:22:12) (in thread): > I have done that but am not seeing any result

Peace Daniel (07:27:52) (in thread): > Hey there, I noticed you referenced suppl table 1I’myour curation for signatures. I believe you can be more specific like suppl table s1 or s2 whichever the case maybe as I had some difficulty searching for a table 1

Blessing Laweh (07:27:53): > Good timezones guys! Assistance needed please. So I just finished the 1st task, moving to the 2nd. I requested for an account waiting for BugSig mail. I aslo noticed there are no new articles to review. What’s the next step please?

NWAKAEGO VINCENT (07:28:19): > Hi every one i’m glad to inform you that my second task is completed and needs review, I am happy i could do thishttps://bugsigdb.org/Study_923 - Attachment (BugSigDB): Influence of aerobic exercise training on mice gut microbiota in Parkinson’s disease - BugSigDB > Accumulating evidence shows that gut microbial dysbiosis may represent a risk factor for Parkinson’s disease (PD).Exercise has a positive effect on microbiota in general.The effect of aerobic exercise training (AET) on the gut microbial environment in PD remains to be explored.

Oluwatomisin Omojokun (07:28:53): > Hello, kindly review the following Articles with missing NCBIhttps://bugsigdb.org/Category:Pages_with_missing_NCBI_ID - Attachment (BugSigDB): Category:Pages with missing NCBI ID

Mildred Anashie (07:29:15) (in thread): > Please be patient articles will be uploaded

Mildred Anashie (07:29:42) (in thread): > You can check your spam folder for the mail > > It might have been sent

Rahila-me (07:30:03) (in thread): > Follow what@Mildred Anashiesaid

Blessing Laweh (07:30:53) (in thread): > OK thanks for your feedback.

Aleru Divine (07:30:55) (in thread): > While you wait for articles being uploaded you could find some tasks to help with here.https://bugsigdb.org/Help:Cleanup#Links_to_lists_of_pages - Attachment (BugSigDB): Help:Cleanup

Blessing Laweh (07:31:37) (in thread): > Also, when they are uploaded would I be assigned to one or I just pick the one I like?

Blessing Laweh (07:32:00) (in thread): > Thank you@Aleru Divine

Mildred Anashie (07:32:02) (in thread): > You pick one and comment under, asking it to be assigned to you

Blessing Laweh (07:32:26) (in thread): > OK noted. Thanks@Mildred Anashie:purple_heart:

NWAKAEGO VINCENT (07:32:50) (in thread): > how do identify the taxon without id?

Oluwatomisin Omojokun (07:34:47) (in thread): > The taxa written in orange without no link and quality control

Rahila-me (07:35:06) (in thread): > s = strain

Mildred Anashie (07:36:40) (in thread): > Please go through the discussion page to know the ones thatcan’tbe resolved > > Saves you time

Mildred Anashie (07:38:48) (in thread): > Hi@NWAKAEGO VINCENTwell done on completing your second task > > Please ensure you add the link to your study under the issue assigned to you on GitHub > And inform the mentors that the study is ready for review

Blessing Laweh (07:42:08) (in thread): > @Aleru DivineI followed the link you sent me to help with some tasks. I want to help with the 1st clean up task (Pages with missing NCBI ID) > > I want to be sure, what I’m to do is find the correct NCBI ID for the study in the Taxonomy website (?) And put it in the page right?

Aleru Divine (07:43:15) (in thread): > Yesthat’scorrect@Blessing Laweh

Mildred Anashie (07:43:44) (in thread): > You find it and inform the mentors here before making edits > > Also go through the discussion page to guide you on the ones thatcan’tbe resolved > > So you focus on the ones that needs to be resolved

NWAKAEGO VINCENT (07:44:11) (in thread): > alright, thank you

Blessing Laweh (07:45:09) (in thread): > OK@Mildred Anashiethanks for the heads up:+1:

Aleru Divine (07:45:17) (in thread): > Also take note of thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710142898336359 - Attachment: Attachment > <!here>, Good morning all, > Attention! Attention!! Attention!! > Just a little observation I want to point out, please if you are done with your second curation and you go to help clean up on BugsigDb please when you open a work and it has March 2024 as its date of curation please leave it alone and look for another probably 2023 down. > Reason, I don’t know how BugsigDb Algorithm works but once a curator curates anything and save it , it automatically keeps your work on Needs clean_up even when your are still working on that study util you are done.

Blessing Laweh (07:48:38) (in thread): > Thank you@Aleru DivineLiza only mentioned March 2024…and instructed to move to 2023 instead. What if there’s a page dated Jan/Feb 2024 can we work/edit that? > > I hope this question makes sense:sweat_smile:

Mildred Anashie (07:49:47) (in thread): > Yes I guess you can > > As March is for this cohort

Leenaa Al-Amin (07:50:10) (in thread): > hello, I want to delete the entire signature and all its information not edit

Blessing Laweh (07:50:31) (in thread): > OK! Thanks for your responses, they are highly appreciated.:purple_heart:

Aleru Divine (07:51:25) (in thread): > Yes it makes sense.I think you can work on Jan and Feb.

Nana (07:57:44): > @Peace SandyI asked you about how I don’t think my study mentioned any Sequencing platform used as it Sequencing type is WMS..you said I should drop a link so you confirm since Saturday you have not gotten back to me > Is also possible for a study not to have the Significance threshold mentioned like p or q value for the same study could not find any: here is the article once again: > cc:@Chioma Onyido@Esther Afuapehttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.780568/full - Attachment (Frontiers): Frontiers | Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode

Nana (07:58:45) (in thread): > Thanks guys, strain actually it was autocorrect that changed it

Esther Afuape (07:59:56) (in thread): > Deleted:white_check_mark:

Nana (08:00:53): > <!channel>: > For newcomers, when you go to github to request for a paper to curate and you see that someone else has requested for that paper, leave it alone and look for an empty paper that no one has requested for and request for it, that’s the one that will be assigned to you. You don’t request for a paper that has already been assigned to someone else. No two people that work on one paper. Thank you all.

Scholastica Urua (08:01:54) (in thread): > Hello@Nana, Svetlana said they’ll go through our still open questions. > Let’s be patience, I’m positive they’ll get to your question.

Peace Daniel (08:03:05) (in thread): > Alright Nana, you welcome

Mildred Anashie (08:03:30) (in thread): > Yea@Scholastica Uruais right

Peace Sandy (08:04:28) (in thread): > @Nanaplease be patient they are many unanswered questions and yours will be attended too

Juliana Oluwatobi (08:09:11): > Noted

Nana (08:13:13) (in thread): > Ok..thank you all

Nana (08:13:48) (in thread): > :ok_hand:

Mildred Anashie (08:22:29) (in thread): > For the P value you might have to use the default 0.05 > > I came across a few results reported using P=0.001 > But we should wait for the mentors response

Leenaa Al-Amin (08:30:05) (in thread): > hello@Desire Oluwarotimi@Mildred Anashiethank you for your reviews yesterday, please what are your github handles so I can tag you

Leenaa Al-Amin (08:30:53) (in thread): > thank you:pray:

Mildred Anashie (08:32:41) (in thread): > You are welcome@Leenaa Al-Amin@MyleeeA

Peace Daniel (08:37:41): > Hey guys, new issues have been added on GitHub for the second contribution.

Amarachi Lewachi (08:41:25): > @Aleru DivineHow do you find incomplete studies to complete their curation. I would like to do so as well

Aleru Divine (08:42:40) (in thread): > I go to studies that have no experiments on the help: pagehttps://bugsigdb.org/Help:Cleanup - Attachment (BugSigDB): Help:Cleanup

Mildred Anashie (08:43:17) (in thread): > Hi Amarachi > > Check herehttps://bugsigdb.org/Special:Ask/-5B-5BState::Incomplete-5D-5D/mainlabel%3D/offset%3D0/format%3Dol/searchlabel%3DIncomplete-20pages-20(marked-20as-20incomplete-20by-20curator) - Attachment (BugSigDB): Special:Ask/-5B-5BState::Incomplete-5D-5D/mainlabel=/offset=0/format=ol/searchlabel=Incomplete-20pages-20(marked-20as-20incomplete-20by-20curator)

Scholastica Urua (08:43:59) (in thread): > Hi@Amarachi Lewachiyou can also check the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Help:Contents > …

Scholastica Urua (08:44:50) (in thread): > Please endeavor to alert the mentors before you work on previous curation though.

Svetlana Ugarcina Perovic (08:45:45) (in thread): > @Nanayes, indeed, the authors did not state the sequencing platform; leave it blank. As for the other question,@Mildred Anashieanswered it.

Nana (08:48:46) (in thread): > @Svetlana Ugarcina Perovicnoted thanks

NWAKAEGO VINCENT (08:51:01) (in thread): > I will do that now

Muqtadirat Yussuff (08:51:19) (in thread): > @Peace Danielhi, there are only two supplementary tables, 1 and 2 which is why I wrote it like that but I’ll check again. Maybe I missed the naming, thank you so much

Svetlana Ugarcina Perovic (08:51:40) (in thread): > @Rahila-mebe careful, s stands for SPECIES

Peace Daniel (08:55:21) (in thread): > I’mreferring to how it was named in your article

Muqtadirat Yussuff (08:57:58) (in thread): > Ohh, okay, I get now. I’ll change that, thank you. > > What are your thoughts on the experiments and signature section by the way?

Amanda Adoyi (09:01:23): > Hi:slightly_smiling_face:Found “unknown Gammaproteobacteria” in the paperhttps://bugsigdb.org/Study_799/Experiment_2/Signature_1I understand that you@Chioma Onyidohad looked it up but I came across the id 86473. I would like to understand why these classifications differ in the database. There appears to be little to no difference besides the rank, as one is unknown and the other is ‘species’. - Attachment (BugSigDB): Study 799/Experiment 2/Signature 1 > Source: Table 4. Description: Mean relative abundance of phyla and genera in HIV-positive individuals without COPD versus HIV-negative individuals without COPD…

Peace Daniel (09:05:43): > Under studies that have no experiments, I noticed https://bugsigdb.org/Study_857 already exists as https://bugsigdb.org/Study_733 (and Is reviewed) > > I suggest study 857 is deleted, can I go ahead to delete this?@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

Svetlana Ugarcina Perovic (09:12:35) (in thread): > Deleted. Thanks!

Mildred Anashie (09:14:47) (in thread): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyJust drawing your attention to this:pray:

Esther Afuape (09:15:38) (in thread): > HiI’llcheck it out in a bit

Scholastica Urua (09:24:11): > Hello@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyidoand everyone. > > I found this incomplete study without experiments and signatures and I’d love to complete it. > Link:https://bugsigdb.org/Study_585Please can I go ahead? - Attachment (BugSigDB): Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer - BugSigDB > Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa.The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear.

Esther Afuape (09:24:27) (in thread): > Please do

Scholastica Urua (09:24:47) (in thread): > Thank you Esther

Muqtadirat Yussuff (09:24:47) (in thread): > Hello@Svetlana Ugarcina Perovic, I identified two NCBI ID yesterday and I haven’t gotten a response if I should edit or perhaps note it somewhere on BugSigDB. > > If it’s not an inconvenience, may I tag you on the thread again? Thank you

Emem Eduoku (09:26:31) (in thread): > not yet@idiaru Angela

Esther Afuape (09:27:08) (in thread): > @Muqtadirat Yussuffplease tag me on it

Muqtadirat Yussuff (09:28:30) (in thread): > @Esther Afuapehere it is, thank you

Desire Oluwarotimi (09:32:46) (in thread): > You are welcome@Leenaa Al-Amin@RotimiDesire

Esther Afuape (09:34:08) (in thread): > Yeah you can go ahead

Desire Oluwarotimi (09:35:28): > Good afternoon everyone.@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI found an incomplete study. Although it says it has been reviewed already, it doesn’t have any experiment at all. So, I’d like to work on it. > > Here is the link.https://bugsigdb.org/Study_784Can I go ahead? - Attachment (BugSigDB): Metagenomic assessment of gut microbial communities and risk of severe COVID-19 - BugSigDB > BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections.However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

Mildred Anashie (09:36:01) (in thread): > It’s a bit confusing most times and I see that the ID shows Unculture, Unclassified, unidentified and unknown Gammaproteobacteria > > What I understand is that taxas with unknown tags typically refer to taxa that have not been confidently identified or classified at the species level, “uncultured” or “unclassified” species often refer to taxa that have been identified but have not yet been successfully cultured or classified to a known taxonomic group > > I’m of the opinion that Most studies use term interchangeably, I think it mostly depends on context >
> I don’t know if this answers anything:woman-shrugging:

Amanda Adoyi (09:37:13) (in thread): > @Mildred AnashieIt helps me big time but also keeps me questioning the situation. I can’t tell if both ids refer to the same taxon.

Svetlana Ugarcina Perovic (09:37:49) (in thread): > @Peace Sandyplease take a look, this one you presented recently at the team meeting.

Mildred Anashie (09:38:28) (in thread): > Okay > > > Thank you:pray:

Amanda Adoyi (09:39:52): > Aloha. I would like to know if modifying your curation is possible even if you have indicated that it’s ready for review and maybe…just maybe review of your work has begun?

Blessing Ene Anyebe (09:40:22) (in thread): > Yea it is

Desire Oluwarotimi (09:40:49) (in thread): > @Amanda AdoyiYou can always modify your curation

Mildred Anashie (09:41:09) (in thread): > In my opinion it is possible

Muqtadirat Yussuff (09:41:49) (in thread): > I believe it is possible

Svetlana Ugarcina Perovic (09:42:41) (in thread): > If the GitHub issue with your curated paper is with tag****“needs review” ****that means now it’s in our hands under review and you are kindly asked to not make any changes while we are reviewing it.

Ima-obong (Aimah) (09:43:14) (in thread): > Oh wow

Amanda Adoyi (09:43:44) (in thread): > Thanks@Svetlana Ugarcina PerovicThis should probably be pinned because a lot of people may not know this really important fact.

Ima-obong (Aimah) (09:43:57) (in thread): > Thanks@Svetlana Ugarcina Perovic..noted

Victoria (Burah) Poromon (09:44:04): > Hello@Svetlana Ugarcina Perovic,@Peace Sandy,@Chioma Onyido,@Esther AfuapeUnder the incomplete studies, I noticed study 783 and 872 were incomplete. But their DOI’s took me to a study that I believe has already been curated under study 873. > > Please kindly check this out.Here’sthe link to both studies.https://bugsigdb.org/Study_872https://bugsigdb.org/Study_783 - Attachment (BugSigDB): - BugSigDB > … - Attachment (BugSigDB): - BugSigDB > …

Mildred Anashie (09:44:36) (in thread): > Thanks@Svetlana Ugarcina PerovicNoted

Muqtadirat Yussuff (09:45:17) (in thread): > Wow, we all thought it was allowed

Blessing Ene Anyebe (09:45:20) (in thread): > Thank you@Svetlana Ugarcina Perovicfor clearing that up > > Thank you@Amanda Adoyifor the question

Ima-obong (Aimah) (09:45:59): > Quick reminder!!.. > Hello, just incase you’re wondering what next to do, there are a few papers on GitHub yet to be assigned…you can request for one now.

Amarachi Lewachi (09:46:19) (in thread): > @Amanda AdoyiThank you for this question.@Svetlana Ugarcina PerovicThank you for your response. I believe it should be pinned as I was equally unaware of this fact.

Amarachi Lewachi (09:47:04): > If I am done with my second contribution do I get to update it on outreachy or do I wait until it is reviewed?

Svetlana Ugarcina Perovic (09:47:15) (in thread): > Once you share with us a bugsigdb link with your curated study andclaim it for review, we assume that you finished your curation and it gets tag “needs review”. From that moment, we are working on it.

Amanda Adoyi (09:47:33) (in thread): > @Amarachi LewachiI was virtually running to you because we talked about this possibility.

Ima-obong (Aimah) (09:47:51) (in thread): > Yes you should….it takes a while for papers to be reviewed

Amarachi Lewachi (09:48:08) (in thread): > @Amanda AdoyiLuckily I saw your post immediately.

idiaru Angela (09:49:01) (in thread): > You can update it now, then wait till its reviewed to input the merged date

Muqtadirat Yussuff (09:49:29) (in thread): > That means I have to submit the paper I marked complete and can no longer edit, oof. > However it’s nice knowing this a bit early on, thank you@Amanda Adoyifor this question

Idiat Alli (09:50:29) (in thread): > @idiaru Angelareally, we can add it tentatively?

Svetlana Ugarcina Perovic (09:50:53) (in thread): > @Muqtadirat Yussuffit means that once you claim it on the GitHub Issue that is ready for review, you are no longer working on it.

Mildred Anashie (09:51:09) (in thread): > Please update it on outreachy

idiaru Angela (09:51:15) (in thread): > @Idiat Alliyes, using the link to the curation

Idiat Alli (09:52:34) (in thread): > Okay thank you@Mildred Anashie@idiaru Angela

Amarachi Lewachi (09:53:05) (in thread): > Thank you all so much

Muqtadirat Yussuff (09:54:37) (in thread): > I wasn’t planning on changing the paper I got from GitHub. I got permission to work on an incomplete curation and I marked as complete before posting here for reviews from fellow contributors. > > I haven’t informed mentors I’m through, does it also mean it can’t be changed? Since I’ve marked the form complete? Or it’s only applicable to papers marked “needs review” on GitHub?@Svetlana Ugarcina Perovic

Amanda Adoyi (09:58:18) (in thread): > I think that when you go to the issue on github and indicate that it’s ready for review, that’s when the “needs review” tag is placed there.

Barakat Akinsiku (10:00:46): > Hello everyone, how do we know an incomplete study we want to undertake hasn’t been taken up by someone else already?

Muqtadirat Yussuff (10:01:01) (in thread): > @Amanda AdoyiI wasn’t talking about a paper issued to us on GitHub. However going further, I don’t plan on marking papers complete unless I’m pretty sure it’s done. Was just asking about that particular issue

Desire Oluwarotimi (10:02:40) (in thread): > @Barakat AkinsikuI think that’s one of the reasons we are asked to post it on the group. > > If someone else is working on it, they will surely signify when they see it. You could even end up working on it together with such individual. I mean it’s open source, so why not?

Scholastica Urua (10:02:52) (in thread): > I think that’s why the links are posted on this platform to avoid such.

Emem Eduoku (10:04:23): > Hello everyone. If alpha diversity test showed no statistically significant difference between H0 and H1, how does this differ from the relative abundance of the signatures. I am confused as I thought there need to be alpha diversity for us to have increased and decreased signatures

Barakat Akinsiku (10:04:57) (in thread): > Oh I see@Desire Oluwarotimi, thanks. Thanks Scholastica

Mildred Anashie (10:05:04) (in thread): > @Muqtadirat YussuffI think@Svetlana Ugarcina Perovicis referring to just the GitHub issues as that is part of the task assigned to us and it will be scored

Muqtadirat Yussuff (10:05:59) (in thread): > @Mildred Anashiethank you for making it clearer. I was just trying to cover all bases but again thank you

Desire Oluwarotimi (10:07:11) (in thread): > Hi@Emem EduokuIf your alpha diversity is indicating that there’s no statistically significant difference, it’ll mean that it is unchanged, thus neither increased or decreased. > > It’s different from signatures because this is only referring to differentially abundant taxas when a group pair are compared.

Emem Eduoku (10:08:49) (in thread): > so alpha diversity has nothing to do with the signatures we will be documenting right?@Desire Oluwarotimi

Scholastica Urua (10:09:11) (in thread): > Hi Emem, the presence or absence of statistically significant differences in alpha diversity does not preclude the possibility of detecting differential microbial signatures. > So whether the alpha diversity is increased, decreased or unchanged, you can still identify signatures.

Ima-obong (Aimah) (10:09:48) (in thread): > Hello@Barakat Akinsikupost the links here and tag the mentors to it

Aleru Divine (10:10:56) (in thread): > Yes@Emem Eduokualpha diversitydoesn’taffect the differential abundance of taxa.So whether it increases or decreases or remains unchanged.It has nothing to do with it.

Desire Oluwarotimi (10:11:32) (in thread): > @Emem EduokuWhile alpha diversity is independent of the signatures you are curating, I think there’s still a connection point between them and it is that they belong to the same experimental groups.

Mildred Anashie (10:12:28) (in thread): > I think what affects the experiment is if the results are significant or not > > Not the alpha diversity, if alpha diversity is not significant you record unchanged

Oluwatomisin Omojokun (10:16:02): > Hello@Svetlana Ugarcina Perovic, i found a study without no experiment and signature, i have complete ithttps://bugsigdb.org/Study_333, Kindly review. Thank You - Attachment (BugSigDB): Maternal antimicrobial use at delivery has a stronger impact than mode of delivery on bifidobacterial colonization in infants: a pilot study - BugSigDB > OBJECTIVE: To investigate factors related to bifidobacterial colonization in early infancy, with a focus on maternal antimicrobial use at delivery.STUDY DESIGN: A cross-sectional pilot study was performed.

Melysssa Minto (10:16:11): > @Melysssa Minto has left the channel

Bolanle Wahab (10:16:23) (in thread): > @Emem Eduokuit differs, it just means that the groups are similar, but specific taxa within the two groups still varies

Ruth Bamgbose (10:17:08) (in thread): > Yeah, while alpha diversity assess the overall diversity within the group, relative abundance of signatures focuses on specifictaxa that shows difference between the groups.

Bolanle Wahab (10:19:01): > Hello @svetlana_up @Afuape Esther@Chioma OnyidoI found this incomplete study experiment without signatures > Link:https://bugsigdb.org/Study_321/Experiment_2Please can I complete it? - Attachment (BugSigDB): Study 321/Experiment 2 > …

Emem Eduoku (10:20:51) (in thread): > Thank you all for the clarification@Desire Oluwarotimi@Mildred Anashie@Aleru DivineAnother question. Is it possible not to have confounders in the study? I am still not sure the study i am working on has confounders

Mildred Anashie (10:21:37) (in thread): > Yesit’spossible > I believe not all study designs allow controlling for Confounders

Scholastica Urua (10:22:20) (in thread): > Yes@Emem Eduoku, it is very possible not to have confounders. The researchers may not have accounted for confounders.

Aleru Divine (10:22:41) (in thread): > Yesthat’spossible@Emem Eduoku

Emem Eduoku (10:22:55) (in thread): > Yes@Mildred Anashiebut i have two conflictinng scenarios for the confounders

Aleru Divine (10:24:34) (in thread): > @Emem EduokuCould you share your article or an excerpt?

Mildred Anashie (10:25:44) (in thread): > What are the conflicting scenarios?@Emem Eduoku

Victoria (Burah) Poromon (10:26:08) (in thread): > With regards to my earlier message, I also found other incomplete studies that already exist on the database with a different study number. > > Under studies that have no experiments. > Study 883, 883 and 884 have the same link. And that article has already been curated under study 899.

Samreen Aftab (10:27:11): > Good day everyone. > In the paperhttps://bugsigdb.org/Study_837/Experiment_4/Signature_2, I found a missing NCBI Id for Erysipelatoclostridiaceae. From google search, I found this page. Are both of them interchangeable? Can I replace******Erysipelatoclostridiaceae with the NCBI id of ****Coprobacillaceae? > > Please correct me if I’m wrong, this is my first time working with microbiomes and scientific terms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (PNG): image.png

Emem Eduoku (10:27:24) (in thread): > This is the first one. It says they couldn’t strictly control for medication and diet which may have confounding effect but they did rule put some medications and dietary habit - File (JPEG): 20240311_152514.jpg

Aleru Divine (10:31:35) (in thread): > @Emem EduokuBugSigDB requests for “confounders controlled for” and from this image it states that > > “We could not strictly control for medication and diet of our subjects and this may have confounding effects on the results, We did rule out some medication and dietary habits that could strongly affect the gut microbiome.” > > So non of the confounders were controlled for or at least “strictly controlled for”

Aleru Divine (10:32:00) (in thread): > Could you share the other?

Emem Eduoku (10:32:57) (in thread): > And the second one where some clinical PD features were quantified and associated with microbial composition > Does this count as confounders? - File (JPEG): 20240311_152949.jpg

Scholastica Urua (10:33:05) (in thread): > @Emem Eduokufrom my point of view, medication and diet are confounders in this case because they could not strictly control for them. Though some medications and diet were ruled out, that does not include all medications and diet which could still skew the result of the study.

Bolanle Wahab (10:34:10) (in thread): > @Samreen AftabI’d suggest you leave it at that instead of changing it, NCBI is used when BugSigDBdoesn’tshow whatyou’relooking for

Emem Eduoku (10:34:21) (in thread): > Are confounders only ruled out? Can they also be quantified and used in checking the effect on the composition like in my 2nd image above?

Aleru Divine (10:34:38) (in thread): > @Emem EduokuThe second image doesn’t count as confounder.

Mildred Anashie (10:35:57) (in thread): > AlsoI’dadvice you check the discussion page to know if this has been mentioned there

Emem Eduoku (10:38:37) (in thread): > So in this study we can say there were no confounders

Aleru Divine (10:43:49) (in thread): > @Emem EduokuYeah, theyweren’texactly “controlled for” > > Even while the researchers made efforts to address potential confounders related to medication and diet in their study, they acknowledged limitations in their ability to control for these factors completely.

Mildred Anashie (10:43:58) (in thread): > YesThat’smy opinion, there was no Confounders controlled for

Peace Sandy (10:44:17) (in thread): > Okay@Svetlana Ugarcina PerovicI will

Adenike Oladimeji-Kasumu (10:47:08) (in thread): > I advise that you do not interchange them as the NCBI ID is what is being made use of in BugSigDB. As@Bolanle Wahabas said, you should leave it at that.

Emem Eduoku (10:48:38) (in thread): > So I’d like to know what the point was for them doing a correlation between relative abundance and the clinical features of the condition. I thought the purpose of this correlation is to measure the relationship between variables, which is what confounders are

Samreen Aftab (10:49:00) (in thread): > Okay, thank you guys.

Adenike Oladimeji-Kasumu (10:52:51): > Hello everyone, I want to say well done to everyone:hugging_face:There’s so much support here so I encourage everyone to keep going and not to give up. > Also, I am open to reviewing your work if you are ready. You can drop the link here. > Cheers everyone

idiaru Angela (10:55:25) (in thread): > Hi@Muqtadirat YussuffI think you missed one of the alpha diversity metric that was measured

Emem Eduoku (10:59:00) (in thread): > @Svetlana Ugarcina PerovicI’d like to know if the correlation test done using Spearman’s correlation on the features of the condition does not make these features count as confounders

Isoken Ibizugbe (11:00:04) (in thread): > I also found this incomplete study experiment without signatures. Please can it be assigned to mehttps://bugsigdb.org/Study_931/Experiment_1

Aleru Divine (11:02:16) (in thread): > @Emem EduokuWhile you’re correct, I think the purpose of correlating the relative abundance with clinical features of PD(this particular correlation) is to explore potential associations or relationships between gut microbiota composition and the disease and its manifestations. > > Can u see table 3? Might throw more light

Samreen Aftab (11:02:54): > Hi guys, I found a missing NCBI id for Proteobacteria in the studyhttps://bugsigdb.org/Study_933Can I edit it? - File (PNG): image.png

Joan C. Chukwuemeka (11:05:11): > @Samreen Aftabttps://bugsigdb.org/Study_933is for a current applicant. You need to let the person know about your findings - File (PNG): image.png

Samreen Aftab (11:05:49) (in thread): > Oh okay, sure!

Millicent Adzepa (11:06:14): > Hello Good morning everyone, please I need help with my account request, > I requested an account to start my second task, after filling the forms I waited for 2 hours without any confirmation link in my email, so I figured that I might have missed a letter in my email, then decided to request a new one which i got the confirmation within few minutes, clicked on the linked and it was successful. > I tried logging in and could not, so I requested for reset of password . then the attached email was sent. Please how do I go about it.@Svetlana Ugarcina Perovic@Chioma Onyido@Esther AfuapeThank you. this has been my issue since Saturday - File (JPEG): WhatsApp Image 2024-03-09 at 9.26.33 PM.jpeg

Michael Adekanye (11:06:55): > Hi, > Please if statistical analysis methods used in a research can’t be found or listed when curating/adding experiment in bugsigdb. What can be done?

Emem Eduoku (11:07:54) (in thread): > @Aleru Divinehere’s table S3 - File (JPEG): 20240311_160700.jpg

Joan C. Chukwuemeka (11:07:59) (in thread): > @Isoken Ibizugbehttps://bugsigdb.org/Study_931/Experiment_1is a study being worked on by a current outreachy applicant. You need to inform that person. We’re not to make edits on such ones.:pray: - File (PNG): image.png

Mildred Anashie (11:08:03) (in thread): > I think you leave it blank > > What statistical method was used though?

Aishat Ijiyode (11:08:15) (in thread): > Thank you ladies. I have requested for one article

Scholastica Urua (11:08:41) (in thread): > You can leave that part blank@Michael Adekanyeif it was not mentioned.

Aleru Divine (11:09:12) (in thread): > Thanks

Emem Eduoku (11:09:30) (in thread): > And here’s the correlation matrix for the features and the relative abundance - File (JPEG): 20240311_160817.jpg

Esther Afuape (11:09:46): > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonymon NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replaceEscherichia coli withEscherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the2-hour videoof<@U1LCB8WEA>solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always askBEFOREyou make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose: - Attachment (Loom): BugSigDB Category:Pages with missing NCBI ID > Two hours of correcting unmapped NCBI taxonomy IDs

Scholastica Urua (11:12:19) (in thread): > Thank you Esther for this clarification.

eneje promise (11:12:29): > Hello everyone,@Svetlana Ugarcina Perovic. I have been assigned to work on Characteristics and correlations of the oral and gut fungal microbiome with hypertension. Kindly assist point out what I am supposed to do?

Joan C. Chukwuemeka (11:12:35) (in thread): > @Michael AdekanyePlease can you share the article ?

Joan C. Chukwuemeka (11:13:34) (in thread): > @eneje promiseIs this your second contribution? what help do you need?

Mildred Anashie (11:14:01) (in thread): > @Emem EduokuThis figure 3 shows the characteristics of the participants in my opinion this might be inclusion criteria and how it correlates with the gut Microbiota of the participants

Aleru Divine (11:14:13) (in thread): > @Emem Eduokusee the description of the figure 6 “The correlation matrix based on the Spearman’s correlation distance confirmed correlations between the relative abundance of the top 65 abundant genera and clínical features.” > > I think this proves that thespearman’scorrelation was used to indeed confirm the relationship between the relative abundance of the gut microbiota composition and the clinical features of PD.

Aishat Ijiyode (11:14:14): > Hello everyone, there’s new articles to curate now. If you’ve not gotten an article for your second contribution please check now

Aleru Divine (11:15:57) (in thread): > Alright@Aishat IjiyodeGoodluck on your second contribution.Don’thesitate to ask questions whenyou’restuck/experiencing difficulties:heart:

Muqtadirat Yussuff (11:16:29) (in thread): > Hi@eneje promiseYou should add a new study on BugSigDB and fill in the forms such as the body site, condition, experiment, signatures e.t.c. > > If you try adding a new study and it says the DOI isn’t unique then that means that particular paper is already in the database which you’d search for and proceed to edit the required fields. > > If you’re not really sure what the required fields involve, you should already curated papers but if you’ve done your first curation, it’s the same process you’re to follow. Do ask questions to fellow contributors when you get stuck

Mildred Anashie (11:17:42) (in thread): > Thank you@Esther Afuape:pray:

Emem Eduoku (11:18:58) (in thread): > @Mildred Anashienot exclusion criteria. For the H1 group these features in Table S3 were identified and also quantified to find a relation with the features and the relative abundance

Esther Afuape (11:19:18) (in thread): > Nice catch@Victoria (Burah) Poromonall deleted:white_check_mark:

Emem Eduoku (11:19:32) (in thread): > I think that’s why I am confused but from what you guys explained I’ll go with no confounders

Aleru Divine (11:20:12) (in thread): > @eneje promisehave a look at this previous study > > Link to study:https://bugsigdb.org/Study_600Also look at this video on how to add a study on BugSigDB > > Link to video:https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=4&t=160s - Attachment (BugSigDB): Alteration of the fecal microbiota in Chinese patients with Parkinson’s disease - BugSigDB > Emerging evidences suggest that gut microbiota dysbiosis plays a role in Parkinson’s disease (PD).However, the alterations in fecal microbiome in Chinese PD patients remains unknown.This case-control study was conducted to explore fecal microbiota compositions in Chinese PD patients. - Attachment (YouTube): Adding a study to bugsigdb.org

Mildred Anashie (11:20:20) (in thread): > I said inclusion not exclusion > > Inclusioncriteria’sand Confounders are a bit confusing

Scholastica Urua (11:21:27) (in thread): > Hello@eneje promiseplease go through a step-by-stepwalk-throughof how to add a new study through the curation interface of BugSigDB. - Attachment (YouTube): Adding a study to bugsigdb.org

Isoken Ibizugbe (11:21:29) (in thread): > Thanks, I will take note of the date next time.

idiaru Angela (11:23:03) (in thread): > You should also read the curation policy that can be found on the help page. It also serves as a guide

Aleru Divine (11:24:05) (in thread): > @Michael Adekanyecould you share the article please.I agree with leaving it blank.But just to be sure:hugging_face:

Esther Afuape (11:24:47) (in thread): > All sorted:white_check_mark:

Aleru Divine (11:25:25) (in thread): > Thanks for this@Esther Afuape:sweat_smile:

Mildred Anashie (11:27:08) (in thread): > Oh > > Thanks a lot:hugging_face:Can I ask why 783 appeared that way? > > Just curious:see_no_evil:

Victoria (Burah) Poromon (11:28:08) (in thread): > Thank you.

Esther Afuape (11:28:49) (in thread): > I’mnot sure…seems someone manually entered the metadata to create the study but theydidn’tcurate it.

Michael Adekanye (11:31:37) (in thread): > Only two was listed there that I could pick from. I tried writing them,but they won’t stay. - File (PDF): Progression of Parkinson’s disease is associated with gut dysbiosis_ Two-year follow-up study - PMC.pdf

idiaru Angela (11:34:21) (in thread): > Hey@Muqtadirat YussuffI also noticed that two types of samples were collected both oral and fecal samples > But only noticed oral samples accounted for or is there a reason for that?

Adenike Oladimeji-Kasumu (11:35:43) (in thread): > Thank you@Esther Afuapefor shedding light to this

Emem Eduoku (11:36:48) (in thread): > @Mildred AnashieI’m further confused now. The H1 group were later subdivided into two groups based on severity and I think this is where those features stated were used. > > The mild and the severe group were compared against the control for the differential abundance using a different statistical analysis

Aleru Divine (11:36:56) (in thread): > @Michael Adekanyeyou mean the statistical test right?

Michael Adekanye (11:37:20) (in thread): > Yeah@Aleru Divine

Mildred Anashie (11:37:28) (in thread): > Okay > This makes sense, Thank you for responding:hugging_face::bouquet:

Mildred Anashie (11:38:13) (in thread): > Please share link to your paper

Michael Adekanye (11:39:40) (in thread): > I will check the help page and probably relay this issue thru talk page to@Svetlana Ugarcina Perovic

Aleru Divine (11:40:35) (in thread): > I see wilcoxon there. - File (JPEG): IMG_7797

Muqtadirat Yussuff (11:41:38) (in thread): > Hey@idiaru Angela, I accounted for only the oral microbiome because it’s the main study of the paper. It appears they were comparing with a fecal microbiome research that was previously carried out.

Aleru Divine (11:42:15) (in thread): > @Michael Adekanyetype Mann-Whitney in the provided column - File (JPEG): IMG_7799

Barakat Akinsiku (11:42:53) (in thread): > Hi@eneje promiseyou can read this guide on how to get started. It has links to several videos that are also helpfulhttps://github.com/waldronlab/BugSigDBcuration/issues/94

Emem Eduoku (11:43:43) (in thread): > Let me know if you can access this@Mildred Anashie - File (PDF): Download.article.pdf

Mildred Anashie (11:44:05) (in thread): > It says between year 0 and 2 wilcoxon was used > > And between stable and deteriorated groups Mann Whitney was used > > If these are two experiments you are considering then > There are the same thing on BugSigdb like Divine has highlighted

Aleru Divine (11:44:38) (in thread): > Additionally, there was MHT correction > > “For multiple comparisons of bacterial counts between the deteriorated and stable groups, the false discovery rate (FDR) was calculated using the Benjamini and Hochberg method.”

Emem Eduoku (11:45:18) (in thread): > I’ll appreciate clarity on the number of experiments to add and the confounders. Those are the areas i am struggling with

Ruth Bamgbose (11:46:14) (in thread): > Thank you@Esther Afuape

Emem Eduoku (11:46:31) (in thread): > @Scholastica Urua@Aleru Divineplease see the link to my paper and help me with the confounders and number of experiments to curate for

Aleru Divine (11:48:36) (in thread): > I’llcheck this out@Emem Eduoku

Michael Adekanye (11:49:21) (in thread): > I thought that part was just select all/any statistical test that was used

Joan C. Chukwuemeka (11:50:07) (in thread): > @Michael AdekanyeThe statistical test that was used to get the differential abundant organisms between the groups is the one to be curated@Scholastica Urua:point_up_2:

Ruth Bamgbose (11:50:55) (in thread): > Also check out the canvas . It explains some key points more clearly. - File (JPEG): IMG_5658

Mildred Anashie (11:52:27) (in thread): > The statistical test that was used for differential abundance > > And It’s not clearly stated here

Mildred Anashie (11:54:34) (in thread): > I would start with identifying what the groups here are and the significant results@Michael Adekanyecan you give more insights > Haven’t gone through the whole paper

Joan C. Chukwuemeka (11:55:00) (in thread): > @Mildred AnashieThe literature review process helps to understand and know which it is.@Michael Adekanyelet me check the article and get back to you

Michael Adekanye (11:55:47) (in thread): > @Joan C. ChukwuemekaThank you. I will be expecting your feedback.

Michael Adekanye (11:59:11) (in thread): > @Mildred AnashieIn the statistical analysis part ehn, a lot of statistical method was used. While trying to select, only two found during curation.@Joan C. Chukwuemekastated above that the test used to get the differential abundant organism is the only one needed. That makes sense. Now I have to dig to get that, since it’s not clearly stated.

Scholastica Urua (12:03:44) (in thread): > Let me check the paper out@Emem Eduoku

Mildred Anashie (12:06:08) (in thread): > @Michael Adekanyeyour significant results are in table 2 and supplementary table 2 > > And both tables state Wilcoxon soI’dgo with wilcoxon

Michael Adekanye (12:08:37) (in thread): > @Mildred AnashieI will have to go back into it. I think I missed some information. Thank you.

Michael Adekanye (12:10:33) (in thread): > I guess the best thing here is to ask for help and take time. Probably I’m in a rush to finish. Thank you guys.

eneje promise (12:10:58) (in thread): > Thank you all

Aleru Divine (12:16:05) (in thread): > @Emem Eduokuthe article says they could not strictly control for medication and diet of the subjects and this may have confounding effects on the results.So I believe this means no confounder was controlled for.For the number of experiments, I see comparisons between > > PD and healthy controls > Mild PD and healthy controls > Severe PD and healthy controls.I think the second and third comparisons came from the fact that they wanted to check if truly the gut microbiota differed at different PD stages.

idiaru Angela (12:19:58) (in thread): > Thank you@Esther Afuape

Scholastica Urua (12:20:27) (in thread): > @Emem EduokuI have been able to identify 2 experiments — > > Experiment 1: > Group 0 - HC (n = 14) > Group 1 - PD (n = 24) > > Experiment 2: > Group 0 - mild PD (MPD) group > Group 1 - severe PD (SPD) group > > I could also see — > Antibiotic exclusion: 3 months > Matched on: age, gender > > For the confounders, I’m still on the fence about that.

Emem Eduoku (12:24:16) (in thread): > Thanks@Scholastica Uruaand@Aleru Divine

NWAKAEGO VINCENT (12:27:30): > Hi@Suru Olaitancan i have a look at your article

Suru Olaitan (12:28:22) (in thread): > Thank you@NWAKAEGO VINCENTfor your help > I’ll send the link now

Suru Olaitan (12:29:01) (in thread): > https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.00164/full?utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field&journalName=Frontiers_in_Microbiology&id=419818 - Attachment (Frontiers): Frontiers | Comparison of Small Gut and Whole Gut Microbiota of First-Degree Relatives With Adult Celiac Disease Patients and Controls

Suru Olaitan (12:30:06) (in thread): > I’m having issues in identifying my statistical test and determining if there’s an MHT correction, LDA score, and the Alpha Diversity

idiaru Angela (12:33:54) (in thread): > @Suru OlaitanHave you tried checking the supplementary materials

Mildred Anashie (12:36:42) (in thread): > @Emem EduokuI do not see any Confounders controlled forAnd I see three experiments like Divine pointed out, see attached images for more clarity on where to look in the paper - File (PNG): IMG_2199 - File (PNG): IMG_2198

idiaru Angela (12:37:59) (in thread): > Hi@Muqtadirat YussuffI think you missed one of the alpha diversity metric that was measured

Suru Olaitan (12:38:33) (in thread): > @Aleru DivineYes, I have

Aleru Divine (12:39:14) (in thread): > I’llcheck this out soon

Muqtadirat Yussuff (12:40:20) (in thread): > Oh which one please? Can you share a screenshot?@idiaru Angela

Ima-obong (Aimah) (12:40:27) (in thread): > Thank you@Esther Afuape

NWAKAEGO VINCENT (12:40:51) (in thread): > check your sequencing process, i saw ANOSIM, ANOVA test for the statistical testing

Ima-obong (Aimah) (12:42:20) (in thread): > @eneje promiseplease take a look at this curation policy too, very helpfulhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

idiaru Angela (12:43:16) (in thread): > @Muqtadirat Yussuffyou accounted for faith and Shannon but not for observed ASV - File (JPEG): Screenshot_20240311_174229_Chrome.jpg

idiaru Angela (12:49:41): > Hi everyone, hope we are all having a splendid time. > how feasible is it for a study to employ two study designs and when that is the case, are both the study designs accounted for?@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido

Muqtadirat Yussuff (12:51:09) (in thread): > Thank you, I did not really know about ASV’s but I just checked the channel and yeah you’re right. Thank you so much@idiaru Angela

Mildred Anashie (12:52:39) (in thread): > It’s possible for a study to have two study designs > > See this@idiaru Angelahttps://bugsigdb.org/Study_16 - Attachment (BugSigDB): Melatonin prevents obesity through modulation of gut microbiota in mice - BugSigDB > Excess weight and obesity are severe public health threats worldwide.Recent evidence demonstrates that gut microbiota dysbiosis contributes to obesity and its comorbidities.

idiaru Angela (12:54:11) (in thread): > @Muqtadirat Yussuffyou’re welcome! If I notice any other disparities I’ll let you know

Ima-obong (Aimah) (12:55:40) (in thread): > We had this issue a few days back, but we were yet to hear from the mentors if the two study designs could be accounted for… > > I’ll say you tag the mentors on this question

idiaru Angela (12:55:48) (in thread): > Thank you@Mildred Anashie

Bolanle Wahab (12:56:48) (in thread): > @idiaru Angelait’s feasible, they’d most likely focus on different aspects of your study but as long as you’re comparing those aspects, they should be accounted for

Suru Olaitan (12:57:06) (in thread): > Thank you@NWAKAEGO VINCENTI also saw that Wilcoxon was used..Initially the option was not popping up when I tried adding it to my study > But I have just seen an alternative name for it > > So my issue now is, which do I go with? > I have 2 experiments by the way….

Ima-obong (Aimah) (12:58:22) (in thread): > Okay I just checked the link that@Mildred Anashieshared and two study designs were listed…save to say you can account for both of them.

Esther Afuape (12:58:39) (in thread): > Hello > It’s possible that they carried out a smaller study within a much larger study. For instance, they can carry out a case-control and carry out a cross-sectional observational study within it. I’ll say report the primary study design of the paper > Check out this old discussion too:https://community-bioc.slack.com/archives/C04RATV9VCY/p1699209219040239?thread_ts=1699204378.759969&channel=C04RATV9VCY&message_ts=1699209219.040239 - Attachment: Attachment > A study can only have one study design. Although it is possible to create two studies from the same publication for each of the study designs, in this case I feel that the distinction between case-control and cross-sectional observational (not case-control) is not important enough to warrant a separate study. Since it seems that the “primary” study is case-control, I would just include everything under that design. If there were a mixture of RCT and a case-control study, or longitudinal + case-control, I think it would be more important to separate those into separate studies because their epidemiological interpretation is so different.

Suru Olaitan (12:58:59) (in thread): > Experiment 1 > Group 0 - Healthy Controls > Group 1 - FDRs of patients with CeD > > Experiment 2 > Group 0 - Healthy Controls > Group 1 - Patients with CeD

Ima-obong (Aimah) (12:59:37) (in thread): > Thanks for this@Esther Afuape

Esther Afuape (13:00:50) (in thread): > What are the 2 designs you’re confused about?@idiaru Angela

Scholastica Urua (13:01:59) (in thread): > Thank you Esther

idiaru Angela (13:02:56) (in thread): > @Esther AfuapeThank you for answering > It’s between a meta analysis and a case control study design > The authors carried out a case control study then collected other data sets to create a meta analysis that was finally used for the statistical analysis

Mildred Anashie (13:03:11) (in thread): > Thank you for this@Esther AfuapeWent through the thread it was really insightfulI’lllike to tag you to a study we were confused about yesterday, I think it is case control and the original curator thinksit’sa Laboratory experiment because both were done in the study

Esther Afuape (13:05:28) (in thread): > So they collected other data sets and analyzed it in a case-control fashion?@idiaru Angela

Mildred Anashie (13:05:50) (in thread): > @Esther Afuape

idiaru Angela (13:09:19) (in thread): > Yes@Esther Afuape

Adedoja Isaac (13:11:12) (in thread): > Thank you so much for this info@Esther Afuape

Esther Afuape (13:12:00) (in thread): > It’sa meta analysis@idiaru Angela

idiaru Angela (13:12:45) (in thread): > Thank you so much for your time@Esther Afuape:heart_hands:

Aleru Divine (13:15:14) (in thread): > @Suru Olaitanideally this study aims to compare the Small Gut and Whole Gut Microbiota of First-Degree Relatives With (Adult Celiac Disease Patients and Controls) > > So I’m thinking > > FDR(1) vs CeD(0)FDR(1) vsDC(0)However according to Figure 3. There was also another comparison which was the differentialabundanceofCeD vs DCIdon’tknow ifit’sokay to add this comparison since it was stated.

Scholastica Urua (13:16:46) (in thread): > @Esther AfuapeThank you for providing additional insight. Over the weekend, we encountered a study that was quite perplexing; there were differing opinions on whether it should be classified as cross-sectional or case-control. Could you please take a look at it? Thank you.:pray:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709950539504309 - Attachment: Attachment > Good morning from India. I wanted to know if I have judged my paper “cross-sectional observation, not case-control,” right? > https://www.nature.com/articles/s41531-023-00554-5

Suru Olaitan (13:17:35) (in thread): > Ohhh..okay@Aleru Divine, Thank you for pointing this out > I’m still a bit unsure of what do though

Joan C. Chukwuemeka (13:18:37) (in thread): > @Michael Adekanyehere are my few findings so far. > 1. data transformation here seems to be raw counts and not relative abundance. > 2. Statistical test - Mann-Whitney (Wilcoxon) is available on BugSigDB.P-value was calculated byWilcoxon signed-ranktest, and was corrected by the Benjamini and Hochberg method to calculate the false discovery rate (FDR) (q-value).there was also MHT correction. > 3. your curation of signature is from table 2 and table s2(supplementary material). the experiment/contrasts seems to be between year 0 and Year 2, though part of the text seems to compare deteriorated grp to stable group > I’ve attached a copy of the article with few annotations I made on it. Trust this helps - File (PNG): image.png - File (PDF): progression_of_parkinson_s_disease_is_associated_with_gut_dysbiosis_two-year_follow-up_study-_pmc.pdf

Aleru Divine (13:21:32) (in thread): > Thank you so much@Esther AfuapeI am currently curating a study that had two study designs, now I know which to keep and which to discard.

Suru Olaitan (13:23:56) (in thread): > @Esther Afuape@Peace Sandy@Chioma OnyidoWould you be kind enough to help me go through my issue, please??

Adedoja Isaac (13:25:36): > Hello everyone > Can we record our second contribution on the Outreachy website now even when it hasn’t been reviewed yet?

Mildred Anashie (13:26:11) (in thread): > I think you can > > Just leave the merge date blank for now

Aleru Divine (13:27:04) (in thread): > Yes@Adedoja Isaacwe can, but leave the merge date for when it finally gets reviewed.

Bolanle Wahab (13:27:22) (in thread): > @Esther Afuapethank you for clearing this:heart:

Adedoja Isaac (13:28:11) (in thread): > Okay, Thank you very much@Aleru Divine@Mildred Anashie

Aleru Divine (13:29:01) (in thread): > Happy to help@Adedoja Isaac

Mildred Anashie (13:30:34) (in thread): > Very clear > > Nicely done@Joan C. Chukwuemeka:thumbsup:

Scholastica Urua (13:41:51) (in thread): > Well done@Joan C. ChukwuemekaThis is detailed.

Peace Daniel (13:42:16) (in thread): > Hello@Chioma Onyido@Esther Afuape@Peace SandyPlease could you help us out here:pray:

Aleru Divine (13:43:40) (in thread): > I agree@Mildred Anashieand@Scholastica Uruathis is really well detailed.Well done@Joan C. Chukwuemeka:clap:

Ima-obong (Aimah) (13:49:12) (in thread): > Yes sure

Amanda Adoyi (14:01:39) (in thread): > This! Thank you.

Joan C. Chukwuemeka (14:33:51) (in thread): > Thanks everyone:relaxed:. Glad to help

Joan C. Chukwuemeka (14:37:48) (in thread): > Thanks@Esther Afuape

Abiola Salako (14:39:24) (in thread): > @Svetlana Ugarcina PerovicThanks for all you do. The challenge I faced was with the first contribution even though it was easy to navigate through I found the EFO difficult to find. However, upon reading the Curator’s policy everything became understandable. For the second contribution, my paper wasn’t difficult to curate but one of my co-contributors still came through for me.

Esther Afuape (14:44:02) (in thread): > What groups were compared in the curatable results?@Mildred Anashie

Abiola Salako (14:44:29) (in thread): > please@NWAKAEGO VINCENT, always record whatever contribution you make on Outreachy.

Abiola Salako (14:51:47) (in thread): > @Svetlana Ugarcina PerovicI never knew. Thank you for making that known to us.

Mildred Anashie (14:52:56) (in thread): > BD patients vs Healthy controls > BD-recipient mice vs healthy control-recipient group > PBS-treated group vs BD-recipient mice > > > This is what I saw@Peace Danielconfirm this

Peace Daniel (14:57:51) (in thread): > The last one was actually BD feces treated group vs healthy control feces mice

Abiola Salako (14:59:21) (in thread): > Well said@Joan C. Chukwuemeka

Esther Afuape (15:00:34) (in thread): > Seems like it’ll have to be 2 different studies since the study designs are very different for the results provided<@UBNSEMS3S>@Svetlana Ugarcina Perovicplease confirm:pray:

Abiola Salako (15:02:37) (in thread): > Thank you@Esther Afuapefor this clarification

Abiola Salako (15:04:59) (in thread): > @eneje promisemake sure you go through the duration policy as shared by@Ima-obong (Aimah)

Abiola Salako (15:06:54) (in thread): > @Aleru DivineThank you for always helping out

Modinat Ganiyu (15:09:40): > Hello Everyone! I can’t seem to get the curation policy link, can you help out please?

UBNSEMS3S (15:10:00) (in thread): > Does it state what kind of GLM they used?

Flourish Ralph (15:10:16) (in thread): > @Esther Afuapeplease can you provide more clarification on this?

Aleru Divine (15:10:21) (in thread): > Here@Modinat Ganiyuhttps://community-bioc.slack.com/files/U05UTDTUHMH/F06133YQJHH/curation_policy_-_bugsigdb.pdf - File (PDF): Curation Policy - BugSigDB.pdf

Muqtadirat Yussuff (15:10:23) (in thread): > Hi@Modinat Ganiyuhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Abiola Salako (15:11:23) (in thread): > Thank you@Esther Afuapefor clearing my doubts!

Abiola Salako (15:11:53) (in thread): > @Adedoja Isaacyes, please.

Abiola Salako (15:13:05) (in thread): > @Modinat Ganiyuhere is the link.https://bugsigdb.org/Curation_Policy#Study_Design - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Modinat Ganiyu (15:18:50) (in thread): > Thank you so much:heart:

UBNSEMS3S (15:19:03) (in thread): > Oh yeah we’ve had these two-in-one studies before. It should just be one study with multiple experiments. I would pick case-control and experimental and note for the laboratory experiment signatures that they were laboratory experiments in the group 1 description, and same goes for the case-control experiments.

Peace Daniel (15:23:19) (in thread): > Okay, thank you so much

Mildred Anashie (15:26:25) (in thread): > Thank you@C. Mirzayi (please do not tag this account)This simplifies everything

Mildred Anashie (15:27:15) (in thread): > @Peace Danielwe were both right:smile::blush:

Peace Daniel (15:30:05) (in thread): > Thank you Anashie

Emem Eduoku (15:40:11): > Hi everyone, when entering the source of the signature, can we have multiple sources? Say Figure 1 and Table 1. > > I’m asking because my study has multiple tables and figures for the different Taxa levels in the microbiome and since we are to document all taxa levels I don’t know which to pick

Svetlana Ugarcina Perovic (15:42:32) (in thread): > Yes, the signature can have multiple source; for eaxmple:Source:Figure 1, Table 1 and text

Mildred Anashie (15:42:53) (in thread): > You can enter signatures from different sources > > Just make sure you indicate in the source > > If you check other studies that have been curated, you would find something like Fig 4 and Result text

Scholastica Urua (15:43:19) (in thread): > Yes, I’ve seen it in other curations

Mildred Anashie (16:00:30): > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy<@UBNSEMS3S>and everybody > I am currently working on a study, it’s a RCT and participants were divided into Cognitively Normal and Mild Cognitive Impairment. An intervention was done using diets (MMKD and AHAD) > > I’m finding a bit of difficulty interpreting the results > > The contrasts I’ve identified are > CN vs MCI:white_check_mark:Post MMKD (CN) vs Post AHAD (CN) > Post MMKD (MCI) vs Post AHAD (MCI) > Or > Post MMKD (CN) vs Post AHAD (MCI) > Post MMKD (MCI) vs Post AHAD (CN) > The article doesn’t state how this comparison was done and I am not sure which it should be also the Fig is not clear to me (Fig 3d and Fig 4) > > I can also see results in Fig 3a and Fig 3b > Showing Pre MMKD (CN) vs Post MMKD (CN) > Pre AHAD (CN) vs Post AHAD (CN) > Pre MMKD (MCI) vs Post MMKD (MCI) > Pre AHAD (MCI) vs Post AHAD (MCI) > > For this other four I see it says “There was no significant change in diets” not sure if I should enter the experiments or not > > The article made reference to Fig 3c but I doubt that’s curatable > > I’m attaching images - File (JPEG): IMG_2206 - File (PNG): IMG_2205 - File (PNG): IMG_2203 - File (JPEG): IMG_2204

Mildred Anashie (16:04:28) (in thread): > This is the link to the studyhttps://www.thelancet.com/journals/ebiom/article/PIIS2352-3964(19)30554-7/fulltext:pray:

Modinat Ganiyu (16:31:57): > Hi everyone. Please, is it a must to fill the PMID & URI space or I can go ahead to fill just the DOI? - File (PNG): image.png

Mildred Anashie (16:32:41) (in thread): > If you use the PMID it will auto populate the other information

Aleru Divine (16:32:46) (in thread): > If the PMID is available, you can fill it. > Plus it helps automatically populate the rest of the data. > > If itisn’t, the you can just fill the DOI and the URL

Mildred Anashie (16:33:01) (in thread): > But if youcan’tfind the PMID you can use DOI

Bolanle Wahab (16:33:17) (in thread): > @Modinat GaniyuIfthey’reboth available,you should

Modinat Ganiyu (16:33:38) (in thread): > Please where can I find the PMID because I saw only DOI

Mildred Anashie (16:33:52) (in thread): > https://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Mildred Anashie (16:34:12) (in thread): > Search for your study using the link

Aleru Divine (16:34:24) (in thread): > Search your paper on the NIH websitehttps://www.ncbi.nlm.nih.gov/ - Attachment (ncbi.nlm.nih.gov): National Center for Biotechnology Information

Modinat Ganiyu (16:35:56) (in thread): > @Mildred AnashieAND@Aleru Divineyou mean I should use the link to search for the title of my study?

Aleru Divine (16:36:11) (in thread): > Yes, exactly

Mildred Anashie (16:36:46) (in thread): > Yes either of the links should work just fine

Modinat Ganiyu (16:37:41) (in thread): > Oh! Thanks so much:heart:But please where did you see this link? I did not come across this

Eniola Adebayo (16:39:17) (in thread): > Hi@Svetlana Ugarcina Perovic@Esther Afuape

Mildred Anashie (16:41:12) (in thread): > I’m not sure I remember well but the videos in the onboarding materials gave info on how to get the PMID and where to search

Aleru Divine (16:41:23) (in thread): > You can just search your paper title on google and open the link for National Institutes of Health(NIH) you’ll surely find your PMID there and if it is not that means it’s unavailable. > > In this case, you can leave it blank and fill the other details manually - File (JPEG): IMG_7809 - File (JPEG): IMG_7810

Idiat Alli (16:42:03) (in thread): > Yea, there’s a link to input your article topic that will give you the PMID

Modinat Ganiyu (16:42:39) (in thread): > @Mildred Anashieand@Aleru Divinethanks for helping out

Idiat Alli (16:42:50) (in thread): > https://pubmed.ncbi.nlm.nih.gov/Use the above link

idiaru Angela (16:43:16): > Hi everyone, > In a situation where there are two tables, one stating the genus and the other Stating both genus and species, which should be curated

Modinat Ganiyu (16:43:38) (in thread): > @Idiat Allithe link is used for what please?

Idiat Alli (16:44:12) (in thread): > Your PMID

Amanda Adoyi (16:46:42) (in thread): > You know…you can curate more than one table/figure as long as the data matters…ie there is comparison of taxa abundance between two groups.

Mildred Anashie (16:47:15) (in thread): > Is there any supporting information saying they further identified the taxa to specie level? > > I know we are to curate all taxas

Bolanle Wahab (16:47:54) (in thread): > @idiaru AngelaI think you should curate the one that states both genus and species if it gives you more information about all taxa relevant to your study

idiaru Angela (16:49:45) (in thread): > @Amanda Adoyiboth tables include the same organisms but one includes both the genus and species

idiaru Angela (16:50:02) (in thread): > @Mildred Anashieyes

Modinat Ganiyu (16:50:53) (in thread): > @Idiat Allithank you:heart:

Aleru Divine (16:50:55) (in thread): > I’d say curate the table stating both the genus and species level, while focusing on the species and if there is one where the speciesisn’tmentioned, you can curate the genus.https://community-bioc.slack.com/archives/C04RATV9VCY/p1703538114617659?thread_ts=1703267775.871189&channel=C04RATV9VCY&message_ts=1703538114.617659 - Attachment: Attachment > “curate only species for those that have their species mentioned, then to curate all the phylum and any genus that doesn’t have its species mentioned.” yes, in other words

Amanda Adoyi (16:51:57) (in thread): > If it’s exactly the same, then perhaps like@Bolanle Wahabstated the second table holds more info. However in the event that there is a difference and it’s relevant…no crime there to curate all of em I think.

Adenike Oladimeji-Kasumu (16:52:56) (in thread): > Hello@Mildred AnashieAlthough I am still going through your paper, I can see that the two groups been studied are Normal cognitive (CN) and the impaired (MCI). > And yes, you have rightly outlined the contrasts in the study. > I do not think the 4 Pre vs Post(s) are relevant though since there were no changes. My opinion…, perhaps the mentors can Put more light on this.

idiaru Angela (16:53:10) (in thread): > Thank you@Aleru Divineand@Amanda Adoyi:heart_hands:

Mildred Anashie (16:53:26) (in thread): > I’d go with@Aleru Divinesuggestion

Adenike Oladimeji-Kasumu (16:56:39) (in thread): > @Modinat Ganiyucopy the title of your article and paste on the search bar of the link that@Idiat Allijust posted > The PMID will be generated. > It will help to auto populate your curation as you begin.

Amanda Adoyi (16:57:52) (in thread): > @Aleru Divinethat’s interesting…I remember asking about it because I felt like I was repeating myself… the answers I find here regarding this seem so conflicted tho. I hear “curate all” then “just species if present” aye…:woman-facepalming:

idiaru Angela (16:59:47) (in thread): > @Amanda AdoyiI have the same confusion. Checked past messages but they were also contradictory so I decided to ask again

Aleru Divine (17:00:41) (in thread): > Even the curation policy says to “curate all taxa no matter of their taxonomic levels”. > > Also goes on to say > “Enter only the highest taxonomic rank mentioned on the paper (e.g. for genus level enter Clostridium, for species level enter Staphylococcus > aureus or Lactobacillus zeae.” > > I feel you

Amanda Adoyi (17:01:01) (in thread): > @Svetlana Ugarcina Perovichi. We keep getting conflicting answers regarding what taxa levels to curate. We might need some clarity.

Aleru Divine (17:03:05) (in thread): > She’s answered this before, herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1703538114617659?thread_ts=1703267775.871189&channel=C04RATV9VCY&message_ts=1703538114.617659 - Attachment: Attachment > “curate only species for those that have their species mentioned, then to curate all the phylum and any genus that doesn’t have its species mentioned.” yes, in other words

Mildred Anashie (17:03:36) (in thread): > YeaIt’sactually confusing in studies were it is not clearly stated

Adenike Oladimeji-Kasumu (17:04:03) (in thread): > @Amanda AdoyiIt was a comment from you and@Mildred Anashiethat helped when I was confused too… > When I read the supplementary materials and looked up the organisms on the NCBI site, I checked each of them one after the other and saw that the ones mentioned in the species level of my paper are the same ones the Genus was referring to, I had to edit my signatures and used the Species instead.

Mildred Anashie (17:05:50) (in thread): > Thank you@Adenike Oladimeji-KasumuHopefully I can get more insights

Aleru Divine (17:20:23) (in thread): > Hi@Mildred AnashieI am currently going through this paper and I must sayI’vecome up with a lot of comparisons:sleepy:I’mtrying to narrow it all down becauseit’scomparing how the diets (MMKD and AHAD) alters the gut microbiome in subjects with MCI.

Blessing Ene Anyebe (17:36:11) (in thread): > Thank you so much@Esther Afuapethis is well noted.

Blessing Ene Anyebe (17:41:37) (in thread): > Great approach and helpful one too@Adenike Oladimeji-Kasumu

Abiola Salako (17:41:37) (in thread): > @Amanda Adoyithose two statements from the curation policy are truly conflicting. But I’ve gained clarity with what@Aleru Divineshared as answered by@Svetlana Ugarcina Perovic.

idiaru Angela (17:44:50): > Hello house, > Is anyone up for reviewing my curation? Your input would be highly appreciated. > Here is the link to the studyhttps://bugsigdb.org/Study_946And here is the link to the articlehttps://movementdisorders.onlinelibrary.wiley.com/doi/10.1002/mds.29300If you’re going to review it please send hi in the replies. Thank you - Attachment (BugSigDB): Integrated Multi-Cohort Analysis of the Parkinson’s Disease Gut Metagenome - BugSigDB > BACKGROUND: The gut microbiome is altered in several neurologic disorders, including Parkinson’s disease (PD).

Aleru Divine (17:52:37) (in thread): > Here’smy conclusion@Mildred Anashie > 1. CN vs MCI: This initial comparison establishes differences in gut microbiome composition between the two groups. > 2. Pre MMKD vs Post MMKD and Pre AHAD vs Post AHAD (For MCI and CN): These comparisons assess the changes in gut microbiome composition after each dietary intervention group (MMKD and AHAD). > 3. Post MMKD vs Post AHAD (For MCI and CN): These comparisons evaluate the differential effects of MMKD and AHAD on the gut microbiome composition, of each group > 4. Post MMKD (CN) vs Post MMKD (MCI) / Post AHAD (CN) vs Post AHAD (MCI): These comparisons specifically examine how the effects of MMKD and AHAD on the gut microbiome differ between each group > I look forward to seeing other inputs.

Aleru Divine (17:54:35) (in thread): > That’sone way to do it@Adenike Oladimeji-Kasumu:+1:

Adenike Oladimeji-Kasumu (18:00:48) (in thread): > Hi@idiaru AngelaI will join to take a look and let you know my observations.

idiaru Angela (18:08:04) (in thread): > Thank you:face_holding_back_tears:@Adenike Oladimeji-Kasumu

Chioma Onyido (20:12:30) (in thread): > Hi@Bolanle Wahabthis study has been reviewed. I wonder whyit’ss showing under incomplete studies category.

Bolanle Wahab (21:41:00) (in thread): > Okay, thanks@Chioma Onyido

Scholastica Urua (22:34:34) (in thread): > Whether to curate the highest or lowest taxonomy level is a bit of a tough and confusing one.:sweat_smile:I’ve gone through this thread, and it’s really insightful. Thank you, everyone.@Aleru Divine, thank you for tagging the previous thread.

Modinat Ganiyu (22:49:21): > Hi everyone. > In the Alpha Diversity section, I don’t seem to understand what Shannon, Chao1 and the rest stands for. The meaning is not also included in the curation policy. I have higher inter-individual diversity (β) and lower intra-individual diversity (α) in my paper and other different places where I can deduce diversity from but I don’t understand these terms under alpha diversity. Can anyone please put me through? - File (PNG): image.png

Scholastica Urua (22:52:45) (in thread): > currently going through this@Mildred Anashie. I’ll let you know my findings.

Scholastica Urua (23:03:54) (in thread): > Hello@Modinat GaniyuAfter going through a paper, I find it particularly helpful to specifically search (Ctrl + F) for each metric to determine if it’s mentioned in the paper. It’s easier to miss tiny details when going through the bulk of the paper. I hadn’t come across alpha diversity metrics before BugSigDB (so grateful for this opportunity). While researching, here is an excerpt I found online. Hope this helps. > > “In alpha diversity analysis, several diversity metrics are commonly used to quantify the diversity within a single sample or community; > > 1. Chao1: Chao1 is a richness estimator that estimates the total number of species or OTUs (Operational Taxonomic Units) in a community based on the observed number of species and the abundance distribution of rare species. It takes into account both the number of species observed and the number of rare species that are likely present but not detected. > > 2. Shannon index: The Shannon diversity index calculates the entropy or uncertainty of species distribution within a community. It takes into account both species richness and evenness, meaning it considers both the number of species present and their relative abundances. A higher Shannon index value indicates higher diversity within the community. > > 3. Simpson index: The Simpson diversity index measures the probability that two randomly selected individuals in a community belong to the same species. It ranges from 0 to 1, with higher values indicating lower diversity (more dominance by a few species) and lower values indicating higher diversity (more even distribution of species). > > 4. Richness: Richness simply refers to the number of different species or OTUs present in a community. It provides a measure of species richness or diversity without considering the relative abundance of each species. > > 5. Pielou’s Evenness: Pielou’s evenness index, also known as the evenness index or evenness measure, quantifies how evenly individuals are distributed among the different species in a community. It takes into account both species richness and the distribution of individuals among those species. A value of 1 indicates perfect evenness, where all species have equal abundance, while a value closer to 0 indicates unevenness, with one or a few species dominating the community. > > These metrics are often used together to provide a comprehensive assessment of alpha diversity within a microbial community.”

Mildred Anashie (23:06:46) (in thread): > Well done@Scholastica Urua

Mildred Anashie (23:08:51) (in thread): > Also@Modinat Ganiyuif you click beside each of themyou’dget information for each > > See image - File (JPEG): 29334039-c971-4c5f-9201-43b7f18340da

Scholastica Urua (23:11:32) (in thread): > @Modinat GaniyuHigher inter-individual diversity (β) and lower intra-individual diversity (α) implies an increase in beta diversity and a decrease in alpha diversity respectively. > > Also check the ‘pop-ups’@Mildred Anashiementioned for further clarity.

Mildred Anashie (23:11:49) (in thread): > Thank you@Scholastica Urua

Mildred Anashie (23:17:15) (in thread): > @Aleru DivineThank you too > > But I feel like if I record for number 3 and number 4 I’ll have redundancy > > As the signatures are almost the same if not same > > Check fig 3d and Fig 4 > > I need help deducing the comparison done in figure 4 > > Also the 2 comparison you are proposing, it was said that no significant change was observed, so Ican’ttell if I should record the experiments without signatures or with signatures > And Ican’ttell which signature increased or decreased in each group, itwasn’tstated

2024-03-12

Ruth Bamgbose (00:03:23) (in thread): > @C. Mirzayi (please do not tag this account)no itdoesn’t,it just says generalized linear models were used.

Desire Oluwarotimi (00:56:18) (in thread): > @Scholastica UruaThat was detailed. Weldone.

Aleru Divine (01:11:48) (in thread): > I am also worried about the redundancy,:sleepy:If no significant change was observed, I don’t think you need to record them.For fig 4 they compared increased and decreased abundance in CN and MCI after the MMKD and AHAD diet.Just that they grouped it to Phyla, families and genera.I don’t know if we should consider (ALL) I alsodon’tknow how.

idiaru Angela (01:27:26) (in thread): > Hi everyone, good morning > Is there anyone willing to help I reviewing my curation, your input would be highly appreciated.

Aleru Divine (01:38:36) (in thread): > @idiaru Angelagood morning:sunny:I’dlove to help you review your curation:hugging_face:

Mildred Anashie (01:49:34) (in thread): > Okay that means Fig 3a and b should not be recorded? > > As for fig 4 and Fig3d let me be more explicit > > I believe the log fold change (Positive and Negative shows increase and decrease) > The red is for post AHAD and green is for post MMKD, but if you observeyou’llsee that we have the same signature increasing in both colors for both groups (I think my confusion in interpreting lies here)

Desire Oluwarotimi (01:55:51): > Good morning mentors and fellow contributors.:sunny:I’m looking forward to doing more with you all today. Let’s get it.:sunglasses:

Bolanle Wahab (01:58:11) (in thread): > Hi@idiaru Angela

Aleru Divine (02:01:38) (in thread): > Good morning:sunny:@Desire Oluwarotimilet’sgoooooo:fire:

Mildred Anashie (02:03:09) (in thread): > Good morning:smiley:@Desire OluwarotimiThis is encouraging, thank you:pray:

Mildred Anashie (02:04:18) (in thread): > Hi@idiaru AngelaI’minterested

Aleru Divine (02:14:24) (in thread): > Fig 3b indicates pre and post diet inclusion for CN and MCI:cold_sweat:I think it should be recorded but then I see some of the taxa also included in 3d.Maybe record 3d cos it has all the taxa still.For fig 4. I thinkyou’recorrect on the log fold change interpretation.Yes I see same signature increasing in both groups:cold_sweat:especially with Bifidobacteriaceae,there’seven a (*) probably indicating the same level of abundance.What I also noticed is that some taxa were more increased in CN than in MCI.I am still not sure what is to be done, maybe to record the one that is more increased or decreased?

Eniola Adebayo (02:15:07) (in thread): > Good morning@Desire Oluwarotimi

Joan C. Chukwuemeka (02:22:13) (in thread): > @Mildred AnashieGood morning, trust you had a restful night. Here are my thoughts after brief read of the paper:Study design- Randomised controlled trial (RCT)Body site - fecesStatistical test- LEfSE (Linear discriminatory analysis [LDA] Effect Size)****?LDA score- 2(not yet seen where it’s specified though..but I think that’s a default);p-value= <0.05Alpha diversities (Chao 1, observed OTU’s {Richness}, & Shannon)seems unchanged. Check Results Text section & the supplementary material.Data transformation- Relative abundanceUnder Section 2.5, that is fecal microbiome analysis, we have:*****Sequencing type - 16S, @V4 region(From the article,16S rRNA gene sequencing was performed as previously described[28–32] -you may need to check the articles referenced to know how the 16S sequencing was done)Sequencing platform -Illumina******Possible contrasts/Experiment- > 1.Cognitive Normal (CN) vs Mild Cognitive Impairment(MCI) > 2. Post-Modified Mediterranean ketogenic diet (MMKD) in CN vs Post-Modified Mediterranean ketogenic diet (MMKD) in MCI > 3. Post-American Heart Association Diet (AHAD) in CN Vs Post-American Heart Association Diet (AHAD) in MCIResearch focus is on MCI, so CN is the likely right control group.****Possible Curatable microbial Signature sources.- Results Text - Sections 3.1 & 3.3 (results from correlation - 3.2/3.4 are not Curated in Bugsigdb.) > - Figures 1f, 1g, 1h, 1m - that’s the ones with significant results. They’re marked with asterisks () > - Figure 3d****Note that a negative LDA score is decreased abundance and vice versa.******

Barakat Akinsiku (02:34:45) (in thread): > Good morning@Desire Oluwarotimi

Abiola Salako (02:35:57) (in thread): > Thank you@Scholastica Urua

Abiola Salako (02:37:13) (in thread): > Good morning@Desire Oluwarotimi

Abiola Salako (02:38:06) (in thread): > @idiaru AngelaI’m interested

Joan C. Chukwuemeka (02:38:17) (in thread): > @Mildred Anashie@Aleru DivineFig 3a and 3b doesn’t seem Curatable: Firstly, it’s looks like a relative abundance report of CN and MCI individually, with no differential abundance really shown:thinking_face:. Secondly, how would we account for the taxa classified as “Others”?.:woman-shrugging:Fig 3d has more taxa info, and contains what’s already in Fig 4, So I don’t really think fig 4 should be curated, to avoid redundancy. > > For the interpretation:Negative Log fold change is decreased abundance, While positive Log fold change is Increased abundance > *****The asterisks points to statistical ***significance at p<0.05 - That is, the one that is Statistically significant is marked asterisks

Blessing Ene Anyebe (02:43:34) (in thread): > Good morning@Desire Oluwarotimi:orange_heart::rocket:

Scholastica Urua (02:48:56) (in thread): > Good morning Desire

Adedoja Isaac (02:55:26) (in thread): > Good morning@Desire Oluwarotimi

Barakat Akinsiku (03:03:28): > Good morning* bugsigdbiers *:smile:hope we’re all getting ready to have an awesome day.@Svetlana Ugarcina Perovic@Chioma Onyido@Esther AfuapeI found an incomplete study which I’ll like to contribute to:https://bugsigdb.org/Study_714Is it okay to go ahead? - Attachment (BugSigDB): Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells - BugSigDB > Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in metabolic fuel utilization that elevates circulating ketone bodies; however, the consequences of these compounds for host-microbiome interactions remain unknown.

Ima-obong (Aimah) (03:13:22) (in thread): > Woah..Thank you@Scholastica Urua…and@Modinat Ganiyualso note that we are only to account for alpha diversity and not beta diversity… good luck with your curation.

Mildred Anashie (03:20:37) (in thread): > Good morning and Thank you@Joan C. Chukwuemekathe first point you raised has been recorded for the study already > > Also I’ll go with not curating 3a and 3b because I was also concerned with how I’d record signatures > > However my concern is with the asterisks you mentioned, I see that with just Bifidobacteriaceae(family) and Bifidobacterium(genera) which I believe is interpreting the same thing

idiaru Angela (03:20:39) (in thread): > Thank you:heart_hands:@Aleru Divine@Mildred Anashie@Abiola Salako@Bolanle WahabThe links to the article and link to the curation are above.

Aleru Divine (03:29:00): > Hello and good morning@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandyand everyone:sunny:I am currently curating a meta-analysis study(this is a study design where researchers combine results from different studies.) and I am confused regarding what to use for my Target regions since there were multiple study cohorts in the analysis. > > Do I compare all at once and take the lowest and highest regions or do I just leave it? > > Your input would be really appreciated.

Joan C. Chukwuemeka (03:29:38) (in thread): > @Mildred AnashieMost figures in literature come with keys, like an explanation of its features. If you check the description of the figure below it, you’d see that the asterisks (*) points to having p value of less than 0.05, which is what was used to determine statistical significance in the study, hence why it’s a superscript beside the p-value. > > For the Bifidobacteriaceae(family) and Bifidobacterium(genera), Yes, they’re interpreting the same thing. What I think happened there is the classified under phyla, went further to check family levels, and then went further to check at genera level. > Does this explain it?

Mildred Anashie (03:32:38) (in thread): > Yes@Joan C. ChukwuemekaI understand what you’re talking about the asterisk and I see it is stated that way but the results were not presented that way apart from the Bifidobacteriaceae family, hence the confusion in interpretation

Aleru Divine (03:32:59) (in thread): > @Mildred Anashieand@Joan C. Chukwuemekayeahthey’reinterpreting the same bacteria just under different levels.I agree:sweat_smile:

Joan C. Chukwuemeka (03:34:50) (in thread): > Yes, you get@Aleru Divine.:slightly_smiling_face:We refuse to be confused…:grinning:Figure 3d is a much better source. Hence why I’d choose it over Figure 4

Mildred Anashie (03:36:32) (in thread): > Alright then > > I buy your idea of working with Fig 3d > > If Idon’tget more input from the mentorsI’llstick to that

Aleru Divine (03:38:01) (in thread): > So do I:sweat_smile:@Mildred AnashieThanks for the detailed explanation@Joan C. Chukwuemeka

Ima-obong (Aimah) (03:38:10) (in thread): > Just went through this convo and I must say I’ve been helped, my first curation, I followed the instruction “curate for all taxa levels” on the curation policy… > As I can’t edit now, I’ll be curating for the highest taxonomic levels in subsequent papers.. > > Thanks@Aleru Divineand everyone who contributed to this convo.

Aleru Divine (03:40:22) (in thread): > Here’s the link to the article, the target regions are in table 1:pray:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6226189/ - Attachment (PubMed Central (PMC)): Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer > Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa. The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity …

Scholastica Urua (03:41:24) (in thread): > I got confused while looking at the material:sweat_smile:. Looking at it with you all’s input is more enlightening:pray:. > Thanks@Joan C. Chukwuemeka@Aleru Divine

Scholastica Urua (03:41:59) (in thread): > Hi@Aleru DivineI’m currently working on this.

Scholastica Urua (03:42:48) (in thread): > https://bugsigdb.org/Study_585 - Attachment (BugSigDB): Re-purposing 16S rRNA gene sequence data from within case paired tumor biopsy and tumor-adjacent biopsy or fecal samples to identify microbial markers for colorectal cancer - BugSigDB > Microbes colonizing colorectal cancer (CRC) tumors have the potential to affect disease, and vice-versa.The manner in which they differ from microbes in physically adjacent tissue or stool within the case in terms of both, taxonomy and biological activity remains unclear.

Aleru Divine (03:42:49) (in thread): > @Scholastica UruaI completely understand:sweat_smile::grin:

Aleru Divine (03:45:04) (in thread): > I got the permission to work on this study on March 10th from@Peace Sandyhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710087571032459 - Attachment: Attachment > Hello again everyone, :sweat_smile: > > @Svetlana Ugarcina Perovic @Esther Afuape @Peace Sandy @Chioma Onyido > > I found this incomplete study (experiment is marked as incomplete) and there are no signatures. > > I’d like to complete the curation > > Here is the link > https://bugsigdb.org/Study_585 > > Can I go ahead?

Scholastica Urua (03:45:22) (in thread): > I noticed the different target regions and different antibiotic exclusion criteria. I was confused on what to do but I included worries in the Talk page while awaiting review and feedback.

Mildred Anashie (03:46:05) (in thread): > Thank you@Aleru Divine@Joan C. Chukwuemeka:heart:

Scholastica Urua (03:49:56) (in thread): > Oh mine:face_with_open_eyes_and_hand_over_mouth:So sorry for the confusion@Aleru Divine:pray:I got permission to work on it so I went ahead.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710163451481819?thread_ts=1710163451.481819&cid=C04RATV9VCY - Attachment: Attachment > Hello @Svetlana Ugarcina Perovic @Esther Afuape @Peace Sandy @Chioma Onyido and everyone. > > I found this incomplete study without experiments and signatures and I’d love to complete it. > Link: https://bugsigdb.org/Study_585 > > Please can I go ahead?

Aleru Divine (03:57:32) (in thread): > That’s okay@Scholastica UruaSince you’re already working on this, do you want to work together?I can go ahead and find another to work on:sweat_smile:if you’re nearly finished.But I’ll be on the lookout for when you finish so I can check the citation.I am really invested in this:hugging_face:

Scholastica Urua (04:07:24) (in thread): > @Aleru DivineI’m nearly finished with the curation and will soon put it up for review. I’m currently going through it again to ensure I haven’t missed anything. Your input and feedback would be greatly appreciated. Working on a meta-analysis presents unique challenges as it involves combining results from multiple studies into one cohesive analysis. > > Could you please share your thoughts on the location of the subjects? Additionally, identifying the experiments and groups to curate proved to be somewhat challenging. I’m eager to hear your feedback.:pray:

Bolanle Wahab (04:08:19) (in thread): > @Aleru DivineI think you should compare the results for all the target regions across the different cohorts, but I’m not sure you’re supposed to take the higher and lower regions if it wasn’t specified in the study. > Determining the regions depends on the statistical analysis used for difference in abundance for each target regions, I’m still going through the article though.

Joan C. Chukwuemeka (04:08:29) (in thread): > Good morning@Peace Sandy, Trust you’re doing fine. Please I’m still hoping to hear from you on this, before I proceed.

Aleru Divine (04:12:01) (in thread): > For all the studies included, the regions were specified actually.But Ididn’tknow which to take

Aleru Divine (04:14:17) (in thread): > Sure thing@Scholastica UruaI’mstill reading through the paper.

Mildred Anashie (04:17:49) (in thread): > I think going forward@Scholastica Uruaand@Aleru Divineif you come across a study thatyou’dlike to work on you can search for it here on BugSigdb and if youdon’tfind it then no one is working on it as we were asked to seek permission before going forward so I believe everyone will post what they intend to work on here > > This is what I do, and it made me realize that a lot of incomplete studies are already being worked on > > Unless of course a case whereyou’dlike to collaborate

Bolanle Wahab (04:22:56): > Hello @svetlana_up @Afuape Esther @Peace Sandy @Chioma Onyido and everyone. > I found a study experiment without signatures :https://bugsigdb.org/Study_467/Experiment_11Can I go ahead with it? - Attachment (BugSigDB): Study 467/Experiment 11 > …

Bolanle Wahab (04:24:27): > Hello @svetlana_up @Afuape Esther @Peace Sandy @Chioma Onyido and everyone. > I checked this study like I did with the one I found yesterday and saw there were no signatures but@Chioma Onyidosaid it had already been reviewed > Please How do we know the ones to actually work with?

Mildred Anashie (04:25:56) (in thread): > I think the ones that do not have the reviewed tag

Scholastica Urua (04:28:44) (in thread): > Like@Mildred Anashiesaid, I think we should work on those without the ‘Reviewed’ tag. Like those tagged ‘incomplete’ or ‘needs review’. > This is because the initial curator and subsequent reviewer may have had reasons for not including signatures.

Muqtadirat Yussuff (04:29:08): > Hi everyone, hello mentors@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyI’m done with a curation and would like to submit it for a review. Thank youhttps://bugsigdb.org/Study_761 - Attachment (BugSigDB): The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study - BugSigDB > The oral microbiome, like the fecal microbiome, may be related to breast cancer risk.Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana.

Leenaa Al-Amin (04:29:47) (in thread): > hi@idiaru AngelaI’m would love to review it

Ima-obong (Aimah) (04:32:38): > Hello everyone… > in my paper,acutediarrheais the condition, but in the drop down,chronicdiarrhoeaandDiarrheaare listed.. > Butacutediarrheaandchronicare not the same aschronicspans over an extended period while acute is just for a few hours to days… > > I’m thinking of pickingDiarrheaas my option…or should I leave it blank asacutediarrheamay not be same in meaning withdiarrhea****.****.Thank you.

Peace Sandy (04:33:26) (in thread): > Have you commented that your paper needs review on GitHub

Ima-obong (Aimah) (04:34:15) (in thread): > Congratulations@Muqtadirat Yussuff..leave a comment on GitHub alongside your completed study link

Peace Sandy (04:34:29) (in thread): > @Joan C. Chukwuemekaplease proceed

Muqtadirat Yussuff (04:34:38) (in thread): > I wasn’t issued this paper on GitHub, I found an incomplete curation and was given permission to go ahead@Peace Sandy

Bolanle Wahab (04:34:38) (in thread): > Thank you@Scholastica Urua@Mildred Anashie

Blessing Ene Anyebe (04:35:28) (in thread): > I think picking Diarrhea only will suffice, but this is a personal opinion. You may now add it to the talk page that the precise condition is “acute” Diarrhea.

Peace Sandy (04:35:40) (in thread): > Okay

Scholastica Urua (04:37:21) (in thread): > I agree with@Blessing Ene Anyebe. Going for Diarrhea may work since it can either be acute or severe. And also make a discussion on talk page to prompt reviewers.

Muqtadirat Yussuff (04:37:29) (in thread): > You should go with diarrhea and add acute diarrhea to the discussion section of your curation

Ima-obong (Aimah) (04:38:37) (in thread): > Alright…thank you everyone..I appreciate your help

Mildred Anashie (04:39:24) (in thread): > Hi@Muqtadirat YussuffI came across this study under pages with Missing NCBI and I was curious about the Prevotella 1, Prevotella 2, Prevotella 6 or so > > > I was going to share to know if what I think is right and can be effected > > I went through the paper and I discovered the signatures you curated were from Supp. Table 1 and in my opinion Supp. Table 2 is what should have be curated (I could tell that the values presented in bold are the significant values, But identifying the decrease and increase was what was tasking) > > For the Prevotella I noticed there were all species and I found this on NCBI (See attached image),I’mwondering if this can be used to replace the taxas and then a comment left on the talk page stating the actual ones found in the paper@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther Afuape:pray: - File (JPEG): IMG_2229

Ima-obong (Aimah) (04:40:22) (in thread): > Please@Blessing Ene Anyebeand@Scholastica Uruais the talk page same as the discussion page for missing NCBI IDs? Or it’s another one…thank you

Scholastica Urua (04:42:35) (in thread): > It’s another one. Let me send you steps on how to go about it.

Ima-obong (Aimah) (04:43:02) (in thread): > Thank you soo much ..that will be really helpful

Rahila-me (04:45:43): > Please in alpha diversity which one will represent ACE, cos its not among the listed one

Bolanle Wahab (04:45:59) (in thread): > @Aleru DivineI went through the article and didn’t see any specifications, I noticed V1-V3 were the most consistent though, do you think it might be appropriate to go with that?

Mildred Anashie (04:46:30) (in thread): > I believe ACE is also curated for richness

Peace Sandy (04:47:10) (in thread): > @Rahila-meACE can be curated for richness

Bolanle Wahab (04:48:59) (in thread): > @Rahila-meACE represents richness of your subjects

Rahila-me (04:49:29) (in thread): > Thumps up guys.:raised_hands:

Ima-obong (Aimah) (04:51:07) (in thread): > Thank you@Scholastica Urua..I really appreciate this

Scholastica Urua (04:51:29) (in thread): > Steps on creating a ‘Talk’ page; > 1. Open your curation > 2. Click on the three dots above (Image 1) > 3. Click on ‘Discussion’ (Image 2) > 4. A talk page will be created were you can write up your discussion. > 5. When done, scroll down to save page. > Hope this helps. > PS: I’m using this study as a sample, I’m not making any edits to it. - File (JPEG): Talk 1.JPG - File (JPEG): Talk 2.JPG - File (JPEG): Talk 3.JPG

Scholastica Urua (04:51:55) (in thread): > You’re welcome@Ima-obong (Aimah)

Bolanle Wahab (04:52:34) (in thread): > Thank you for this@Scholastica Urua

idiaru Angela (04:56:37): > Good morning everyone, Happy Bugsigdbing@Chioma Onyido@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandyhttps://bugsigdb.org/Study_599I found this incomplete study and I’d love to complete it. Do I have the permission to do that? - Attachment (BugSigDB): Changes in Bacteroides and the microbiota in patients with obstructed colorectal cancer: retrospective cohort study - BugSigDB > BACKGROUND: The relationship between intestinal obstruction due to colorectal cancer (CRC) and the gut microbiota remains largely unknown.The aim of this study was to investigate the potential association between alterations in gut microbiota and CRC in the presence of intestinal obstruction.

Blessing Ene Anyebe (04:56:37) (in thread): > Thank you sharing@Scholastica Urua:orange_heart:

Ima-obong (Aimah) (04:58:02) (in thread): > Please check the date…this is may be a current curation as the date reads 2024,…but I’m not sure either

Bolanle Wahab (05:01:35) (in thread): > @Scholastica Urua@Mildred Anashiethe curations tagged ‘needs review’ have recent curated dates and have most likely not been reviewed by our mentors

Esther Afuape (05:02:58): > Hello<!channel>Before you start working on an incomplete study, please search for the number of that study here to be sure nobody else has started working on it.Tap on bugSigDB and select the search option

Ima-obong (Aimah) (05:03:49) (in thread): > Thank you@Esther Afuape.. noted

Mildred Anashie (05:04:33) (in thread): > I suggest you leave them as it appears there are no more incomplete studies unless the mentors say otherwise

Svetlana Ugarcina Perovic (05:04:57): > Good morning:star-struck:Thanks to@Chioma Onyidohttps://github.com/waldronlab/BugSigDBcuration/issuesis full of new papers. > NOTE: Before claiming for new one, please make sure that you finished your previous curation and claim it for review in the corresponding GitHub issue of your paper with a link to your bugsigdb curation. Thanks!Happy BugSigDB-ing!Your mentors<@U1LCB8WEA><@UBNSEMS3S>@Peace Sandy@Esther Afuape@Chioma Onyidoand@Svetlana Ugarcina PerovicP.S. If you maybe skip this post by@Esther Afuapeon how to solve NCBI taxonomy issues, please do check it outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189 - Attachment: Attachment > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonym on NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replace Escherichia coli with Escherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the 2-hour video of @U1LCB8WEA solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose:

Desire Oluwarotimi (05:06:44) (in thread): > BugSigDB-ing is a fun word and I like it.:joy:

Suru Olaitan (05:07:42) (in thread): > @Esther Afuape@Peace Sandy@Chioma Onyido

Scholastica Urua (05:08:01) (in thread): > It’s been fun BugSigDBing with you all:hugging_face:Thank@Chioma Onyido:heart_eyes:Hello@Svetlana Ugarcina Perovicplease can we claim new papers to review on GitHub while waiting for our second contribution to be reviewed?

Svetlana Ugarcina Perovic (05:08:43) (in thread): > @Barakat Akinsikuintroduced “bagsigdbiers” but actually we invented “BugSigDB-ing” in the previous outreachy round w/@Peace Sandy@Chioma Onyidoand@Esther Afuape

Desire Oluwarotimi (05:09:17) (in thread): > @Scholastica UruaYes, you can.

Aleru Divine (05:09:52) (in thread): > @Bolanle Wahabyou’re correct. It’s the most consistent. That’s one way to look at it. Well done for this observation.:+1:Another way I was thinking was, taking V1-V6 > > Because the target regions altogether ranges from V1-V6. > > V1 (lowest target region among all) > V6 (highest target region among all).@Scholastica Uruawhat do you think?:sweat_smile:

Desire Oluwarotimi (05:09:59) (in thread): > @Svetlana Ugarcina PerovicBugSigDB-ing is actually a very creative one.

Joan C. Chukwuemeka (05:10:05) (in thread): > Alright

Ima-obong (Aimah) (05:12:25) (in thread): > Bugsigdbing..thats a fun word right there:smile:Thanks for the update@Svetlana Ugarcina Perovic

Esther Afuape (05:12:56) (in thread): > Hi@Suru OlaitanIf you check the subheading “Sequence Processing and Bacterial Community Analysis”, everything you need is there, the statistical test and whether MHT was carried out. Figure 1 contains the alpha diversity measurement.

Aleru Divine (05:14:16) (in thread): > Thank you@Svetlana Ugarcina Perovic:sweat_smile:BugSigDB-ing does have a certain ring to it.

Suru Olaitan (05:15:04) (in thread): > Okay , Thank you so much > I’m also not sure on what my groups should be for experiment…It seems like I have up to 3 comparisons > Could you please help with that as well?@Esther Afuape

Abiola Salako (05:16:26) (in thread): > Bugsigdbing have it:joy:@Svetlana Ugarcina Perovic

Mildred Anashie (05:16:53) (in thread): > Thank you@Svetlana Ugarcina PerovicGood morning:sun_with_face:By the way BugSigdbing does it for me:smiley:

Joan C. Chukwuemeka (05:16:54) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thanks for the update:slightly_smiling_face:

idiaru Angela (05:18:45) (in thread): > @Ima-obong (Aimah)it’s Jan 2024 > So I doubt it for someone in our cohort

Leenaa Al-Amin (05:19:46) (in thread): > Thanks for the update!@Svetlana Ugarcina Perovic

idiaru Angela (05:21:15) (in thread): > @Esther AfuapeNoted:pray:

Ikeh Darlington Ikeh (05:22:25) (in thread): > Hi@Esther Afuape! Thank you for this clarification,however,I’mstill a bit not clear on this subject.Let me explain; in my study,I saw some signatures that were not matched on the NCBI taxonomy, while some were giving me IDs of related bacteria but not exactly same name as indicated in my paper, so I left it in BugSigBD exactly as written in the paper, but there were showing red when saved.Is this correct practice or not?

Joan C. Chukwuemeka (05:23:03) (in thread): > Quite an interesting finding at@Mildred Anashie

Mildred Anashie (05:25:02) (in thread): > @Ikeh Darlington IkehI believe some taxas can be left in orange if all efforts to match them has been made with no positive results > > IfI understand your question

Ikeh Darlington Ikeh (05:26:23) (in thread): > Exactly what I did.

Barakat Akinsiku (05:28:21) (in thread): > Thank you for the update and fun-word:smile:@Svetlana Ugarcina Perovic

Modinat Ganiyu (05:31:00) (in thread): > Thank you so much everyone, your response goes along way in curating my paper. Much love from here:heart:

Ikeh Darlington Ikeh (05:31:30) (in thread): > @Scholastica Uruaplease when is the next office hour? I think a separate Chanel should be created for the meetings, its links and notes so they don’t get lost in this thread. Also so that we all can keep track of it and put it in our schedule.

Svetlana Ugarcina Perovic (05:32:38) (in thread): > @Aleru Divine@Scholastica UruaI’m happy to see you working together

Svetlana Ugarcina Perovic (05:33:09) (in thread): > You have to specify V regions for every study as it is reported in the paper

Aleru Divine (05:33:48) (in thread): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (05:34:53) (in thread): > Thank you@Svetlana Ugarcina Perovic.

Aleru Divine (05:35:21) (in thread): > @Svetlana Ugarcina Perovicthis is a meta-analysis study and there are about 10 different studies being analyzed. > > What should be done in this case?

Svetlana Ugarcina Perovic (05:36:17) (in thread): > <@U1LCB8WEA>could you please advise on this? Thanks!

Scholastica Urua (05:36:22) (in thread): > @Aleru DivineI was thinking same thing; V1 - V6.@Svetlana Ugarcina Peroviccan this work? Since it’s a meta-analysis.

Scholastica Urua (05:40:00) (in thread): > Also note; > > The exclusion of antibiotics was not standardized across the different CRC-associated studies, as each study employed different criteria. For instance, in one study, cases with previous chemotherapy and antibiotic use were excluded. > > In two other studies, patients who had not taken antibiotics for at least a month prior to sample collection were included. In another study, only patients who had not taken antibiotics for two months were included. > > Additionally, in yet another study, patients who had taken antibiotics in the last three months prior to sample collection were excluded. > > The remaining studies did not provide details regarding antibiotic exclusion criteria. > > Please how should this be accounted for?

Esther Afuape (05:41:36) (in thread): > I thinkwe’veused this before for all the numbered prevotella species. Ifyou’resurethey’respecies, then yes, you can

Modinat Ganiyu (05:42:03) (in thread): > @Scholastica UruaI want to ask where you get details on how you curate papers because there are lots of information in the paper that is easy to disregard some information due to oversight. And the curation policy doesn’t do enough justice in explaining the terms in details but you seem to get a hang of it. Please what link or act can help me better curate my paper. > > For example: Statistical test on my paper shows Random forest, anova, regression. Its a lot. Please how/what can I do to help me curate this paper better.

Mildred Anashie (05:44:08) (in thread): > Hi@Modinat GaniyuIcan’tanswer for scholastica:smiley:butI’dadvice that you ask questions here if you are unsure about anything, it helps alot > > Also for statistical test you curate the one that was used for the differential abundant taxas

Mildred Anashie (05:45:42) (in thread): > Oh that’s great > > Thank you:blush:@Esther Afuape@Muqtadirat YussuffI’d effect my observations, I hope this is okay

Abiola Salako (05:47:23) (in thread): > @Modinat GaniyuAside from reading the curation policy you need to watch some other videos and other documentation you were provided with just before you started your first contribution and read most of the write-ups being shared here from the previous cohorts. Thank you. I hope this helps.

Modinat Ganiyu (05:49:24) (in thread): > @Mildred Anashiebut it isn’t specifically stated that one is for differential abundant taxas. > > > Is there a key word I should look for or something else please?

Muqtadirat Yussuff (05:49:43) (in thread): > @Mildred AnashieThank you but please don’t, I’d like to re read the material first. I initially considered using sp 1 -8 but that feels like it’s encompassing all and it’s just 1, 2 and 6 that were in the table

U1LCB8WEA (05:51:25) (in thread): > Extremely well-described, thank you@Esther Afuape!!!

Mildred Anashie (05:51:41) (in thread): > If you have identified figures that contain the differential abundant taxas, it’s mostly stated in the footnote > > Also some papers state it, but you can share screenshots I could help with that and share how I was able to identify it

Scholastica Urua (05:52:14) (in thread): > Hi@Modinat Ganiyu, the onboarding materials actually cover all aspects comprehensively. I’ve had to read them numerous times to fully grasp the content (and I still refer back to them occasionally when I get confused:sob:). > > Additionally, I’ve found it helpful to ask questions on the platform when I encounter difficulties. It’s surprising how sometimes the questions others ask are ones you hadn’t even considered, yet their answers turn out to be just what you need to progress. So, reading through threads can be incredibly beneficial. > > Regarding the statistical test, as@Mildred Anashiepointed out, you curate the one used for the assessment of differential abundance. > > Furthermore, as mentioned by@Chioma Onyidoduring the last office hour, some papers may utilize multiple statistical tests. However, it’s essential to distinguish between them, as one test might be employed for calculating the p-value, while another could be for determining differential abundance.

Esther Afuape (05:52:39) (in thread): > Hi@Eniola Adebayoplease confirm if the TG5 mentioned in the paper for that study is a genus. If it is, then you’re right. Please add it to the unresolved taxonomy on the discussion page. > Well done!:bouquet:

idiaru Angela (05:53:13) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you for the update > And thank you to the creative people that coined > BugSigDB-ing:sweat_smile:

Mildred Anashie (05:56:10) (in thread): > That’sfine > > You can use 1-8 and leave a note in the discussion page stating the exact ones found in the paper, I think that will help

Adedoja Isaac (05:56:16): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (05:56:37) (in thread): > Please@Modinat Ganiyu, you can include a snapshot/link to your work so we can figure it out together. We’re all here to learn and help each other while BugSigDB-ing.

Muqtadirat Yussuff (05:58:02) (in thread): > Thank you so much for your help and understanding@Mildred Anashie

U1LCB8WEA (05:58:09) (in thread): > What I would probably do in the case of meta-analysis where there isn’t a consistent answer, would be just to leave that field blank since none of the ones under discussion here are mandatory. But honestly all of the solutions already proposed here are reasonable!:sweat_smile:In any case, discussion like this what you’ve pointed out@Scholastica Uruashould definitely go on the “Discussion” page for this study, so it will be available to anyone wondering in the future why you made the choice you did.

U1LCB8WEA (05:58:43) (in thread): > Also since antibiotics is free-form, you could simply write in the range of criteria applied in that box.

Scholastica Urua (05:59:35) (in thread): > Thank you Levi, I will do that.

Mildred Anashie (05:59:50) (in thread): > @Esther Afuapeplease can you help with this:pray:I’vegot inputs from fellow applicants butI’mstill not sure on how to proceed

Aleru Divine (06:00:24) (in thread): > Thank you so much for the input@Levi Waldron

U1LCB8WEA (06:00:37) (in thread): > You’re welcome

U1LCB8WEA (06:00:39) (in thread): > !

Modinat Ganiyu (06:00:58) (in thread): > @Scholastica Uruaand@Mildred Anashiespecial thanks to you. > > I’m sorry if my questions are weird, I’m new to the system that’s why. Even after carefully reading and watching all the materials, I still find it confusing when curating. > Kindly help, here is the linkhttps://journals.asm.org/doi/10.1128/spectrum.02368-23#tab-citations

Hamidat Mohammed (06:06:33) (in thread): > Thanks for the Update@Svetlana Ugarcina Perovicand thank you@Chioma Onyido

Scholastica Urua (06:06:34) (in thread): > @Ikeh Darlington IkehOffice hours is usually held at 9 AM EDT (eastern daylight time) every Thursday. The link is posted on the platform before then by the mentors.

Esther Afuape (06:06:44) (in thread): > Hi@Mildred Anashiefigure 3a to disn’tcuratable, figure 4 is. However,I’mnot sure what “all” means in figure 4

Scholastica Urua (06:08:06) (in thread): > Thank you Esther:pray:

idiaru Angela (06:11:08) (in thread): > @Leenaa Al-Aminthank you!

Aleru Divine (06:12:09) (in thread): > Thanks you for the input@Esther Afuape

Aleru Divine (06:12:56) (in thread): > That rules out fig 3:sweat_smile:

Evelyn Mary Attah (06:13:11) (in thread): > @Scholastica Urua, thank you very much

Mildred Anashie (06:13:17) (in thread): > Okay…Thank you@Esther AfuapeAll means both CN and MCI in my opinion and what i picked from the study but the focus was on the two groups and the diet intervention from the text and the note beneath the figure

Mildred Anashie (06:15:32) (in thread): > Yea@Aleru DivineHow ironic:joy:

Aleru Divine (06:15:58) (in thread): > :sweat_smile::sweat_smile:

Scholastica Urua (06:16:51) (in thread): > Hi@Modinat Ganiyu, scanning through your paper, I identify LefSe as the statistical test with LDA of 3 and p value of 0.005. > > Please@Mildred Anashiewhat do you think? - File (JPEG): LefSe (3).JPG - File (JPEG): LefSe analysis.JPG

Precious Orakwe (06:17:07): > Please what am I suppose to put here - File (PNG): Screenshot_20240312-101031.png

Joan C. Chukwuemeka (06:18:43) (in thread): > @Esther Afuapedoesn’t the * which points to statistical significance not mean that only Bfidobacteriaceae is significant?:thinking_face:

Aleru Divine (06:19:07) (in thread): > 1. Tick the terms of service(always read the terms of service) > 2. Tick the I’m not a robot > 3. Request for an account. > 4. Wait for a confirmation email. > They’ll send your account details.

Scholastica Urua (06:19:23) (in thread): > Are you trying to request an account on BugSigDB? If yes, under the additional notes, you can include a brief description of yourself. > And also do what@Aleru Divinesaid.

Bolanle Wahab (06:20:32) (in thread): > @Precious Orakweifyou’rereferring to the additional notes and websites,you can leave them blank unless you have a cover letter or something you feel should be known about you

Mildred Anashie (06:21:13) (in thread): > @Joan C. ChukwuemekaI don’tthink so > > I think it’s because of the prominent reduction it had in both diet interventions > > See this image - File (JPEG): IMG_2231

Modinat Ganiyu (06:21:43) (in thread): > @Scholastica UruaPlease again can you send the link or materials that I can go through to make me better understand how to curate. > Or what has really helped you in getting the key info from your data. Thank you!

Aleru Divine (06:22:12) (in thread): > @Scholastica Uruathere’salready a space provided for personal biography above this one.

Mildred Anashie (06:22:35) (in thread): > Yes > > The statistical test is LEfSe

Precious Orakwe (06:22:59) (in thread): > Thanks everyone, I am done

Scholastica Urua (06:23:31) (in thread): > That’s right@Aleru Divine. Thanks > > In that case it can be left blank or include any additional notes of choice.

Aleru Divine (06:23:33) (in thread): > Well done@Precious Orakwe

Esther Afuape (06:23:37) (in thread): > @Mildred Anashieso like post-MMKD(group 1) in all participants vs post-AHAD(group 0) in all participants is one experiment, then, signature is decrease in post-MMKD (bifidobacterium, bifidobacteriacea). > > Then you do post-MMKD vs post-AHAD in MCI. Signature is decrease in abundance (bifidobacteriacea, bifidobacterium)

Adegboye Rukayat (06:23:40) (in thread): > @Esther AfuapeThank you

Precious Orakwe (06:24:39) (in thread): > Thank you all for your assistance, I so much appreciate

Esther Afuape (06:25:01) (in thread): > You have to be careful to tell relative abundance figures apart from significance abundance figures. Figure 3 is for relative abundance

U1LCB8WEA (06:25:17) (in thread): > Note for anyone with “Administrator” privileges onbugsigdb.org, which include the privilege of deleting pages. When deleting an experiment, you should first delete all its signatures, and when deleting a Study, you should first delete all its signatures and experiments. Otherwise they end up as “orphaned” signatures and experiments, like this signature (#13 athttps://bugsigdb.org/Help:Cleanup#Orphaned_Signatures). After double-checking that Experiments 2 and 4 should really be gone, their “orphaned” signatures should now also be deleted. Alumni,@Chioma Onyido@Esther Afuape@Peace SandyI can assign administrator privileges to you if you’d like to help with this. - Attachment (BugSigDB): Help:Cleanup

Mildred Anashie (06:26:19) (in thread): > Saw it mentioned under statistical test@Modinat Ganiyu - File (PNG): Lefse.PNG

Scholastica Urua (06:27:13) (in thread): > Hi Modinat, we can jump on a call if that’s okay by you.:pray:I’ll provide my details in your inbox

Mildred Anashie (06:27:40) (in thread): > Yes@Esther Afuapethis is totally right…. And I’ll definitely pay more attention to that going forward:pray:

Modinat Ganiyu (06:27:55) (in thread): > @Scholastica UruaThat would be great. Thanks a lot

Esther Afuape (06:28:11) (in thread): > We still have administrator privileges:sweat_smile:@Levi Waldron

Mildred Anashie (06:28:33) (in thread): > Thank you@Scholastica Urua

U1LCB8WEA (06:31:18) (in thread): > Oh great!:sweat_smile:

Aleru Divine (06:31:46) (in thread): > Thanks again@Esther Afuape:pray:I can’t believe I read that and I missed it:sleepy:

Idiat Alli (06:40:49) (in thread): > Happy BugSigDB-ing to me:blush:

Joan C. Chukwuemeka (06:41:31) (in thread): > Okay..<@U1LCB8WEA>. Good morning and Thanks for the info.

Aishat Ijiyode (06:45:54) (in thread): > Hi please I am confused on something. When adding signatures, If in my article, the microorganisms doesn’t exactly decrease and increase. Like there are some that increase for the disease and there are some that increase for the healthy control group, do I use the one that increase for the healthy control group as signature 2? (because the dropdown says decrease)

Esther Afuape (06:47:05) (in thread): > <@U1LCB8WEA>I’ma bit confused. Thisisn’tfrom study 213 considering the description?https://bugsigdb.org/Study_213/Experiment_1/Signature_1Butit’sattached to it - Attachment (BugSigDB): Study 213/Experiment 1/Signature 1 > Source: Figure 2. Description: Figure 2 Forest plot of fold change of select genera (G) and species (S) in both the New York University and National Cancer Institute…

Mildred Anashie (06:48:20) (in thread): > The ones that increased in your control group should be the decrease for the case group in my opinion

U1LCB8WEA (06:48:58) (in thread): > Yeah, there is the unfortunate side-effect of orphaned pages that when eg study 213 is deleted and leaves orphaned pages, they can get “adopted” when a new Study 213 is created.

Aishat Ijiyode (06:49:03): > Hi please I am confused on something. When adding signatures, If in my article, the microorganisms doesn’t exactly decrease and increase. Like there are some that increase for the disease and there are some that increase for the healthy control group, do I use the one that increase for the healthy control group as signature 2? (because the dropdown says decrease)

Esther Afuape (06:49:57) (in thread): > Do I just delete them? Ican’treally tell where they are from as they are attached to other studies

Ima-obong (Aimah) (06:51:13) (in thread): > @Aishat Ijiyodesome papers may have increased signatures only for both control and group 1…hence in the absence of decreased signatures in group 1, you can append the increased signatures in the control group as your decreased in group 1

U1LCB8WEA (06:51:22) (in thread): > Yes, just delete the orphaned or now mismatched signatures, they belong to a page that no longer exists.

Mildred Anashie (06:51:49) (in thread): > Yes@Aishat IjiyodeThe increase for the control group is decreasing in case group

Esther Afuape (06:52:39) (in thread): > Oh now I get it!Cleaning them up now:rocket:

Aishat Ijiyode (06:53:06) (in thread): > Thank you so much for your help

Desire Oluwarotimi (06:53:06) (in thread): > Hi@Aishat AdebayoTake for example, you have a group pair as; > Health control vs Disease (0 vs 1) > > You should should have the increased abundance for the diseased group as your increased signature and the increased abundance for the health control as your decreased signature as long as they are provided.

Scholastica Urua (06:53:14) (in thread): > I noticed the other tests too@Mildred Anashie. I picked LEfSe analysis when using Fig. 2 as source for your signature. I noticed there’s a more than one experiment in this study.

U1LCB8WEA (06:53:45) (in thread): > Maybe also check the history of the parent pages to see who accidentally left the orphaned pages, to make sure they know not to do it any more:slightly_smiling_face:

U1LCB8WEA (06:55:19) (in thread): > Oh I said something incorrect, the previous version of study 213 does still exist, in the history of that page.

U1LCB8WEA (07:03:02) (in thread): > See the reference near the top ofhttps://bugsigdb.org/w/index.php?title=Study_213&action=historyto deleted edits - looks like the relevant deletion was by@Svetlana Ugarcina Perovicin October:wink: - Attachment (BugSigDB): Composition of gut microbiota in infants in China and global comparison - BugSigDB > Symbiotic gut microbiota is essential for human health, and its compositional changes have been associated with various complex disorders. - File (PNG): IMG_2254

Mildred Anashie (07:11:40) (in thread): > Yes I noticed that too > > It’s saying T-test was used for the second group

Modinat Ganiyu (07:13:05) (in thread): > @Scholastica UruaThanks so much for taking your time to explain these things to me, it really goes a long way to curate my paper > > Love you loads:smiling_face_with_3_hearts:

Scholastica Urua (07:13:43) (in thread): > You’re welcome@Modinat Ganiyu:hugging_face::heart_eyes:

Chioma Onyido (07:16:03) (in thread): > @Scholastica Uruaexplains it well.:+1:Here’s how to navigate thediscussion pagefeature on bugsigdb and an example of how it was used by myself and@Esther AfuapeI hope this helps. - File (JPEG): talk page 1.jpg - File (JPEG): talk page 2.jpg - File (JPEG): talk page 3.jpg

Joan C. Chukwuemeka (07:17:23) (in thread): > @Esther AfuapeThanks for the input. > > Please will it be feasible for you to use this paper as a case study to explain relative abundance and significant differential abundance during the next office hour? > > In some articles, It’s easy to differentiate, in others like this one, it’s kind of tricky and not easily ascertained.:pray:I believe it’ll be helpful

Mildred Anashie (07:17:53) (in thread): > @Esther AfuapeI know we have established what should be done > > But I’m still concerned about the groups you suggested > 1) The sample size that’ll be used when comparing the post-MMKD(group 1) in all participants vs post-AHAD(group 0) in all participants > 2) Making AHAD the control group whereas it was also a diet intervention (I’m wondering if this works because AHAD didn’t establish any significant result) > I think the group comparison is between CN and MCI > 3) We are ignoring the results the other results that were established within results text and working with just the Bifido….. sinceit’sthe only one that showed significant in the figure > > I hopeI’mnot mixing things up

Mildred Anashie (07:23:33) (in thread): - File (JPEG): IMG_2232

Odigiri Great Alume (07:23:36) (in thread): > Good evening@Esther Afuape@Svetlana Ugarcina Perovic@Chioma Onyidolooking at this study. I think that > 1. The comparison groups are CN (group 0) and MCI (group 1). > 2. Figure 4 is curatable, specifically 4b and c. > 3. MMKD and AHAD were treatments given to these comparison groups. And from the footnote of figure we could see where it says “******MMKD and AHAD induce specific changes in the gut microbiom of subjects diagnosed with MCI vs CN”******Therefore, in my opinion I believe the comparison should be: CN Vs MCI (for Post MKKD) and CN vs MCI (for AHAD). Looking also at the footnote we know that only asterisk:eight_spoked_asterisk:bacteria taxa yielded significant results hence only those should be curated. Which will then be CN vs MCI (For post MMKD) as the experiment of CN Vs MCI for Post AHAD didn’t yield significant results. However, the experiment for CN vs MCI (for post AHAD) can be created with no signatures If think:thinking_face:. > 4. In summary I think the only experiment that yielded significant results and is has curatable signatures in figure 4 Will be CN (group 0) vs MCI (group 1) for post MMKD. and only reduce taxa (bifidobacterium and bifidobacteriaceae) were recorded As decreased based on text and on the figure. > > > Please:pleading_face:my view

Chioma Onyido (07:23:43) (in thread): > Ohh I see it now, this is noted.

Mildred Anashie (07:31:08) (in thread): > Hi@Precious Orakwewell done:thumbsup:Nowyou’dwait for your account to be approved and claim an issue on GitHub if youhaven’tYou claim by dropping a comment on the issue you intend to work on asking it be assigned to you

Oluwatomisin Omojokun (07:33:17) (in thread): > Thanks for the update. duly noted, thanks@Svetlana Ugarcina Perovic

Esther Afuape (07:35:21) (in thread): > @Mildred Anashieall participants will be MCI and CN, right? The sample size will be the addition of their sample sizes. > For your second question, a comparison between 2 groups makes an experiment. A controldoesn’talways have be the group without any test carried out on it or in this case, without any intervention. I always prefer to make the group with the significant or main change the group 1. > I hope you understand me

Esther Afuape (07:36:14) (in thread): > @Odigiri Great Alumeare you saying thereshouldn’tbe an experiment for all participants?I think there should be one for it since it has significant results

Precious Orakwe (07:36:18): > How will I know that a paper duration has been assigned to me, please

Scholastica Urua (07:37:21) (in thread): > When you are the first to request a paper on the GitHub issues, one of the mentors will reply ‘assigned’. And also the paper will be tagged “assigned” in red.

Peace Sandy (07:37:37) (in thread): > Hi@Precious OrakweHave you claimed a paper on GitHub

Idiat Alli (07:39:45) (in thread): > @Precious Orakweyou have to first comment on the paper that you want to curate it and ensure no-one has commented before you

Adenike Oladimeji-Kasumu (07:40:22) (in thread): > After you have asked for the paper to be assigned to you on GitHub, a mentor will tag it as assigned. You will also receive a mail to notify you.@Precious Orakwe

Idiat Alli (07:40:47) (in thread): > @Precious Orakweif you have commented by tagging our mentors. You will keep checking the page to see if it has been assigned to you

Oluwatomisin Omojokun (07:41:11) (in thread): > You can check under the Github issues which you need to curate and see if the mentors assigned the issue to you. it will be label in red

Chioma Onyido (07:47:42) (in thread): > Hi@Suru OlaitanI see 2 curatable figures in your study, figures 2 and 3; the first shows Pairwise comparisons done using Wilcoxon tests while the second shows differential abundance results using DeSeq2. Sometimes, researchers carry out different statistical tests to compare the identified taxa produced. If each of the statistical tests produces different signatures (respectively) asin your case, then I suggest you create separate experiments.

Flourish Ralph (07:47:52) (in thread): > Noted@Svetlana Ugarcina Perovicthank you!

Suru Olaitan (07:48:41) (in thread): > Okay > Thank you so much@Chioma Onyido

Abiola Salako (07:49:31) (in thread): > Thank you@Chioma Onyido

Abiola Salako (07:52:16) (in thread): > You’ll see a red label ‘assigned’ if you were the first person to claim it@Precious Orakwe

Amanda Adoyi (07:52:34): > Good day people:slightly_smiling_face:I would like to know if when your paper indicates a particular genus to be abundant in a case, and states that “using a feature classifier closest BLAST hits for its representative sequence was * particular specie * with an identity of say 99.8%” do you record that specie as fact or just record the genus? I know we are meant to be as accurate as possible.@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy

Chioma Onyido (07:53:05) (in thread): > You’re welcome!

Amanda Adoyi (07:55:07) (in thread): > For me it has got to be avoiding extraneous taxa…recording only what is required. Getting more clarity as I go but definitely that.

Odigiri Great Alume (07:55:30) (in thread): > @Esther Afuapeumhm I understand totally. Just that my doubt for having a experiment for all participants stems from > 1. That will mean that a pair wise comparison was done. Which I agree with however, in supp figure 1. We see that both MMKD and AHAD was given at the baseline and endpoint making it difficult to determine which intervention should be considered group 1 or 0. But if we make AHAD group 0 Because it had no significant result and MMKD group 1 because it has significant result. What if we come across studies like this were both groups have sig results. How do we then determine the group ?:thinking_face:. > 2. If we do this, then both experiments you suggested(AHAD vs MMKD for all, and AHAD vs MMKD for MCI) will have same signatures then, and wouldn’t be comparing CN vs MCI as that was stated in the footnote that it’s what they are trying to achieve. But from my view, Im thinking that this comparison between CN vs MCI was only further stratified based on the treatments or interventions (AHAD and MMKD) to see the effect they have on these comparison groups (CN vs MCI). AHAD had no effect while MMKD had effect. > Lastly, I also believe that the reason we have significant result for ALL is them just simply summarizing that “when we look at all the participants(CN and MCI) that’s received both AHAD and MMKD, only participants that received MMKD yielded significant results” and we can see that the MCI participants are part of the ALL which makes sense while thesame taxas that were recorded for MCI will appear in ALL.:thinking_face:

Chioma Onyido (07:56:23) (in thread): > Ohh didn’t realize you already made an illustration, this is good!

Mildred Anashie (07:58:12) (in thread): > Wheeewww:woman-facepalming:I have understood you now and It’s clear > > I also picked something from your explanation “Making the group with the significant results the Group 1”. Noted:white_check_mark:Thank you for always taking out time to clarify things:heart:

Mildred Anashie (08:00:10) (in thread): > So@Odigiri Great Alumeyou are saying since they are comparing the effect of the diet on the participants the initial participants should maintain the groups?

idiaru Angela (08:01:12) (in thread): > The confusion of species vs genus:sweat_smile:I do think the species should be curated seeing that the confidence level is very high@Amanda Adoyi

Amanda Adoyi (08:02:14) (in thread): > Thank you. That’s my suspicion too.

Mildred Anashie (08:02:32) (in thread): > I also think the species should be curated

Abiola Salako (08:02:46) (in thread): > @Amanda AdoyiWhen your paper indicates a particular genus to be abundant in a case and specifies a particular species with a high identity percentage, it’s best to record both the genus and the species, but since we’re to curate just either of the species or genus, I think you can just record only the genus. Let’s await more responses from@Svetlana Ugarcina Perovic@Chioma Onyido.

Esther Afuape (08:03:40) (in thread): > @Odigiri Great Alumein that case, you can use any as group 0 or 1, just be consistent with it throughout your curation > For question 2, you could be right. Effect of the interventions on CN and MCI is the main thing andwe’realready creating an experiment for that. Itwon’thurt to create an experiment for all andit’sfine to leave it out too I guess

Odigiri Great Alume (08:03:41) (in thread): > @Mildred Anashieyes I guess. That’s what I think:grin:

Aleru Divine (08:05:19) (in thread): > @Amanda AdoyiIn this case I think curating the species is ideal.

Esther Afuape (08:09:54) (in thread): > Record both ifyou’rein doubt. Better than missing one of them

Amanda Adoyi (08:10:59) (in thread): > @Esther Afuapethank you

Mildred Anashie (08:13:23) (in thread): > Hmmmmm > I thought I figured this out already:woman-gesturing-ok:@Odigiri Great AlumeI understood from the angle@Esther Afuapepointed out and I’m also understanding your point as well > > I’m on a crossroad here

Esther Afuape (08:13:51) (in thread): > @Chioma Onyidoplease check this out@Mildred Anashieyou might have to confirm this during the office hour

Scholastica Urua (08:18:39) (in thread): > Thank you@Chioma Onyido

Mildred Anashie (08:19:24) (in thread): > Okay:pray:Hopefully@Chioma Onyidois able to help us out and we get it resolved before the office hour

Adedoja Isaac (08:24:29) (in thread): > Thank you@Esther Afuape

Precious Orakwe (08:29:12) (in thread): > Thanks to everyone, I appreciate your assistance

Mildred Anashie (08:41:00) (in thread): > @Esther AfuapeCan I request for another paper to be assigned to me while I waitI’vecurated this based on your inputs and my understanding awaiting@Chioma Onyidoopinion > > PS: This is not my second contribution that requires grading, already submitted that for review

Mildred Anashie (08:45:16) (in thread): > @Precious Orakweyou can start going through the paper though > > If you are the first to request on it

Peace Sandy (08:47:09) (in thread): > Have you requested for the paper to be assigned to you@Precious Orakwe

Peace Daniel (09:01:01): > I’vecompleted my second contribution and I can say it was a longgggg and exciting ride butI’velearnt a whole lot and (Ihad to research a lot:smiling_face_with_tear:) > Special thanks to@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Esther Afuape@Chioma Onyido@Peace Sandy@Mildred Anashieand everyone for answering questions and clarifying things:tada::purple_heart:

Esther Afuape (09:02:37) (in thread): > @Joan C. Chukwuemeka@Mildred Anashiehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697468494614279?thread_ts=1697450304.857849&channel=C04RATV9VCY&message_ts=1697468494.614279 - Attachment: Attachment > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

Peace Sandy (09:04:12) (in thread): > @Mildred AnashieThis is a good paper to present during the office hour

Mildred Anashie (09:05:12) (in thread): > NowI’mhappyit’sall done:hugging_face:Well done@Peace DanielI admire your patience

Joan C. Chukwuemeka (09:05:55) (in thread): > Thanks@Esther Afuape. I’ve seen that discourse earlier. I just feel it will provide a more practical and relatable clarification when a paper as this is used to present

Mildred Anashie (09:06:52) (in thread): > Thank you@Esther Afuape:blush:I’vesaved it for later,it’samazing how we learn and forget most times:see_no_evil:

Scholastica Urua (09:07:02) (in thread): > Thank you@Esther Afuape. Difference between relative and differential abundance makes more sense to me now.:pray:

Mildred Anashie (09:07:31) (in thread): > Okay@Peace SandyI’llbring it up:pray:

Chioma Onyido (09:07:57) (in thread): > Ohh, I remember this particular argument, took us a while to finally realize the difference between Relative abundance and differential abundance, with this explanation by Chloe coupled with more experienceyou’llget a full grasp. Give it time.:wink:

Aleru Divine (09:08:13) (in thread): > Thanks for sharing this@Esther Afuape

Chioma Onyido (09:09:00) (in thread): > And I definitely agree with bringing this paper up during the office hour for more clarity esp for those who missed the discussion.

Odigiri Great Alume (09:10:42) (in thread): > @Chioma Onyidoway to go ma’am

Chioma Onyido (09:11:19) (in thread): > It’s@Esther Afuape:raised_hands:

Oluwatomisin Omojokun (09:15:29): > Hello@Svetlana Ugarcina Perovic,@Peace Sandy,@Chioma Onyido,@Esther AfuapeUnder the studies with no experiment, I noticed study 882 has been curated and awaiting reviewed under study 899. > Please kindly check this out. > Here’s the link to both studies.https://bugsigdb.org/Study_899https://bugsigdb.org/Study_882 - Attachment (BugSigDB): Microbial communities associated with honey bees in Brazil and in the United States - BugSigDB > Honey bee colony losses worldwide call for a more in-depth understanding of the pathogenic and mutualistic components of the honey bee microbiota and their relation with the environment. - Attachment (BugSigDB): - BugSigDB > …

Peace Sandy (09:20:56) (in thread): > I suggest that you leave study 822 it’s already marked as reviewed and study 899 needs review but has been completed by the curator > > You can check out other studies on the clean up page

Peace Daniel (09:21:12) (in thread): > I think this issomeone’swork, check the date

Esther Afuape (09:21:35) (in thread): > @Joan C. Chukwuemekaokay…I’llmention it still during the meeting

Oluwatomisin Omojokun (09:22:09) (in thread): > The study is 882 not 822

Peace Sandy (09:23:30) (in thread): > 882 does not have any experiments probablyit’sa duplicate that needs to be deleted

Oluwatomisin Omojokun (09:25:20) (in thread): > Yes,@Peace Sandy

Peace Sandy (09:25:49) (in thread): > Okay,I’mtrying to understand your initial question with the studies

Peace Daniel (09:26:58) (in thread): > 882 is a duplicate as it has the same DOI as 899. Also 899 is assigned to someone cuz the date says march

Oluwatomisin Omojokun (09:27:33) (in thread): > The Doi link in 882 is a curated study under 899.

Peace Sandy (09:27:51) (in thread): > Okay

Peace Sandy (09:29:18) (in thread): > I’ll go through them and delete study 882 > > Thank You for pointing it out@Oluwatomisin Omojokun

Oluwatomisin Omojokun (09:29:53) (in thread): > That’s really helpful. thanks@C. Mirzayi (please do not tag this account)

Leenaa Al-Amin (09:39:34): > Hello everyone,@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoI found this incomplete study without experiments and signatures and I’d like to complete it. > > Here is the linkhttps://bugsigdb.org/Study_784Can I go ahead? - Attachment (BugSigDB): Metagenomic assessment of gut microbial communities and risk of severe COVID-19 - BugSigDB > BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections.However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

Esther Afuape (09:43:57) (in thread): > @Peace Sandyhave you checked out this study?

Peace Sandy (09:45:45) (in thread): > I noticed they is an issue with deletion of this study

Peace Daniel (09:46:05) (in thread): > Can you search if it has already been resolved as I found it under closed issues on GitHubhttps://github.com/waldronlab/BugSigDBcuration/issues/153

Peace Sandy (09:46:30) (in thread): > @Esther Afuapethe study is complete and has been reviewed but when you click on it youcan’tsee the experiment directly under it and I wonder why

Peace Sandy (09:48:22) (in thread): > @Esther Afuapehttps://bugsigdb.org/Study_784/Experiment_1 - Attachment (BugSigDB): Study 784/Experiment 1 > …

Esther Afuape (09:49:42) (in thread): > Ahh

Esther Afuape (09:50:17) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

UBNSEMS3S (10:04:53) (in thread): > Then yes curate as linear regression

Glorious Katushabe (10:05:53): > Hello Team, I am in the process of creating account with BugSigDB, a confirmation link was sent to my email and a password was not. how do i go about it in order to login and start curation.

Aleru Divine (10:08:50) (in thread): > Another email will be sent to you with your username and password.Just be in the lookout for that

Abiola Salako (10:11:52) (in thread): > Be patient and wait for it as@Aleru Divinesuggested.

Glorious Katushabe (10:12:12) (in thread): > Thank you team

Abiola Salako (10:16:46) (in thread): > Thank you for the clarification@Esther Afuape

UBNSEMS3S (10:19:59) (in thread): > Sounds like a bug. I’ll file a report.

UBNSEMS3S (10:23:41) (in thread): > Bug reported:https://github.com/waldronlab/BugSigDB/issues/221 - Attachment: #221 Study 784 Experiments not showing but exist > https://bugsigdb.org/Study_784 shows no experiments on the page but they do exist: https://bugsigdb.org/Study_784/Experiment_1 > > I tried refreshing the page under … > Refresh but that did not resolve the issue.

Samreen Aftab (11:02:16): > Hello guys, since the last two days, I’ve been on the bugsigdb website trying to find some issue to solve, but I’m unable to find any, and almost all the incomplete papers have already been taken up. I’m still waiting for my second contribution to be reviewed. Can anyone guide me on what else I can do ? Thank you.

Aleru Divine (11:03:29) (in thread): > @Samreen Aftabyou can request for a new issue on GitHub while you wait for the review.

Bolanle Wahab (11:04:27) (in thread): > @Samreen Aftabnew issues have been added on GitHub,you can check

Scholastica Urua (11:06:36) (in thread): > New issues were added this morning. They’re still some unassigned ones. You can check now.

Ruth Bamgbose (11:07:22) (in thread): > Alright thank you<@UBNSEMS3S>

Samreen Aftab (11:10:19) (in thread): > Okay, thank you guys

Mildred Anashie (11:23:46) (in thread): > Yea@Samreen AftabYou can request for a new issue to be assigned to you once you are done with your assigned issue and you await review

NWAKAEGO VINCENT (11:50:00) (in thread): > thank you@Abiola Salako

Modinat Ganiyu (12:10:06): > Hello Everyone! I’m trying to delete one of the created experiment but it keeps redirecting to this page. Can anyone please help out on how I can delete the created experiment - File (PNG): image.png

Mildred Anashie (12:11:07) (in thread): > Hi@Modinat Ganiyuwe do not have permission to do this > > The mentors can do that for you however@Chioma Onyido@Svetlana Ugarcina Perovic@Esther Afuape

Scholastica Urua (12:11:13) (in thread): > Hi@Modinat Ganiyuwe do not have permission to delete, only the mentors. > > Please mention the page link and tag the mentors.

Mildred Anashie (12:11:51) (in thread): > Yea > > Drop the page link and the experiment you want to delete

Hamza Haji (12:15:33): > :wave:Hello, team! I have already made my first contribution and was waiting to complete my second contribution in order to make my final application in the outreachy program. The bugsigdb page in the outreachy program website now states that the microbiome curation project is closed to new applicants. Just wanted clarification on this.@Svetlana Ugarcina Perovic@Esther Afuape@Desire Oluwarotimi@Peace Sandy. Thank you.

Modinat Ganiyu (12:15:41) (in thread): > Thank you so much

Aleru Divine (12:16:56) (in thread): > @Hamza Haji, did you record your first contribution?

Aleru Divine (12:17:30) (in thread): > If you did, then not to worry,you’realready an applicant for this project.

Hamza Haji (12:18:26) (in thread): > @Aleru DivineYes, I recorded my first contribution on sunday.

Hamza Haji (12:18:48) (in thread): > Thank you@Aleru Divine.

Aleru Divine (12:19:04) (in thread): > Then go ahead and complete your second contribution:hugging_face:

Scholastica Urua (12:19:07) (in thread): > Like@Aleru Divinesaid, you’re already an applicant if you’ve recorded your first contribution. I just notice you are still able to record more contributions . > > Provided you’ve recorded your first.

Hamza Haji (12:22:56) (in thread): > Thank you@Aleru Divine@Scholastica Urua. Is there a way the bugsigdb team can confirm if one’s first contribution has been recorded by the team. My contribution link had opened a blank page?

Aleru Divine (12:23:50) (in thread): > @Hamza Hajii believe as long as you submitted, it has been recorded.It was the same for everyone.

Scholastica Urua (12:24:02) (in thread): > Since you filled and submitted the first contribution form, the mentors already have what they need.

Hamza Haji (12:25:52) (in thread): > @Aleru Divine@Scholastica UruaI really appreciate how helpful and quick your responses are.

Aleru Divine (12:26:34) (in thread): > :hugging_face::hugging_face:

Scholastica Urua (12:26:51) (in thread): > You’re welcome@Hamza Haji:sparkling_heart:

Modinat Ganiyu (12:42:45) (in thread): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuapeplease kindly help delete the Experiment 2 in my study. Here’s the link to the studyhttps://bugsigdb.org/Study_883. Thank you!

UBNSEMS3S (12:45:42) (in thread): > Deleted.

Modinat Ganiyu (12:49:33) (in thread): > @C. Mirzayi (please do not tag this account)Thank you so much

Praise Agbetuyi (13:13:34) (in thread): > Thank you so much<@U01MW62UDQR>

Scholastica Urua (13:51:30): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandyand everyone, please I would appreciate your assistance in reviewing this curation.:pray:https://bugsigdb.org/Study_955Here are some of my observations; > > 1. I opted for a case-control study design because the study aimed to compare healthy controls with cases. > > 2. Duodenal and sigmoid mucosal samples were collected from participants for biopsy. While I found “duodenal mucosa” listed among the body sites, I couldn’t find “sigmoid mucosa.” After searching the Uber-anatomy ontology, I selected “mucosa of the sigmoid colon” as it appeared to be the closest term. Is this an appropriate choice? > > 3. In this study, nineteen PD patients and twenty-two healthy controls were enrolled. Gastrointestinal endoscopes were used to collect duodenal and sigmoid mucosal samples for biopsy. One control only had a duodenal biopsy due to inadequate preparation for colon cleansing, resulting in a reduced number of sigmoid mucosal control samples to 21. > > 4. Alpha diversity is somewhat unclear to me. I find this excerpt from the study to be contradictory (I would appreciate further clarification on this if possible, as I may not be fully grasping the point): > “Compared to the duodenal mucosa of controls or PD patients, Kruskal–Wallis analysis showed that the microbiotic diversity of sigmoid mucosa was significantly richer according to the Shannon and Simpson diversity indices (P < 0.05). There was no significant difference in the diversity of the duodenal or sigmoid mucosa between the controls and PD patients according to the Chao1, Shannon, and Simpson diversity indices (P > 0.05).” > For Experiment 1 (duodenal mucosal samples), I curated increased Shannon and Simpson indexes and unchanged Chao1 index, while for Experiment 2 (sigmoid mucosal samples), I curated decreased Shannon and Simpson indexes and unchanged Chao1 index. > > 5. Some of the taxa are highlighted red:face_holding_back_tears:, I’m still working to identify them on the NCBI taxonomy website. > > Please I’m really looking forward to your feedback. - Attachment (BugSigDB): The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson’s disease - BugSigDB > Parkinson’s disease (PD) is the second most common neurodegenerative disease but still lacks a preclinical strategy to identify it.The diagnostic value of intestinal mucosal α-synuclein (αSyn) in PD has not drawn a uniform conclusion.

idiaru Angela (13:51:57): > Hello everyone, I hope we’re having a grand time. I have a question and I’d love various inputs. > If you have a study that has multiple cohorts but alpha diversity metrics revealed increase in just one of the cohorts how is it reported > Note that all the cohorts were used in the statistical analysis but the information about the difference in alpha diversity was also stated@Chioma Onyido@Esther Afuape@Peace Sandy@Svetlana Ugarcina PerovicI’d like some clarity, Thank you

Aleru Divine (13:55:04) (in thread): > Hi@idiaru Angelacan you share the article please.

Scholastica Urua (13:55:44) (in thread): > @Idiat Alliwhen you say multiple cohorts, does that involve different experiments? > If it does, then maybe you’ll state the different alpha diversity index under different experiments. > I may be wrong since I dont have access to the paper.

Scholastica Urua (13:56:11) (in thread): > Please share the link:pray:

idiaru Angela (13:58:47) (in thread): > @Aleru Divine@Scholastica Uruahttps://movementdisorders.onlinelibrary.wiley.com/doi/10.1002/mds.29300That is the link. Also the screenshot shows where it was stated. I don’t think it involves different experiments because all the cohorts were used to determine the differential abundance - File (JPEG): Screenshot_20240312_185701_Chrome.jpg

Aleru Divine (14:00:16) (in thread): > @Scholastica Urualet me carefully go through the article and your curation.For your point number 2, yes I think you made the appropriate choice

Scholastica Urua (14:07:01) (in thread): > Thank you so much@Aleru Divine:hugging_face::heart_eyes:

Scholastica Urua (14:08:17) (in thread): > I’m looking through the article@idiaru Angela

Leenaa Al-Amin (14:18:01) (in thread): > from what i’ve read, each cohort is a seperate experiment, increase in alpha diversity for the TBC cohort, alpha diversity is unchanged in the RUMC cohort@idiaru Angela

idiaru Angela (14:19:09) (in thread): > @Scholastica Uruaafter going through the article I made 2 observations > For the alpha diversity metrics, richness was also accounted for in the paragraph just above the excerpt you lifted. > Also, I think for Experiment 1( duodenal mucosa samples) it should be decreased for both Chao1, Shannon and Simpson while for Experiment 2 (sigmoid mucosa samples) it should be increased Shannon and Simpson while Chao1 is not recorded since it wasn’t explicitly stated > What do you think?

idiaru Angela (14:20:46) (in thread): > @Leenaa Al-AminThe study is a meta analysis so all the cohorts were used in the statistical analysis therefore its impossible to curate them into different experiments as they were evaluated for differential abundance together

idiaru Angela (14:20:59) (in thread): > Thank you@Scholastica Urua

Leenaa Al-Amin (14:28:20) (in thread): > let me go through the entire study

Mildred Anashie (14:33:52) (in thread): > Hi@Scholastica UruaI’ve gone through the study and I agree with your curation > > However for the Alpha diversity it’s truly confusing, I can deduce two things from that > 1) The sigmoid mucosa of PD patients had significantly richer microbial diversity compared to controls and duodenal mucosa of either controls or PD patients, based on the Shannon and Simpson diversity indices. > Sigmoid- Richness will be increased, Shannon and Simpson will be decreased > Duodenal- All indices will be decreased > > 2) Since there were no significant differences in microbial diversity between controls and PD patients in either the duodenal or sigmoid mucosa based on the Chao1, Shannon, and Simpson diversity indices it’ll be unchanged in both groups:thinking_face:This is a bit confusing:face_with_diagonal_mouth:

idiaru Angela (14:35:55) (in thread): > Thank you@Leenaa Al-Amin

Chioma Onyido (14:44:07) (in thread): > 1:white_check_mark:2:white_check_mark:3. Not sure what you’re asking here..? > 4. I haven’t taken a proper look into your paper yet but from the excerpt you provided. > > No sig diff in the diversity of duodenal mucosa or sigmoid mucosabetweencontrols and PD patients (2 experiments here; one for duodenal mucosa comparing PD and control and the second for sigmoid mucosa comparing PD and control) acc to Chao1, Shannon and Simpson=Meaning: for this, I would curate unchanged for the alpha diversity measures in this expt. And I’ll do same for experiments created for sigmoid mucosa samples. Becauseno sig difference = unchanged. > > **You’re right to curate the respective alpha diversities for each of the samples. > > This part “Compared to the duodenal mucosa of controls/ PD patients, … diversity of sigmoid mucosa was sig richer acc to Shannon and Simpson”, this means they compared Duodenal mucosa to Sigmoid mucosa and sigmoid was found to be sig higher (acc. to the alpha diversity results) > > Did they show differential abundant results for this too? If so, an expt. can be created for this (Group 1: Sigmoid mucosa of PD patients vs Group 0: Duodenal mucosa of PD patients). > If so, this should be curated as increased for Shannon and Simpson, Chao wasn’t mentioned and should be left blank. > > 5. I’d look out for heterotypic/ homotypic synonyms. And do further search on uniprot.:wink:

Mildred Anashie (14:54:42) (in thread): > Thank you@Chioma Onyido:heart:

Abiola Salako (14:55:08) (in thread): > Thank you@Chioma Onyidofor providing this clarity.

Aleru Divine (14:55:10) (in thread): > @Scholastica Urua@Chioma Onyidofor alpha diversity, > > I see “There was no significant difference in the diversity of the duodenal or sigmoid mucosa between the controls and PD patients according to the Chao1, Shannon, and Simpson diversity indices”Doesn’tthis mean that for both the duodenal and sigmoid mucosa that alpha diversity was unchanged?I’mstill confused:cold_sweat:

Mildred Anashie (14:57:47) (in thread): > My second interpretation as well@Aleru DivineJust that I was throwing away the information that showed significance > But looking at it again the other two groups vs control is unchanged and I suspectthere’sanother experimentthat’sshowing the increase diversity which is doudenal vs sigmoid but without signatures:thinking_face:

Chioma Onyido (14:59:48) (in thread): > Yes@Aleru Divine:thumbsup:that will make it two separate experiments as Scholastica has rightly curated. > > My mistake, thanks for pointing that out I corrected my response (1st paragraph).

Mildred Anashie (15:02:09) (in thread): > So@Chioma Onyidothis means weshouldn’tpay attention to the information that talked about increase in the diversity of doudenal and sigmoid?

Aleru Divine (15:02:26) (in thread): > Thanks@Chioma Onyido@Mildred Anashie

Chioma Onyido (15:04:50) (in thread): > :sweat_smile:I addressed that part in my response, (3rd paragraph under number 4).

idiaru Angela (15:09:57) (in thread): > Thank you for the clarification@Chioma Onyido

Scholastica Urua (15:13:44) (in thread): > Thank you so much everyone for your response.:sparkling_heart:This is engaging and insightful.@Chioma OnyidoIf I understand this part correctly, all the alpha diversity measures present here for both experiments are unchanged… right?:point_down:****“Meaning: for this, I would curate unchanged for the alpha diversity measures in this expt. And I’ll do same for experiments created for sigmoid mucosa samples. Becauseno sig difference = unchanged.”**Also regarding the excerpt, there is no differential abundant results for that (I’ll still go through the article again to make sure). Can I still go ahead to create this experiment (Group 1: Sigmoid mucosa of PD patients vs Group 0: Duodenal mucosa of PD patients) without signatures? > > PS; no. 3 is an observation, not a question:pray:.

Mildred Anashie (15:14:32) (in thread): > Idon’thave a full grasp on how Meta analysis are curated@idiaru AngelabutI’dlook into it to see if I can pick anything

Scholastica Urua (15:16:03) (in thread): > Thank you@Chioma Onyidofor the clarification:hugging_face:.

Chioma Onyido (15:20:15) (in thread): > Now, I’m not sure if to curate if there are no differential abundance results.<@UBNSEMS3S>a likkle light here pleassee > > You can go ahead with other curations, pending when Chloe responds. > If none, I’d suggest you bring it up during the next office hour. If to curate such results where alpha diversity was presented but no differential abundance result, meaning the expt. will not have signatures.

Scholastica Urua (15:21:53) (in thread): > I think this a meta analysis like@idiaru Angelamentioned. This is because it pools data from two independent studies. > We had an interesting discussion this morning between myself,@Aleru Divine, Svetlana and Levi. Below is the link, it might provide more insight:point_down:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710228540842369 - Attachment: Attachment > Hello and good morning @Svetlana Ugarcina Perovic @Esther Afuape @Chioma Onyido @Peace Sandy and everyone :sunny: > > I am currently curating a meta-analysis study(this is a study design where researchers combine results from different studies.) and I am confused regarding what to use for my Target regions since there were multiple study cohorts in the analysis. > > Do I compare all at once and take the lowest and highest regions or do I just leave it? > > Your input would be really appreciated.

Chioma Onyido (15:23:15) (in thread): > Although In the past, we’ve curated experiments (with sig alpha diversity results) without signatures.:eyes:

Mildred Anashie (15:23:23) (in thread): > @Chioma OnyidoI think you can curate experiment without signatures if the experiment is significant > > WhatI’munsure of is if a significance in alpha diversity can be considered as significance for an experiment (I hope this makes sense:sweat_smile:)I’llwait for<@UBNSEMS3S>response though

Scholastica Urua (15:25:34) (in thread): > Thank you@Chioma Onyido, I’ll bring it up during office hour.

idiaru Angela (15:26:07) (in thread): > @Scholastica Uruajust went through that discussion. Helped me clarify some things. Thank you:heart_hands:

Aleru Divine (15:26:09) (in thread): > I’dreally love to know becauseI’malso at the crossroads.I have two experiments in my study with alpha diversity metrics but without any mention on differential abundance.Ididn’tcurate themI’dlove to know if I can.:pray:

Aleru Divine (15:27:52) (in thread): > That’scorrect@Scholastica Urua

Scholastica Urua (15:34:17) (in thread): > I also agree with what@Leenaa Al-Aminsaid. One experiment (TBC cohort) had an increased alpha diversity while the other (RUMC samples) was unchanged. > > So@idiaru AngelaI think you can record different alpha diversity measures for the separate experiments. Hope this is right though:thinking_face: - File (JPEG): alpha.JPG

idiaru Angela (15:39:56) (in thread): > @Scholastica Uruathe reason I didn’t create a separate experiment is that while there were multiple cohorts, there was joint modelling of all the data sets to provide differential abundance data. > Creating a separate experiment would mean there would be no signatures.

Mildred Anashie (15:41:58) (in thread): > @idiaru AngelaGoing through the thread, it might be best to leave the Alpha diversity section blank:woman-shrugging:As Idon’tthink you should separate the experiments

Scholastica Urua (15:43:04) (in thread): > Forgive me, I didn’t go through the part accounting for differential abundance. Like we discussed in the morning, you can leave it blank and create a talk page discussing what informed your choice.

Bolanle Wahab (15:44:11) (in thread): > This entire thread has been insightful, I’d really like more light on differential abundance cause I’m currently working on a study without differential results in alpha diversities:pray:

idiaru Angela (15:52:08) (in thread): > Thank you so much@Mildred Anashie@Scholastica Uruain grateful for your inputs

Eniola Adebayo (16:30:55) (in thread): > Thankyou:blush:

Modinat Ganiyu (16:40:12): > Hello@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica Uruaand everyone, please kindly:pray:review this curation. Here is the linkhttps://bugsigdb.org/Study_883My paper do not specifically state the ‘Confounders controlled for’ and this screenshot is where I see the content is somehow related to the that. Feel free to state your opinions, they’re are highly welcome - Attachment (BugSigDB): Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups - BugSigDB > The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies.The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system. - File (PNG): image.png

Amanda Adoyi (16:46:56): > As far as open source goes this is a great project. Thanks everyone for the support :) > I would also like to point out that I think there aren’t any more issues left.
> Happy curation :)

Svetlana Ugarcina Perovic (16:57:19) (in thread): > We would also like to point out thata bugsigdb curator aims for quality over quantity. Happy bugsigdb-ing!

Bolanle Wahab (16:59:14) (in thread): > @Modinat Ganiyufrom the screenshot, these are likely confounding factors in your study but not all of them would be in the dropdown so I think you should record the ones there like Age, Gender, cough and point out the rest in a talk page.

UBNSEMS3S (17:00:19) (in thread): > You cannot control for confounders in a LEfSe analysis.

UBNSEMS3S (17:01:33) (in thread): > @Bolanle WahabAnalyzing confounders descriptively (as is presented in a demographics table) isnot the same thing as controlling for them. You only control for confounders if they specifically state they entered those variables as covariates in a model (aka “adjusted for” them).

Bolanle Wahab (17:10:25) (in thread): > @C. Mirzayi (please do not tag this account)oh,I’msorry my bad, Ididn’ttake note of the LeFSe analysis.Thanks for the correction.

UBNSEMS3S (17:12:03) (in thread): > Yeah you can curate an experiment with no signatures if there was no significant results.

Mildred Anashie (17:18:01) (in thread): > @Svetlana Ugarcina Perovic:smile:Point noted:white_check_mark:

Scholastica Urua (17:18:30) (in thread): > Thank you Chloe:pray:

Peace Daniel (17:27:17): > Hello guys, just to be sure. Do I need to curate this? I personallydon’tthink so but would love opinions - File (JPEG): IMG_2286

Juliana Oluwatobi (17:30:23): > Please I have not completed my first task I mistakenly hit submit, please what do I do?

Desire Oluwarotimi (17:32:48) (in thread): > Hi@Peace DanielI don’t think this particular figure itself can be curated. You might want to look at other figures that can be curated in your paper.

Peace Daniel (17:32:59) (in thread): > I think you can re-do it but someone said earlier BugSigdb is no longer accepting first contributions. > > Can someone else confirm this please?

Peace Daniel (17:33:31) (in thread): > Yes, I needed a confirmation. Thank you Desire

Svetlana Ugarcina Perovic (17:33:51) (in thread): > As of today, this project is closed to new applications.

Precious Orakwe (17:35:59) (in thread): > Thank you@Svetlana Ugarcina Perovicand@Amanda Adoyifor the update

UBNSEMS3S (17:37:51) (in thread): > No we don’t curate metabolites, generally speaking.

Mildred Anashie (17:38:51) (in thread): > Thank you<@UBNSEMS3S>for the confirmation > In this case, can this experiment be curated?There’sa significance in alpha diversity but no significant results stated

Aleru Divine (17:40:28) (in thread): > Thanks@C. Mirzayi (please do not tag this account):pray:

Peace Daniel (17:44:05) (in thread): > Noted. Thank you@C. Mirzayi (please do not tag this account)

UBNSEMS3S (17:44:15) (in thread): > Confirmed.

Mildred Anashie (17:46:12) (in thread): > @Aleru DivineI guessyou’dhave to enter the experiments you mentioned

Aleru Divine (17:53:41) (in thread): > Yes yes:hugging_face:thanks@Mildred Anashie

Juliana Oluwatobi (17:59:04) (in thread): > Please will there be grace for those who had difficulty completing the task yesterday

Modinat Ganiyu (18:10:07) (in thread): > Thank you@C. Mirzayi (please do not tag this account)for the clarification

Modinat Ganiyu (18:11:00) (in thread): > Please I need feedback from my curation guys

Abiola Salako (23:07:13) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Scholastica Urua (23:10:01) (in thread): > Thank you<@UBNSEMS3S>

2024-03-13

Kelechi Madubuko (00:45:44) (in thread): > Good morning@Svetlana Ugarcina Perovic@Chioma OnyidoI’ve completed my first contribution but I’m yet to be assigned a paper to curate for my second contribution as all the issues opened yesterday have been assigned to other BugSigDBers. Thank you as i wait for new issues to be opened so I can record my second contribution.

Adedoja Isaac (01:18:24) (in thread): > Good Morning@Kelechi MadubukoWeldone on completing the first contribution. The mentors will add some more papers so that you can contribute as well.

Kelechi Madubuko (02:01:35) (in thread): > Ok. Thank you@Adedoja Isaac

Modinat Ganiyu (02:25:51): > Good Morning everyone:blush:I’m happy to inform you that I’ve completed my second contribution and it was indeed a learning experience for me. > Thank you everyone for taking out time to answer my questions and special thanks to my fellow contributors@Scholastica Urua@Mildred Anashiefor always willing to help and guide through any confusion for clarity. > Here is the ink to the curated paperhttps://bugsigdb.org/Study_883All feedbacks would be appreciated:pray: - Attachment (BugSigDB): Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups - BugSigDB > The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies.The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system.

Mildred Anashie (02:27:46) (in thread): > Good morning@Modinat GaniyuI’m happy to always help > Congratulations and well done on completing your second contribution:bouquet::heart:

Desire Oluwarotimi (02:33:14) (in thread): > Good morning@Modinat GaniyuWeldone and congratulations on the milestone.:+1:

Eniola Adebayo (02:37:34) (in thread): > Good morning@Modinat GaniyuWell done:thumbsup:

Modinat Ganiyu (02:39:05) (in thread): > Please kindly review my curation:pray:

assel (03:03:02): > Good morning@Svetlana Ugarcina Perovic@Chioma OnyidoI’ve been completed my first contribution, now I’m waiting to be assigned for a second contribution.:pray:

Aleru Divine (03:04:01) (in thread): > Well done@Modinat Ganiyu:clap:

Aleru Divine (03:04:32) (in thread): > Well done@assel:clap:Did you request an issue yet?

Barakat Akinsiku (03:06:01) (in thread): > Good morning@asseland well done. You’ll have to comment under an issue once new ones are uploaded to be assigned. Happy bugsigd-ing

Mildred Anashie (03:15:14) (in thread): > Good morning@asselSomeone said they are no more available issues,you’llhave to be patient till the mentors upload more > > When they do, you comment on one and ask it be assigned to you

assel (03:20:37) (in thread): > Thank you, no I didn’t, all issues were already assigned :(

Aleru Divine (03:22:34) (in thread): > Okay@asseljust like Mildred said, more issues will be uploaded soon.Just be on the lookout:hugging_face:

Scholastica Urua (03:29:26) (in thread): > Well done@Modinat Ganiyu

Scholastica Urua (03:29:57) (in thread): > I’ll go through it with you:hugging_face:

Scholastica Urua (03:39:27) (in thread): > Hello@assel, hope you recorded your first contribution before the project was closed yesterday?

Ima-obong (Aimah) (03:41:41) (in thread): > @assel.. congratulations..keep your eyes on the GitHub page more issues will be uploaded

Leenaa Al-Amin (04:14:17) (in thread): > Good morning. Well done!@Modinat Ganiyu. I’ll help review it :)

idiaru Angela (04:26:53) (in thread): > Good morning@Modinat Ganiyucongratulations. Would review the curation now

assel (04:33:14) (in thread): > OMG I’m not sure (((

Adedoja Isaac (04:36:08) (in thread): > Weldone@assel

Amanda Adoyi (04:39:07): > Aloha and good morning:slightly_smiling_face:I am without work at the moment. Please employ me in the review of your curation if you would like to. Thank you in advance.

Scholastica Urua (04:40:40) (in thread): > Hi@asselhopefully you did but please check to make sure. If you did, then you’re already an applicant of the project. If not, you’ll have to apply to another project that’s still open (for the purpose of outreachy). > > Also, you can still contribute to BugSigDB regardless of outreachy owing to the fact that BugSigDB is open source. (Hope this is correct@Svetlana Ugarcina Perovic)

Peace Daniel (04:46:55) (in thread): > :sweat_smile:will take you up on that soon

Amanda Adoyi (04:47:38) (in thread): > @Peace DanielYes please.

Scholastica Urua (04:51:13) (in thread): > Hello@Modinat GaniyuI noticed there is no Exp. 2, just jumped from 1 to 3 (is this an issue from BugSigDB?:thinking_face:). From the article, I think two experiments is okay which is what you did. > > From my observation, the signatures are correctly assigned to the increased and decrease abundance groups. I don’t have anything else to add. Lets see what follow contributors have to say. > > Well done Modinat:+1:

Mildred Anashie (04:52:07) (in thread): > @Scholastica UruaI remember she asked that her Experiment 2 be deleted > I thinkthat’swhyit’sin that order

Oluwatomisin Omojokun (04:53:52) (in thread): > Good morning, Bugsigdb enthusiasts!:sunny:Rise and shine, for today is another opportunity to contribute to the amazing world of Bugsigdb! Your dedication and passion make a real difference in the global community. > Remember, every line of code, every article update, and every NCBI missing link you fix make brings us one step closer to building a more inclusive, innovative, and collaborative future. > So, let’s seize the day with enthusiasm, creativity, and a shared commitment to making Bugsigdb! software accessible and impactful for everyone. Together, we can accomplish great things! > Wishing you all a productive and fulfilling day ahead!

idiaru Angela (04:55:05) (in thread): > Hey@Amanda AdoyiI’d like to employ you here:sweat_smile:. Thank you

Scholastica Urua (04:56:19) (in thread): > Oh, maybe that’s why@Mildred AnashieDo you think experiment 3 should be deleted and re-entered as 2?:thinking_face:@Peace Sandy@Chioma Onyido@Esther Afuape

Mildred Anashie (04:57:51) (in thread): > I would have suggested she edited the experiment 2 and delete 3 instead butit’sdone already andI’mnot sure the order matters, I thinkit’sthe information that matters:smile::woman-shrugging:

Scholastica Urua (05:00:16) (in thread): > Okay, if the order does not matter, then I’d leave it.

Mildred Anashie (05:00:54) (in thread): > @Scholastica Urua#my opinion:smile:

Amanda Adoyi (05:09:36) (in thread): > @idiaru AngelaYes:slightly_smiling_face:

Svetlana Ugarcina Perovic (05:14:09): > Good morning:potted_plant:Today I have a special invitation for you:join us next week at MVIF, a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > Microbiome Virtual International Forum > is free, 3 hours in total, > happens every month, and > covers microbiomes from different niches and hosts (not only the human gut!). > > Attending MVIF is a good way to learn about the latest microbiome research and catch opportunities for networking.You can register for free at https://microbiome-vif.org - File (PNG): program_March24 (1).png

Blessing Ene Anyebe (05:14:45) (in thread): > Yaaaaay thank you@Svetlana Ugarcina Perovic:orange_heart::rocket::rocket:

Desire Oluwarotimi (05:16:13) (in thread): > Thank you@Svetlana Ugarcina PerovicE-see you there:joy:

Leenaa Al-Amin (05:16:22) (in thread): > thank you!@Svetlana Ugarcina Perovic

Adegboye Rukayat (05:17:22): > Hello everyone, I am just getting to know that we have to send the link to our second contribution to the mentors for review. I have done that just now, but please how will I know if it has been reviewed by the mentors. Thank you

Barakat Akinsiku (05:17:37) (in thread): > Thank you!@Svetlana Ugarcina Perovic

Muqtadirat Yussuff (05:18:24) (in thread): > Thank you:sparkles:@Svetlana Ugarcina Perovic

Adedoja Isaac (05:18:35) (in thread): > Good morning!@Oluwatomisin OmojokunThis message is exactly what I needed to get pumped for the day. Let’s crush some bugs and make Bugsigdb even better! Thank youuuu:hearts:

Chioma Onyido (05:19:08) (in thread): > Awesome! Been looking forward to the next MVIF since the last one.:grin:

Adedoja Isaac (05:20:05) (in thread): > Thank youuu:hugging_face::hugging_face:@Svetlana. See you there

Mildred Anashie (05:20:19) (in thread): > Thank you for the invite@Svetlana Ugarcina Perovic:sparkles:

Scholastica Urua (05:20:30) (in thread): > Thank you@Svetlana Ugarcina Perovic. Looking forward to it:dancer:

Muqtadirat Yussuff (05:21:27) (in thread): > Hi@Adegboye Rukayat, Did you send the link privately? We’re not to do that as it is preferable to converse about non sensitive information publicly. You just need to inform them the curation is ready for review on GitHub

Mildred Anashie (05:21:37) (in thread): > I thinkYou’llsee a reviewed tag attached to it on GitHub

Svetlana Ugarcina Perovic (05:22:06) (in thread): > In the GitHub issue where you are assigned as a curator, you will receive our feedback once we evaluate your curation. Thank you for your patience!

Adegboye Rukayat (05:22:55) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (05:24:23) (in thread): > Thank you so much for sharing this@Svetlana Ugarcina PerovicLooking forward to it

Rahila-me (05:24:54) (in thread): > Looking forward to it

Barakat Akinsiku (05:25:03): > Hi Bugsigdbiers, good morning! Hope we’re all having a great day > > I’m curating a study that has two experiments; a case-control experiment contrasting the gut microbiota between Parkinson Disease patients and healthy individuals and another, an in-vivo laboratory experiment on rats to study the pathway and genes which could play a part in neurobehavioural symptons and Parkinson’s disease progression. Is it safe to curate only the human part of the study since that of the rats has nothing directly related to relative abundance in gut microbiota? > > Also, in the instance where it is stated that drugs were excluded without specifying if the drugs are antibiotics or stating the duration of exclusion, can we still record it as an exclusion? - File (PNG): b1.png

Adegboye Rukayat (05:25:35) (in thread): > @Muqtadirat YussuffYes, I did that on GitHub

Adegboye Rukayat (05:26:00) (in thread): > Thank you@Mildred Anashie

Adegboye Rukayat (05:26:38) (in thread): > Alright, thank you@Svetlana Ugarcina Perovic

Mildred Anashie (05:27:30) (in thread): > For the exclusion I think if antibiotics were not directly stated then you leave it blank

Scholastica Urua (05:27:52) (in thread): > Hi@Barakat Akinsikufor your second question, I think if antibiotic exclusion was not specifically stated it’s best to leave it.

Rahila-me (05:27:59): > @Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyidoplease i have highlighted in this pdf with red ink what is supposed to be an increase and decrease signature of the case group (DN) yet no figure or table in the article to back it up. There is only one SUPPLEMENTAL FILE 1, at the end of the study i have checked that too: > here is the link to pdf file highlighted part can you help me take a look:zhang-et-al-2022-alterations-of-the-gut-microbiota-in-patients-with-diabetic-nephropathy.pdfthen this the article:https://journals.asm.org/doi/10.1128/spectrum.00324-22waiting for your kind reply

Nana (05:28:42) (in thread): > I am present already cannot wait

Mildred Anashie (05:28:44) (in thread): > Did they have differential abundant results for the second experiment? > > My opinion is, if they did then you should curate it but if not you might have to leave it

Kelechi Madubuko (05:28:51) (in thread): > Nice one@Svetlana Ugarcina PerovicI will be there. Already registered

Eniola Adebayo (05:29:36) (in thread): > Itshould be specifically stated that antibiotics are excluded. I think you curate the experiment that have only differential abundance results@Barakat Akinsiku

Barakat Akinsiku (05:30:54) (in thread): > Noted, thank you guys

Scholastica Urua (05:32:11) (in thread): > @Barakat AkinsikuFor the first question,<@UBNSEMS3S>mentioned this earlier;https://community-bioc.slack.com/archives/C04RATV9VCY/p1710277923151239?thread_ts=1710265890.754799&cid=C04RATV9VCY - Attachment: Attachment > Yeah you can curate an experiment with no signatures if there was no significant results.

Oluwatomisin Omojokun (05:33:02) (in thread): > I will gladly be there to acquire more knowledge on the latest research on the microbiome. Thank you@Svetlana Ugarcina Perovic

Barakat Akinsiku (05:33:38) (in thread): > Thank you@Scholastica UruaI’ll go through it

Eniola Adebayo (05:36:19) (in thread): > The pdf you highlighted is not showing on my device.If I get your question right, looking at your article, figure 3 has LEfSe analysis results and other results that curatable.

NWAKAEGO VINCENT (05:37:40) (in thread): > registered already:heart:

Bolanle Wahab (05:38:57) (in thread): > Thank you:partying_face:@Svetlana Ugarcina Perovic

Adegboye Rukayat (05:44:48) (in thread): > @Amanda Adoyican you help me take a look at my curationhttps://bugsigdb.org/Study_925although I have tagged the mentor for review, I am honestly kind of scared lol, like I don’t know if I did it right. I knew I watched the How to add a study video and I followed the guidelines to the best of my knowledge. Your criticism will go a long way in helping me better at curating. Thank you - Attachment (BugSigDB): - BugSigDB > …

Adenike Oladimeji-Kasumu (05:48:51) (in thread): > @Rahila-meFigure 3 is curatable as@Eniola Adebayomentioned. Check the text before Figure 3 as it explains the relative abundance. > > The link to your highlighted article cannot open, I think that cannot be shared though. - File (JPEG): Screenshot_20240313-104635.jpg - File (JPEG): Screenshot_20240313-104502.jpg

Bolanle Wahab (05:49:26) (in thread): > @Barakat Akinsikuyes, I think it’s safe to curate the human part of all the data pertains to human gut microbiota

Adenike Oladimeji-Kasumu (05:53:26) (in thread): > From the Text above Figure 3, the organisms were already mentioned. That is which was increased and the deceased abundance. For some, the Genus level was mentioned and species name for others. > You might need to take a closer look at the organisms mentioned in that text and compare each with the ones in figure 3. In so doing, you would be able to differentiate the increased signatures from the decreased. > > I hope this helps.

Amanda Adoyi (05:54:09) (in thread): > @Adegboye RukayatWould love to. On it in a while. Also please don’t be scared of ‘bugsigdb-ing’ or the mentors. It appears they love us asking questions:sweat_smile:. But seriously be free here about your concerns.

idiaru Angela (06:00:51) (in thread): > Thank you@Svetlana Ugarcina Perovic:relieved:

idiaru Angela (06:03:46) (in thread): > Hey@Adegboye Rukayatour mentors have informed us that once your issue is tagged reviewed on Github no changes should be made on it. Also I agree with@Amanda Adoyiwe’re all here learning so please don’t be scared:blush:

Adegboye Rukayat (06:04:37) (in thread): > @Amanda AdoyiThank you, The questions being asked by other BugSigDBers have been really helpful and also I don’t hesitate to voice out my concerns example is this:face_with_peeking_eye:. Thank you once again

Amanda Adoyi (06:06:01) (in thread): > @idiaru AngelaAye. That line skipped my sight.@Adegboye RukayatI’m afraid if you’ve done that on github you should kindly not modify your curation.

Modinat Ganiyu (06:06:34) (in thread): > Thank you for your feedbacks:pray:At first, I duplicated an extra experiment than I needed and I tried deleting one but couldn’t so, I had to tag our mentors for the request and thankfully@C. Mirzayi (please do not tag this account)deleted Experiment 2 which I asked for. > I actually thought deleting Experiment 2 will automatically change Experiment 3 to Experiment 2 because at this time I had already done a lot under Experiment 3. Little do I know that the Experiment number wouldn’t change. And right now I know I can’t duplicate another to correct.@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic<@U1LCB8WEA>@Peace Sandy@Chioma Onyidoplease what can I do to change Experiment 3 to Experiment 2 as I only have 2 Experiments in my paper?

idiaru Angela (06:06:35) (in thread): > Kindly help me review my curation. Thank you@Amanda Adoyi

Amanda Adoyi (06:07:00) (in thread): > @idiaru AngelaAlready on it:slightly_smiling_face:

U1LCB8WEA (06:09:40) (in thread): > Wecan’trename an experiment,butit’sok to skip from experiment 1 to 3.

U1LCB8WEA (06:12:10) (in thread): > This is because page history is an important part of the wiki, and renaming a page would make it complicated to represent that history. Also note that deleted pages are not truly gone, if you navigate to that page in the future, you will still see links to the deleted material.

Scholastica Urua (06:14:16) (in thread): > I came across an incomplete study that started from Experiment 2. Now I understand why. > > Thank you for clarifying<@U1LCB8WEA>:hugging_face:

Ima-obong (Aimah) (06:17:43) (in thread): > Already registered!!..Will be there no matter what:partying_face:

Ruth Bamgbose (06:23:48) (in thread): > Thank you@Svetlana Ugarcina Perovic. Looking forward to it.

Rahila-me (06:24:25) (in thread): > No, I have done curation for 2 signatures already, i have to also compare T2DM and DN where now DN will be the case study, And i have to provide an increase and decrease taxon for DN which the supplemently material did not provide to the best of my knowledge. my study has 3 different experiments and 2 different conditions. @Mentors please i still need help

Adegboye Rukayat (06:30:25) (in thread): > @idiaru AngelaOh okay. Thank you.@Amanda Adoyican you check and give me your honest feedback while I await the mentor’s response.

assel (06:30:57) (in thread): > I saw few NEW issues on github. Please check it

Adenike Oladimeji-Kasumu (06:31:40) (in thread): > Alright. I guess I’m the one not getting your question. Since I saw that different color bars were used to represent each group in Fig 3. > The mentors would help but you have to tag them by their names.

Nana (06:33:00) (in thread): > @Rahila-meI have checked it out, yes others the figures you people are pointing to has to do when she compares with a healthy group. Now she wants to compare T2DM against DN. At Liza I’m right

assel (06:34:32) (in thread): > Hello, can u please tell how did you inform them through github? Thank u in advance

Abiola Salako (06:34:57) (in thread): > @Kelechi MadubukoThere are a few new issues on GitHub, kindly check it.

Scholastica Urua (06:35:03) (in thread): > Good morning@Chioma Onyido:boom:I implemented the corrections you pointed out and also added another experiment (Group 1: Sigmoid mucosa of PD patients vs Group 0: Duodenal mucosa of PD patients) without signatures. > > I still have some questions about this other part of the study:point_down:; is this another experiment? is it curatable?:thinking_face:(So many questions:sweat_smile:) > > Really looking forward to your response. Thank you:pray: - File (JPEG): Correlation analysis.JPG

Mildred Anashie (06:36:44) (in thread): > Just click on one of the issues and drop a comment thatyou’lllike it to be assigned to you > > Ensure ithasn’tbeen assigned to anyone yet

Abiola Salako (06:37:08) (in thread): > @asselcongratulations there are a few new issues on GitHub kindly check it.

Mildred Anashie (06:38:36) (in thread): > Can I see Fig 6? > The text looks likeit’sresults for relative abundance@Scholastica Urua

assel (06:39:42) (in thread): > no, I meant after completing a second curation, how we can inform mentors that we’ve done.

Abiola Salako (06:39:47) (in thread): > Thank you for the clarification@Levi Waldron

assel (06:40:13) (in thread): > and they can review it

Scholastica Urua (06:40:42) (in thread): > Hi@Amanda Adoyi, there are more open issues on GitHub at the moment.

Mildred Anashie (06:40:50) (in thread): > By leaving a comment under the issue with a link to the study you curated on BugSigdbThey’lladd a “needs review” tag and you patiently wait for it to be reviewed

Muqtadirat Yussuff (06:41:14) (in thread): > Make another comment that the curation is ready for review on the GitHub issue you were assigned to

Muqtadirat Yussuff (06:41:40) (in thread): > Don’t attempt editing the curation once you do that though

assel (06:42:00) (in thread): > THANK You!!

Rahila-me (06:42:37) (in thread): > Nana exactly my point

Abiola Salako (06:42:56) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic. Looking forward to it already

Modinat Ganiyu (06:43:17) (in thread): > Thank you:blush:@Svetlana Ugarcina Perovic

assel (06:43:26) (in thread): > Thank you very much

Adenike Oladimeji-Kasumu (06:43:46) (in thread): > Okay… I’m sorry I misunderstood you@Rahila-me

Scholastica Urua (06:44:33) (in thread): > @Mildred Anashiehere’s a link to the curation;https://bugsigdb.org/Study_955 - Attachment (BugSigDB): The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson’s disease - BugSigDB > Parkinson’s disease (PD) is the second most common neurodegenerative disease but still lacks a preclinical strategy to identify it.The diagnostic value of intestinal mucosal α-synuclein (αSyn) in PD has not drawn a uniform conclusion. - File (JPEG): Fig 6.JPG

Chioma Onyido (06:47:44) (in thread): > @Rahila-meIf there’re no figures showing the diff abundance for T2DM vs DN, try also to read within text. If further reading still shows no abundance results for T2DM vs DN, then curate only the alpha diversity results (if there are any). > > Remember in bugsigdb, experiments are only created for comparisons made.

Amanda Adoyi (06:47:52) (in thread): > @Scholastica UruaThanks

Modinat Ganiyu (06:48:41) (in thread): > @Amanda AdoyiPlease kindly review my curationhttps://bugsigdb.org/Study_883I’d appreciate it if you can. Thank you! - Attachment (BugSigDB): Upper respiratory tract microbiome profiles in SARS-CoV-2 Delta and Omicron infected patients exhibit variant specific patterns and robust prediction of disease groups - BugSigDB > The role of the upper respiratory tract (URT) microbiome in predicting lung health has been documented in several studies.The dysbiosis in COVID patients has been associated with disease outcomes by modulating the host immune system.

Amanda Adoyi (06:49:36) (in thread): > @Modinat GaniyuWill get to it soon. Thanks.

Rahila-me (06:51:22) (in thread): > @Adenike Oladimeji-Kasumuyou do not have to apologies please, you did nothing wrong you were only trying to help and i really appreciate that:people_hugging::people_hugging:

Chioma Onyido (06:53:35) (in thread): > Our focus on bugsigdb is differential abundance results, gene expression results on the other hand are not curated on bugsigdb.

Scholastica Urua (06:54:24) (in thread): > Thank you Chioma:tulip:

Idiat Alli (06:54:52): > Good morning everyone > There is an article uploaded to be curated. Fastest finger:blush:

Kelechi Madubuko (06:57:15) (in thread): > Thank you@Abiola Salako@asselI’ve been assigned an issue

Precious Orakwe (06:57:59): > Good day team, please I need help on how to start my second contribution, the issue has been assigned to me on GitHub, I want to know how and where you start. Thank you

Rahila-me (06:58:01) (in thread): > @Chioma Onyido<@UBNSEMS3S>i have read in between lines, please what can you infer from this screen shots. To report signature for increase and decrease in DN when T2DM becomes the group 0 and DN becomes the group 1 - File (PNG): chi3.png - File (PNG): chi 2.png - File (PNG): chi 1.png

Ima-obong (Aimah) (06:59:07) (in thread): > Hello@Precious Orakwehere is the curation policy, please read through it to know how to curate your paperhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Rahila-me (06:59:54): > @Precious Orakwego to this website:https://bugsigdb.org/Main_Pageclick on Add a study, read your article and fill the required information from the article to the input fields - Attachment (BugSigDB): Main Page > …

Ima-obong (Aimah) (06:59:57) (in thread): > Also, have you requested for an account already?

Abiola Salako (07:00:36) (in thread): > Thank you@Chioma Onyido

Barakat Akinsiku (07:00:53) (in thread): > Hi@Precious OrakweYou add a study from your bugsigdb homepage. Follow the steps in the curation policy as shared by Aimah

Ima-obong (Aimah) (07:01:13) (in thread): > If you have, then sign in to your account, it takes you to the homepage, then you click on add a study and you start curating from the paper assigned to you

Rahila-me (07:01:27): > @Precious Orakweunderstand your article very well before answering the questions . you can achieve this if your account has been approved

Abiola Salako (07:03:21) (in thread): > @Precious Orakwekindly read through the curation policy as shared by@Ima-obong (Aimah)to know what and what not to curate.

Scholastica Urua (07:04:07) (in thread): > Hi@Precious Orakwethis video will guide on how to document your curation:point_down:Step-by-step guidance on how to document a signature in BugSigDB (link) > > Also go through the onboarding materials for further clarification.https://github.com/waldronlab/BugSigDBcuration/issues/94. > > I hope this helps. Please feel free to ask questions anywhere you experience hiccup. We are all here to help. - Attachment (YouTube): Adding a study to bugsigdb.org - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday at: https://us02web.zoom.us/j/2737200499. Attendance by all applicants is highly encouraged. Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Contributions > > Remember to record your contributions in Outreachy at https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/microbiome-study-curation/contributions/

Precious Orakwe (07:11:13) (in thread): > Thanks @everyone for your warm assistance and thanks@Mildred Anashiefor her guide

Modinat Ganiyu (07:12:59) (in thread): > @Precious Orakwewatch the video using the link@Scholastica Uruasent to guide you on how to add a study and start curating the paper assigned to you but before that, create BugSigDB account using this linkhttps://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Bolanle Wahab (07:18:49): > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyidoand everyone. > I’m currently working on a study that investigated the gut microbiome in PD and the impact on disease progression and the use of device assisted therapy over 12months > I have been able to deduce these contrasts: > Healthy Control(HC) vs PD > PD patients with slower progression v faster progression > I’m confused about the comparisons for the DAT cohort cause it has a subgroups: LCIG and DBS > Should I compare HC with DAT, or compare HC with each of the subgroups. > Please if there are other experiments I’m missing, I’d appreciate your inputs. ThanksHere’sa link to the article:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9152137/ - Attachment (PubMed Central (PMC)): The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies > Altered gut microbiome (GM) composition has been established in Parkinson’s disease (PD). However, few studies have longitudinally investigated the GM in PD, or the impact of device-assisted therapies.To investigate the temporal stability of GM …

Adegboye Rukayat (07:25:51) (in thread): > Thank you@Scholastica Urua

Adegboye Rukayat (07:26:23) (in thread): > Yes yes, thank you@Idiat Alli

Idiat Alli (07:31:47) (in thread): > You are welcome@Adegboye Rukayat

Aleru Divine (07:36:47) (in thread): > @Bolanle WahabI think you should compare with each sub groups because according to Fig 7 it was done that way. > > Also consider the different time points/intervals because they pointed that out because they mentioned some over representations and I think that matters in the curation.

Aleru Divine (07:37:53) (in thread): > Thank you for the invitation@Svetlana Ugarcina Perovic:hugging_face:

Bolanle Wahab (07:47:05) (in thread): > @Aleru DivineSo to clarify,I’mcomparing:LCIG vs DBS at each time points separately?

Aleru Divine (07:52:17) (in thread): > @Bolanle WahabYes I thinkthat’sthe best way to go about it.Because they highlighted the over representations at different time points.Would’vebeen different if theydidn’t

Bolanle Wahab (07:56:57) (in thread): > Alright,Thank you so much.

Aleru Divine (07:58:33) (in thread): > Not LCIG vs DBS > > It should be PD vs each sub group.PD vs LCIG > PD vs DBS > > Becausethey’reboth an intervention andthey’retrying to study the effects of these interventions on the gut microbiome.Does this make sense?

Bolanle Wahab (08:08:08) (in thread): > It does make sense. > But how about PD vs DAT as a group because they took samples from the participants Pre DAT and initiated LCIG and DBS at the same timepoints?

Amanda Adoyi (08:08:44) (in thread): > @Adegboye RukayatAlright.

Aleru Divine (08:11:42) (in thread): > Then in this case it should be > Pre DAT vs LCIG > Pre DAT vs DBS

Aleru Divine (08:16:07) (in thread): > I think so because they they provided information on the differentially abundant taxa differently, not as DAT but as DBS and LCIG - File (JPEG): IMG_7917

Bolanle Wahab (08:29:59) (in thread): > I noticed that too, I was just confused because some information were presented for DAT as a group butI’dgo with your idea and duplicate the experiment and add their signatures. > Thank you for your time@Aleru Divine

Joan C. Chukwuemeka (08:35:13) (in thread): > Thanks for the invite@Svetlana Ugarcina Perovic

Aleru Divine (08:35:40) (in thread): > Registered and looking forward to it:white_check_mark:Thanks again:hugging_face:@Svetlana Ugarcina Perovic

Aleru Divine (08:36:20) (in thread): > Alright@Bolanle WahabYou’rewelcome:hugging_face:

Peace Daniel (08:45:41): > Can we like inform people before making certain changes?For instance,I think Pseudomonadota is close to Proteobacteria and you might want to confirm instead of just making edits.It’snot nice:pray:

Modinat Ganiyu (09:14:20) (in thread): > Thanks so much:pray:for your response, for clarifying and stating reasons its like that<@U1LCB8WEA>This makes me feel better

Faith Ifeoluwa Alexander (09:15:27): > Good Afternoon everyone.@Mildred Anashiepls I need your help. I am stuck in Curating my paper.

Chioma Onyido (09:15:48) (in thread): > Apologies Peace. > Applicants should not work or edit the curations by current applicants.It’sgood to always check the dates (the study was curated) before attempting to correct or review any study.

Ima-obong (Aimah) (09:17:06) (in thread): > Hello..maybe you can share the issue on the channel here… others will be more than willing to assist too.

Aleru Divine (09:17:32) (in thread): > Hi@Faith Ifeoluwa Alexanderwhat’sthe issue?

Ima-obong (Aimah) (09:18:17) (in thread): > @Chioma Onyidothanks for this, please can it be pinned too?

Faith Ifeoluwa Alexander (09:18:51) (in thread): > The article I was assigned to is on the ncbi website and I don’t know if I should import it onto the BugSigdb site

Faith Ifeoluwa Alexander (09:19:43) (in thread): > I have watched the YouTube video but I don’t understand how to go about it now.

Aleru Divine (09:20:17) (in thread): > Can you share the title please.But even if itisn’ton the NCBI website, you can fill the data manually.Just set it to manual.

Ifenna Muonagolum (09:20:24) (in thread): > Hello everyone, can someone explain the below goals to me in simple terms “A microbial signature is findings of bacterial taxa that differed between one condition of interest and another via statistical testing.” I’ve read it again and again but yet to understand what is required of me.

Ima-obong (Aimah) (09:20:31) (in thread): > No..I don’t think you need to..you could download it if need be, but you can read it from wherever and just input your answers to the questions on the bugsigdb study page

Ima-obong (Aimah) (09:23:09) (in thread): > On your bugsigdb homepage, click on add a study, then input the study design, DOI of the paper and the PMID which can be found on the PubMed page then set it to complete and it will populate the other Fields… > Then you click on add an experiment

Ima-obong (Aimah) (09:23:52) (in thread): > Oh..first of…do you have an account?..did you request for one?

Faith Ifeoluwa Alexander (09:23:52) (in thread): > The title is Effect of Parkinson’s disease and related medications on the composition of Fecal bacteria microbiota@Aleru Divine

Peace Daniel (09:23:58) (in thread): > If you stilldon’tunderstand you can post the link here

Scholastica Urua (09:24:08) (in thread): > Hello@Faith Ifeoluwa Alexandercan you please drop the link of the issue on GitHub? It will be easier to help that way.

Faith Ifeoluwa Alexander (09:25:37) (in thread): > Okay. Let me get it then

Mildred Anashie (09:27:24) (in thread): > Hi@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (09:27:49) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/217 - Attachment: #217 Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota > Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - Weis et al - NPJ Parkinsons Disease
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884491/

Faith Ifeoluwa Alexander (09:28:41) (in thread): > Hello@Mildred Anashie. How are you doing?

Aleru Divine (09:29:27) (in thread): > Hi@Ifenna MuonagolumI totally understand you and let me try and break it down. > 1. Microbial Signature: This refers to specific patterns or characteristics observed in the types of bacteria present in a particular environment or sample. > 2. Condition of Interest: This is the specific situation or state being studied. It could be a disease, a particular environmental condition, or any other factor of interest in the research. > 3. Statistical Testing: Researchers use statistical methods to analyze data and determine if there are significant differences between groups. In this context, statistical testing is used to identify which bacterial taxa (types of bacteria) show notable differences between the condition of interest and another condition. > Putting it all together, a microbial signature is essentially a set of bacterial taxa that are identified as different or distinctive between two conditions based on statistical analysis. It helps researchers or curators(us) understand how the composition of bacteria varies under different circumstances, which can provide insights into the factors influencing microbial communities.

Peace Daniel (09:29:34) (in thread): > Just fill in the PMID31815177

Mildred Anashie (09:29:38) (in thread): > Follow the steps@Ima-obong (Aimah)has shared > > AlsoI’llgo through the paper to see if I can highlight a few things for you

Faith Ifeoluwa Alexander (09:29:44) (in thread): > @Peace DanielI have a BugSigDB account.

Faith Ifeoluwa Alexander (09:30:17) (in thread): > Where do I find the doi?

Scholastica Urua (09:31:01) (in thread): > @Faith Ifeoluwa Alexanderdoi:10.1038/s41531-019-0100-xThis is the doi to your article

Mildred Anashie (09:31:18) (in thread): > @Faith Ifeoluwa Alexanderinsert the PMID@Peace Danielshared every other field will auto populate in the add a study field

Faith Ifeoluwa Alexander (09:31:19) (in thread): > I found it too

Aleru Divine (09:31:51) (in thread): > Here is your article on PMIDhttps://pubmed.ncbi.nlm.nih.gov/31815177/THE PMID and DOI are beneath the authors names. - Attachment (PubMed): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - PubMed > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders. PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS). Such alterations and functional gastroi …

Ima-obong (Aimah) (09:33:04) (in thread): > Your study design is case-control..add that with the DOI and the PMID and you’re good to go …next is to click on the “add a new experiment”

Scholastica Urua (09:33:11) (in thread): > Well written@Aleru Divine

Aleru Divine (09:34:00) (in thread): > Thank you@Scholastica Urua:hugging_face:

Faith Ifeoluwa Alexander (09:34:43) (in thread): > No need for URL?

Mildred Anashie (09:35:30) (in thread): > Add the PMID and it should auto complete the rest@Faith Ifeoluwa Alexander

Scholastica Urua (09:35:40) (in thread): > Not necessarily@Faith Ifeoluwa Alexander, it will auto populate or it can be left blank

Faith Ifeoluwa Alexander (09:35:49) (in thread): > Okay.

Ima-obong (Aimah) (09:37:39) (in thread): > This is awesome@Aleru Divine:clap:

Faith Ifeoluwa Alexander (09:38:07) (in thread): > Okay, it has auto-populated the article and I have clicked on Add an Experiment.

Rahila-me (09:38:23) (in thread): > @Chioma Onyidohola

Ima-obong (Aimah) (09:39:01) (in thread): > @Faith Ifeoluwa Alexander..please go through this curation policy, it will give you a proper understanding of what is required of the curation.https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Rahila-me (09:39:03) (in thread): > I made this statement on monday, thanks for saying it again

Scholastica Urua (09:41:17) (in thread): > Nice going@Faith Ifeoluwa Alexander. > You can check out this step-by-step guidance on how to document a signature in BugSigDB (link). - Attachment (YouTube): Adding a study to bugsigdb.org

Bolanle Wahab (09:41:49) (in thread): > This is really nice@Aleru Divine@Ifenna Muonagolumyou can also check out@Chioma Onyido‘s blog where she compared Microbial Signature to ID card. > Here’s the link:https://chiomaonyido.wordpress.com/2024/01/03/bugsigdb-ing-chronicles-1/comment-page-1/#comments - Attachment (…tales (and tips) from a bioCurious opensource bébé…): BugSigDB-ing Chronicles 1- A 4-Step Contribution Guide > The BugSigDB-ing toolkit are the tools and techniques used in BugSigDB-ing, and they include (but not limited to) the ontology and taxonomy browsers, as well as the special rules that curators/revi…

Faith Ifeoluwa Alexander (09:42:16) (in thread): > I can’t seem to find the location of the experiment in the article.

Ifenna Muonagolum (09:47:11) (in thread): > Thank you@Aleru Divine

Aleru Divine (09:47:34) (in thread): > You’rewelcome!

Aleru Divine (09:48:37) (in thread): > @Ifenna Muonagolumjust to be sure, does it make sense to you now? > > You ask questions if it is still unclear.

Peace Daniel (09:49:38) (in thread): > You’dneed to read your article very carefully to find those details. Also I suggest you highlight important sentences so you can easily find them when you start curating

Ifenna Muonagolum (09:51:01) (in thread): > @Aleru Divineit’s still a little bit unclear. But let me read it again and again. I believe it will get clearer.

Faith Ifeoluwa Alexander (09:51:36) (in thread): > Is it possible that the location of Subjects is not included in an article?

Scholastica Urua (09:52:17) (in thread): > Hello again@Faith Ifeoluwa Alexanderplease take your time to go through the article like@Peace Danielsuggested. You’ll definitely find it. If not, this is what the curation policy has to say; - File (JPEG): Location.JPG

Aleru Divine (09:53:32) (in thread): > Alright then:thumbsup:be sure to ask where youdon’tunderstand.Maybe I can throw more light.

Peace Daniel (09:54:04) (in thread): > Fecal sampling was performed in 2015. In order to collect samples at home, subjects were provided with sterile containers (MED AUXIL fecal collector set, Süsse, Gudensberg, Germany) and introduced to the collection procedure. Samples were sent to the Institute of Microecology in Herborn, Germany, frozen immediately and then stored at −20 °C until further analysis. Fecal calprotectin concentrations were measured by an enzyme-linked immunosorbent assay as reported previously.16

Ikeh Darlington Ikeh (09:54:37) (in thread): > Perfectly said. In addition, all the information you need about curating your article is on the bugsigbd help page.Link belowhttps://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Help:Contents > …

Mildred Anashie (09:55:11) (in thread): > @Faith Ifeoluwa AlexanderScholastica is right, the curation policy states how to find the location, but if you go through your methods you’ll see the location there

Faith Ifeoluwa Alexander (09:57:13) (in thread): > @Peace Danielpls how did you figure this out?

Ikeh Darlington Ikeh (09:57:58): > Dear team bugsigdb, if you need help with your curation and seem not to be getting the response to answer your questions or late response, the help page of the bugsigbd website is very helpful and contains almost all the tips and tricks to help you. See link below.https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Help:Contents > …

Peace Daniel (09:58:25) (in thread): > By reading the methods in your article

Faith Ifeoluwa Alexander (09:59:04) (in thread): > I just found it now. Let me settle down. My Baby was fussing earlier.

Michael Adekanye (09:59:33) (in thread): > Thank you@Joan C. Chukwuemeka

Aleru Divine (09:59:34) (in thread): > @Faith Ifeoluwa Alexanderthe location is usually always stated and ifit’snot, you can just leave it blank.To find the location, most of the time it might be in the introduction, materials and method or sampling section.

Peace Daniel (10:00:10) (in thread): > Alright faith, sorry about that:purple_heart:

Scholastica Urua (10:00:29) (in thread): > I’ve realized that most times you’ll find the location in your abstract or method under the sample collection section (like in your case)@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (10:01:01) (in thread): > Thank you. I was feeding him & trying to work on the article at the same time.

Faith Ifeoluwa Alexander (10:01:54) (in thread): > Okay@Scholastica Urua. Guess mine is at the Sample collection area.

USLACKBOT (10:04:33): > This message was deleted.

Aleru Divine (10:05:03) (in thread): > It’severy Thursday@Michael Adekanye:hugging_face:

Michael Adekanye (10:05:19) (in thread): > Oh my bad.

Joan C. Chukwuemeka (10:05:24): > Office hour is every Thursday@Michael AdekanyeInfo on the Office hour is also on the GitHub page:https://github.com/waldronlab/BugSigDBcuration/issues/95

Ima-obong (Aimah) (10:05:26) (in thread): > No..every Thursday

Mildred Anashie (10:05:27) (in thread): > It’s stated Thursdays on the onboarding material

Abiola Salako (10:07:08) (in thread): > @Peace Danielwe all should be calming down:joy:

Michael Adekanye (10:11:47) (in thread): > @Joan C. Chukwuemeka1. how do get to know it’s raw counts? > 2. The statistical test will to be chosen is either the one for p-value or relative abundance, right?

Mildred Anashie (10:13:18) (in thread): > Hi@Michael AdekanyeThe statistical test is the one used for differential abundance

Mildred Anashie (10:14:32) (in thread): > Go through this for Data transformationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697145085673689?thread_ts=1697141457.022309&channel=C04RATV9VCY&message_ts=1697145085.673689 - Attachment: Attachment > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio -> Rare. ANCOM > > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

Abiola Salako (10:14:52) (in thread): > @Faith Ifeoluwa AlexanderDo take your time to read through the curation policy and read your article well following the instructions in the materials shared by@Ima-obong (Aimah)&@Scholastica Urua.

Joan C. Chukwuemeka (10:15:19) (in thread): > For raw counts, The researchers stated, “bacteria count” in different parts of the paper. I’ll try to point you to an excerpt shortly,@Mildred Anashieis right about the statistical test.

Scholastica Urua (10:16:15) (in thread): > Thanks@Mildred AnashieThis will also helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1699808143495129?thread_ts=1699704087.950319&cid=C04RATV9VCY - Attachment: Attachment > Oh wow > Could you correct this list please? @Levi Waldron > > ANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance

Faith Ifeoluwa Alexander (10:16:17) (in thread): > I am doing that along with the video. Thank you.

Abiola Salako (10:17:17) (in thread): > @Aleru Divine:raised_hands:

Joan C. Chukwuemeka (10:19:49) (in thread): > Alright..@Michael Adekanyecheck the highlighted in the image. Such statements gives you a hint to know it’s likely raw counts. - File (PNG): image.png

Chioma Onyido (10:21:19) (in thread): > Excerpt from Image 1: this is not the original results from the paper, the paper was only making reference to previous results published by other researchers elsewhere (check the citation beside it). > Excerpt from image 2 and 3: no comparisons made, only relative abundance was stated. > > Conclusion: Please curate the differential abundance results for other expts from the Lefse figures as advised by your peers, > Ifthere’san alpha diversity result and no diff abundance result for T2DM vs DN,it’svery okay to curate only that with no signatures.

Joan C. Chukwuemeka (10:22:48) (in thread): > @Michael AdekanyeThe result table below points to that too. - File (PNG): image.png

Michael Adekanye (10:32:28) (in thread): > @Joan C. Chukwuemeka:+1:Raw counts and Mann-Whitney(wilcoxon), will this work?

Ifenna Muonagolum (10:35:51) (in thread): > @Aleru DivineThank you for your writeup it helped a lot. So I’ve read it, solved the questions that followed, and submitted it. What is the next thing to do?

Joan C. Chukwuemeka (10:36:52) (in thread): > From Online research, I found that Raw counts can be used in the Mann-Whitney U test with some caveats.******Here’s the info I got online:*******the Mann-Whitney U test (Wilcoxon rank-sum test) can be performed on both *******raw counts******* and *******relative abundance******* data.Here’s a breakdown: > ******Raw counts:******* Represent the unprocessed number of times each element (bacteria) is observed in a sample. > ******Relative abundance:******* Expresses the proportion of each element (bacteria) within a group relative to the total count. It’s usually presented as a percentage or a proportion. > *****Mann-Whitney U test:******* This non-parametric test is suitable for comparing two independent groups and assessing if their medians differ significantly.Here’s why both data types work for the test: > ******Non-parametric:******* The Mann-Whitney U test doesn’t assume any specific underlying distribution for the data. It relies on the ranks of the observations instead of their actual values. > ******Ranks:******* During the test, the data points (raw counts or relative abundance values) from both groups are ranked together, assigning numerical positions based on their order from smallest to largest. > Therefore, the Mann-Whitney U test focuses on the relative ordering of the data points, making it suitable for analyzing both raw counts and relative abundance data as long as they represent measurements on the same scale.*****Points to consider:****** > * ******Interpretation:******* While both can be used, the interpretation of the results might differ slightly. > > ******Raw counts:******* Reflect the direct difference in the number of observed bacteria between groups. > ******Relative abundance:******* Indicates a proportional difference, which can be helpful when comparing groups with varying total bacterial counts. > > ******Normalization:******* When using raw counts, it’s crucial to ensure the data is normalized for any group size differences that might skew the results. > *****Conclusion:********The Mann-Whitney U test is a versatile tool for comparing two groups and can be applied to both raw count and relative abundance data in microbiome analysis. Choosing the appropriate data type depends on the specific research question and how you want to interpret the results.**However, I stand to be corrected<@U1LCB8WEA>@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape

Aleru Divine (10:37:13) (in thread): > Is this for the first task? Did you start recording your contribution on the Outreachy website?

Michael Adekanye (10:40:12) (in thread): > @Joan C. ChukwuemekaThank you so so much.

Rahila-me (10:40:13) (in thread): > ok..thank you

Joan C. Chukwuemeka (10:41:27) (in thread): > You’re Welcome. Glad to help.:hugging_face:

Oluwatomisin Omojokun (10:46:05): > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma OnyidoUnder the Studies that have no Experiments, > I noticed the following study to be duplicated or incomplete > Study 878, 888 , 895, 901, 936- Need to be deleted > Study 887 has no record on the Bugsigdb site which I would love to work on it. > Duplicated studies are: > 898 (deleted) and 899 (need review) > 915 (deleted) and 902 (need review) > 889, 916 (deleted) and 887 (need review) > 937, 938, 940, 943 are the same with no experiment and signature > 962, 963, 964, 965 are the same with no experiment and signature

Peace Sandy (10:47:30) (in thread): > Thank you for pointing it outI’lltake a look

Ifenna Muonagolum (10:54:54) (in thread): > Yes, it is for the first task. Is it to be recorded on the Outreachy website?

Aleru Divine (10:57:01) (in thread): > Yes it is.Idon’tthink you can record anymore since this project is closed for new applicants.I’mso sorry about that.

Michael Adekanye (10:57:56) (in thread): > It’s raw counts(from the highlighted text) and Mann-Whitney can be used. > Please anyone that has an objection or will like to add to what’s been talked about in the thread. Kindly help@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA> - File (JPEG): Screenshot_20240313-155247.jpg

Glorious Katushabe (11:02:39): > Hello team, my study has 3 groups ( samples are categorized into three groups: no transplant group (NT) , lung transplant event-free group (EF) , and lung transplant chronic rejection group (CR) and I am finding hardships in identifying group 1. and results are in this form NT vs EF, NT vs CR and EF vs CR, The LEfSe analysis exhibited significant differences between groups. I tried to create each as an experiment but I am getting a comment that there is no difference from previous experiment. Should I combine CR and EF and name it Lung Transplant to form group 1. your guidance is highly appreciated.

Joan C. Chukwuemeka (11:03:03) (in thread): > @Oluwatomisin OmojokunSome of these experiments are likely “work-in-progress” by other contributors.

Aleru Divine (11:04:00) (in thread): > @Glorious Katushabeyou will need to create 3 experimentsand below are the different groups. > 1. NT(group 0/control group) vs EF(group1) > 2. NT(group 0/control group) vs CR(group1) > 3. EF(group 0) vs CR(group1 because it is the high severity group)

Mildred Anashie (11:05:08) (in thread): > Hi@Glorious KatushabeIf the results are presented in the format you shared, you should curate based on what@Aleru Divinejust shared

Abiola Salako (11:06:09) (in thread): > Yes. Create 3 experiments as said by@Aleru Divine

Scholastica Urua (11:14:49) (in thread): > @Glorious Katushabeyou should create 3 experiments just like you and@Aleru Divinementioned. > Please what do you mean by “there is no difference from previous experiment.”? Can you drop a snapshot of the message?

Rahila-me (11:17:39) (in thread): > You will create 3 different experiment with its own unique signatures for each based on differential abundance mentioned in the study

Nana (11:18:51) (in thread): > @Peace Sandypeople are still working and editing ooh

UBNSEMS3S (11:23:45) (in thread): > Yes Mann-Whitney can be used for count data.

UBNSEMS3S (11:23:59) (in thread): > And that’s what’s depicted in that table that was posted.

UBNSEMS3S (11:26:10) (in thread): > According to that methods snippet that Michael posted, it looks like they also fitted a linear model for those 10 bacterial taxa so that should be curated as well.

Peace Daniel (11:28:30) (in thread): > I’m calm, just stating:blush:

U1LCB8WEA (11:35:24): > <!channel>coming up, the 3-hour monthly Microbiome Virtual International Forum, on Mar 20 (western hemisphere) or Mar 22 (eastern hemisphere). Organized by@Svetlana Ugarcina Perovic, myself, and others from around the world. There will be a keynote talk “Strain-specific gene function prediction and the Human Microbiome Bioactives Resource,” several short talks and “highlights” (our online version of posters), and networking. It’s a great way to learn more broadly about the field of microbiome studies and meet others in the field. Registration is free:https://www.microbiome-vif.org/en-US/-/future-events/mvif27-20-2122-march-2024-prof-curtis-huttenhower - Attachment (microbiome-vif.org): MVIF.27 | 20 & 21/22 March 2024 > with Keynote talk by Prof. Curtis Huttenhower

Svetlana Ugarcina Perovic (11:40:59) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710321249373689 - Attachment: Attachment > Good morning :potted_plant: > > Today I have a special invitation for you: join us next week at MVIF, a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > Microbiome Virtual International Forum > is free, 3 hours in total, > happens every month, and > covers microbiomes from different niches and hosts (not only the human gut!). > > Attending MVIF is a good way to learn about the latest microbiome research and catch opportunities for networking. > You can register for free at https://microbiome-vif.org

U1LCB8WEA (11:41:51) (in thread): > Great minds think alike,butdon’tnecessarily catch up on Slack posts:joy:

Bolanle Wahab (11:43:44) (in thread): > Already Registered,can’twait:partying_face:

Mildred Anashie (11:44:19): > Hello team:blush:Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyI’m currently working on a study, it’s a laboratory experiment and I’m unsure if my interpretation of the Alpha diversity is correct. > Chao1 and Simpson =Unchanged > > Also the paper used Rat and Mice interchangeably would I be right to pick one when entering the host? > > The images attached are where alpha diversity was mentioned and shown > > Here’s the link to the studyhttp://dx.doi.org/10.1155/2022/9110560 - File (JPEG): IMG_2284 - File (JPEG): IMG_2283

Bolanle Wahab (11:53:52) (in thread): > @Mildred AnashieI think ‘no discernable variation’ implies there was neither increase nor decrease, so you’re right to select Unchanged

Aleru Divine (11:56:41) (in thread): > Registered and looking forward to it:hugging_face:

Scholastica Urua (12:02:48) (in thread): > @Mildred AnashieI’ll also go with unchanged for alpha diversity. > > I can see mice recurring in the objective of the study. This is most likely the host I assume. - File (JPEG): mice.JPG

Aleru Divine (12:03:19) (in thread): > @Mildred AnashieI think your interpretation is correct. > > As for the second point, use mice as host because the section 2.2 which describes the animals refers to mice.

Bolanle Wahab (12:04:45) (in thread): > Also Mice seems like the main subject of the experiment according to the objective of the study - File (PNG): IMG_9634

Eniola Adebayo (12:11:40) (in thread): > Mice model was mostly used@Mildred Anashie

Abiola Salako (12:12:47) (in thread): > Already registered:smiling_face_with_3_hearts:

Abiola Salako (12:17:57) (in thread): > Thanks for the clarification@C. Mirzayi (please do not tag this account)

Barakat Akinsiku (12:19:30) (in thread): > Already registered!

Flourish Ralph (12:19:47) (in thread): > Registered and looking forward to the conference!:slightly_smiling_face:

Kelechi Madubuko (12:22:51) (in thread): > Registered! I will be there

Barakat Akinsiku (12:23:34) (in thread): > Yeah, mice re-occured more@Mildred Anashie

Adedoja Isaac (12:53:18) (in thread): > In!:boom:Will be there:white_check_mark:

Glorious Katushabe (13:02:08) (in thread): > Thank you team for your comments, I am being helped

Mildred Anashie (13:21:31) (in thread): > Thank you everyone for your inputs needed to share for accuracy:pray:

UBNSEMS3S (14:31:29): > Hi everyone, > > Just a reminder that we have our team meeting and office hours at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. > > Please note that the US just experienced daylight savings time. This meansfor many of you the meeting will be an hour earlier than last week. Please double check the meeting time with your local time using this link:https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179

Michael Adekanye (14:31:53): > Hi Team, > The cofounders controlled for the study I am working on is not clearly stated. I tried checking whether I could get it through statistical analysis in the research. I couldn’t get it. > Any hints on getting it or it can left blank since it’s not stated.

Muqtadirat Yussuff (14:32:20) (in thread): > Hi, you can leave it blank

Mildred Anashie (14:32:25) (in thread): > Yes it can be left blank if it’s not stated

UBNSEMS3S (14:32:33) (in thread): > If they didn’t state any clearly (usually using words like “adjusted for” or “controlled for”) they probably didn’t control for any confounders. Controlling for confounders is fairly uncommon in microbiome research currently.

Michael Adekanye (14:32:57) (in thread): > Thank you.

Mildred Anashie (14:33:55) (in thread): > Thank you for the reminder:pray:<@UBNSEMS3S>

Benedicta Imelda (14:34:24): > I am having problems getting an account on bugsigdb main page > Please I need help

Desire Oluwarotimi (14:34:26) (in thread): > Thank you<@UBNSEMS3S>

UBNSEMS3S (14:35:17) (in thread): > I just approved your account.

Bolanle Wahab (14:35:54) (in thread): > Thank you:heart:@C. Mirzayi (please do not tag this account)Our meeting time is now 2pm Nigerian time

Benedicta Imelda (14:36:24) (in thread): > Thank you so much

Michael Adekanye (14:36:50) (in thread): > A Google meet, right?

Desire Oluwarotimi (14:37:35) (in thread): > Nah, it’s zoom now.@Michael Adekanye

Bolanle Wahab (14:37:53) (in thread): > @Michael Adekanyeit’sa zoom link

UBNSEMS3S (14:38:16) (in thread): > Please use the zoom link above. I’ll be hosting this time around and Zoom is easiest for recording and posting after for people who can’t make it.

Scholastica Urua (14:38:23) (in thread): > Thank you<@UBNSEMS3S>

Michael Adekanye (14:38:49) (in thread): > The last one was a Google meet,right?

Mildred Anashie (14:39:32) (in thread): > Yes@Michael Adekanye

Michael Adekanye (14:41:03) (in thread): > So I was refreshing the zoom link I saw prior to that. I kept refreshing and refreshing till I couldn’t refresh no more.

Michael Adekanye (14:41:18) (in thread): > It’s noted now. Thank you.

Flourish Ralph (14:55:43) (in thread): > Noted@C. Mirzayi (please do not tag this account)thank you

Flourish Ralph (14:56:50): > Hi everyone, > I’ll like to get your input on a study I’m curating; > > What do I do in a situation where the study says that there are statistically significant differences in alpha diversity but doesn’t state if it’s an increase or decrease? (Both text and the figure)@Svetlana Ugarcina Perovic@Esther Afuape@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy

Aleru Divine (14:57:59) (in thread): > Thank you for the update@C. Mirzayi (please do not tag this account)

Mildred Anashie (14:58:18) (in thread): > Hi@Flourish RalphCan you show how it was stated? > Like an excerpt or screenshot

Blessing Ene Anyebe (14:59:18) (in thread): > Thank you@C. Mirzayi (please do not tag this account):sparkles:

Desire Oluwarotimi (14:59:40) (in thread): > Hmmm. Quite tricky. > > I think it’s going to be quite uncertain that it’s not stated in the paper at all. > > Sometimes, we miss these things.@Flourish Ralph

Flourish Ralph (15:00:37) (in thread): > @Mildred Anashie - File (JPEG): IMG_2857

Flourish Ralph (15:01:26) (in thread): - File (JPEG): IMG_2859

Desire Oluwarotimi (15:03:34) (in thread): > @Flourish RalphIt says there was no significant difference at week 2 after surgery, this means that alpha diversity was unchanged. > > However, there was a difference at week 4.

UBNSEMS3S (15:04:00) (in thread): > You can tell if it’s increased or decreased from the box and whiskers plots. For instance, ACE is increased in WT_AB is increased relative to WT_Control.

UBNSEMS3S (15:05:02) (in thread): > A-E have alpha diversity measures that can be curated.

Mildred Anashie (15:05:06) (in thread): > I see significance in Ace and PD whole tree > > I know we curate Ace but I don’t know if we curate PD_whole tree > > And Its increased in Ace but others seem to be unchanged > > My interpretation:woman-shrugging:

Flourish Ralph (15:05:42) (in thread): > Yes@Desire Oluwarotimi, baseline and week 2 have no significance. I’m trying to know exactly what the change in alpha diversity is at week 4. If it’s an increase or a decrease.

Desire Oluwarotimi (15:05:48) (in thread): > @Mildred AnashieI think we can. PD whole tree is Faith.

Mildred Anashie (15:06:58) (in thread): > Oh yes that’s true > > Phylogenetic diversity

Desire Oluwarotimi (15:07:05) (in thread): > @Flourish Ralph<@UBNSEMS3S>already helped out.

Desire Oluwarotimi (15:07:45) (in thread): > Each of those plots represent the alpha diversity related to the paper.

Flourish Ralph (15:07:49) (in thread): > Thank you!@C. Mirzayi (please do not tag this account)

Flourish Ralph (15:07:59) (in thread): > Thank you guys

UBNSEMS3S (15:08:19) (in thread): > The horizontal square bracket indicates a significant difference. Since the median value of red is higher than the median value of blue, there is a difference between the two and red is increased relative to blue. - File (PNG): image.png

UBNSEMS3S (15:08:47) (in thread): > There is no difference between blue and green or green and red however! If there were, they’d have a bracket pointing to them.

Flourish Ralph (15:09:50) (in thread): > Ah I see, I understand better now@C. Mirzayi (please do not tag this account), I appreciate your help:grin:

Mildred Anashie (15:11:28) (in thread): > <@UBNSEMS3S>I was thinking the one with significance are the ones with the asterisks above the brackets, that was how I interpreted it:thinking_face:

UBNSEMS3S (15:13:26) (in thread): > Oh yes they have to have an asterisk. That’s a weird way of doing it. Usually you don’t include the brackets if they’re non-significant.

Mildred Anashie (15:14:40) (in thread): > Oh I see > > So in this case we curate all as significant because of the brackets? > > Just for clarity

Bolanle Wahab (15:15:06) (in thread): > @C. Mirzayi (please do not tag this account)please how about in situations where you’re given only the p values of the alpha diversities without indicating increase or decrease?

UBNSEMS3S (15:15:17) (in thread): > No you were right. B, D and E should not be curated because they are not significant.

UBNSEMS3S (15:15:46) (in thread): > @Bolanle WahabIf they don’t give you any indication, then yeah you can’t curate that unfortunately.

Flourish Ralph (15:16:06) (in thread): > So what will B, D, and E be recorded as in alpha diversity?@C. Mirzayi (please do not tag this account)

Mildred Anashie (15:16:41) (in thread): > Okay > > Thank you<@UBNSEMS3S>:hugging_face:

UBNSEMS3S (15:17:00) (in thread): > @Flourish RalphNo difference.

Mildred Anashie (15:17:28) (in thread): > I think Unchanged@Flourish Ralph

Flourish Ralph (15:17:29) (in thread): > I see, noted

Bolanle Wahab (15:17:58) (in thread): > @C. Mirzayi (please do not tag this account)Okay, thank you

Michael Adekanye (15:20:51) (in thread): > Since this thread is about alpha diversity. > In my case, alpha diversity wasn’t named at all. > Only sentences like “Total fecal bacteria counts were decreased in 2 years in all PD patients”. Can the alpha diversity be gotten from such?

Mildred Anashie (15:22:04) (in thread): > @Michael AdekanyeI doubt that sentence implied Alpha diversity > Ifit’snot mentioned I think the best option is to leave it blank

UBNSEMS3S (15:22:31) (in thread): > Yeah that doesn’t sound like diversity to me. Total counts is not a diversity measure.

UBNSEMS3S (15:22:57) (in thread): > Unless it’s something like “total counts ofunique taxa” which is another way of saying richness.

Mildred Anashie (15:24:53) (in thread): > This is insightful, if I came across that I probably would have ignored it > > Thank you for mentioning that<@UBNSEMS3S>:pray:

Michael Adekanye (15:25:15) (in thread): > To add to the information gotten from the paper: > “The composition of gut microbiota was analyzed using Yakult intestinal Flora-SCAN(YIF-SCAN).”

UBNSEMS3S (15:26:20) (in thread): > Never heard of YIF-SCAN

Michael Adekanye (15:31:25) (in thread): > I hope this will help. - File (JPEG): IMG-20240313-WA0002.jpg

Michael Adekanye (15:36:27) (in thread): > Or is there a way to get it from here? - File (JPEG): IMG-20240313-WA0003.jpg

Flourish Ralph (15:37:53) (in thread): > @C. Mirzayi (please do not tag this account)Amongst Pielou, Shannon, inverse Simpson, and richness in the BugSigDB edit, which is ace and sobs?

Mildred Anashie (15:38:52) (in thread): > Ace is richness@Flourish Ralph

Barakat Akinsiku (15:39:11) (in thread): > This is a really interesting thread. I’ve learnt a lot. Thank you@C. Mirzayi (please do not tag this account)

Flourish Ralph (15:39:34) (in thread): > Okay, what about sobs please?

Mildred Anashie (15:40:40) (in thread): > I’m notsure of sobs > > Pleaselet’swait forChloe’sresponse on that

Desire Oluwarotimi (15:41:30) (in thread): > Yeah. > > Ace is richness. I’m not sure about sobs either.

Ima-obong (Aimah) (15:44:59) (in thread): > Woah…Such an insightful thread.. > > Thanks to everyone for the amazing responses

Barakat Akinsiku (15:51:35) (in thread): > And I’m also curious, in situations like this where there’s no square brackets or asterisks, how do we determine increased or decreased alpha diversity?<@UBNSEMS3S>@Mildred Anashie - File (PNG): b.png

Scholastica Urua (15:52:28) (in thread): > This thread is insightful and interesting. Thanks you<@UBNSEMS3S>. > > Save this thread for later:sweat_smile:

Esther Afuape (15:53:26) (in thread): > Sobs is observed species

Flourish Ralph (15:57:23) (in thread): > Thank you@Esther AfuapeHowever,there’sno standalone sobs tag. The tags left to classify arePielou, Shannon, and inverse Simpson in the BugSigDB edit. Which of them refers to observed species (sobs)?

Aleru Divine (15:58:50) (in thread): > This is really insightful.Thank you@C. Mirzayi (please do not tag this account)@Mildred Anashie@Flourish Ralph:pray:

Esther Afuape (15:58:53) (in thread): > I thinkit’sused to describe richness also. The result often correlates with that of richness

Abiola Salako (15:59:17) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Flourish Ralph (16:01:23) (in thread): > Noted thank you

Adegboye Rukayat (16:03:46) (in thread): > <@UBNSEMS3S>Thank you

Abiola Salako (16:09:17) (in thread): > This is such an interesting read. Thank you@C. Mirzayi (please do not tag this account)for your contributions.

Mildred Anashie (16:10:07) (in thread): > @Barakat AkinsikuI reallycan’tinterpret the image, I’ll leave that for<@UBNSEMS3S>to respond to:hugging_face:The text says “Varied Significantly” > I’m not sure if it’s trying to indicate an increase or decrease > But I’m gearing towards decrease:thinking_face:

Abiola Salako (16:11:28) (in thread): > @Scholastica Uruayou got that right”Save this thread for later”:grinning:

Bolanle Wahab (16:16:48) (in thread): > @Barakat Akinsikuin the study where only p values were given, the graph looked similar to this and I asked@C. Mirzayi (please do not tag this account), she said itcan’tbe curated so unless your study says otherwise,you should probably leave it.

Barakat Akinsiku (16:17:27) (in thread): > Thank you@Mildred AnashieYeah, let’s wait for@C. Mirzayi (please do not tag this account)’s response

Barakat Akinsiku (16:17:57) (in thread): > Okay, thanks@Bolanle Wahab

Adenike Oladimeji-Kasumu (16:41:47): > Hello<@UBNSEMS3S>,@Svetlana Ugarcina Perovic,@Chioma OnyidoI was assigned a paper to work on with PMID 34776854. Upon entering the PMID, it says “must be unique”. so, I assume that the study already exist. Could you please help me check the study if it is completed or if I can still work on it. Also, please help with the link to the study. Thank you.

Muqtadirat Yussuff (16:43:03) (in thread): > Hi, it’s already in the database, you can search for the article title and see what pops up. You don’t need the mentors for that

Adenike Oladimeji-Kasumu (16:46:12) (in thread): > @Muqtadirat YussuffI have searched for the Title of the Article On the BugSigDB page but it says “There were no results matching the query.” Or is there another way to search?

Muqtadirat Yussuff (16:47:58) (in thread): > To my knowledge there isn’t. What’s the title by the way?

Adenike Oladimeji-Kasumu (16:48:25) (in thread): > “Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson’s Disease Cohort”

Muqtadirat Yussuff (16:49:38) (in thread): > Hmm, gimme a few minutes please

Muqtadirat Yussuff (16:53:24) (in thread): > Yeah I can’t find the title or PMID. Doesn’t seem to be in the database, should I attempt creating it?

Desire Oluwarotimi (16:54:07) (in thread): > @Adenike Oladimeji-KasumuHave you tried the manual option as well?

Adenike Oladimeji-Kasumu (16:58:33) (in thread): > @Desire OluwarotimiYeah, that is what I just did. I have been able to create the study. Thank you guys

Joan C. Chukwuemeka (18:00:41) (in thread): > Thanks for the update<@UBNSEMS3S>Based on that, Office hour for tomorrow, 14 March 2024 will be at these times: > 09:00 AM EST, > 13:00 (1:00PM) UTC, > 14:00 (2:00PM) WAT, > 16:00 (4:00PM) EAT, > 18:30 (6:30PM) IST; > > For time zone not stated, you can check -https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Grace Paul (18:10:50) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic. Look forward to it

Aleru Divine (19:24:28): > Hello everyone,@Svetlana Ugarcina Perovic@Esther Afuape<@UBNSEMS3S>@Chioma Onyido@Peace SandyI would really appreciate your input on this:pray:I am currently curating this paper that compared microbial diversity and composition in six different gastrointestinal sites. > > I have curated the experiments and differential abundances of each of the six sites. > > However, there were 2 additional considerations > 1. The paper also considered the effects of H. pylori infection in the microbial composition of both the cardia and non-cardia specimens. > 2. The effects of H.pylori infection and pH value on the microbial characteristics of gastric juice. > Both of these comparisons had no mention of differential abundances of bacteria, but they did mention some alpha diversity measures. > > My concerns are: > 1. Do I go ahead to curate these as experiments even if they were not the primary focus? And if yes, > 2. About the alpha diversity in the second consideration(gastric juice specimen), I am confused as to how to curate it because of the multiple groups mentioned and would really love all your thoughts and inputs on this. > I have attached images and a link to the paper. > > Thank you in anticipation:pray:https://journals.asm.org/doi/10.1128/spectrum.00645-21 - File (PNG): IMG_7927 - File (PNG): IMG_7928

Mildred Anashie (19:52:53): > Hi@Aleru Divinethe comparison in the gastric juice seems to be a bit confusing but I think there’s an experiment to be curated from the cardia and non-cardia > > I’ll go through the paper though to try to figure this out more

Aleru Divine (20:01:13) (in thread): > @Mildred Anashiethank you:pray:Yes I understand the cardia and non cardia case but the gastric juice is just so confusing:sleepy:

Bolanle Wahab (21:02:27) (in thread): > @Aleru DivineI’m not so sure but it looks like separate experiments for gastric juice:H pylori negative Vs H pylori positiveH pylori positive(high pH) Vs H pylori negative(high pH)H pylori positive (low pH) Vs H pylori negative (low pH)But then again, I’m a little confused about this part

Abiola Salako (21:05:21): > 1)I want to believe it’s okay to include the additional considerations as experiments, even if they weren’t the primary focus@Aleru Divine. But let’s wait to hear from@Svetlana Ugarcina Perovic@Esther Afuape.

Aleru Divine (21:56:23) (in thread): > @Bolanle Wahabthe paper doesn’t really make the comparisons. It stated that the observed ASVs and Shannon index decreased across the groups. > > My interpretation: all the groups had a decrease in observed ASVs and Shannon index.So ifI’mcurating maybe I would make it 1 experiment(sinceit’sthe same for all) > > It is just very confusing:face_with_diagonal_mouth:

Nitya Singhal (22:12:04) (in thread): > Yes, yes in the first contribution, you have to simply read the article and answer the questions in the quiz. Primary focus shall be on the highlighted words. So sorry for the late reply.@Evelyn Mary Attah

Hamza Haji (22:45:20): > Hello team. I am curating a paper that investigates several conditions, altogether termed Gastrointestinal cancers. The paper states them as colorectal cancer, esophageal cancer, gastric cancer and others. When curating this paper the term gastrointestinal cancer is not available so I’ve filled out the individual cancers. My challenge is that the paper does not mention what the ‘other’ cancers are. Should i fill out the cancers mentioned only since the form does not accept the term ‘others’?https://bugsigdb.org/Special:FormEdit/Experiment?Experiment%5BBase%20page%5D=Study_978&reload=1&returnto=Study_978 - Attachment (BugSigDB): Special:FormEdit/Experiment

Hamza Haji (22:52:10): > Also, how does one fill out confounders that are not in the list of allowed values? For example, the confounders in this study include age, gender, Cancer type, MSI, bmi, drug, EBER status, allergy and prior treatment, most of which are not in the list of allowed values?

Aleru Divine (23:05:23) (in thread): > Hi@Hamza Hajiif I’m not mistaken, this sounds a lot like the paper I’m currently curating. > > Could you check it out to clear my doubts please > > Link to my paper.https://journals.asm.org/doi/10.1128/spectrum.00645-21

Aleru Divine (23:17:02) (in thread): > I re-read your issue and I believe it isn’t.:sweat_smile:Kindly share your paper so I can go through it and see if I can catch anything. > > Thanks!

Hamza Haji (23:26:59) (in thread): > Hello@Aleru DivineHere’s the articlehttps://aacrjournals.org/cancerimmunolres/article/8/10/1251/466881/The-Gut-Microbiome-Is-Associated-with-Clinical

Hamza Haji (23:27:33) (in thread): > They are different papers:sweat_smile:

Aleru Divine (23:27:48) (in thread): > @Hamza HajiConsidering that the paper investigates various cancers within the digestive system, it may be beneficial to use the term ‘Digestive system cancers’ to encompass all related conditions. > > I found this a few days ago on BugSigDB, this page describes Digestive system cancer and lists some of its aliaseshttps://bugsigdb.org/Digestive_system_cancer - Attachment (BugSigDB): Digestive system cancer > Aliases…

Aleru Divine (23:29:48) (in thread): > @Hamza HajiThat’srelieving to hear:sweat_smile::pray:thanks for sharing.

Hamza Haji (23:33:27) (in thread): > Digestive system cancer works. Thank you@Aleru Divine.

Aleru Divine (23:34:47) (in thread): > That’sgreat news@Hamza Haji:hugging_face:

Aleru Divine (23:48:46) (in thread): > I believe this calls for the attention of the mentors.@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Peace Sandy@Chioma Onyido@Esther AfuapeAlsoI’drecommend exploring closely related terms as these might be among the list of allowed values.

2024-03-14

Scholastica Urua (00:10:18) (in thread): > Nice point@Aleru Divine. Digestive system cancer does work well because all the other types@Hamza Hajimentioned are cancers that can originate in various parts of the digestive system.

Mildred Anashie (00:10:42) (in thread): > Hi@Hamza Hajiyou should fill most of those in full > > > E.g BMI should be entered as Body Mass Index > Let’s see if it works for all while we wait for the mentors

Scholastica Urua (00:13:32) (in thread): > If I remember correctly, I think@Esther Afuapementioned earlier that if the confounders are mentioned, it should be filled out even when they’re not among the list of accepted values.:thinking_face:

Hamza Haji (00:22:57) (in thread): > Thank you@Aleru Divine@Mildred Anashie@Scholastica Urua.

Mildred Anashie (00:50:39) (in thread): > Hi@Aleru DivineI’ve gone through the paper and I think the gastric juice also has different pairwise comparisons done and this groups where defined in the paper - File (JPEG): IMG_2298

Mildred Anashie (00:52:23) (in thread): > I think the experiments should be accounted for, I see results in Table S4 I don’t know if it should be curated though, as they tagged it Relative abundance of dominant genus

Scholastica Urua (01:40:56) (in thread): > Going through the article@Aleru DivineI’m also thinking since the alpha diversity measures are decreased in all the groups curating as 1 will be a better option. > “The observed ASVs and Shannon index values were lower in H. pylori-positive participants than in H. pylori-negative participants both in cardia (Fig. 3A and B) and noncardia (Fig. 3C and D) specimens.” > > For the Gastric pH, I’m stumped because a lot of groups are mentioned here under group definition.:disappointed_relieved:Although I think it should also have an experiment. > > Waiting to hear the mentors opinion because I’d to know what should be done in this case.

Faith Ifeoluwa Alexander (01:43:35): > Good Morning everyone. Pls, I have been searching for Statistical test in the paper I was assigned to curate? I have searched the Bioinformatics & Statistics section of my paper and yet I can’t seem to find it. Pls, help!

Mildred Anashie (01:44:36) (in thread): > Hi@Faith Ifeoluwa Alexanderplease share your paper

Faith Ifeoluwa Alexander (01:45:50) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/217 - Attachment: #217 Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota > Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - Weis et al - NPJ Parkinsons Disease
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884491/

Aleru Divine (01:46:41) (in thread): > @Mildred Anashiethat’sthe issue.They stated “relative abundance of genus” and we are not supposed to curate that.SoI’lljust record without experiments then.

Aleru Divine (01:50:01) (in thread): > @Scholastica Uruayes I agree with you. I had no problem with the cardia and non cardia specimens.My issue is with the multiple groups mentioned relating to the gastric juice specimens.Hopefully the mentors can help clarify this:pray:

Aleru Divine (01:51:09) (in thread): > Thank you so much for all your inputs and for going through the paper@Bolanle Wahab@Mildred Anashie@Scholastica Urua:heart:

Svetlana Ugarcina Perovic (02:00:01): > <!channel>Hello everyone, two important messages today:good_luck:1. We will be having**** our weekly team meeting and Outreachy office hours ****at 9 AM EDT today at:https://us02web.zoom.us/j/2737200499. > > Find out the time in your local time zone here:https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179PLEASE NOTE: this is an hour earlier for those of us not yet in daylight savings time!SAVE THE DATE for the next two meetingshttps://github.com/waldronlab/BugSigDBcuration/issues/952. In the next days, we will be releasing**** our review feedback with a curation scorein the GitHub issues, one by one. Please be patient while waiting for yours – you could check them out and learn from them, just search for a label:reviewed. - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world. - Attachment: #95 Office Hours > Welcome, Outreachy applicants! > > My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Svetlana (pronouns: she/her) on the BugSigDB project and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on our GitHub repo: #94 > > Also, between now and Monday, April 1st, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participate or observe these meetings as well as ask questions. > > These meetings are scheduled for:
> Thursday March 7**, 9-10 AM ET* (Zoom Link TBA)
> *Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Thursday March 14, 9-10 AM ET (https://us02web.zoom.us/j/2737200499)
> Thursday March 21, 9-10 AM ET (https://us02web.zoom.us/j/2737200499)
> Thursday March 28, 9-10 AM ET (https://us02web.zoom.us/j/2737200499) > > Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179
> PLEASE NOTE: this is an hour earlier for some countries due to daylight savings time! > > We are happy to meet with you on a different day or time upon request. Thank you!

Mildred Anashie (02:02:29) (in thread): > @Faith Ifeoluwa AlexanderThis is from your paper “differences in OTU counts between PD and controls using a two-sided Wilcoxon–Mann–Whitney test for unpaired”. Also i think the Data transformation is raw counts

Aleru Divine (02:02:33) (in thread): > @Faith Ifeoluwa Alexanderthanks for sharing your paper.I see some info on statistical analysis in your paper and in the section you mentioned. > > Check images below. > 1. P-values for alpha diversity was calculated using ANOVA > 2. The package coin version 1.2–2 was used to compute differences in OTU counts between PD and controls using a two-sided Wilcoxon–Mann–Whitney test > I also saw from the same section that “Statistical analyses resulting in p-values were corrected using a false discovery rate (FDR) correction for multiple testing.” > > This means that there was MHT correction. - File (PNG): IMG_7929

Faith Ifeoluwa Alexander (02:04:31) (in thread): > Now I am even more confused.

Mildred Anashie (02:04:54) (in thread): > Noted > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (02:05:39) (in thread): > Noted@Svetlana Ugarcina PerovicThank you so much! > Looking forward to the office hours today:hugging_face:

Faith Ifeoluwa Alexander (02:06:13) (in thread): > @Mildred AnashieRelative abundance is written all over my paper.

Bolanle Wahab (02:06:43) (in thread): > @Aleru DivineApparently there are other groups mentioned, although didn’t specify if there were comparisons but if atall, there can be one experiment for gastric juice: Lower group Vs Higher group, and then probably list the information for the sub groups in a talk page. > Waiting for our mentors now:cold_sweat:

Aleru Divine (02:07:20) (in thread): > @Faith Ifeoluwa Alexanderrelative abundance is not to be used for curating differential abundance.But yes use that as your data transformation.

Faith Ifeoluwa Alexander (02:08:14) (in thread): > @Aleru Divineis my statistical test ANOVA or Wilcoxon?

Mildred Anashie (02:09:42) (in thread): > We are saying “The statistical test used is Wilcoxon-Mann-Whitney test” > > MHT=Yes > > For the data transformation that statement indicates Raw counts in my opinion

Bolanle Wahab (02:12:16) (in thread): > @Faith Ifeoluwa Alexanderaccording to the points@Aleru Divinehighlighted in the screenshot, Your statistical test should be Wilcoxon

Faith Ifeoluwa Alexander (02:12:24) (in thread): > But@Aleru Divinementioned ANOVA.

Faith Ifeoluwa Alexander (02:12:50) (in thread): > Okay.

Mildred Anashie (02:13:31) (in thread): > ANOVA was used for the Alpha Diversity@Faith Ifeoluwa Alexander

Bolanle Wahab (02:13:54) (in thread): > @Svetlana Ugarcina Perovicthank you

Faith Ifeoluwa Alexander (02:14:13) (in thread): > Which p-value is the correct one as I am seeing different p-values?

Aleru Divine (02:16:46) (in thread): > @Bolanle Wahabthis makes sense.If I understood you perfectly, you mean > > Group 0 would belower pH and H.pylori negative (LN)and > > Group 1 would be higher pH and H.pylori negative.Is that correct? > > Since the group 1 has the highest severity, maybe all the other groups would be group together as 0.What do you think? > > I’ll definitely leave a note.Thanks:pray:

Mildred Anashie (02:17:15) (in thread): > This is also from your paper > > “One bacterial family and three genera were found to be significantly different in relative abundance between PD and controls (p < 0.05).”

Bolanle Wahab (02:18:54) (in thread): > @Faith Ifeoluwa Alexander - File (PNG): IMG_9638

Aleru Divine (02:19:02) (in thread): > Yes@Faith Ifeoluwa Alexanderthe correct statistical test for differential abundance is Wilcoxon.You’llfind it as Mann-Whitney(wilcoxon).

Victoria (Burah) Poromon (02:21:03): > Hello everyone, Good morning > Please I’d like to make some clarifications. > 1. How do we record Ace and Sobs alpha diversity? I read somewhere here that PD whole tree is same as Faith’s. > 2. Can group sample sizes be left blank if the study really didn’t specify? I have read the material through and through this time and looked at the figures and supplemental tables. Nothing specifies the sizes for each group, n was equal to so many things throughout the paper, for example (3, 4, 6, 10, 4-6, 9-10). Ps: this paper only has 2 contrasting groups. And none of these numbers were specific for any group at any point. > 3. If MHT correction wasn’t mentioned throughout the study, but you find out through the supplemental table that p values were corrected. Do you go ahead and say yes in this situation? > 4. I have a taxa that looks like this [Paraprevotellaceae], it’s no where on NCBI and UNIPROT. Can I go ahead and curate this taxa? > 5. Lastly can 1 taxa be differentially abundant in two contrasting groups? This paper has Coriobacteriaceae as a differentially abundant taxa in the two contrasting group. > @Svetlana Ugarcina Perovic,@Esther Afuape,@Peace Sandy,@Chioma Onyido,<@UBNSEMS3S>I will really appreciate your opinion’s on these.

Eniola Adebayo (02:21:05) (in thread): > Thankyou@Svetlana Ugarcina Perovic

Faith Ifeoluwa Alexander (02:26:26) (in thread): > Thank you everyone. Pls, I can only see that the test subjects were age matched. Doesn’t it matter that their sexes were stated?

Aleru Divine (02:27:05) (in thread): > @Victoria (Burah) Poromon > 1. Ace is richness and Sobs is observed species. > 2. It should be left blank since it was not specified. > 3. If MHT correction was found in the supplemental material,itshould be included.I believe including information from the supplemental material ensures your interpretation of the study is based on a comprehensive understanding of the study. > Check this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710356210762269 - Attachment: Attachment > Hi everyone, > I’ll like to get your input on a study I’m curating; > > What do I do in a situation where the study says that there are statistically significant differences in alpha diversity but doesn’t state if it’s an increase or decrease? (Both text and the figure) > > @Svetlana Ugarcina Perovic @Esther Afuape @C. Mirzayi (please do not tag this account) @Chioma Onyido @Peace Sandy

Mildred Anashie (02:30:04) (in thread): > Idon’tthink it matters,what’simportant is that both groups were age matched

Faith Ifeoluwa Alexander (02:30:36) (in thread): > Okay. Thank you.

Evelyn Mary Attah (02:30:53): > Hello@Desire Oluwarotimi, can you kindly guide me on how to claim my paper for review?

Victoria (Burah) Poromon (02:32:16) (in thread): > Thank you!@Aleru Divine, very interesting thread:smile:

Eniola Adebayo (02:32:37) (in thread): > If the p value is adjusted, then it is yes for MHT > For the sample size read in between the lines very well, ifit’snot specified then I think you should leave it blank > For q5, you still curate it@Victoria (Burah) Poromon

Faith Ifeoluwa Alexander (02:33:27) (in thread): > Pls how do I check for confounders controlled? Is it age stratification or model adjustment?

Mildred Anashie (02:34:14) (in thread): > Hi@Victoria (Burah) Poromonfor the Alpha diversity > > Faith is same as PD > Ace is Richness > Sobs is species observed which also correlates with Richness > > The MHT I think you can check the paper for either adjusted for, FDR, q value, Benjamini-Hochberg or Bonferroni > > For the sample size ifthere’sa figure that has the characteristics of the participants or subjects you can check it, it might carry the information

Aleru Divine (02:36:06) (in thread): > 1. Go to GitHub and look at the issues listed for any unassigned issue that no one has requested. > 2. Comment your name and your interest in curating the paper. > 3. It’llbe assigned to you. Just check your mail or keep checking the issues page. > 4. Once assigned, you can start curating. > Link to issues page:https://github.com/waldronlab/BugSigDBcuration/issues?page=1&q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22

Victoria (Burah) Poromon (02:36:24) (in thread): > @Eniola AdebayoOkay thanks. I have read between the lines and checked all supplemental materials. Andthere’sreally no sample size specified.

Mildred Anashie (02:39:14) (in thread): > Idon’tthink any stratification or model adjustment was done here > > For the Confounders controlled for, your paperdoesn’tstate it > > You can Ctrl+f and type words like Confounders, controlled for, covariates > And Ididn’tfind in your paper

Aleru Divine (02:39:29) (in thread): > They’reusually stated in the paper most of the time.

Bolanle Wahab (02:40:28) (in thread): > Yes I think, this only makes sense.You’rewelcome@Aleru Divine

Faith Ifeoluwa Alexander (02:40:43) (in thread): > Okay. I didn’t see any too so I am going to leave it blank.

Eniola Adebayo (02:42:51): > How do I record Fisher alpha diversity?@Svetlana Ugarcina Perovic<@UBNSEMS3S>

Evelyn Mary Attah (02:42:51) (in thread): > Hello@Aleru Divine, I have curated a paper, I was asked to claim it for review and I copied the link to the curated one, posted it on GitHub and tagged the mentor to review it but I’m still seeing “needs review” on it.

Bolanle Wahab (02:43:39): > @Faith Ifeoluwa Alexander - Attachment: Attachment > If they didn’t state any clearly (usually using words like “adjusted for” or “controlled for”) they probably didn’t control for any confounders. Controlling for confounders is fairly uncommon in microbiome research currently.

Victoria (Burah) Poromon (02:43:45) (in thread): > @Mildred Anashie, thank you.@Aleru Divinealready clarified the alpha diversity one. > > So for MHT correction. It wasn’t mentioned in the paper. But p-value adjustments are mentioned in the supplemental material. > > For the sample size,I’vechecked all figures, andthere’sno specific size for the groups

Mildred Anashie (02:45:21) (in thread): > MHT will be Yes in my opinion > > And just maybe the sample size should be left blank > > What kind of study is it though?

Victoria (Burah) Poromon (02:46:39) (in thread): > @Mildred AnashieIt’sa laboratory experiment using mice

Eniola Adebayo (02:47:12) (in thread): > They are working on reviewing the curationshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710396001560269 - Attachment: Attachment > Hello everyone, two important messages today :good_luck: > > 1. We will be having our weekly team meeting and Outreachy office hours at 9 AM EDT today at: https://us02web.zoom.us/j/2737200499. > > Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179 > PLEASE NOTE: this is an hour earlier for those of us not yet in daylight savings time! > > SAVE THE DATE for the next two meetings https://github.com/waldronlab/BugSigDBcuration/issues/95 > > 2. In the next days, we will be releasing our review feedback with a curation score in the GitHub issues, one by one. Please be patient while waiting for yours – you could check them out and learn from them, just search for a label:reviewed.

Eniola Adebayo (02:50:26) (in thread): > Is the laboratory experiment what you used to curate your study@Victoria (Burah) Poromon

Mildred Anashie (02:52:39) (in thread): > In some laboratory experiments the number is usually relative to all groups (like same number in each group)I’mreally unsure of how to go about this one

Victoria (Burah) Poromon (02:53:13) (in thread): > @Eniola AdebayoYes

Faith Ifeoluwa Alexander (02:53:22) (in thread): > I need some clarification for the Alpha Diversity section.

Victoria (Burah) Poromon (02:55:26) (in thread): > @Mildred AnashieYeah. But thisdidn’teven mention the total number of mice they started with.

Faith Ifeoluwa Alexander (02:57:15) (in thread): > Do I have fill in all the fields in the Alpha Diversity section?

Mildred Anashie (02:58:47) (in thread): > No just the ones mentioned in your paper

Bolanle Wahab (02:58:49) (in thread): > @Faith Ifeoluwa AlexanderNo, only the ones mentioned in your study

Faith Ifeoluwa Alexander (02:59:35) (in thread): > Okay. How do I know if they are increased or decreased?

idiaru Angela (02:59:55) (in thread): > For 5 I think different species of the taxa might be in the two contrasting groups but if they didn’t specify you might want to curate them as specified@Victoria (Burah) Poromon

Aleru Divine (03:01:48) (in thread): > @Evelyn Mary Attahthey’rereviewing it.When new issues are uploaded, you can claim one and start working on it while you wait for this to be reviewed.

idiaru Angela (03:02:23) (in thread): > @Evelyn Mary Attahyes, we’ve been told it might take a few days to be reviewed to we need to be patient. But you have already claimed it for review

Eniola Adebayo (03:02:41) (in thread): > For question 4@Victoria (Burah) Poromonhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189 - Attachment: Attachment > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonym on NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replace Escherichia coli with Escherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the 2-hour video of @U1LCB8WEA solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose:

Mildred Anashie (03:02:47) (in thread): > @Faith Ifeoluwa AlexanderIt’smostly stated as increase or decrease and whenthere’sno significance it’s unchanged > > In this case Richness and Chao1 decreased and Shannon and Simpson is unchanged - File (PNG): IMG_2299

Bolanle Wahab (03:03:51) (in thread): > It should be stated there, if not, there should be figures that would give you information on that

Faith Ifeoluwa Alexander (03:04:47) (in thread): > Observed serves for Richness right?

Eniola Adebayo (03:04:49) (in thread): > @Evelyn Mary Attahhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710164561168739?thread_ts=1710164392.226189&channel=C04RATV9VCY&message_ts=1710164561.168739 - Attachment: Attachment > If the GitHub issue with your curated paper is with tag “needs review” that means now it’s in our hands under review and you are kindly asked to not make any changes while we are reviewing it.

Faith Ifeoluwa Alexander (03:05:33) (in thread): > Okay@Mildred Anashie.

Bolanle Wahab (03:14:48): > Hi everyone > Hi@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther Afuape > 1. Please How do I know the abundance of these signatures, they only gave information on Underrepresentation and over representation of the taxa, > 2. If the two groups of the same experiment have different p values, which one are we supposed to choose? > I’d really appreciate your inputs. Thanks - File (PNG): IMG_9642 - File (PNG): IMG_9639 - File (PNG): IMG_9641 - File (PNG): IMG_9640

Aleru Divine (03:15:29) (in thread): > @Eniola AdebayoFisher alpha diversity measures evenness

Mildred Anashie (03:18:00) (in thread): > @Nanaasked the question a few days ago > Did you get an answer? > > But in my opinion this can denote increase and decrease@Bolanle Wahab

Aleru Divine (03:20:32) (in thread): > @Bolanle Wahabunderrepresentation would mean decrease in abundance and over representation would be increase.

Peace Daniel (03:22:16) (in thread): > Yes@Hamza Hajiyou’dfind BMI when typed in full > Try what@Mildred Anashiesaid

Bolanle Wahab (03:24:24) (in thread): > Thanksss:blush:Had to be sure

Victoria (Burah) Poromon (03:24:44) (in thread): > Yeah, I agree with@Aleru Divine

Raihanat Adewuyi (03:25:19) (in thread): > Under representation in the study means decreased in abundance and over representation Is an increase in abundance@Bolanle Wahab

Scholastica Urua (03:38:18) (in thread): > Hello@Victoria (Burah) PoromonFor Question 4. > If a taxa is no where on NCBI and UNIPROT. It’s better to go ahead and curate it rather than skipping it. The curation will then be grouped with those with missing NCBI ID and can be corrected in future.

Victoria (Burah) Poromon (03:41:03) (in thread): > Thank you everyone:yellow_heart:

Scholastica Urua (03:42:15) (in thread): > I agree with what everyone says@Bolanle Wahab. Under representation and over representation would be for decreased and increased, respectively.

Rahila-me (03:49:29) (in thread): > <@UBNSEMS3S>from this image it means no significant difference across all the 3 group. so it can be curated? and when curating in each of the experiment the 3 alpha diversity mentioned will remain unchanged throughout each experiment? - File (PNG): Screenshot 2024-03-14 084318.png - File (PNG): Screenshot 2024-03-14 084451.png

Mildred Anashie (03:52:13) (in thread): > @Rahila-mein my opinion your interpretation is correct > > The text says there was no obvious changes among the groups

Bolanle Wahab (03:52:48) (in thread): > Please Is it possible thatthere’sneither increase or decrease in Abundance of taxa?

Aleru Divine (03:53:24) (in thread): > Yes I believe so.I had one study that recorded no significant change.

Mildred Anashie (03:53:38) (in thread): > Yesit’spossible > > It will indicate no significance in the experiment

Bolanle Wahab (03:53:50) (in thread): > So i can leave it blank? > Thanks

Scholastica Urua (03:53:56) (in thread): > I think there are some studies that do not specify the alpha diversity measures used. so its possible.

Scholastica Urua (03:54:35) (in thread): > Better to leave blank in such case

Mildred Anashie (03:56:20) (in thread): > If an experiment is not significant I believe itshouldn’tbe recorded > If it is significant with no significant taxas then it should be recorded without signatures > > If you are talking about Alpha diversity it should be left blank

Rahila-me (04:02:16) (in thread): > @Mildred AnashieThanks dear

Rahila-me (04:03:08) (in thread): > <@UBNSEMS3S>the image interpretation?

Blessing Ene Anyebe (04:18:25) (in thread): > Thank you@Svetlana Ugarcina Peroviclooking forward to the office hour and our review season! Thank you

Abiola Salako (04:25:14) (in thread): > Thank you@Svetlana Ugarcina Perovic

Barakat Akinsiku (04:30:54): > Hi everyone, good morning > I have a few questions regarding taxa and NCBI. > For listed significant taxas in a study that have a noname tag exampleBacteriodales noname, and which have no taxa ID on NCBI, can we still go ahead and record them as missing NCBI or we should leave them out? > Also, if an OTU is reported only as Bacteria, without the species or genus being specified, should we still go ahead and record it as Bacteria or leave it out from a list of signatures?@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@C. Mirzayi (please do not tag this account)@Chioma OnyidoI also want to know how to determine increase or decreased alpha diversity when it’s only specified as significant (invsimpson below), thank you - File (PNG): b2.png - File (PNG): b.png

Scholastica Urua (04:36:00) (in thread): > @Barakat Akinsikufrom this image, I think the alpha diversity measure (which is inverse simpson in this case) is decreased in the case group. > > For the first question, if you have done a thorough search on Uniproct and NCBI and you still can’t find the ID, I think its better to go ahead to record it rather than skip it. This way it can be group under experiment with missing NCBI ID and corrected in future.

Muqtadirat Yussuff (04:37:17) (in thread): > Hey@Scholastica Uruacan you please explain your reason for determining it’s decreased using this image?

Abiola Salako (04:37:57) (in thread): > @Scholastica Urua, since the study mentioned varied significantly, How did you arrive at ‘decreased’? Why not ‘Increased’? Kindly give your reason, please. Thank you.

Barakat Akinsiku (04:40:01) (in thread): > Thanks@Scholastica UruaHow did you determine the decrease?

Joan C. Chukwuemeka (04:42:02) (in thread): > @Barakat AkinsikuThe median value line for PD is lower than that of control that’s how it’s decreased. The alpha diversity here is inverse-simpson. > We had a similar conversation with<@UBNSEMS3S>last night. > > Good morning all

Scholastica Urua (04:42:11) (in thread): > Please check this thread where<@UBNSEMS3S>made a mention of it yesterday. > Hope this explains it better.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710356210762269 - Attachment: Attachment > Hi everyone, > I’ll like to get your input on a study I’m curating; > > What do I do in a situation where the study says that there are statistically significant differences in alpha diversity but doesn’t state if it’s an increase or decrease? (Both text and the figure) > > @Svetlana Ugarcina Perovic @Esther Afuape @C. Mirzayi (please do not tag this account) @Chioma Onyido @Peace Sandy

Mildred Anashie (04:42:47) (in thread): > YeaIt’sdecreased also in my opinion

Rahila-me (04:43:26) (in thread): > @Barakat Akinsikuread this thread, it will help:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710356210762269

Ima-obong (Aimah) (04:46:21) (in thread): > @Victoria (Burah) Poromonfor the question about******Paraprevotellaceae******, I know about******Prevotella; a******genus of CFB bacteria in the family of******Prevotellaceae******.. > And******Paraprevotella******is also a genus just like******Prevotella******in the same family of*****Prevotellaceae > *****This makes me wonder if******Paraprevotellaceae******could also be assumed to be a type of******Prevotellaceae******which is a family of the CFB bacteria… > > Although, while watching the Video onMissingNCBIIDs, this same signature(Paraprevotellaceae)was treated in the video byLevi, and he had concluded by stating in the discussion page that; > “Paraprevotellaceaelooks like the******Prevotellaceae******family, but he’s not certain”… > > My advice would be to open a discussion page on your study and add that bothParaprevotellaceaeandPrevotellaceaecould be considered as the same family of bacteria and you can also reference Levi in the Missing NCBI video.. > Best of luck.

Mildred Anashie (04:46:25) (in thread): > Bacteriodales noname might have to be entered that way in my opinion > > Bacteria exists on NCBI so I guess it can be recorded@Barakat Akinsiku - File (PNG): IMG_2308

Scholastica Urua (04:47:43) (in thread): > @Barakat AkinsikuFor your second question, if an OTU is reported only as Bacteria, without the species or genus being specified… Is it significantly abundant? If yes, it should be documented like@Mildred Anashiementioned

Barakat Akinsiku (04:48:11) (in thread): > Thanks@Joan C. Chukwuemekafor the explanation, thanks everyone > > Okay@Mildred Anashie,@Scholastica Uruathanks

Victoria (Burah) Poromon (04:48:35) (in thread): > @Ima-obong (Aimah)Thank you so much. This is very helpful!

Aleru Divine (04:49:10) (in thread): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy:pray::pray:please I need your help with clarification on this.

Ima-obong (Aimah) (04:49:18) (in thread): > You’re welcome@Victoria (Burah) Poromon

Abiola Salako (04:51:37) (in thread): > @Scholastica UruaThank you. It’s even obvious in the image that the alpha diversity measure is decreased in the case- group.

Joan C. Chukwuemeka (04:59:59): > @Victoria (Burah) Poromonthere’s already a topic on the discussion page onParaprevotellaceae. I think it’ll be better to document your findings under same heading. - File (JPEG): Screenshot_2024-03-14-09-56-58-744_com.android.chrome.jpg

Victoria (Burah) Poromon (05:07:36): > @Joan C. Chukwuemekathank you,I’lldo this

Svetlana Ugarcina Perovic (05:21:20) (in thread): > Here it ishttps://bugsigdb.org/Study_973 - Attachment (BugSigDB): Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson’s Disease Cohort - BugSigDB > Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson’s disease (PD), but the influence of geographic location has received little attention.

Abiola Salako (05:23:00): > Hello everyone,@Esther Afuape@Chioma Onyido@Peace Sandywhat do I do to a body site(pooled Nasopharyngeal or Throat Swab) that wasn’t included in the drop-down menu? After checking the environmental ontology through the link provided I still didn’t get any accurate answer. Let’s assume I got an answer, which of the responses am I going to work with? Thank you.

Bolanle Wahab (05:33:24) (in thread): > @Abiola Salakothis looks like it has something to do with respiratory tract or similar > Can you share the link to your article?

Muqtadirat Yussuff (05:37:13) (in thread): > @Abiola SalakoIf it isn’t in the drop-down you’d have to pick the closest like respiratory tract which@Bolanle Wahabsuggested but please share the link to your article

Abiola Salako (05:40:23) (in thread): > Yes. You’re right. nasopharyngeal swab is one type of nasal swab, IT IS used to look for bacteria or viruses that cause respiratory infections. HERE IS THE Link to the study@Bolanle Wahabhttps://journals.asm.org/doi/10.1128/spectrum.02196-22#fig1

Adenike Oladimeji-Kasumu (05:41:35) (in thread): > Thank you so much@Svetlana Ugarcina Perovicfor responding. I was able to add the study. I’m curating it already.

Blessing Laweh (05:42:50) (in thread): > Noted, thank you@Svetlana Ugarcina Perovic:pray:

Bolanle Wahab (05:44:31) (in thread): > @Abiola SalakoUpper Respiratory tract and throat are your likely body sites

Abiola Salako (05:44:57) (in thread): > @Bolanle WahabI know

Svetlana Ugarcina Perovic (05:45:09) (in thread): > Great!@Adenike Oladimeji-Kasumukeep up the good work!

Ima-obong (Aimah) (05:45:29) (in thread): > @Abiola Salako.. if there’s throat in the drop-down..I think you should use that…cause throat swab sample means mucus gotten from the throat

Abiola Salako (05:46:05) (in thread): > No throat swab in the drop-down menu

Ima-obong (Aimah) (05:47:07) (in thread): > Just throat will be fine

Bolanle Wahab (05:47:09) (in thread): > Throat swab is not a part of the body,it’sused to collect samples for experiment, just throat is fine

Barakat Akinsiku (05:47:35) (in thread): > @Abiola Salakofor body site and condition you can always choose the closest thing that describes the term you’re trying to search for.

Peace Sandy (05:53:36) (in thread): > Noted

Scholastica Urua (06:20:55): > Hello everyone, for those without papers to curate there are more now available on GitHub. Please just like@Svetlana Ugarcina Perovicsaid, we should prioritize quality over quantity. I’ll be sure to drop my questions here when I get stuck:sweat_smile:. > Really love collaborating with you all:hugging_face:.

Abiola Salako (06:21:09) (in thread): > Thank you everyone.

U1LCB8WEA (06:21:47) (in thread): > @Barakat Akinsikunote the spelling,Bacter******oi********dales noname, notBacter********io********dales noname. This seems equivalent tounclassified Bacteroidales(taxid 185291, no rank).@Mildred Anashie,Bacteriais not incorrect, but it provides less information about the lineage thanunclassified Bacteroidales does, which at least tells us the order.** - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Svetlana Ugarcina Perovic (06:22:50): > TIP: to search quickly for a study e.g. you are not sure if it’s already curated or not, in the main page go to “Search BugSigDB” in the top right corner and type in a PMID of paper of your interest. - File (PNG): Screenshot 2024-03-14 at 10.25.00.png

Levi Waldron (06:24:41) (in thread): > You’re welcome!:blush:

Mildred Anashie (06:26:35) (in thread): > Thank you<@U1LCB8WEA>Definitely noted > > I understood from her question that She mentioned both Bateroidales noname and Bacteria although Ididn’tgo through the paper to know if both were mentioned > > Would it be okay to curate Bacteria if it was stated that way?

Levi Waldron (06:34:52) (in thread): > One more note - I haven’t read the paper, but if based on the rank of other things being reported you think it should be of a certain rank, there may be other options, like “uncultured Bacteroidales bacterium” for a species from the orderBacteroidales. ”Bacteroidales incertae sedis” could refer to a group of bacteria that might represent an unclassified genus, family, or multiple genera, thought to belong toBacteroidales.

Levi Waldron (06:37:07) (in thread): > Ahh I missed the part aboutBacteriabeing reported. If they reported that there were more or lessBacteriaas a whole between the groups then yes you could use that. Not many experiments are designed to estimate changes in overall bacterial load, although it is possible.

Rahila-me (06:43:59): > @Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido > 1. In EFO i did not find type 2 diabetes mellitus (T2DM) as a condition however i found diabetes mellitus so i entered it, is this correct > 2. in matched-on gender can be replaced with sex? > 3. In the study Abstract it stated 15 Con, 15 DN, 15 T2DM but then moving down at results it says 14 Con, 12 DN, 12 T2DM then in Materials and Methods it says 15 Con, 15 DN and 15T2DM…please which should i ignore here is image for better understanding: - File (PNG): Screenshot 2024-03-14 113409.png - File (PNG): Screenshot 2024-03-14 113445.png - File (PNG): Screenshot 2024-03-14 113541.png

Mildred Anashie (06:48:22) (in thread): > @Rahila-methis implies that some samples were excludedI’lladvice you go with the final samples not the initial samples

Desire Oluwarotimi (06:49:17) (in thread): > Hi@Rahila-meIf you couldn’t find T2DM, using diabetes mellitus like you said might be a correct move. > > Yes, Gender can be replaced with sex. > > You should go with the 14 HC, 12 DN and 12 T2DM. The other samples were excluded due to some disqualification of some sort.

Scholastica Urua (07:09:03) (in thread): > @Rahila-methe final sample sizes are to be curated; that is 14, 12, 12 respectively.

assel (07:19:29): > Hello team, can u please share with your experience about creation a BugSigDB account, I did it yesterday but still no email about BugSigDB account.

Desire Oluwarotimi (07:21:54) (in thread): > Hi@asselMy experience with creating a BugSigDB account was seamless. > > Please check your email’s spam folder. You might have something there. > > And if nothing, indicate for one of the mentors to help you out.

Scholastica Urua (07:22:34) (in thread): > Sometimes the message is delivered to your spam.

Scholastica Urua (07:23:41) (in thread): > If you still don’t see it, tag the mentors so they can help you out like@Desire Oluwarotimisuggested.

assel (07:28:12) (in thread): > Thank u!!! Indeed it is there )))

Scholastica Urua (07:29:04) (in thread): > Happy BugSigDB-ing@assel:hugging_face:

Oluwatomisin Omojokun (07:30:32) (in thread): > Majority of the study has the same DOI, I think two study should not have the same DOI or URL or I’m wrong@Peace Sandy.

Rahila-me (07:31:30) (in thread): > ok..Thanks guys:raised_hands:

Mildred Anashie (07:50:07) (in thread): > Thanks a lot@Levi WaldronThis information just helped me solve a taxa now:pray::blush:

Rahila-me (07:52:39): > @Oluwatomisin Omojokunwhat you should be concerned with is the PMID which is the unique ID that’s why no study has same PMID

Oluwatomisin Omojokun (07:54:02): > Exactly my point@Rahila-me

Svetlana Ugarcina Perovic (08:37:42): > IMPORTANT: when the GitHub issue with your curation is claimed for review and got a label****“needs review” ****any edits from this point are not allowed. - File (PNG): Screenshot 2024-03-14 at 13.32.28.png - File (PNG): Screenshot 2024-03-14 at 13.37.00.png

Desire Oluwarotimi (08:45:12): > Hi Guys. It’s only fifteen minutes more to the office hour. > > See you there.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710354689619439 - Attachment: Attachment > Hi everyone, > > Just a reminder that we have our team meeting and office hours at 9 AM EDT tomorrow at https://us02web.zoom.us/j/2737200499. > > Please note that the US just experienced daylight savings time. This means for many of you the meeting will be an hour earlier than last week. > > Please double check the meeting time with your local time using this link: https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179

Scholastica Urua (08:45:43) (in thread): > Thanks for the reminder@Desire Oluwarotimi

Blessing Ene Anyebe (08:45:48) (in thread): > Thanks for the reminder@Desire Oluwarotimi

Aleru Divine (08:48:50) (in thread): > Looking forward to it:sparkles:

Rahila-me (08:49:22) (in thread): > 2pm Nigeria time

Nana (09:01:45): > It’s time please all should join

Blessing Laweh (09:05:07): > Help the zoom link is not loading?

Rahila-me (09:05:30): > same here, thought it was my network

Blessing Laweh (09:06:03): > good to know it’s not just me lols

Rahila-me (09:06:41): > maybe is just the 2 of us

Ima-obong (Aimah) (09:06:52): > Been trying since 1:50pm

Aleru Divine (09:07:04): > It works for me

Rahila-me (09:07:13): > you see

Mildred Anashie (09:08:28): > Ican’tjoin too

Abiola Salako (09:09:05): > I’ve been unable to join as well

Kelechi Madubuko (09:10:35): > I can’t join too

Rahila-me (09:11:19): > @Aleru Divinecan you please let them know that the zoom link is not working for must of us

Rahila-me (09:12:00): > please send the link you joined with

Peace Sandy (09:12:44) (in thread): > Please try again

Eniola Adebayo (09:12:46): > Ican’tjoin

UBNSEMS3S (09:13:14): > https://us02web.zoom.us/j/2737200499

Rahila-me (09:14:59): > <@UBNSEMS3S>it keeps loading

Ima-obong (Aimah) (09:15:26): > Still can’t join

Adenike Oladimeji-Kasumu (09:15:51): > @C. Mirzayi (please do not tag this account)still can’t join the meeting. Please help

Blessing Ene Anyebe (09:16:21): > Likewise

Adenike Oladimeji-Kasumu (09:17:33): > The link returns “Unable to connect”

Kelechi Madubuko (09:17:51): > I still can’t join the meeting.. keeps loading but not connecting

Eniola Adebayo (09:18:26): > I have not been able to join too

Mildred Anashie (09:20:25) (in thread): > its same for me

Abiola Salako (09:23:09): > Still can’t join

EBERE ADEKOGBE (09:33:33): > Also I can’t join

Chioma Onyido (09:34:36): > Apologies guys.It’sprobably connection issues. > The good news is that the meeting is recorded and the recording will be posted after the meeting!

Blessing Laweh (09:38:19) (in thread): > Woukd be exoecting, thanks@Chioma Agu

Kelechi Madubuko (09:39:34) (in thread): > Ok. I guess I just have to wait for the recording then

Blessing Ene Anyebe (09:39:35) (in thread): > Thank you so much@Chioma Onyido:orange_heart:

Evelyn Mary Attah (09:41:28): > hello@Desire Oluwarotimi, can you kindly assist me to review this paper I’m working on? here’s the linkhttps://bugsigdb.org/Study_976thank you. - Attachment (BugSigDB): HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome - BugSigDB > This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals.

Desire Oluwarotimi (09:42:36) (in thread): > Hi@Evelyn Mary AttahI will go through it when I can.

Eniola Adebayo (09:46:58) (in thread): > Thankyou:pray:

Nana (09:50:29): > @C. Mirzayi (please do not tag this account)https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.780568/full - Attachment (Frontiers): Frontiers | Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode > Microbiota colonization is a dynamic process that impacts the health status during an individual’s lifetime. The composition of the gut microbiota of newborn…

Scholastica Urua (10:06:26): > Thank you<@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovicfor the insightful office hour:hugging_face:

Michael Adekanye (10:11:46): > Please can someone help go through the paper I’m working on. It’s not much. I don’t want to miss some information. A second eye might help. > 1. It looks it might involve two experiments. > a)Stable and Deteriorated group. > b) Year 0 and year 2 > 2. Alpha diversity part with signature to look out for. - File (PDF): progression_of_parkinson_s_disease_is_associated_with_gut_dysbiosis_two-year_follow-up_study-_pmc.pdf

Michael Adekanye (10:12:39) (in thread): > Yes it was. Thank you guys for your time.

Muqtadirat Yussuff (10:15:47) (in thread): > I can if you’re fine getting the feedback tonight or tomorrow

Blessing Laweh (10:18:58): > Hello. I need help please. I want to create a new study from the article I was assigned but I can’t open it. I was able to open it like 30mins ago but now I keep getting an error message. I’ve tried other means and checked my network. Anyone available to help me with this please? I’d greatly appreciate it, thanks

Barakat Akinsiku (10:19:52) (in thread): > Thanks so much@Levi WaldronThis helped a lot:pray:

Aleru Divine (10:19:55) (in thread): > @Blessing Lawehplease send me the link so I could check too

Scholastica Urua (10:20:29) (in thread): > Sorry for the inconvenience@Blessing Laweh

Bolanle Wahab (10:20:44) (in thread): > @Blessing Lawehdo you mean a link to your article or on BugSigDB?

Michael Adekanye (10:21:11) (in thread): > @Muqtadirat Yussuffplease I’ll be very happy. Looking forward to hearing from you.

Blessing Laweh (10:21:55) (in thread): > Thanks@Aleru DivineHere it ishttps://journals.asm.org/doi/10.1128/spectrum.01901-21#fig5

Aleru Divine (10:22:36) (in thread): > It works just fine from my end@Blessing Laweh - File (PNG): IMG_7936

Blessing Laweh (10:22:38) (in thread): > No it’s fine@Scholastica Urua, thank you

Aleru Divine (10:23:01) (in thread): > @Blessing LawehHave you tried restarting your device?

Bolanle Wahab (10:23:20) (in thread): > Same here

Michael Adekanye (10:23:24) (in thread): > Please I guess you can convert it to pdf so you don’t have issues like this later.

Scholastica Urua (10:23:39) (in thread): > I think it’s adding a new experiment she meant. Am I right@Blessing Laweh?

Blessing Laweh (10:23:40) (in thread): > That would be my last resort. Let me do that now. Thanks for your help

Blessing Laweh (10:24:05) (in thread): > The bugsigdb page is loading well@Scholastica Uruait’s just the article. I wanted to be sure nothing happened to the website. Since it worked for Divine and Bolanle, I’ll try it again

Scholastica Urua (10:24:21) (in thread): > Okay, I misunderstood you

Bolanle Wahab (10:24:35) (in thread): > @Blessing Lawehhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8865484/Try this - Attachment (PubMed Central (PMC)): Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing > The microbiota plays an important role in human health and disease development. The lung microbiota profile in pulmonary tuberculosis (TB) patients and the effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively. …

Aleru Divine (10:25:57) (in thread): > @Blessing LawehI downloaded it, just in case it stillwon’topen.I’llsend it via dm ifthat’sokay by you.

Blessing Laweh (10:27:23) (in thread): > It’s still not opening@Bolanle Wahab…:thinking_face:

Aleru Divine (10:27:41) (in thread): > Let me send it over then:hugging_face:no worries

Blessing Laweh (10:27:49) (in thread): > I’d appreciate the PDF, thank you

Abiola Salako (10:27:52) (in thread): > @Blessing Lawehkindly log out & re log in into the page

Blessing Laweh (10:28:25) (in thread): > Thanks for your help everyone. Thanks a lot

Bolanle Wahab (10:29:10) (in thread): > @Blessing Lawehit’sprobably your browser then, Let Divine rescue you in your dm:sweat_smile:

Abiola Salako (10:29:51) (in thread): > @Evelyn Mary Attahokay.

Blessing Laweh (10:30:00) (in thread): > I know right lols. Thanks for the alternative link also, I appreciate:purple_heart:

Aleru Divine (10:32:47) (in thread): > You’rewelcome Blessing:hugging_face:

Abiola Salako (10:35:41) (in thread): > @Scholastica Uruacould you please give a brief of the office hour?

Scholastica Urua (10:37:48) (in thread): > @Abiola SalakoIt was mostly a question and answer session and it was recorded. Chloe promised to drop the recording as soon as its available:pray:

Abiola Salako (10:38:24) (in thread): > Alright. Thank you.

Adedoja Isaac (11:19:37) (in thread): > Thanks@Chioma Onyido

Faith Ifeoluwa Alexander (12:03:03) (in thread): > I would love to listen to the recording too. I missed it due to network issues.b

Faith Ifeoluwa Alexander (12:04:02): > Pls, as regards Adding a Signature, I need help. I don’t know which Figure I am to enter in as the Source. Pls, Help!!

Joan C. Chukwuemeka (12:05:23) (in thread): > @Faith Ifeoluwa AlexanderSource is simply where you are curating the microbial signatures from. It can be figures, tables, result text, or combinations of them

Bolanle Wahab (12:05:34) (in thread): > @Faith Ifeoluwa Alexanderplease send your article

Adenike Oladimeji-Kasumu (12:05:56) (in thread): > Hello@Faith Ifeoluwa AlexanderIt is the figure that describes the Taxa abundance. Could be the Genus or the species level, depending on what you have. > Can you share the link to your Article to a better look at it?

Faith Ifeoluwa Alexander (12:06:00) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/217 - Attachment: #217 Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota > Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - Weis et al - NPJ Parkinsons Disease
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884491/

Abiola Salako (12:07:45) (in thread): > @Faith Ifeoluwa AlexanderThis is an excerpt from the curation policy on adding signature source > > “Source > The figure/table number where the signatures are found Abundance in Group 1 > Whether the abundance has increased or decreased in the Group 1 (exposed group) > A separate signature should be created for the increased and decreased group. > For example: Signature 1 is for increased abundance in exposed group. Signature 2 is for decreased in exposed group.”

Bolanle Wahab (12:08:36) (in thread): > You could check Differences in Microbiota Composition,Table 2@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (12:08:41) (in thread): > @Abiola SalakoI read that in the Curation Policy but I don’t understand where it applies in my Paper.

Faith Ifeoluwa Alexander (12:10:27) (in thread): > @Bolanle WahabThank you.

Bolanle Wahab (12:12:17) (in thread): > After the table, you’d see the relative abundance of the signatures of PD patients compared to your controls

Faith Ifeoluwa Alexander (12:13:46) (in thread): > Yeah, I am reading through that again now@Bolanle Wahab.

Abiola Salako (12:16:42) (in thread): > Under the result section in your article, check where they mentioned differential abundance analysis for the microbiomes, most time would point out a table/ figure showing the images of the increased/ decreased microbiomes. I’m unable to look into your paper at the moment due to….@Faith Ifeoluwa Alexander

Adenike Oladimeji-Kasumu (12:19:25) (in thread): > @Faith Ifeoluwa AlexanderYou might have to study Table 2 and the text that follows. Those are the only places where I could find the Signature abundance in your paper. - File (JPEG): Screenshot_20240314-171735.jpg - File (JPEG): Screenshot_20240314-171625.jpg

Adedoja Isaac (12:20:18) (in thread): > The figure is always referenced in the paragraph where you found the differencial abundance. It’s always clickable to. Once you click the figure reference, it leads you to the legend or image.

Mildred Anashie (12:21:03) (in thread): > Hi@Faith Ifeoluwa Alexanderhave you figured it out?

Glorious Katushabe (12:23:22): > Hello team, how do I delete an experiment?

Faith Ifeoluwa Alexander (12:23:59) (in thread): > Not yet. Yes I found the Table but I am stuck on how to describe the Signature & where to find it’s abundance. > > I was using my Laptop before but I had to switch to my phone when the network and my Laptop started misbehaving.

Mildred Anashie (12:25:01) (in thread): > Hi > > Tag the mentors to this post > > With a link to the study and the experiment you want to delete

Adedoja Isaac (12:25:05) (in thread): > @Glorious KatushabeTag an adminstrator to delete an experiment

Faith Ifeoluwa Alexander (12:26:37) (in thread): > I don’t understand what you said@Adedoja Isaac.

Glorious Katushabe (12:31:03) (in thread): > thank you

Adedoja Isaac (12:31:32) (in thread): > @Faith Ifeoluwa AlexanderThis is what I mean. As an example - File (JPEG): Screenshot_20240314_172858_Chrome.jpg

Adedoja Isaac (12:32:05) (in thread): > When you click on those, it leads you to the source image

Faith Ifeoluwa Alexander (12:32:47) (in thread): > @Adedoja Isaacthese figures were not included in my paper.

Faith Ifeoluwa Alexander (12:34:13) (in thread): > @Mildred Anashiepls help me out.

Adedoja Isaac (12:34:32) (in thread): > @Scholastica Uruaonce talked about putting texts as reference too if you can’t find image. But you can confirm from the mentors.

Mildred Anashie (12:35:40) (in thread): > Let me try to go through the article but@Adenike Oladimeji-Kasumualready pointed to table 2 > I think the results you are looking for should be there

Faith Ifeoluwa Alexander (12:36:57) (in thread): > All I need is a pointer and I will get the rest. Then I don’t know how to describe the signature too.

Mildred Anashie (12:38:26) (in thread): > Are you talking about source description?

Faith Ifeoluwa Alexander (12:39:00) (in thread): > Yeah. Sorry I meant source description.

Adedoja Isaac (12:39:15) (in thread): > Ohhhh

Scholastica Urua (12:39:43) (in thread): > Yes@Adedoja Isaacif the source is from the text, you can use ‘Text’ as source. Then if its from table, figure then ‘Table’ and ‘Figure’ respectively just like@Joan C. Chukwuemekamentioned.

Faith Ifeoluwa Alexander (12:40:14) (in thread): > Then a pointer to how to find the abundance.

Faith Ifeoluwa Alexander (12:40:44) (in thread): > Yeah I got that part@Scholastica Urua. Mine is a Table.

Faith Ifeoluwa Alexander (12:41:35) (in thread): > I am confused on how to describe the source and how to find the abundance.

Joan C. Chukwuemeka (12:41:55) (in thread): > @Faith Ifeoluwa AlexanderSource description example. that is, what’s the source about? - File (PNG): image.png

Mildred Anashie (12:42:05) (in thread): > You describe the source using information about the table(since yours is a table)

Joan C. Chukwuemeka (12:42:35) (in thread): > @Faith Ifeoluwa Alexandercan you share a snippet of the table?

Faith Ifeoluwa Alexander (12:42:58) (in thread): > Okay@Joan C. Chukwuemeka

Chioma Onyido (12:44:58) (in thread): > Hi@Glorious KatushabeWhich experiment would you like to delete?

Bolanle Wahab (12:45:02) (in thread): > @Faith Ifeoluwa Alexanderyou can see the signatures and their abundance depending on your experiment here. - File (PNG): IMG_9644 - File (PNG): IMG_9643

Faith Ifeoluwa Alexander (12:46:38) (in thread): > Okay so there is no figure. I was looking out for figures.

Joan C. Chukwuemeka (12:47:33) (in thread): > @Faith Ifeoluwa AlexanderSource is not always in figures and I think yours is clearly stated within the result text

Faith Ifeoluwa Alexander (12:47:46) (in thread): > @Joan C. Chukwuemekathis is the snippet I can capture. - File (JPEG): Screenshot_20240314-174417.jpg

Bolanle Wahab (12:48:38) (in thread): > There’sno figure

Faith Ifeoluwa Alexander (12:51:13) (in thread): > So if I am right my description should be “16S rRNA analysis showing the differences in the relative abundance of microbiota between PD and Healthy controls” Is that right?

Adenike Oladimeji-Kasumu (12:52:01) (in thread): > Exactly@Joan C. ChukwuemekaThat’s what I was trying to point out. Table 2 and the text that follows explains the signature abundance.

Adedoja Isaac (12:52:52) (in thread): > Ctrl+F and type “abundance”

Adedoja Isaac (12:53:12) (in thread): - File (JPEG): Screenshot_20240314_175135_Chrome.jpg - File (JPEG): Screenshot_20240314_175146_Chrome.jpg - File (JPEG): Screenshot_20240314_175206_Chrome.jpg - File (JPEG): Screenshot_20240314_175154_Chrome.jpg - File (JPEG): Screenshot_20240314_175219_Chrome.jpg

Adedoja Isaac (12:53:27) (in thread): > Here are some screenshots

Faith Ifeoluwa Alexander (12:54:15) (in thread): > Yeah I got how to find the abundance now. It’s either increased or decreased.

Joan C. Chukwuemeka (12:54:23) (in thread): > @Faith Ifeoluwa AlexanderExcerpt from your paper:PD patients treated with entacapone showed significantly higher relative abundances of the families Enterococcaceae, Bifidobacteriaceae, and the Clostridiales family XI, as well as of the genera Peptoniphilus, Anaerococcus, the Eubacterium brachy group, Sellimonas, Bifidobacterium, and Enterococcus, ******when compared to the controls******From the above, an experiment that is******PD patients treated with entacapone (group 1) VS controls(group 0) ****will have the above listed taxa under “Increased abundance for group 1”:Enterococcaceae, Bifidobacteriaceae, Clostridiales XI, Peptoniphilus, Anaerococcus, Eubacterium brachy group, Sellimonas, Bifidobacterium, and Enterococcus.Be careful though to pick out differential abundant taxa, not just relative abundance. The comparison (“******when compared to the controls”) ****tells you that it’s differential abundance not just relative abundance

Faith Ifeoluwa Alexander (13:00:27) (in thread): > So pls, help me check if this description is right: > > “16S rRNA analysis showing the differences in the relative abundance of microbiota between PD and Healthy controls” > > Is that right?

Ima-obong (Aimah) (13:11:01) (in thread): > @Faith Ifeoluwa Alexander..the description is okay

Faith Ifeoluwa Alexander (13:13:03) (in thread): > Thank you so much@Ima-obong (Aimah). I apprecaite this.

Ima-obong (Aimah) (13:13:35) (in thread): > You’re welcome

Habiba Saad (13:21:02): > hey there@Chioma Onyido@Peace Sandy@Esther Afuapei have completed my 3rd contribution. i will be very pleased if someone reviews my contributions.:v::blush::innocent:.https://bugsigdb.org/Study_983 - Attachment (BugSigDB): Fusobacterium is associated with colorectal adenomas - BugSigDB > The human gut microbiota is increasingly recognized as a player in colorectal cancer (CRC).While particular imbalances in the gut microbiota have been linked to colorectal adenomas and cancer, no specific bacterium has been identified as a risk factor.

Iman Ngwepe-Ntshibida (13:43:53) (in thread): > Registered:blush:

Qi (13:57:46): > @Qi has left the channel

Abiola Salako (14:25:00) (in thread): > Well done@Habiba Saad

Scholastica Urua (14:49:12) (in thread): > Nice one@Habiba Saad

Faith Ifeoluwa Alexander (14:50:13) (in thread): > Hello Everyone, pls do I enter all organisms indicated to be of increased relative abundance in the NCBI section of adding a signature?

Ima-obong (Aimah) (14:52:53) (in thread): > Yes .. Increased for group1 and decreased for group 1 as well making it two signatures

Faith Ifeoluwa Alexander (14:54:59) (in thread): > But those of decreased relative abundance will be recorded in Signature 2 right?

Ima-obong (Aimah) (14:55:52) (in thread): > Yes in signature 2

Faith Ifeoluwa Alexander (15:25:08) (in thread): > Okay. > > Pls, again is it possible for an organism to be in increased and decreased relative abundance at the same time in a patient with the same condition but different treatments?

Amanda Adoyi (15:26:11) (in thread): > This is good news. Was unavoidably absent today and worried about that.

Mildred Anashie (15:29:05) (in thread): > @Faith Ifeoluwa Alexanderfor some reason Ihaven’tbeen able to open the paper but I think thisshouldn’tbe right > > AlthoughI don’tfully understand what you mean by different treatments:thinking_face:

Adedoja Isaac (15:35:23) (in thread): > @Faith Ifeoluwa AlexanderYes! It is possible. I think situation like this is called Treatment impact. Treatments can alter the relative abundance of organisms. An organism that’s initially abundant might decrease with one treatment, while another treatment might have the opposite effect.

Adedoja Isaac (15:36:13) (in thread): > But what do you mean by “at the same time”?

Faith Ifeoluwa Alexander (16:13:09) (in thread): > @Adedoja Isaacyou have said it all. What I meant at the same time is that it was first in decreased relative abundance in one situation. Then it became increased in relative abundance with the presence of a Calprotein.

Mildred Anashie (16:13:50) (in thread): > Is this for different experiments?

Faith Ifeoluwa Alexander (16:15:44) (in thread): > Yes. It decreased in PD Patients but it increased in PD patients who are Calprotein positive.

Adenike Oladimeji-Kasumu (16:17:17) (in thread): > This seems like it’s a different experiment. You have to first record the signature abundance for the first experiment (that is, before the introduction of Calprotein). So, then it is possible that one or more organisms that were decreased in the first experiment now have an increased abundance in the second experiment (that is after the introduction of Calprotein)

Faith Ifeoluwa Alexander (16:19:44) (in thread): > It was in the part of the article where relative abundance was reported.

Faith Ifeoluwa Alexander (16:20:05) (in thread): > It’s not a different experiment.

Faith Ifeoluwa Alexander (16:21:28) (in thread): > So it is safe to record it in ncbi for both decreased & increased relative abundance then?

Faith Ifeoluwa Alexander (16:24:10): > @Adedoja IsaacFaecalibacterium was in decreased abundance in this part of the article. - File (JPEG): Screenshot_20240314_175135_Chrome.jpg

Faith Ifeoluwa Alexander (16:28:36): > Faecalibacterium was in increased relative abundance in the part where Calprotectin Positive PD Patients were reported. - File (JPEG): Screenshot_20240314_175146_Chrome.jpg

Faith Ifeoluwa Alexander (16:31:56) (in thread): > @Adenike Oladimeji-KasumuI just started a new thread about what I am talking about.

Adenike Oladimeji-Kasumu (16:34:18) (in thread): > Yes, I now see what you mean.

Faith Ifeoluwa Alexander (16:34:34) (in thread): > Alright

Adenike Oladimeji-Kasumu (16:35:18) (in thread): > Yes@Faith Ifeoluwa AlexanderI now see it from your perspective. I am not so sure about it .

Adenike Oladimeji-Kasumu (16:36:18) (in thread): > In this page, I see that the article began to talk about the signature abundance with significance to the effect of the medications. The paper (according to its title is supposed to focus on the effects of PD and the related medications), this is why I thought it should be curated as another experiment. If not, you would just have to curate for only PD vs control. > However, I am not too sure about this. Perhaps our other colleagues or mentors can shed more light on it. > > Well done @Faith Ifeoluwa Alexander - File (JPEG): Screenshot_20240314-212853.jpg

Faith Ifeoluwa Alexander (16:41:12) (in thread): > Yes. So I think it is safe to record it for both increased & decreased relative abundance then.
> > Thank you@Adenike Oladimeji-Kasumu

Adenike Oladimeji-Kasumu (16:42:03) (in thread): > Let’s see what other opinions we’d get

Aleru Divine (16:43:44) (in thread): > @Michael Adekanyeyou’re right about number 1 they took samples from two different time points. > > Year 0 from 36 patients > Year 2 from 28 patients > > The patients were divided into 2 groups yes, depending the degree of worsening of UPDRS scores > > About the signatures, I observed that they talked a lot about decrease in bacterial counts. So mostly there was decrease in abundance. > > I included an image below. > You can find more on the discussion section. > > Additionally, there’s a mention of Table S2 which is a supplemental material. I think you’ll find more info on the bacterial counts/differential abundances there. I couldn’t access it. > > I am yet to find anything on alpha diversity measures - File (JPEG): IMG_7941

Adedoja Isaac (16:51:21) (in thread): > @Adenike Oladimeji-KasumuI feel the same way. That’s a good point and I I completely agree with you. The study seems to take a turn towards the medication’s impact too, which should be a separate experiment. Curating for PD vs control and medication abundance separately would allow focus on each aspect in more detail.

Faith Ifeoluwa Alexander (16:54:20) (in thread): > So you feel I should create another study for the medication impact separately?

Adedoja Isaac (16:55:24) (in thread): > Another experiment under the study

Adenike Oladimeji-Kasumu (16:55:43) (in thread): > Not a different study but a second experiment

Faith Ifeoluwa Alexander (16:55:45) (in thread): > Okay and that will be Experiment 2?

Adenike Oladimeji-Kasumu (16:56:12) (in thread): > Yes

Faith Ifeoluwa Alexander (16:56:55) (in thread): > But how do I then focus only on the effect of the medications in Experiment 2? It wants to turn my head now o.

Faith Ifeoluwa Alexander (16:57:53) (in thread): > Then how do I find the relative abundance between PD and healthy control alone now? My head is boiling already.

UBNSEMS3S (17:00:54): > Office Hours recording. Thanks all that attended. - File (MPEG 4 Video): video1485903245.mp4

Adenike Oladimeji-Kasumu (17:01:25) (in thread): > Be calm. You would get it right, I’m certain:hugging_face:The Signature abundance between PD and Controls were discussed before the paragraph that started discussing medications.

Adenike Oladimeji-Kasumu (17:03:29) (in thread): > You can take a break from it now and look again in the morning:hugging_face:Sometimes, that’s how I ease myself of stress. Take a break and go back:blush:

Adedoja Isaac (17:03:39) (in thread): > Skim through and identify the specific sections dedicated to the medications. > Don’t let head boil o:grin:

Faith Ifeoluwa Alexander (17:03:52) (in thread): > Okay. I read the write up below Table 2 and I don’t need to do another Experiment. The study compared control, Parkinson’s Disease samples and the sex attributes(male or female), presence or absence of Calprotectin and medication with L-dopa and Entacapone.

Adenike Oladimeji-Kasumu (17:04:18) (in thread): > I was just going to make a post to ask about this. Thank you for sharing@C. Mirzayi (please do not tag this account)

Adedoja Isaac (17:07:01) (in thread): > I’ve tried@Adenike Oladimeji-Kasumu’s suggestion to take a break and it works. You’d come back and find them easily and you start wondering why it was stressful earlier:grin:Weldone@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (17:26:20) (in thread): > Okay. But I have a screenshot to share. The question marks & red alert sign in the Quality Control part is confusing me. Is it normal or is it a sign that I made a mistake? - File (JPEG): Screenshot_20240314-222452.jpg

Aleru Divine (17:27:59) (in thread): > Thank you so much for sharing<@UBNSEMS3S>

Faith Ifeoluwa Alexander (17:35:20) (in thread): > Thank you so much for Sharing<@UBNSEMS3S>

Faith Ifeoluwa Alexander (17:56:14): > Hello everyone. Pls, is something wrong with my Signature? It’s showing some red & purple tag in the Quality control part of my Signature. Pls, what does it mean & must I correct it? And pls do I do to correct it as well. Thank you. - File (JPEG): Screenshot_20240314-222452.jpg

Blessing Laweh (18:04:23) (in thread): > Thanks for this:pray:@C. Mirzayi (please do not tag this account)

Joan C. Chukwuemeka (18:12:47) (in thread): > @Faith Ifeoluwa AlexanderRed alert sign under quality control is not something to be worried about…see the image attached which explains quality control signs - File (JPEG): IMG_20240314_230910.jpg

Muqtadirat Yussuff (19:50:18) (in thread): > Hi, it means the NCBI ID is missing, to fix it you can try matching the specie to an ID on NCBI. Go through this to understand mapping NCBI IDs to taxahttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189 - Attachment: Attachment > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonym on NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replace Escherichia coli with Escherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the 2-hour video of @U1LCB8WEA solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose:

Olajumoke Adeoyo (20:12:05) (in thread): > Hi Iman, If you haven’t gotten a reply yet. I added the link to the test as my contribution URL. Can someone confirm if this is right please?

Muqtadirat Yussuff (20:21:49) (in thread): > Hi@Michael Adekanye, regarding question one you are right about two experiments; year 0 (36 patients) and year 2 (28 patients) which were further divided into two groups. > > 2. There was decrease in bacterial abundance “Total fecal bacterial counts were decreased in 2 years in all PD patients, as well as in both the deteriorated and stable groups”. The discussion section has most of the info regarding differential abundance. Lactobacillus appears to be unchanged though - File (PNG): Screenshot 2024-03-15 011559.png - File (PNG): Screenshot 2024-03-15 011944.png

Muqtadirat Yussuff (20:45:52) (in thread): > Hi@Mildred Anashie, sorry it’s late but you can effect your observations, thank you

Hamza Haji (21:43:04): > Hello team. I have just finished my second contribution. It has been a challenging but interesting activity. I would appreciate a review, so that I may improve my curations. I am also open to reviewing curations from other contributors in the meantime.@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy@Chioma Onyido@C. Mirzayi (please do not tag this account). Thank you team.https://bugsigdb.org/Study_978 - Attachment (BugSigDB): - BugSigDB > …

Scholastica Urua (21:59:04) (in thread): > Thank you<@UBNSEMS3S>

Scholastica Urua (22:00:37) (in thread): > Well done@Hamza Haji

Olajumoke Adeoyo (22:04:33): > Hi everyone, I have a question about adding signatures to the paper I’m curating. In the experiment, for taxas where the name of the species was not specified, but rather the genus, family, order, and class were specified instead, should I include them in the signature? Please check the image below for better understanding. - File (PNG): bugsigdb 2.PNG

Olajumoke Adeoyo (22:08:39) (in thread): > Welldone, let me run through it.

Mildred Anashie (22:09:13) (in thread): > Hi@Olajumoke AdeoyoNo you don’t include them you record them without the classification > > For e.g g_oscillibacter will be recorded as Oscillibacter

Mildred Anashie (22:10:26) (in thread): > Yesit’sright

Olajumoke Adeoyo (22:16:42) (in thread): > I’m asking if higher classifications should be recorded e.g the family oscilliospiraceae could be referring to any species. Cause I read something similar from the curation policy but I don’t quite understand. Please, read policy below. > > (Sometimes papers report an unclassified species, but provide classification up to the genus level. Such unclassified species should be excluded from the curation as opposed to curating the taxon up to the genus level. In general, differential abundance of a certain species does not necessarily imply differential abundance of the corresponding genus. (Note that this equally applies to the case of unclassified higher taxonomic levels such as the case of an unclassified genus where classification is provided up to the family level).

Mildred Anashie (22:24:41) (in thread): > In my opinion > You record all

Mildred Anashie (22:26:16) (in thread): > Thank you<@UBNSEMS3S>for sharing this, been waiting to listen again:pray:

Olajumoke Adeoyo (22:30:26) (in thread): > okay, thank you so much but I would love to have further clarification on that policy.

2024-03-15

Abiola Salako (00:50:29) (in thread): > Thank you@C. Mirzayi (please do not tag this account).

Abiola Salako (00:54:53) (in thread): > Well done@Hamza Haji

Joan C. Chukwuemeka (01:00:00): > @Faith Ifeoluwa AlexanderFor the taxa in red, that usually happens when what is inputted is not available in NCBI: Either a mistyped one or taxa not yet available in NCBI. > > To Resolve the Eubacterium brachy.. Taxa ID is 35517(see image below) > > For Clostridiales XI, most Clostridial clusters are not available on NCBI, however the closest I found to clostridiales XI is******Peptostreptococcaceae******(Taxonomy ID: 186804). I think this will be a good fit as its rank is Family and it has “Clostridium cluster XI” as a heterotypic synonyms. (Image attached 2). > > Perhaps<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Peroviccan confirm this further? > > These should resolve the taxa in red. - File (JPEG): IMG_20240314_234711.jpg - File (JPEG): IMG_20240315_000213.jpg

Aleru Divine (01:03:34) (in thread): > Well done@Hamza Haji:clap:I have a lot of experiments to curate in my current study butI’llfind the time to review this:hugging_face:

Aleru Divine (01:04:35) (in thread): > @Olajumoke AdeoyoI’d suggest you record all in this case

Mildred Anashie (01:09:59) (in thread): > <@UBNSEMS3S><@U1LCB8WEA>could you please throw more light on this aspect of the curation policy stated by@Olajumoke AdeoyoThank you:pray:

Joan C. Chukwuemeka (01:23:33) (in thread): > Good morning@Faith Ifeoluwa Alexanderthis response is for your question. Hoping it helpshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710478800324829 - Attachment: Attachment > @Faith Ifeoluwa Alexander For the taxa in red, that usually happens when what is inputted is not available in NCBI: Either a mistyped one or taxa not yet available in NCBI. > > To Resolve the Eubacterium brachy.. Taxa ID is 35517(see image below) > > For Clostridiales XI, most Clostridial clusters are not available on NCBI, however the closest I found to clostridiales XI is Peptostreptococcaceae (Taxonomy ID: 186804). I think this will be a good fit as its rank is Family and it has “Clostridium cluster XI” as a heterotypic synonyms. (Image attached 2). > > Perhaps @UBNSEMS3S @U1LCB8WEA @Svetlana Ugarcina Perovic can confirm this further? > > These should resolve the taxa in red.

Abiola Salako (01:33:45) (in thread): > @Mildred Anashie@Aleru DivineIsn’t it that the ones with the rank ‘family’ should be checked in the NCBI taxonomy browser while adding ‘bacterium’ to get an ID for them? Because of this part of the curation policy that says: > ‘For species that are only classified to higher levels of the taxonomy than genus (for example only their family or order are known), try adding “bacterium” to the family in your NCBI taxonomy browser search, order etc. E.g. see Clostridiales bacterium (Taxonomy ID: 1898207, unclassified species from the Eubacteriales order). Eubacteriales is a heterotypic synonym for Clostridiales.’ > > Could you both please make it clear to me? Thank you.

Desire Oluwarotimi (01:47:58) (in thread): > Weldone@Hamza Haji

Desire Oluwarotimi (01:52:32) (in thread): > Hi@Olajumoke AdeoyoI think that as long as the species weren’t specified, there’s absolutely no reason to worry about them. > > Include only what was provided to you.@C. Mirzayi (please do not tag this account)mentioned not trying to guess results in yesterday’s office hour.

Scholastica Urua (01:59:43) (in thread): > I agree with@Desire OluwarotimiI feel only taxa specified should be curated.

idiaru Angela (02:24:21) (in thread): > Nice work@Hamza Hajiill definitely check it out ad give you feed back

Blessing Ene Anyebe (02:34:49) (in thread): > Thank you for sharing@C. Mirzayi (please do not tag this account)

Scholastica Urua (02:48:40) (in thread): > Hello@Hamza Haji, > > Nice effort in curating this study. While I haven’t delved into the details extensively, I’d like to mention my observations: > > 1. It appears that the citation was not fully populated. To remedy this, consider including the PMID (‘32855157’ in your case) or manually completing the citation details. > > 2. In your curation, ‘Gender’ is mentioned as one of the confounders, yet it’s not listed on BugSigDB. A potential alternative could be ‘Sex’, which is available and might align better with the database. > > 3. I noticed that in Signature 1 (Exp 1), some taxa are highlighted in red. To address this, you can utilize theNCBI taxonomy browserto search for any missing NCBI IDs. Additionally, some of your taxa are not entered correctly; for instance, instead of ‘NCBI:txid28050’, input ‘28050’. > > I hope this few observations help. I’ll let you know more when I go through the details of the article.:pray:Well done… - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Oluwatomisin Omojokun (03:24:13) (in thread): > well done@Habiba Saad

Oluwatomisin Omojokun (03:26:16) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Peace Daniel (03:42:49) (in thread): > Hover around the purple tagyou’dsee a description

Svetlana Ugarcina Perovic (04:39:02): > Happy Friday! :upside_down_face:This week was full of your GREAT discussions in the channel here, where we couldlearn from each other. > Thank you for all your questions: We’ve been trying to respond asap and we ask for your patience given the large volume of requests and reviews. > > P.S. Here is the Office Hours recording from this week:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710450054675839 - Attachment: Attachment > Office Hours recording. Thanks all that attended.

Joan C. Chukwuemeka (04:43:07): > Thanks@Svetlana Ugarcina Perovic, You Bugsigdb mentors are all Amazing.:white_check_mark::blush:

Mildred Anashie (04:44:21) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:hugging_face::hugging_face:Yes, I learnt a lot personally andI’mGrateful > > Thank you to you and the other mentors for always responding:heart:

Peace Daniel (04:48:34) (in thread): > Thank you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)

Barakat Akinsiku (04:49:04) (in thread): > Thank you@Svetlana Ugarcina Perovicand Happy Friday! It has indeed been a great week of learning

Svetlana Ugarcina Perovic (04:54:35): > AND, a kind reminder:pray:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710419862129939 - Attachment: Attachment > IMPORTANT: when the GitHub issue with your curation is claimed for review and got a label “needs review” any edits from this point are not allowed.

Scholastica Urua (04:57:28) (in thread): > Thank you and all the other mentors for the wonderful job you’re doing. Happy Friday@Svetlana Ugarcina Perovic

Aleru Divine (05:09:44) (in thread): > Good morning@Svetlana Ugarcina Perovicand happy Friday!:partying_face:Thanks to the office hours yesterday, I now have a better understanding of the study I’m curating, particularly in interpreting the alpha diversity measures from the figures.:partying_face:Thanks again<@UBNSEMS3S>for the in-depth explanation yesterday:pray:Thank you to all the mentors and fellow contributors for all the assistance.Your support is truly appreciated.This has been an incredible journey for me so far.:blush:Wishing you all a wonderful weekend ahead!:clinking_glasses::hugging_face:

Desire Oluwarotimi (05:17:53) (in thread): > Thank you@Svetlana Ugarcina PerovicLooking forward to doing more.

idiaru Angela (05:26:16) (in thread): > Happy Friday@Svetlana Ugarcina Perovic. Thank you to all the mentors and fellow contributors. You guys are truly incredible:heart_hands:

Abiola Salako (05:29:53) (in thread): > Big thanks to you and other mentors for all you do@Svetlana Ugarcina Perovic

Faith Ifeoluwa Alexander (05:31:03) (in thread): > Yes, I did. But I don’t understand it.

Peace Daniel (05:41:14) (in thread): > Hold on,I’llcheck it out so I can explain better

Faith Ifeoluwa Alexander (05:41:47) (in thread): > Okay.

Scholastica Urua (05:56:21): > Hello everyone and Happy Friday! > > A big thanks to<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>@Chioma Onyido@Peace Sandy@Esther Afuapefor consistently answering questions and resolving issues. The office hour yesterday was greatly appreciated. > Thank you, fellow contributors, for all your assistance.:hugging_face:Please I need your help reviewing this curation in case I missed something;https://bugsigdb.org/Study_980Here are some of my observations and questions: > > 1. LEfSe was used to identify several significantly different taxa between the two groups in both experiments. LDA score was reported as Log10, so I left that field blank. I have made a discussion on the ‘Talk page’ concerning that. But I’m thinking should I proceed and use 1 since Log10 is mathematically 1?:thinking_face:2. This excerpt is from EXP. 1: “No significant differences in species richness and evenness were observed between HCs and patients with NAFLD in median alpha diversity (observed species, Chao1, Shannon, and Simpson diversity indices) (Fig. 2C).” To my understanding, this means all alpha diversity measures employed are unchanged. However, Fig. 2C (image attached) threw me off. Please take a look at it and let me know what you think. > > 3. Curating the signatures has been particularly challenging, especially for EXP. 1 with 24 and 51 taxa for the increased and decreased groups, respectively, especially since most of the taxa did not appear automatically:disappointed_relieved:. I was able to resolve some of them, but there are a couple I couldn’t resolve. One such is Fusobacteria. Fusobacteriia and Fusobacteria (not on BugSigDB) were both increased in the NAFLD group. Fusobacteriia is available as a homotypic synonym of Fusobacteria. Should I omit Fusobacteria since they are both the same? How should this be curated? > > 4. This excerpt is from EXP. 2: “We discovered that the number and evenness of flora species, as well as the Shannon and Simpson diversity indices, decreased in patients with NAFL compared with NASH (Fig. 4A).” I assumed that ‘number’ here represents the richness of species diversity, so I documented it under ‘Richness’. Is this okay? > > I’m patiently looking forward to your feedback:pray: - File (JPEG): fig 2c.JPG

Kelechi Madubuko (06:08:37) (in thread): > Thanks for dropping this recording timely@Svetlana Ugarcina PerovicThis would be quite a useful resource to make up for those of us who were unable to join

Blessing Ene Anyebe (06:18:45) (in thread): > Thank you for sharing the recording@Svetlana Ugarcina PerovicThe support of everyone here has been truly amazing. I am elated to be a part of it as well. Huge shoutout to every contributor! > > Our mentors, you all are amazing! Thank you:orange_heart:@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy(This time the tag is not a question.:new_moon_with_face::sweat_smile:)

Esther Afuape (06:44:51) (in thread): > @Joan C. Chukwuemekathe relative abundance and differential abundance question was answered at the beginning of the meeting. Please check the recording

Faith Ifeoluwa Alexander (06:45:15): > Hello Everyone. I am having issues accessing BugSigDB site. Is it only from my end or a general issue???

Scholastica Urua (06:46:24) (in thread): > Hi@Faith Ifeoluwa Alexander, the site is working just fine on my end. Please check your network connection.

Faith Ifeoluwa Alexander (06:46:55) (in thread): > I can’t access it at all on my browser.

Faith Ifeoluwa Alexander (06:47:24) (in thread): > I have turned my network on & off severally. It’s the same thing.

Habiba Saad (06:47:33) (in thread): > yes its working fine.

Rahila-me (06:47:57) (in thread): > Faith network is bad

Scholastica Urua (06:48:14) (in thread): > Have you tried using a different network?

Adedoja Isaac (06:48:18) (in thread): > Hi@Scholastica UruaI agree with most of your curation… > > For LDA score: It is reasonable to leave the LDA score field blank if it was reported as Log10. Logarithms are a mathematical concept, and most people might not expect to see them directly in the LDA score field. Leaving it blank avoids confusion and maintains consistency with how other scores are likely presented. So I think Including “Log10” or “1” might be misinterpreted as the actual LDA score, which could lead to confusion for others who aren’t familiar with the mathematical conversion. So, I feel it’s best to leave it blank. Let’s hear from our mentors and other contributors tho… > > To Alpha diversity: You are right. The text excerpt you provided says that there are no significant differences in alpha diversity measures between the two groups. However, Fig. 2C shows some p-values that are “not statistically significant” (represented by ns). This inconsistency can be due to chance variation or because the alpha diversity measures were not adjusted for multiple comparisons. So, recording as Unchanged I think would be very correct. > > For Fusobacteria curation: You are right and I also agree that Fusobacteriia is a homotypic synonym of Fusobacteria. Fusobacteriia is a higher taxonomic level encompassing the entire genus Fusobacteria and potentially other related genera. In this case, Fusobacteriia is a homotypic synonym of Fusobacteria. they represent the same taxonomic level (genus in this case). So, like you said, I think the recommended approach may be to choose the name that is most commonly used … Fusobacteria is the more common term, so you can omit Fusobacteriia. > > And Species richness: Yes, I totally agree with you. The word “number” in the study refers to the richness of species diversity, so it is correct to document it under “Richness”. In the context of species diversity, “number” is often used interchangeably with “richness.” Both terms refer to the total number of species, not the abundance of any individual species. The study reference mentions “number and evenness of flora species.” Evenness refers to how uniformly distributed the abundance is among the species. Since evenness is considered, it implies that “number” refers to the total count of species (richness) and not the abundance of any particular species. But I’d love to know what other contributors feel about this part too.

Faith Ifeoluwa Alexander (06:49:22) (in thread): > Nope. I don’t have another network.

Faith Ifeoluwa Alexander (06:49:49) (in thread): > It’s only MTN I am using to access the internet and it has been horrible since yesterday.

Scholastica Urua (06:50:26) (in thread): > So for the inconvenience Faith

Faith Ifeoluwa Alexander (06:50:30) (in thread): > I wonder how Slack is even working.

Faith Ifeoluwa Alexander (06:53:11) (in thread): > Thank you so much@Joan C. Chukwuemeka. But I don’t get what you mean. Are you suggesting I use their Taxa IDs instead of the names?

Adedoja Isaac (06:53:54) (in thread): > @Faith Ifeoluwa AlexanderThe network you’re using has some issues. I faced the same yesterday. And the Reason why slack is working is because it doesn’t reall need a very strong network to work as an app. So like@Scholastica Uruasaid, changing your network would work just fine.

Joan C. Chukwuemeka (06:56:14) (in thread): > Okay@Esther Afuape

Adegboye Rukayat (06:56:46) (in thread): > @Faith Ifeoluwa AlexanderMtn network has been really bad for the past few days. I think it is best you switch network till they resolve their network issue.

Scholastica Urua (06:57:07) (in thread): > Thank you so much for your review@Adedoja Isaac:pray:

Joan C. Chukwuemeka (06:57:28) (in thread): > @Faith Ifeoluwa AlexanderYou can use either… Once you input the ID and save it will show the taxa name too

Adegboye Rukayat (06:58:36) (in thread): > Keep in mind Glo too is not that strong but better than MTN.

Faith Ifeoluwa Alexander (06:59:35) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the good job you and every other Mentors are doing for us. A big thank you to my fellow contributors who have been super helpful in curating my paper. If not for your support, I don’t know how I would have been able to do this. Thank you so so much. > > And as for me I am not resting on my oars this weekend. I will be working on finishing up my Curation. > > Happy Friday everyone!

Faith Ifeoluwa Alexander (07:00:38) (in thread): > Okay. Is Airtel better? So I can know which to switch to.

Joan C. Chukwuemeka (07:01:17) (in thread): > Airtel is fair… That’s what I’m using currently

Adegboye Rukayat (07:03:16) (in thread): > I think I will also have to switch to Airtel. Thanks@Joan C. Chukwuemeka

Abiola Salako (07:06:59) (in thread): > 3)For the taxa resolution issue, if Fusobacteriia and Fusobacteria are essentially the same I think it’s okay to curate it as one signature@Scholastica Urua4) Yes, assuming ‘number’ represents richness in species diversity, documenting it under ‘Richness’ seems appropriate based on your interpretation of the text@Scholastica Urua

Faith Ifeoluwa Alexander (07:07:35) (in thread): > Okay. Thanks.

Faith Ifeoluwa Alexander (07:08:20) (in thread): > You said the red & purple tag under quality control is nothing to be worried about. Pls, explain in simpler terms for me. Thank you.

Faith Ifeoluwa Alexander (07:08:50) (in thread): > Okay. Thank you. Let me switch to Airtel then.

Scholastica Urua (07:09:35) (in thread): > Thank you@Abiola Salako

Joan C. Chukwuemeka (07:14:04) (in thread): > 1. See thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710515023935049?thread_ts=1710514443.652329&cid=C04RATV9VCY > 2. The alpha diversity are unchanged here. If you look at the bar line on the figures in 2C, you’ll see “ns” which means “not significant” > 3. Homotypic synonym can be used. However, let the two taxa reported be noted down in a talk or discussion page. > 4. Pls can you share fig. 4A for a clearer view and response? - Attachment: Attachment > Yes I was incorrect yesterday–we use the default score of 2 if missing.

Mildred Anashie (07:14:34) (in thread): > Hi@Scholastica UruaFor the LDA score usually if it isn’t mentioned using 2 works just fine (I’m not sure if it can work here as Log10 was Mentioned instead) > > The excerpt interprets no significance, also if you look closely at the Fig2C you can tell that there was no significance (ns) and it’s safe to assume the P value here is 0.05 as all the values are above 0.05 > > For the signatures I also happen to be stuck with being able to find some signatures in NCBI in the paper in curating:pensive:Also for the Fusobacteria and Fusobacteriia since one is the homotypic synonym of the other using the one with the Taxonomy ID should suffice in my opinion > > I agree that number could imply richness > > Well done on your curation:blush:

Scholastica Urua (07:20:03) (in thread): > Thank you@Joan C. Chukwuemeka@Mildred AnashieI totally understand question 2 now:hugging_face:Fig. 4A as requested Joan - File (JPEG): Fig 4A.JPG

Peace Daniel (07:24:16) (in thread): > With this image you shared, I think number has to be a measurement index

Peace Daniel (07:25:23) (in thread): > Is it safe to say number means richness?

Mildred Anashie (07:27:19) (in thread): > This 4a is a bit confusing for the evenness as Simpson and Shannon represents evenness and they are already mentioned, I think Pielou should represent this evenness that was used here and work for this

Scholastica Urua (07:28:54) (in thread): > I think so too@Mildred Anashie. I documented the evenness for Pielou.

Peace Daniel (07:29:24) (in thread): > Take a look at this - File (PNG): IMG_2295

Faith Ifeoluwa Alexander (07:30:39) (in thread): > Airtel is working fine now. Thank you everyone.

Joan C. Chukwuemeka (07:37:36) (in thread): > They provide further information about the taxa. If you hover a mouse over them you’d see the info. If you check the snippet I sent from the BugSigDB, it has what each one is pointing to.

Barakat Akinsiku (07:38:34) (in thread): > Hi@Scholastica Uruathe default for LDA if not mentioned is 2 but since it was written log1 maybe leave it blank. Also the last signature with the noname tag could it fall under unclassified peptostreptococcaceae? I also agree you can use the homotypic synonym of Fusobacteria in its place

Faith Ifeoluwa Alexander (07:40:21) (in thread): > Yes, the red one was telling me it was a contaminant.

Scholastica Urua (07:40:27) (in thread): > Thank you@Peace Daniel@Barakat Akinsiku

Faith Ifeoluwa Alexander (07:41:17) (in thread): > While the purple tag was telling me that the indicated taxa is found in other body parts.

Joan C. Chukwuemeka (07:42:27) (in thread): > Okay… From the figure, number should be Richness. Evenness, perhaps is Pielou.

Joan C. Chukwuemeka (07:43:13) (in thread): > Yea… you get it now. Well done:+1:

Faith Ifeoluwa Alexander (07:44:21) (in thread): > So to resolve the taxa in red, do I input the numbers only without adding txid?

Joan C. Chukwuemeka (07:44:32) (in thread): > Yes

Faith Ifeoluwa Alexander (07:44:43) (in thread): > Okay. Thank you.

Faith Ifeoluwa Alexander (07:47:35) (in thread): > I have resolved it. Thank you so much.

Faith Ifeoluwa Alexander (07:48:13) (in thread): > The taxa are all in green now.

Joan C. Chukwuemeka (07:53:03) (in thread): > You’re welcome@Faith Ifeoluwa Alexanderglad to help:hugging_face:

Ima-obong (Aimah) (08:20:57) (in thread): > Thank you<@UBNSEMS3S>for sharing

Idiat Alli (08:31:07) (in thread): > Thank you<@UBNSEMS3S>

Amanda Adoyi (08:43:41): > Halo:slightly_smiling_face:Being away for a day feels like a century here. Not happening again aye…Thank you for the recording@Svetlana Ugarcina Perovicand thanks everyone for answering questions I’m quite sure I’d ask soon. If you would like a review, happily would help in the best way I can. Danke :)

Peace Daniel (08:51:54) (in thread): > Welcome back Amanda:purple_heart:

idiaru Angela (08:57:53) (in thread): > Happy to have you back@Amanda Adoyi

Amanda Adoyi (08:59:45) (in thread): > omw I could cry. Y’all are awesome. Love this project. Good chance I’ll be doing this a lifetime…perhaps.

Peace Daniel (09:18:44): > Hey y’all:wave:So I’m trying to source for the NCBI ID for unidentified Ruminococcaceae > I couldn’t find this but I saw unclassified Oscillospiraceae and it’s heterotypic synonym is unclassified Ruminococcaceae

Peace Daniel (09:21:14) (in thread): > I don’tthink I can interchange unidentified for unclassified

Joan C. Chukwuemeka (09:22:40) (in thread): > @Peace DanielUnclassified Oscillospiraceae is fine.. since it’s a heterotypic synonym > > You can also put a note in the discussion page for the actual reported taxa on the Paper

Peace Daniel (09:25:45) (in thread): > But unidentified doesn’t mean the same as unclassified in plain English so it’s quite confusing > When you say unidentified it means ithasn’tbeen identified yet but unclassified means it has been identified but not classified > > I dunno…this my thoughts on it

Mildred Anashie (09:28:42) (in thread): > Yea@Joan C. Chukwuemekais right > > I think some papers use it interchangeably, and I think the closest way of identifying the taxa works in recording on BugSigdbYou can use that, justleave a note

Scholastica Urua (09:32:16) (in thread): > I think you should use it but make a note on the talk page.

Amanda Adoyi (09:38:01) (in thread): > Heterotypic synonyms are tricky though. While homotypic synonyms definitely refer to the exact same taxon, heterotypic may refer to different strains. They seem more…..subjective maybe. Does that matter in this curation task though?

Amanda Adoyi (09:40:25): > Aloha my people. I’ve got to know, if you’ve dealt with duplicate studies (same PMID) how do you go about it with the mentors? Just report here? Because they seem very obvious and I’m sure someone may have pointed them out before, just that I see nothing on the talk/discussion page.

UBNSEMS3S (09:40:40) (in thread): > Yes we curate the taxa as specified in the paper to the best of our ability. This includes taxa at any rank: genus, family, order, etc.If they are presenting taxa at a rank higher than species (genus, etc.), do not attempt to curate a species.That specific part of the curation policy is discussing the specific case where the paper to be curated has a taxon like “unclassified Clostridiales species.”

Peace Daniel (09:41:06) (in thread): > I’lluse that and write a note in the discussion page > > > I just thought it seemed quite different…

Hamza Haji (09:41:16) (in thread): > Thank you@Olajumoke Adeoyo@Desire Oluwarotimi@idiaru Angela@Abiola Salako@Aleru Divine

UBNSEMS3S (09:42:31) (in thread): > What is the PMID?

Mildred Anashie (09:43:09) (in thread): > Thank you for the clarification<@UBNSEMS3S>:pray:

Hamza Haji (09:43:33) (in thread): > Thank for your time@Scholastica UruaI really appreciate the feedback. For the taxa highlighted in red, I could not find them in the NCBI database.

Amanda Adoyi (09:43:38) (in thread): > Hi:slightly_smiling_face:Oh yea. It’s29234019

Ima-obong (Aimah) (09:43:56) (in thread): > It’s been a moment.. I listened through this recording and I must say a big thank you to the mentors for recording this meeting …could really have missed alot.@Aleru Divinequestions were an eye opener for me and I learnt a whole lot of new principles as regards curation.. > > Thank you again to all the mentors for taking the time to answer these questions, I really appreciate the support. > > I believe my next curation will be error-free:100::smiling_face_with_3_hearts:…Thank you .

UBNSEMS3S (09:45:29) (in thread): > Looks like this study was curated twice because of two different study designs–that’s how we did it back in the early days of the project when it was just an Excel spreadsheet. I would not try to change it now.

Amanda Adoyi (09:45:54) (in thread): > Alright. Thank you.

idiaru Angela (09:46:00) (in thread): > @Hamza Hajiyou should check to confirm that they have no homotypic synonyms or check uniprot. For those that have homotypic synonyms, they can be entered via their Taxonomy ID

Amanda Adoyi (09:47:03) (in thread): > <@UBNSEMS3S>How do I figure out which one is intended to be left alone? Or perhaps I should try some other task besides checking out duplicate work?

UBNSEMS3S (09:48:53) (in thread): > Thanks for bringing this ambiguity in the language to my attention. I’ve added some clarification to the curation policy.

Scholastica Urua (09:49:30) (in thread): > Thanks for clarifying<@UBNSEMS3S>

Aleru Divine (09:49:49) (in thread): > Thank you so much for the clarification<@UBNSEMS3S>

UBNSEMS3S (09:49:53) (in thread): > Any study that has been marked as reviewed should probably be left alone.

Amanda Adoyi (09:50:06) (in thread): > Alright

UBNSEMS3S (09:53:31) (in thread): > It’s nice to see a paper controlling for so many confounders.

Aleru Divine (09:54:01): > Hello@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI accidentally added a signature twice and would like for it to be deleted.Please help me delete Signature 3 in experiment 6 from this study. > > Thank you so much:pray:https://bugsigdb.org/Study_953 - Attachment (BugSigDB): Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China - BugSigDB > The objective of this study was to describe and compare the dynamic microbiota characteristics in the gastrointestinal (GI) tract in Chinese participants via high-throughput sequencing techniques.

UBNSEMS3S (09:55:09) (in thread): > Deleted.

Aleru Divine (09:55:41) (in thread): > Thank you so much<@UBNSEMS3S>

Abiola Salako (10:06:14) (in thread): > @Ima-obong (Aimah)very well said:smiling_face_with_3_hearts:

idiaru Angela (10:08:11) (in thread): > @Hamza HajiThese are some of my observations > 1. The paper already included the ncbi taxa ID for some of the taxa that you curated, so you curate just the taxa ID and it would show up in the data base > 2. The second signature that includes the decreased abundance has not been curated but it was included in the experiment

Abiola Salako (10:11:23) (in thread): > Thanks for the clarification@C. Mirzayi (please do not tag this account)

Amanda Adoyi (10:29:49): > Aloha again:slightly_smiling_face:So I found this study with missing NCBI Id. Under experiment 6 signature 1, I saw that there was no id for “un-Allorhizobium-Neorhizobium Pararhizobium-Rhizobium”. I’m wondering if ‘un’ here signifies the exclusion of the genera from that experiment as opposed to an inclusion…so would an id be expected to be found? Would appreciate any input.<@UBNSEMS3S>@Chioma OnyidoI really got to know if this is a possibilityhttps://bugsigdb.org/Study_835

Mildred Anashie (10:39:51) (in thread): > It’stotally fine, Alright:thumbsup:

Nitya Singhal (10:43:31): > Hey, I wanna know how to add another experiment?@Peace Sandy@Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account)

Amanda Adoyi (10:45:25) (in thread): > Just under the heading (subject of your study), you should find a “Add another experiment” button I believe.

Mildred Anashie (10:47:41) (in thread): > Hi@Nitya Singhaljust go above the study page (where you’d find study design) you’d see “Add experiment”

Victoria (Burah) Poromon (10:54:03): > Hi everyone, good afternoon > > I just want to clarify. If the LDA score is not stated in a paper, do you leave that blank or fill in the default score?

Aleru Divine (10:55:17) (in thread): > @Victoria (Burah) Poromonif the statistical test used was LEfSe, then you would have to use the default score.

Victoria (Burah) Poromon (10:56:15) (in thread): > Yes it was. > Thank you

Ikeh Darlington Ikeh (10:58:03): > Hi everyone! I am really impressed with the level of collaboration in this community. It is really awesome to see everyone wanting to help answer questions and contribute and such is the spirit of teamwork. > > Most times when I see a question I want to respond to as a “not-very-fast-typer” before I finish typing “jack” an appropriate and correct response and answer is already there. Kudos to everyone. Let’s keep that spirit and grow#bugsigdbtogether. Each contribution here is a growth to BugSigDB and the science and tech community, whether you know it or not. > > Thank you everyone!

Abiola Salako (10:59:17) (in thread): > Yes. Use the default score@Victoria (Burah) Poromon

Aleru Divine (11:01:41) (in thread): > @Ikeh Darlington IkehTeam work makes the dream work:muscle::muscle:Great work everyone:clap::clap::clap:

UBNSEMS3S (11:03:43) (in thread): > Yes I was incorrect yesterday–we use the default score of 2 if missing.

Victoria (Burah) Poromon (11:05:12) (in thread): > Thank you<@UBNSEMS3S>

Amarachi Lewachi (11:15:15) (in thread): > Its lovely to experience this level of teamwork.

Victoria (Burah) Poromon (11:34:16): > Hi everyone > Is it possible for one taxa to be differentially abundant in two contrasting groups? - File (JPEG): IMG_7531

idiaru Angela (11:35:35) (in thread): > Yes it is possible

Mildred Anashie (11:35:40) (in thread): > Like you are contrasting A vs B andit’spresent in both A and B?

Victoria (Burah) Poromon (11:36:12) (in thread): > Yes yes@Mildred Anashie

Joan C. Chukwuemeka (11:36:49) (in thread): > @Victoria (Burah) PoromonThis looks like a case of different taxa level being reported. A larger view of the figure may give more insight

Mildred Anashie (11:37:07) (in thread): > Wow > > Idon’tthinkI’vecome across that:thinking_face:

Victoria (Burah) Poromon (11:37:49) (in thread): > @idiaru Angela, wow.Ididn’tknow this

Joan C. Chukwuemeka (11:37:57) (in thread): > Is it increased in both? or increased in one and decreased in the other?@Victoria (Burah) Poromon

Victoria (Burah) Poromon (11:38:31) (in thread): > Hi@Joan C. ChukwuemekaIt is increased in one and decreased in the other.

Joan C. Chukwuemeka (11:38:59) (in thread): > Oh, then it’s possible.

Victoria (Burah) Poromon (11:40:24) (in thread): > I’mshik shak shok:sweat_smile:@Joan C. ChukwuemekaThank you

Mildred Anashie (11:41:05) (in thread): > @Joan C. Chukwuemekaifit’sA vs B andit’sabundant in A and also abundant in B that meansit’llbe recorded as both increase and decrease in the same experiment > > This is possible?

Peace Daniel (11:41:23) (in thread): > YesI’vecome across this in my present curation

Joan C. Chukwuemeka (11:41:27) (in thread): > You’re welcome:grinning:@Victoria (Burah) Poromon

idiaru Angela (11:42:12) (in thread): > @Victoria (Burah) PoromonI think it’s possible because it could be that different species of the same genus or phylum are abundant in the 2 contrasting groups but the species weren’t specified so it should probably be curated as seen

Aleru Divine (11:42:32) (in thread): > That makes sense@idiaru Angela

Joan C. Chukwuemeka (11:43:38) (in thread): > @Mildred AnashieIt’s increased in one and decreased in the other according to@Victoria (Burah) Poromon. > So, If the decrease is in the control group (group 0), and increase is in the case group (group 1), it will be recorded as increase, cos it’s the case group signature that is curated. Do you get?

Chioma Onyido (11:43:46) (in thread): > Yesit’spossible.I’vecome across this and we had a discussion with@Svetlana Ugarcina Perovica while ago about why this is. Let me look for the thread, should be among my saved items…

Aleru Divine (11:44:19) (in thread): > @Victoria (Burah) Poromonif it increased in one and decreased in the other, maybe itwasn’ta mistake.

Victoria (Burah) Poromon (11:46:03) (in thread): > @idiaru AngelaYes I curated as seen. But I’m seeing it for the first time and I just wanted clarity on it. Thank you:blush:

Mildred Anashie (11:46:42) (in thread): > Okay@Joan C. Chukwuemekait’sclearer now > > Thank you@Chioma OnyidoI’minterested in that thread

Victoria (Burah) Poromon (11:46:46) (in thread): > @Chioma OnyidoThank you.

Victoria (Burah) Poromon (11:47:16) (in thread): > @Aleru Divine, it is increased in one and decreased in the other

Chioma Onyido (11:47:32) (in thread): > Ohh got it! > > “******Different bacterial strains may have different biological properties due to the different genes:*********** > *******for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98%****”https://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639 - Attachment: Attachment > During today’s talk by Liao Herui (PhD Student of City University of Hong Kong) about his work on strain identification analysis (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10433603/), I remembered our discussion on why some signatures have the same species in decrease and increase reported? > > One of Liao’s slides had a nice illustration and helpful comment that I would like to share with you: > Different bacterial strains may have different biological properties due to the different genes:** > for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98% [https://pubmed.ncbi.nlm.nih.gov/30837975/]

Victoria (Burah) Poromon (11:48:48) (in thread): > Thank you so much@Chioma Onyido

Joan C. Chukwuemeka (11:49:01) (in thread): > Thanks<@UBNSEMS3S>@Scholastica UruaI think this should answer the question you asked earlier on LDA score vs Log 10

Scholastica Urua (11:50:03) (in thread): > Thank you@Chioma OnyidoDidn’t know it was possible

Aleru Divine (11:50:41) (in thread): > Thank you@Chioma Onyidothis makes so much sense:sweat_smile:

Scholastica Urua (11:51:11) (in thread): > I think so@Joan C. ChukwuemekaThanks:pray:

Chioma Onyido (12:01:35) (in thread): > I know right? I thought so too.You’rewelcome!

Chioma Onyido (12:03:23) (in thread): > I think I mistakenly deleted the thread.:woman-facepalming:Let me re-share.

Mildred Anashie (12:04:54) (in thread): > I can still see it though@Chioma OnyidoAnd it makes sense, thank you

idiaru Angela (12:05:19) (in thread): > Thank you@Chioma Onyido:blush:

Aleru Divine (12:05:29) (in thread): > Yeah me too.Unlessthere’smore.@Chioma Onyido

Chioma Onyido (12:05:41) (in thread): > Ican’t. Probably my network:sweat_smile:That’sgreat then.

Chioma Onyido (12:23:54) (in thread): > @Flourish Ralph

Modinat Ganiyu (12:24:19): > Hello Everyone! > Thanks:blush:to you all for helping out. To those who ask the questions, thank you. To those who answer, respond and/or redirect questions to our mentors, I appreciate. I want to take this moment to review curations. So anyone who want a review on his/her curation, you’re welcome, I’m open for now.

Flourish Ralph (12:24:48): > Hi everyone:wave:I have a question; can there be experiments without signatures in tow?@Svetlana Ugarcina Perovic@Esther Afuape@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy

Flourish Ralph (12:25:23) (in thread): > Thank youuu

Esther Afuape (12:25:28) (in thread): > Yes > Ifthere’san alpha diversity result but no significant taxa reported

Joan C. Chukwuemeka (12:26:26): > @Flourish RalphBased on a review I got recently, I’m told it’s possible if alpha diversity was done for it

Flourish Ralph (12:26:48) (in thread): > Noted, thank you!

Flourish Ralph (12:27:04) (in thread): > Okay, thank you for this

Aleru Divine (12:28:57) (in thread): > @Flourish RalphYeah:sweat_smile:I am currently curating experiments without signatures > > Twinssssss:people_hugging:

Modinat Ganiyu (12:30:06) (in thread): > Yeah, I think its possible so far its not stated

Abiola Salako (13:10:43) (in thread): > Thank you@Chioma Onyido

Flourish Ralph (13:17:58) (in thread): > @Aleru Divine:rolling_on_the_floor_laughing:‘Where have you been????’:index_pointing_at_the_viewer:

fetlework gubena arage (14:23:21): > Hello Everyone!

fetlework gubena arage (14:23:58): > I have a question I have finished curating my second paper what am i going to do next

Aleru Divine (14:27:16) (in thread): > Hi@fetlework gubena aragecongratulations on completing your second curation. > > You can do the following: > 1. Submit for review > 2. Record your contribution on the Outreachy website(leave the “merge date” for when you receive feedback) > 3. While you wait for the review, you can proceed to claim another article for curation on GitHub(if available) or look for other ways to contribute via the help page. > Link to page:https://bugsigdb.org/Help:Cleanup#Links_to_lists_of_pages - Attachment (BugSigDB): Help:Cleanup

Mildred Anashie (14:27:20) (in thread): > Hi@fetlework gubena aragecongratulations > > Please go herehttps://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Help:Contents > …

fetlework gubena arage (14:29:46) (in thread): > Thank you Aleru how can I record it on Outreachy website

Mildred Anashie (14:32:27) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcUse this link to record your first contribution - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Mildred Anashie (14:32:45) (in thread): > For the second use the link to the study you just completed

Abiola Salako (14:32:51) (in thread): > @fetlework gubena arageyou can also post it here for fellow contributors who might be interested in reviewing it before the final submission.

Aleru Divine (14:34:00) (in thread): > Go to Record a contribution.Repeat the steps you took while you recorded the first contributionUse the link of the study you curated as the contribution link.

Muqtadirat Yussuff (15:22:44): > Hi everyone, how are we doing? Does anyone need a second input on their curation?

Oluwatomisin Omojokun (15:22:58) (in thread): > Did you record the first contribution and how did you get the link@Aleru Divine

Aleru Divine (15:23:34) (in thread): > For the first contribution, the survey link is the link.

Mildred Anashie (15:23:35) (in thread): > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcThis is the link - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Aleru Divine (15:24:17) (in thread): > Yes, this link posted by@Mildred Anashie:point_up_2:

Scholastica Urua (15:24:31) (in thread): > Hello@Muqtadirat Yussuff:hugging_face:

Muqtadirat Yussuff (15:25:56) (in thread): > Hi@Scholastica Urua, how are you doing?

Oluwatomisin Omojokun (15:26:13) (in thread): > okay, thanks@Mildred Anashie@Aleru Divine

Scholastica Urua (15:29:09) (in thread): > Very well, thank you. How do you do Yussuff?

Eniola Adebayo (15:33:52) (in thread): > Hi@Muqtadirat Yussuff

Muqtadirat Yussuff (15:34:57) (in thread): > I’m doing okay, thank you. What are you up to if I may ask?@Scholastica Urua

Muqtadirat Yussuff (15:35:09) (in thread): > Hey@Eniola Adebayo, how are you?

Eniola Adebayo (15:36:07) (in thread): > I’m doing good. Thank you > Hope you’re good too@Muqtadirat Yussuff

Muqtadirat Yussuff (15:40:53) (in thread): > I am, thank you for asking@Eniola Adebayo. How’s your time at BugSigDB going by the way?

Flourish Ralph (15:41:07) (in thread): > Hi@Muqtadirat YussuffI’llneed your input soon

Mildred Anashie (15:42:21): > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyHi everyone > > This signatures are from the study I just finished curating and I haven’t been able to find them on the NCBI taxonomy browser or Uniprot > > Thought to share it here incase anybody has an idea on what could best fit any of them or could search where I haven’t:relaxed:before I open a talk page for them > > Thank you:blush:I’m looking forward to your help and responses > > Coriobacteriaceae UCG 002 unclassifed > Coriobacteriaceae UCG 002 > Ruminococcaceae UCG 010 unclassifed > Eubacterium coprostanoligenes group unclassifed > Ruminiclostridium 9 > Eubacterium brachy group unclassifed > Candidatus Saccharimonadas > Eubacterium nodatum group > unclassifed > *Family XIII > > Also if anyone would like to review the curation here’s the linkbugsigdb.org/Study_960

Scholastica Urua (15:45:21) (in thread): > I finished curating this earlier;https://bugsigdb.org/Study_980but there are some taxa with missing NCBI taxa ID. I was able to resolve some but there are still some more unresolved. I’m going over it again with fresh eyes to try and resolve more (if I can). > > I wouldn’t mind you taking a long at it too@Muqtadirat Yussuff. Thanks:pray: - Attachment (BugSigDB): Role of intestinal flora in the development of nonalcoholic fatty liver disease in children - BugSigDB > In China, 45% of adolescents with obesity develop fatty liver disease, a condition that increases the long-term risk of developing cirrhosis and liver cancer.

Muqtadirat Yussuff (15:48:55) (in thread): > @Flourish Ralphalright, I’ll be waiting

Muqtadirat Yussuff (15:49:33) (in thread): > @Scholastica UruaI’ll go through, please give me a while as network as been terrible lately. Thank you

Aleru Divine (15:50:34) (in thread): > Looking forward to the responses:pleading_face::crossed_fingers:@Mildred Anashie

Eniola Adebayo (15:52:19) (in thread): > It’sbeen amazing, I have learnt a lot and I have been able to apply those lessons. I’m enjoying the BugSigDB community@Muqtadirat Yussuff

Aleru Divine (15:57:31) (in thread): > @Mildred AnashieI am currently occupied with curating the multiple experiments in the studyI’mworking on, regardless, I will make the time to carefully review your curation.Will get back to you whenI’mdone:heart:

Mildred Anashie (15:59:00) (in thread): > I would appreciate that > > Thank you@Aleru Divine:heart:and well done on that curation:raised_hands:

Peace Daniel (16:00:03) (in thread): > Currently taking a look at this, I’m sure you found Candidatus saccharimonadale…right? > > Would search thoroughly in case I find something Anashie

Bolanle Wahab (16:08:56) (in thread): > @Mildred AnashieI have a few unclassified signatures that Icouldn’tfind as well, I was thinking of just leaving a note on the discussion page.I’mstill searching though,I’lllet you know if I find any > ButI’mhere for the responses too just incase:smiling_face_with_tear:and if you eventually find them, let me know how please.

idiaru Angela (16:14:13) (in thread): > @Mildred Anashiewould review and give feedback

Esther Afuape (16:21:05) (in thread): > Don’tforget to check that I thread I made again ifyou’restill confused on entering taxa:eyes:

Bolanle Wahab (16:29:29) (in thread): > @Esther Afuapethank you Esther, for example, there’s a match for Ruminococcaceae UCG in your thread and@Mildred Anashielist says Ruminococcaceae UCG 010 unclassified, please are they the same thing and > can we do the same match for similar cases like that?

Mildred Anashie (16:29:59) (in thread): > Sure I have that in mind@Esther AfuapeI made this post though to know if they can be resolved, I hopethat’sokay > > Also is it okay to drop a note on the talk page or I could leave them the way they are

Joan C. Chukwuemeka (18:53:48) (in thread): > @Mildred Anashieis this your second curation? If not, can one edit to resolve any taxa that is found?

Joan C. Chukwuemeka (19:00:24) (in thread): > @Mildred AnashieThis is for Eubacterium brachy - File (JPEG): IMG_20240314_234711.jpg

Mildred Anashie (20:56:54) (in thread): > Eubacterium Brachy already exists in the curation@Joan C. ChukwuemekaThe one listed is Eubacterium brachy group unclassified,both were mentioned

Scholastica Urua (21:23:54) (in thread): > Hello@Mildred AnashieI’m going through this, I’ll let you know if I find any.

Scholastica Urua (21:27:56) (in thread): > Lemme add a few more under this thread hope that’s okay:pray:. They’re in my curation and I’ve been going through them for hours and can’t seem to resolve them; > > Christensenellaceae R-7
> Ruminococcaceae
> Lachnospiraceae ND3007
> Prevotellaceae UCG-001
> Lachnospiraceae UCG-003
> Ruminococcaceae UCG-010
> PrevotellaceaeUCG_001
> Prevotellaceae Ga6A1
> Peptostreptococcaceae noname

Akinbode Mariam (22:59:30): > Hello guys , i just finished my second contribution. i intentionally went through the channel before starting and to be honest everything i needed to ask was already answered thanks to everyone that took their time to answer:hugging_face:@Svetlana Ugarcina Perovic@Mildred Anashie@Peace Sandy@Esther Afuape. i am open to reviewing curations from others, also pls review my contribution so i know if i’m on the right track.https://bugsigdb.org/Study_995 - Attachment (BugSigDB): Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson’s disease - BugSigDB > Growing evidences show that gut microbiota is associated with the pathogenesis of Parkinson’s disease (PD) and the gut-brain axis can be promising target for the development of the therapeutic strategies for PD.

2024-03-16

Mildred Anashie (00:05:06) (in thread): > That’stotally fine@Scholastica UruaThis thread might be helpful for the last onehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710411707183289?thread_ts=1710405054.603599&channel=C04RATV9VCY&message_ts=1710411707.183289 - Attachment: Attachment > @Barakat Akinsiku note the spelling, Bacteroidales noname, not Bacteriodales noname. This seems equivalent to unclassified Bacteroidales (taxid 185291, no rank). @Mildred Anashie, Bacteria is not incorrect, but it provides less information about the lineage than unclassified Bacteroidales does, which at least tells us the order_._

Peace Daniel (00:41:54) (in thread): > Congratulations on completing your curation:clap:

Faith Ifeoluwa Alexander (00:57:21): > Hello Everyone. Good Morning. Please I just need clarity on my paper. Is it possible to have up to 6 experiments in a Study?

Joan C. Chukwuemeka (01:00:00): > Hello all, > I have some questions regarding a study I’m currently curating. > First here’s an Excerpt from the study and the figures mentioned. > > Excerpt:
> 16S rRNA gene sequencing (16S-seq) revealed significant shifts in the gut microbiota between the two diets (Figures 1C and S1A; Table S1), including an altered relative abundance of the Actinobacteria, Bacteroidetes, and Firmicutes phyla (Figure 1D). 19 genera were significantly different with Bifidobacterium showing the greatest decrease on the KD (Figure 1E). > > Metagenomic sequencing of paired stool samples from the two diet arms confirmed the reduction of several bifidobacterial species on KD (Figures 2A and 2B; Table S2).<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape<@U1LCB8WEA>@Peace Sandy@Chioma OnyidoQuestions: > 1. Looking at Figure 1D and 1E and the supporting texts excerpts above, are both Curatable? Taking a 2nd look, I’m thinking 1D maybe like just relative abundance, while 1E is the differential abundance that should be Curated and then DeSeq2 as statistical test?:thinking_face: > 2. If signatures from both are Curatable, then which statistical type will be curated? will it be both? Cause according to the description of the figures, Figure 1D is a result of paired Wilcoxon test, while Figure 1E is a result of DeSeq2.? > 3. They made mention of another sequencing type - Metagenomic sequencing. However, the figures reported to show the outcome of that doesn’t seem Curatable - Figures 2A and 2B:thinking_face:

Desire Oluwarotimi (01:04:13) (in thread): > Hi@Faith Ifeoluwa AlexanderYes, it is very much possible to have 6 or more experiments in a study. > However, this is dependent on the number of group comparisons for which there were differential abundance and alpha diversity results in the study.

Faith Ifeoluwa Alexander (01:05:47) (in thread): > Okay. So the group comparison for my study is for Parkinson’s Disease Patients, Healthy Controls and medications the PD Patients were treated with.

Desire Oluwarotimi (01:08:37) (in thread): > Can you share the link to the paper please?

Faith Ifeoluwa Alexander (01:08:53) (in thread): > https://bugsigdb.org/Study_984 - Attachment (BugSigDB): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders.PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS).

Aleru Divine (01:15:21) (in thread): > Hi Joan, good morning:sunny:I observed the following, > 1. Only Figure 1E is curatable as 1D is showing the relative abundance.If you could provide the link to the paper, maybe I can be sure on what statistical test was used.But from the excerpt you provided it should be DeSeq2 sincewe’reonly supposed to consider the statistical test used for differential abundance. > 2. 1E is the one curatable so DeSeq2 > 3. To answer this I would really like read the paper in question:pray:because it looks like there were 2 sequencing methods used. > Hope this helps:pray:

Aleru Divine (01:16:53) (in thread): > It’svery possible@Faith Ifeoluwa AlexanderI have over 40 experiments in the studyI’mcurating.I don’t think there is a limit to the number of experiments we are to curate.

Faith Ifeoluwa Alexander (01:17:25) (in thread): > Wow! That is a lot,@Aleru Divine. Well Done! > > I just even noticed the groups in my paper are more than 6.

Aleru Divine (01:18:43) (in thread): > Congrats on completing your curation:partying_face:

Faith Ifeoluwa Alexander (01:23:21) (in thread): > @Desire Oluwarotimiwhat can you deduce from my paper?

Bolanle Wahab (01:34:27) (in thread): > @Joan C. Chukwuemeka > 1. You’re right, 1D doesn’t show any significant difference between the groups, 1E shows differential abundance and should be curated > 2. You should go with the statistical test for 1E > 3. The figure only shows metagenomic sequencing details of your subject compared to the other type. > Sending your article would help

Desire Oluwarotimi (01:36:24) (in thread): > @Faith Ifeoluwa AlexanderYes, you have quite a number of experimental groups. Here are the ones I found; > > PD vs Controls > Female Controls vs Male controls > Female PD vs Male PD > PD patients with elevated levels of fecal calprotectin vs Calprotectin negative controls. > PD patients with normal calprotectin levels vs Controls. > PD patients with normal calprotectin levels vs Calprotectin positive PD patients. > PD patients treated with L-dopa vs Controls. > PD patients who were not treated with L-dopa vs Control group. > PD patients who were not treated with L-dopa vs PD patients treated with L-dopa. > PD patients treated with entacapone vs Control group. > PD patients with a hypokinetic-rigid (HR) phenotype vs Control group. > PD patients with a tremor dominant (T) phenotype vs Control group. > HY stage of 1 to 2.5 vs Control group. > HY stage of 3 to 4 vs Control group. > HY stage of 1 to 2.5 vs HY stage of 3 to 4.

Faith Ifeoluwa Alexander (01:37:55) (in thread): > :exploding_head:Wait must they be listed like this????

Faith Ifeoluwa Alexander (01:38:20) (in thread): > I skipped the gender control groups.

Desire Oluwarotimi (01:38:26) (in thread): > I found these in the section titled “Differences in microbiota composition” under the Results part of your paper. > > When there are a lot of them like this, it is very easy to miss out some. So, I’d advice you go through them again.

Faith Ifeoluwa Alexander (01:39:11) (in thread): > Do I then delete the ones I have done & start from the beginning???

Desire Oluwarotimi (01:39:59) (in thread): > When comparing gender control groups, they mentioned a few taxas. This means you can’t skip it.

Abiola Salako (01:40:04) (in thread): > Well done@Akinbode Mariam

Abiola Salako (01:40:30) (in thread): > Yes,@Faith Ifeoluwa Alexanderit’s very possible.

Desire Oluwarotimi (01:40:47) (in thread): > I don’t think you necessarily have to delete. > > You can simply make edits where necessary.

Faith Ifeoluwa Alexander (01:41:13) (in thread): > I mean I didn’t arrange them in the order that you listed them out.

Desire Oluwarotimi (01:45:17) (in thread): > Even if you didn’t, you can make edits instead of asking the mentors to delete. > > I think you should only be looking to delete when the experiment or signature is wrong and you don’t need to make edits.

Faith Ifeoluwa Alexander (01:46:31) (in thread): > So I have to arrange them in the order that they were listed out in the study. Is that right?

Desire Oluwarotimi (01:46:51) (in thread): > Hi@Joan C. ChukwuemekaCan you share the link to the article please? > I’d like to go through before coming to conclusions.

Desire Oluwarotimi (01:48:06) (in thread): > I think so, Yes. > > Please go through the study again. > I already pointed out the part that’ll provide the needed info.

Faith Ifeoluwa Alexander (01:48:15) (in thread): > Pls, I am asking so I will know how & where to make corrections.

Faith Ifeoluwa Alexander (01:49:04) (in thread): > Yeah. I know that part of the study because that is where I am getting all the experiments from.

Faith Ifeoluwa Alexander (01:49:47) (in thread): > One more question pls. So for the groups where no significant differences were observed, how do I add their signatures?

Desire Oluwarotimi (01:52:47) (in thread): > For the groups that didn’t provide any taxa at all, I think you should only create such experiment if there’s a corresponding alpha diversity.

Faith Ifeoluwa Alexander (01:57:29) (in thread): > Okay. Thank you because some of the groups don’t have taxas started in them.

Faith Ifeoluwa Alexander (02:02:15) (in thread): > Also in the group of PD patients with hypo kinetic rigid Phenotype, only the increased relative abundance was reported, no decreased relative abundance was reported. > > Similarly, only the decreased relative abundance was reported for PD patients with a tremor dominant Phenotype and no increased relative abundance as reported. So how do I add the signature of that?

Faith Ifeoluwa Alexander (02:02:53) (in thread): > Can an experiment have only one signature?

Aleru Divine (02:03:15) (in thread): > @Faith Ifeoluwa Alexanderthis is a lot of experiments:people_hugging:Thanks for helping out@Desire Oluwarotimi

Desire Oluwarotimi (02:03:32) (in thread): > You only have to curate what was provided and Yes, you can have a single signature.@Faith Ifeoluwa Alexander

Mildred Anashie (02:07:26) (in thread): > Concerning your question about decreased and increased signature you’d record only the decreased that was mentioned@Faith Ifeoluwa Alexander

Mildred Anashie (02:08:00) (in thread): > Waiting for the link too@Joan C. Chukwuemeka

Faith Ifeoluwa Alexander (02:08:15) (in thread): > Okay. Thank you@Mildred Anashie. I didn’t know that an experiment can have a single signature.

Faith Ifeoluwa Alexander (02:09:10) (in thread): > Thank you so much@Desire Oluwarotimi. You have been very helpful. Thanks a lot. I appreciate your help.

Scholastica Urua (02:10:56) (in thread): > Thanks@Mildred Anashie

Muqtadirat Yussuff (02:15:02) (in thread): > Hi@Scholastica Urua, I haven’t been able to get good results but regarding* **Ruminococcaceae *I found this and the taxa id it was merged into isOscillospiraceae - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (PNG): Screenshot 2024-03-16 070925.png

Faith Ifeoluwa Alexander (02:15:46) (in thread): > One last question pls, is it possible for an experiment to not have a signature? > > In the case where there is no taxa reported for a group.

Aleru Divine (02:16:37) (in thread): > Yesthat’spossible@Faith Ifeoluwa AlexanderI have a few of those too.I confirmed this from the mentors.

Faith Ifeoluwa Alexander (02:16:58) (in thread): > Okay. Thank you so much@Aleru Divine.

Desire Oluwarotimi (02:17:11) (in thread): > Feel free to ask as many questions. > > Yes it possible, but remember that there needs to be alpha diversity.

Faith Ifeoluwa Alexander (02:17:55) (in thread): > Wait, does each experiments have different Alpha diversities???

Faith Ifeoluwa Alexander (02:18:37) (in thread): > In my study, only 4 Alpha Diversities were reported across board for all the groups.

Desire Oluwarotimi (02:18:57) (in thread): > Yes, they should and it’s very possible that the alpha diversity tallies all through.

Scholastica Urua (02:19:56) (in thread): > @Joan C. Chukwuemekafor questions 1 and 2, I’d go with curating 1E since that’s showing the differential abundance.

Desire Oluwarotimi (02:21:39) (in thread): > @Esther Afuapeclarified this in a post she made sometime but I can’t seem to find it again. > > Can someone help please?

Faith Ifeoluwa Alexander (02:21:59) (in thread): > I can only see four Alpha diversities in my study.

idiaru Angela (02:22:57) (in thread): > Hey@Akinbode MariamWeldone on your curation. Going through I have some observations, can I proceed?

Scholastica Urua (02:25:37) (in thread): > Nice looking out@Desire OluwarotimiThat’s a lot of experiments@Faith Ifeoluwa Alexander, good luck with the curation:muscle:

Desire Oluwarotimi (02:26:21) (in thread): > I’m trying to look for that post from@Esther Afuapebut I can’t find it. > > I believe it’ll further clarify the alpha diversity thing.

Scholastica Urua (02:29:27) (in thread): > Well done@Akinbode Mariam

Faith Ifeoluwa Alexander (02:33:42) (in thread): > Okay. Thank you so much@Desire Oluwarotimi. I have to start all over again from Experiment 1.

EBERE ADEKOGBE (02:39:22) (in thread): > Thank you for this recording, was worried I was not in the meet up yesterday, as I tried several times to join but to no avail. Listening to the recording has really helped my understanding of how to curate better!@Svetlana Ugarcina Perovic@Chioma Onyido

Joan C. Chukwuemeka (03:05:36) (in thread): > Thanks guys.@Aleru Divinefor question 3, > 2 sequencing methods were mentioned in the paper - 16S rRNA and Metagenomic (although other experiments were done cos the study used both human and mice) > 1. Within the abstract (Summary), it was stated that metagenomic and metabolomic analyses were done. > 2. Within results text 16S rRNA was stated and the metagenomic was stated like a confirmatory procedure within the result text. However, the figures reported to show the outcome of metagenomic Sequencing doesn’t also seem Curatable - Figures 2A and 2B:thinking_face:(the referenced table S2 is just a list.) Both sequence types were described in the methods too. > link to the paper -https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7293577/ - Attachment (PubMed Central (PMC)): Ketogenic diets alter the gut microbiome resulting in decreased intestinal Th17 cells > Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in metabolic fuel utilization that elevates circulating ketone bodies; however, the consequences of these compounds for host-microbiome interactions remain unknown. Here, … - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Joan C. Chukwuemeka (03:07:09) (in thread): > the table s2 - File (PNG): image.png

Aleru Divine (03:13:37) (in thread): > @Joan C. ChukwuemekaIndeed there were 2 sequencing methods.In your second point, you mention the Metagenomic was like a confirmatory procedure, meaning the first was 16S.I’dsuggest to go with 16S since it was the first.This is just a thought.Going through the paper now:pray:thanks for sharing

Desire Oluwarotimi (03:14:44) (in thread): > Hi@Akinbode MariamYou might want to go through your paper and curation again. > > You won’t be having just one experiment because the paper has about four groups; Control, MPTP, MPTP + Acu and MPTP + Non-Acu. I don’t think they involved the last in any experiment though. > > Also, there were mentions of before and after acupuncture treatment which I think makes everything a bit dynamic.

Scholastica Urua (03:16:18) (in thread): > @Joan C. ChukwuemekaHaven’t gone through the paper yet but I have a question. Is alpha diversity reported for the metagenomic sequencing? > I curated this paper with two different sequencing methods and both reported significantly abundant taxa and alpha diversity so I curated for both.

Aleru Divine (03:21:00) (in thread): > @Scholastica Uruacorrect:+1:

Faith Ifeoluwa Alexander (03:21:19): > Hello, Once again everyone. Pls how do I get permission to delete a Signature? > > In the process of correcting my experiments, I have an experiment that doesn’t have 2 signatures and I now have to delete the 2nd signature I added to the previous group.

Samreen Aftab (03:22:07): > Hello guys. In my study, studies were performed on rats as well as humans. So I’m required to create experiments for both right?

Mildred Anashie (03:22:08) (in thread): > Hi@Faith Ifeoluwa AlexanderPlease ask the mentors to delete it for you by tagging them

Mildred Anashie (03:22:26) (in thread): > With a link to the study and what you want to delete

Faith Ifeoluwa Alexander (03:23:08) (in thread): > @Mildred Anashiedo you have any idea of how long it will take for mentors to respond?

Mildred Anashie (03:23:40) (in thread): > They collected samples from rats and humans? > > Results were reported for both?

Mildred Anashie (03:24:24) (in thread): > Immediately they see it > > Plus it’s weekend so Ican’ttell, butyou’llhave to be patient

Desire Oluwarotimi (03:24:26) (in thread): > I think they’ll attend to you as soon as they see it.

Desire Oluwarotimi (03:25:55) (in thread): > Yes, you have to create all experiments as provided in the study. Rats and Humans. > > I think I’ve come across something like this before.

Faith Ifeoluwa Alexander (03:26:45) (in thread): > On second thought,@Desire Oluwarotimiwas it stated anywhere categorically that experiments must follow the order that they were stated in the paper?

Joan C. Chukwuemeka (03:27:15) (in thread): > Interestingly@Scholastica Urua@Aleru Divine, I’m yet to see alpha diversity measures within the paper.:thinking_face:

Faith Ifeoluwa Alexander (03:27:15) (in thread): > I am asking to save time.

Samreen Aftab (03:27:17) (in thread): > Yes@Mildred Anashie - File (PNG): image.png - File (PNG): image.png

Faith Ifeoluwa Alexander (03:27:44) (in thread): > @Mildred Anashiepls give your input to my question.

Desire Oluwarotimi (03:28:00) (in thread): > I don’t think so. > > But I always do.

Mildred Anashie (03:28:23) (in thread): > No@Faith Ifeoluwa AlexanderIdon’tthink it has to follow the orderWhat’simportant is recording allexperiment’s reportedin the paper

Faith Ifeoluwa Alexander (03:29:07) (in thread): > Okay, then I will have to arrange it the way I have arranged it earlier. So I won’t have to delete anything.

Desire Oluwarotimi (03:30:46) (in thread): > Yes, you really do not have to delete the experiments you already have.

Scholastica Urua (03:33:40) (in thread): > Still going through your paper, will let you if I find something

Bolanle Wahab (03:35:56) (in thread): > 2A and 2B doesn’t show exact results of metagenomic sequencing but the samples that were already sequenced in Table S2, 16S was the main method used and the other one was used to confirm the resultsThey’rebasically saying the same thing, one is just confirming the other,I’dgo for just 16S, just suggesting. - File (PNG): IMG_9648

Joan C. Chukwuemeka (03:36:21) (in thread): > However, I think its possible not to have alpha diversity measures as the curation policy advices that the section be left blank, if not done.@Chioma Onyido@Peace Sandy<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape<@U1LCB8WEA> - File (PNG): image.png

Joan C. Chukwuemeka (03:46:14) (in thread): > Mistakenly deleted the images. Here they are: - File (JPEG): IMG_20240316_012631.jpg - File (JPEG): IMG_20240316_012645.jpg

Samreen Aftab (03:54:37): > Hey everyone. I’m currently working on this paperhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9657043/Can anyone tell me whether the study design is case control (since it has results between AD and healthy controls) or if it is laboratory design (since rats are used in the experiment)? Should I put both study designs here? > Thank you. - Attachment (PubMed Central (PMC)): Modulation of the Gut Microbiota in Memory Impairment and Alzheimer’s Disease via the Inhibition of the Parasympathetic Nervous System > The gut microbiota has been demonstrated to play a critical role in maintaining cognitive function via the gut-brain axis, which may be related to the parasympathetic nervous system (PNS). However, the exact mechanism remains to be determined. We investigated …

idiaru Angela (04:01:48) (in thread): > Hey@Samreen AftabFigure 1 is not curatable tho. It shows relative abundance not differential abundance

Muqtadirat Yussuff (04:03:21) (in thread): > Hi, I’m unsure if it’s possible to have multiple study designs but I would go with case control as the human patients seem to be the main study of the paper. If it’s possible then go with both > > Hi mentors, is it possible to have multiple study designs?<@UBNSEMS3S>@Esther Afuape@Peace Sandy

idiaru Angela (04:06:06) (in thread): > Hey@Muqtadirat Yussuff@Samreen Aftabthe mentors have confirmed that it is possible but quite uncommon. In most instances one study design is nested in another study design which is the primary design

Samreen Aftab (04:07:05) (in thread): > Thank you@idiaru Angela. I’ll go with case control then.

Muqtadirat Yussuff (04:07:10) (in thread): > Thank you@idiaru Angela, that’s good to know

idiaru Angela (04:09:08) (in thread): > @Samreen Aftabfrom what I can see, I think it is a lab experiment using rats but the results were validated using previous human studies

Samreen Aftab (04:10:43) (in thread): > @idiaru AngelaI’m actually confused, because experiments have been performed on both humans and rats, and there is significant data for both experiments

Samreen Aftab (04:15:02) (in thread): > <@UBNSEMS3S>@Esther Afuape@Peace Sandycan you please help me determine the study design of my paper?

Mildred Anashie (04:16:39) (in thread): > Yes Figure 1isn’tcuratable > > Please share your paper

Aleru Divine (04:17:22) (in thread): > Hi@Samreen Aftabfrom the abstract and then table 1, this seems like a meta-analysis study to me.Also from the abstract, it mentions the hypothesis from the study was further validated in rats. - File (PNG): IMG_7958

Mildred Anashie (04:18:02) (in thread): > Yes experiments can exists without signatures

idiaru Angela (04:19:42) (in thread): > @Aleru DivineI did consider that possibility but I think they only validated it but didn’t pool the data sets together so I still think it’s a lab experiment@Samreen AftabI think the significant data reported weren’t performed by the authors but were from the previous 4 studies that they had mentioned in the beginning of the article

Samreen Aftab (04:20:31) (in thread): > @Aleru Divineokay, thank you. > Also I should include the experiments for both humans and rats, I suppose?

Samreen Aftab (04:21:32) (in thread): > @idiaru AngelaOkay. This is confusing:smiling_face_with_tear:

Aleru Divine (04:22:45) (in thread): > From what you stated@idiaru Angelathat would mean a meta-analysis study design.

Peace Daniel (04:25:43) (in thread): > Ihaven’tread your article but you can have two study designshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710090998459309 - Attachment: Attachment > Hi @Chioma Onyido @Peace Sandy @Esther Afuape > Can a study design be both case-control and a laboratory experiment? > A link to my article > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-018-0520-6

Scholastica Urua (04:27:05) (in thread): > @Joan C. ChukwuemekaI haven’t noticed any alpha diversity mentioned for the WMS which is possible. Like you mentioned the curation policy advices that the section be left blank in such case.

Mildred Anashie (04:28:29) (in thread): > My connectionisn’tletting me open the paperI’vehad very poor internet connection, I really cannot make an input:disappointed:

Aleru Divine (04:28:58) (in thread): > So do you suggest different experiments?@Joan C. Chukwuemeka@Scholastica Urua

Samreen Aftab (04:30:09) (in thread): > @Aleru Divine@Peace Danielaccording to this, the experiment was not performed on humans, rather, data was collected from previous human studies. So should I add experiments for humans as well? > And it should be a meta-analysis study right? > I’m sorry, I’m a little confused about this:sweat_smile: - File (PNG): image.png

Scholastica Urua (04:30:36) (in thread): > If there’s no alpha diversity and no differential abundant taxa mentioned. should the experiment be curated at all? Just thinking

Samreen Aftab (04:31:08) (in thread): > @Mildred Anashiehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9657043/here - Attachment (PubMed Central (PMC)): Modulation of the Gut Microbiota in Memory Impairment and Alzheimer’s Disease via the Inhibition of the Parasympathetic Nervous System > The gut microbiota has been demonstrated to play a critical role in maintaining cognitive function via the gut-brain axis, which may be related to the parasympathetic nervous system (PNS). However, the exact mechanism remains to be determined. We investigated …

Aleru Divine (04:35:02) (in thread): > @Scholastica Urua@Joan C. ChukwuemekaAnd Metagenomic sequencing sort of confirmed the decrease in the genus Bifidobacteria for individuals on the KD diet which was already evident from 16S sequencing.I suggest going with 16S.

EBERE ADEKOGBE (04:37:04) (in thread): > Hello all, please can I get a review of my second contribution? Thank you as you do. > Here is the link:https://bugsigdb.org/Study_913 - Attachment (BugSigDB): - BugSigDB > …

Aleru Divine (04:37:38) (in thread): > Yes@Samreen Aftabit should be a meta analysis study.This confirms that:+1:

Samreen Aftab (04:38:28) (in thread): > Thank you@Aleru Divine:hugging_face:

Scholastica Urua (04:38:50) (in thread): > You’re right@Aleru Divine. Since they’re both saying the same thing right?

Aleru Divine (04:39:17) (in thread): > Yeah:sweat_smile:

Aleru Divine (04:39:46) (in thread): > @Mildred AnashieI’mso sorry about your internet connection.

Mildred Anashie (04:44:06) (in thread): > Okay@EBERE ADEKOGBELet me try to see if I can open it, I’ll make an input if I can

Scholastica Urua (04:45:12) (in thread): > Okay@EBERE ADEKOGBE

Aleru Divine (04:45:15): > Hello hello everyone:hugging_face:, Good morning and happy Saturday!:sunglasses:

Chioma Onyido (04:47:09) (in thread): > Aleru is right, it is a meta-analysis study because samples were pooled from 4 different studies (see Table 1), > It is also a laboratory experiment because it was validated in rat models and taxa was also reported. > Yes, a study can have 2 study designs. See this response from Chloe, on how to curate such studies: > “Oh yeah we’ve had these two-in-one studies before. It should just be one study with multiple experiments. I would pick case-control and experimental and note for the laboratory experiment signatures that they were laboratory experiments in the group 1 description, and same goes for the case-control experiments”.

Abiola Salako (04:48:54) (in thread): > @EBERE ADEKOGBEI tried reaching the page it wasn’t getting through. Will probably check later.

Aleru Divine (04:49:16) (in thread): > Thanks for the clarification@Chioma Onyido:pray:

Samreen Aftab (04:51:01) (in thread): > Thank you so much@Chioma Onyido

Scholastica Urua (04:52:13) (in thread): > Good morning@Aleru Divine:hugging_face:

Samreen Aftab (04:52:27): > In meta-analysis studies, are we supposed to create experiments to record signatures which have been pooled from previous different studies?

Chioma Onyido (04:52:32) (in thread): > You’rewelcome. Brilliant discussion!:+1:

Peace Daniel (04:53:03) (in thread): > Thank you@Chioma Onyido

Bolanle Wahab (04:53:18) (in thread): > Good morning Divine and a Happy Saturday to you too:heart:

Peace Daniel (04:53:29) (in thread): > I was reading your article earlier butthere’syour response@Samreen Aftab:blush:

Samreen Aftab (04:53:40) (in thread): > Good morning@Aleru Divine. I hope you have a great day!:heart:

Abiola Salako (04:55:48) (in thread): > Good morning@Aleru Divine

Barakat Akinsiku (04:58:01) (in thread): > Good Morning@Aleru DivineHappy Saturday!

Abiola Salako (05:01:27) (in thread): > @Samreen AftabThis thread would be helpful in answering some of your questions about the Meta-Analysis project you’re curating.

idiaru Angela (05:02:30) (in thread): > Thank you so much for the clarification@Chioma OnyidoWe were both right:sweat_smile:@Aleru Divine

Scholastica Urua (05:02:45) (in thread): > Thanks@Chioma Onyidofor clarifying

Joan C. Chukwuemeka (05:02:51) (in thread): > Yes@Aleru Divine@Scholastica UruaI already Curated 16S rRNA, however, I needed to confirm that I won’t need to curate metagenomic, where the figure references aren’t curatable as differential abundance and no alpha diversity for it too. > Thanks for the support. > > Hope you’re Curation is going well@Aleru Divine? Won’t mind collaborating with you on it, once I’m done with this:blush:

Barakat Akinsiku (05:03:22) (in thread): > Hi@Samreen Aftabare the studies part of what your meta analysis is focused on? If so I think yes especially if the signatures represent taxa with differential abundance

Abiola Salako (05:04:33) (in thread): > @Samreen AftabI have tagged you to a thread that would be helpful answering your questions. Kindly read through it.

Aleru Divine (05:05:10) (in thread): > You’re welcome@Joan C. Chukwuemekamy curation is going well, thanks for asking. > > I am however done with the curation.But I have to go through it again and would really appreciate a review > > Thank you so much for this:pray:https://bugsigdb.org/Study_953 - Attachment (BugSigDB): Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China - BugSigDB > The objective of this study was to describe and compare the dynamic microbiota characteristics in the gastrointestinal (GI) tract in Chinese participants via high-throughput sequencing techniques.

Abiola Salako (05:07:01) (in thread): > Thank you@Chioma Onyido

Joan C. Chukwuemeka (05:11:21) (in thread): > Alright then… Well done@Aleru Divine

Scholastica Urua (05:12:43) (in thread): > Well done@Aleru Divine, this is a lot of experiments:raised_hands::muscle:

Mildred Anashie (05:15:50) (in thread): > Well done:raised_hands:@Aleru Divine

Mildred Anashie (05:16:15) (in thread): > Happy Saturday:heart:

Aleru Divine (05:19:32) (in thread): > Thank you so much:pray:@Joan C. Chukwuemeka@Scholastica Urua@Mildred AnashieI’ll appreciate your reviews.Also check the discussions page for some notes.

Bolanle Wahab (05:20:52) (in thread): > You’redoing great@Aleru Divine:partying_face:

Aleru Divine (05:21:34) (in thread): > Thank you:pray:@Bolanle Wahab

Mildred Anashie (05:23:18) (in thread): > Yes you are to record experiments based on what is reported in the paper@Samreen Aftab

Samreen Aftab (05:26:15) (in thread): > Yes@Abiola Salakothank you

Abiola Salako (05:28:56) (in thread): > You’re welcome

Scholastica Urua (05:57:37) (in thread): > Good one@EBERE ADEKOGBEHere are some observations I made while reviewing your curation and article: > > It seems that the citation is not fully populated. To address this, consider including the PMID (‘38087200’ in your case) or manually completing the citation details. > > The description of your groups could be clearer. It should be readily apparent which groups are being contrasted without needing to read the article in detail. For instance, the ‘N group’ for group 0 lacks specificity regarding whether they are healthy controls or another case group. Providing clearer descriptors such as ‘Healthy controls (N group)’ or ‘Non-Orthokeratology (OK) lens wearers (N group)’ would enhance clarity. Similarly, instead of ‘L group’ for group 1, consider using ‘Orthokeratology (OK) lens wearers (L group)’ for better understanding. > > For the signature, figure 4 appears to be a better source for curation compared to figure 6. Figure 6 may not be suitable for curation purposes.:thinking_face:Keep up the good work, and I look forward to seeing other opinions.

Mildred Anashie (05:58:53): > Thank you@Scholastica UruaIhaven’tbeen able to go through the paper

Flourish Ralph (06:01:31) (in thread): > Happy Saturday:hugging_face:

Mildred Anashie (06:18:31) (in thread): > I agree with@Scholastica Uruaobservations concerning the group names > OK lens wearers vs Non Ok lens wearers > > The PMID will auto populate the abstract and the study name > > Then the signatures should rather come from Fig 4 and not Fig 6 > Also your Alpha diversity indices are in Fig 2 > > See the images attached > Well done on your curation@EBERE ADEKOGBE - File (PNG): IMG_2401 - File (PNG): IMG_2399

Peace Daniel (06:25:44) (in thread): > Well done@Mildred Anashie@Scholastica Urua

Samreen Aftab (07:01:55) (in thread): > @Aleru DivineUm, meta-analysis involves analyzing data from existing studies to draw conclusions about a specific research question or hypothesis. > However, in my study, experiments were performed on rats. So shouldn’t it be meta-analysis and laboratory experiment both?

Mildred Anashie (07:03:45) (in thread): > See this@Samreen Aftabhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710578829868969?thread_ts=1710575677.388369&channel=C04RATV9VCY&message_ts=1710578829.868969 - Attachment: Attachment > Aleru is right, it is a meta-analysis study because samples were pooled from 4 different studies (see Table 1), > It is also a laboratory experiment because it was validated in rat models and taxa was also reported. > Yes, a study can have 2 study designs. See this response from Chloe, on how to curate such studies: > “Oh yeah we’ve had these two-in-one studies before. It should just be one study with multiple experiments. I would pick case-control and experimental and note for the laboratory experiment signatures that they were laboratory experiments in the group 1 description, and same goes for the case-control experiments”.

Aleru Divine (07:05:17) (in thread): > @Samreen AftabYes it should be both.I thinkthat’sallowed.Thanks@Mildred Anashiefor sharing:pray:

Samreen Aftab (07:05:45) (in thread): > Ah yeah, I missed that part. Thank you@Mildred Anashie:heart:

Abiola Salako (07:06:40) (in thread): > Thank you Mildred

Ima-obong (Aimah) (07:26:56) (in thread): > Yea.. happy weekend:partying_face:

Faith Ifeoluwa Alexander (07:31:16) (in thread): > Happy Working weekend to you too@Aleru Divine.

Akinbode Mariam (09:06:48) (in thread): > @idiaru Angelapls go ahead

Peace Daniel (09:18:58): > Good day everyone, > I’m trying to find a suitable condition for my curation and the closest I found was fibroblast growth factor 21 measurement. > Is it fine to use this? > Link to my curationhttps://bugsigdb.org/Study_961 - Attachment (BugSigDB): Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson’s disease mouse model via modulating gut microbiota and metabolic homeostasis - BugSigDB > AIMS: The effects of FGF21 on Parkinson’s disease (PD) and its relationship with gut microbiota have not been elucidated.

Akinbode Mariam (09:19:14) (in thread): > @Desire Oluwarotimipls can you explain i am a bit lost, is the first experiment correct ? or i should go ahead and add Control, MPTP, MPTP + Acu and MPTP + Non-Acu. ? the is the link so you understand better .Download article.pdfSupplementary data.docx

Aleru Divine (09:26:55) (in thread): > @Peace DanielI believe Parkinson’s disease is the condition.

Peace Daniel (09:27:44) (in thread): > I thought so as well but what was being studied was FGF21

Bolanle Wahab (09:27:44) (in thread): > @Peace DanielWhy not go for Just PD? > The study observed the effect of FGF21 on PD mice , it’s not a condition

Aleru Divine (09:28:12) (in thread): > @Peace DanielThe researchers were investigating the effects of fibroblast growth factor 21 (FGF21) on Parkinson’s disease (PD) using a mouse model

Peace Daniel (09:28:51) (in thread): > And I just editedParkinson’sdisease:sweat_smile:Alright, thanks for the clarification

Peace Daniel (09:29:26) (in thread): > But can you take a look at this > > The Condition is what is being contrasted in the experiment, not something shared by both groups. > Example: objective: To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients. > Condition: effect of a probiotic strain Bacillus clausii UBBC-07, not IBD.

Desire Oluwarotimi (09:29:53) (in thread): > @Akinbode MariamI don’t quite understand what you have as your first experiment. > > But you should have; > Controls vs MPTP > Controls vs MPTP + Acu > MPTP vs MPTP + Acu.

Aleru Divine (09:30:27) (in thread): > Well:thinking_face:let me read again:nerd_face:

Peace Daniel (09:31:31): > Hello@Chioma Onyido@Esther Afuape@Peace SandyThere’sa duplicate curation on this study with PMID:30366118Andthey’veboth been reviewed

Aleru Divine (09:33:05) (in thread): > Where did you get the above reference from?:pray:

Peace Daniel (09:33:24) (in thread): > From the canvas in this slack group

Akinbode Mariam (09:33:31) (in thread): > @Peace DanielPD is the condition looks similar to what im working on. pls can you guys help me out, im not sure my experiment is meant to be just 1, what do you think ?https://bugsigdb.org/Study_995 - Attachment (BugSigDB): Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson’s disease - BugSigDB > Growing evidences show that gut microbiota is associated with the pathogenesis of Parkinson’s disease (PD) and the gut-brain axis can be promising target for the development of the therapeutic strategies for PD.

Peace Daniel (09:33:47) (in thread): > I’vebeen thinking for awhile now, thanks for joining in@Aleru Divine:sweat_smile:

Akinbode Mariam (09:34:11) (in thread): > okay thank you

Peace Daniel (09:34:36) (in thread): > Okay@Akinbode Mariamwill take a look

Aleru Divine (09:35:17) (in thread): > @Peace DanielI think FGF21 is an intervention and not the condition.So I still stand with PD.Would like to hear from the mentors.@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy:pray:

Peace Daniel (09:36:05) (in thread): > Alright, hoping to get some feedback soon

Peace Daniel (09:38:20) (in thread): > Thanks for your feedback,I’llbe reverting back toParkinson’sdisease till I get a different view:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Aleru Divine (09:38:34) (in thread): > Checking this out now@Akinbode Mariam

Aleru Divine (09:38:57) (in thread): > Okay@Peace Daniel:sweat_smile:

Mildred Anashie (09:40:19) (in thread): > The condition isParkinson’sdisease@Peace Daniel

Desire Oluwarotimi (09:41:34) (in thread): > @Peace DanielThe condition is Parkinson’s Disease. > > It was only checking the effect of FGF21 on PD.

Peace Daniel (09:42:18) (in thread): > Thank you all,Parkinson’sit is

Aleru Divine (09:43:04) (in thread): > Thanks everyone:heart:

Peace Daniel (09:46:55) (in thread): > @Akinbode Mariamwere randomly allocated into four groups: the control group (only saline, n = 6), the MPTP group (n = 10), the MPTP + Acu group (n = 9), and the MPTP + Non-acu (n = 5).

EBERE ADEKOGBE (09:49:00) (in thread): > @Mildred Anashie@Scholastica UruaThank you for your reviews. Will make the necessary corrections, but concerning the PMID I did add it, but it was not auto generating that is why I left it blank. Concerning that of the group names, I used the OK group and it was not accepting it so I decided to go with the L and N group.

Bolanle Wahab (09:49:15) (in thread): > @Akinbode Mariamthere’s more than one experiment: > Control vs MPTP > CONTROL vs MPTP +Acu > Control vs MTPT + non acu > MPTP Acu vs MPTP non-acu > There’s probably more, still checking

Aleru Divine (09:52:10) (in thread): > @Akinbode MariamI see 4 groups mentioned in the animals and group allocation. > 1. Control group > 2. MPTP group > 3. MPTP + Acu group > 4. MPTP + Non-acu group > So I don’t think your experiment should be 1 > > > Going further I see comparisons for control, MPTP and MPTP + Acu group. > > There should be about 3/4 experiments:thinking_face:. I’m still looking at the paper - File (JPEG): IMG_7962

Desire Oluwarotimi (09:53:30) (in thread): > I mentioned the MPTP + Non acu earlier but the reason I left it out for grouping was because I didn’t see any differential results done for it. > > I probably missed it.

Mildred Anashie (09:54:23) (in thread): > Yes the experiment and groups listed by@Peace Danieland@Aleru Divineis what I observed too > You have about 3 experiments with alpha diversity but with significant results for just two(supp Table S1) > Check your supplemental information Fig S1 is showing the diversity indices

Scholastica Urua (09:54:34) (in thread): > @EBERE ADEKOGBEyou should try the PMID again, maybe it was a network glitch. Hopefully it works this time

EBERE ADEKOGBE (09:55:00) (in thread): > Probably so. I will try it again

Aleru Divine (09:55:21) (in thread): > You’reright@Desire Oluwarotimiand@Mildred Anashie

Peace Daniel (10:23:30): > Hi Aishat on BugSigdb > You worked on study951, while going through missing ID’s I noticed your experiment 1 signature 1 for morococcus cerebrosus is1056807You should check it again and edit.

Peace Daniel (10:25:14) (in thread): > Also you should add your PMID to your curation

Mildred Anashie (10:34:15) (in thread): > @Akinbode MariamAlso the experiments I propose are > Control vs MPTP (signatures reported) > MPTP vs MPTP+Acu group (signatures reported) > Control vs MPTP+Acu (They might be significant results) > MPTP + Acu vs MPTP + Non Acu (no significant results) > > > Fig 4 and Fig S1 for the number of experiments and alpha diversity@Aleru Divineplease help confirm the statistical test used here and which should be curated between Table S1 or Fig 4G

Samreen Aftab (10:38:41): > Hello guys, basic query, but can anyone teach me how to read figures like these? For example, how can I draw conclusions about the differential abundances of signatures from this figure? - File (PNG): image.png

Aleru Divine (10:38:55) (in thread): > On it

Aleru Divine (10:40:37) (in thread): > Give me some time to load the paper:pleading_face:

Peace Daniel (10:40:43) (in thread): > Taxa’s with green bar in front are abundant in health, those in orange are abundant in positive and so on

Samreen Aftab (10:43:26) (in thread): > That’s simple:smiley:Thank you@Peace Daniel

Desire Oluwarotimi (10:46:17) (in thread): > @Samreen AftabTaxa in green bar is an increased abundance in health, orange an increased abundance in positive and blue an increased abundance in MD.

Aleru Divine (10:50:34) (in thread): > @Mildred AnashieI say Fig 4G because the description of Table S1 is “List of bacterial genera with significant differences in relative abundance between gut microbiota of control, MPTP and MPTP+Acu groups.” Meaning it is showing the relative abundance. > > Curate Fig 4G it shows the differential abundance.

Desire Oluwarotimi (10:51:55) (in thread): > Why does@Mildred Anashiesay there may not be significant result for control vs MPTP + Acu?

Mildred Anashie (10:52:18) (in thread): > Okay, Thank you:blush:Was skeptical on which she should curate

Mildred Anashie (10:55:21) (in thread): > @Desire OluwarotimiI said there might be > > Because I was trying to figure out where the significant resultsshe’llbe curating isIf she’sworking with Fig 4G thenthere’ssignificant results for the experiment

Desire Oluwarotimi (10:57:43) (in thread): > Oooh. No issues. I get you now. > > I just wanted to know why you were doubting because I believe there’s significant results.

Samreen Aftab (11:09:56): > Can I say that environment is a confounder controlled for? - File (PNG): image.png

Desire Oluwarotimi (11:16:20) (in thread): > @Samreen AftabIn this case, I think No. > > That line was only trying to explain how each animals were housed and catered for.

Aleru Divine (11:17:24) (in thread): > I agree with@Desire Oluwarotimi.@Samreen AftabI don’t think this counts as a confounder.The animas were housed in a controlled environment.That’sdifferent thing.

Idiat Alli (11:53:33) (in thread): > Yea exactly

fetlework gubena arage (12:00:46) (in thread): > https://bugsigdb.org/Study_994Thank you all for your help here is the contribution. your feedback is appreciated.@Svetlana Ugarcina Perovic@Aleru Divine<@UBNSEMS3S> - Attachment (BugSigDB): Increased rectal microbial richness is associated with the presence of colorectal adenomas in humans - BugSigDB > Differences in the composition of the gut microbial community have been associated with diseases such as obesity, Crohn’s disease, ulcerative colitis and colorectal cancer (CRC).

Mildred Anashie (12:17:12) (in thread): > Hi@fetlework gubena arageif your contribution is ready for review by the mentors you should drop a comment on the issue on GitHub informing them there > > However if you need a fellow applicants review before submission then this is okay

Habiba Saad (13:04:28): > hey there everyone. hope all of you doing well. i have a question. do we have permission to edit missing NCBI IDs? if yes then do we have to mention it somewhere that we have corrected it?

Muqtadirat Yussuff (13:06:51) (in thread): > You have to get permission here before making an edit

Mildred Anashie (13:07:15) (in thread): > You can resolve them but before making edits you inform the mentors here stating what you found and what you intend to edit it to

Scholastica Urua (13:14:59) (in thread): > You have to mention the correction you found here so that the mentors can collaborate it. Then they’ll give you go ahead to edit.

Peace Daniel (13:23:18) (in thread): > Please confirmit’snot a curation by someone in this outreachy session,we’renot allowed to edit that

Samreen Aftab (13:37:01): > Why does it give contrasting results for Enterobacteriaceae, Pseudomonadaceae, and Streptococcaceae? - File (PNG): image.png - File (PNG): image.png

Scholastica Urua (13:48:31) (in thread): > Hi@Samreen Aftabfrom what the mentors said, a taxa can be both in the increase and decrease group.

Aleru Divine (13:50:39) (in thread): > It happens sometimes@Samreen Aftab:sweat_smile:Seen that twice today.

idiaru Angela (13:53:38) (in thread): > @Samreen Aftabsee thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710517652414799?thread_ts=1710516856.042729&cid=C04RATV9VCY - Attachment: Attachment > Ohh got it! > > “Different bacterial strains may have different biological properties due to the different genes: > for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98%” > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639

Samreen Aftab (16:09:32): > Are MGISEQ-2000 and MiSeq the same thing?

Mildred Anashie (16:12:24) (in thread): > I don’t think they are:thinking_face:Presumably No

Mildred Anashie (16:14:41) (in thread): > The MiSeq and MGISEQ-2000 are both types of sequencing platforms used in genomics research. > 1. MiSeq: It’s a benchtop sequencer manufactured by Illumina. It’s known for its flexibility, relatively low cost per run, and suitability for small to medium-sized projects. MiSeq is commonly used for targeted sequencing, amplicon sequencing, small genome sequencing, and microbial genomics. > 2. MGISEQ-2000: Produced by MGI Tech, a subsidiary of BGI Group, the MGISEQ-2000 is a high-throughput sequencing platform. It’s designed for large-scale genomic projects and can process a high volume of samples simultaneously. It’s known for its fast turnaround time and cost-effectiveness for large-scale projects such as population genetics, cancer genomics, and metagenomics. > Both platforms have their strengths and are used based on the specific requirements of the project, including throughput, cost, and turnaround time. > > Online search*

Peace Daniel (16:16:01) (in thread): > They’re not although I think they’re both used for sequencing

Samreen Aftab (16:17:21) (in thread): > My paper mentions MiSeq but it is not in the drop-down. What should I do?

Peace Daniel (16:18:28) (in thread): > I believeit’sillumina Yh?

Mildred Anashie (16:20:01) (in thread): > Just check, I think you might find Illumina or WMS

Samreen Aftab (16:21:03) (in thread): > Okayy, thank you!

Chioma Onyido (17:09:28) (in thread): > @Peace Daniel, for your question it depends. > I’d say everyone’s right about the condition being PD. Additional information: If they compared the FGF + MPTP against the MPTP group to access the effect of FGF (which I think they did in one of the LeFSE results) then the condition here will probably not be PD. Because both groups received MPTP shots (to induce PD right?), so for this experimentit’sreasonable to use FGF as the condition.

Samreen Aftab (17:09:41): > Hey guys! I’ve just wrapped up curating my second paper (phew, it took me a solid 12 hours!), and I’m feeling pretty accomplished right now. > This one was a bit trickier than the last, but I’ve learned a ton along the way. BigSigDB has been an awesome platform for me to dive into a whole new field that’s totally different from what I’m studying in college. > Here’s my curationhttps://bugsigdb.org/Study_997Here’s the paper:https://pubmed.ncbi.nlm.nih.gov/36362360/I’d love to hear your thoughts and feedback on the curation. Thanks a bunch for all your support!:heart: - Attachment (BugSigDB): Modulation of the Gut Microbiota in Memory Impairment and Alzheimer’s Disease via the Inhibition of the Parasympathetic Nervous System - BugSigDB > The gut microbiota has been demonstrated to play a critical role in maintaining cognitive function via the gut-brain axis, which may be related to the parasympathetic nervous system (PNS).However, the exact mechanism remains to be determined. - Attachment (PubMed): Modulation of the Gut Microbiota in Memory Impairment and Alzheimer’s Disease via the Inhibition of the Parasympathetic Nervous System - PubMed > The gut microbiota has been demonstrated to play a critical role in maintaining cognitive function via the gut-brain axis, which may be related to the parasympathetic nervous system (PNS). However, the exact mechanism remains to be determined. We investigated that patients with mild cognitive impair …

Scholastica Urua (17:11:05) (in thread): > Well done@Samreen Aftab:muscle:

Mildred Anashie (17:18:18) (in thread): > Well done@Samreen Aftab

Peace Daniel (17:33:39) (in thread): > Thank you@Chioma OnyidoYes it was compared FGF21 + MPTP vs MPTP > For the comparison between Control and MPTP is it safe to say this is Parkinson’s disease and the other FGF21? > > Also can I use FGF21 measurement since it was the closest I found on EFO?

Peace Daniel (17:36:20) (in thread): > Well done@Samreen Aftabwould let you know if I find anything:purple_heart:

Raihanat Adewuyi (17:45:12): > Hello@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy@Esther Afuape. I mistakenly added a signature twice and i would like for it to be deleted please. Signature 3 in experiment 1 from the below study. Thankshttps://bugsigdb.org/Study_935 - Attachment (BugSigDB): Systematic analysis of gut microbiome reveals the role of bacterial folate and homocysteine metabolism in Parkinson’s disease - BugSigDB > Parkinson’s disease (PD) is the most common progressive neurological disorder compromising motor functions.However, nonmotor symptoms, such as gastrointestinal (GI) dysfunction, precede those affecting movement.

Chioma Onyido (18:21:35) (in thread): > Hmmm…The definition of ‘FGF21 measurement’ on the ontology site makes me second guess (I might be wrong) using it as a suitable condition: “Quantification of the amount of fibroblast growth factor 21 in a sample”. > > Perhaps ‘response to treatment’ or ‘response to growth factor’?@Peace Sandy@Esther Afuapea likkle help here please..:eyes:

Chioma Onyido (18:23:34) (in thread): > Deleted.

idiaru Angela (18:55:24) (in thread): > Well done@Samreen Aftab

Abiola Salako (19:08:39) (in thread): > Yes@Samreen Aftabit’s that simple:joy:

Abiola Salako (19:12:55) (in thread): > What you shared didn’t point to any Confouder@Samreen Aftab

Abiola Salako (19:15:56) (in thread): > Well-done@Samreen Aftab

Aleru Divine (22:02:49) (in thread): > Well done@Samreen Aftab

Desire Oluwarotimi (23:34:43) (in thread): > Weldone@Samreen Aftab

2024-03-17

Scholastica Urua (00:59:42): > Hello everyone and Happy Sunday! How are we all doing today?:hugging_face:I just want to put this out here. During my second contribution, I made a mistake in my choice of study design, which was kindly corrected by@Chioma Onyidoduring her review and grading of my curation. My article repeatedly mentioned conducting a cross-sectional study so by default I chose that as a study design when, in fact, the appropriate design should have been a case-control study (it was obvious too:sweat_smile::sweat_smile:). > > While browsing through the pinned messages, I stumbled upon some valuable information by<@U1LCB8WEA>that I found particularly helpful. I thought it might be beneficial to share it in case someone else encounters a similar situation and wants to avoid making the same mistake in the future. > > Thanks to the help from the mentors and my fellow contributors, I’m improving day by day.:heart_hands: - File (JPEG): Study design.JPG

Scholastica Urua (01:01:19) (in thread): > Here’s a link to the thread, in case you want to read the rest;https://community-bioc.slack.com/archives/C04RATV9VCY/p1678803364578459 - Attachment: Attachment > Hi everyone - we are behind on reviewing second contributions, so I have a request: if you have done second contribution, please wait until it is reviewed before starting on a third contribution. Otherwise, we are worried about having you move ahead too far before getting feedback, which could result in repeating the same mistakes. Instead, I would recommend a couple other things if you have more time you’d like to spend on bugsigdb: > 1. review your own contribution again on anything you’re unsure of, keeping in mind that accuracy is the primary concern and the most important aspect we will be assessing. Some common mistakes are: a) incorrect study design. For example, if participants are selected for an observational study based on the outcome or exposure of interest, then this is a case-control study. If they are selected without regard to the outcome or exposure and then the outcome/exposure are simply identified, then this may be a “cross-sectional observational, not case-control”. Case-control is much more common. b) Entering for Condition something that is shared by all participants, rather than what was contrasted between group 1 and group 0. Or, entering for Condition or Body site an ontology term that is too specific, not specific enough, or entering multiple terms when a single term would be more precise and correct. c) Entering invalid taxa when these could have been mapped to valid terms in the NCBI taxonomy. If your microbial names are showing in orange then check again whether it is possible to match them to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi . Not all taxa can be mapped, so if you cannot find a valid match then leave it as-is. See https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID for some challenges that have and haven’t been solved in the wiki, and a long video of me trying to solve scientific nomenclature problems. d) basic errors like reversing the “increased” and “decreased” abundance in group 1 signatures, putting the control group as group 1, entering taxa that weren’t identified as significantly different, or not entering taxa that were identified as significantly different. > 2. You could look at at https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID to see if there are any taxonomic issues you think you can solve (very challenging!) or at the corresponding page (https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID). I would rather that for now you not yet make corrections in the wiki, but resolving scientific nomenclature would be a very interesting discussion to have here.

Adedoja Isaac (01:41:09) (in thread): > Thank you for bringing out this thread:pray:

Manisha Nair (01:41:12): > Hello everyone, I’ve completed my first article curation. Please review my curation as this is completely different from the field I study. > Please help in rectifying or addressing any missing elements. > My curation:https://bugsigdb.org/Study_990Link to the article:https://journals.asm.org/doi/10.1128/spectrum.00189-23 - Attachment (BugSigDB): The efficacy of prevention for colon cancer based on the microbiota therapy and the antitumor mechanisms with intervention of dietary Lactobacillus - BugSigDB > Gut microbiota and their secreted metabolites have an influence on the initiation and progression of colon cancer.

Aleru Divine (02:05:26) (in thread): > Thank so much for sharing this@Scholastica Urua:heart:

Peace Daniel (02:28:05) (in thread): > Good morning@Chioma OnyidoI found FGF21 on the ontology site butcouldn’tfind it on BugSigdb

Chioma Onyido (03:26:46) (in thread): > Hmmm the ‘FGF21’ you identified is probably not an EFO term..?Let’swait to have the input of other mentors, which will most likely be by Monday.

Peace Daniel (03:31:07) (in thread): > Okay, thank you

Ifeyinwa Ohondu (03:32:14): > Hi guys. When the name of the taxon does not autocomplete on bugsigdb and we do a search on NCBI and find it’s a hypotypic synonym or basionym. Do we go ahead and use the current name or type in the numerical tax ID?

Habiba Saad (03:34:32) (in thread): > use the current name and if you find the synonym then add the ncbi id of it.

Aleru Divine (03:35:38) (in thread): > If it’s a synonym, then it’s fine. It is stated in the curation policy@Ifeyinwa OhonduYou can go ahead and use the ID.

Chioma Onyido (03:40:02) (in thread): > Yeah you can go ahead with the rest of your curation.:+1:

Ifeyinwa Ohondu (03:42:17) (in thread): > Okay. Thanks@Habiba Saadand@Aleru Divine

Ruth Bamgbose (03:45:23) (in thread): > Thanks for sharing this@Scholastica Uruait is really helpful:sparkles:

Desire Oluwarotimi (04:12:45) (in thread): > This is kind of you. > > Thank You@Scholastica Urua

Flourish Ralph (04:24:58) (in thread): > Thank you for this@Scholastica Urua

Mildred Anashie (04:41:50) (in thread): > Thanks@Scholastica Urua:heart:Study designs can be confusing most times

Mildred Anashie (04:43:39) (in thread): > You paste the ID of the synonym it’s accepted on BugSigdb andit’llautomatically replace the name when you mark the page as complete

Blessing Ene Anyebe (04:58:08) (in thread): > Thank you for sharing@Scholastica UruaIt is beautiful to see you sharing your learning in this way as well. Well-done:orange_heart:

Habiba Saad (05:01:35): > hey there i have found the missing signature of erysipelotrichaceae UCG-003 by an alternative name of bacterium LF3 on midas field guide. is this correct? kindly guide me mentors@Svetlana Ugarcina Perovic@Peace Sandy - File (PNG): 1st.PNG - File (PNG): 2nd.PNG

Habiba Saad (05:10:19) (in thread): - File (PNG): 3rd.PNG

Scholastica Urua (05:43:00) (in thread): > Hello@Manisha Nair, well done on your curation. > > Your study correctly identifies two distinct groups, which aligns with your curation:+1:. However, I observed a few points that may need attention: > > The appropriate statistical test to measure taxa significantly abundant in the contrasting group should be LefSe (in your curation), not ANOVA or T-Test. > > The significance threshold (P-value) is set at 0.05. > > I also noticed that the signatures for both experiments are incomplete. Figure 3 illustrates additional taxa that should be included. > > These are some of the things I observe, I don’t know if anyone else has a varying opinion.:pray: - File (JPEG): 2.JPG

Faith Ifeoluwa Alexander (05:52:33) (in thread): > Hello@Habiba Saad. Good morning. I believe that since you found the taxa with the same name on the NCBI website, then it is correct. > > Before@Svetlana Ugarcina Perovicresponds, I hope my input helped.

Faith Ifeoluwa Alexander (05:56:29) (in thread): > In my case, I used a mix of both. If you input the numerical ID, it will automatically change to the name when it displays on the signature part of the main page of the study.

Modinat Ganiyu (06:02:28) (in thread): > Thanks for sharing@Scholastica UruaThis is helpful

Faith Ifeoluwa Alexander (06:09:17) (in thread): > This is quite helpful. Thank you@Scholastica Urua.

Faith Ifeoluwa Alexander (06:17:34): > Phew! I just finished my second contribution and I must say it was a daunting task. I learnt a lot and understood how to curate a study better.
> > I went from thinking I had to add one experiment to adding 16 experiments and at some point, I made some mistakes. But all in all, I had a helpful community back here that helped guide me through it all. > > I am thankful for all the help I was able to get from you all as they made this contribution much easier than it would have been without help. > > Here is the link to my study:https://bugsigdb.org/Study_971Here is also the link to the article I curated:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884491/Pls, help me do a quick review of it and point my attention to anything I might have left out. > > Thank you so much, everyone. It was quite insightful working here with eveyone. - Attachment (BugSigDB): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders.PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS). - Attachment (PubMed Central (PMC)): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders. PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous …

Faith Ifeoluwa Alexander (06:22:19): > I would like to give back the support I was given to anyone who needs it. So I would be giving my support to anyone who needs it in this beautiful community. > > Once again, I am thankful to everyone who helped me out while curating my study. Thank you so so much!!:pray:

Manisha Nair (06:46:06) (in thread): > Thank you so much@Scholastica Urua

idiaru Angela (06:46:21) (in thread): > Well done@Faith Ifeoluwa AlexanderI’ll check it out and give you feedback

Habiba Saad (07:01:24): > are all these same? the signature Ruminococcaceae_NK4A214 found on midas field guide is only with a name NK4A214 and a family ofOscillospiraceae. when found on ncbi taxonomyOscillospiraceaeheterotypic name appear asRuminococcaceae. is this correct or just garbage in and garbage out? @Svetlana Ugarcina Perovic**** ****@Peace Sandy**** ****<@UBNSEMS3S>**** **** - File (PNG): bug.PNG - File (PNG): midas.PNG - File (PNG): ncbi.PNG

Faith Ifeoluwa Alexander (07:01:48) (in thread): > Thank you so much.

Evelyn Mary Attah (07:05:02): > Hello@Scholastica Urua@Desire Oluwarotimi, Kindly assist me with reviewing my curation and here’s the link=https://bugsigdb.org/Study_987, . Was a bit confusing and hoping for some clarifications especially about the NCBI area. Thank you very much:heart: - Attachment (BugSigDB): Interaction between Cervical Microbiota and Host Gene Regulation in Caesarean Section Scar Diverticulum - BugSigDB > Cesarean section scar diverticulum (CSD) has become a formidable obstacle preventing women receiving CS from reproducing.However, the pathogenesis of CSD remains unexplored.In this study, we characterized the cervical microbiota, metabolome, and endometrial transcriptome of women with CSD.

Faith Ifeoluwa Alexander (07:05:44): > Pls, what do I do after finishing my study curation. Do I need to do anything?

Blessing Ene Anyebe (07:07:09) (in thread): > Inspiring:sweat_smile:Congratulations@Faith Ifeoluwa Alexander:orange_heart:

Modinat Ganiyu (07:07:20) (in thread): > Well done@Manisha NairYou’ve done great@Scholastica Uruais right. The significance threshold (P-value) is 0.05 instead of 0.0001 > > Also, the statistical test to measure taxa should be LefSe and not ANOVA or T-Test. > > Lastly, I feel the experiments should be 3. The last one should be between the Living bacteria group (LB) and Inactivated bacteria group (IB). I’m seeing some valid details about the 2 groups (This is what I observed, I don’t know if anyone else has a contradicting opinion.:pray: - File (PNG): image.png

Manisha Nair (07:08:09) (in thread): > Thanks a lot@Modinat Ganiyu

Aleru Divine (07:08:12) (in thread): > Hi@Faith Ifeoluwa Alexanderyou can submit the link to the study for curation. Submit the same way you request to claim on GitHub. > > Then proceed to the outreachy website to record your contribution. > > Link to contribution is the link to your study.

Bolanle Wahab (07:08:14) (in thread): > Well done:heart:@Faith Ifeoluwa Alexander

Scholastica Urua (07:08:44) (in thread): > You need to put it up for review by commenting under the GitHub issue. Then proceed to record on Outreachy site.

idiaru Angela (07:08:46) (in thread): > @Faith Ifeoluwa Alexanderyou can first wait for co contributors interested in reviewing your curation to do that. > Then when you’re satisfied with the curation, comment on the issue asking for a review with the study link on Github. Don’t forget to record your contribution on outreachy

Scholastica Urua (07:09:54) (in thread): > Hi@Evelyn Mary Attah, I’ll get on it as soon as possible:pray:

Faith Ifeoluwa Alexander (07:11:01): > And am I to register my curation on the outreachy website now?

Mildred Anashie (07:11:46) (in thread): > Yes you are@Faith Ifeoluwa Alexander

Mildred Anashie (07:12:01) (in thread): > You can leave the merge date tillit’sreviewed

Muqtadirat Yussuff (07:12:29) (in thread): > Yes and for the merged date, you’d fill that when the mentors have reviewed it

Aleru Divine (07:12:42) (in thread): > Yes I agree with@idiaru Angela, before you submit please make sure you have no other edits to make as it is not acceptable.So submit after feedback from co-contributors > > Once you submit for review, youaren’tallowed to make anymore edits.:pray:

Faith Ifeoluwa Alexander (07:13:48) (in thread): > Okay. Let me wait for co-contributor to review it then before submitting. Pls, I have put a link to the study in an earlier post. Pls, anyone is welcome to help me look through it.

Scholastica Urua (07:14:06) (in thread): > Yes, you are

Habiba Saad (07:17:33) (in thread): > @Mildred Anashiedo we have to leave the merge date blank?? if so how do we know if our curation is reviewed?

Mildred Anashie (07:18:13) (in thread): > You will see the review on the issue on GitHub and the review tag will also be added

Scholastica Urua (07:42:02) (in thread): > @Habiba Saadyou’ll leave the merged date until your curation is reviewed. In addition to what@Mildred Anashiesaid, when your curation is reviewed GitHub will also send you a notification mail.

Scholastica Urua (07:49:26) (in thread): > @Modinat GaniyuI saw that comparison between LB and IB group too but the study also mentioned there was no statistical difference between LB group and IB group. That’s why I didn’t mention it. Or should it be curated?:thinking_face:

Habiba Saad (07:50:28) (in thread): > and for signature 2 write lactobacillus not lactobacilli as written in figure 1

Desire Oluwarotimi (07:54:54) (in thread): > Hi@Evelyn Mary AttahHere’s the details of what I noticed; > > I think your statistical test should be just LEfSe and not Spearman correlation. Spearman correlation was used for other things aside determining differential abundance. > > Also, I think the source for your signatures are wrong. Fig 2a is the figure that you can curate and it should be the source.

Desire Oluwarotimi (07:55:28) (in thread): > @Aleru Divine@Mildred AnashieDo you guys mind taking a look at this?

Manisha Nair (07:56:17) (in thread): > @Scholastica UruaI’m having difficulty in undertaking the figure 3g. The green bars indicate taxa that increased in living group and orange indicates the taxa that is decreased in control group right? > Also, how do I figure out the taxa decreasing in living group.

Habiba Saad (08:00:23) (in thread): > @Desire Oluwarotimii think you are right.

Aleru Divine (08:02:03) (in thread): > Checking it out now:pray:@Desire Oluwarotimi

Mildred Anashie (08:03:40) (in thread): > Okay > On it@Desire Oluwarotimi

Scholastica Urua (08:06:19) (in thread): > So the results for both experiments are from the same source (fig 3g). The first image is Control (red) vs Living (green). So those with green bars will be documented under increased abundance for LB while those with red bars will be decreased abundance for LB. > > I don’t know if you get my point@Manisha Nair

Aleru Divine (08:12:45) (in thread): > You’re correct@Desire Oluwarotimi.:thumbsup:An excerpt to further confirm this “LEfSe (linear discriminant analysis effect size) was used for differential analysis of cervical microbiota abundance.” > > This is what spearman’s correlation was used for@Evelyn Mary Attah“We used Spearman correlation analysis to construct the correlation network between genus in Microbiome Analyst with R > 0.8 and P < 0.05 as cutoff values” > > Source of microbial signatures is Fig 2A > > Correct again@Desire Oluwarotimi:clap::clap:

Desire Oluwarotimi (08:13:44) (in thread): > Thank You.@Aleru Divine:pray:

Scholastica Urua (08:14:40) (in thread): > I agree with@Desire Oluwarotimi. Statistical test should be Lefse and figure 2a be curated instead. Also LDA is 2 not 3. Still going through it for more details…

Mildred Anashie (08:14:41) (in thread): > I totally agree with this@Desire Oluwarotimiand@Aleru Divine

Desire Oluwarotimi (08:15:07) (in thread): > Thank You.@Mildred Anashie

Modinat Ganiyu (08:15:14) (in thread): > @Scholastica UruaThat’s my thought anyway:blush:and it’s weekend,@C. Mirzayi (please do not tag this account)<@U1LCB8WEA>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandywould have clarified it for us

Faith Ifeoluwa Alexander (08:15:19): > @idiaru Angelapls have you been able to go through my curation?@Mildred Anashie,@Joan C. Chukwuemeka,@Aleru Divine,@Desire Oluwarotimi,@Adedoja Isaac,@Scholastica Uruapls help me review my curation.:pray:

Desire Oluwarotimi (08:15:24) (in thread): > Thank You@Scholastica Urua

Aleru Divine (08:15:35) (in thread): > That’scorrect@Scholastica Urua

Aleru Divine (08:15:52) (in thread): > Thanks everyone:pray::saluting_face:

Aleru Divine (08:18:43) (in thread): > Will go through this now@Faith Ifeoluwa Alexander

Manisha Nair (08:19:27) (in thread): > @Scholastica Uruathanks for clarification. I’m understood your explanation. > > I have one more question. I read that ‘c_clostridia’ refers to class Clostridia belonging to order Clostridiales. Should I include both separately, or is it sufficient to only write ‘Clostridiales’? There are several others like this in the barchart. - File (JPEG): IMG_20240317_174612.jpg

Scholastica Urua (08:19:50) (in thread): > What do we think about the data transformation? Relative abundance instead?:thinking_face:

Mildred Anashie (08:20:04) (in thread): > Okay@Faith Ifeoluwa Alexander

Mildred Anashie (08:21:01) (in thread): > Thank you for picking that@Scholastica UruaYesit’sRelative abundance not raw counts

Desire Oluwarotimi (08:22:12) (in thread): > Yes@Scholastica UruaYou are right.

Aleru Divine (08:23:57) (in thread): > Additionally, theyweren’tmatched on any factors.

Mildred Anashie (08:29:14) (in thread): > No they were not > > So@Evelyn Mary AttahThe data transformation here is Relative Abundance:white_check_mark:No Matched on:white_check_mark:Signature source is Fig 2a not Figure 1:white_check_mark:Statistical test is just LEfSe:white_check_mark:Every other thing is okay, well done:thumbsup:Also when you enter taxas and they appear in orange, you can search for them on NCBI and copy the ID and paste on BugSigdb to replace the orange taxas, I hope this is clear > > Observations from@Desire Oluwarotimi@Aleru Divine@Scholastica Urua

Desire Oluwarotimi (08:31:41) (in thread): > @Faith Ifeoluwa AlexanderAntibiotics exclusion is 3 months.

Scholastica Urua (08:34:15) (in thread): > Will go through it too@Faith Ifeoluwa Alexander

Scholastica Urua (08:37:05) (in thread): > @Manisha NairI haven’t been able to load up the image you dropped. But from the source fig 3g both are mentioned as increased. Firstly it’s “Order: Clostridiales belonging to the Class: Clostridia” (not the other way round, I think:thinking_face:). Personally, I’d curate both because there are more than one ‘order’ in a ‘class’ and it could be talking about any one of them. But I’m not really sure:disappointed_relieved:.@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeplease we’ll appreciate your input here:pray:

Manisha Nair (08:41:19) (in thread): > @Scholastica UruaReally appreciate your help:blush:Also, should I add a third experiment as suggested by@Modinat Ganiyu. Please clarify@Svetlana Ugarcina Perovic@Chioma Onyido<@U1LCB8WEA><@UBNSEMS3S>

Faith Ifeoluwa Alexander (08:45:16) (in thread): > @Desire OluwarotimiAntibiotics was stated not to be reported in the article.

Faith Ifeoluwa Alexander (08:47:50) (in thread): > @idiaru AngelaBut the Mann-Whitney Test was also mentioned in the article. Now I am confused.

Faith Ifeoluwa Alexander (08:50:19) (in thread): > ANOVA was used to measure Alpha Diversity@idiaru Angela

idiaru Angela (08:51:04) (in thread): > Oh you’re right@Faith Ifeoluwa Alexander

Mildred Anashie (08:52:14) (in thread): > ANOVA was used for Alpha diversity@idiaru AngelaMann Whitney was used for the OTU counts

Faith Ifeoluwa Alexander (08:53:33) (in thread): > @Desire Oluwarotimisee the screenshot below for the Antibiotics report. - File (JPEG): Screenshot_20240317-135221.jpg

Desire Oluwarotimi (08:54:13) (in thread): > @Faith Ifeoluwa AlexanderYes, I’ve seen that. > You are right.

Mildred Anashie (09:03:14) (in thread): > I think your Data transformation is Raw counts and not Relative abundance

Faith Ifeoluwa Alexander (09:07:10) (in thread): > @Mildred Anashiebut all over the paper, what was reported was Relative Abundance. Not a mention of raw counts.

EBERE ADEKOGBE (09:09:38) (in thread): > Thank you@Scholastica Uruafor sharing

Faith Ifeoluwa Alexander (09:12:31) (in thread): > @Mildred Anashiewhy do you think it is raw counts?

Mildred Anashie (09:27:14) (in thread): > Let me try to confirm my statement > > I might be wrong, still cross checking though

Evelyn Mary Attah (09:38:54) (in thread): > Thank you so much for the clarity @everyone, really helpful

Mildred Anashie (09:54:54) (in thread): > This was confusing me - File (JPEG): IMG_2432

Mildred Anashie (09:55:29) (in thread): > It’sclearer now@Faith Ifeoluwa AlexanderYou are right - File (JPEG): IMG_2433

Adedoja Isaac (09:58:54) (in thread): > Okay@Faith Ifeoluwa AlexanderWill go through too

Aleru Divine (10:00:08) (in thread): > Idon’tsee any problem so far.I’mgoing through the signatures right now.I’ma bit confused I hope I get a hang of it.:pray:

Faith Ifeoluwa Alexander (10:01:25) (in thread): > What are you confused about pls?@Aleru Divine

idiaru Angela (10:04:44) (in thread): > @Faith Ifeoluwa Alexandergoing through I didn’t notice any revisions:blush:

Joan C. Chukwuemeka (10:07:39) (in thread): > Okay…@Faith Ifeoluwa AlexanderI’ll revert here, when I do.

Manisha Nair (10:10:47) (in thread): > @Scholastica Urua@Modinat GaniyuI’ve included the rectifications (except adding a third experiment). Please take a look.

Aleru Divine (10:12:51) (in thread): > @Faith Ifeoluwa AlexanderI don’tsee Peptostreptococcaceae on the table or text.How did you get that?

Faith Ifeoluwa Alexander (10:14:29) (in thread): > Yes. It’s the synonym for Clostridales. I registered it but it kept showing red so@Joan C. Chukwuemekashowed me the taxa synonym on NCBI

Aleru Divine (10:14:50) (in thread): > Okay:thumbsup:

Faith Ifeoluwa Alexander (10:15:38) (in thread): > What do you mean by revision?@idiaru Angela

Aleru Divine (10:16:15) (in thread): > It seems like you recorded relative abundances > > “The Clostridiales family XI and the genus Peptoniphilus were observed at higher relative abundances in the PD dataset.”We’reonly to curate the differential abundance

Faith Ifeoluwa Alexander (10:19:20) (in thread): > I don’t think so@Aleru Divinebecause the signature section automatically populated the rest of increased or decreased relative abundance part for me. And the results were reported in relative abundance.

Faith Ifeoluwa Alexander (10:21:17) (in thread): > Why did you think it’s differential abundance that should be recorded?

Aleru Divine (10:23:36) (in thread): > BugSigDB curates only differential abundance

Faith Ifeoluwa Alexander (10:25:28) (in thread): > So where will I find the differential abundance in the article? And how do I record it?

Evelyn Mary Attah (10:31:55) (in thread): > Hello@Mildred Anashie, Can you kindly put me through on this “Also when you enter taxas and they appear in orange, you can search for them on NCBI and copy the ID and paste on BugSigdb to replace the orange taxas” Not really clear please, Thank you.

Aleru Divine (10:32:15) (in thread): > According to your curation, you said you used table 2. > > That shows the differential abundance. > > Whatever you’re curating from the text should not be relative abundance as that is not to be curated.

Faith Ifeoluwa Alexander (10:33:35) (in thread): > So where do I find it, can you send a screenshot of which part of the article, I should use for my signature?

Faith Ifeoluwa Alexander (10:34:37) (in thread): > Pls, where do I make corrections specifically?

Aleru Divine (10:35:22) (in thread): > Search whatever taxa appears in orange in the taxonomy browser. > > Copy the ID and paste in place of the name, it should replace the name. > > Taxonomy browser link:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Aleru Divine (10:35:57) (in thread): > Ididn’tgo through all the signatures.I just wanted to make sure youweren’trecording relative abundance.

Aleru Divine (10:36:36) (in thread): > It seems like all your signatures were gotten from text. It should be from the table. I thought you used the table since you mentioned it as your source.

Mildred Anashie (10:36:50) (in thread): > Thank you@Aleru Divine

Faith Ifeoluwa Alexander (10:37:47) (in thread): > I asked if I was to record figures but I was told it was the names of the taxa that I should record.

Akinbode Mariam (10:38:11) (in thread): > Thank you all so much i will go ahead and correct it now@Peace Daniel@Aleru Divine@Desire Oluwarotimiand@Mildred Anashie

Faith Ifeoluwa Alexander (10:38:33) (in thread): > The text I used was under the Table I cited. The text better explained the results in the table.

Faith Ifeoluwa Alexander (10:39:10) (in thread): > Can you pls make me understand this cuz it looks like I have been wasting time thinking I was doing the right thing.

Aleru Divine (10:39:55) (in thread): > Idon’tunderstand the table.That was why I was confused earlier.:cold_sweat:

Faith Ifeoluwa Alexander (10:40:09) (in thread): > I remember citing the description for my signature here and everyone said I was doing the right thing.

Mildred Anashie (10:42:07) (in thread): > @Aleru Divineit was a bit confusing for me because I didn’t find differential abundant results > > I hopeI’mnot mixing things up

Aleru Divine (10:42:28) (in thread): > I thinkit’sthe table 2

Mildred Anashie (10:43:11) (in thread): > But just Table 2 seems to be showing curatable results

Faith Ifeoluwa Alexander (10:43:11) (in thread): > I cited Table 2 in my signature description.

Aleru Divine (10:43:38) (in thread): > Not just citing it, you have to curate the data from it

Faith Ifeoluwa Alexander (10:44:05) (in thread): > Pls, can you explain further and simpler cuz I am lost right now.

Aleru Divine (10:45:24) (in thread): > Table 2 contains curatable results for your signatures.The texts talks more about relative abundance.

Faith Ifeoluwa Alexander (10:46:06) (in thread): > So am I to input the numbers in table 2?

Faith Ifeoluwa Alexander (10:46:24) (in thread): > And how do I go about inputting the numbers?

Faith Ifeoluwa Alexander (10:51:55) (in thread): > @Aleru Divinepls make what you are saying understandable to me. I am so lost right now cuz I don’t know what you mean.

Aleru Divine (10:53:01) (in thread): > The taxa is what you’re inputting not numbers. The taxa in the table. Now the problem is interpreting the table.Ihaven’tfigured it out yet.

Faith Ifeoluwa Alexander (10:55:48) (in thread): > I have gone back to the Table and the table shows their p values. I believe that the text below explains the Table in words.

Faith Ifeoluwa Alexander (10:58:04) (in thread): > If we are to interpret the table, don’t you think that will be a task that is too technical for a literature review?

Aleru Divine (10:59:07) (in thread): > My problem is the “relative abundance” keyword.

Faith Ifeoluwa Alexander (11:05:48) (in thread): > I found this reviewed paper and this is a screenshot of it. - File (JPEG): Screenshot_20240317-160503.jpg

Faith Ifeoluwa Alexander (11:07:05) (in thread): > This reviewed paper used relative abundance to describe all its signatures.

Faith Ifeoluwa Alexander (11:07:14) (in thread): > And it is a reviewed paper.

Aleru Divine (11:09:00) (in thread): > From one of the mentorshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710327215805919?thread_ts=1710265890.754799&channel=C04RATV9VCY&message_ts=1710327215.805919 - Attachment: Attachment > Our focus on bugsigdb is differential abundance results, gene expression results on the other hand are not curated on bugsigdb.

Aleru Divine (11:12:59) (in thread): > I guess we need to take this to the mentors.I am confused too:pray:

Faith Ifeoluwa Alexander (11:14:17) (in thread): > I searched for the word differential abundance on google & this was the result. - File (JPEG): Screenshot_20240317-161323.jpg

Faith Ifeoluwa Alexander (11:15:26) (in thread): > In other words, either the abundance of the taxa was increased or decreased.

Faith Ifeoluwa Alexander (11:16:05) (in thread): > Okay, walk me through how you have been curating your paper.

Adedoja Isaac (11:17:09): > Hi@Chioma Onyido@Peace Sandy@Levi Waldron@Svetlana Ugarcina PerovicPlease when recording the signature data, should I be focusing on relative abundance or differential abundance?

Aleru Divine (11:17:56) (in thread): > I have been curating differential abundance and not relative abundance.Usually from a table, figure or stated in the text.Relative abundance is usually also stated but Idon’tcurate anything that has to do with relative abundance.

Aleru Divine (11:18:45) (in thread): > Here’ssomething to helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710327215805919?thread_ts=1710265890.754799&channel=C04RATV9VCY&message_ts=1710327215.805919 - Attachment: Attachment > Our focus on bugsigdb is differential abundance results, gene expression results on the other hand are not curated on bugsigdb.

Faith Ifeoluwa Alexander (11:19:41) (in thread): > Okay. How is the differential abundance being reported in your paper?

Faith Ifeoluwa Alexander (11:20:05) (in thread): > Like how do you recognize the differential abundance?

Aleru Divine (11:21:26) (in thread): > It is usually stated in text or the description of a table or a figure.Sometimes not exactly “differential abundance” but it’s never “relative abundance”

Mildred Anashie (11:26:20) (in thread): > Yea@Adedoja Isaacjust like what it says in what Divine shared > > You focus on differential abundance

Evelyn Mary Attah (11:39:21) (in thread): > @Aleru Divine@Mildred Anashie@Scholastica Urua@Desire OluwarotimiThank you so much, really appreciate:heart:

Blessing Laweh (11:58:44): > Hello Team. Thanks for your help all through, you guys are amazing!!! > > I’m done with curating a paper and it needs review. I’d greatly appreciate if anyone can help me with the review, thanks.:heart_hands:https://bugsigdb.org/Study_988 - Attachment (BugSigDB): Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing - BugSigDB > The microbiota plays an important role in human health and disease development.The lung microbiota profile in pulmonary tuberculosis (TB) patients and the > effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively.

Samreen Aftab (12:06:54): > If anyone is free, can you review my paper?https://bugsigdb.org/Study_997I’d love to review yours :) - Attachment (BugSigDB): Modulation of the Gut Microbiota in Memory Impairment and Alzheimer’s Disease via the Inhibition of the Parasympathetic Nervous System - BugSigDB > The gut microbiota has been demonstrated to play a critical role in maintaining cognitive function via the gut-brain axis, which may be related to the parasympathetic nervous system (PNS).However, the exact mechanism remains to be determined.

EBERE ADEKOGBE (12:17:08) (in thread): > Yes,@Adedoja Isaac. Focus on differential Abundance, as they both rightly said!

idiaru Angela (12:37:01) (in thread): > Sure@Samreen AftabI’ll review and give feedback

Isoken Ibizugbe (12:43:59) (in thread): > I’ll like to review it.

Idiat Alli (12:45:31) (in thread): > Very correct answers:ok_hand:

Adedoja Isaac (13:04:33) (in thread): > @Faith Ifeoluwa AlexanderPlease note. Thank you so much everyone:pray:

Isoken Ibizugbe (13:32:22) (in thread): > Great job. Study design is good, as the experiment was done on rats in the lab and on previous human study. You divided the experiments in to 5, but as I went through I saw two experiments which were done on rats and the findings from previous studies. Can you please point out where you found the other ones. Thanks

Samreen Aftab (13:38:47): > @Isoken Ibizugbesomeone said here that I’m required to put down the findings from previous data as well, so I created experiments to record the signatures from previous studies. > So experiments 1,2,3 are signatures from results of previous studies, and 4,5 are signatures from the experiments performed on rats. > Thank you for reviewing my paper <3

Isoken Ibizugbe (13:40:47) (in thread): > Ok, thanks. You did great:heavy_check_mark:

Isoken Ibizugbe (13:42:11) (in thread): > I’ll like to review it.

Blessing Laweh (13:43:43) (in thread): > Thank you@Isoken Ibizugbe. I’d greatly appreciate your review:pray:

Isoken Ibizugbe (14:22:15) (in thread): > If you’re sure your work is ready for review from the mentors, then you should click complete.

Abiola Salako (14:37:55) (in thread): > Thanks for sharing@Scholastica Urua

idiaru Angela (14:42:13) (in thread): > Hey@Samreen Aftabit’s a good curation. Some of my observations about the curation include > 1. The statistical test used in experiment 1 wasn’t included however it was stated in the article > 2. Noticed that for experiments 2 and 3, you curated for relative abundance but in BugsigDB only differential abundance is curated. So you might want to review those curations

Abiola Salako (14:42:35) (in thread): > @Ifeyinwa Ohonduyou can paste the taxonomy ID of the synonym. It’s acceptable.

idiaru Angela (14:42:47) (in thread): > Hey@Blessing LawehI’ll review and get back to you

Abiola Salako (14:44:38) (in thread): > Well done@Faith Ifeoluwa Alexander

Abiola Salako (14:48:50) (in thread): > Thank you all for your input

Abiola Salako (14:49:36) (in thread): > @Habiba SaadYea, you are.

Abiola Salako (14:54:09) (in thread): > @Adedoja IsaacWe focus on differential abundance!

Abiola Salako (14:55:30) (in thread): > Okay@Blessing Laweh

Abiola Salako (15:03:43) (in thread): > @Isoken Ibizugbeher project has a meta-analysis study design.

Isoken Ibizugbe (15:05:02) (in thread): > @Abiola Salakoyes it does

Ifeyinwa Ohondu (17:36:35): > Hi guys. Who is up for a review?https://bugsigdb.org/Study_928 - Attachment (BugSigDB): Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease - BugSigDB > Chronic granulomatous disease (CGD) is caused > by defects in any 1 of the 6 subunits forming the nicotinamide > adenine dinucleotide phosphate oxidase complex 2 (NOX2), > leading to severely reduced or absent phagocyte-derived > reactive oxygen species production.

idiaru Angela (19:46:37) (in thread): > Hey@Ifeyinwa Ohondu, Nice work. One of the things I picked up from your curation is that some of the taxonomy in red can be resolved if you remove the “group” at the end and match it on the ncbi taxonomy browser > 2. For antibiotics exclusion, only the period of exclusion is usually noted. You can see the curation policy on the BugsigDB website for more info

idiaru Angela (19:54:34) (in thread): > @Ifeyinwa OhonduI also noticed that this experiment with significant differences in alpha diversity was also missing from the curation. > 4. For Experiment 3, I noticed that you specified Fig 5 as the source for the signature but I’m not sure Fig 5 is actually curatable. I’d like other opinions on that though - File (JPEG): Screenshot_20240318_005248_Chrome.jpg

idiaru Angela (20:10:17) (in thread): > Hey@Blessing LawehNice work! > My observations include > 1. You have some unresolved taxa in your curation. These are the ones showing in red. But they can actually be resolved by matching them in the ncbi taxonomy database and inputing the taxonomy ID instead > 2. In this study, there seems to be more than 1 expriment. For instance in Fig 4, there is differentially abundant taxa enriched in the UTG group > 3. I also seem to notice that you might have some experiments that do not have signatures but are statistically significant. > 4. If you also look through the results once again, you’d notice that there are some differentially abundant taxa that have been mentioned among the groups the study was carried out on. > If you need anymore clarification, I’m willing to help

Raihanat Adewuyi (20:43:45) (in thread): > Thanks

2024-03-18

Samreen Aftab (00:40:24) (in thread): > @idiaru Angelathank you. > 1. I’m confused about the statistical test, is it LefSe? > 2. I curated from this figure showing the LDA scores. This can be curated right? - File (JPEG): IMG_20240318_100819.jpg

Ifeyinwa Ohondu (01:16:48) (in thread): > Thanks for the insights:pray:@idiaru Angela

Ima-obong (Aimah) (01:39:53) (in thread): > @Ifeyinwa Ohonduyou did an amazing job with your curation, weldone. > I think in a situation where the family and genus has been mentioned for a particular signature, you should curate only the genus..same for genus and species, in this case, curate only the species…Take******Lachnospiraceae and Lachnospiraceae N230…******for example.

Ima-obong (Aimah) (01:53:24): > Hello everyone…welcome to a fresh week. Like we say in Nigeria “We go again this week”:star-struck:Have a fun-filled “bugsigdbing” week:partying_face:Cheers:wine_glass:

assel (02:16:57): > Hello everyone, I didn’t expect that these papers can be so interesting:+1:However , I have some questions. May be you can help me, as far as I can see there is only one experiment in my article ( I’m not sure:upside_down_face:). BUT it mentioned two diversities (Alfa and Beta) ,does it mean I should write down TWO experiments? Please Please Please My article -https://www.frontiersin.org/articles/10.3389/fnagi.2022.881872/full#S11, mu curation -https://bugsigdb.org/Study_981 - Attachment (Frontiers): Nutritional Intake and Gut Microbiome Composition Predict Parkinson’s Disease > BackgroundModels to predict Parkinson’s disease (PD) incorporating alterations of gut microbiome (GM) composition have been reported with varying success.ObjectiveTo assess the utility of GM compositional changes combined with macronutrient intake to develop a predictive model of PD.MethodsWe performed a cross-sectional analysis of the GM and nutritional intake in 103 PD patients and 81 household controls (HCs). GM composition was determined by 16S amplicon sequencing of the V3-V4 region of bacterial ribosomal DNA isolated from stool. To determine multivariate disease-discriminant associations, we developed two models using Random Forest and support-vector machine (SVM) methodologies.ResultsUsing updated taxonomic reference, we identified significant compositional differences in the GM profiles of PD patients in association with a variety of clinical PD characteristics. Six genera were overrepresented and eight underrepresented in PD patients relative to HCs, with the largest difference being overrepresentation of Lactobacillaceae at family taxonomic level. Correlation analyses highlighted multiple associations between clinical characteristics and select taxa, whilst constipation severity, physical activity and pharmacological therapies associated with changes in beta diversity. The random forest model of PD, incorporating taxonomic data at the genus level and carbohydrate contribution to total energy demonstrated the best predictive capacity [Area under the ROC Curve (AUC… - Attachment (BugSigDB): Nutritional Intake and Gut Microbiome Composition Predict Parkinson’s Disease - BugSigDB > BACKGROUND: Models to predict Parkinson’s disease (PD) incorporating alterations of gut microbiome (GM) composition have been reported with varying success.OBJECTIVE: To assess the utility of GM compositional changes combined with macronutrient intake to develop a predictive model of PD.

Mildred Anashie (02:18:08) (in thread): > Yes@Ifeyinwa OhonduI agree with@idiaru Angelasome of the taxas in orange in your paper can be solved such as Escherichia Shigella (if it’s a species, then see attached image) > > Antibiotic exclusion you use duration of exclusion > > I see NIH vs PIDTC (patients with CGD without a history of IBD or active IBD and all patients with CGD regardless of their IBD status) is not recorded for > From Fig 3c and fig E4c > > Fig E6 also shows Active IBD (Yes) vs No Active IBD and history of IBD (Yes) vs No History of IBD (I don’t know how curatable it is) > > Alpha diversity indices includes Fischer for some of the experiments (Not sure which of the indices represents Fischer) > > Also I don’t think Fig5 is curatable > > Well done on your curation:partying_face::raised_hands:

Barakat Akinsiku (02:20:17): > Good morning BugSigdbiers, welcome to a new week. > > I wish us all an awesome week of curating and learning:blush::star-struck:

Mildred Anashie (02:20:19) (in thread): > Forgot to attach the images > > Also this experiment in FigureE5 patients under 12 and above 12 has alpha diversity results and significant results I think it should be curated - File (PNG): IMG_2453 - File (PNG): IMG_2454

Mildred Anashie (02:26:28) (in thread): > Hi@asselI’ll go through your curation but we record only for Alpha diversity and not Beta diversity > And Alpha and Beta doesn’t translate to the number of experiments in the paper > > What defines an experiment is the comparison done as well as groups contrasted

Ima-obong (Aimah) (02:27:15) (in thread): > Weldone@asselIn our curation we are only concerned with alpha diversity..beta diversity is not needed

Ima-obong (Aimah) (02:29:18) (in thread): > Please also check out this curation policy for better understandinghttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Abiola Salako (02:30:14) (in thread): > @Ifeyinwa OhonduWell done on your curation, In addition to what has been said, I also observed that you omitted the PMID of your study.

Abiola Salako (02:34:10) (in thread): > @asselGood Morning. Well done on your curation. I observed that you didn’t add a study design to your work.

Eniola Adebayo (02:35:40): > Good morning everyone, it’s a new week, good luck as you go ahead hitting those goals you set for yourself this week. Glad to do this open source thing with you all. Have a productive week!

Bolanle Wahab (02:48:12) (in thread): > Good morning@asselWeldone:heart:BugSigDB only records Alpha diversity. > I think you’re right to have one experiment though, the other comparison showed result for relative abundance and we’re supposed to record just differential abundance. > Then the Statistical test is ANOVA, PERMANOVA was used for beta diversity.

assel (02:49:30) (in thread): > Thank you guys !!! What about statistical analysis , should I write all of them? or choose only one? Computational and Statistical Analyses > Data was assessed by Levene’s test to determine homogeneity of variances. Clinical data comparisons between groups were performed using Student’st-tests and χ2-tests (SPSS v.26 SPSS Inc., Chicago, IL, United States) for quantitative and categorical variables, respectively. Pairwise Spearman correlations assessed non-parametric associations between microbiota and clinical covariates. For all tests, ap< 0.05 was considered statistically significant. All microbiome statistical comparisons and data visualizations were performed with R (v.3.5.1) and figures were generated with ggplot2 (v.3.1.0).

Bolanle Wahab (02:49:57) (in thread): > Good morning@Barakat Akinsikuand everyone, Thank you and I hope we all have an amazing week ahead:heart:

Habiba Saad (02:51:15) (in thread): > for eubacterium xylanophilum its available on uniprot and ncbi i don’t know why bugsigdb did not recognize it and shows red review needed.

Mildred Anashie (02:57:39) (in thread): > Its ANOVA just like what@Bolanle Wahabsaid - File (PNG): assel.PNG

assel (02:57:52) (in thread): > Thank u@Bolanle Wahabfor notes. What do u think should I choose for Alfa diversity statistical analysis tool? I’m a beat confused

assel (02:58:20) (in thread): > Anova only?

Mildred Anashie (02:59:36) (in thread): > Yes, we record the statistical test used for the differential abundant taxa

Mildred Anashie (03:00:32) (in thread): > Your Alpha diversity is unchanged for Shannon and Simpson in Fig 1

Habiba Saad (03:00:54) (in thread): > @Blessing LawehPMID is missing > antibiotic exclusion is not what you wrote in it. I think this study did not conduct any antibiotic exclusion. > for signatures showing in red try to write full name for example instead of writing M Tuberculosis write mycobacterium tuberculosis.

Bolanle Wahab (03:03:28) (in thread): > Yes, Just ANOVA@assel

Blessing Laweh (03:10:01) (in thread): > Thank you@idiaru AngelaI had a feeling there should be another experiment but didn’t know how to go about it. Thanks for pointing that out. I’ll look through it. > > Please, If you don’t mind explaining 3 and 4 a little bit more. I’d appreciate that, thanks > .

Blessing Laweh (03:13:42) (in thread): > Thank you@Habiba Saadfor your review. I tried inputing the PMID but I was getting an error message in red letters. Is there a way I can bypass this? > > About the Antibiotics inclusion, there were parts in the study that mentioned using Anti-TB drugs for 2weeks to 2.4months for a group and 6months for another group that why I included it. I don’t know, shouldn’t they be like the same?

Habiba Saad (03:17:28) (in thread): > while writing pmid ensure that there is no spaces before or after. its antibiotic exclusion not inclusion.

Joan C. Chukwuemeka (03:18:56) (in thread): > Good morning all, > Trust we had a good weekend. Happy BugSigDB-ing:seedling:On this incomplete studyhttps://bugsigdb.org/Study_714that I’m working to complete: > Based on the excerpt in the 1st Image - the result text and corresponding figures, figure 4G is relative abundance, Figure 4H says relative abundance but seems to point to differential abundance too, Here’s the statement that got me thinking, “Relative abundances of two genera(Bifidobacterium and Lactobacillus) that are******significantly different ****comparing HFD89 to KD (FDR <0.05, DESeq2)”. Which is it?:thinking_face:@Esther Afuape@Chioma Onyido<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>@Peace SandySecondly, I already have a curation that shows thatBifidobacterium and Lactobacillus are decreased in abundance for HFD vs KD in the Mice experiment (FDR <0.1, DESeq2) (as seen in the 2nd/3rd image). If Fig. 4H is differential abundance, is there need to curate it, hence it’s still similar outcome? and the mice experiments in the study were follow up studies for the human cohort?:woman-shrugging:Study link -https://doi.org/10.1016/j.cell.2020.04.027 - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

assel (03:21:07) (in thread): > Does it mean that I shouldn’t add any Signatures? because of “unchanged” Alfa diversity?:face_with_rolling_eyes:OMG I’m so confused

Abiola Salako (03:24:50) (in thread): > @asselNo. What you’re to choose under the alpha diversity section has been mentioned by@Mildred Anashie: “Shannon & Simpson which are both unchanged.@asseland remember that the signatures we curate are the ones obtained from the statistical test showing ‘differential abundance’

Blessing Laweh (03:25:32) (in thread): > Imagine!@Habiba Saadinclusion, exclusion (why did I think:woman-facepalming:omg. Thank you for pointing that out:sweat_smile:)

Habiba Saad (03:26:34) (in thread): > let me know if your pmid issue resolves or not.

Bolanle Wahab (03:28:27) (in thread): > Not necessarily@asselunchanged alpha diversity just means the diversity within the groups you’re comparing are similar. > > If there are signatures that shows differential abundance, you should curate them

idiaru Angela (03:37:55): > It’s a new week!! I hope we all have a productive and fun week:dizzy:. Happy BigSigDB- ing everyone > If you’re still in need of co- contributor reviews, I’m available this morning:blush:.

Scholastica Urua (03:42:46): > Hello everyone, I hope you had a wonderful weekend.:hugging_face:Please we’ll appreciate your thoughts on this:pray:@Mildred Anashieand I have been reviewing@Mkpouto Shedrackcuration;https://bugsigdb.org/Study_985. However, we find ourselves at a crossroads regarding signatures to curate for each experiment. Here’s our current understanding: > > There are four experiments outlined: > > 1. Healthy vs CKD (all) (curatable result in Figure 3) > 2. Healthy vs H-CKD > 3. Healthy vs NC-CKD > 4. Healthy vs d-CKD > > We’ve encountered difficulty in identifying significant results for the other three experiments where CKD was separated into different groups. The article primarily references Figure 4 and other figures which do not appear to be curatable. We concluded that only Experiment 1 will have signatures, while the other experiments should still be curated but without signatures. > > Could you kindly review this and share your thoughts? - Attachment (BugSigDB): Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor - BugSigDB > The intimate correlation of chronic kidney disease (CKD) with structural alteration in gut microbiota or metabolite profile has been documented in a growing body of studies.

Scholastica Urua (03:54:15): > Hello<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyI came across this incomplete curation under ‘Experiments that have no Signatures’https://bugsigdb.org/Study_672. > > I’ll love to work to complete it. - Attachment (BugSigDB): Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial - BugSigDB > The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health.

Peace Sandy (03:55:44) (in thread): > You can go ahead

Scholastica Urua (03:56:08) (in thread): > Thank you@Peace Sandy

idiaru Angela (03:59:23) (in thread): > @Blessing Lawehfor 3 see this thread where our mentor gives some clarification.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710519928024379?thread_ts=1710519888.679079&cid=C04RATV9VCYIt’s possible to curate an experiment that has alpha diversity even when the differentially abundant organisms aren’t mentioned as far as the comparison was made > For 4. In the result text there is a comparison between groups that was made that actually has differentially abundant organisms but the experiment has not yet been curated so I was pointing you in that direction - Attachment: Attachment > Yes > If there’s an alpha diversity result but no significant taxa reported

idiaru Angela (04:13:49) (in thread): > Hey@Samreen Aftabfrom the screenshot you can see one of the statistical test. In my opinion, I think that because you are doing a meta analysis and a lab experiment you have different statistical tests for different experiments. > The Fig you sent is curatable however experiment 2 and 3 were not curated from that figure but from relative abundance that was stated in text - File (JPEG): Screenshot_20240318_091112_Chrome.jpg

Blessing Laweh (04:30:57) (in thread): > Thanks for these@idiaru AngelaI’d get to it in the next hour. If you don’t mind. Can you help me review it later?

Barakat Akinsiku (04:33:37) (in thread): > Same here@Bolanle Wahab:hugging_face:

Samreen Aftab (04:38:05) (in thread): > @idiaru AngelaI have curated from both the figure and text, since the text gives us an idea about the differential abundance between the groups. I’m confused now:sweat_smile:

Samreen Aftab (04:42:04): > Hello everyone. I have a question. In my study I’ve curated signatures from both the text and the figure. Is it okay to curate signatures from text like this , since it gives us an idea about the differential abundance between the groups. Please help me out, I’m confused. Thank you. - File (JPEG): IMG_20240318_140950.jpg - File (JPEG): IMG_20240318_140936.jpg

Barakat Akinsiku (04:46:50) (in thread): > Yes@Samreen AftabI believe it is. If you notice, the authors just repeat what is already in the figures as part of their discussion segment

Ima-obong (Aimah) (04:55:23) (in thread): > @Samreen AftabYes you can..the tables most times are for reference purposes

idiaru Angela (04:58:28) (in thread): > Hey@Joan C. Chukwuemekafor the first one, in my opinion it only points to relative abundance. I don’t think the figure gives information about the differential abundance > For 2. I think Fig 3G should be curated (though I’m not sure I understand your question right:sweat_smile:)

Scholastica Urua (04:59:35) (in thread): > Yes@Samreen Aftab, you can curate signatures from text. Just remember to fill ‘Text’ as your source if that’s what you are using.

idiaru Angela (04:59:58) (in thread): > @Samreen Aftabthe text you sent is talking about relative abundance though and that cannot be curated on BugSigDB

idiaru Angela (05:00:39) (in thread): > @Samreen Aftabonly the figure you sent gives an idea about differential abundance

Mildred Anashie (05:00:47) (in thread): > If the text is showing differential abundance then yes you can curate from there

idiaru Angela (05:01:29) (in thread): > In the statement in the text, it was explicitly stated relative abundance though@Samreen Aftab

idiaru Angela (05:02:13) (in thread): > Definitely:blush:@Blessing Laweh

Peace Sandy (05:02:53) (in thread): > Hi@Samreen AftabPlease go through this thread by@C. Mirzayi (please do not tag this account)It is really helpful,she also talked about signature sourceshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1704320770281189

Idiat Alli (05:03:00) (in thread): > @Samreen Aftabcurate only for differential abundance

Samreen Aftab (05:09:55) (in thread): > @Peace Sandy@Mildred AnashieI’m so sorry but doesn’t the statement “In the ET-B participants, the relative abundance of Bacteroidaceae, Phocaeicola, Halomonadaceae, Pseudomonadaceae, Enterobacteriaceae, and Streptococcaceae decreased in the order of the healthy (n= 125), MCI (n = 141), and AD (n = 103) groups” imply that these signatures have a decreased abundance for HC (Group 0) vs MCI (group 1)? Again, I’m so sorry for the confusion guys.:sweat_smile: - File (JPEG): IMG_20240318_140936.jpg

Scholastica Urua (05:12:09) (in thread): > Thank you@Peace Sandy, I just went through the thread. It’s really insightful.

Samreen Aftab (05:13:14) (in thread): > Thank you@Peace Sandy

Mildred Anashie (05:14:55) (in thread): > @Samreen Aftabthe text is pointing to Figure 1b > > What does fig 1b show?

Samreen Aftab (05:16:28) (in thread): > @Mildred Anashieit shows the relative abundance

Ima-obong (Aimah) (05:26:35): > Hello mentors@Peace Sandy,@Chioma Onyido…if one finds an incomplete study with no PMID, DOI or even the name of the paper, how do they get to see the paper that was used to curate the study being that they want to complete the curation…. > E.g, Study895 under “study without experiment section” > > Thanks

Barakat Akinsiku (05:30:47) (in thread): > @Ima-obong (Aimah)was the url or link to the paper not included? I know if a paper has no PMID you are to manually enter the details but even at that, you should include the link to the paper so reviewers can have access to it

Peace Sandy (05:30:50) (in thread): > Look for signature sources that points you to differential abundance

Ima-obong (Aimah) (05:31:17) (in thread): > Nope ..no URL

Barakat Akinsiku (05:33:33) (in thread): > Hmm that’ll be tough. Maybe search on Google or pubmed with the title of the study (usually that will at least be entered) and hope the paper turns up

Ima-obong (Aimah) (05:34:33) (in thread): > Thank you…but like I said, the study name wasn’t entered either, neither the abstract.

Scholastica Urua (05:35:48) (in thread): > @Ima-obong (Aimah)if it does not have any identifying data, I think it means no paper is linked to it. I suggest look for another incomplete study.

Bolanle Wahab (05:36:23) (in thread): > @Ima-obong (Aimah)I think someone has raised an issue about 895 and said it needs to be deleted

Ima-obong (Aimah) (05:36:33) (in thread): > Okay..just wanted the mentors to confirm that@Scholastica Urua

Mildred Anashie (05:37:00) (in thread): > In this case it was probably created on error by the initial curator and the original study probably already exists and this should be deleted

Mildred Anashie (05:38:11) (in thread): > We curate differential abundant results not relative abundance@Samreen Aftaband you should do what@Peace Sandysaid

Barakat Akinsiku (05:39:33) (in thread): > If there’s no title, abstract or identifying information best to look for another experiment@Ima-obong (Aimah)

Peace Sandy (05:41:04) (in thread): > Hi@Ima-obong (Aimah)Please work on another experiment,I’lltake a look at the study. Thank you for pointing it out

Mildred Anashie (05:41:47): > Hello everyone, I hope you had a wonderful weekend. > > Hi@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido@Esther AfuapeIs it possible that an entire study will not have curatable signatures?:thinking_face:I found this studyhttps://bugsigdb.org/Study_761under pages with Missing NCBI and tried to solve the Prevotella1,2,6Iwent through the article andnoticedthe curator recorded signatures from Supp table 1. > I’m tryingto reviewthe study because I think the table shouldn’t have been curated > Also noticed thatall the results were presented as correlation results and I can’t find differential abundance results in the studyThe statistical test is linear regression and they did some sort of model adjustment(just pointing this out)Can you help me go through it to point out what shouldor can becurated from here?Thank you:pray: - Attachment (BugSigDB): The oral microbiome and breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in the Ghana Breast Health Study - BugSigDB > The oral microbiome, like the fecal microbiome, may be related to breast cancer risk.Therefore, we investigated whether the oral microbiome was associated with breast cancer and nonmalignant breast disease, and its relationship with the fecal microbiome in a case-control study in Ghana.

Abiola Salako (05:43:27) (in thread): > Thank you@Peace Sandy

Ima-obong (Aimah) (05:43:56) (in thread): > Thank you@Barakat Akinsiku,@Scholastica Urua@Bolanle Wahab@Mildred Anashieand@Peace Sandyfor all your replies..thank you

Scholastica Urua (05:45:03) (in thread): > Also, just to point out@Mildred Anashie, the curation is done by a current applicant. So you can also notify them of your findings.

Mildred Anashie (05:46:46) (in thread): > Yes it was an incomplete study he was trying to complete and said I could effect corrections@Muqtadirat Yussuffplease confirm this

Leenaa Al-Amin (05:48:06) (in thread): > hello, what about these as the abundant signatures for the NC-CKD and the d-CKD compared to the healthy controls? it seems these are the species specifically abundant in those groups as opposed to the other CKD-groups - File (JPEG): IMG_4756

Mildred Anashie (05:49:43) (in thread): > Hi@Leenaa Al-AminThat has Fig 4 as reference,we have difficulty interpreting Fig 4

Scholastica Urua (05:51:40) (in thread): > Fig 4 doesn’t look curatable@Leenaa Al-Amin, hence our confusion.

Svetlana Ugarcina Perovic (05:53:53): > Happy Monday!NEW Microbiome Digest is out https://microbiomedigest.com/2024/03/18/march-18-2023/Microbiome Digestis a widely-read daily compilation of scientific literature related to microbiomes. It aggregates recent research papers, reviews, and news articles concerning the microbiome field. The digest serves as a valuable resource for researchers, clinicians, and anyone interested instaying updated on the latest advancements and discoveries in microbiome research. It typically covers topics such as the role of microbiomes in health and disease, microbial ecology, microbiome therapeutics, and methodological advances in microbiome studies. It is founded by Elisabeth Bik and ran by volunteers. > On the right side, you can select, in Archives and Categories, a month or category of microbiome science that you are particularly interested in.:potted_plant:We wish you a good BugSigDB-ing week!<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina PerovicNOTE: *this is not a list of papers for bugsigdb curation; here, in our outreachy project, we are curating only carefully selected papers in the GitHub issues - Attachment (Microbiome Digest - Bik’s Picks): March 18, 2023 > Today’s digest features the human gut microbiome atlas of Africa, sociobiome, a large human gut Bacteroidales culture collection, Patescibacteria in global waste water treatment plants, and m…

Blessing Ene Anyebe (05:55:01) (in thread): > This would help in the understanding micro biome in detail. Thank you@Svetlana Ugarcina Perovicfor sharing. > Happy new week everyone:orange_heart::sparkles:

Scholastica Urua (05:55:44) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicHappy Monday!

Idiat Alli (05:56:00) (in thread): > Well done@Faith Ifeoluwa Alexander

Ima-obong (Aimah) (05:57:09) (in thread): > Thank you

Barakat Akinsiku (05:57:16) (in thread): > Thank you@Svetlana Ugarcina Perovic

Idiat Alli (05:58:04) (in thread): > Thanks@Svetlana Ugarcina PerovicHappy New week:sparkles:

idiaru Angela (05:58:18) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovicand Happy Monday:dancer:. I hope you have a wonderful week.

Bolanle Wahab (05:59:15) (in thread): > Thank you:heart:

Oluwatomisin Omojokun (06:01:56) (in thread): > Exactly@Peace Daniel

Nana (06:06:24) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovicthis will go along to understand microbiome better

Rahila-me (06:07:43) (in thread): > @Svetlana Ugarcina PerovicThanks for sharing. Happy Monday too

Oluwatomisin Omojokun (06:07:51) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovicand happy new week

Samreen Aftab (06:08:03): > the 16S region should be V3-V4 or V2-V4? - File (PNG): Screenshot from 2024-03-18 15-35-02.png

Aishat Ijiyode (06:09:11) (in thread): > Thank you so much for sharing@Svetlana Ugarcina PerovicHappy Monday everyone. Cheers to a productive week

Modinat Ganiyu (06:09:18) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovicand have a great day

Abiola Salako (06:09:41) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic

Oluwatomisin Omojokun (06:10:31): > Good morning@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy. Please kindly add new article for curation. Thank you

Aleru Divine (06:11:49) (in thread): > Thank you so much for sharing@Svetlana Ugarcina Perovicand Happy Monday!:hugging_face:

Idiat Alli (06:12:11): > @Samreen AftabI actually came across something like this but I couldn’t differentiate which is the upper bound and the lower bound. Let’s be on the look out for responses

Bolanle Wahab (06:12:52) (in thread): > @Samreen Aftabthis doesn’t give much information but the regions depends on the taxa level of the signature you curated

Samreen Aftab (06:13:30) (in thread): > @Bolanle Wahabthank you

Aishat Ijiyode (06:15:08) (in thread): > After we read up on an article that pick our interest, are we to curate a study on the articles please?

Mildred Anashie (06:15:25) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicHappy Monday:bouquet:

Scholastica Urua (06:16:40) (in thread): > @Aishat Ijiyodewe are to curate those listed on BugSigDB’s GitHub issues or other incomplete experiments on BugSigDB.

Svetlana Ugarcina Perovic (06:16:40) (in thread): > Discussed herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710237489267499?thread_ts=1710228540.842369&cid=C04RATV9VCY - Attachment: Attachment > What I would probably do in the case of meta-analysis where there isn’t a consistent answer, would be just to leave that field blank since none of the ones under discussion here are mandatory. But honestly all of the solutions already proposed here are reasonable! :sweat_smile: In any case, discussion like this what you’ve pointed out @Scholastica Urua should definitely go on the “Discussion” page for this study, so it will be available to anyone wondering in the future why you made the choice you did.

Bolanle Wahab (06:17:36) (in thread): > @Aishat Ijiyodeif it is assigned to you, yes you are to curate it

Mildred Anashie (06:19:15) (in thread): > @Aishat Ijiyodeyou curate only articles on the GitHub repo that are assigned to you

Scholastica Urua (06:20:40) (in thread): > Thanks@Svetlana Ugarcina Perovic. I’ve been looking for this thread to post here.:sweat_smile:‘Save for later’:hugging_face:

Bolanle Wahab (06:20:40) (in thread): > @Svetlana Ugarcina Perovicthank you:sweat_smile:

Aishat Ijiyode (06:20:49) (in thread): > for the articles in the Microbiome Digest that@Svetlana Ugarcina Perovicshared earlier in this thread, are we to read them only or also curate them?

Svetlana Ugarcina Perovic (06:21:05) (in thread): > *this implies in case of meta-analysis as well as reusing public data for a study

Bolanle Wahab (06:21:58) (in thread): > @Idiat Allithis should be useful to you too

Aishat Ijiyode (06:22:04) (in thread): > okay now I understand we are to read them, I wanted to be sure. Thank you so much everyone

Idiat Alli (06:22:05) (in thread): > @Aishat Ijiyodeyes you can curate articles on github

Idiat Alli (06:23:30) (in thread): > Oh. Thank you@Svetlana Ugarcina Perovic@Bolanle Wahab

Muqtadirat Yussuff (06:25:09) (in thread): > Hi@Mildred AnashieI did give the go ahead but for NCBI mapping. If you notice any issue could you bring please it forward to me? As I asked for review regarding this curation especially the experiments section and I wasn’t informed I curated the wrong table

Glorious Katushabe (06:25:12): > Hello@Svetlana Ugarcina Perovic<@UBNSEMS3S>please delete experiment 3 that I had added. find my study link ashttps://bugsigdb.org/Study_958 - Attachment (BugSigDB): Analysis on the change of gut microbiota and metabolome in lung transplant patients - BugSigDB > Previous studies have shown that the gut microbiota and its metabolites are > associated with the success of organ transplantation.However, the specific changes in > the gut microbiota of lung transplant patients remain unclear.

Samreen Aftab (06:25:25): > Also guys , the condition in my study is mild cognitive impairment, however it is not in the drop - down. Can I use memory impairment instead?

Scholastica Urua (06:25:45) (in thread): > Hello@Oluwatomisin OmojokunWhile waiting for more issues to be uploaded, some other ways you can contribute to BugSigDB are; > > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Idiat Alli (06:26:30) (in thread): > Noted, I left it blank:slightly_smiling_face:

Aleru Divine (06:27:02) (in thread): > Hey@Samreen AftabI think using cognitive impairment is fine.Can you find that?

Svetlana Ugarcina Perovic (06:27:12) (in thread): > NOTE: this is not a list of papers for bugsigdb curation; we are curating only carefully selected papers in the GitHub issues

Mildred Anashie (06:27:26) (in thread): > Okay@Muqtadirat YussuffYou can keep an eye on this thread possibly ifthere’sa response regarding that you can implement it > > Although I mentioned it when I told you about the NCBI ID

idiaru Angela (06:27:36) (in thread): > @Samreen AftabI don’t think memory impairment and cognitive impairment mean the same thing though

Idiat Alli (06:27:37) (in thread): > Yea@Aleru Divineif she can find that

Samreen Aftab (06:28:13) (in thread): > @idiaru Angelasince my study is about memory impairment, that’s why:sweat_smile:

Idiat Alli (06:28:20) (in thread): > @Samreen Aftabcheck your article for more terms

Scholastica Urua (06:28:55) (in thread): > @Samreen AftabCognitive Impairment is available on BugSigDB so you can use that like@Aleru Divinesuggested.

Svetlana Ugarcina Perovic (06:29:03) (in thread): > Deleted.

Idiat Alli (06:29:06) (in thread): > Check for cognitive impairment like@Aleru Divinesaid

idiaru Angela (06:29:40) (in thread): > Okayyy@Samreen Aftab

Adenike Oladimeji-Kasumu (06:29:51) (in thread): > Although they are related concepts, Cognitive impairment is broader… But I think you can use it if that’s the only option you can find. > Do well to still get a Mentor’s opinion.

Samreen Aftab (06:30:07) (in thread): > Ah, okay thank you@Scholastica Urua@Aleru Divine

Mildred Anashie (06:30:37) (in thread): > Yea > > Cognitive impairment should be okay

Glorious Katushabe (06:31:11) (in thread): > Thank you

Abiola Salako (06:32:45) (in thread): > Yes,@Samreen Aftab. Cognitive Impairment is okay.

Leenaa Al-Amin (06:35:58) (in thread): > alright@Mildred Anashie@Scholastica UruaI’ve tried interpreting it as well and it has proven difficult:sweat_smile:I’d love to hear the opinions of others

Mildred Anashie (06:40:14) (in thread): > :laughing:Thank you for your effort@Leenaa Al-Amin

Ikeh Darlington Ikeh (06:45:31): > Any help guys will be appreciated with love. How do i curate the following: Unknown Class, Unknown family, Unknown order, Uncultured? - File (PNG): image.png

Aleru Divine (06:48:05) (in thread): > In my opinion, I thinkit’sbest to leave them out.You could include a note on the discussions page, mentioning their existence.But theseweren’tidentified.Sothere’snothing to search and no way of knowing(that I know of):thinking_face:

Oluwatomisin Omojokun (06:48:10) (in thread): > i am working already on them. Thanks@Scholastica Urua

Ima-obong (Aimah) (06:48:53) (in thread): > I would leave them out, and make a note on the discussion page

Mildred Anashie (06:49:45) (in thread): > Yea I think it should be left out like Divine suggested > > I knowthere’san ID for unknown bacteria but thatdoesn’tseem to be the case here soI’mnot sure it can fit here@Ikeh Darlington Ikeh

Ima-obong (Aimah) (06:49:58) (in thread): > And I’ll also check if the unknown class, and genus has its species mentioned, then I’ll curate the species only

idiaru Angela (06:52:22) (in thread): > I agree with@Aleru Divineleaving a note on the discussion page would probably be best

Bolanle Wahab (06:54:06) (in thread): > @Ikeh Darlington IkehI also think you should remove them and leave a note that you removed them due to missing taxa information.

Abiola Salako (06:54:55) (in thread): > @Ikeh Darlington IkehI think it’s better to leave them out and make a report on the talk page.

Idiat Alli (06:58:37) (in thread): > @Ikeh Darlington Ikehit was stated in a thread to leave what wasn’t stated

Joan C. Chukwuemeka (06:58:39) (in thread): > Figure 3G has already been curated.@idiaru AngelaQuestion is: > * Is Figure 4h differential abundance or just relative abundance? It has a description:“********Relative abundances *****of two genera (Bifidobacterium and Lactobacillus) that are *******significantly different ******comparing HFD89 to KD (FDR <0.05, DESeq2)” > * If Fig. 4H is differential abundance, is there need to curate it as a 3rd experiment, since I already have an experiment that shows thatBifidobacterium and Lactobacillus are decreased in abundance for HFD vs KD in the Mice experiment (FDR <0.1, DESeq2) (as seen in the 2nd/3rd image). > https://community-bioc.slack.com/files/U05UTDTUHMH/F06PT4GH70W/image.pnghttps://community-bioc.slack.com/files/U05UTDTUHMH/F06PZMVC17D/image.pnghttps://community-bioc.slack.com/files/U05UTDTUHMH/F06PKAGT3KR/image.png - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Ima-obong (Aimah) (06:59:16): > Hello mentors@Chioma Onyido@Peace SandyI found this study under study with missing experiments and though it only has the DOI as part of its study design, The DOI is incorrect when you try to search for the paper as the study has no paper name or abstract and URL attached to it.. > > I think it should be deleted or looked into… Thanks.https://bugsigdb.org/Study_901 - Attachment (BugSigDB): - BugSigDB > …

Idiat Alli (06:59:35) (in thread): > Discussed herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710237489267499?thread_ts=1710228540.842369&cid=C04RATV9VCY

Grace Paul (07:01:19) (in thread): > Hi@Ikeh Darlington Ikeh, i think since you have the values for increasing and decreasing sp. It seems curatable to me. I think you can look each organism up and get those information. C. Bacilli for example (Binomial name:Bacillus cereusDomain: Bacteria > Phylum: Bacillota > Class: Bacilli > Order: Bacillales > Family: Bacillaceae > Genus: Bacillus > Species: B. cereus)

idiaru Angela (07:03:29) (in thread): > @Joan C. ChukwuemekaI understand better now. > In my opinion Fig 4h is just relative abundance because even the graph gives the percentage of the relative abundance I highly doubt it points to differential abundance

Amanda Adoyi (07:17:40): > Guten tag and hello:slightly_smiling_face:Hope your morning is going awesomely. It’s a new day and I am ecstatic to get back on the reviewing wagon this week; really helping me learn more with each paper. Thanks to those who have employed me but I’m in need of more if you’d like. Bring on the papers. Grazie.

Scholastica Urua (07:18:27) (in thread): > Hello to you too@Amanda Adoyi

Mildred Anashie (07:19:39) (in thread): > Hello@Amanda Adoyi:blush:

Aleru Divine (07:20:04) (in thread): > Good day@Amanda Adoyi:hugging_face:I do have a paperthat’sI’d loveto be reviewed:pleading_face:Thank you so much:pray:Link:https://bugsigdb.org/Study_953Note: it is quite lengthy 🫨 - Attachment (BugSigDB): Microbial Diversity and Composition in Six Different Gastrointestinal Sites among Participants Undergoing Upper Gastrointestinal Endoscopy in Henan, China - BugSigDB > The objective of this study was to describe and compare the dynamic microbiota characteristics in the gastrointestinal (GI) tract in Chinese participants via high-throughput sequencing techniques.

Mildred Anashie (07:20:34) (in thread): > We’dlike to employ you here to get your opinion@Amanda Adoyi:grin:

Scholastica Urua (07:21:46) (in thread): > I’m working on this incomplete study and everyone’s input will be appreciated. It’s a bit challenging knowing which groups to curate and not to curate.:pray:https://bugsigdb.org/Study_672 - Attachment (BugSigDB): Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial - BugSigDB > The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health.

Amanda Adoyi (07:23:18) (in thread): > Thanks all. Thanks@Aleru Divineand@Scholastica Urua. Will get to them soon.

Joan C. Chukwuemeka (07:31:14) (in thread): > @Ikeh Darlington IkehIs there a supplemental material?

Amanda Adoyi (07:31:51): > So em…I can’t be the only one who now thinks about conditions a little differently now. I knew something like that in the past but I mean, the craziness of signatures of tiny, really tiny, not easily seen by the naked eye organisms determining so much of physiology and behaviour. Who wants to bet that the first biologists/ doctors to point this out were stoned? I mean I’ll check what actually happened but it’s just damn fascinating. Just thinking out loud in text. Okay continue your bugsigdb-ing.

Idiat Alli (07:34:12) (in thread): > Hi@Amanda Adoyi

Joan C. Chukwuemeka (07:35:33) (in thread): > Okay. Thanks@idiaru Angela@Aleru Divine@Esther Afuapeany input to this please?

Muqtadirat Yussuff (07:36:48) (in thread): > Hi, can I join the review bandwagon? I have gaps and I feel reviewing more papers would help@Aleru Divine@Scholastica Urua

Scholastica Urua (07:38:04) (in thread): > Of course@Muqtadirat Yussuff. I’ll really appreciate your feedback:pray:

Faith Ifeoluwa Alexander (07:38:09): > Good Morning, everyone. Pls, I can’t find the differential abundance in my paper. I need HELP!!!!!

Aleru Divine (07:40:44) (in thread): > Yes please@Muqtadirat Yussuffthank you so much for this:pray:

Oluwatomisin Omojokun (07:51:24) (in thread): > @Faith Ifeoluwa Alexander, you can share the article, so that others can help out.

Bolanle Wahab (07:52:32) (in thread): > You’re not alone@Amanda AdoyiI guess it just proofs that in life, even the smallest things can play important roles in complex systems. > And I doubt they were stoned:joy::joy::joy:I mean careful attention to details is one of the qualities of a scientist.

Adenike Oladimeji-Kasumu (07:52:38) (in thread): > Hi@Faith Ifeoluwa AlexanderYou can use Ctr +F on the Paper to search for related words e.g. increased, Taxa, abundance, Etc. Or if there is/are supplementary material(s), you can check them to be sure.

Bolanle Wahab (07:53:34) (in thread): > @Faith Ifeoluwa Alexanderdo you mind sharing your article?

idiaru Angela (07:56:34) (in thread): > Hello@Amanda Adoyi

Faith Ifeoluwa Alexander (07:57:04) (in thread): > Okay. Let me share it now.

Amanda Adoyi (07:57:46) (in thread): > @Bolanle WahabLolz. I get this. I’m in an academic field where I have got to believe the power of the minute but still this blows my mind aye…

Faith Ifeoluwa Alexander (07:57:53) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884491/ - Attachment (PubMed Central (PMC)): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders. PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous …

Amanda Adoyi (08:05:11) (in thread): > @Faith Ifeoluwa AlexanderFirst off, take a deep breath; you scared me with the exclamation marks. lolz. Secondly, I found a subheading “Differences in microbiota composition”…if you read through you may find what you are looking for. You could also look up figure 2 and you can check out the text in detail. In the introduction (abstract?) comparisons were made and some significant taxa pointed out. This is just based on glancing through so you may have to check em out more.

Adenike Oladimeji-Kasumu (08:06:47): > Hi everyone, Please who is interested in helping to take a look at my curation? Here is the link:https://bugsigdb.org/Study_973and this is the link yo the paper:https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2021.756951/full. I like that your observations, most especially in respect to my curated signatures. - Attachment (BugSigDB): Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson’s Disease Cohort - BugSigDB > Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson’s disease (PD), but the influence of geographic location has received little attention. - Attachment (Frontiers): Frontiers | Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson’s Disease Cohort > Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson’s disease (PD), but the influence of geographic locati…

Amanda Adoyi (08:07:47) (in thread): > @Adenike Oladimeji-Kasumupointed out supplementary tables which honestly is advice that goes a long way; I nearly missed what I hope is important info in my curation by ignoring those.

Iman Ngwepe-Ntshibida (08:08:01): > Hi team, I’m working on a lab study. There seems to be no clear distinction with regards to the group sizes, 30 rats were randomly placed in the two. And both groups are exposed however the SA group is classed as the control. Can we assume a 50/50 split in the size ? And as per the policy, is it ok to class MP group as 1 even though it is not a case-control study. - File (PNG): grouped.PNG - File (PNG): groups.PNG

Faith Ifeoluwa Alexander (08:08:27) (in thread): > @Amanda Adoyiwhat I found in that part of the article you mentioned are relative abundances and we are asked to curate for differential abundance. So that is the problem I am facing.

Idiat Alli (08:08:49) (in thread): > Very true@Amanda Adoyi,supplementary materials is fully packed with information > Do check@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (08:09:12) (in thread): > I have the supplementary table open on my laptop and I can’t seem to understand it.

Aleru Divine (08:09:40) (in thread): > There could be additional info in the materials and methods/sample collection.Could you share your paper please:pray:

Adenike Oladimeji-Kasumu (08:10:44) (in thread): > Hello Everyone. I have posted the link to my work here, I would love your Reviews@Amanda Adoyiand everyone who is interested.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710763607985719 - Attachment: Attachment > Hi everyone, Please who is interested in helping to take a look at my curation? Here is the link: https://bugsigdb.org/Study_973 and this is the link yo the paper: https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2021.756951/full. I like that your observations, most especially in respect to my curated signatures.

Iman Ngwepe-Ntshibida (08:10:56) (in thread): > @Aleru DivineHey Aleru, this is paperhttps://journals.asm.org/doi/10.1128/spectrum.01437-23

Mildred Anashie (08:11:09) (in thread): > Hi@Faith Ifeoluwa AlexanderSo yesterday@Aleru Divineand I spent a lot of time on your paper and it was a bit confusing due to the relative abundance that was repeatedly mentioned but we think curating from text is okay > > Relative abundance between groups can be curated in my opinion > > But you can confirm this from the mentors and others opinions

Aleru Divine (08:11:13) (in thread): > Thanks

Scholastica Urua (08:11:40) (in thread): > @Iman Ngwepe-NtshibidaFrom the image you provided, I’d say you can group ‘MP’ as 1 and ‘SA’ as 0 since they received the saline.

Faith Ifeoluwa Alexander (08:12:29) (in thread): > Maybe I should tag the mentors to ask.@Mildred Anashie.

Mildred Anashie (08:13:25) (in thread): > Yes that would be best in my opinion@Faith Ifeoluwa Alexander

Amanda Adoyi (08:15:07) (in thread): > @Faith Ifeoluwa AlexanderI’m not sure it’s all relative abundance. In a sentence I found that > “…PD patients treated with L-dopa showed significantly higher relative abundances ofEnterococcaceae,Clostridialesfamily XI, and the generaPeptoniphilusandFinegoldia, whileFaecalibacteriumand theRuminococcus gauvreauiigroup were significantly decreased when compared to the controls.” > There appears to be a comparison between groups regarding the taxa mentioned. > If your paper happens to be one where you must read everyline to determine when differential abundance is implied…em…that’s a lot.

Faith Ifeoluwa Alexander (08:15:38): > @Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account)@Esther Afuapepls can relative abundances between groups be curated as I can not find differential abundances in my paper? > > Thank you so much for your anticipated responses.

Aleru Divine (08:16:04) (in thread): > @Iman Ngwepe-Ntshibidacheck Fig. 1 description for your sample sizes. > > I hope that helps - File (PNG): IMG_7974

Iman Ngwepe-Ntshibida (08:16:14) (in thread): > Thanks@Scholastica Urua, this policy is what was throwing me off - File (PNG): control.PNG

Scholastica Urua (08:17:37) (in thread): > @Iman Ngwepe-Ntshibidait’s also mentioned here that SA is control group. - File (JPEG): SA.JPG

Iman Ngwepe-Ntshibida (08:18:10) (in thread): > @Aleru Divinemany thanks:blush:

Adenike Oladimeji-Kasumu (08:18:13) (in thread): > Please I need reviews:pray:

Faith Ifeoluwa Alexander (08:18:26) (in thread): > I curated for the relative abundance between groups but I was later told that we are meant to curate for differential abundance & that has kept me in a knot since yesterday as I can’t find the differential abundance in my paper.

Bolanle Wahab (08:19:28) (in thread): > Your study found differential abundance in fecal microbiota composition between PD patients and healthy controls. Faecalibacterium and Fusicatenibacter were lower in PD patients compared to controls. there was also Clostridiales in PD patients. > > Peptoniphilus, Finegoldia, Faecalibacterium, Fusicatenibacter, Anaerococcus, Bifidobacterium, Enterococcus, and Ruminococcus were also found in patients undergoing medication with L-dopa and entacapone ( PD patients) , compared to healthy controls > I think you can curate these. - File (PNG): IMG_9668

Scholastica Urua (08:19:29) (in thread): > Also note that the study design is not case-control. It’s more like a time series / longitudinal observational study.

Bolanle Wahab (08:19:56) (in thread): > I agree with@Mildred Anashie

Ikeh Darlington Ikeh (08:20:16) (in thread): > @Joan C. Chukwuemekathere are supplementary materials, but non detailing the unknown, unclassified and uncultured signatures. > > I think I will go with the popular response here! leave them out and open a discussion page for it.

Oluwatomisin Omojokun (08:20:19) (in thread): > This is what i found in the article ’’PD patients treated with L-dopa showed significantly higher relative abundances ofEnterococcaceae,Clostridialesfamily XI, and the generaPeptoniphilusandFinegoldia, whileFaecalibacteriumand theRuminococcus gauvreauiigroup were significantly decreased when compared to the controls. However, there were no significant differences on genus or family levels between PD patients who were not treated with L-dopa and the control group or the PD patients treated with L-dopa. > PD patients treated with entacapone showed significantly higher relative abundances of the familiesEnterococcaceae, Bifidobacteriaceae, and theClostridialesfamily XI, as well as of the generaPeptoniphilus, Anaerococcus, theEubacterium brachygroup,Sellimonas, Bifidobacterium, andEnterococcus, when compared to the controls. However, theRuminococcus gauvreauiigroup and the genusFaecalibacteriumwere significantly decreased in this relation.

Faith Ifeoluwa Alexander (08:20:49) (in thread): > Let me share the study I curated here again.

Iman Ngwepe-Ntshibida (08:21:09) (in thread): > Thought it fell under lab experiment . I get it now.

Faith Ifeoluwa Alexander (08:21:14) (in thread): > @Bolanle Wahabwhat you pointed out is what I curated.

Faith Ifeoluwa Alexander (08:22:26) (in thread): > This is the link to my curated study:https://bugsigdb.org/Study_971 - Attachment (BugSigDB): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders.PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS).

Amanda Adoyi (08:23:14) (in thread): > We maybe seem to be carried away by terms a bit much. You won’t explicitly find “differential abundance” but it’s implied, comparisons were made and taxa mentioned regarding that comparison. But…all the confusion would likely be put to rest with the mentors feedback. So rest easy@Faith Ifeoluwa Alexander

Scholastica Urua (08:23:44) (in thread): > Yeah, you may be right. Lab rats were used in the experiment.@Aleru Divinecan you confirm this please

Bolanle Wahab (08:23:53) (in thread): > @Faith Ifeoluwa Alexanderlet’s keep our fingers crossed and wait for responses from our mentors:smiling_face_with_tear:

Aleru Divine (08:25:30) (in thread): > Yes rats were used.@Scholastica Uruaso do we go with laboratory experiment in this case? Even if it was a time series? > > I think so:thinking_face:

Faith Ifeoluwa Alexander (08:26:29) (in thread): > Thank you@Amanda AdoyiMy brain has been boiling hot since yesterday. Finding the differential abundance, I couldn’t rest.

Scholastica Urua (08:30:56) (in thread): > Laboratory experiment might be a better study design for this because animals were utilized under controlled laboratory conditions, I think:thinking_face:

Aleru Divine (08:32:37) (in thread): > Yeah I agree@Scholastica Urua@Iman Ngwepe-Ntshibida

Svetlana Ugarcina Perovic (08:36:40) (in thread): > differential abundance testing == comparing the (relative) taxonabundance between twogroups

Svetlana Ugarcina Perovic (08:37:17) (in thread): > I believe this is your paper to curatehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6884491/?

Joan C. Chukwuemeka (08:37:35) (in thread): > @Faith Ifeoluwa AlexanderBugSigDbB curation focuses on******Differential abundance ****not******relative abundance. ****This post from@Esther Afuapehas actually cleared my understanding of the two concepts. > > “Another struggle of mine was telling apart relative abundance and differential abundance results. ******Relative abundance gives you an idea of the proportion of a microbe in a single sample *****while *******differential abundance compares the abundance levels between different samples or conditions.******* I’m glad this is one thing I no longer struggle with.” *https://kunmiwrites.wordpress.com/2023/12/29/everyone-struggles-week-3-of-outreachy/ - Attachment (The everyday chronicles): Everyone struggles-Week 3 of Outreachy > Everyone struggles (link to image source) Transitioning into tech is not for the faint-hearted. This is what my almost 2 years of attempting to transition into tech has taught me. Going into devops…

Svetlana Ugarcina Perovic (08:37:38) (in thread): > Yes, the results there are curatable.

Joan C. Chukwuemeka (08:39:16) (in thread): > Thanks@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&cid=C04RATV9VCYthis is quite helpful to me too and answers some previous questions I asked. - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Faith Ifeoluwa Alexander (08:47:31) (in thread): > Yes@Svetlana Ugarcina Perovicthat is my paper you tagged there.

Joan C. Chukwuemeka (08:48:10) (in thread): > This is sorted.

Faith Ifeoluwa Alexander (08:48:49) (in thread): > Thank you so much@Svetlana Ugarcina Perovic. It means I am right on track.

Esther Afuape (08:52:07) (in thread): > Figure 1D is curatable,figure 1Eisn’tcuratable to me. Itdoesn’tshow the significance differences between the 2 groups as 1D does. Both 16s sequencing and WMS were carried out in the study so you have to know which one is carried out for the resultsyou’recurating. Results in figure 1 are from 16s sequencing

Esther Afuape (08:52:58) (in thread): > Alright then

Mildred Anashie (08:54:30) (in thread): > @Esther Afuapecould you help us out here:pray:

Isoken Ibizugbe (09:00:14) (in thread): > @Amanda Adoyiyes that is true

Isoken Ibizugbe (09:05:05) (in thread): > Hi@Adenike Oladimeji-Kasumucan i get back to you on this later, it might not be thorough but I’ll give my observations. Thanks

Adenike Oladimeji-Kasumu (09:05:41) (in thread): > I’d appreciate that@Isoken Ibizugbethank you

Faith Ifeoluwa Alexander (09:06:59) (in thread): > @Amanda Adoyipls can you help me review my study curation?

Amanda Adoyi (09:12:37) (in thread): > @Faith Ifeoluwa Alexandersure. would love to.

idiaru Angela (09:18:41) (in thread): > I’ll check and give you review@Adenike Oladimeji-Kasumu

Faith Ifeoluwa Alexander (09:21:51) (in thread): > Okay.@Amanda Adoyihere is the link to my study curation:https://bugsigdb.org/Study_971 - Attachment (BugSigDB): Effect of Parkinson’s disease and related medications on the composition of the fecal bacterial microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disorders.PD patients suffer from gastrointestinal dysfunctions and alterations of the autonomous nervous system, especially its part in the gut wall, i.e., the enteric nervous system (ENS).

Ikeh Darlington Ikeh (09:32:59): > Hi team, I can’t find “Rikenellaceae RC9 gut group” on NCBI, can I use the nearest taxon “Rikenellaceae bacterium 4-1-11” or “Rikenellaceae” or “unclassified Rikenellaceae”?

Mildred Anashie (09:36:45) (in thread): > Hi > Rikenellaceae RC9 gut group does not seem unclassifiedI’mthinking you leave it like that and leave a note:woman-shrugging:Others opinions might differ though

Adenike Oladimeji-Kasumu (09:38:51) (in thread): > Thank you@idiaru Angela

idiaru Angela (09:43:58) (in thread): > I agree with@Mildred Anashieit would be best if you record the taxa like that. It seems to me like a different strain other than it being unclassified

Olajumoke Adeoyo (10:14:37) (in thread): > @Ikeh Darlington Ikehwe were asked to refrain from making guesses. I suggest leaving it as it is.

Bolanle Wahab (10:23:11): > Hi@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther Afuape@Svetlana Ugarcina PerovicI’d like to delete Experiment 6/signature 2 please > I mistakenly added the same signature twice. Thank youhttps://bugsigdb.org/Study_966 - Attachment (BugSigDB): The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies - BugSigDB > BACKGROUND: Altered gut microbiome (GM) composition has been established in Parkinson’s disease (PD).However, few studies have longitudinally investigated the GM in PD, or the impact of device-assisted therapies.

Svetlana Ugarcina Perovic (10:25:31) (in thread): > deleted

Bolanle Wahab (10:32:02) (in thread): > Thank you so much

idiaru Angela (10:37:19): > Hey everyone, there are several unassigned papers that have been added on github if you’re in need of a second or third paper for curation

Ikeh Darlington Ikeh (10:42:15): > Hi everyone, I believe when you are curating for “differential abundance”, the data transformation field on BugSigBD should be “raw counts” not “relative abundance”. Please correct me if I am wrong and does this statement in my study say otherwise? > > “We identified 923 total operational taxonomic units (OTUs) at a 97% similarity level. Of these, 876 were shared between the two groups, and 24 and 23 OTUs were specific to the control and infected groups, respectively.”@Peace Sandy@Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account)

Samreen Aftab (10:56:10): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9657043/pdf/ijms-23-13574.pdfcan anyone go through my paper and help me out with the signatures? From the figure, I cannot find any decreased abundance for MCI vs HC or AD vs HC, so should I just curate the signatures for increased abundance?

Muqtadirat Yussuff (10:58:40) (in thread): > Hi, it’s okay to curate for just increased abundance if there is no hint of decreased and vice versa. I haven’t gone through your paper though

Joan C. Chukwuemeka (11:02:35) (in thread): > @Ikeh Darlington IkehIt can be either. > > see thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697145085673689?thread_ts=1697141457.022309&channel=C04RATV9VCY&message_ts=1697145085.673689 - Attachment: Attachment > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio -> Rare. ANCOM > > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

idiaru Angela (11:08:13) (in thread): > Hey@Ikeh Darlington IkehI think the excerpt above points to raw counts. But it’s a bit hard to know for sure except I go through the paper

Faith Ifeoluwa Alexander (11:08:49) (in thread): > One of our mentors have explained that differential abundance is equal to relative abundance between groups so the statistical test used will determine what your data transformation is.

Faith Ifeoluwa Alexander (11:10:27) (in thread): > @Amanda AdoyiI am yet to get a response from you as regards your review of my study curation.

Ikeh Darlington Ikeh (11:10:43) (in thread): > https://github.com/waldronlab/BugSigDBcuration/files/14564953/Download.article.pdfLink to article

Amanda Adoyi (11:14:32) (in thread): > @Faith Ifeoluwa Alexandersorry bout that but was in the middle of reviewing some other curations. Good thing is you can get multiple reviews from everyone here so thank God for open source. I’ll get to it soon:pray:

Scholastica Urua (11:15:57) (in thread): > @Ikeh Darlington Ikehit can be either “raw counts” or “relative abundance”. Also remember there are other data transformation so it all depends on your study.

Faith Ifeoluwa Alexander (11:18:10) (in thread): > You made it a downloadable file making it impossible to access it without downloading.

Faith Ifeoluwa Alexander (11:19:58) (in thread): > Well LeFSe test and 16S rRNA analysis was mentioned in your paper so your data transformation will be relative abundances.

Faith Ifeoluwa Alexander (11:22:19) (in thread): > I know but some of our co-contributors checked it yesterday which led to the relative abundance question & clarification. So with that question cleared, I wanted a new review of my curation with the new perspective provided.

idiaru Angela (11:22:24) (in thread): > Looking at the article it wasn’t explicitly stated so I might have to agree with@Faith Ifeoluwa Alexander

Esther Afuape (11:26:14) (in thread): > Hi@Mildred Anashie@Scholastica UruaI’mnot sure what the difference between the heat maps in figure 4 is. They all compare the same groups.I’llsay you should focus on the lefse result in the paper

Faith Ifeoluwa Alexander (11:26:41) (in thread): > Yes. You can only curate for abundances available but curate the experiments and don’t add signatures if there are no taxa reported for the experiments.

Scholastica Urua (11:30:41) (in thread): > Thank you@Esther Afuape. Just to confirm your point, does it mean only one experiment; Healthy vs CKD should be curated? Because the Lefse result is for the Healthy vs CKD experiment.:pray:

Mildred Anashie (11:33:56) (in thread): > @Scholastica UruaI thinkshe’ssaying the results reported within text for the other experiments is whatwe’llhave to curate

Scholastica Urua (11:35:36) (in thread): > Oh, I get it now > Thanks@Mildred Anashie

Mildred Anashie (11:36:48) (in thread): > I hopeI’mright:satisfied:

Aishat Ijiyode (11:37:33): > When I pasted the DOI and and url to my curation, it did not auto populate the details of the study, I did it again same thing. This is the first time I’m experiencing this so I’m wondering if this is something that happens normally, is it perfectly normal?

Scholastica Urua (11:37:46) (in thread): > There are more unassigned issues available on GitHub now@Oluwatomisin Omojokun

Mildred Anashie (11:38:25) (in thread): > Might be your connection > > Use the PMID > Did you get anything like “must be unique”? > Were you able to complete and save the page?

Scholastica Urua (11:38:51) (in thread): > @Aishat Ijiyodeyou can try to fill it out manually

Joan C. Chukwuemeka (11:39:00) (in thread): > @Aishat IjiyodeIt’s PMID that auto-populates not DOI

Oluwatomisin Omojokun (11:41:23) (in thread): > Thanks@Scholastica Urua

Aishat Ijiyode (11:42:05) (in thread): > Oh…there is no PMID in the article > > I was able to save the page

Aishat Ijiyode (11:42:33) (in thread): > this is the articlehttps://journals.asm.org/doi/10.1128/spectrum.03190-23

Aananditaa (11:43:04): > Hii everyone! I recently curated this article:https://pubmed.ncbi.nlm.nih.gov/26170900/Could you please review my curation:https://bugsigdb.org/Study_996This will be really helpful. I can review yours as well :) - Attachment (PubMed): Virulence genes are a signature of the microbiome in the colorectal tumor microenvironment - PubMed > This work identifies bacterial taxa significantly correlated with colorectal cancer, including a novel finding of an elevated abundance of Providencia in the tumor microenvironment. We also describe the predicted metabolic pathways and enzymes differentially present in the tumor-associated microbiom … - Attachment (BugSigDB): Understanding of the Site-Specific Microbial Patterns towards Accurate Identification for Patients with Diarrhea-Predominant Irritable Bowel Syndrome - BugSigDB > Fecal microbial community could not fully represent the intestinal microbial community.However, most studies analyzing diarrhea-dominant irritable bowel syndrome (IBS-D) were mainly based on fecal samples.

Scholastica Urua (11:43:13) (in thread): > You can copy the article name and check it on pubmed for the PMID

Mildred Anashie (11:44:04) (in thread): > Try pasting it herehttps://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Scholastica Urua (11:44:26) (in thread): > @Aishat IjiyodeThis should be your PMID: 37461449

Aishat Ijiyode (11:45:11) (in thread): > I just did that

Aishat Ijiyode (11:45:17) (in thread): > Thank you so much

Esther Afuape (11:47:57) (in thread): > Ifthere’sa part of the result text that you can curate from,that’sfine butdon’tworry about figure 4. Ifthere’snothingcuratablefor the other experiments within result text, curate only that lefse result.

Akinbode Mariam (11:55:52) (in thread): > Hi guys@Aleru Divineand@Mildred Anashiei am still a bit confused so if i am to edit the first experiment now are you saying my group 1 will be control group ? cos i already have healthy control as group 0. question2, the n in each group does it also mean the sample size? question 3, will my lab analysis and statiscal analysis remain the same for each experiment ? also is my LdA 2.5 ? Lastly how do i know if my alpha diversity is increased or decreased? so sorry the questions are a lot but i thought i figured it out , thanks to you guys that corrected me.https://bugsigdb.org/Study_995 - Attachment (BugSigDB): Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson’s disease - BugSigDB > Growing evidences show that gut microbiota is associated with the pathogenesis of Parkinson’s disease (PD) and the gut-brain axis can be promising target for the development of the therapeutic strategies for PD.

Blessing Laweh (12:03:03) (in thread): > Hello@idiaru AngelaI’m about to start making these corrections, but I realised there’s np option to add an new experiment aside ‘Duplicate this experiment’. Do I duplicate the experiment and edit to add the new experiment or what?

idiaru Angela (12:05:45) (in thread): > @Blessing Lawehyou should not duplicate the experiment. There is a add experiment tag just below study information. It would add a new experiment for you - File (JPEG): 1710777900899.jpeg

Samreen Aftab (12:06:23): > this figure shows only increased abundance and no decreased abundance right? - File (PNG): image.png

Mildred Anashie (12:07:25) (in thread): > This are the experiments > You now have four experiments not one > Control (Group 1) vs MPTP (Group 1) (signatures reported) > > MPTP (Group 0) vs MPTP+Acu group(Group 1) (signatures reported) > > Control (Group 0) vs MPTP+Acu (Group 1) (Signatures reported) > > MPTP + Acu (Group 0) vs MPTP + Non Acu (Group 1) (no significant results) > > Fig 4G has some results@Aleru Divineplease confirm this

Faith Ifeoluwa Alexander (12:08:07) (in thread): > I didn’t know how to read LDA scores but does this table have a text below it?

Samreen Aftab (12:08:49) (in thread): > @Faith Ifeoluwa AlexanderLinear discriminant analysis (LDA) scores of the bacteria at the genus level

Blessing Laweh (12:13:12) (in thread): > I’ve been searching for it…@idiaru Angela - File (PNG): Screenshot 2024-03-18 171008.png

Mildred Anashie (12:13:14) (in thread): > Yes the n is the sample size for all the groups > > LDA is 2.5 and LEfSe is the statistical test > For the Alpha diversity indices being decreased, increased or unchangedI’mstill trying to figure that out

Faith Ifeoluwa Alexander (12:14:36) (in thread): > I guess it should be increased abundance.

idiaru Angela (12:14:56) (in thread): > You are still in the wrong page. Clink the link in blue then you’d find the right page@Blessing Laweh

Blessing Laweh (12:16:07) (in thread): > Ahhhh got it. Thanks@idiaru Angela

Peace Sandy (12:16:12) (in thread): > @Samreen Aftabfrom the except you shared, I think green is the healthy control that should be your decreased abundance

Joan C. Chukwuemeka (12:19:01) (in thread): > @Faith Ifeoluwa Alexander@Samreen AftabPositive LDA score implies increased abundance, while negative LDA score implies decreased abundance

Mildred Anashie (12:22:04) (in thread): > @Samreen Aftabfrom the figure you have shown > > > If you have an experiment as Health vs MCI > The signatures reported as increased in health are the decreased abundance in the group 1 which is MCI > > In this the taxas in blue will be increased while those in green will be decreased > This is an example of how you can interpret it

Samreen Aftab (12:22:39) (in thread): > Thank you@Mildred Anashie@Peace Sandythis cleared my confusion:blush:

Scholastica Urua (12:22:49) (in thread): > @Samreen Aftabif these are two different experiments; > Healthy control vs MCT (Blue is increased, green is reduced) > Healthy control vs AD (Red is increased, green is reduced)

Kelechi Madubuko (12:25:33): > Hello@Peace Sandy@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma OnyidoI mistakenly added experiment 2 and 3 to my study while I was trying to edit experiment 1. Please I need experiment 2 and 3 deleted. Thank you. Here’s the linkhttps://bugsigdb.org/Study_975 - Attachment (BugSigDB): Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson’s Disease from India - BugSigDB > OBJECTIVES: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson’s disease (PD).

Kelechi Madubuko (12:28:44): > Hello fellow BugSigdbers.. I just finished curating my first paper for my second contribution. Your reviews are highly welcome.https://bugsigdb.org/Study_975 - Attachment (BugSigDB): Dysbiosis of the Beneficial Gut Bacteria in Patients with Parkinson’s Disease from India - BugSigDB > OBJECTIVES: Recent advancement in understanding neurological disorders has revealed the involvement of dysbiosis of the gut microbiota in the pathophysiology of Parkinson’s disease (PD).

Akinbode Mariam (12:47:13) (in thread): > oh thank you@Mildred Anashie

Amanda Adoyi (12:59:31) (in thread): > Would certainly contribute my perspective tonight@Faith Ifeoluwa Alexander

Aishat Ijiyode (13:29:45): > Hi all, there’s a confusion when recording the alpha diversity in my paper. It is a longitudinal study, and the main group are uninfected and infected infants, and both consist of South africans and Nigerians, this is what I have in the study > > do I ignore the alpha diversity aspect totally or how do I go about it since the increase and decrease is not referring to the main groups > link to the paper-https://journals.asm.org/doi/10.1128/spectrum.03190-23 - File (PNG): image.png - File (PNG): image.png

Aishat Ijiyode (13:39:04): - File (PNG): image.png

idiaru Angela (13:42:40) (in thread): > @Aishat Ijiyodefrom the second image, I think there is a comparison group between the south Africa and Nigeria infants and the alpha diversity was noted

idiaru Angela (13:44:12) (in thread): > @Aishat Ijiyodecan you send the article for more clarification?

Svetlana Ugarcina Perovic (13:51:18) (in thread): > Deleted.

Aishat Ijiyode (13:56:38) (in thread): > There is alpha diversity, but it is not between the infected and uninfected infants

Aishat Ijiyode (14:00:05) (in thread): > https://journals.asm.org/doi/10.1128/spectrum.03190-23

idiaru Angela (14:08:21) (in thread): > Yes its very possible that the comparison was made@Aishat Ijiyode

Praise Agbetuyi (14:27:02): > Hi, amazing curators. Thank you for all the support thus far, I do appreciate it. I have a couple of concerns that I would like assistance with: > The statistical analysis used in my paper is not listed in the drop-down menu. I’m unsure of how to proceed in this situation. > In my study, the major grouping consists of Parkinson’s disease (PD) patients with or without motor complications. However, the number of participants in each group is not specified. I have attached the paper to this message. Thank you:hugging_face: - File (PNG): image.png - File (PDF): 1-s2.0-S1353802021004673-main.pdf

Scholastica Urua (14:30:25) (in thread): > What’s the name of the test used@Praise Agbetuyi?

idiaru Angela (14:32:08) (in thread): > From the article you sent, a comparison was done at week 1 to assess the microbial composition of the Nigerian infants vs the South africa infants. And there was statistical difference. In my opinion that should serve as an experiment@Aishat Ijiyode

idiaru Angela (14:33:06) (in thread): > Can you send the screenshot from the article where the statistical analysis was mentioned@Praise Agbetuyi

Praise Agbetuyi (14:47:39) (in thread): > This is the screenshot of the area where the statistical analysis was mentioned - File (PNG): image.png

Mildred Anashie (14:55:40) (in thread): > From this, the statistical test is wilcoxon which is available on BugSigdb (See image in what to use) - File (JPEG): IMG_2467

Habiba Saad (14:56:27) (in thread): > for wilcoxxon use mann whitney > for for ancova use ANOVA

idiaru Angela (14:57:20) (in thread): > @Praise Agbetuyifrom the screenshot you sent, the statistical analysis used is actually Wilcoxon rank-sum test.

Praise Agbetuyi (14:58:04) (in thread): > Okay. Thank you so much

idiaru Angela (14:58:49) (in thread): > @Habiba Saadwilcoxon rank sum test is available in the data base and ANCOVA wasn’t used to test for differential abundance so it doesn’t need to be curated

Habiba Saad (15:06:15) (in thread): > @Peace Sandy@Esther Afuape

Mildred Anashie (15:26:03) (in thread): > Ehhhmmmm > > Not to sound confused but I think the linear regression should be curated also > > I think they also tried to assess the relationship between taxa abundance and other variables (e.g., sex, age, medication doses) while considering multiple factors simultaneously > > The Ancova on the other hand seemed to have been used to control for Confounders:thinking_face:I’m trying to look for alpha diversity results and significant results too@Esther Afuape@Chioma Onyidoplease help me here:pray:Is the linear regression just showing relative abundance and should be left? - File (PNG): IMG_2470

idiaru Angela (15:28:36) (in thread): > @Mildred AnashieI agree with the note on Ancova > But I think the linear regression was only used for relative abundance

Mkpouto Shedrack (15:35:45) (in thread): > Thank you so much everyone for your comments and contributions

EBERE ADEKOGBE (15:39:51) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Eniola Adebayo (15:40:25): > Hi, will anyone be kind enough to help me review my curation. Thank youbugsigdb.org/Study_968

Ima-obong (Aimah) (15:42:55) (in thread): > Sure@Eniola Adebayowill get on it ..

Mildred Anashie (15:43:47) (in thread): > You are welcome@Mkpouto ShedrackThis should help you with your curation:grin:Had fun doing this@Scholastica Uruaup for more collaborations

Eniola Adebayo (16:03:09) (in thread): > Thankyou:pray:

Abiola Salako (16:03:57) (in thread): > @Eniola AdebayoWell done on your Curation. Have you tried checking the taxas in orange through the NCBI browser? If No, please do and if you didn’t get any meaningful results through the NCBI you can google search their genus/ species names and refill them through the NCBI taxonomy Browser.

Eniola Adebayo (16:06:08) (in thread): > I checked NCBI, but I will use the google search for it. Thank you:pray:

Abiola Salako (16:23:17) (in thread): > Please do,@Eniola AdebayoThis afternoon while working on a paper I concluded a microbiome had no name and taxonomy ID and was about to leave it just the way it was, I thought to check Google and to my greatest surprise, I found the name, searched for its ID through the NCBI browser and everything came out well:grinning:

Eniola Adebayo (16:25:59) (in thread): > Will definitely check it out.Thank you:blush:

Ima-obong (Aimah) (16:29:15) (in thread): > @Eniola Adebayo..I don’t know but I think your group 1 for both Experiments 1 and 2 are the same…for instance in experiment 1, group1 is named as “Alzheimer’s group and the description you gave is that they are patients with Alzheimer’s disease.. > > Also in experiment two, the group1 is still referred to as Alzheimer’s patients… > > Also in the method’s section of your paper, I saw that the test was conducted between individuals with Alzheimer’s disease and healthy controls and I didn’t see a sub grouping in it.

Eniola Adebayo (16:32:46) (in thread): > That’scorrect. The difference between experiment 1 and 2 is the statistical analysis used. > There are no sub-groups

Ima-obong (Aimah) (16:37:19) (in thread): > Okay awesome

Praise Agbetuyi (18:10:28) (in thread): > Thank you@Mildred Anashie@idiaru Angela@Scholastica Urua@Habiba Saad. > > I tried looking at the grouping again, but couldn’t get the number of participants for each group

idiaru Angela (18:51:57) (in thread): > @Praise Agbetuyihave you looked through the supplementary materials?

Praise Agbetuyi (19:58:39): > Good morning, Amazing Curators! It’s another day to make meaningful contributions, share ideas, help members of the community make their journey smoother, say hello:grin:, ask questions without fear of being talked down or ignored, and check up on fellow members. This is me wishing you a beautiful Tuesday filled with energy and the right vibes!

Praise Agbetuyi (20:01:50): > Guess what, I just finished my second contribution, and I know this week will be a time to learn more and make more rich curations. Please, I would like my curation to be reviewed. Thank you.https://bugsigdb.org/Study_1006/Experiment_1 - Attachment (BugSigDB): Study 1006/Experiment 1 > …

Praise Agbetuyi (20:04:34) (in thread): > I checked, but there was no link to a supplementary material

Mildred Anashie (22:15:47) (in thread): > Did you figure the sample size out?@Praise Agbetuyi

Scholastica Urua (23:57:06) (in thread): > Same here@Mildred Anashie:hugging_face:

2024-03-19

Ima-obong (Aimah) (02:27:10) (in thread): > @Praise Agbetuyicongratulations on completing your curtaion. Will go through it and give you feedback. > Also, don’t forget to record it on the outreachy site as your second contribution

Muqtadirat Yussuff (02:51:02): > Hello everyone, > > I hope you’re all doing well! I’ve noticed a bit of a dip in activity lately and wanted to check in with everyone. How are things going with your learning and contributions to the project? And of course, how are you all doing outside of our work on research papers? > > This also extends to our wonderful mentors@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido<@UBNSEMS3S>and thank you for your support and guidance > > I do hope we’re all doing alright, have a beautiful day and thank you for this community:sparkles:

Mildred Anashie (02:52:19) (in thread): > Congratulations on finishing your second contribution:confetti_ball:

Scholastica Urua (03:06:18) (in thread): > Hello@Muqtadirat Yussuffthanks for checking in. I’m doing very well. Hope you’re doing good yourself?

Nitya Singhal (03:10:06): > I am not able to find any confounders. Kindly helphttps://www.nature.com/articles/s41531-023-00554-5#MOESM1 - Attachment (Nature): Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease > npj Parkinson’s Disease - Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease

Nitya Singhal (03:10:40) (in thread): > Thanks for the concern. I am doing great. Hope you are fine too.

Mildred Anashie (03:11:02) (in thread): > Thank you@Muqtadirat YussuffI do appreciate you checking inI’mdoing good and you?

Nitya Singhal (03:12:14): > Kindly suggest what kind of signature can be added in my paperhttps://www.nature.com/articles/s41531-023-00554-5#MOESM1

Aleru Divine (03:12:24) (in thread): > Hey@Muqtadirat Yussuffthanks for checking in.Ihaven’tbeen feeling too well but I’m getting a bit better:heart:

Nitya Singhal (03:14:24) (in thread): > @Svetlana Ugarcina Perovic@Chioma Onyido@Scholastica Urua<@UBNSEMS3S>

Faith Ifeoluwa Alexander (03:15:24) (in thread): > Thank you for this@Muqtadirat Yussuff. That is so thoughtful of you.

Scholastica Urua (03:15:32) (in thread): > Hello@Nitya Singhal, I’ll check and revert back.

Faith Ifeoluwa Alexander (03:16:26) (in thread): > @Aleru DivineSorry about your health & thank God you are getting better.

Aleru Divine (03:17:04) (in thread): > It seems anti-PD medication was a confounder controlled for. > > Here > > “To eliminate the confounding factor of anti-PD medication, we selected de novo PD patients as disease controls.” > > I am not very certain, could you look at this:pray:@Scholastica Urua@Mildred Anashie@Desire Oluwarotimi

Nitya Singhal (03:18:47) (in thread): > @Aleru DivineBut there is no such option available in the drop down of confounders

Muqtadirat Yussuff (03:19:09) (in thread): > Hey@Scholastica Urua,@Nitya Singhal,@Mildred AnashieI’m doing a bit okay, thank you guys:blue_heart:

Mildred Anashie (03:19:31) (in thread): > Sorry about your health@Aleru Divine

Muqtadirat Yussuff (03:20:00) (in thread): > Ouch@Aleru Divine, do take care of yourself and gets lots of rest. I hope you get better real soon , sorry:blue_heart:

Ima-obong (Aimah) (03:20:29): > Hello everyone…If you are in need of new papers to curate, please check the GitHub page now. Best of luck:tada:

Aleru Divine (03:20:46) (in thread): > That’s true.I just checked.I tried “medication”I didn’tsee it either.In this case you could leave a note on the discussions page

Aleru Divine (03:21:18) (in thread): > Thank you everyone:pray:

Mildred Anashie (03:24:31) (in thread): > You are right@Aleru Divineit seems medication will be most appropriate but itdoesn’tseem available

Nitya Singhal (03:24:55) (in thread): > Sorry, I didn’t get it. Discussion page as in?@Aleru Divine

Nitya Singhal (03:25:43) (in thread): > @Aleru Divine@Mildred Anashie@Desire Oluwarotimi@Peace Daniel

Mildred Anashie (03:26:10) (in thread): > The signatures will be added based on significant results for the experiment you are recording

Nitya Singhal (03:27:31) (in thread): > Can you explain a little bit more?@Mildred Anashie

Bolanle Wahab (03:29:16) (in thread): > @Muqtadirat YussuffLife gets overwhelming sometimes butI’mgrateful.Thank you for checking in though:pleading_face:, > I hope you’re well too? > And take care@Aleru Divine:heart:

Mildred Anashie (03:29:47) (in thread): > So the comparisons made in your study makes up the experiments you would record and the signatures you will record are those taxas that were reported as being differentially abundant and are either increased or decreased for the Groups

Faith Ifeoluwa Alexander (03:29:59): > Good Morning, everyone. > > Just one last look at my paper and I realized that I got my differential abundance from text but I also had a Table that gave the figures showing the differential abundance. > > So do I cite “Text” as the source of my curation or the “Table” since the “Text” only gave a clearer explanation of the Table in words?

Mildred Anashie (03:30:35) (in thread): > I think you use both text and table as source

Rahila-me (03:30:42): > @Faith Ifeoluwa AlexanderTable is what to site

Scholastica Urua (03:30:51) (in thread): > Hi@Aleru DivineI see the excerpt but I’m actually confused if that means medication is a confounder or not.:thinking_face:If it is a confounder, it can be added even if its not on the list@Nitya Singhal

Aleru Divine (03:31:14) (in thread): > Check on page tools, when you click on the 3 dots,you’llsee “discussion”.Then you can add this text. - File (JPEG): IMG_7747

Faith Ifeoluwa Alexander (03:32:05) (in thread): > Okay. Thank you, I will add the Text before submitting the paper for review. Thank you@Mildred Anashie. > > And I sent you a DM yesterday but you are yet to respond. Thanks.

Barakat Akinsiku (03:36:35) (in thread): > Hi@Faith Ifeoluwa Alexanderyou can cite both

Faith Ifeoluwa Alexander (03:36:55) (in thread): > Okay.@Rahila-me.

Faith Ifeoluwa Alexander (03:37:30) (in thread): > Okay. Thanks,@Barakat Akinsiku.

Barakat Akinsiku (03:38:32) (in thread): > Hi@Muqtadirat Yussuffthanks for checking in.@Aleru Divineso sorry to hear that. Hope you get better soon. Try to get enough rest:hugging_face:

Aleru Divine (03:38:59) (in thread): > I found some of the taxa on the table, the text gave a better explanation so both will be ideal in this case.

Aleru Divine (03:39:54) (in thread): > @Scholastica UruaI was too, hence the tag:sweat_smile::cold_sweat:

Scholastica Urua (03:40:13) (in thread): > @Nitya Singhalthis will guide you on making a discussion/talk page;https://community-bioc.slack.com/archives/C04RATV9VCY/p1710233489795919?thread_ts=1710232358.053269&cid=C04RATV9VCY - Attachment: Attachment > Steps on creating a ‘Talk’ page; > 1. Open your curation > 2. Click on the three dots above (Image 1) > 3. Click on ‘Discussion’ (Image 2) > 4. A talk page will be created were you can write up your discussion. > 5. When done, scroll down to save page. > Hope this helps. > PS: I’m using this study as a sample, I’m not making any edits to it.

Nitya Singhal (03:41:06) (in thread): > Is parkinson’s disease a confounder?

Scholastica Urua (03:41:33) (in thread): > Sorry about your health@Aleru Divine

Barakat Akinsiku (03:42:34) (in thread): > @Nitya Singhalcontrolled for or adjusted for are terms to check for when determining confounders. In this case medication could be one but like others suggested leave an explanation on the talk page since it does not exist in the options

Mildred Anashie (03:43:01) (in thread): > Parkinson’smight be the condition in the study

Ima-obong (Aimah) (03:43:26) (in thread): > Hello@Praise Agbetuyi, I went through your curation and I didn’t see the study design section, hence I couldn’t get a link to your paper to review your curation deeply . > Also, for your confounders, some of them like: duration of illness, daily L-dopa dose, catechol-o-methyl, waering off etc are showing warning indicators because they are not in the list of allowed values. > Also, your signatures are also showing warning indicators because their names don’t match… > > Maybe you could share a link to your paper, I’d love to go through it as well.. > > In the meantime, here is a link to the curation policy, you should check it out for a better understanding…Best Wisheshttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > Microbial Signature Curation Project Policy…

Nitya Singhal (03:43:48) (in thread): > For condition, I chose “essential tremor”. what do you think about it@Mildred Anashie?

Rahila-me (03:44:10) (in thread): > yea we normally site table or figures depending on the one the study specified, text are usually for indebt understanding of those figures or tables

Nitya Singhal (03:44:13) (in thread): > ok got you@Barakat Akinsiku

Muqtadirat Yussuff (03:44:21) (in thread): > @Bolanle WahabMan I really feel the whole life gets overwhelming thing but yeah I’m well, thank you. > > Don’t forget to occasionally take a step back to breathe and decompress:blue_heart:

Bolanle Wahab (03:47:56) (in thread): > Thank you so much@Muqtadirat Yussuff:heart:

Mildred Anashie (03:49:50) (in thread): > It’s Essential Tremor, The study is checking how ET patients can differ from PD patients are in my opinion > > And Parkinson doesn’t seem like a confounder here

Rahila-me (03:52:37): > hello all, we only enter test used for the one that mentioned differential abundant, not the one that says significantly difference between taxon?

Faith Ifeoluwa Alexander (03:54:32) (in thread): > You add an experiment for it with no signature because it was also tested which gave the result of no significant difference.

idiaru Angela (03:55:35) (in thread): > Yes, we only enter the test used for differential abundance in each experiment@Rahila-me

Rahila-me (03:58:16) (in thread): > ok guys..thanks

idiaru Angela (03:58:21) (in thread): > Hey@Muqtadirat Yussuffthank you for checking in. I hope you’re doing okay too

idiaru Angela (03:59:47) (in thread): > Sending major good vibes your way:heart_hands:@Aleru Divine

Aleru Divine (04:16:06) (in thread): > Thanks@idiaru Angela:heart:and everyone:heart:

Joan C. Chukwuemeka (04:20:31) (in thread): > @Muqtadirat YussuffI’m good, thanks for asking. > > You’d get better soon@Aleru Divine:pray:

Abiola Salako (04:25:21) (in thread): > @Muqtadirat YussuffThank you for checking in and@Aleru DivineI wish you a quick recovery.

Abiola Salako (04:31:37) (in thread): > Yes. We only enter the statistical test used for differential abundance@Rahila-me

Ikeh Darlington Ikeh (04:33:18): > Hello everyone, I can’t find the appropriate ontology from the EFO site for the condition: “Maternal glucocorticoid levels during pre- and postnatal periods” nor “Gut bacterial signature in wild primates.” > > My study is “The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels” > > What do I do from here?@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Scholastica Urua@C. Mirzayi (please do not tag this account)

Kelechi Madubuko (04:33:39) (in thread): > Thank you

Muqtadirat Yussuff (04:42:24) (in thread): > I am, thanks for asking:blue_heart:@idiaru Angela

Adedoja Isaac (04:44:19) (in thread): > Hi@Ikeh Darlington IkehYou can look for existing EFO terms that encompass your specific study. > For example, Maternal hormone levels (EFO_0004632) kind of accurately captures the concept of glucocorticoid levels during pregnancy and postpartum period in Animals.

Abiola Salako (04:49:47) (in thread): > @Ikeh Darlington IkehIf you can’t find the appropriate ontology terms on the EFO site, you might consider looking at related terms or broader categories that could encompass your concepts as stated by@Adedoja Isaac.

Blessing Ene Anyebe (05:12:04) (in thread): > @Muqtadirat YussuffThank you so much for asking. I am doing well, How are you doing as well? > > I am so sorry@Aleru DivineI wish you speedy recovery. Like you I have been very strong but I am getting better and I hope to get stronger.

Zaynab Aderonke Ogunnubi (05:12:28): > Hi, everyone! Trust we are having a good morning. > > I’m curating my second article and I need help with reviews and adding a signature:https://bugsigdb.org/Study_949 - Attachment (BugSigDB): Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host - BugSigDB > BACKGROUND: Intestinal helminths are extremely prevalent among humans and animals.In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry.

Peace Daniel (05:32:46) (in thread): > Hello@Chioma Onyido@Esther Afuape@Peace SandyPlease I need help with selecting a close condition for FGF21

Peace Daniel (05:35:35) (in thread): > Do you still need help@Nitya Singhal

Rahila-me (05:40:05): > @Chioma Onyidocan this be curated for?@Peace Sandy - File (PNG): Screenshot 2024-03-19 103820.png

Peace Sandy (05:44:24) (in thread): > Hi@Rahila-meYes it can

Mildred Anashie (05:46:24) (in thread): > Yes it can@Rahila-meWhat I see from this is that the red are increased for control and the green are increased for pjs, from the taxas listed by the right

Adenike Oladimeji-Kasumu (05:59:57) (in thread): > Sure, it can.:+1:

Zaynab Aderonke Ogunnubi (06:14:28) (in thread): > The signature is supposed to be between the control group vs the case group right?@Peace Sandy@Mildred Anashie@Peace Daniel@Aleru Divine

idiaru Angela (06:22:11) (in thread): > Yes@Zaynab Aderonke Ogunnubi

Aleru Divine (06:23:24) (in thread): > That’sright@Zaynab Aderonke Ogunnubiit is usually between the case and the control from that particular experiment.

Mildred Anashie (06:28:14) (in thread): > Yes@Zaynab Aderonke OgunnubiWhat Divine said is right > > The increased for the control will be your decreased signatures for the case and the increased for the case will be your increased signatures for the experiment you are recording

Zaynab Aderonke Ogunnubi (06:35:13) (in thread): > Thank you@idiaru Angela,@Aleru Divineand@Mildred Anashie. So, the alpha diversity test was between 3 groups: (1) Infected vs Non infected, (2) Infected host vs parasites, and (3) Parasites of different sex or origins. But the microbiome identification was done between 2 and 3.

Rahila-me (06:37:43) (in thread): > ok..thanks.

Mildred Anashie (06:43:31) (in thread): > This means that you would possibly have 3 experiments since you have alpha diversity for all and the first might not have signatures since youdon’thave significant results for it and the other two would have signatures recorded based on your statement

Mildred Anashie (06:46:14) (in thread): > (1) Infected vs Non infected(No signatures recorded)(2) Infected host vs parasites(signatures)(3) Parasites of different sex or origins (signatures) > > My understanding of your statement

Aleru Divine (06:48:31) (in thread): > Yes@Mildred AnashieI agree with you.@Zaynab Aderonke OgunnubiIf you have alpha diversity metrics for 3 groups, you would have 3 experiments regardless.In the case where there are no signatures for some groups, you can simply leave that out and curate the available signatures.

Amanda Adoyi (06:52:28): > Aloha my fave people :) Just found out thanks to@Flourish Ralphthat “Faith” is the same as “PD whole tree”. Just pointing it out for anyone who comes across this and doesn’t realize its importance.

Zaynab Aderonke Ogunnubi (06:52:30) (in thread): > Oh, wow! So, that means there would be an experiment for each of them. Can you help me review what I’ve done so far, so, I can know if I’m on the right track?

Aleru Divine (06:53:59) (in thread): > Sure:+1:

Aleru Divine (07:08:21) (in thread): > I see one experiment so far and no signatures added yet.

Zaynab Aderonke Ogunnubi (07:09:20) (in thread): > Yes@Aleru Divine, that’s the experiment for the infected vs non-infected. I became confused when I got to the signatures part

Mildred Anashie (07:12:03) (in thread): > I see same too@Zaynab Aderonke OgunnubiI think you’d go ahead to add the other ones with signatures

Aleru Divine (07:12:28) (in thread): > Also@Zaynab Aderonke Ogunnubisamples were collected from several intestinal regions.“Luminal content samples were collected from several intestinal regions (duodenum, jejunum, ileum, cecum, colon)” for both infected and non-infected.Also seen in Fig. 1B(alpha diversity) > > Please take note of that as those are different experiments.

Zaynab Aderonke Ogunnubi (07:19:56) (in thread): > I actually classified them all as intestines.

Zaynab Aderonke Ogunnubi (07:20:41) (in thread): > If I’m to record them separately, that means there would be about 7 experiments recorded?

Mildred Anashie (07:22:07) (in thread): > I thinkyou’dhave to record all 7 experiments if there are significant results for them > > I apologize Ihaven’tgone through the paper yet

Aleru Divine (07:23:18) (in thread): > Yes that would be 5. Iadviseyou to record separately because they were compared separately.As you can see in Figure 1B.Different alpha diversity(chao1) results for each intestinal region.Just take your time and do this.:pray:

Zaynab Aderonke Ogunnubi (07:25:51) (in thread): > Whew:smiling_face_with_tear:… Thanks a lot.

Mildred Anashie (07:28:26) (in thread): > I see what Divine is saying > > There’s alpha diversity for infected and non infected for the different intestinal sites

Nitya Singhal (07:29:36): > Hey all, > I just completed my second curation and would like some of you to review my curation. Thank you.https://bugsigdb.org/Study_931@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido - Attachment (BugSigDB): Association of fecal short-chain fatty acids with clinical severity and gut microbiota in essential tremor and its difference from Parkinson’s disease - BugSigDB > Diagnosis of essential tremor (ET) at an early stage can be difficult, especially when distinguishing it from healthy controls (HCs) and Parkinson’s disease (PD).

Aleru Divine (07:30:04) (in thread): > And they differ, so it should be curated differently.

Barakat Akinsiku (07:33:39): > Hi everyone, hope we’re having a great day > > I’m curating the following study examining the effects of oats diet on antibiotic induced dysbiosis and have a couple of questions.https://journals.asm.org/doi/10.1128/spectrum.02376-23A total of 72 female mice were used for the experiments and were fed standard diet for 2 weeks (control). The mice were randomly picked and subdivided into 4 diet trials: always dextrose, always oats, prophylactic oats and recovery oats. A further group was created from each diet trial which had amoxicillin included in their diet and mice without amoxicillin (control). > My question is how to determine sample size since the number of randomly selected mice into the different groups was not given. > (2) Alpha diversity (Shannon and Faith) decreased in each group from day 2 for all diets except prophylactic oats which decreased at day 5 and then alpha diversity increased back to pre-amoxicillin levels as early as day 9 for always dextrose, 11 for always oats, 6 for prophylactic oats, and 7 for recovery oats groups. How can this be reported? > (3) Should I focus on creating an experiment for the only group with differentially abundant taxa Always Dextrose (Group 0) vs prophylactic oats( Group 1) see Figure 3, or create experiments for all groups with decreased alpha diversities but no signatures? Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy - File (PNG): b1.png - File (PNG): b3.png

Zaynab Aderonke Ogunnubi (07:34:43) (in thread): > So, mostly everything about the first 5 experiments will be the same asides the body site.

Mildred Anashie (07:35:08) (in thread): > Hi@Nitya Singhalwell done on your curation > > Ifit’sready for review by the mentors thenyou’dinform them by leaving a comment with the study link on GitHub

Esther Afuape (07:35:29) (in thread): > Hi@Peace DanielI go with@Chioma Onyidosuggestion.Response to treatment seems like the best fit since it was an intervention

Mildred Anashie (07:36:38) (in thread): > You’dhave to check if the alpha diversity is same for all

Zaynab Aderonke Ogunnubi (07:37:14) (in thread): > Yeah, I’d look out for that.

Aleru Divine (07:42:11) (in thread): > Hello@Barakat Akinsikuyour sample sizes are in the description for figure 1.

Aleru Divine (07:44:03) (in thread): > For number 3. You create experiment for all the groups compared.Whether or not there was differential abundance stated.You can leave out signatures for the ones without signatures.

Barakat Akinsiku (07:48:02) (in thread): > Thanks@Aleru Divine

Nitya Singhal (07:50:46) (in thread): > Thank you so much@Mildred Anashie. Would you like to review my curation before I submit it further?

Nitya Singhal (07:51:35) (in thread): > Problem solved. Thank you for asking@Peace Sandy

Aleru Divine (07:53:14) (in thread): > For the alpha diversity, I’d suggest you do a pair wise comparison for each group. > > You can see this video from the last office hours for more clarity.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710450054675839 - Attachment: Attachment > Office Hours recording. Thanks all that attended.

Nitya Singhal (07:53:22): > Hey, lovely people, I have completed my curation, so if anyone wants me to review their paper, I am available. Thank you.:smile:

Aleru Divine (07:53:47) (in thread): > I’mnot very certain,I’dwelcome other opinions:pray:

Mildred Anashie (07:54:15) (in thread): > Iwouldn’tmind

Nitya Singhal (07:57:39) (in thread): > That’s great. Please review the curation and lemme know if I missed out on something.

USLACKBOT (08:30:20): > This message was deleted.

Oluwatomisin Omojokun (08:34:06): > Good day, i am working on my curation on a laboratory experiment ’’ Microbial, proteomic, and metabolomic profiling of the estrous cycle in wild house mice’’https://journals.asm.org/doi/10.1128/spectrum.02037-23#F1My question is how to curate the study since there was no group 0 and group 1 given. > 2. Should I focus on creating an experiment for just only the microbiome and leave out the part for proteomic and metabolomic profiling 3. Do I create a signature for different estrous cycles for the oral and vagina or group them together. Thank you

Ikeh Darlington Ikeh (08:35:02) (in thread): > @Aleru DivineI have same challenge with my paper. See figure 2https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01596-w - Attachment (BioMed Central): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - Microbiome > Background During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. Results In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. Conclusions In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract

Aleru Divine (08:38:08) (in thread): > @Ikeh Darlington IkehI’m not sure what your challenge is.

Ikeh Darlington Ikeh (08:41:39) (in thread): > @Aleru DivineIn Fig 2A, comparing Group 0=Rich Season and Group 1= Lean Season. How do I curate the signatures given that each of the signatures in the figure are present in both groups?

Aleru Divine (08:48:36) (in thread): > Figure 2A is not curatable. > > Idon’tthink it satisfies thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549As you can see it is comparing in one group each.Solet’sfind what other figure is curatable or carefully check texts and supplemental resources. - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Aleru Divine (08:51:34) (in thread): > @Ikeh Darlington Ikehsee figure 8

Scholastica Urua (08:53:37) (in thread): > Well done@Nitya Singhal

Aleru Divine (08:53:42) (in thread): > From the description “Relative abundance of the 20 most abundant (top) families and (bottom) genera observed in fecal samples of wild Assamese macaques collected during the rich (R, green bars) and the lean season (L, blue bars) at the Phu Khieo Wildlife Sanctuary (Thailand).” > > I believe you can curate this.

Abiola Salako (08:54:05) (in thread): > Well done,@Nitya Singhal

Bolanle Wahab (09:10:10) (in thread): > Hi@Oluwatomisin OmojokunYour study used a longitudinal study design and samples were collected at different timepoints. > The first day of sample collection or day 0 is the baseline (control) and you’d compare that sample to the other samples collected at the different timepoints stated in your article > 2. I don’t think you should leave out any part of the experiment cause they focused on each mice at different stages of their estrous cycle > 3. I think you should curate signatures for each stages as long as they had differential abundant results

Olajumoke Adeoyo (09:14:25) (in thread): > wow, I did not know this. Thank you@idiaru Angela

Bolanle Wahab (09:15:52) (in thread): > https://waldronlab.slack.com/files/UBNSEMS3S/F06Q0HTRXFB/video1485903245.mp4You can watch this from our last office meeting from 42:11,@C. Mirzayi (please do not tag this account)explained how to curate longitudinal study design. - File (MPEG 4 Video): video1485903245.mp4

Oluwatomisin Omojokun (09:16:36) (in thread): > Thanks@Bolanle Wahab

Mildred Anashie (09:16:39) (in thread): > You would curate all the existing significant experiments in the study

Peace Daniel (09:27:49) (in thread): > Thank you so much@Esther Afuape@Chioma Onyido

Oluwatomisin Omojokun (09:45:07) (in thread): > I thought we were only interested in the microbiomes. do I have to curate proteomes and metabolomes.

Bolanle Wahab (09:59:04) (in thread): > @Oluwatomisin Omojokunno, you don’t. > Just the stages of estrous cycle in the vaginal and oral microbiome. > You could mention them in the discussion page though if the analysis connects with microbiome results in any way, I’m not sure@Esther Afuape@Chioma Onyidoplease help

Oluwatomisin Omojokun (10:00:03) (in thread): > Thanks@Bolanle Wahab

Praise Agbetuyi (10:07:52) (in thread): > Thank you@Ima-obong (Aimah)and@Mildred Anashie. > > > My paper is closed access and was not available through SciHub. > > > I attached the paper here.

Praise Agbetuyi (10:08:41) (in thread): > https://community-bioc.slack.com/files/U06N460QF70/F06Q13TE8AZ/1-s2.0-s1353802021004673-main.pdf - File (PDF): 1-s2.0-S1353802021004673-main.pdf

Scholastica Urua (10:20:28) (in thread): > @Oluwatomisin Omojokunyou can curate the experiments without signatures if the study does mention the increased and decreased taxa (microbiome).

Aleru Divine (10:23:29) (in thread): > Thanks everyone:heart:

Amanda Adoyi (10:36:04): > Hi@Svetlana Ugarcina Perovic@Esther Afuape<@UBNSEMS3S>for experiments where no signatures are recorded even though the groups are explicitly defined, should they be curated or ignored? In such a case, there would be no signatures in the curation.

idiaru Angela (10:38:37) (in thread): > They should be curated@Amanda Adoyi. > See the recording for the last office hour for more clarification by@C. Mirzayi (please do not tag this account)https://community-bioc.slack.com/archives/C04RATV9VCY/p1710450054675839?thread_ts=1710450054.675839&cid=C04RATV9VCY - Attachment: Attachment > Office Hours recording. Thanks all that attended.

Mildred Anashie (10:38:47) (in thread): > Hi@Amanda Adoyicheck this thread outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710277923151239?thread_ts=1710265890.754799&channel=C04RATV9VCY&message_ts=1710277923.151239 - Attachment: Attachment > Yeah you can curate an experiment with no signatures if there was no significant results.

Amanda Adoyi (10:39:31) (in thread): > Thanks

idiaru Angela (10:39:37) (in thread): > Hey@Iman Ngwepe-NtshibidaI’ll check it out and give you feedback

Mildred Anashie (10:41:21) (in thread): > @Oluwatomisin Omojokungoing through this study i think the comparison for the microbiome is what you are curating and i observed it was done between the oral vs vaginal microbiome and not at different time points

Idiat Alli (10:46:21) (in thread): > Thanks@Muqtadirat Yussuff. I hope you’re good too

Joan C. Chukwuemeka (10:48:58) (in thread): > I think curation of experiments without signatures are for ones that have alpha diversity done:thinking_face:If there’s no alpha diversity and no signatures, are we to curate that?@Chioma Onyido<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape@Levi Waldron@Peace Sandy

Idiat Alli (10:49:28) (in thread): > @Aleru Divineget well soon:melting_face::melting_face:

Mildred Anashie (10:50:24) (in thread): > @Joan C. Chukwuemekaifthere’sno alpha diversity and significant results then itshouldn’tbe curated

Joan C. Chukwuemeka (10:52:28) (in thread): > My thoughts too@Mildred Anashie, Just wanted to get the perspective of the mentors and be certain we’re on the same line of thought as regards that.

Mildred Anashie (10:53:09) (in thread): > Okay@Joan C. ChukwuemekaCheck this outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710277923151239?thread_ts=1710265890.754799&channel=C04RATV9VCY&message_ts=1710277923.151239 - Attachment: Attachment > Yeah you can curate an experiment with no signatures if there was no significant results.

Scholastica Urua (10:53:34) (in thread): > @Joan C. Chukwuemekathe first thread Mildred posted actually clarifies that. so if there’s no alpha diversity and significant results then it shouldn’t be curated

Idiat Alli (10:58:41) (in thread): > Well done on your second contribution:clap:@Nitya Singhal

Bolanle Wahab (11:01:01) (in thread): > Hi@Oluwatomisin OmojokunI think Mildred is right, the samples were only collected at different days and then they did a pairwise comparison. > But then@Mildred Anashiethis is an excerpt from one of the supplementary materials > “Individual identity was included as a random effect to account for repeated sampling of the same mouse.”

Habiba Saad (11:01:19): > hey there everyone, is this supplementary figure 6b curatable? - File (PNG): fig6.PNG

Scholastica Urua (11:04:01) (in thread): > @Habiba SaadI think fig 6b is curatable because it shows bacteria that were differentially abundant between smokers and non smokers

idiaru Angela (11:05:14) (in thread): > I think it is@Habiba Saad. It shows the differential abundance between smokers and non smokers at week 0. So using the plot you can tell which increased and which decreased

Habiba Saad (11:05:26) (in thread): > if it is how we would know if it increased or decreased? and which one

idiaru Angela (11:07:17) (in thread): > @Habiba Saadyou can tell from the median line of the box plot . For instance lautropia has an increased median line in smokers compared to non smokers. That denotes increased relative abundance in smaokers

Scholastica Urua (11:09:36) (in thread): > @idiaru Angelais right. Although the image does not seem to capture which color represents smokers and which is non smokers. > Except I’m missing something

idiaru Angela (11:10:21) (in thread): > @Scholastica Urualook under the PCA plot, you’d see the color codes

Habiba Saad (11:11:24) (in thread): > @idiaru Angelait is but how would each signature will be compared for increase and decrease for example for lautropia nonsmoker is increase and for smokers decreased, but for treponema non smokers decrease and smokers increase so how it will curate in the signature in bugsigdb ?

Mildred Anashie (11:12:14) (in thread): > @Bolanle Wahabdid they include results for the different time points? I didn’t find that, the comparisons i saw was oral vs vaginal and oral vs vaginal samples in individual phases of the estrous cycle and i see results reported in text

Scholastica Urua (11:14:10) (in thread): > @Habiba Saadcan you include a link to your study?

Habiba Saad (11:14:39) (in thread): > https://journals.asm.org/doi/10.1128/spectrum.01757-21

idiaru Angela (11:14:40) (in thread): > @Habiba SaadI don’t think you need to curate lautropia for decrease too.( I’d like others opinion on this) . In my opinion there’s increased abundance in lautropia then decrease abundance in the remaining 2 taxa and should just be curated like that

Habiba Saad (11:17:11) (in thread): > another question do I have to make another experiment for this?@idiaru Angela@Scholastica Urua

Scholastica Urua (11:18:35) (in thread): > Lemme scan through the article

idiaru Angela (11:22:04) (in thread): > @Habiba Saadif you haven’t already made an experiment with these two contrasting groups, I think you should. If however you already have, I think the taxa just need to be added to the signature

Scholastica Urua (11:23:19) (in thread): > @Habiba Saadthis excerpt should tell you which is increased or decreased. - File (JPEG): s vs ns.JPG

Mildred Anashie (11:28:16) (in thread): > Hi@Nitya Singhalwell done on your curation:clap:The antibiotic exclusion should be just the duration and in this case “one month” is enough > > The p value is 0.05 not 0.082 > > LDA is 2 > They were matched on Age, sex and BMI > > You should also look at Table S5 for significant signatures and compare with the text you curated from > > Every other thing is okay in my opinion

Bolanle Wahab (11:41:32) (in thread): > Ididn’teither,it’sprobably worth mentioning in the discussion page I guess

Joan C. Chukwuemeka (12:56:24) (in thread): > @Habiba SaadCLR i.e. Centered-log ratio is a type of data transformation > > I’ll try to go through your paper and see what insights I can draw from it. I’ll revert to you once I do.

Joan C. Chukwuemeka (13:07:24): > Good afternoon/evening<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Levi Waldron@Chioma Onyido@Peace Sandy@Esther AfuapeI have completed this experiment that was found in “Studies with incomplete experiment”https://bugsigdb.org/Study_714and it’s ready for review.<!here> - Attachment (BugSigDB): Ketogenic Diets Alter the Gut Microbiome Resulting in Decreased Intestinal Th17 Cells - BugSigDB > Very low-carbohydrate, high-fat ketogenic diets (KDs) induce a pronounced shift in metabolic fuel utilization that elevates circulating ketone bodies; however, the consequences of these compounds for host-microbiome interactions remain unknown.

Habiba Saad (13:11:39) (in thread): > thank you so much guys@idiaru Angela@Scholastica Urua:heart:

Scholastica Urua (13:12:57): > Hello everyone, please I need some help with this:pray:: > > I believe the sequencing type used here is Polymerase Chain Reaction (PCR), and the sequencing platform is the Pacific Biosciences Sequel platform (I filled in PacBio RS). > > Q1. Is this accurate? There seems to be a repeated mention of 16S rRNA, which has caused some confusion for me. I’m accustomed to seeing 16S/WMS paired with Illumina as the sequencing type and platform, respectively:sweat_smile:. It’s quite intriguing to encounter something different. > > Regarding alpha diversity, here’s an excerpt: > “We assessed various indices in the α-diversity analysis, including observed species (Sob, indicating operational taxonomic unit (OTU) numbers), Chao (indicating species richness), Good’s coverage (indicating the coverage of OTUs with low abundance), Simpson (indicating species diversity), Shannon (indicating species evenness), and phylogenetic diversity (PD)-whole tree (indicating the coverage of OTUs with low abundance). The comparison between patients with PA and healthy individuals is summarized in Fig. S1.” > > Q2. How is ‘Good’s coverage’ curated in BugSigDB? > Q3. Based on Fig. S1, which indices would you say have increased or decreased? > > Here’s a link to the study;https://bugsigdb.org/Study_1015@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido<@UBNSEMS3S> - Attachment (BugSigDB): Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing - BugSigDB > The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders. - File (TIFF): Fig S1.tif

Scholastica Urua (13:14:55) (in thread): > Also, I only curated 1 experiment because the study did not show alpha diversity or differential abundance of microbes between the four clinical phenotypes of PA. Is this okay?:thinking_face:Image of sequencing type and platform is below; - File (JPEG): PCR.JPG

Nitya Singhal (13:29:48) (in thread): > I can’t find table s5 though@Mildred Anashie

Nitya Singhal (13:32:38) (in thread): > In antibiotic exclusion, the info icon says, “Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any),” so I included other criteria as well. Will that be wrong?@Mildred Anashie

Scholastica Urua (13:35:50) (in thread): > @Nitya SinghalBugSigDB only focuses on antibiotic exclusion so@Mildred Anashieis right. You might want to stick with only the antibiotic duration.

Nitya Singhal (13:38:14) (in thread): > ok ok

Nitya Singhal (13:45:29) (in thread): > In which experiment LDA is 2?@Mildred Anashie

Habiba Saad (14:09:19) (in thread): > Pac bio is correct > i dont think we need to curate for goods coverage on bugsigdb.

Aleru Divine (14:18:11): > Good eveningeveryone,@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma OnyidoFor my sample size,the paperstates n = 4-5 mice.I went with this as they didn’t exactly specify. But I’m getting this warning message.““-5” can not be assigned to a declared number type with value 4.”What do I do in this situation?:pray: - File (JPEG): IMG_7987 - File (JPEG): IMG_7985

Scholastica Urua (14:20:51) (in thread): > @Aleru Divinewhat if you go with one value, maybe 5 because that’s the highest. Then include a discussion on the talk page…

Aleru Divine (14:22:01) (in thread): > That sounds like a great idea.Thanks@Scholastica Urua:blush:

Mildred Anashie (14:26:29) (in thread): > I’m not sure how Goods coverage is curated > > My interpretation of the Alpha diversity from S1 is that > Sobs=increased in case > Chao=increased in case > Good coverage= unchanged > Simpson= not so sure, but I think unchanged > Shannon = increased in health > PD=increased in case > > The mentors opinions will help better

Ruth Bamgbose (14:26:59) (in thread): > Oh, I also have this issue with the paperI’mcurating was just about to ask

Desire Oluwarotimi (14:27:40) (in thread): > I’d suggest that you wait for a mentor’s opinion on this.@Scholastica Uruamight be right by the way.@Aleru Divine

Mildred Anashie (14:28:49) (in thread): > Is there no table or any other information with information on the mice?@Aleru Divine:thinking_face:

Joan C. Chukwuemeka (14:28:51) (in thread): > @Aleru Divinehad this issue in the last experiment I curated for an incomplete study, I went with 4 though. I reasoned that 4-5 meant, it may be up to 5 or not:shrug:@Mildred Anashiein my own case there wasn’t

Scholastica Urua (14:31:42) (in thread): > Thanks@Habiba Saadand@Mildred AnashieI went with increased for chao, simpsons and faith but I’m not so sure if that’s correct.

Mildred Anashie (14:33:33) (in thread): > @Nitya Singhalcheck under statistical analysisyou’dget information for the LDA > > Also the Table S5 was mentioned in the paper > > Download the supplementary information, also Ctrl + f supplement should help you find it

Mildred Anashie (14:35:16) (in thread): > Okay@Joan C. ChukwuemekaYou have a point with your reason for picking 5

Aleru Divine (14:37:29) (in thread): > Another table says 4-6 and another 4-5

Aleru Divine (14:38:06) (in thread): > 4 is consistent so I guessI’llgo with that.

Joan C. Chukwuemeka (14:38:18) (in thread): > I picked 4, that may be more feasible for you too@Aleru Divine

Desire Oluwarotimi (14:39:10) (in thread): > An error is inevitable given that they were inconsistent with the numbers/range.@Aleru Divine

Aleru Divine (14:41:36) (in thread): > So what do you suggest? In this case?:thinking_face:

Ruth Bamgbose (14:42:15): > Hello every one,@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Esther Afuape@Peace Sandy@Chioma OnyidoI have some questions regarding the paper I’m curating.https://www.mdpi.com/2072-6643/14/3/412 > 1. The way I see it the condition being studied is the impact of postnatal iron supplementation, but I’ve checked the drop down and ncib and the only terms I can find that relate are, mouse postnatal and postnatal, I don’t know what I’m to put down as condition > 2. I’m confused on how to curate the sample sizes as it is mentioned in the study as “3 litters per group, n = 27-29 per group” > 3. Also, ruminococcus 2 is abundant, do I record it as ruminococcus, i am not sure about this. - File (JPEG): IMG_5662

Desire Oluwarotimi (14:42:33) (in thread): > Wait for the mentors’ opinion I guess.

Esther Afuape (14:44:50) (in thread): > Haven’tseen a range of values for a sample size before@Svetlana Ugarcina Perovic<@UBNSEMS3S>

idiaru Angela (14:50:39) (in thread): > For 2@Aleru Divinehas the same issue. You can monitor this thread for when the mentors give an answerhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710872291722169?thread_ts=1710872291.722169&cid=C04RATV9VCY@Ruth Bamgbose - Attachment: Attachment > Good evening everyone, > > @Svetlana Ugarcina Perovic @UBNSEMS3S @Esther Afuape @Peace Sandy @Chioma Onyido > > For my sample size, the paper states n = 4-5 mice. > > I went with this as they didn’t exactly specify. But I’m getting this warning message. > > ““-5” can not be assigned to a declared number type with value 4.” > > What do I do in this situation? :pray:

Scholastica Urua (15:33:52) (in thread): > Hello@Esther Afuape, please can you help out here:pray:

Svetlana Ugarcina Perovic (15:54:32) (in thread): > me neither@Esther Afuape

Ruth Bamgbose (15:54:36) (in thread): > Thanks@idiaru Angela, I will

Svetlana Ugarcina Perovic (15:55:48) (in thread): > Where there isn’t a consistent answer, it is ok just to leave that field blank but with a note why.

Aleru Divine (16:16:18) (in thread): > Noted! Thank you@Svetlana Ugarcina Perovic@Esther Afuapeand everyone:heart:

UBNSEMS3S (17:10:43) (in thread): > Yeah it’s not uncommon for animal studies to not consistently report sample size for some reason.

UBNSEMS3S (17:31:12) (in thread): > Yes looks like at least three experiments to me.

Oluwatomisin Omojokun (18:03:44) (in thread): > Thanks everyone@Mildred Anashie.@Bolanle Wahab. i am almost done with the curation, i will post it soon for review. Thanks

Aleru Divine (19:03:49) (in thread): > Leaving it blank then.:pray:thanks<@UBNSEMS3S>and everyone again:heart::sweat_smile:

Olajumoke Adeoyo (23:33:17) (in thread): > Hi@Aishat Ijiyode, > To the best of my knowledge, your study appears to be a longitudinal study conducted in two different locations. Since it’s a longitudinal study, the timeframe is crucial. You’re focusing on infants at week 1 and infants at week 15, whether they are iheu or ihuu. These are the major groups you’re examining. > Considering this, I suggest creating two experiments: Experiment 1 for South Africans and Experiment 2 for Nigerians. This way, you can record the alpha diversity for week 1 and week 15 infants in both locations. > I hope you get me?. You can tag our mentors for further clarifications.

Nitya Singhal (23:47:05) (in thread): > Hey@Mildred Anashie, are you referring to the LDA as 2 from this statement? > > “Linear discriminant analysis (LDA) effect size (LEfSE) analysis was used for between-group comparisons (ET vs. HC, ET vs. PD) with an alpha cutoff of 0.05 and an effect size cutoff of 2.0.”

2024-03-20

Mildred Anashie (00:30:46) (in thread): > Yes in my opinion@Nitya Singhal

Scholastica Urua (01:29:38): > Hello everyone, good morning:sun_with_face::sunny:This is a kind reminder of the MVIF today. See you all there:hugging_face:.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710321249373689?thread_ts=1710321249.373689&cid=C04RATV9VCY - Attachment: Attachment > Good morning :potted_plant: > > Today I have a special invitation for you: join us next week at MVIF, a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > Microbiome Virtual International Forum > is free, 3 hours in total, > happens every month, and > covers microbiomes from different niches and hosts (not only the human gut!). > > Attending MVIF is a good way to learn about the latest microbiome research and catch opportunities for networking. > You can register for free at https://microbiome-vif.org

Aleru Divine (01:49:30) (in thread): > Yes@Scholastica Uruathanks for the reminder.See you there:hugging_face:

Peace Daniel (01:53:03) (in thread): > Good day and thanks for the reminder:blush:

Svetlana Ugarcina Perovic (02:00:00): > Good morning:tulip:There’s still time to register for todays’ MVIFhttps://www.microbiome-vif.org/en-USIt’s a 3 hour event about the latest microbiome science: > 1. a keynote and Q&A: this time Curtis Huttenhower will present their workhttps://huttenhower.sph.harvard.edu/home/ > 2. 3 short talks* and Q&A session with speakers > 3. highlights & networking session where you can meet other microbiome researchers > FUN FACT: one of the studies, that will be presented as a short talk. has been curated very recently by YOUhttps://github.com/waldronlab/BugSigDBcuration/issues/179See you at MVIF!*<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace Sandy@Svetlana Ugarcina Perovic - Attachment: #179 Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices > Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices – Kun Huang – Cell Reports Medicine > > https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(24)00049-1 - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Mildred Anashie (02:01:18) (in thread): > Thank you@Scholastica Urua:hugging_face:

idiaru Angela (02:02:23) (in thread): > Good morning@Svetlana Ugarcina Perovic:cherry_blossom:. Thank you for the reminder.

idiaru Angela (02:06:08): > Good morning Everyone, > As a way of clarification, if an experiment was done to determine the bacteria composition of the soil in the habitat of a particular organism and it yielded significant results, > Would I curate that kind of experiment on BugsigDB? > I’d appreciate your response Thank you@Chioma Onyido@Esther Afuape@Peace Sandy@Svetlana Ugarcina Perovic

Mildred Anashie (02:08:25) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you for the reminder

Scholastica Urua (02:08:45) (in thread): > Good morning@Svetlana Ugarcina Perovic

Scholastica Urua (02:25:35): > Good morning@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape:boom:I encountered a blocker in my recent curation and really need your assistance. Could you please help me interpret these alpha diversity measures? Additionally, is it possible for a statistical test not to be mentioned in a paper? I’ve gone through my article several times, and it seems that the statistical test isn’t mentioned at all. > Here’s a link to my curation -https://bugsigdb.org/Study_1015Thank you for your help. - Attachment (BugSigDB): Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing - BugSigDB > The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders. - File (TIFF): Fig S1.tif

Desire Oluwarotimi (02:27:50) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you.

Peace Daniel (02:43:37) (in thread): > Could this be (in reference to case) > Increased > Increased > Unchanged > Decreased > Decreased > Increased > > ?? > How did you read it@Scholastica Urua

Mildred Anashie (02:47:09) (in thread): > Hi@Scholastica UruaThis is from you:grin:https://community-bioc.slack.com/archives/C04RATV9VCY/p1709714631523339?thread_ts=1709713879.191869&channel=C04RATV9VCY&message_ts=1709714631.523339 - Attachment: Attachment > Yes @Bolanle Wahab leave blank if the study doesn’t specify a statistical test.

Scholastica Urua (02:57:08) (in thread): > Thanks@Mildred Anashie:hugging_face:This is actually the first time I’m encountering this.

Scholastica Urua (02:59:12) (in thread): > @Peace Danielthis is how I documented it in my curation;Chao1 increasedSimpson increasedFaith increased

Aleru Divine (03:00:33) (in thread): > Good morning@Svetlana Ugarcina Perovicand everyone:sunny:Looking forward to it:hugging_face:

Aleru Divine (03:02:40) (in thread): > @Scholastica Uruaif no statistical test was mentionedit’ll be okay to leave it blank.Let me look at the alpha diversity:crossed_fingers::sweat_smile:

Scholastica Urua (03:03:57) (in thread): > Thank you@Peace Daniel@Mildred Anashie@Aleru Divine

Peace Daniel (03:06:27) (in thread): > Hm, alright we hope to hear from the mentors soon@Scholastica UruaBut why do you think Simpson was increased?

Aleru Divine (03:13:57) (in thread): > For Shannon and Simpson I see no significant difference.(There is but I’d consider it insignificant):face_with_peeking_eye:I’d wait for an input from the mentors@Scholastica Urua

Ima-obong (Aimah) (03:17:21) (in thread): > Thank you@Svetlana Ugarcina Perovic.. looking forward to it

Scholastica Urua (03:19:01) (in thread): > I’m not so sure why@Peace Daniel:pensive:Thank you@Aleru Divine

Peace Daniel (03:20:11) (in thread): > Alright then, we wait

Aleru Divine (03:21:19) (in thread): > Hi@idiaru AngelaGood morning.Is this a paper assigned to you for curation?

idiaru Angela (03:21:36) (in thread): > Yesss

Aleru Divine (03:25:29) (in thread): > I like to believe it is relevant.This is because I think papers are carefully selected beforethey’reput up for curation.And like you said, it yielded significant results.So yeah, I think it is curatable.Please can you a link to the paper?I’dlike to read it:pleading_face:it seems different.

idiaru Angela (03:28:21) (in thread): > https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03150-yHere it is@Aleru DivineThere are other curatable experiments that I have already recorded. I just wanted to know if I should exclude the one on soil or not - Attachment (BioMed Central): Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs - BMC Microbiology > Background Frogs are critical economic animals essential to agricultural ecosystem equilibrium. However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings. While frog-associated microbiota contribute to elemental cycling and immunity, the effects of frog sex and health on gut bacteria remain understudied, and the relationship between frog habitat and soil microbes is unclear. We aimed to determine how frog sex, health status and habitat influence symbiotic bacteria and community assembly mechanism to provide guidance for sustainable frog farming and conservation. Results We employed 16S rRNA sequencing to investigate gut microbiota differences in relation to frog sex and health status. We also compared symbiotic communities in frog-aggregation, native and soybean soil on the farm. Results showed that gut bacterial β-diversity and taxonomy were markedly influenced by frog sex and health. Healthy frogs had more robust gut bacterial metabolism than frogs infected with MID. Cooccurrence network analysis revealed that healthy female frogs had more complex microbial network structure than males; however, diseased males showed the greatest network complexity. The assembly mechanism of gut bacteria in male frogs was dominated by deterministic processes, whereas in female frogs it was dominated by stochastic processes. Among symbiotic bacteria in frog habitat soils, deterministic processes predominantly shaped the community assembly of soybean soil. In particular, soybean soil was enriched in pathogens and nitrogen functions, whereas frog-aggregation soil was markedly increased in sulphur respiration and hydrocarbon degradation. Conclusion Our study reveals that sex mainly alters the interaction network and assembly mechanism of frog intestinal bacteria; MID infection significantly inhibits the metabolic functions of intestinal bacteria. Furthermore, diverse frog habitat soils could shape more symbiotic bacteria to benefit frog farming. Our findings provide new horizons for symbiotic bacteria among frogs, which could contribute to sustainable agriculture and ecological balance.

Aleru Divine (03:35:07) (in thread): > Oh! Okay.I think the mentors would be in the best position to answer that.

Aleru Divine (03:35:21) (in thread): > Let me take a look now:pray:thanks for sharing

Nana (03:41:29) (in thread): > @Scholastica Uruawhat will you enter for coverage?

Scholastica Urua (03:43:17) (in thread): > @NanaI‘m unsure of that as well. I actually asked in my previous post how ’Good coverage’ is documented but I didn’t get an answer.

Preethi grace Manthena (03:53:51): > Hii Everyone, I hope everyone is doing great !

Preethi grace Manthena (03:57:08): > I’ve just completed my first task, I’ve filled the curation form. Can anyone please help me in recording the contribution, what are the dates I should enter specifically. Your response will helpful for me and Thank You:handshake:

Aleru Divine (03:57:50) (in thread): > @idiaru Angelait looks pretty curatable to me. But maybe wait and get a “go ahead” from the mentors.

Mildred Anashie (03:58:09) (in thread): > Hi@Preethi grace ManthenaWell done on completing your first contribution

Mildred Anashie (03:58:36) (in thread): > The datesyou’llenter for the first contribution will be the date you started and the date you finished

Muqtadirat Yussuff (03:59:07) (in thread): > Hi, for your start date input the date you started the curation and for the merge date input the date you completed it. > > For second curation upwards the merge date would be when the mentors have assigned the “reviewed” tag to your GitHub issue but for the first curation, you don’t need this

idiaru Angela (04:00:12) (in thread): > @Aleru Divinesame thing I thought. but I haven’t yet seen a curation on soil bacteria. so I just want a confirmation. thank you Aleru

Preethi grace Manthena (04:01:11) (in thread): > Thank you for your responses@Mildred Anashie@Muqtadirat Yussuff, Is the date I’ve started my curation work, or The date I’ve informed here as a applicant

Mildred Anashie (04:01:47) (in thread): > The date you started the contribution

Muqtadirat Yussuff (04:01:50) (in thread): > @Preethi grace Manthena, it’ll be the date you started curation

Scholastica Urua (04:02:44) (in thread): > Hello@Preethi grace Manthenawell done on completing your first task. > > Just to be clear, are you referring to the Qualtrics form? > Also, please have you recorded any contribution on Outreachy before now? this is because the Bioconductor project is closed for new entry.

Preethi grace Manthena (04:03:16) (in thread): > okay thank you so much:slightly_smiling_face:. I’ve got u@Mildred Anashie@Muqtadirat Yussuff

Preethi grace Manthena (04:05:28) (in thread): > yes mam, I’ve submitted qualtrics form today, this is my first contribution in outreachy, as ive occupied with my exams in academics, i’m unable to do it before, apoligies for this delay mam@Scholastica Urua

Abiola Salako (04:06:18) (in thread): > Thanks for the reminder@Svetlana Ugarcina Perovic.

Scholastica Urua (04:07:50) (in thread): > @Preethi grace ManthenaI’m also a fellow applicant. Nice to e-meet you:hugging_face:. > I not sure you can still record contribution on outreachy since the project is closed. That’s why I’m asking…

Abiola Salako (04:08:30) (in thread): > Yes,@idiaru Angela. Let’s wait and hear from the mentors

Preethi grace Manthena (04:09:42) (in thread): > Haan, I’ve checked it in website, I’ll confirm with the mentor once they are online, Btw@Scholastica Uruasorry for mis -understanding.

Preethi grace Manthena (04:10:14) (in thread): > Nice to meet you too:handshake::blush:

Abiola Salako (04:13:58) (in thread): > @Preethi grace Manthenawell done on completing your first contribution.

Idiat Alli (04:24:59) (in thread): > Good morning@Svetlana Ugarcina Perovic

Bolanle Wahab (04:25:50): > Hi everyone@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther AfuapeThis is quite long but Please help me out:smiling_face_with_tear:So my study has two samples and each of the samples were divided into 2 portions each and kept at different storage conditions at different times too. > I’ve been able to list out the storage conditions for differential analysis > Excerpt from the study: > > “Differential abundance analysis. Differential abundance analyses were performed using DESeq (31) at sample matrix level (P1, P2, S1, and S2) using the raw count table. Custom DESeq sizeFactors were used, taking the total sums for the different samples divided by the mean total sums for all of the samples. Pairwise comparisons of the abundance of the genera were performed between storage conditions using DESeq2. Based on the PCoA plots and raw dissimilarities, the differences between 0 h and 64 h (–80°C), 0 h and 64 h (22°C), and 0 h and 64 h (5°C) were further assessed through the use of MA plots with the genera colored according to the same criteria as in the CCA (see above). Comparison of the same genera or AMR genes across the different samples was performed by extracting log2 fold change and generating box plots to compare across all samples and scatter plots to compare the two pig feces and sewage samples separately.” > > My first question now is what are the sample sizes cause I can’t find them, they weren’t specified or I probably missed it > > 2. How do I attach each sample to the various storage conditions? Should I curate them separately (i.e P1 and P2 separately, S1 and S2 separately) or together?Thank you > Study link:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/ - Attachment (PubMed Central (PMC)): Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns > Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. …

Idiat Alli (04:36:16) (in thread): > Thank you for the reminder@Scholastica Urua

Mildred Anashie (04:46:47) (in thread): > Hi@Bolanle Wahabfrom the Alpha diversity Figure (Fig1b) and Fig4 this looks like you have a lot of experiments to curate > > And you might have to record the experiments for P1 vs P2 at all the storage conditions (both time and temperature) and S1 vs S2at all the storage conditions (both time and temperature) > > Others opinions might differ, still reading through to confirm this

Bolanle Wahab (04:56:13) (in thread): > @Mildred AnashieI thought so too, they actually narrowed it down to 3 storage conditions for differential analysis. > Another question now is, do you think this implies I’m also going to compare pig vs sewage at each conditions too? - File (JPEG): IMG_9686

Abiola Salako (05:00:19) (in thread): > 1) the sample sizes may be provided elsewhere in the supplementary materials@Bolanle WahabDid you check if your study has supplementary materials?

Mildred Anashie (05:05:40) (in thread): > Yes in Fig1b and Fig 4 it’s same, the study said they focused on 0h, 16h and 64h > > You have forP1vs P20 hours16 hours-80°C16 hours-20°C16 hours-5°C16 hours-22°C > 64hours-80°C64hours-20°C64hours-5°C64hours-22°CAnd youalso haveforS1 vs S20 hours16 hours-80°C16 hours-20°C16 hours-5°C16 hours-22°C64 hours-80°C64 hours-20°C64 hours-5°C64 hours-22°C

idiaru Angela (05:06:08) (in thread): > @Mildred AnashieI don’t think all of them are statistically significant though. Or am I missing something:thinking_face:

Bolanle Wahab (05:07:47) (in thread): > @Abiola Salakoit does butit’snot there,I’mstill going over the entire article again though

Mildred Anashie (05:09:23) (in thread): > The text below is from your paper and I think the sample size is mentioned there > It seems one feaces sample was collected from the first pig (P1) and same for the second pig (P2) > Also for the sewage samples S1=1 sample and S2=1 sample > > This is my opinion > > Microbiome samples. > > Two pig feces and two domestic sewage samples were collected for this study. The pig feces samples were obtained from two individual animals right after defecation at two different conventional pig production farms in Denmark on separate occasions and were transported within 3 h to the laboratory in a cooling box. The unprocessed domestic sewage was collected at a local wastewater treatment facility (Lyngby-Taarbaek Forsyningen) on separate occasions as 20-liter inlet water in 5-liter sterilized plastic bottles, transported in cooling boxes to the laboratory within 20 min, and placed into a refrigerator at 5°C. Sedimentation of the sewage was commenced immediately using 50-ml Falcon tubes and two centrifuges (Eppendorf 5810R, Hamburg, Germany; program: 10 min at 10,000 × g). Sedimentation of the entire sewage sample was completed within 12 h. > > Each individual pig feces sample and sewage pellet was thoroughly homogenized in a 50-ml Falcon tube with a sterile wooden spatula and distributed into two large aliquots in 50-ml Falcon tubes, respectively. One aliquot for each of the four original microbiome samples, respectively, was spiked with a freshly prepared mock community (see below), and all samples were homogenized with a sterile wooden spatula to take into account that the mixing might have an effect on community composition. Small aliquots for each sample storage condition were prepared in Eppendorf tubes and either processed immediately (storage for 0 h) or stored at a certain temperature (−80°C, −20°C, 5°C, or 22°C) for a specific period of time (16 h, 64 h, 4 months, 8 months, or 12 months) (described in detail below). Additional aliquots underwent 2 to 4 freeze-thaw cycles at different time points (40 h, 64 h, or 88 h) (described in detail below).

Bolanle Wahab (05:10:27) (in thread): > @Mildred Anashiethe storage condition for differential abundance were actually pointed out. > 0h and 64hrs (-80) > 0h and 64hrs(22) > 0h and 64hr(5) > 0hr as the baseline

Bolanle Wahab (05:13:32) (in thread): > @Mildred Anashiesee here > Itdidn’tspecify for each,it’sactually conflicting - File (PNG): IMG_9688

Abiola Salako (05:15:46) (in thread): > @Mildred Anashiewhat do you think of this except from her work? - File (JPEG): Screenshot_20240320_101414_Chrome.jpg

Mildred Anashie (05:19:36) (in thread): > @idiaru Angelawe have alpha diversity indices for the storage conditions they focused on for both samples > I don’t know if she should curate all but I believe those results are either increased, decreased or unchanged

Mildred Anashie (05:21:16) (in thread): > @Bolanle Wahabread from the beginning of where the 304 was mentioned, I mean from the start right under results > > I believethat’swhere the screenshot is a from

idiaru Angela (05:21:23) (in thread): > Okayy I see what you’re saying now@Mildred Anashie

Bolanle Wahab (05:24:14) (in thread): > @Mildred Anashieso you’re saying I should take each sample as 1, literally? > Now thatI’mthinking about it,you’reright, I was just thinking about how everything would amount to 304, forgettingI’mnot curating all the storage conditions

Mildred Anashie (05:27:42) (in thread): > @Abiola Salakomy opinion of that is that > > They are investigating how storage temperature and duration impact two types of samples: pig feces and sewage. And in the experiments done, samples were stored at different temperatures, room temperature, refrigerated, frozen and for varying durations 0hours, 16hours, 64hours, 4months, 8months and 12months > > Although the last three (4months, 8months and 12months) was excluded > > This is what I think about that

Ikeh Darlington Ikeh (05:28:00): > Hi everyone, taking a look at the figure below, I believe it is curatable, the challenge is which group to classify as group 0 and 1. Since the figure describes “the effect of different maternal predictors moderated by Age at sampling on the differential relative abundance of bacterial genera during the rich season.” > > From my understanding, the relative abundance of certain bacteria genera responded to maternal glucocorticoid (GC) levels during early gestation (Early-preGC), and this effect is amplified with increasing age. 14.1% precisely exhibited this pattern amongst which 4.7% and 9.4% showed increased and decreased abundance as age (early pre-GC) increased respectively. > > How will I define group 0 and 1 ? > > Link to paper belowhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01596-w@Chioma Onyido@Joan C. Chukwuemeka@Peace Sandy@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account) - Attachment (BioMed Central): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - Microbiome > Background During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. Results In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. Conclusions In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract - File (PNG): image.png

NWAKAEGO VINCENT (05:31:35) (in thread): > thank you<@UBNSEMS3S>

Mildred Anashie (05:34:02) (in thread): > So@Bolanle Wahaball of this is my opinion and what I understand > > Maybe the mentors opinions might differ > > I think the 304 was gotten after “Triplicate DNA isolations were performed for each storage condition”. (See the images attached) - File (JPEG): IMG_2541 - File (JPEG): IMG_2540

Bolanle Wahab (05:38:47) (in thread): > Okay. Thank you so much you guys@Mildred Anashie@Abiola Salako@idiaru Angela:heart::heart:

idiaru Angela (05:39:23) (in thread): > From the article you shared@Ikeh Darlington IkehI think the definitions for group 0 and 1 are in the figure description

Nana (05:50:43) (in thread): > Ok

Victoria (Burah) Poromon (05:51:50): > Hello everyone, Good morning.I’ma bit confused about something, so I want to clarify. > > I curated these as Matched On factors. Because the study mentioned that there were no significant differences in them between the two groups in the study. > Which meansthey’resimilar in both groups. > > I want to know if this is okay? - File (JPEG): f7dbd764-b14d-4b80-b769-8a4e98c13e50

Muqtadirat Yussuff (05:53:18) (in thread): > Hi, did the study state these were “matched”? if not, you’re not to curate as matched

Mildred Anashie (05:54:02) (in thread): > Hi, If the study doesn’t state that they were matched on those factors I don’t think you should curate them as matched on > > To be sure you can Ctrl + find and type Matched

Aleru Divine (05:54:33) (in thread): > Good morning@Victoria (Burah) Poromon.I think one thing that would qualify them in this case would be the “matched on” keyword not similarity.

Victoria (Burah) Poromon (05:56:02) (in thread): > Okay okay > Thank you guys,I’lljust leave that blank then

Nana (05:57:53): > @Peace Sandy@Svetlana Ugarcina Perovic@Chioma Onyidoplease what test is used in this study from this image, is sequencing platform present and LDA is mentioned in the paper but a value is never attached to it, should I leave it blank. Below is the attached image for better clarification - File (JPEG): IMG-20240320-WA0003.jpg - File (JPEG): IMG-20240320-WA0002.jpg - File (JPEG): IMG-20240320-WA0001.jpg

NWAKAEGO VINCENT (05:58:13): > I studied microbiology as my first degree in Nigeria but after graduation you don’t really know what to do with the course since there is little or no room for you to practice it. this project has really enlightened me and i am so proud i studied this course, at least now i can contribute my quota to the microbiome community by engaging frequently in the microbiome curation project:smiling_face_with_3_hearts:. whosoever established this community had me in mind

Nana (05:59:13) (in thread): > As@Mildred Anashiesuggested is the easiest way to spot matched on

Victoria (Burah) Poromon (05:59:49) (in thread): > @Mildred AnashieYeah, I did control find, and it’s not specified. Thank you. I’ll just leave it blank

Mildred Anashie (06:00:30) (in thread): > Hi@NanaI think recording 2 for the LDA is okay if a figurewasn’tmentioned but there was mention of LDA

NWAKAEGO VINCENT (06:05:04): > hope we are getting ready for today’s event guys:dancer:

Ikeh Darlington Ikeh (06:09:16) (in thread): > @Nanafor statistical tests, there’s KW, LEfse, Chi-Square

Mildred Anashie (06:23:43) (in thread): > @Nanafor the statistical test I see Kruskal Wallis and LEfSe mentioned for differential abundance from what you shared and it’s possible to have multiple statistical tests but I’d advise you take a look at the figure or table you are curating signatures from it might guide you > > This might help youhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709738863990949?thread_ts=1709738698.328209&channel=C04RATV9VCY&message_ts=1709738863.990949 - Attachment: Attachment > Yes, you can have multiple statistical tests. However, be sure that the test is for differential abundance, and not for p-value. You should check the description of the figure or table you’re curating the result from to be certain of the test being carried out for that comparison/experiment

Nana (06:32:42) (in thread): > @Mildred Anashieis 2 default value for LDA?

Svetlana Ugarcina Perovic (06:36:20) (in thread): > Yes it is

Mildred Anashie (06:37:25) (in thread): > Yes it ishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709738784493999?thread_ts=1709738367.253199&channel=C04RATV9VCY&message_ts=1709738784.493999 - Attachment: Attachment > The default LDA value is 2.00 in LefSe. For p value they stated: “P values < 0.05 were considered statistically significant.”

Rahila-me (07:08:33): > Ace index is for richness

Joan C. Chukwuemeka (07:09:05) (in thread): > Yes@Rahila-me

Precious Orakwe (07:17:33) (in thread): > Good day house, please am stuck here, I don’t know what to do, - File (PNG): Screenshot_20240320-120735.png - File (PNG): Screenshot_20240320-120759.png - File (PNG): Screenshot_20240320-121019.png

Precious Orakwe (07:18:42) (in thread): > Good day house, I need help here, I don’t know what to do here: - File (PNG): Screenshot_20240320-120735.png - File (PNG): Screenshot_20240320-120759.png - File (PNG): Screenshot_20240320-121019.png

Blessing Ene Anyebe (07:22:37): > Starts in an hour…….:partying_face::partying_face::partying_face: - Attachment: Attachment > Good morning :tulip: > > There’s still time to register for todays’ MVIF https://www.microbiome-vif.org/en-US > > It’s a 3 hour event about the latest microbiome science: > 1. a keynote and Q&A: this time Curtis Huttenhower will present their work https://huttenhower.sph.harvard.edu/home/ > 2. 3 short talks* and Q&A session with speakers > 3. highlights & networking session where you can meet other microbiome researchers > *FUN FACT: one of the studies, that will be presented as a short talk. has been curated very recently by YOU https://github.com/waldronlab/BugSigDBcuration/issues/179 > > See you at MVIF! > @U1LCB8WEA @UBNSEMS3S @Chioma Onyido @Esther Afuape @Peace Sandy @Svetlana Ugarcina Perovic

Mildred Anashie (07:29:22) (in thread): > Hi@Precious Orakweyou’llhave to carefully read the article you are curating to identify the experiments done which will help in filling the group and sample size sections > > Also identify which of the alpha diversity indices was used in the paper and if it increased, decreased or is unchanged (not significant) > > And the signatures you will record will be taxas reported as being differentially abundant (significantly increased or decreased) for the experiments you are curating

Mildred Anashie (07:34:02) (in thread): > Also go through the curation policyhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > …

Aleru Divine (07:35:02): > Hello@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace SandyI’dlike to deletesignature 3 from experiment 7 in this study.https://bugsigdb.org/Study_1008Thank you so much! - Attachment (BugSigDB): External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells - BugSigDB > Gut microbiota are involved in many physiological functions such as metabolism, brain development, and neurodegenerative diseases.Many microbes in the digestive tract do not maintain a constant level of their relative abundance but show daily oscillations under normal conditions.

Precious Orakwe (07:36:37) (in thread): > The alpha diversity I saw in the study, there is nothing like increased or decrease, that’s why am confused

Mildred Anashie (07:46:44) (in thread): > You can share with me let me try to go through it

Precious Orakwe (08:18:05) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9127079/#s2title - Attachment (PubMed Central (PMC)): Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer’s Disease and Obesity > Lifestyle choices, external environment, aging, and other factors influence the synthesis of melatonin. Although the physiological functions of melatonin have been widely studied in relation to specific organs, the systemic effects of endogenous melatonin …

Barakat Akinsiku (08:28:49): > Hey everyone, the microbiome MVIF event starts in 30 minutes. Let’s get set and ready:partying_face::partying_face:

Nana (08:30:22) (in thread): > @Precious Orakwefor the screenshot you sent here..the answers will be found in the paper you are curating . Carefully read it through then the curation policy on bugsigdb org is another place to find all you seek.

Scholastica Urua (09:00:56) (in thread): > It’s time:hugging_face:

Svetlana Ugarcina Perovic (09:04:22) (in thread): > Deleted.

Precious Orakwe (09:04:40) (in thread): > I have done that, yet I can’t understand anything

Aleru Divine (09:04:45) (in thread): > Thank you so much!

Precious Orakwe (09:05:22) (in thread): > Like in the signature, I don’t know what to put as the source and description

Precious Orakwe (09:05:39) (in thread): > I can’t understand. Single that from that part

Kelechi Madubuko (09:05:50): > We’re live now.. Let’s join up guys - Attachment: Attachment > Good morning :tulip: > > There’s still time to register for todays’ MVIF https://www.microbiome-vif.org/en-US > > It’s a 3 hour event about the latest microbiome science: > 1. a keynote and Q&A: this time Curtis Huttenhower will present their work https://huttenhower.sph.harvard.edu/home/ > 2. 3 short talks* and Q&A session with speakers > 3. highlights & networking session where you can meet other microbiome researchers > *FUN FACT: one of the studies, that will be presented as a short talk. has been curated very recently by YOU https://github.com/waldronlab/BugSigDBcuration/issues/179 > > See you at MVIF! > @U1LCB8WEA @UBNSEMS3S @Chioma Onyido @Esther Afuape @Peace Sandy @Svetlana Ugarcina Perovic

Nana (09:07:32) (in thread): > Does your study contain supplemental material or figures or tables? These are the places that point to signatures that will be curated

Precious Orakwe (09:15:05) (in thread): > These are some of the tables and figures I saw in my supplementary materials, is this what you meant, if test what next should I do? - File (PNG): Screenshot_20240320-141120.png - File (PNG): Screenshot_20240320-141112.png - File (PNG): Screenshot_20240320-141053.png - File (PNG): Screenshot_20240320-141043.png

Iman Ngwepe-Ntshibida (10:05:20): > Is the livestream on a short break ?

Joan C. Chukwuemeka (10:05:36): > Yes@Iman Ngwepe-Ntshibida

Nana (10:41:54) (in thread): > Theses ones are not curatble oooh

Mildred Anashie (10:54:37) (in thread): > Look for where they are talking about differential abundance

Habiba Saad (11:31:24): > Having curated Kun D Huang’s paper on BugsiGDB, it’s truly an honor to be in touch regarding his work. The research on ‘Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices’ is both valuable and insightful. It’s wonderful to see collaboration and knowledge-sharing within the community. His presentation at MVIF was incredibly informative, offering many useful insights and understandings of microbiome studies.

Svetlana Ugarcina Perovic (11:35:52) (in thread): > Just sharing with others, if they wanna check it outhttps://bugsigdb.org/Study_876 - Attachment (BugSigDB): Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices - BugSigDB > The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained.Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM.

Ima-obong (Aimah) (11:40:21) (in thread): > @Habiba Saadfeels surreal knowing you curated this paper .. you’re doing amazing:clap:

Peace Daniel (11:48:51) (in thread): > Well done@Habiba Saad:clap:For gender, you can try sex and when you type BMI as body mass indexyou’dfind the drop down

Preethi grace Manthena (11:55:53): > Hii everyone, May I know how much time it will take to receive the confirmation mail to create account in bugSigDB

Mildred Anashie (11:56:30) (in thread): > Hi > > Check your spam folder, it might have been sent

Mildred Anashie (11:57:17) (in thread): > Well done on your curation:hugging_face:

Preethi grace Manthena (11:58:00) (in thread): > Hey@Mildred Anashie, Thanks alot, I’ve got that:handshake::heart:

Peace Daniel (12:01:43): > Hi everyone > > I’m open to peer reviews, if you need one please tag me to it:wave:

Victoria (Burah) Poromon (12:10:23): > Hello@Svetlana Ugarcina Perovic,@Esther Afuape,<@UBNSEMS3S>,@Peace Sandy,@Chioma OnyidoPlease I’d like to delete signature 3 from experiment 1 in this study.https://bugsigdb.org/Study_1020Thank you. - Attachment (BugSigDB): Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma - BugSigDB > BACKGROUND: Oral microbiome dysbacteriosis has been reported to be associated with the pathogenesis of advanced esophageal cancer.However, few studies investigated the potential role of oral and gastric microbiota in early-stage intramucosal esophageal squamous carcinoma (EIESC).

idiaru Angela (12:23:09): > Hello@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido@C. Mirzayi (please do not tag this account)I’d like to know If it is okay to curate an experiment that established the microbial composition of soil from from different spaces in the habitat of frogshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710914768843159?thread_ts=1710914768.843159&cid=C04RATV9VCY - Attachment: Attachment > Good morning Everyone, > As a way of clarification, if an experiment was done to determine the bacteria composition of the soil in the habitat of a particular organism and it yielded significant results, > Would I curate that kind of experiment on BugsigDB? > I’d appreciate your response Thank you > @Chioma Onyido @Esther Afuape @Peace Sandy @Svetlana Ugarcina Perovic

Victoria (Burah) Poromon (12:25:17): > Hello everyone, > > Should this be recorded as 2 different taxa?:eyes:Lachnospiraceae andClostridium > - File (JPEG): 08035f25-cb34-41f4-bc96-3c857889c801

Mildred Anashie (12:33:19) (in thread): > I’mthinking you record as one or just the genus:thinking_face:Waiting for others opinions because thisdoesn’tlook like it should be guessed:joy:

Peace Daniel (12:36:52) (in thread): > I’m not sure but take a look at this > > The family Lachnospiraceae is a phylogenetically and morphologically heterogeneous taxon of the class Clostridia, phylum Firmicutes.https://link.springer.com/referenceworkentry/10.1007/978-3-642-30120-9_363 - Attachment (SpringerLink): The Family Lachnospiraceae > The family Lachnospiraceae is a phylogenetically and morphologically heterogeneous taxon of the class Clostridia, phylum Firmicutes. The family, described on the basis of 16S rRNA gene sequence analysis, contains a high number of as yet not reclassified species of…

Peace Daniel (12:38:23) (in thread): > I think she should record just the genus as well@Mildred Anashie

Muqtadirat Yussuff (12:41:57) (in thread): > I think you’d record as one

idiaru Angela (12:42:36) (in thread): > I also agree with@Mildred Anashieto record just the genus

Blessing Ene Anyebe (12:43:59) (in thread): > Well done on your curation@Habiba Saad:orange_heart:

Scholastica Urua (12:55:28) (in thread): > Hi@Peace Danieldo you mind reviewing my curation please:pray:https://bugsigdb.org/Study_1015 - Attachment (BugSigDB): Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing - BugSigDB > The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders.

Peace Daniel (12:58:54) (in thread): > Not at all,I’lldo my best:hugging_face:

Svetlana Ugarcina Perovic (13:04:15) (in thread): > Deleted.

Scholastica Urua (13:11:56) (in thread): > Thank you:pray:Looking forward to your feedback

Aleru Divine (13:14:50) (in thread): > YeahI’drecord the genus too@Victoria (Burah) Poromon

Victoria (Burah) Poromon (13:16:52) (in thread): > Thank you so much.

Victoria (Burah) Poromon (13:19:16) (in thread): > Thank you everyone!:sweat_smile:

Oluwatoyosi Victoria Olanrewaju (13:58:51): > Hello Ladies, I need help please. I’ve been stuck here for days and don’t know how to proceed. So I’m about to start adding a signature but what exactly is the source and description and how can I find it on my paper. Here’s a link to my paper please help a sister outhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5718049/ - Attachment (PubMed Central (PMC)): Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease > The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders. However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored. Synucleinopathies are characterized by … - File (PNG): Screenshot 2024-03-20 195142.png

Joan C. Chukwuemeka (14:04:02): > Good evening all, > I and@Ikeh Darlington Ikehare working on the curationbugsigdb.org/study_911We’re at a diverging point on choice of statistical test that was used as well as EFO condition. > Seehttps://github.com/waldronlab/BugSigDBcuration/issues/173We’re calling 911 on the group…:blush:So, we seek insights from others<!here> - Attachment: #173 The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels > The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels – Simone Anzà et al. – Microbiome 2023
> https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01596-w

Scholastica Urua (14:05:43) (in thread): > @Oluwatoyosi Victoria Olanrewajuthe source is were you find the abundant taxa listed. I’ll look at your paper and get back to you.

Aleru Divine (14:05:53) (in thread): > Hi@Oluwatoyosi Victoria Olanrewajuso your signatures are the differentially abundant taxa that were identified and stated in the article. > > Source: could be a figure, a table or from text. > > Description: Provide a detailed description of your source. So it is clear to a reader. > > I looked at your article, Figure 6E looks like a good source.The description is provided below the figure, you can use that. - File (PNG): IMG_7990 - File (PNG): IMG_7991

Peace Daniel (14:06:53) (in thread): > The source is asking for the table, figure or text you found those signatures andthere’salways a description attached to the figure which you can use

Peace Daniel (14:07:02) (in thread): > What experiment would this be? Share a link to yourstudy on BugSigdb

Oluwatoyosi Victoria Olanrewaju (14:07:29) (in thread): > Omg thank you so much, there was a lot of figures so I got confused

Oluwatoyosi Victoria Olanrewaju (14:08:10) (in thread): > https://bugsigdb.org/Special:FormEdit/Signature?Signature%5BBase%20page%5D=Study%20910%2FExperiment%201&reload=1&returnto=Study_910@Peace Danielthis is it - Attachment (BugSigDB): Special:FormEdit/Signature

Peace Daniel (14:09:51) (in thread): > No, you sent a link to edit. Please go back and share a link that looks like thishttps://bugsigdb.org/Study_961 - Attachment (BugSigDB): Fibroblast growth factor 21 ameliorates behavior deficits in Parkinson’s disease mouse model via modulating gut microbiota and metabolic homeostasis - BugSigDB > AIMS: The effects of FGF21 on Parkinson’s disease (PD) and its relationship with gut microbiota have not been elucidated.

Oluwatoyosi Victoria Olanrewaju (14:10:47) (in thread): > Oh my bad - Attachment (BugSigDB): Gut Microbiota Regulate Motor Deficits and Neuroinflammation in a Model of Parkinson’s Disease - BugSigDB > The intestinal microbiota influence neurodevelopment, modulate behavior, and contribute to neurological disorders.However, a functional link between gut bacteria and neurodegenerative diseases remains unexplored.

Scholastica Urua (14:11:08) (in thread): > Just checked your article,@Aleru Divineis right. Fig. 6E should be your source

Oluwatoyosi Victoria Olanrewaju (14:12:58) (in thread): > Thank you so much ladies, I truly appreciate@Aleru Divine@Peace Daniel@Scholastica Urua

Peace Daniel (14:19:03) (in thread): > Not quite sure about your definition for group 1 > Just write 3 months for your antibiotic exclusion > > And yes, fig 6E is curatable

Oluwatoyosi Victoria Olanrewaju (14:20:03) (in thread): > Ok all noted, I wanted to ask if I’m on track

Aleru Divine (14:21:11) (in thread): > @Joan C. Chukwuemeka@Ikeh Darlington IkehI agree with the condition you’ve gone with.It makes sense.My reason is, they investigated the effect of pre and postnatal maternal glucocorticoid levels.That would mean how the bodies responded to it.Let me check the statistical test.

Peace Daniel (14:21:33) (in thread): > Sure, you can always share for review onceyou’redone. Good luck:purple_heart:

Oluwatoyosi Victoria Olanrewaju (14:22:13) (in thread): > Appreciate you@Peace Daniel:heart:

Sidra Khan (14:25:24): > Hi, I’m curating a study, while I’m adding DOI for this study. I’m not getting the other fields auto-filled. Could someone guide me how to fix this unexpected behaviour or I’m doing something wrong? - File (PNG): image.png - File (PNG): image.png

Mildred Anashie (14:26:06) (in thread): > Add the PMID instead

Mildred Anashie (14:26:47) (in thread): > I’mseeing ANCOM-BC and linear regression being mentioned not certain which it is yet

Ikeh Darlington Ikeh (14:30:59) (in thread): > We have identified two statistical tests, the ANCOM-BC and Linear Regression.IfI’mcorrect,@Joan C. Chukwuemekais of the opinion that only ANCOM-BC should be listed since it uses a Linear Regression Framework. However,I’mof the opinion that since the data field allows for more than one tests to be listed that we go ahead and list both since they are both available for selection in the statistical test field.

Aleru Divine (14:31:49) (in thread): > This is quite confusing@Mildred AnashieI see > > “The absolute abundance data were modeled by ANCOM-BC using a linear regression framework.” > And > “ANCOM-BC analyses at phylum, family, and genus level for rich and lean season.” > > 🫨

Aleru Divine (14:33:12) (in thread): > Here’sanother excerpt “All analyses were performed in R Studio (Version 3.6.1) using the packages glmmTMB [57] and ancombc”:thinking_face:

Sidra Khan (14:36:02) (in thread): > Thank you@Mildred Anashie:ok_hand:

Aleru Divine (14:40:10) (in thread): > I think the statistical test is ANCOM-BC > > Here’s why: - File (PNG): IMG_7992

Ikeh Darlington Ikeh (14:54:17) (in thread): > @Aleru DivineYou’re correct, but I still think both tests were used as they serve different purpose in determining the resultant differential abundances. ANCOM-BC was used to determine the differentially abundant taxas while linear regression was used to understand/determine the relationship between the identified taxas and the predictors (pre-GC to post-GC) > > “The absolute abundance data were modeled by ANCOM-BC using a linear regression framework”

Joan C. Chukwuemeka (14:58:31) (in thread): > My thoughts too@Aleru Divine.@Ikeh Darlington Ikehmy understanding is that the linear regression pointed out is the framework which is utilised by ANCOM-BC.<@UBNSEMS3S>@Chioma Onyido<@U1LCB8WEA>@Svetlana Ugarcina Perovic@Esther Afuape@Peace SandyPlease your expertise is needed here?:pray:

Abiola Salako (16:02:54) (in thread): > Yes, if it was me I would record only the genus@Victoria (Burah) Poromon

Sidra Khan (16:09:23): > How to delete the accidentally duplicated experiment? I’m getting the following error? - File (PNG): image.png

Mildred Anashie (16:09:56) (in thread): > We do not have permission to delete > > You can request a mentor deletes it for you

Mildred Anashie (16:10:17) (in thread): > Just state the experimentyou’dlike to delete and add a link to the study

Muqtadirat Yussuff (16:10:18) (in thread): > Hi, just inform the mentors and they’d delete it

Aleru Divine (16:10:39) (in thread): > @Sidra KhanYou’dhave to tag the mentors as only they have the permission to delete.

Sidra Khan (16:11:07) (in thread): > ok thanks everybody:tulip:

Bolanle Wahab (16:12:44) (in thread): > @Mildred Anashie@Abiola Salako@idiaru Angelahi, do you think this study used a longitudinal study design since samples were analyzed on different days but then it’s experimental as well, what do you think please?

Abiola Salako (16:13:34) (in thread): > @Sidra Khantag the mentors with the study link.

Mildred Anashie (16:17:39) (in thread): > In my opinion it’s just experimental

Habiba Saad (16:23:34): > @Svetlana Ugarcina Perovic@Peace Sandykindly delete experiment 1 signature 2 fromhttps://bugsigdb.org/Study_1003 - Attachment (BugSigDB): The Impact of Mouthwash on the Oropharyngeal Microbiota of Men Who Have Sex with Men: a Substudy of the OMEGA Trial - BugSigDB > Mouthwash is a commonly used product and has been proposed as an alternative intervention to prevent gonorrhea transmission.However, the long-term effects of mouthwash on the oral microbiota are largely unknown.

idiaru Angela (16:23:38) (in thread): > I agree with@Mildred Anashieon this one. Its more experimental because the laboratory conditions like temperature were controlled

Muqtadirat Yussuff (16:24:00): > Hello mentors@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma Onyido<@UBNSEMS3S>, I found this curation with**Rhodobacteraceae__HIMB11without an NCBI ID and I believe it isRhodobacteraceae bacterium HIMB11 with an ID of 1366046Please review and let me now if I can edit, thank you.Here’s the curation link **https://bugsigdb.org/Study_855 - Attachment (BugSigDB): Tear film microbiome in Sjogren’s and non-Sjogren’s aqueous deficiency dry eye - BugSigDB > PURPOSE: To understand the bacterial microbiome changes associated with Sjogren’s syndrome (SS) and non-Sjogren’s syndrome (NSS) aqueous-deficient dry eyes compared to healthy eyes.

Bolanle Wahab (16:25:32) (in thread): > Thank you:heart:

Nana (16:31:04) (in thread): > Enter the id it is the correct one

Sidra Khan (16:31:37): > Hello mentors@Svetlana Ugarcina Perovic@Peace Sandy@C. Mirzayi (please do not tag this account). I’m working on this studyhttps://journals.asm.org/doi/10.1128/spectrum.00344-21, I have accidentally added experiment 4 kindly delete it. Here is the link to the curation:https://bugsigdb.org/Study_1044Thanks for your assistance. - Attachment (BugSigDB): The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients - BugSigDB > Infection and rejection are the two most common complications after lung transplantation (LT) and are associated with increased morbidity and mortality.We aimed to examine the association between the airway microbiota and infection and rejection in lung transplant recipients (LTRs).

Joan C. Chukwuemeka (16:31:39) (in thread): > @Muqtadirat Yussuffhave you checked if taxa level on the Paper forRhodobacteraceae_HIMB11, and the taxa level forRhodobacteraceae bacterium HIMB11 NCBI are the same?

Abiola Salako (16:32:58) (in thread): > @Bolanle WahabThe study appears to be experimental in design. It involves manipulating storage conditions (such as temperature and time) and observing the effects on microbiome composition. This aligns with the characteristics of an experimental study where researchers actively intervene or manipulate variables to observe their effects. So I agree with@Mildred Anashieand@idiaru Angela

Muqtadirat Yussuff (16:35:40) (in thread): > @Nanadon’t I need a go ahead for that?

Muqtadirat Yussuff (16:36:35) (in thread): > @Joan C. ChukwuemekaHmm, no but I cross referenced my search results with uniprot and NCBI, I got a match

Nana (16:38:59) (in thread): > In ncbi and uniprot.. check the rank level if it is the same as on the paper then enter the id. That’s all. It will appear as the name when you save

Chioma Onyido (16:39:25) (in thread): > Deleted.:white_check_mark:

Nana (16:39:40) (in thread): > When you check on ncbi or uniprot you don’t enter with underscore

Chioma Onyido (16:42:05) (in thread): > Deleted.:white_check_mark:

Muqtadirat Yussuff (16:43:18) (in thread): > @NanaI didn’t use the underscore but alright, I’ll check the paper. Thank you

UBNSEMS3S (16:45:35) (in thread): > Nice catch.

Nana (16:46:16) (in thread): > Urw

UBNSEMS3S (16:47:54) (in thread): > ANCOM-BC uses a linear model. In this case, just curate it as ANCOM.

Mildred Anashie (16:49:12) (in thread): > @Joan C. Chukwuemeka@Ikeh Darlington IkehDoubt cleared

UBNSEMS3S (16:49:18): > Hi everyone, > > Just a reminder that we have our team meeting and office hours at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. Looking forward to seeing you there.

Ikeh Darlington Ikeh (16:50:22) (in thread): > Yeah! very well cleared…Thanks@C. Mirzayi (please do not tag this account)for the clarification

Abiola Salako (16:50:46) (in thread): > Alright. Thanks for the reminder@C. Mirzayi (please do not tag this account)

Mildred Anashie (16:51:00) (in thread): > Thank you for the reminder<@UBNSEMS3S>Looking forward to it:hugging_face::hugging_face:

idiaru Angela (16:51:08) (in thread): > Looking forward to seeing you too. Thanks for the reminder@C. Mirzayi (please do not tag this account)

Ikeh Darlington Ikeh (16:51:47) (in thread): > Awesome!

Scholastica Urua (16:51:56) (in thread): > Thank you for the reminder<@UBNSEMS3S>. Looking forward to it.

Mildred Anashie (16:55:48) (in thread): > Hi<@UBNSEMS3S>@Chioma Onyido@Esther Afuapecould you please help out here:pray:This is still confusing

Chioma Onyido (16:56:15) (in thread): > I enjoyed this discussion. Always keep in mind thatit’sthestatistical test used for differential abundance is what you should curate on bugsigdb.Thanks<@UBNSEMS3S>for the clarification.:white_check_mark:

Sidra Khan (16:59:19) (in thread): > Thanks for the reminder@C. Mirzayi (please do not tag this account)

Kelechi Madubuko (17:01:25) (in thread): > Ok noted. Thank you Chloe

Chioma Onyido (17:08:57) (in thread): > Hi@idiaru AngelaGood question! > I presented a similar paper in the past where sig taxa results were reported for different environments, I remember that they compared household to work environment. > > Ifit’s not from an actual body site of the host species, then itshould takebe curated.See curation policy for host species.

Ima-obong (Aimah) (17:09:06): > Hello everyone, and my efficient mentors@Chioma Onyido@Peace Sandy@Esther AfuapeI have a confusing situation here and I sincerely will appreciate your input no matter how long it takes for it to come in:blush:My study’s condition is biological ageing inPeople living with HIV(PLWH)as group 1 andPeople living without Hiv(PLWOH)as control … > The body sites were listed to be colon, Ileum, blood and Feces > > My major problem is in the figures I’m to curate fromFig.4cshowsDifferential bacterial abundancebetweentissue(colon, ileum) and fecal sampleson a logscale. And the comparisons include;colon Vs feces(red),Ileum Vs Feces(blue)andIleum Vs colon(green).WhileFig4Dshows logscaledifferences in bacterial abundance across colon(triangle), ileum(square) and feces(circle) between PLWH(group1) and PLWOH(control)..Question is: am I to curate from both figures?, and if so, especially forFig4c, since the comparison is between thesamplesand not thegroupsit self, am I to create new experiments for each of them? > > And if yes, what will my group 1 and 0 be for those Experiments > E.g. group 1: colon Vs ileum of PLWH > group 0: colon Vs Ileum of control…?? > > > > Secondly,Fig5Ashows spearman’s rank correlation analysis depictingassociations between colonic microbiomes increased (top row) or decreased (bottom row) in PLWH…Can I also curate this figure 5? > > Thanks alot..really:pray::pray:. > > Here is a link to the paper, I greatly appreciate in advance whatever input you make cause my eyes hurt already from looking at this paper:sob::joy:https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4 - Attachment (BioMed Central): Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging - Microbiome > Background People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV — influenced by the infection itself, ART usage, sexual orientation, or other associated factors — affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. Results PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. Conclusions We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract - File (JPEG): IMG-20240320-WA0016.jpg - File (JPEG): IMG-20240320-WA0015.jpg

Chioma Onyido (17:09:34) (in thread): > should not*

Ima-obong (Aimah) (17:11:18) (in thread): > Fig 4 - File (JPEG): IMG-20240320-WA0015.jpg

Ima-obong (Aimah) (17:11:43) (in thread): > Fig 5 - File (JPEG): IMG-20240320-WA0016.jpg

idiaru Angela (17:12:31) (in thread): > Thank you very much:saluting_face:@Chioma Onyido

Bolanle Wahab (17:12:57) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Aleru Divine (17:16:34) (in thread): > Thanks for the reminder<@UBNSEMS3S>

Blessing Ene Anyebe (17:27:40) (in thread): > Thank you@C. Mirzayi (please do not tag this account)Looking forward to it!

Praise Agbetuyi (17:48:01) (in thread): > Yes, the sample size is a total of 223 patient

Chioma Onyido (17:54:27) (in thread): > Fig 4d shows diff abundance between people living with HIV on antiretroviral therapy and controls. > You see the increased abundance by the right and decreased by the left…? > So you curate for each of the samples; feces, ileum and colon (indicated by the shapes) > **You curate following the significance thresholds color indicators by the bottom left of the image (Hint: you should curate only significant results). > > Fig 4c shows diff abundance between the samples- tissue and fecal generally. Theydidn’tsay ifit’sfor control or case samples (…Ididn’tsee that in the figure). > > Here you curate with same strategy as above, looking out for only significant results. > Not sure about which to use as group 0 or 1 here but whichever you choose,you’ve to be consistent.

Chioma Onyido (17:54:53) (in thread): > For your question on spearman correlation, we only curate differential abundance results in bugsigdb.

Abiola Salako (17:55:53) (in thread): > Thanks for the clarification@Chioma Onyido

Ima-obong (Aimah) (17:57:37) (in thread): > @Chioma Onyido…I feel soo relieved:dancer::hugging_face:…Thank youuuuu. I really appreciate your response.

Chioma Onyido (18:01:35) (in thread): > Curating certain figures can be challenging at times, soit’sgood to ask questions especially when you’re not sure. Glad to help!:cherry_blossom:

Joan C. Chukwuemeka (18:15:07) (in thread): > Thanks<@UBNSEMS3S>

Ima-obong (Aimah) (18:15:50) (in thread): > Thank you@Chioma Onyido..but please I still need a little clarity on the threshold colour indicators of the bottom left.. > > And also curating only significant results…for the Fig4D, does the FDR indicator represent the nonsignificant ones while the P indicators rep the significant ones? > > Thanks alot for taking out the time to help me out…I really appreciate It:pray:

Joan C. Chukwuemeka (18:21:27) (in thread): > @Ima-obong (Aimah)FDR is False Discovery Rate, it’s usually a pointer that MHT Correction was done

Ima-obong (Aimah) (18:28:15) (in thread): > Thank you@Joan C. Chukwuemeka…so that means the signatures with the FDR indicators are insignificant right? And should not be curated?

Joan C. Chukwuemeka (18:32:25) (in thread): > That’s not what it implies… It’s like an adjusted p-value…. If you check the description for the figure, you’ll understand it. > > Here’s the description: Log-scale differences in bacterial abundance across colon (triangle), ileum (square), and feces (circle) between PLWoH and PLWH on ART. Analysis incorporated bacterial taxa with > 1% mean relative abundance. Linear models estimated abundance changes, and adjustments for multiple tests used the Benjamini–Hochberg method. *****Significance markers: FDR < 0.05 (purple), FDR < 0.1 (cyan), and P < 0.05 (green)**************Meanwhile, do you have experiments/ contrasts like these in your curation? > PLWH on ART vs. PLWoH for body site as feces > > PLWH on ART vs. PLWoH for body site as colon > > PLWH on ART vs. PLWoH for body site as Ileum.

Ima-obong (Aimah) (18:36:56) (in thread): > Yes….I do have those Experiments… > > Sincerely…thank you so much for explaining the significant markers….. I’m really grateful:pray::pray:

Joan C. Chukwuemeka (18:43:10) (in thread): > Okay…@Ima-obong (Aimah)So to interpret for example: > We need to find out what the significance level the researchers set/used. > > If significance was set P < 0.05(green), the ones that are P > 0.05(no colour) will be seen as not significant. In essence the ones in green will be Curated. Same for FDR. > > So check through the Paper to ascertain the significance level for the p-value and FDR used by the researchers. > > Hope this helps?

Ima-obong (Aimah) (18:48:15) (in thread): > This is really, really helpful@Joan C. Chukwuemeka….thank youuuuu

Praise Agbetuyi (19:00:01): > Good morning, BugSigDB > > It’s Thursday, Curator, A great day is set to unfold > > Alright, I would like to remind you of our team meeting and office hours today at 9 AM EDT. Please find below the link to join the meeting:https://us02web.zoom.us/j/2737200499I look forward to seeing all of you there. > P.S. To convert the meeting time to your local time zone and set a reminder, please visit the link:https://www.worldtimebuddy.com/ - Attachment (Worldtime Buddy): World Clock & Time Converter > Effortless time conversion and world time. Schedule conference calls, webinars & online meetings, plan travel and track flight arrival time across time zones.

Habiba Saad (21:56:13): > hello mentor I have found this signature TG5 without an NCBI id and found it in ncbi with a taxonomy id of1500835. in the following study in bugsigdbhttps://bugsigdb.org/Study_157/Experiment_2/Signature_2. kindly review it so i can edit. thanks<@UBNSEMS3S>@Chioma Onyido@Svetlana Ugarcina Perovic@Peace Sandy - Attachment (BugSigDB): Study 157/Experiment 2/Signature 2 > Source: Table 3 Description: Relative abundance of significant microbiota in the ESCC group compared to the Healthy control group Abundance in Group 1: decreased…

2024-03-21

Mildred Anashie (00:24:53) (in thread): > Hi@Habiba SaadThere’sa comment on TG5 on the talk page you should check it out

Svetlana Ugarcina Perovic (02:00:02): > <!channel>Good morning, everyone:good_luck:We will be having**** our weekly team meeting and Outreachy office hours ****at 9 AM EDT today at:https://us02web.zoom.us/j/2737200499. > Find out the time in your local time zone here:https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179We have a question for you:What’s the best/most fun and least fun part while BugSigDB-ing? Feel free to leave a comment below.<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic

Desire Oluwarotimi (02:00:58) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for the reminder. > > Most fun part has to be the collaboration on the platform that aids curation into BugSigDB. The least fun part is definitely curating a difficult paper. Although it can be challenging, I get to learn how to approach curation better in the end.

fetlework gubena arage (02:07:23) (in thread): > Good morning@Svetlana Ugarcina Perovicand evryon.

Akinbode Mariam (02:07:48) (in thread): > Good morning guys

fetlework gubena arage (02:11:41) (in thread): > For me the best part of BugSigDB-ing is exploring new studies every day and gaining knowledge from new researches while curating. The other best part is the community. It is very open and friendly; always there to help me with any challenge.

Mildred Anashie (02:14:55) (in thread): > Good morning@Svetlana Ugarcina PerovicFor me the less fun part while BugSigdb-ing is going through a very confusing paper but I get so happy and satisfied whenI’mable to figure out the paper mostly with the help of community members and the most fun part is entering and recording the information on BugSigdb (The process is always so smooth)and the knowledge I gain:hugging_face::yellow_heart:

Himel Mallick (02:21:47): > @Himel Mallick has left the channel

Scholastica Urua (02:22:13) (in thread): > Good morning@Svetlana Ugarcina Perovic:sunny:The best part for me is going through a paper and being able to figure the curatable details, also discovering new things about microbiome everyday. > > The less fun part I’d say is going through a confusing paper and encountering blocks. Another fun part for me is getting past those blocks through help and collaboration from fellow contributors. It’s really exciting to experience how helpful everyone in the community is:hugging_face:.

Akinbode Mariam (02:25:47) (in thread): > Best/most fun while BugsigDB-ing for me will be the discovery part, learning and having a better understanding of the complex relationships between bacteria and their environments. and also the satisfaction i get when i finally figure out my paper. the least fun part is thinking i figured it out and then going back to read over my paper carefully. it can be frustrating!! but the community always comes to my aid with every roadblock i face which doesnt make it all bad at the end of the day.

Akinbode Mariam (02:30:28) (in thread): > hi@Mildred Anashieyou havent gotten back to me on the alpha diversity.@Aleru Divinealso is my study design laboratory experiment case study or relative abundance@Esther Afuapehttps://bugsigdb.org/Study_995 - Attachment (BugSigDB): Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson’s disease - BugSigDB > Growing evidences show that gut microbiota is associated with the pathogenesis of Parkinson’s disease (PD) and the gut-brain axis can be promising target for the development of the therapeutic strategies for PD.

Flourish Ralph (02:36:03) (in thread): > Good morning!@Svetlana Ugarcina PerovicI think the fun part has to be taking something absolutely complex and breaking it down into more understandable bits, reminds me of copywriting and product design. > > Plus I love the collaboration here, you get to exchange knowledge and get new information,makes learning fun. > > The less fun part is interacting with a studythat’swayyyyy different from whatyou’vealready worked on, but then again, I like a good challenge.:thumbsup:

idiaru Angela (02:37:08) (in thread): > Good morning@Svetlana Ugarcina Perovicand everyone here:cherry_blossom:. I’d say the most fun part has to be the collaboration. It’s so satisfying to know that whenever I encounter a road block I have a community full of people to help out. Makes me feel less alone when I encounter changes curating. > The least fun part or BugsigDB-ing is sitting for hours trying to figure out a very confusing or contradictory paper:smiling_face_with_tear::eyes:

idiaru Angela (02:38:51): > Hi everyone, good morningI have finished this curation and I love peer reviews. I’d highly appreciate any feedback I get. Thank you:heart_hands: - Attachment (BugSigDB): Sex, health status and habitat alter the community composition and assembly processes of symbiotic bacteria in captive frogs - BugSigDB > BACKGROUND: Frogs are critical economic animals essential to agricultural ecosystem equilibrium.However, Meningitis-like Infectious Disease (MID) often affects them in agricultural settings.

Ima-obong (Aimah) (02:50:48) (in thread): > Good morning@Svetlana Ugarcina PerovicFun part for me is reading the study papers; I get to learn alot from the Introduction, to sampling methods as I have a background in biological sciences.. > > The not so fun part? Interpreting the results and curating signatures with unmatched names:hugging_face:… But I get more fulfilled when I can figure them out.

Adedoja Isaac (02:54:44) (in thread): > For me, the best part is curating an easy ast paper. While the less fun part is curating a confusing paper

Peace Daniel (03:03:25) (in thread): > Good morning@Svetlana Ugarcina PerovicThe best part for me is completing my curation and researching:woman-cartwheeling:The less fun part for me is being stuck on a confusing paper

Peace Daniel (03:05:17) (in thread): > Well done:clap:

idiaru Angela (03:12:49) (in thread): > Thank you@Peace Daniel

Mildred Anashie (03:22:33): > Hi everyone andGood morning:sunny:Hi@Chioma Onyido@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy<@UBNSEMS3S>@Levi WaldronThank you for always easing the process of curation with your insights and help:hugging_face:I believe I’m almost done with this study I’m curating, however I can’t seem to find the best term for the condition. > The condition is “White Nose Syndrome” and I found Geomyces on EFO (see attached image),I’mskeptical if that can replace it > > Here’s a link to the paper for anyone who’d like to review, Thank you:blush::face_with_peeking_eye:https://bugsigdb.org/Study_1022 - Attachment (BugSigDB): White-nose syndrome restructures bat skin microbiomes - BugSigDB > Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases.Instead of single organisms being associated with disease, community characteristics may be more relevant. - File (JPEG): IMG_2566

Peace Daniel (03:27:31) (in thread): > Hey Anashie,well done on your curation > > Did you search “Pseudogymnoascus destructans” as a condition?

Mildred Anashie (03:29:54) (in thread): > YesIt’snot available on BugSigdb anddidn’tfind the EFO term for that

Peace Daniel (03:34:36) (in thread): > Alright, this is close enough

Oluwatomisin Omojokun (03:41:51) (in thread): > Good morning@Svetlana Ugarcina Perovicand everyone here. The most fun part is working with amazing people on the platform, being able to collaborate with them, their suggestions, review, and answer when I am curating a confusing or difficult study is really amazing . Kudos to everyone.:+1::gratitude-thank-you:The least fun part or Bugsigdb is always working for hours because there is a lot to do during this contribution stage and also trying to figure out a very confusing study:smiling_face_with_tear:

Aleru Divine (03:48:30) (in thread): > Hi@Mildred Anashiegood morning.I’vetried to search for a closely related term too but Icouldn’tfind any.:sleepy:

Scholastica Urua (03:49:22) (in thread): > Hello@Mildred AnashieI think Geomyces is the closest I can find from my search too. Let’s wait and hear from the mentors. > > Well done on your curation

Aleru Divine (04:06:32) (in thread): > Hi@Svetlana Ugarcina Perovic, good morning, and thanks for the reminder. > > The best part for me is when I get to work on a new paper. It’s exciting to learn about new research and their results, especially when I’m able to understand as I read through. It feels really good:sweat_smile:Plus, knowing that I have a great team to help me if I ever run into problems makes it even better. Everyone here is amazing:heart:Before, the least fun part was trying to figure out or interpret alpha diversity. But now, with the help of some clarification from the mentors and with each new paper, I learn more and I don’t get stuck on that anymore. > > Right now, I’m really looking forward to every new paper I’m assigned because it means I get to discover new studies, new perspectives, and new results.

Victoria (Burah) Poromon (04:07:09) (in thread): > Hello@Svetlana Ugarcina PerovicI believe the most fun part for me is being able to fish out every data in a study. > > The not so fun part is curating a confusing study.

Aleru Divine (04:08:11) (in thread): > I believe it is a laboratory experiment@Akinbode Mariam

Victoria (Burah) Poromon (04:17:10): > Good morning everyone, > > If your study used 2 different samples (saliva & gastric biopsy) but you only have differential abundance result from 1 sample (saliva). > > Do you record 2 body sites or just the one with the results?:eyes:

Mildred Anashie (04:18:24) (in thread): > My opinion is Ifthere’salpha diversity results for both samplesyou’d haveto record for both > > Although only saliva will have signatures > Experiments can exist without signatures

Aleru Divine (04:19:05) (in thread): > You record both body sites.Did they have different alpha diversity measures? > If they did thenthey’dbe different experiments.But only the saliva would have signatures > > Please can you share your paper:pray:

Victoria (Burah) Poromon (04:21:03) (in thread): > They have the same alpha diversity results. Unchanged

Victoria (Burah) Poromon (04:21:35) (in thread): > Sure@Aleru Divine

Mildred Anashie (04:21:43) (in thread): > The alpha diversity was mentioned for both sites differently?

Desire Oluwarotimi (04:21:46) (in thread): > I agree with@Mildred Anashieand@Aleru DivineAnd since they both have alpha diversity results, I think recording for both of them is the best thing to do.

Victoria (Burah) Poromon (04:22:44) (in thread): > https://bugsigdb.org/Study_1020 - Attachment (BugSigDB): Characteristics of the oral and gastric microbiome in patients with early-stage intramucosal esophageal squamous cell carcinoma - BugSigDB > BACKGROUND: Oral microbiome dysbacteriosis has been reported to be associated with the pathogenesis of advanced esophageal cancer.However, few studies investigated the potential role of oral and gastric microbiota in early-stage intramucosal esophageal squamous carcinoma (EIESC).

Victoria (Burah) Poromon (04:24:49) (in thread): > @Mildred Anashieuhmm, it said “there was no significant difference in alpha diversity between the groups in both samples”

Victoria (Burah) Poromon (04:26:58) (in thread): > @Desire OluwarotimiRight > I thought about this, but it will mean that i am just duplicating the experiment but only one will have signatures:eyes:Because they have similar alpha diversity results

Aleru Divine (04:27:17) (in thread): > But the alpha diversity was measured differently,there’sa figure for that.You would have two experiments.One for each body sites gastric biopsy and one for saliva.

Mildred Anashie (04:27:47) (in thread): > Those are two different experiments@Victoria (Burah) PoromonRecord separately

idiaru Angela (04:28:06) (in thread): > Yes@Aleru Divinethe study will have 2 experiments

Scholastica Urua (04:29:14) (in thread): > From your paper@Victoria (Burah) Poromonfrom your paper there are two separate experiments so they’ll be recorded separately.

Desire Oluwarotimi (04:29:53) (in thread): > @Victoria (Burah) PoromonLike they’ve all said, you’ll have two separate experiments.

Victoria (Burah) Poromon (04:30:33) (in thread): > Uhmmm > I see I see > > Thank you guys:hugging_face::hugging_face:

Mildred Anashie (04:32:09) (in thread): > Thank you guys:yellow_heart:

Mildred Anashie (04:51:13) (in thread): > @Akinbode Mariamthe study design is laboratory experiment in my opinion > > The alpha diversity in my opinion is interpreted asControl (Group 1) vs MPTP (Group 1)Chao1is decreasedRichnessis unchangedShannonis unchangedMPTP (Group 0) vs MPTP+Acu group(Group 1)Chao1is increasedRichnessis increasedShannonis unchangedControl (Group 0) vs MPTP+Acu (Group 1)Chao1 is increased > Richness is increased > Shannon unchangedMPTP + Acu (Group 0) vs MPTP + Non Acu (Group 1)Chao1is increasedRichnessis increasedShannonis unchanged

Nana (05:14:33) (in thread): > You record 2 body sites.

Nana (05:15:36) (in thread): > 3pm Nigeria time abi?

idiaru Angela (05:16:34) (in thread): > @Nana2pm Nigerian time

Nana (05:20:11): > Good morning@Peace Sandywhat I have in the Cladogram for CRC is the same for Lefse bar and I ask will I create signatures for both below is the image

Mildred Anashie (05:21:18) (in thread): > Good morning > > I think you should focus on the LEfSe bar (B) > > Can I see the footnote please > ((Figure description)

Desire Oluwarotimi (05:24:08) (in thread): > Hi@NanaBased on experience from previously curated papers, I think both B and C carry the same information but in different formats. > > However, I think B is quite easier to curate.

Scholastica Urua (05:26:07) (in thread): > Hello@NanaI think you should only curate the LeFse bar and use fig B as your source.

Aleru Divine (05:29:17) (in thread): > @Nanathe image is not clear, but as you said,they’rethe same, I’d suggest to curate the taxa from the LEfSe bar.

Abiola Salako (05:31:30) (in thread): > Good Morning@Svetlana Ugarcina PerovicThanks for the reminder. > > For me, the not-so-fun part is trying to figure out which signatures to curate especially with articles that are not too easy to understand. Although I have learnt one life lesson from it, imbibing the habit of being patient and paying attention to every little detail. > > The most fun part is having a reliable community of people to seek help and collaborate with for the successful curation of studies.

Nana (05:35:09) (in thread): > Thanks guys:ok_hand::ok_hand:

Nana (05:35:44) (in thread): > Ok .thank you

Blessing Ene Anyebe (05:52:09) (in thread): > Hello@Svetlana Ugarcina Perovic, thank you for the kind reminder! > > The least fun part for me is getting stuck figuring the complete details required to make a quality curation (especially around the numbers of experiments conducted in a long-study:sweat_smile:). Now I have learnt from other contributors’ help how to navigate that phase and the satisfaction isrewarding. > > The fun parts for me is figuring differential abundance because I struggled with it earlier, and its also fun/lovely seeing the collaboration and support everyone shares here.:orange_heart:

Ikeh Darlington Ikeh (06:01:29): > Hi everyone!, please when a taxa is denoted at the end with (UN) what does it mean? Uncultured or Unclassified? for example Bacilli RF39 (UN)

Mildred Anashie (06:02:21) (in thread): > Hi > > I think it could be any, they might be more information in text ifthat’sgotten from a figure or table > Have you checked?

Ikeh Darlington Ikeh (06:03:37) (in thread): > No further information in text. I didn’t find any?

idiaru Angela (06:05:26) (in thread): > Hi. I think it typically means uncultured. It usually refers to taxa that have been identified only by genetic sequencing but not culturing in a lab. > In other context tho I think a few authors may use it for unclassified(I’m not sure)

Esther Afuape (06:20:06) (in thread): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>there’sno sure way to tell the significant diversities here,I’malso not sure if I should use the long bars to measure the directions?

Peace Daniel (06:40:09) (in thread): > I think it means uncultured

Oluwatomisin Omojokun (06:46:32) (in thread): > it can be both uncultured and unclassified, some authors use it interchangeably

Barakat Akinsiku (06:46:35) (in thread): > Hi@Svetlana Ugarcina Perovicgood morning! > > My most favourite part of BugSigDB-ing is the daily learnings about new research in microbiome study from the papers I’m curating and also the warm, helpful community. > > The not-so-fun part? Trying to figure out ncbi missing taxa names with numerical digit appendages:joy:

Adenike Oladimeji-Kasumu (06:47:22) (in thread): > “(UN)” typically stands for “Uncultured” rather than “Unclassified.” > When a taxon is labeled as “Uncultured,” it means that the microorganism represented by that taxon has not been successfully cultured or grown in a laboratory setting as@idiaru Angelaalready stated.

Adenike Oladimeji-Kasumu (06:48:23) (in thread): > I suggest you can curate Bacilli sp but check to be sure it is on the ontology site.

U1LCB8WEA (06:48:46) (in thread): > Ha - for me the most fun thing is trying to figure out ncbi taxonomic names - it’s like solving a mystery for me:smile:

Desire Oluwarotimi (06:50:42) (in thread): > I’m assuming there’s no least fun thing then:joy:<@U1LCB8WEA>

Peace Daniel (06:51:27) (in thread): > That’sa first:sweat_smile:@Levi Waldron

Akinbode Mariam (06:51:43) (in thread): > Thanks@Mildred Anashie@Aleru Divine@Esther Afuapebut can you read this statement again concerning the experiment 4.( Interestingly, the acupuncture treatment significantly increased the number of observed OTUs and the Shannon index. We also found that Chao1 index, observed OTUs, and Shannon index were not increased significantly in the MPTP + Non-acu group compared to the MPTP group (Fig. S1A–C).) Doesnt it mean that the Chao1 and shannon would be descreased ?? for the Mptp + Non Acu group ?

Scholastica Urua (06:51:54) (in thread): > This is actually interesting. I feel uncultured and unclassified are two different things. Uncultured may mean organisms that have not been successfully grown in a laboratory culture, while Unclassified may refer to organisms that have been cultured but taxonomic classification is unresolved. But I’m not sure how either are denoted.

Peace Daniel (06:52:26) (in thread): > Haven’treally encountered this so far, but I can only imagine:hugging_face:@Barakat Akinsiku

Mildred Anashie (06:53:27) (in thread): > Yes > > I thought MTPT + non Acu was group 0

Joan C. Chukwuemeka (06:55:08) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for the reminder. > > Best/fun part of BugSigDB-ing is being able to decipher hidden yet curatable information from complex articles and the detective mode I activate to resolve NCBI missing IDs:sunglasses:, cause that makes me research more and increase my Microbiome knowledge. e.g. I learnt about other taxonomy databases like GTDB and SILVA in the process:seedling:Least fun part,,,hmmm… that was when I was still unsure about how to decipher between relative abundance and differential abundance, and then interpreting Log-fold figures especially the ones with box-plot.:face_with_peeking_eye:.. but, all of that is clear now. Quite comfortable with them now:nerd_face:

Chioma Onyido (06:55:11) (in thread): > I agree. This is a good issue to bring up during the office hour today.:wink:

Peace Daniel (06:55:14) (in thread): > @Adenike Oladimeji-Kasumudon’tknow about bacili so but I found this while making a search earlierhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=423410 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Ikeh Darlington Ikeh (06:55:15) (in thread): > @Mildred Anashie@ are you certain that experiments with Signatures can be curated on bugSigDB ? I don’t think I have seen any curation without signature on BugSigDB. Please can you refer me to any you know so I can study, because my current paper has experiments without signatures and I am skipping them. Hopefully this will clarify me.

Scholastica Urua (06:57:12) (in thread): > Yes@Ikeh Darlington Ikehthey can. Please refer to this thread from<@UBNSEMS3S>https://community-bioc.slack.com/archives/C04RATV9VCY/p1710277923151239?thread_ts=1710265890.754799&cid=C04RATV9VCY - Attachment: Attachment > Yeah you can curate an experiment with no signatures if there was no significant results.

Mildred Anashie (06:57:33) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710277923151239?thread_ts=1710265890.754799&channel=C04RATV9VCY&message_ts=1710277923.151239Go through this thread - Attachment: Attachment > Yeah you can curate an experiment with no signatures if there was no significant results.

Akinbode Mariam (06:57:39) (in thread): > oh okay how did you determine the richness in each ?@Mildred Anashie

Aleru Divine (06:57:55) (in thread): > Also yes@Ikeh Darlington Ikehexperiments without signatures can be curated.I had one of those and the mentors said it was okay to go ahead with the curation.

Mildred Anashie (06:59:31) (in thread): > I used the description for Fig S1 and tried to interpret the image from my understanding

Mildred Anashie (07:01:06) (in thread): > N/B@Ikeh Darlington Ikehif it says the experiment wasn’t significant I doubt there’s any point in curating it > > I have several experiments curated without signatures

Adenike Oladimeji-Kasumu (07:02:02) (in thread): > I have checked the ontology website, Bacilli sp is not identified. I did not find any synonymous microorganism.@Ikeh Darlington IkehI am not sure on how you would curate that organism. You can check the site that@Peace Danieljust dropped too

Mildred Anashie (07:06:57) (in thread): > @Scholastica Uruasee Chioma’s response

Ikeh Darlington Ikeh (07:07:12) (in thread): > @Aleru Divinecan I see the curation on BugSugDB so I can study it and know if it’s similar to mine?

Scholastica Urua (07:08:17) (in thread): > Okay@Chioma Onyidoreally looking forward to the office hour. Thanks:hugging_face:

Mildred Anashie (07:08:35) (in thread): > There’san example herehttps://bugsigdb.org/Study_1022 - Attachment (BugSigDB): White-nose syndrome restructures bat skin microbiomes - BugSigDB > Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases.Instead of single organisms being associated with disease, community characteristics may be more relevant.

Aleru Divine (07:11:40) (in thread): > https://bugsigdb.org/Study_861 - Attachment (BugSigDB): Resilience of the respiratory microbiome in controlled adult RSV challenge study - BugSigDB > This study of healthy adults revealed no major changes in the bacterial community of the respiratory tracts following RSV inoculation, suggesting that the adult respiratory microbial community is resilient to viral perturbations https://bit.

Ikeh Darlington Ikeh (07:17:54) (in thread): > @Mildred Anashie@Aleru DivineWow! I never knew, would have skipped those experiments. Thanks a million times over!

Mildred Anashie (07:18:30) (in thread): > You are welcome > > We are all learning:hugging_face:

Aleru Divine (07:18:48) (in thread): > That’salright,I’vebeen there:sweat_smile:

Mildred Anashie (07:19:59) (in thread): > Also just to point out > > If you study the link I shared,you’llrealize that there were more experiments than I recorded but it stated that there were not significant so I didn’t record them

Ikeh Darlington Ikeh (07:25:41) (in thread): > @Mildred AnashieNoted! I’ll check if there’re curatable, comparing with your paper. thanks so much

Ikeh Darlington Ikeh (07:36:24) (in thread): > For me! It gives me joy seeing my name among the curators, like the satisfaction and feeling of achievement it gives me is thrilling. Every other process from studying the papers to curating is fun until I get to the not so fun part of inputting bacterial strains that can’t be identified by BugSigDB and NCBI. However, the entire process has enlightened me more and that is also fun.

Joan C. Chukwuemeka (07:54:08) (in thread): > @Ima-obong (Aimah)glad to help:hugging_face:

Praise Agbetuyi (08:02:36) (in thread): > Thank you,@Svetlana Ugarcina Perovic, for the reminder. For me, the most fun part of the experience is seeing that a significant number of mentors and fellow curators are responding to my questions and addressing my concerns. It’s truly amazing, as I never thought I would enjoy open-source contributions this much since I’m more accustomed to working behind the scenes. On the other hand, um, the least fun part is trying to understand certain terms while curating and, even after grasping them, figuring out how best to report them. Thankfully, there’s a supportive community always ready to help with any concerns. Thank you, BugSigDB

Chioma Onyido (08:10:21) (in thread): > Best part is learning something new every time I curate/ review a study, for example Fecal microbiota transplantation to improve symptoms/ treat diseases.. you’d see something like “freshfaeces was collected and stored…”:sweat_smile:Not so fun part, curating any figure that’s not Lefse!:face_with_peeking_eye:

Ikeh Darlington Ikeh (08:16:18) (in thread): > @Chioma OnyidoThat was also in one of the papers I curated.It’squite funny reading that.And I learnt that Fecal Microbiota Transplantation can be used to treat Constipation in PD patients.

Oluwatomisin Omojokun (08:17:37): > Good afternoon everyone, I need your help on a study am workinghttps://bmcpulmmed.biomedcentral.com/articles/10.1186/s12890-023-02825-6#Sec2My question is > 1. There is more than two alpha diversity a. Gut microbial profiles between Lung cancer patients and benign pulmonary Diseases patients in figure 1 and b. Gut microbial profiles of Lung cancer patients with impaired pulmonary function in fig 3. > should i create them as different experiment since the sample size did not change (but they were re grouped) > 2. I am a little confused about the alpha divesity analysis in the figure above. > Thanks - Attachment (BioMed Central): Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites - BMC Pulmonary Medicine > Background Lung cancer (LC) is one of the most devastating diseases worldwide, there is growing studies confirm the role of impaired lung function in LC susceptibility. Moreover, gut microbiota dysbiosis is associated with LC severity. Whether alterations in gut microbiota and metabolites are associated with long-term lung dysfunction in LC patients remain unclear. Our study aimed to analyze the risk factors in LC patients with impaired pulmonary function based on the characteristics of the gut microbiome and metabolites. Methods Fecal samples from 55 LC patients and 28 benign pulmonary nodules patients were collected. Pulmonary ventilation function was graded according to the American Thoracic Society/ European Respiratory Society (ATS/ERS) method. LC patients were divided into 3 groups, including 20 patients with normal lung ventilation, 23 patients with mild pulmonary ventilation dysfunction and 12 patients with moderate or above pulmonary ventilation dysfunction. The fecal samples were analyzed using 16 S rRNA gene amplicon sequencing and metabolomics. Results The gut microbiome composition between LC patients and benign pulmonary nodules patients presented clearly differences based on Partial Least Squares Discriminant Analysis (PLS-DA). Pulmonary ventilation function was positively correlated with LC tumor stage, the richness and diversity of the gut microbiota in LC patients with moderate or above pulmonary ventilation dysfunction increased significantly, characterized by increased abundance of Subdoligranulum and Romboutsia. The metabolomics analysis revealed 69 differential metabolites, which were mainly enriched in beta-Alanine metabolism, styrene degradation and pyrimidine metabolism pathway. The area under the curve (AUC) combining the gut microbiome and metabolites was 90% (95% CI: 79-100%), indicating that the two species and four metabolites might regarded as biomarkers to assess the prediction of LC patients with impaired pulmonary function. Conclusions Our results showed that microbiome and metabolomics analyses provide important candidate to be used as clinically diagnostic biomarkers and therapeutic targets related to lung cancer with impaired pulmonary function.

idiaru Angela (08:22:25) (in thread): > @Oluwatomisin Omojokungoing through your paper, yes, they need to be curated as separate experiments as they were regrouped

idiaru Angela (08:27:36) (in thread): > The text above the figure that you sent explains it already. That there was no difference between the alpha diversity I.e Unchanged for all alpha diversity metrics. A good way to know just from the figure is to look above each plot when a plot carries * Then it means there is a significant difference. When there is a significant difference, looking at the median line would help you figure out if it increased or decreased. > I hope this answers your question:pray:

Ima-obong (Aimah) (08:30:33): > Good day everyone… > > My Fig4D has These significant markers;FDR<0.05(purple),FDR<0.1(blue),P<0.05(green), andP>0.05(white) > **And I’m to curate only significant signatures based on the colour indicators of these markers. > > But in my paper, there’s been no mention of P value and FDR or q value > For the P-value, I took the default value of 0.05 as my significant value hence the signatures with the indicator of p>0.05 are insignificant and not to be curated… > > My issue is with the FDR value…I don’t know how to decipher which is insignificant from the figure.. > > Will really appreciate your insights on this…Thanks alot:pray::pray: - File (JPEG): IMG-20240320-WA0015.jpg

Blessing Ene Anyebe (08:51:59): > Hello everyone office hour starts in few minuteshttps://us02web.zoom.us/j/2737200499

Desire Oluwarotimi (08:52:46) (in thread): > Hi@Ima-obong (Aimah)It doesn’t look like you can curate that figure to me.

Ima-obong (Aimah) (08:56:27) (in thread): > Okay@Desire Oluwarotimi.. here’s the thread of the question I asked last night and one of the mentors answered in the affirmativehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710968946807999?thread_ts=1710968946.807999&cid=C04RATV9VCY - Attachment: Attachment > Hello everyone, and my efficient mentors @Chioma Onyido @Peace Sandy @Esther Afuape > > I have a confusing situation here and I sincerely will appreciate your input no matter how long it takes for it to come in:blush: > > My study’s condition is biological ageing in People living with HIV(PLWH) as group 1 and People living without Hiv(PLWOH) as control … > The body sites were listed to be colon, Ileum, blood and Feces > > My major problem is in the figures I’m to curate from > Fig.4c shows Differential bacterial abundance between tissue(colon, ileum) and fecal samples on a logscale. And the comparisons include; colon Vs feces(red), Ileum Vs Feces(blue) and Ileum Vs colon(green). > > While Fig4D shows logscale differences in bacterial abundance across colon(triangle), ileum(square) and feces(circle) between PLWH(group1) and PLWOH(control).. > > Question is: am I to curate from both figures?, and if so, especially for Fig4c, since the comparison is between the samples and not the groups it self, am I to create new experiments for each of them? > > And if yes, what will my group 1 and 0 be for those Experiments > E.g. group 1: colon Vs ileum of PLWH > group 0: colon Vs Ileum of control…?? > > > > Secondly, > > Fig5A shows spearman’s rank correlation analysis depicting associations between colonic microbiomes increased (top row) or decreased (bottom row) in PLWH…Can I also curate this figure 5? > > Thanks alot..really :pray::pray:. > > Here is a link to the paper, I greatly appreciate in advance whatever input you make cause my eyes hurt already from looking at this paper:sob::joy: > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4

Desire Oluwarotimi (08:58:23) (in thread): > In that case, I’m not sure how to.

Joan C. Chukwuemeka (08:59:20): > <!here>A study in its figure inputted* Enterococcaceae(UN)and then in the description added this: ““UN” refers to undetermined/unclassified genus, and family or order is therefore reported. > > I’m thinking in this case the signature to curate would be the reported familyEnterococcaceae *and notUnclassifiedEnterococcaceae?Am I right?<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>@Chioma Onyido@Esther Afuape@Peace Sandy

Ima-obong (Aimah) (09:00:57) (in thread): > Okay. Thanks alot

Svetlana Ugarcina Perovic (09:39:33) (in thread): > @Mildred Anashiehttps://www.ebi.ac.uk/ols4/ontologies/mondo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FMONDO_0002041?lang=enfungal infectious disease > “White-nose syndrome is a disease caused by the fungus Pseudogymnoascus destructans.” - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Mildred Anashie (09:56:25) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:pray:

Aleru Divine (10:00:57) (in thread): > Hi@Oluwatomisin OmojokunI’ve looked at your paper and yes, you’ll curate these figures (1 and 3) as different experiments. > 1. One experiment for figure 1 (between lung cancer patients(C) and benign diseases patients(N) > 2. For figure 3 you’ll curate 3 experiments.(this should come from a pair wise comparison of ZC, QD and ZZD. > To address your concern on alpha diversity, I believe there were no significant differences in figure 1. There will be a square bracket on top if there is a significant difference.For figure 3, > > Sobs, Chao1, Ace and Shannon, ZC decreased when compared to ZZD. > > No significant differences in the others.

Scholastica Urua (10:01:44) (in thread): > Thank you<@UBNSEMS3S>for the lecture on confounders:blush:

Oluwatomisin Omojokun (10:02:02) (in thread): > Thank you@Aleru Divine

Peace Daniel (10:03:58): > Thank you@C. Mirzayi (please do not tag this account)for simplifying ways to control for confounders

Svetlana Ugarcina Perovic (10:04:16) (in thread): > UnclassifiedEnterococcaceae

Ajayi Mercy (10:04:46): > BugSigDB is a valuable resource for gaining insight into various bugs, their signatures, and their impact on systems. However, the vast amount of data in BugSigDB can be overwhelming, and locating specific information can be a challenging task, like finding a needle in a haystack.

Roderick Momin (10:05:04): > Hello, should I go ahead and record my Second Contribution at Outreachy? I’m still waiting for the Supplementary Materials to be provided by the author of my the case study I’ve been assigned.

Blessing Ene Anyebe (10:06:16): > Thank you for the insightful section@C. Mirzayi (please do not tag this account)It was interesting to see you go on about regression!:sweat_smile:Thank you so much for sharing more about confounding.:orange_heart:

Amarachi Lewachi (10:07:05): > Thank you@C. Mirzayi (please do not tag this account)for an insightful session. And thank you to all who asked questions. i learnt from your questions.

Scholastica Urua (10:07:10): > Thank you<@UBNSEMS3S>for the lecture on confounders:blush:

Peace Daniel (10:07:23) (in thread): > I don’t understand, waiting for what? > Could you share a link to your paper?

Mildred Anashie (10:07:47) (in thread): > Hi > > Have you submitted for review? > You can record if you are done curating it > But it appears you are still waiting to get the supplemental so you finish curating > > In this case I believe you can ask the mentors to help you get the supplemental

Svetlana Ugarcina Perovic (10:07:52) (in thread): > Do not wait for the author’s reply too long. Sometimes they just do not reply. You could just send a kind reminder. Anyway, continue with your curation without Supplementary material.

Desire Oluwarotimi (10:08:21): > Thank you@C. Mirzayi (please do not tag this account)

idiaru Angela (10:09:03): > Thank you@C. Mirzayi (please do not tag this account). The office hour was very insightful. Thank you to other co-contributors too. I learnt a lot from your questions.

Oluwatomisin Omojokun (10:09:43): > @C. Mirzayi (please do not tag this account),Thank you for the session. it was really explanatory especially the confounding.:gratitude-thank-you:

Aleru Divine (10:10:01): > Thank you<@UBNSEMS3S>for the insightful session today.And thank you to everyone that asked these questions:heart:

Scholastica Urua (10:10:38): > Thank you<@UBNSEMS3S>for the clarification. I’ve made some adjustments and my curation is ready for review. > Thank you@Mildred Anashieand@Peace Danielfor going through the article with me.:hugging_face:https://bugsigdb.org/Study_1015 - Attachment (BugSigDB): Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing - BugSigDB > The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders.

Joan C. Chukwuemeka (10:16:25) (in thread): > Thanks@Svetlana Ugarcina Perovic<@UBNSEMS3S>also responded during the office hour.

Svetlana Ugarcina Perovic (10:17:35) (in thread): > yes, during our meeting I put Chloe’s answer here, just not to be missed

Joan C. Chukwuemeka (10:19:53) (in thread): > Yea…Thanks a lot:hugging_face:

Abiola Salako (10:21:21): > Thank you@C. Mirzayi (please do not tag this account)it was an insightful session.

Roderick Momin (10:38:14) (in thread): > @Svetlana Ugarcina PerovicI’ve waited 14 days (counting weekends) and sent a follow up email to the author. I’d like to submit the paper I’ve curated for review then. Links for convenience: > 1. https://bugsigdb.org/Study_886(Contains talk/discussion page as well) > 2. https://github.com/waldronlab/BugSigDBcuration/issues/89 > Of note, I made a mistake adding Signature 3 and Signature 4 under Experiment 1 which I cannot delete due to not being an admin.

Rahila-me (10:55:08): > Thanks for taking out your time to explain confounder<@UBNSEMS3S>it was insightful

Svetlana Ugarcina Perovic (10:56:53) (in thread): > ok@Roderick Mominall noted

Roderick Momin (11:06:45) (in thread): > I appreciate@Svetlana Ugarcina Perovicthe swift replies.

Mildred Anashie (11:54:18): > The meeting was enlightening thanks to<@UBNSEMS3S>all the mentors and all the questions that were asked > > A few take home points from the meeting > 1. A confounder is a variable that can cause both exposure and outcome and it can lead to bias henceforth the reason researchers control for confounders (they Can either adjust, control for etc. > Ways to control for confounding > 1. Stratified Analysis > Break your study into various groups based on the confounder and analysis between each group. > 2. Linear model/Regression model and add the confounder as a Covariate. > > It needs to be stated that the covariates were included in the model. > (The few I could get:laughing:) > > If there isnt a defined Group 1 and Group 0 you can try to figure out which best fit from the paper. > > Hopefully we’ll get more from the recording:hand_with_index_and_middle_fingers_crossed:

Ima-obong (Aimah) (12:11:53) (in thread): > Thanks for this summary@Mildred Anashie

Barakat Akinsiku (12:17:35) (in thread): > The explanation on confounders was truly enlightening@Mildred AnashieThank you@C. Mirzayi (please do not tag this account)for the insightful session

Aleru Divine (13:31:23) (in thread): > Thanks@Mildred Anashie:hugging_face:

Blessing Ene Anyebe (13:33:53) (in thread): > Thank you for the summary@Mildred Anashie:orange_heart:

Scholastica Urua (13:42:55): > Hello everyone, > I haven’t been able to find this signature on NCBI taxonomy browser or Uniprot; > Ruminococcaceae bacterium UCG-007 > > Thought to share it here in case anybody has an idea. > > Thank you! > I’m looking forward to your help:hugging_face:

Muqtadirat Yussuff (13:46:38) (in thread): > Same with Ruminococcaceae bacterium UCG-005, I think it’s just best to leave them. They don’t seem to have an ID, for now anyway

Mildred Anashie (13:59:54) (in thread): > Yea I agree with@Muqtadirat YussuffI think there are unresolved for now

Scholastica Urua (14:00:30) (in thread): > Thank you@Muqtadirat Yussuffand@Mildred Anashie

Scholastica Urua (14:04:21): > Hello everyone, > > I just completed this curation and will love peer reviews. I’d appreciate any corrections and feedback I get. Thank you:pray:https://bugsigdb.org/Study_1052 - Attachment (BugSigDB): Disturbed microbial ecology in Alzheimer’s disease: evidence from the gut microbiota and fecal metabolome - BugSigDB > BACKGROUND: Gut microbiota (GMB) alteration has been reported to influence the Alzheimer’s disease (AD) pathogenesis through immune, endocrine, and metabolic pathways.This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis.

idiaru Angela (14:05:04) (in thread): > Well done@Scholastica Urua. Would love to review it.

Scholastica Urua (14:05:54) (in thread): > Thank you@idiaru AngelaLooking forward to your feedback:hugging_face:

Adenike Oladimeji-Kasumu (14:06:29) (in thread): > I’ve checked myself and even try to look at some individual Ruminococcaceae species… There’s none similar. > I also think you should leave it as@Muqtadirat Yussuffsuggests

Scholastica Urua (14:07:12) (in thread): > Okay, thank you@Adenike Oladimeji-Kasumu

Adenike Oladimeji-Kasumu (14:10:04) (in thread): > I would also like to review it. Well done:100:Please I am also in need of reviews for my latest curation if you don’t mind. Here’s the link:https://bugsigdb.org/Study_973 - Attachment (BugSigDB): Changes in the Gut Microbiome and Predicted Functional Metabolic Effects in an Australian Parkinson’s Disease Cohort - BugSigDB > Background: There has been increasing recognition of the importance of the gut microbiome in Parkinson’s disease (PD), but the influence of geographic location has received little attention.

Scholastica Urua (14:16:29) (in thread): > Thank you@Adenike Oladimeji-KasumuI’ll get right on yours now.

Sidra Khan (14:21:26) (in thread): > Thanks for the detailed summary:ok_hand:. From where we can get the recording of the session?

Barakat Akinsiku (14:24:30) (in thread): > Well done Scholastica, will also review it

Barakat Akinsiku (14:28:38) (in thread): > @Muqtadirat YussuffRuminococcaceae bacterium UCG-005 actually has an ID. I’ve searched for Ruminococcaceae bacterium UCG-007 but that seems to be unresolved@Scholastica Urua

Peace Daniel (14:45:06) (in thread): > I actual found yours@Muqtadirat Yussuffhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?name=Ruminococcaceae+bacterium+UCG-005 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Scholastica Urua (14:45:57) (in thread): > Nice one@Peace Daniel

Mildred Anashie (14:57:10) (in thread): > It will be shared here in the channel by the mentors whenit’savailable

Svetlana Ugarcina Perovic (15:08:40) (in thread): > Here is<@UBNSEMS3S>’s drawing of the example ;) - File (PNG): Screenshot 2024-03-21 at 14.25.10.png

Mildred Anashie (15:11:27) (in thread): > Well done@Scholastica UruaI’ll glance through again

Scholastica Urua (15:13:41) (in thread): > Hello@Adenike Oladimeji-Kasumu, > > Well done on your curation, these are a few things I noticed: > > 1. It appears that ANOVA was utilized to compare alpha diversities and to test for continuous variables, while Fisher’s exact test was employed for testing categorical variables (as indicated in the excerpt below). However, for the differential abundance analysis, it seems that Mann-Whitney (Wilcoxon) would have been a more appropriate statistical test to employ. > > 2. It’s mentioned that there was a multiple hypothesis testing (MHT) correction performed, specifically a false discovery rate (FDR) adjustment. However, I couldn’t find this detail in your curation. > > 3. Regarding the matching procedure, I couldn’t find evidence suggesting that the participants were ‘matched-on’ any specific criteria. Could you kindly direct me to this information, I may have overlooked it. > > If I come across any other information, I let you know. Cheers:hugging_face: - File (JPEG): ANOVA.JPG - File (JPEG): test.JPG - File (JPEG): test2.JPG

Abiola Salako (15:21:26) (in thread): > Thanks for sharing@Mildred Anashie

Abiola Salako (15:26:55) (in thread): > Well done@Scholastica Uruawould love to glance through it. > > It was a study well-curated.

UBNSEMS3S (15:32:50) (in thread): > Haha if I knew my drawing was going to be screenshotted I would have done a better job with it!

UBNSEMS3S (15:32:53): > Today’s office hours recording. Thank you all for attending and asking excellent questions. - File (MPEG 4 Video): video1477738317.mp4

idiaru Angela (15:33:48) (in thread): > Thank you@C. Mirzayi (please do not tag this account)for your time

Sidra Khan (15:37:06) (in thread): > Thank you for providing the recording@C. Mirzayi (please do not tag this account)

Mildred Anashie (15:39:08) (in thread): > Thank you for sharing<@UBNSEMS3S>:hugging_face:

Eniola Adebayo (15:46:32) (in thread): > Thankyou<@UBNSEMS3S>

Adenike Oladimeji-Kasumu (15:48:37) (in thread): > Thank you so much for this@Scholastica UruaI appreciate you. > I would go through yours in the morning and get back to you

Scholastica Urua (15:50:03) (in thread): > You’re welcome@Adenike Oladimeji-Kasumu. Looking forward to your feedback.

Scholastica Urua (15:50:25) (in thread): > Thank you<@UBNSEMS3S>

Eniola Adebayo (15:53:51) (in thread): > Well done@Scholastica UruaI think this is another name for a signature in experiment 1 that is in red - File (JPEG): IMG_0235

Nana (15:54:23) (in thread): > @C. Mirzayi (please do not tag this account)thank you very much today was very impactful especially your lecture on confounder

Rahila-me (15:56:16): > Please@Peace Sandywhat’s the interpretation of this: Is it increase in the first two then unchange for choa

Svetlana Ugarcina Perovic (15:57:26) (in thread): > correct

Rahila-me (16:22:49) (in thread): > @Svetlana Ugarcina Perovicok.. Thanks:ok_hand:

Scholastica Urua (16:22:51) (in thread): > Thank you@Eniola AdebayoBut I think that’s for ‘Ruminococcaceae’ which I believe is different from ‘Ruminococcaceae bacterium UCG-007’

Rahila-me (16:35:30): > @Svetlana Ugarcina PerovicCan i change this : NCBI BLAST name:firmicutes to Bacillota this does not hav id in ncbi Firmicutes

Svetlana Ugarcina Perovic (16:43:45) (in thread): > Correct. > Btw, this reminded me of one the yesterday MVIF slideshttps://twitter.com/MicrobiomeVIF/status/1770460842531623017/photo/1 - Attachment (X (formerly Twitter)): Microbiome Virtual International Forum (@MicrobiomeVIF) on X > @Roche . @SerenaManara @LeviWaldron1 & another #nomvifwithoutproblems moment :D

Svetlana Ugarcina Perovic (16:45:02) (in thread): > https://twitter.com/GenScript/status/1470271283053178880/photo/1 - Attachment (X (formerly Twitter)): GenScript (@GenScript) on X > #updates :point_right:Some #bacteria have new phylum names! @NCBI Taxonomy to include phylum rank in taxonomic names. https://t.co/rqeI6A0b25 > #microbiome #microbiology #microbiologist #metabolic #taxonomy #Biology #biomedical #Pharmaceutical #microbiota

Rahila-me (17:27:55) (in thread): > @Svetlana Ugarcina Perovicthis is hilarious and at the same time educational. I will save this for view and laugh. This made my night

Nana (17:37:48): > Can I enter this as a signature

Flourish Ralph (18:26:57): > Hi everyone, > > What do I do in a situation where the antibiotics exclusion criteria doesn’t have a clearly stated timeline?@Svetlana Ugarcina Perovic@Esther Afuape@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy - File (JPEG): IMG_3024

idiaru Angela (18:28:00) (in thread): > If you confirm from supplementary materials that it doesn’t, I suggest you leave it blank@Flourish Ralph

Flourish Ralph (18:29:22) (in thread): > There’sno supplementary material that I can see

idiaru Angela (18:30:24) (in thread): > Then I suggest you leave it blank since it’s not clearly defined

Flourish Ralph (18:30:40) (in thread): > Hmm, I see

Flourish Ralph (18:31:48) (in thread): > I also have an issue figuring out the exact disease condition, don’t know if I can just classify it as ‘mental health’ when the intestinal microbiome is also being affected. > > Here’s the link to the study I’m curating, for clarityhttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-02056-3 - Attachment (BioMed Central): Alterations in the intestinal microbiome and mental health status of workers in an underground tunnel environment - BMC Microbiology > Background Working in an underground tunnel environment is unavoidable in professions such as miners and tunnel workers, and there is a concern about the health of these workers. Few studies have addressed alterations in the intestinal microbiome of workers within that environment. Results Fecal samples were collected from the workers before they entered the tunnel (baseline status, BS) and after they left the tunnel (exposed status, ES), respectively (a time period of 3 weeks between them). We analyzed 16S rRNA sequencing to show the changes in microbial composition and self-evaluation of mental health questionnaire was also performed. The results showed that Shannon and Simpson indices decreased significantly from BS to ES. A higher abundance was found in the phylum Actinobacteria, classes Actinobacteria and Deltaproteobacteria, orders Bifidobacteriales, Coriobacteriales, and Desulfovibrionales, families Bifidobacteriaceae, Peptostreptococcaceae, Coriobacteriaceae, Clostridiaceae_1, Desulfovibrionaceae, Pseudomonadaceae, and Microbacteriaceae, and genera Bifidobacterium, Romboutsia, Clostridium sensu stricto, and Leucobacter in ES, while BS showed greater levels of genera Faecalibacterium and Roseburia. The self-evaluation showed that at least one-half of the tunnel workers experienced one or more symptoms of mental distress (inattention, sleeplessness, loss of appetite, headache or dizziness, irritability) after working in the underground tunnel environment. Conclusions Collectively, the underground tunnel environment led to alterations in the intestinal microbiome, which might be relevant to symptoms of mental distress in underground-tunnel workers.

idiaru Angela (18:37:50) (in thread): > I think Mental Health works perfectly:thinking_face:. The intestine is the body site not necessarily the condition

Flourish Ralph (18:44:50) (in thread): > I’ma bit skeptical because of the‘alterations inthe intestinal microbiome’ part:weary:

idiaru Angela (18:46:53) (in thread): > Ohhh > Many topics in many other conditions appear like that. It has no impact on what the condition being studied is

Flourish Ralph (18:57:55) (in thread): > Ahhh, I see > Thank you, Angela!

idiaru Angela (19:00:58) (in thread): > You’re welcome@Flourish Ralph

2024-03-22

Aleru Divine (00:52:56) (in thread): > @Flourish RalphI thinkit’sokay to leave this out ifit’snot clearly stated.You can include a note.

Aleru Divine (00:55:04) (in thread): > @NanaI doubt this should be included. It’s not a taxon.

Aleru Divine (00:56:09) (in thread): > Absolutely hilarious meme:sweat_smile::sweat_smile:

Adenike Oladimeji-Kasumu (01:53:39) (in thread): > In my understanding, You cannot curate this.

Svetlana Ugarcina Perovic (02:00:00): > Good morning, you are ALL doing great. Keep up the good work andHAPPY FRIDAY!Just wanted to share with you some microbiome/bioinformatics learning/fun resources that might be of your interest. Some time ago, I started compiling several lists (& still regularly updating them!):Microbiome eventshttps://github.com/SvetlanaUP/Microbiome-conferences-cMicrobiome podcastshttps://github.com/SvetlanaUP/Microbiome-etc-PodcastsBioinformatics learning resourceshttps://github.com/SvetlanaUP/A-microbiologist-wants-to-compute

Joan C. Chukwuemeka (02:00:01): > @Flourish RalphAn excerpt from your study, “We analyzed 16S rRNA sequencing to show the changes in microbial composition and self-evaluation of mental health questionnaire was also performed” > > The Condition is what is being contrasted in the experiment. In this case, I think the contrast that was done was between the gut/intestinal microbiota status at Baseline and at Exposure. > > So, I think the nearest condition will be along the lines of Intestinal/gut microbiome measurements/evaluation. > > gut microbiome measurement > EFO:0007874

Mildred Anashie (02:09:06) (in thread): > Good morning@Svetlana Ugarcina Perovicand happy Friday to you too:sunny:Thank you for the encouragement and for sharing this information packed filled linksI’llbe sure to check them out > Thank you:blush:

Flourish Ralph (02:12:36) (in thread): > Good morning and Happy Friday@Svetlana Ugarcina PerovicThank you for this:fire:

Flourish Ralph (02:12:58) (in thread): > Thank you@Aleru Divine

Desire Oluwarotimi (02:13:50) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you

Flourish Ralph (02:13:58) (in thread): > Good morning@Joan C. ChukwuemekaDoes this mean the disease condition should be ‘gut microbiome measurement’ and ‘mental health’?

Peace Daniel (02:14:47) (in thread): > Good morning and happy friday:tada:

Amarachi Lewachi (02:24:10) (in thread): > For me the fun part is learning something new during curation and the collaboration on the platform. The challenging part is (or was) getting acquainted with new terms.

Adenike Oladimeji-Kasumu (02:28:47) (in thread): > Happy Friday everyone and to you too@Svetlana Ugarcina Perovic. Thank you for sharing this. Your support always goes a long way.

Scholastica Urua (02:36:23) (in thread): > Good morning and Happy Friday@Svetlana Ugarcina Perovic. Thank you for sharing:hugging_face:I’ll definitely check them out.

Joan C. Chukwuemeka (02:38:48) (in thread): > Good morning@Flourish Ralph, I’m a bit skeptical if mental health should be included. Scanning through the paper, I don’t really see contrasts that involved mental health, especially as info on that was self-evaluated by questionnaire:thinking_face:. > Perhaps the mentors can offer more insight on this.@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy

Joan C. Chukwuemeka (02:44:17) (in thread): > Good morning@Svetlana Ugarcina PerovicHappy Friday too:hugging_face:Thanks for sharing:magic:

idiaru Angela (02:57:57) (in thread): > Good morning@Svetlana Ugarcina Perovicand Happy Friday. Thank you for these resources

Blessing Ene Anyebe (03:07:55) (in thread): > Thank you@C. Mirzayi (please do not tag this account)it was an informative section.:orange_heart:

Blessing Ene Anyebe (03:13:51) (in thread): > Hello@Svetlana Ugarcina Perovichope you are well. Thank you for sharing these resources. Happy Friday!:orange_heart::sparkles:

idiaru Angela (03:19:33) (in thread): > @Flourish Ralphlooking through your paper I think the condition would be Work environment. In the contrast that was made, the intestinal microbiome was checked before exposure to the tunnel and after exposure to the underground tunnel, to me that forms the contrast between the two groups. Since exposure to a tunnel isn’t a term that you can find, I think work environment should work too

Abiola Salako (03:31:28) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for sharing. We’re grateful.

Aleru Divine (03:39:05) (in thread): > Happy Friday@Svetlana Ugarcina PerovicThank you so much for sharing this resources.:hugging_face:

Nana (03:44:33) (in thread): > @Svetlana Ugarcina Perovichappy Friday to you too. Thank you for all you do.

Nana (03:45:34) (in thread): > Ok..thanks

Nana (03:46:41): > @Peace SandyI chose GBS negative as my group 1.. please kindly take a look at the image and know if I am correct.

Aleru Divine (03:52:19) (in thread): > @NanaGBS culture negative should be group 0 as they are unexposed(meaning negative) > > Your group 1 should be GBS culture positive group.

Rahila-me (03:52:42) (in thread): > This i love:dancer:Thank you@Svetlana Ugarcina Perovic

Barakat Akinsiku (03:55:32) (in thread): > Good morning and thank you@Svetlana Ugarcina Perovic

Barakat Akinsiku (03:58:10) (in thread): > Yes@NanaGBS culture negative should be your control Group 0 and GBS culture positive your Group 1

Mildred Anashie (04:10:31) (in thread): > They are both correct in my opinion@NanaCulture positive seems like the group with the condition which is the case group and group 1 is usually the case group > > So I’ll go with GBS culture positive for Group 1 instead of Group 0

Nana (04:12:50) (in thread): > Ok..thanks.

Nana (04:13:28) (in thread): > One more thing if FDR is mentioned in a study, does it mean you will tick MHT to be yes..in the experiment

Mildred Anashie (04:13:47) (in thread): > Yes

Scholastica Urua (04:13:56) (in thread): > @Nanayes to MHT

Aleru Divine (04:14:18) (in thread): > Yes@Nana

Nana (04:14:37) (in thread): > Thanks my lovely guys..una too much

Bolanle Wahab (04:17:39) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you:heart:Definitely checking these out!

Victoria (Burah) Poromon (04:53:52): > Hello, good morning everyone > I just finished curating this study. > > If anyone is still up for peer reviews,I’dreally appreciate it:hugging_face:https://bugsigdb.org/Study_1053 - Attachment (BugSigDB): Profiling the urinary microbiome in men with calcium-based kidney stones - BugSigDB > BACKGROUND: The dogma that urine is sterile in healthy individuals has been overturned by recent studies applying molecular-based methods.Mounting evidences indicate that dysbiosis of the urinary microbiota is associated with several urological diseases.

idiaru Angela (04:54:44) (in thread): > @Victoria (Burah) Poromonwould review and give you feedback. Well-done!

Victoria (Burah) Poromon (04:55:13) (in thread): > Thank you!@idiaru Angela

Nana (05:04:39) (in thread): > Guys the FDR was mentioned only in Fig will I still enter the MHT to be yes?

Scholastica Urua (05:12:41) (in thread): > The fig with the differential abundance taxa right? > I think it t should still be yes@Nana

idiaru Angela (05:13:22) (in thread): > Hello@Victoria (Burah) Poromonwell done again > 1. For the body site I would go with urine as that was the sample that was collected and not the microbe from the bladder exactly. > 2. For the antibiotics exclusion, just the period of exclusion is to be recorded I.e 30days > 3. “The α − diversity indices, including observed species, chao 1 index, ACE index, Shannon diversity index, of the microbiota in HB group were all higher than those of KB group” > From the excerpt above, all alpha diversity metrics increased but i noticed you recorded 2 of them as decreased:thinking_face:

Nana (05:14:12) (in thread): > Yes

Aleru Divine (05:14:27) (in thread): > @Nanaeven if it was mentioned just once, it should still be a yes.But can you share your paper soI’lltake a look.

Scholastica Urua (05:15:45) (in thread): > Well done on curation@Victoria (Burah) Poromon

Victoria (Burah) Poromon (05:23:21) (in thread): > Thank you!@idiaru Angelafor your feedback > So let me explain why I curated different body sites:weary: > 1. The difference between KB and KP group is where the urine was gotten from. So I think curating 2 body sites would be more appropriate?I might have to look at the paper again. Thank you for this > 2. Thank you,I’lledit this one. > 3. Uhmmm, I was looking at the KB group, those are lower.Idunno ifI’mmissing something here:smiling_face_with_tear:thought my curation is supposed to be based on the diseased group (group 1)?

Victoria (Burah) Poromon (05:24:18) (in thread): > @Scholastica Uruathank you! > If you have the time. We could review eachother’scuration? > I’d appreciate it

Oluwatomisin Omojokun (05:28:15): > Good morning everyone > I just finished my curated study. I will like your review because I was confused curating the study especially at the experiment 2. your review will be highly appreciated.https://bugsigdb.org/Study_1051 - Attachment (BugSigDB): Analyzing lung cancer risks in patients with impaired pulmonary function through characterization of gut microbiome and metabolites - BugSigDB > BACKGROUND: Lung cancer (LC) is one of the most devastating diseases worldwide, there is growing studies confirm the role of impaired lung function in LC susceptibility.Moreover, gut microbiota dysbiosis is associated with LC severity.

idiaru Angela (05:29:35) (in thread): > @Victoria (Burah) Poromonfor 1. I totally get it. Its a bit confusing for me too. I however just thought that when intestinal microbes are being analysed the body site is still feces coz that is usually the sample collected, using that reasoning I felt the body site for this study should be urine > For 3. Following your train of thought, that would mean all alpha diversity measures should be decreased then, don’t you think:thinking_face:. I was just trying to point that in the curation some are recorded as increased while some are recorded as decreased

Victoria (Burah) Poromon (05:31:59) (in thread): > Okay. I should probably clarify about this from the mentors. Thank you > > For 3. I got that from fig.2 Simpson’s is increased and the rest are decreased

Nana (05:32:52) (in thread): > Ok

Nana (05:34:43) (in thread): > Here@Aleru Divine - File (JPEG): Screenshot_2024-03-22-10-34-22-81_99c04817c0de5652397fc8b56c3b3817.jpg

Scholastica Urua (05:34:59) (in thread): > That’ll be nice@Victoria (Burah) PoromonI’m going through someone’s one right now but when I’m done I’ll get right on yours. Here’s a link to minehttps://bugsigdb.org/Study_1052 - Attachment (BugSigDB): Disturbed microbial ecology in Alzheimer’s disease: evidence from the gut microbiota and fecal metabolome - BugSigDB > BACKGROUND: Gut microbiota (GMB) alteration has been reported to influence the Alzheimer’s disease (AD) pathogenesis through immune, endocrine, and metabolic pathways.This study aims to investigate metabolic output of the dysbiosis of GMB in AD pathogenesis.

idiaru Angela (05:36:16) (in thread): > @Victoria (Burah) Poromonfor 3. Hmm > From the figure Simpson does look increased while the rest are decreased.

Mildred Anashie (05:36:19) (in thread): > It’s still a Yes for MHT@Nana

Rahila-me (05:36:42) (in thread): > ok…:ok_hand:

Rahila-me (05:36:50) (in thread): > Thanks once again

Mildred Anashie (05:37:04) (in thread): > Congratulations and well done

Rahila-me (05:38:07) (in thread): > Well done@Oluwatomisin Omojokun

idiaru Angela (05:39:09) (in thread): > Well done@Oluwatomisin Omojokun

Victoria (Burah) Poromon (05:39:43) (in thread): > It’sthis figureI’mtalking about:sneezing_face: - File (JPEG): 60f94220-1614-433d-81fe-fa1f5f332f35

idiaru Angela (05:41:19) (in thread): > Yes I noted that. The median line for asv, chao, ace, and Shannon look decreased to me. While Simpson is clearly increased

Victoria (Burah) Poromon (05:41:58) (in thread): > YeahThat’swhat i recorded

Nana (05:42:45) (in thread): > @Victoria (Burah) Poromonwell done

idiaru Angela (05:43:32) (in thread): > Alright@Victoria (Burah) PoromonIf you do get clarification on the body site please tag me. I’d like to know If my thought process regarding that was correct

Victoria (Burah) Poromon (05:44:07) (in thread): > Sure I will@idiaru AngelaMany thanks

Aleru Divine (05:44:45) (in thread): > Thanks@Nana

Aleru Divine (05:45:11) (in thread): > Great job@Oluwatomisin Omojokun:clap:

Nana (05:45:52) (in thread): > For body sites you can look it up on UBERON by clicking on find terms

Nana (05:46:04) (in thread): > If it didn’t appear when typing

Victoria (Burah) Poromon (05:46:45) (in thread): > Yeah@NanaThat’swere I got the two body sites I recorded

Nana (05:49:52) (in thread): > Ok

Oluwatomisin Omojokun (05:52:36) (in thread): > Thank you@Mildred Anashie@Rahila-me@idiaru Angela@Aleru Divine

Ima-obong (Aimah) (05:55:23) (in thread): > Well-done@Oluwatomisin Omojokun

Abiola Salako (06:01:27) (in thread): > Well done@Oluwatomisin Omojokun

Victoria (Burah) Poromon (06:01:31) (in thread): > Hi@Oluwatomisin OmojokunWell done! > > I’m looking at your curation. > Here are some things I’ve noticed > 1. Figure 4A is not curatable, thanks to a review I got from@Mildred Anashieon my first curation. Becauseit’srelative abundance. Only differential abundance is been curated > 2. Firmicutes is same as Bacillota. And Bacteriodes to Bacteroides. I think you missed the o and I > 3. For the matched-on, Idon’tthink they did for this study. Those seem like the data they got from patients. > Well done

Abiola Salako (06:02:47) (in thread): > Well done@Victoria (Burah) Poromon

Victoria (Burah) Poromon (06:03:29) (in thread): > Thank you!@Abiola Salako

Abiola Salako (06:04:04) (in thread): > Yes for MHT@Nana

idiaru Angela (06:05:37) (in thread): > Yes@Oluwatomisin Omojokunonly figure 4c is curatable

Oluwatomisin Omojokun (06:12:40) (in thread): > @Victoria (Burah) Poromon@idiaru Angela, Thank you for the review. I will cross-check.

Abiola Salako (06:14:38): > Good day, everyone. I just finished curating a study and would like some of us to help look through it before the final submission. Thank you as you do.https://bugsigdb.org/Study_977 - Attachment (BugSigDB): Limited Impact of SARS-CoV-2 on the Human Naso-Oropharyngeal Microbiota in Hospitalized Patients - BugSigDB > Numerous studies have reported dysbiosis in the naso- and/or oro-pharyngeal microbiota of COVID-19 patients compared with healthy individuals; however, only a few small-scale studies have also included a disease control group.

idiaru Angela (06:16:20) (in thread): > Hey@Abiola Salakowell done. I’ll review and give you feedback

Abiola Salako (06:17:53) (in thread): > @idiaru AngelaThank you.

NWAKAEGO VINCENT (07:20:29): > the paper i am curating does not have PMID, Do i leave that section blank?https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02387-9 - Attachment (BioMed Central): Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts - BMC Microbiology > Background To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities. This study aimed to investigate the impact of fecal and oral sample collection methods and room temperature storage on collection samples for studies of the human microbiota. Results We collected fecal and oral samples from participants in two Iranian cohorts located in rural Yazd (n = 46) and urban Gonbad (n = 38) and investigated room temperature stability over 4 days of fecal (RNAlater and fecal occult blood test [FOBT] cards) and comparability of fecal and oral (OMNIgene ORAL kits and Scope mouthwash) collection methods. We calculated interclass correlation coefficients (ICCs) based on 3 alpha and 4 beta diversity metrics and the relative abundance of 3 phyla. After 4 days at room temperature, fecal stability ICCs and ICCs for Scope mouthwash were generally high for all microbial metrics. Similarly, the fecal comparability ICCs for RNAlater and FOBT cards were high, ranging from 0.63 (95% CI: 0.46, 0.75) for the relative abundance of Firmicutes to 0.93 (95% CI: 0.89, 0.96) for unweighted Unifrac. Comparability ICCs for OMNIgene ORAL and Scope mouthwash were lower than fecal ICCs, ranging from 0.55 (95% CI: 0.36, 0.70) for the Shannon index to 0.79 (95% CI: 0.69, 0.86) for Bray-Curtis. Overall, RNAlater, FOBT cards and Scope mouthwash were stable up to 4 days at room temperature. Samples collected using FOBT cards were generally comparable to RNAlater while the OMNIgene ORAL were less similar to Scope mouthwash. Conclusions As microbiome measures for feces samples collected using RNAlater, FOBT cards and oral samples collected using Scope mouthwash were stable over four days at room temperature, these would be most appropriate for microbial analyses in these populations. However, one collection method should be consistently since each method may induce some differences.

NWAKAEGO VINCENT (07:21:48) (in thread): > okay, thank you

Mildred Anashie (07:21:58) (in thread): > 34809575Your PMID

idiaru Angela (07:22:52) (in thread): > Hey@NWAKAEGO VINCENT34809575 > That is the pmid

NWAKAEGO VINCENT (07:23:13) (in thread): > how did you find it@Mildred Anashie

idiaru Angela (07:23:40) (in thread): > By searching the topic on PubMed

Mildred Anashie (07:23:43) (in thread): > To get it, you paste your articles name on pubmed or NIH

NWAKAEGO VINCENT (07:25:02) (in thread): > oh really thank you@Mildred Anashie@idiaru Angela

Flourish Ralph (07:27:37) (in thread): > Oh, I see

Flourish Ralph (07:27:59) (in thread): > @Esther Afuape@Chioma Onyido@C. Mirzayi (please do not tag this account)please can you advise?

Flourish Ralph (07:28:24) (in thread): > @Esther Afuape@Chioma Onyido@C. Mirzayi (please do not tag this account)please advise

Nitya Singhal (07:34:39): > Hey everyone > I had a doubt. Do we need to update about our contributions on Outreachy simultaneously or collectively at the end?@Peace Sandy@Chioma Onyido<@UBNSEMS3S>@Svetlana Ugarcina Perovicplease let me know the procedure

Scholastica Urua (07:37:29) (in thread): > @Nitya SinghalI think you can do it either ways. But I think you should upload it gradually so it’s not too much at the end. My opinion though.

Nitya Singhal (07:38:19) (in thread): > Did you wait for the review of your paper before registering the contribution on outreachy?

Nitya Singhal (07:38:29) (in thread): > @Scholastica Urua

Mildred Anashie (07:38:58) (in thread): > Yea@Nitya SinghalI was going to say same thing@Scholastica Uruasaid

Scholastica Urua (07:39:06) (in thread): > @NWAKAEGO VINCENTIn case of next time you can use this link to search for PMID;https://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Nitya Singhal (07:39:24): > Can anyone send me the link for that page where difference between type of study was given. Thank you

NWAKAEGO VINCENT (07:39:55) (in thread): > sure , i will thank you@Scholastica Urua

Nitya Singhal (07:39:59) (in thread): > Did you wait for the review of your paper before registering the contribution on outreachy?@Mildred Anashie

Bolanle Wahab (07:40:23) (in thread): > https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > …

Mildred Anashie (07:40:37) (in thread): > Youdon’thave to wait > > You can record and leave the merge date blank till it is reviewed

Ruth Bamgbose (07:40:38) (in thread): > Check this toohttps://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Scholastica Urua (07:40:40) (in thread): > No@Nitya Singhal, I uploaded before the review.

Nitya Singhal (07:43:34) (in thread): > ok thank you@Mildred Anashie@Scholastica Urua

Aleru Divine (07:45:50) (in thread): > I agree with@Scholastica Uruarecord simultaneouslyso itdoesn’tget overwhelming at the end.Also, you can record before review.

Aleru Divine (07:49:11) (in thread): > I believe this is it.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697727781091049 - Attachment: Attachment > Wheww! What an interesting discussion today! :grin: > If you weren’t able to attend the meeting today, Here’s a summary of what I gathered from the office hour today: > -“Hallmarks of Study Designs”- by @UBNSEMS3S > > 1. Randomized controlled trial (RCT): participants are randomly divided into groups. The treatment group receives the intervention while control group don’t. Here, researchers randomly assign the conditions to people. > Classical example: > 50 people receive the real vaccine, 50 receive the placebo. Other examples: diet, exercise, etc. > > 2. Laboratory experiment: done using animal models, such as rats, pigs, mice, etc. > You’re not randomizing here because they’re all in the same condition. > > 3. Meta-analysis: this is a study design where researchers combine results from different studies. Meta analysis also means Pooling of results. > > 4. Prospective cohort studies: this is a study where researchers recruit a group of people based on a common characteristic (e.g. based on residence) and follow them up over time. > > Classical example #1: all patients recruited in a study who showed signs of depression in the month of October. > Classical example #2: 100 people develop some diseases of interest (cases) and some people don’t (control) > > 5. Longitudinal observational study: time series studies. There is no intervention by the researcher in this kind of study. > Data is collected at multiple time points. > > Classical example: observing COVID participants before and after the event. > > 6. Case control: when you recruit cases ( people with a disease of interest) and controls (people without) similar on some characteristics. You would sometimes see matched on: age, bmi, sex, etc. > > Classical example: Healthy control group (control) and JIA group (case) > > 7. Cross-sectional observational: Contrasting 2 geographical areas or based on some socio-demographical characteristic (for example), usually at a single time point. > > Classical example: community studies where they took 100 people from a neighborhood and contrasted with people from another neighborhood. > > Apologies if I left anything out, the recording will be posted soon. :pray::skin-tone-5:

Praise Agbetuyi (07:55:02) (in thread): > Good afternoon, all the way from Nigeria,@Svetlana Ugarcina Perovic. Thank you for your kind words and for sharing the links to these resources and sites. Do enjoy the rest of your day

Nitya Singhal (08:11:18): - Attachment: Attachment > How did you fill this for the first contribution

Nitya Singhal (08:11:45) (in thread): > @Aleru Divine@Scholastica Urua@Mildred Anashie

Aleru Divine (08:13:09) (in thread): > 1. Date contributions started is the day you were assigned. > 2. Date contribution was accepted is the day you get a feedback. > 3. Contribution URL is the link to your study. > 4. Description is a little description of your contribution.

Scholastica Urua (08:13:49) (in thread): > @Aleru Divinehas already provided the answer.

Nitya Singhal (08:14:56) (in thread): > did you mention the first curation too in which we had to answer to the quiz?

Scholastica Urua (08:15:05) (in thread): > For the accept or merge date, you can leave it blank if the curation has not been reviewed yet.

Scholastica Urua (08:16:16) (in thread): > @Nitya Singhalplease record each contributions separately because they’ll carry different url. So the first recording will be for the first (quiz) task.

Aleru Divine (08:17:01) (in thread): > I recorded the first contribution separately.Link of contribution was the survey link(quiz link).Please record all contributions separately.

Mildred Anashie (08:17:14) (in thread): > You will use the link to the survey and inform them briefly what you did > > Also the dates will be the date you started and finished the first contribution

Nitya Singhal (08:18:14) (in thread): > is it this link?https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Scholastica Urua (08:18:55) (in thread): > Yes, this is the url for the first contribution.

Aleru Divine (08:19:36) (in thread): > Yepthat’scorrect.

Victoria (Burah) Poromon (08:20:15): > Hello@Svetlana Ugarcina Perovic,<@UBNSEMS3S>,@Chioma Onyido,@Peace Sandy,@Esther AfuapeI have a study with 3 groups and Urine from 2 different sites were used > 1. HB- Bladder Urine from healthy patients > 2. KB- Bladder urine from kidney stone patients > 3. KP- Renal Pelvis Urine from kidney stone patients. > 2 comparisons were made. > 1. HB & KB > 2. KB & KP > So my question is this > For both experiments, do I use the same body site? Which is just “Urine” > Or do i record 2 different body sites? Which is Urinary bladder for experiment 1 & Renal pelvis/Ureter for experiment 2 > > I’d really appreciate your response. Thank you!

Nitya Singhal (08:30:10) (in thread): > For second contribution, I have to add the link of my curated study or just the paper?@Scholastica Urua@Aleru Divine

Aleru Divine (08:30:18) (in thread): > Hi@Victoria (Burah) Poromonbladder urine and renal pelvis urine refer to urine collected from different parts of the urinary tract and may have differences in composition and characteristics.In the case where youdon’tfind the exact terms or closely related terms, you can use “urine” and leave a note to indicate that they collected urine samples from different sites.

Aleru Divine (08:31:02) (in thread): > The link to the curated study@Nitya Singhal

Scholastica Urua (08:31:07) (in thread): > You add the link to just your curation.

Victoria (Burah) Poromon (08:33:33) (in thread): > @Aleru Divine, yesI’maware of this and I curated different body sites. But someone reviewed it and she was of the opinion that it should have been just “Urine” for both experiments. > > SoI’mtrying to clarify and be sure of what exactly it should be.

Aleru Divine (08:34:31) (in thread): > I think you should leave it as different body sites.

Mildred Anashie (08:35:24) (in thread): > If the body sites are available on BugSigdb I think it’s okay to use different > But if not, urine in this case works in my opinion

Nitya Singhal (08:37:18) (in thread): > do we have to fill this “Apply for this project” now?@Aleru Divine@Scholastica Urua - File (PNG): image.png

Rahila-me (08:37:28) (in thread): > I will go with what@Mildred Anashiesaid, if it recorded on bugsigdb then record two different body sites

Aleru Divine (08:38:02) (in thread): > This is for whenyou’reready for your final application@Nitya Singhal

Rahila-me (08:39:50) (in thread): > @Aleru Divinehow is it for the last day of submission? that you use the Apply for this project

Rahila-me (08:40:18) (in thread): > The one called final contribution when will that link be clicked and filled?

Victoria (Burah) Poromon (08:40:36) (in thread): > @Mildred AnashieFor Bladder urine, I used the ontology search and found “Urinary bladder” > And for Renal pelvis Urine, I found “Renal pelvis/ureter” > > And these are what I used

Victoria (Burah) Poromon (08:41:04) (in thread): > @Aleru DivineAlright. Thank you

Aleru Divine (08:41:39) (in thread): > @Rahila-meItdoesn’thave to be on the last day.You can apply for a project whenever you feelyou’vemade enough contributions.

Ima-obong (Aimah) (08:41:56): > Hello everyone, > > I’m confused about this, and I’d appreciate your assistance.. > > Alpha diversity (Faith, Richness, Shannon) in colon was said to be lower ..but it was stated in the paper thatsmaller non significant differenceswere observed in feces and ileum..and was recorded in a supplementary figure.. > > My question is, does non significant difference means unchanged or I shouldn’t even curate for feces and ileum? > And also, being listed in a supplementary paper, can I still curate it? > > > Thanks alot - File (JPEG): IMG-20240322-WA0007.jpg - File (JPEG): IMG-20240322-WA0006.jpg

Mildred Anashie (08:42:39) (in thread): > Idon’tthink you should wait for the last day of submission, I think we’ll have to wait for the mentors to give us the timeline for this project > > Also when you apply and submit you can still make edits till the final day

Scholastica Urua (08:43:07) (in thread): > I agree with@Mildred Anashie

Aleru Divine (08:44:15) (in thread): > @Ima-obong (Aimah)from these images provided, there are no significant differences between groups. > > Yea it means unchanged and can be curated.

Mildred Anashie (08:45:14) (in thread): > Feces and ileum seem to be showing unchanged and I think it should be curated > > Also you can curate from supplements, it usually provides us with additional information

Mildred Anashie (08:45:54) (in thread): > @Aleru Divineare you saying itshouldn’tbe curated?

Ima-obong (Aimah) (08:46:44) (in thread): > Okay@Aleru Divineare you saying they should not be curated including that of colon which was said on the paper to be decreased?

Ima-obong (Aimah) (08:47:37) (in thread): > Okay.. I’ve seen the second part

Aleru Divine (08:47:40) (in thread): > No@Mildred Anashie@Ima-obong (Aimah)they’reto be curated but as unchanged.No significant differences = unchanged

Ima-obong (Aimah) (08:48:19) (in thread): > Alright thanks alot@Aleru Divineand@Mildred Anashie

Mildred Anashie (08:48:59) (in thread): > No@Ima-obong (Aimah)you’dcurate the alpha diversity indices based on the comparison done and I think you will curate for all

Nitya Singhal (09:00:30) (in thread): > ok got you@Mildred Anashie@Aleru Divinethank you

Nitya Singhal (09:08:46): > Hey, I had this doubt about the paper I am curating. > I figured out that it is a Longitudinal observation and I think that there are 2 groups… > SCC patients with chemoradiotherapy > SCC patients with surgery > > However, there is a bifurcation in the chemoradiotherapy as responders and non-responders. So kindly help me out with thishttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01677-w - Attachment (BioMed Central): Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer - Microbiome > Background Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein. Results Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva. Conclusions The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC. Graphical Abstract After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella Video Abstract

idiaru Angela (09:21:41) (in thread): > @Mildred Anashieif there was no significant difference in alpha diversity = unchanged and there was no differential abundance for the two groups being compared I don’t think she has to curate those contrasts:thinking_face:

Rahila-me (09:24:30) (in thread): > it will be curated, we curate for unchanged alpha diversity which in this case No significant. it was mentioned

Rahila-me (09:25:49) (in thread): > ok

Rahila-me (09:26:29) (in thread): > so for every contribution you make, you record

Aleru Divine (09:27:24) (in thread): > Hi@Nitya Singhalso far, you’re right with the groups you have identified. I am looking at the paper and the sample sizes aren’t clear to me yet. > > I also see that the surgically treated patients had had paired samples for pre- and post-treatment microbiome analysis. Idon’tknow if this matters.

Ima-obong (Aimah) (09:28:33) (in thread): > @idiaru Angelathere’s actually a differential abundance for the two groups..the alpha diversity is just said to have no significant differences which in this case means unchanged

idiaru Angela (09:29:03) (in thread): > Okayy@Ima-obong (Aimah)that means they would have to be curated

Ima-obong (Aimah) (09:29:55) (in thread): > Yes

Barakat Akinsiku (09:31:46): > Hi everyone, hope we’re all having a great day > > I have just completed this study and would love a peer reviewhttps://bugsigdb.org/Study_1014I wasn’t also able to find these signatures on NCBI taxonomy browser and Uniprot and would appreciate some detective help. There’s a lot more of the MGBC signatures and I’m hoping being able to figure one out will lead to unlocking the others:slightly_smiling_face:Thank you > > prevotella sp 900545525, phocaeicola sp002493165 > Erysipelotrichaceae_NOV MGBC000147, Eubacterium R MGBC120247

Scholastica Urua (09:34:06) (in thread): > That’s right@Rahila-me

Mildred Anashie (09:43:53) (in thread): > Whatyou’vedone seems to work in my opinion sinceit’smore specific > > ButI’mthinking urine generalizes everything > > Either way works

Scholastica Urua (09:49:06) (in thread): > Hello@Barakat AkinsikuI can find both prevotella sp and phocaiecola sp on the NCBI taxonomy browser but I don’t quite understand what those numbers attached to them here means.:thinking_face:

Victoria (Burah) Poromon (09:49:40) (in thread): > Alright@Mildred AnashieI’ll just leave it the way it is and hang on to see if the mentors think otherwise. > Thank you so much.

Scholastica Urua (09:50:07) (in thread): > Hello@Nitya Singhal, I’m going through your paper to see if I can help figure out anything.

Barakat Akinsiku (09:54:49) (in thread): > Exactly@Scholastica Uruathe two signatures are there but I don’t know if the numbers point to a different strain or something

idiaru Angela (09:54:55) (in thread): > Hey@Abiola Salakowell done. Going through I noticed that You didn’t add the antibiotics exclusion period but it was stated in the paper

Muqtadirat Yussuff (09:58:30) (in thread): > I can’t say for sure but mostly, from the few I’ve seen on google, it tends to indicate a different strain but who knows, maybe it’s some unique identifier given by the researchers

Nana (09:59:38) (in thread): > If you don’t find it, then enter exactly what’s on the paper like that on your signature

Nana (10:00:04) (in thread): > Is Bett than entering a wrong Ncbi

Scholastica Urua (10:02:43) (in thread): > Yes@NanaI think its better to enter it like that than to enter the wrong taxa.

Nana (10:02:56) (in thread): > Exactly my point

idiaru Angela (10:03:17) (in thread): > Looking at this for instance, it seems prevotella sp 900545525 is a different strain from prevotella sp - File (JPEG): Screenshot_20240322_150210_Chrome.jpg

Abiola Salako (10:03:33) (in thread): > Oh. I left it blank because antibiotics exclusion wasn’t specifically mentioned but antimicrobial therapy. What do you think? > > Kindly check Fig 4A of the article, do you deem it fit for curation? > > Thank you for your help@idiaru Angela

Nana (10:04:14) (in thread): > It is ooh@idiaru Angela

idiaru Angela (10:05:41) (in thread): > Since antimicrobial encompasses antibiotics I think it’s perfectly right to include the exclusion - File (JPEG): 1711116306850.jpeg

Barakat Akinsiku (10:08:19) (in thread): > That’s an interesting angle@Muqtadirat Yussuff@Nanathat’s what I did but just trying to see if there’s a possibility of unmasking the real thing. Thanks@idiaru AngelaThank you everyone for your input

idiaru Angela (10:10:04) (in thread): > Yes@Abiola SalakoFig 4a is definitely curatable

Abiola Salako (10:12:52) (in thread): > Thank you@idiaru Angela. I curated it initially before changing it. Will have a look at it again. Thank you.

Adedoja Isaac (10:31:22) (in thread): > Hi@Nitya SinghalWill go through it as well now

Nana (10:38:03) (in thread): > Ure

Nana (10:38:05) (in thread): > Urw

Adedoja Isaac (10:49:09) (in thread): > Hi@Barakat AkinsikuThe “sp” often indicates a strain that has not been fully characterized and assigned a species name. Also, “NOV” likely means “novel sequence” and this also suggests the Erysipelotrichaceae sequence may be a newly discovered variant. > And lastly “R” may refer to reference strain for Eubacterium. So looking through it from this point that they may be new and unclassified strains, it’s best to follow@Scholastica Uruaand@Nanasaid. To input it as is.

Barakat Akinsiku (10:56:40) (in thread): > Thank you@Adedoja Isaac

Abiola Salako (10:56:48) (in thread): > @Aleru Divine, is it the link to the study curated on bugSigDB or the link to GitHub where the issue was assigned? Thank you.

Aleru Divine (10:57:38) (in thread): > The link to the study(curation)

Adedoja Isaac (10:58:47) (in thread): > https://pubmed.ncbi.nlm.nih.gov/22719826/Found some useful info here - Attachment (PubMed): Novel bacterial taxa in the human microbiome - PubMed > The human gut harbors thousands of bacterial taxa. A profusion of metagenomic sequence data has been generated from human stool samples in the last few years, raising the question of whether more taxa remain to be identified. We assessed metagenomic data generated by the Human Microbiome Project Con …

Abiola Salako (10:59:01) (in thread): > @Aleru Divinewhat do you also think about figure 4A. Thank you:orange_heart:

Mildred Anashie (11:00:14) (in thread): > Link to the study on BugSigdb@Abiola Salako

Aleru Divine (11:01:00) (in thread): > It’s a curatable figure. You curated it in your study right?

Abiola Salako (11:01:27) (in thread): > Thank you both@Aleru Divineand@Mildred Anashie:100:

Abiola Salako (11:02:36) (in thread): > Not yet. I was trying to be sure if it’s curatable@Aleru Divine

Aleru Divine (11:03:06) (in thread): > Okay

Abiola Salako (11:03:30) (in thread): > Thank you@Aleru Divine

Abiola Salako (11:10:30): > Hi everyone, I was reviewing a colleague’s work and I became confused along the way trying to figure out a blocker so I thought to share it with you all for your insights. > > > If the P-value/FDR in a paper was not stated but the default value of 0.05 can be used as the value > > Now the signatures to be curated have significant markers of > 1. P>0.05, > 2. P<0.05 > 3. FDR <0.05 > 4. FDR <0.1 > > and you’re not to curate any signature with a significant marker that is above 0.05 > > What should be done if a signature’s significant marker <0.1 > > Should it be neglected seeing that 0.1 is larger than 0.05 or should it be curated being that less than 0.1(<0.1) can be any figure including 0.05 either above it or below it? > > Please what do you advise? Thank you.

idiaru Angela (11:14:33) (in thread): > @Abiola Salakomight need to see the article to make any final inference but from what you have typed I think the significance threshold might be 0.1 and if so I think the signatures should be curated:thinking_face:

Abiola Salako (11:17:27) (in thread): > @idiaru Angelahttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01758-4 - Attachment (BioMed Central): Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging - Microbiome > Background People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV — influenced by the infection itself, ART usage, sexual orientation, or other associated factors — affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. Results PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. Conclusions We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract

idiaru Angela (11:28:04) (in thread): > @Abiola SalakoI think a similar question was asked during office hour yesterday. In my opinion the highest threshold stated should be used and I think that is 0.1

Blessing Laweh (11:43:12): > Hello@Svetlana Ugarcina PerovicI’d like to request permission to delete signature 2 (Experiment 1) of this study please, thank you.https://bugsigdb.org/Study_988 - Attachment (BugSigDB): Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing - BugSigDB > The microbiota plays an important role in human health and disease development.The lung microbiota profile in pulmonary tuberculosis (TB) patients and the > effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively.

Abiola Salako (12:05:56) (in thread): > Thank you so much@idiaru Angela. I appreciate your response.

Eniola Adebayo (12:09:05): > Hi, in the study I’m curating, premenopausal was compared with postmenopausal, and some enriched taxa in premenopausal women were stated in the write up and others in the figure, but a taxa (Neisseria) is at the other side of the figure. Should I curate it as increased in post menopausal ?@Esther Afuape@Chioma Onyidohttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03149-5 - Attachment (BioMed Central): Insights into estrogen impact in oral health & microbiome in COVID-19 - BMC Microbiology > Background COVID-19 emerged in late 2019 and has occasioned more than 765 millions cumulative cases and 6.9 millions of deaths globally. Notably, around 70% of patients with severe COVID-19 are men. Therefore, it is to be presumed that women have a hormonal protector factor in inflammation and ACE2 expression. On the other hand, oral health status, and local microbiome can be key factors to respiratory viral infections control. Nevertheless, it has been poorly investigated. In our study 20 premenopausal, 18 postmenopausal and 22 men with COVID-19 were included. Oral health status, viral load, lingual ACE2 expression, as well as microbiome, estrogens and cytokines in saliva were analyzed. Results Our results showed a lower expression of ACE2 in tongue cells of postmenopausal compared with premenopausal (p = 0.05), and a strong negative correlation between saliva estrogen and viral load (r = -0.76; p = 0.001). Respect to IFN-γ (p = 0.05), IL-1β, TNF-α, IL-18, and IL-23 levels were increased in postmenopausal. Oral microbiome signature of premenopausal was characterized by Prevotella melaninogenica (Log2 = 26.68; p = 1.34e-10), Haemophilus (Log2 = 23.99; p = 2.96e-9), and Alloprevotella (Log2 = 7.92; p = 0.0001). On the other hand, Leptotrichia (Log2 = -18.74; p = 0.001), Tanerella (Log2 = -17.08; p = 0.004), and Clostridiales (Log2 = -2.88; p = 0.04) represented the poor oral health group compared with the adequate group which was enriched with the commensal microorganism Neisseria perflava (Log2 = 26.70; p = 1.74e-7). Furthermore, the high viral load group was characterized by Prevotella nanceiensis (Log2 = 19.60; p = 6.06e-8), Prevotella melaninogenica (Log2 = 21.45; p = 9.59e-6), Alloprevotella (Log2 = 23.50; p = 2.70e-7) and bacteria from the red complex Porphyromonas endodentalis (Log2 = 21.97; p = 1.38e-7). Conclusions Postmenopausal and men have a poor oral health status which could be related to a detrimental progression of COVID-19 also linked to a lower expression of ACE2, lower saliva estrogen levels and oral dysbiosis. Nevertheless, functional studies are required for a deeper knowledge. - File (JPEG): IMG_0249 - File (JPEG): IMG_0248

Scholastica Urua (12:13:46) (in thread): > @Nitya SinghalFrom your study I could see that patients are in chemoradiotherapy > and surgery groups. > > This is what I could figure out… > For the Chemotherapy Alone group, participants were divided into; > - Responders (baseline i.e before treatment) > Responders (6 months after treatment) > > - Non-Responders (baseline i.e before treatment) > Non-Responders (6 months after treatment) > > So these might be two separate experiments. There’s more though but I’m still going through the paper to be sure. Let’s wait for input from others cos its still a bit confusing for me…

Mildred Anashie (12:16:18) (in thread): > So I’m thinking the focus should be on the FDR <0.05 and P < 0.05 because 0.1 is not a stringent threshold > > The person can curate those and then leave a note in the discussion page stating why they left out 0.1 > > Others opinions might differ though@Ima-obong (Aimah)this is my opinion

idiaru Angela (12:33:32) (in thread): > @Mildred AnashieI was thinking though that just like our mentor said in the office hour, that when it is not clearly stated the threshold should be the biggest significance mentioned:thinking_face:

Mildred Anashie (12:40:52) (in thread): > Hi@Eniola Adebayocan you point me to the place where this was mentioned in the text?

Mildred Anashie (12:43:50) (in thread): > Ifit’sFig 3c itdoesn’tseem curatable,it’stalking about Bray Curtis which is for Beta diversity in my opinion

Mildred Anashie (12:44:12) (in thread): > I’drather try to curate Fig 3f

Eniola Adebayo (12:48:11) (in thread): > It’snot the Bray Curtis figure. Look at the screenshot attached to the message above (that’sthe one I’m referring to)

Mildred Anashie (12:49:39) (in thread): > Look at the fig description for 3c

Eniola Adebayo (12:52:18) (in thread): > It’sa mistake.It’s3c on the figure

Mildred Anashie (12:57:35) (in thread): > I see what you are saying > > They repeated c twice in the description

Mildred Anashie (12:58:36) (in thread): > Where can I find the text you are talking about?Alsoit’sokay to have the same signature increasing and decreasing in the same experiment (If this is your question) > I learnt that recently from@Chioma Onyido

Ima-obong (Aimah) (12:59:27) (in thread): > Okay noted@Mildred Anashie..thank you

Eniola Adebayo (13:03:43) (in thread): > It’son page 4 under the heading oral micro biome signature (paragraph one). Yes (I can have it in both), but does the figure mean Neisseria increased and decreased in premenopausal?

Mildred Anashie (13:05:25) (in thread): > Go through this thread, it might helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710517426265079?thread_ts=1710516856.042729&channel=C04RATV9VCY&message_ts=1710517426.265079

Eniola Adebayo (13:06:29) (in thread): > Thankyouvery much@Mildred Anashie

Mildred Anashie (13:08:49) (in thread): > I think post menopausal will be your Group 1 and the figure will mean it increased in both Premenopausal and postmenopausal soyou’llhave Neiserria in increased and decreased for this experiment > > This is my opinion

Eniola Adebayo (13:12:18) (in thread): > Okay:ok_hand:. Thank you@Mildred Anashie

Mildred Anashie (13:13:28) (in thread): > Well I think 0.05 should be used in this case because 0.1 seems to be too weak in my opinion > > This is the simplest reason I have after going back and forth through the paper@idiaru AngelaThat’swhy I suggested she leaves a note in the discussion page

Samreen Aftab (13:15:18): > Hello everyone. > Does this statement imply that age and diversity are confounders controlled for? - File (PNG): image.png

Joan C. Chukwuemeka (13:16:26) (in thread): > @Samreen AftabI don’t think so

Mildred Anashie (13:18:31) (in thread): > Itdoesn’tsound like that to me@Samreen Aftab

Eniola Adebayo (13:19:10) (in thread): > Idon’tthink so@Samreen Aftab

Abiola Salako (13:23:00) (in thread): > No, it doesn’t look so@Samreen Aftab

idiaru Angela (13:23:10) (in thread): > Alright@Mildred Anashie

Samreen Aftab (13:25:09) (in thread): > this is my articlehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241752/can anyone help me identify the confounders and matched on for this study?

Aleru Divine (13:26:02) (in thread): > No@Samreen Aftabitdoesn’tlook like confounders

Samreen Aftab (13:27:06) (in thread): > @Aleru Divineis there any specific way to identify matched on and confounders in a study? I always seem to get stuck on that

Abiola Salako (13:27:13) (in thread): > @Samreen AftabFor confounder and matched on, just search the keywords.

idiaru Angela (13:32:27) (in thread): > @Samreen Aftabif a regression analysis was not used in the study it also means confounders were not accounted for. > You can watch the recording of yesterday’s office hour for more clarification on cofoundershttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711049573159649?thread_ts=1711049573.159649&cid=C04RATV9VCY - Attachment: Attachment > Today’s office hours recording. Thank you all for attending and asking excellent questions.

Aleru Divine (13:33:59) (in thread): > Yes@Samreen Aftabyou can search for the key words “confounders” and “matched on” in your paper

Nitya Singhal (14:00:03) (in thread): > so that means there will be 6 experiments- > surgically alone pre-treatment > surgically alone post-treatment > chemoradiotherapy alone (responders (baseline i.e before treatment)) > chemoradiotherapy alone (responders (6 months after treatment)) > Non-Responders (baseline i.e before treatment) > Non-Responders (6 months after treatment)

Nitya Singhal (14:00:22) (in thread): > it is not clear to me

Scholastica Urua (14:12:26) (in thread): > From the explanation Chloe gave yesterday, they’re not confounders@Samreen Aftab

Nana (14:21:37) (in thread): > It is not ooh

Nitya Singhal (14:27:17) (in thread): > @Scholastica Urua@Aleru Divine

Scholastica Urua (14:28:40) (in thread): > Hi@Nitya Singhalplease give me a moment I’ll look through it again:pray:

Flourish Ralph (15:37:32): > Hi everyone, please I need help again.:face_holding_back_tears:I’m meant to curate Clostridiaceae_1 but I can’t find it, also in NCBI. > > Any thoughts? - File (JPEG): IMG_3125

Muqtadirat Yussuff (15:39:39) (in thread): > You can still curate it, it’ll just be flagged for missing an ID

Flourish Ralph (15:40:58) (in thread): > Really? Thank you

Mildred Anashie (15:43:42) (in thread): > Yea@Flourish Ralphyou can curate that way > > It’s okay to have taxas in orange

Muqtadirat Yussuff (15:44:20) (in thread): > Yeah, not every specie has an NCBI ID, you can identify them in curated works when their text color is orange@Flourish Ralph

Peace Daniel (15:46:37) (in thread): > When I search on NCBI what comes up is Clostridiaceae but you can curate it as Clostridiaceae_1

Flourish Ralph (15:47:46) (in thread): > Thank you guys

Aleru Divine (16:19:15) (in thread): > @Nitya SinghalI believe there are 5 experiments to be curated instead of 6 and below are the points that align with that. > 1. Figure 1. Salivary microbiome of patients pre (0) vs post (6 months after treatment). > 2. Figure 2. Significant changes in microbiome after chemoradiotherapy. That is chemoradiotherapy-treated SCC patients at 0 vs 6 months. > 3. Figure 3. Significant change in the salivary microbiome after surgery alone. (That is 0 vs 6 months after surgery). > 4. Figure 4. Between responders and non-responders of chemoradiotherapy at baseline. > 5. Figure 5. Microbiome differences between responders and non-responders to chemoradiotherapy at 6 months.

Aleru Divine (16:32:02) (in thread): > I agree with everyone:sweat_smile:in this case, curate as reported.

Svetlana Ugarcina Perovic (16:55:40) (in thread): > Deleted.

Blessing Laweh (16:56:18) (in thread): > Thank you:pray:

Modinat Ganiyu (18:49:31) (in thread): > Yes@Flourish Ralphcurate it that way, there’s nothing wrong in doing that. It’s just that it’ll show in orange color

Scholastica Urua (20:40:01) (in thread): > @Aleru Divinethank you for taking the time to outline this.:pray:I’ve been so occupied:woman-facepalming:

Nitya Singhal (23:30:28) (in thread): > Thank you soooo much@Aleru DivineReally helpful. Sorted half of worries.

Manisha Nair (23:55:00): > Hello everyone, I need help. Can someone help me identify which transformation technique is being applied in this study? The text mentions both relative abundance and log-centered ratios. Also, since the study refers to qPCR, should I include RT-qPCR in sequencing platform ? Study Link:https://journals.asm.org/doi/10.1128/spectrum.05273-22 - File (PNG): Screenshot 2024-03-23 091534.png

2024-03-23

Nitya Singhal (00:50:11) (in thread): > Hi Manisha, > They used relative abundances as the transformation technique because all the taxon are measured using that technique only. Hope it helps:blush:

Scholastica Urua (01:54:04) (in thread): > Hello@Manisha Nairfor the sequencing platform I can see Illumina. I hope this helps. - File (JPEG): 16.JPG

Bolanle Wahab (02:26:01): > Hi everyone, > Happy Weekend:partying_face:@Chioma Onyido@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Esther AfuapePlease does anyone have any idea what the condition would be for a studythat’sobserving storage conditions of Biological samples and how it affects Microbiome composition? > > Secondly, they examined pig feces and sewage conditions,should I leave the host species and body site for sewage sample blank cause nothing fits? > Thank you

Nitya Singhal (02:38:50) (in thread): > Hey@Aleru Divine, there is not enough data for “Significant changes in microbiome after chemoradiotherapy. That is chemoradiotherapy-treated SCC patients at 0 vs 6 months.” > What shall be done?

Peace Daniel (02:40:29) (in thread): > Can you share a link to your paper?

Nitya Singhal (02:41:19) (in thread): > Also, are these variables the factors, these groups are matched on?@Scholastica Urua@Aleru Divine@Mildred Anashie - File (PNG): image.png

Nitya Singhal (02:42:09) (in thread): > @Peace Daniel

Bolanle Wahab (02:43:44) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/# - Attachment (PubMed Central (PMC)): Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns > Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. …

Peace Daniel (02:53:00) (in thread): > I’m taking a look at a close match for the condition > > For your second question, I suppose you leave it blank > > Was there microbial abundance for the sewage?

Aleru Divine (02:53:48) (in thread): > No, thesearen’tmatched on factors@Nitya Singhal

Aleru Divine (02:54:59) (in thread): > @Nitya Singhalfor the one without enough data, curate what is available.

Peace Daniel (02:58:12) (in thread): > For the first question, this is the closest I could findhttps://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FOBI_0001472 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Bolanle Wahab (03:01:52) (in thread): > @Peace Danielyes there was microbial abundance for sewage.

Mildred Anashie (03:02:16) (in thread): > No@Nitya Singhalthesearen’tmatched on factors like Divine said > > You can Ctrl + F and type matched on and if nothing comes up it’s best to leave it blank

Peace Daniel (03:03:02) (in thread): > Alright, you might have to leave it blank butlet’swait for the opinion of others

Bolanle Wahab (03:03:35) (in thread): > Okay, thank you@Peace Daniel

Peace Daniel (03:05:20) (in thread): > Your questions have been answered:hugging_face:

Aleru Divine (03:06:11) (in thread): > @Bolanle WahabI suggest you include the host species as pig and the body site as feces.The reason I say this is, if you think about it, sewage samplesaren’tparticularly from a body site / host species and since youcan’tfind a closely related term you could leave a note.But I believe you should include the provided host species and body site.

Scholastica Urua (03:06:18) (in thread): > Like@Aleru Divineand@Mildred Anashiesaid , these are not matched on factors.

Peace Daniel (03:07:09) (in thread): > The sewage samples and pig feces are two different things if I understood correctly@Aleru Divine@Bolanle Wahab

Bolanle Wahab (03:08:32) (in thread): > @Aleru DivineI used that when I curated for pig samples, my confusion was because I also had to compare only sewage samples separately

Peace Daniel (03:08:56) (in thread): > Technically speaking, sewage is only made up of waste that has come through the toilet. More generally, however, it can refer to used water, coming from domestic or industrial circumstances, such as toilet water and waste, shower water, kitchen waste, organic matter, and industrial chemicals. > > Can you use humans for this?

Bolanle Wahab (03:10:05) (in thread): > @Peace DanielI thought of that but I doubt it cause itdidn’tsay anything about human microbiome

Aleru Divine (03:10:39) (in thread): > @Bolanle WahabIn that case you could leave the body site blank.Unlessthere’sa close term.Ididn’tfind any at the moment

Bolanle Wahab (03:15:31) (in thread): > @Aleru Divinethankss

Bolanle Wahab (03:18:41) (in thread): > So just for clarity, they actually gave microbial abundance for all the storage conditions but for differential abundance, it says this, that means I should focus on those right - File (JPEG): IMG_9724

Aleru Divine (03:23:23) (in thread): > Yes I think so

idiaru Angela (03:32:03) (in thread): > Hi@Bolanle WahabI don’t think you should curate an experiment with only sewage samples. I also has an experiment that did comparison between microbes that weren’t from any body site. So I confirmed from the mentors if it was okay to curate and they said NO. Look at the thread for morehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710968937518219?thread_ts=1710951789.235799&cid=C04RATV9VCY - Attachment: Attachment > Hi @idiaru Angela Good question! > I presented a similar paper in the past where sig taxa results were reported for different environments, I remember that they compared household to work environment. > > If it’s not from an actual body site of the host species, then it should take be curated. See curation policy for host species.

Bolanle Wahab (03:36:51) (in thread): > @idiaru Angelaoh okay, thank you:heart:

idiaru Angela (03:59:00): > Hi everyone, Happy weekend. > In the image attached differential abundance was explored for different taxa levels, I’d like to clarify if I’d be right to curate for all taxa levels mentioned. Thank you - File (JPEG): Screenshot_20240323_085707_WPS Office.jpg

Peace Daniel (04:04:22) (in thread): > Curate for species

Mildred Anashie (04:05:37) (in thread): > The species seems to include all > I’d definitely curate species > > Not sure about if the other levels should be included

Joan C. Chukwuemeka (04:07:32) (in thread): > @idiaru AngelaGood morning. I think you are to curate all Taxa, except if within the text it was stated that the species level is a breakdown of the Genus level, in which case the species’ level should suffice. > > However, only the differentially significant ones are to be Curated. I see p value captured for each pair. So what’s the significance level set by the researchers? That’ll guide your choice

Mildred Anashie (04:10:27) (in thread): > @Joan C. Chukwuemekaif the significant level is 0.05 then all taxas are significant

idiaru Angela (04:15:04) (in thread): > Thank you all so much for your responses. The significance level is 0.05 so all the taxa were significant. The authors didn’t state that the species were a breakdown of all other taxa in their words “the table reflects the differential abundance at all levels” plus when I did a little research Monoglobaceae which is a family abundant under the control falls under the clostridia class which is abundant under the CAD group. So I thought it would be better to curate all taxa level since a family being abundant in one group didn’t mean the class was also abundant in the same group. So I thought to seek more opinions. Thank you guys so much for your time@Mildred Anashie@Joan C. Chukwuemeka@Peace Daniel

Aleru Divine (04:16:19) (in thread): > @Mildred AnashieYou’reright, the species seems like it looks like it encompasses all the other taxa.But like@Joan C. Chukwuemekasaid,we’renot really sure:thinking_face:I had this in my last curation, I went with curating all taxa levels.I think I did that because I found a similar already reviewed study that curated all taxa levels.

idiaru Angela (04:17:28) (in thread): > Oh@Aleru Divineif its possible to point me to that study I’d really appreciate it

Mildred Anashie (04:18:25) (in thread): > I agree with your opinion@idiaru AngelaAll taxa levels seem more appropriateI’malso facing a similar situation in my current curation although just genus and species were listedI’mgoing with both as not all the listed species were found in the genera

Aleru Divine (04:19:41) (in thread): > On it@idiaru Angela

Aleru Divine (04:20:20) (in thread): > Found ithttps://bugsigdb.org/Study_896 - Attachment (BugSigDB): Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore - BugSigDB > INTRODUCTION: The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome.PPIs are commonly used for the treatment of acid-related disorders.

idiaru Angela (04:23:41) (in thread): > Thank you very much@Aleru Divine

Peace Daniel (04:39:18) (in thread): > Well if not all the listed species are found in the genera.It’sreasonable to curate all taxas

Adedoja Isaac (05:02:12) (in thread): > Hi@idiaru AngelaYes, you would be right to curate for all taxa levels mentioned in the image. The text in the image says: “Differential abundance was explored for different taxa levels, including class, order, family, and species”. This means that the researchers looked at how the abundance of different microbes varied between the two groups being compared (CAD patients and controls) at each of these taxonomic levels. > > Curating for all taxa levels mentioned in the study could be useful because it allows you to see if the differences in abundance are consistent across different taxonomic levels. For example, you might find that a particular class of microbes is more abundant in one group than the other, and that this difference is also reflected at the order and family levels. This would suggest that the difference in abundance is likely to be real and biologically relevant. > > On the other hand, you might find that the differences in abundance are only seen at certain taxonomic levels. For example, you might find that a particular species of microbe is more abundant in one group than the other, but that there is no difference in abundance at the family level. This could be because the species is only distantly related to the other members of its family, or because the difference in abundance is specific to that particular species. > > So, just as@Mildred Anashie@Aleru Divineand@Joan C. Chukwuemekasaid, curating for all taxa levels mentioned in the study can give you a more complete picture of how the abundance of different microbes varies between the two groups being compared.

idiaru Angela (05:07:20) (in thread): > Thank you@Adedoja Isaac

ayesha khan (05:56:04): > hi im still curating , wanted peer reviews .https://bugsigdb.org/Study_993 - Attachment (BugSigDB): Divergent maturational patterns of the infant bacterial and fungal gut microbiome in the first year of life are associated with inter-kingdom community dynamics and infant nutrition - BugSigDB > BACKGROUND: The gut microbiome undergoes primary ecological succession over the course of early life before achieving ecosystem stability around 3 years of age.

idiaru Angela (06:23:21): > Hi everyone, Good morning. I’d love reviews and feedback on this study i curated. I’m also available to review yours if you’d like Thank youhttps://bugsigdb.org/Study_1058 - Attachment (BugSigDB): Alterations in gut microbiota and host transcriptome of patients with coronary artery disease - BugSigDB > BACKGROUND: Coronary artery disease (CAD) is a widespread heart condition caused by atherosclerosis and influences millions of people worldwide.Early detection of CAD is challenging due to the lack of specific biomarkers.

Abiola Salako (06:51:50) (in thread): > Let me save this for later should I come across this study expement in the future. Thanks@Chioma Onyidoand@idiaru Angela.

Aleru Divine (06:54:13) (in thread): > Hi@ayesha khangreat job on your curation. > > I observed the following: > 1. There aren’t any matched on factors. > 2. DESeq2 was used for the differential abundance testing. > 3. There was MHT correction > 4. Sample size for both group in experiment 1 is 99 according to the description of figure 1. > 5. For the signatures in experiment 1, you should curate figure 3C as it is titled “differentially abundant bacteria”. 3A only shows relative abundance. Figure 1 represents alpha and beta diversity. > 6. For experiment 2 the sample size is seen in the figure 2 description and I think all tests were the same for this experiment too. Figure 3F should be curated in this case(differentially abundant fungi) No matched on factors, yes for MHT correction, same sequencing type and platform as experiment 1. > Please carefully go through the paper and check my observations:pray:

Abiola Salako (06:58:21) (in thread): > @ayesha khanWell done on your curation. Kindly go through@Aleru Divineobservations and make changes where necessary. We’re rooting for you:smiling_face_with_3_hearts:

Abiola Salako (06:58:41) (in thread): > Well done@Aleru Divine

Aleru Divine (07:03:09) (in thread): > Hi@idiaru AngelaI’vegone through this andIthink this is very well curated.I have no notes so far:hugging_face:well done!I’llgo through it again just to be sureIdidn’t miss anything.:pray:

idiaru Angela (07:16:50) (in thread): > Thank you so much for going through it@Aleru Divine:heart_hands::heart_hands:

ayesha khan (07:18:56) (in thread): > THANK YOU@Aleru Divine

Scholastica Urua (07:42:28) (in thread): > Hello@idiaru AngelaWell done on your curation. This is well curated from my observation. I do have one thing to point out… > > The discussion page for taxa with missing NCBI ID mentioned this;“Lachnospiraceae_NK4A136was updated to Lachnospiraceae bacterium NK4A136” > > So I think this could work for your Lachnospiraceae_NK4A136_group in orange. - File (JPEG): lach.JPG

idiaru Angela (07:44:23) (in thread): > @Scholastica UruaI think you’re right. Thank you so much:heart_hands:. Will change that now

Barakat Akinsiku (07:45:15) (in thread): > Hi@idiaru AngelaI agree. I’ve just looked at your study and everything checks out. Well done

Barakat Akinsiku (07:49:53) (in thread): > Hi@ayesha khancan you check sagatella copri? I think it’s an homotypic synonym for prevotella copri so you can use its taxonomy ID

Chiemelie Carita Ndibe (07:53:27): > Hello mentors@Svetlana Ugarcina Perovic@Peace Sandy@C. Mirzayi (please do not tag this account). I just concluded the first contribution for Outreachy applicants, I want to confirm how to to record the contribution. Thank you

Adedoja Isaac (07:53:36) (in thread): > Everything is curated perfectly from my check too. Weldone@idiaru Angela

Scholastica Urua (07:56:35) (in thread): > Hello@Chiemelie Carita NdibeHere are steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > When recording the first contribution, the merged date refers to the date you submitted your contribution. > > -The URL is the link to the curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcwill serve as your Contribution URL. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Chiemelie Carita Ndibe (07:58:46) (in thread): > Thank you very much Scholastica.

Barakat Akinsiku (08:00:05) (in thread): > Yes@Chiemelie Carita Ndibefollow the steps Scholastica outlined above

NWAKAEGO VINCENT (08:02:50) (in thread): > @Scholastica Urua@Mildred Anashieshould i create two experiments for this study because i am working on a paper that is comparing fecal samples and oral sample collection but each sample analysed two diferrent methods under both

idiaru Angela (08:03:55) (in thread): > Thank you for your feedback@Barakat Akinsiku@Adedoja Isaac

Scholastica Urua (08:11:43) (in thread): > Please@idiaru Angelacan you kindly point out where the contrast was made. I haven’t gone through your article in detail.:see_no_evil:

idiaru Angela (08:21:43) (in thread): > @Scholastica Uruasee attached screenshots from the results. Seems I was wrong and there us actually more than one contrast. But unlike other papers everything is written in text and there are no tables for easy identification of the comparisons. - File (JPEG): Screenshot_20240323_132004_Samsung Internet.jpg - File (JPEG): Screenshot_20240323_131926_Samsung Internet.jpg - File (JPEG): Screenshot_20240323_131832_Samsung Internet.jpg - File (JPEG): Screenshot_20240323_131807_Samsung Internet.jpg

Mildred Anashie (08:25:24) (in thread): > The comparisons can be picked from the supplemental tables with the differential abundance > > I’m seeing about 4-6 experiments altogether for both samples collected > Still trying to figure out the direction of abundance (increased or decreased)

idiaru Angela (08:26:53) (in thread): > @Mildred Anashieif you don’t mind can you send a picture of the supplementary material that has the differential abundance

Mildred Anashie (08:27:26) (in thread): > https://static-content.springer.com/esm/art%3A10.1186%2Fs12866-021-02387-9/MediaObjects/12866_2021_2387_MOESM2_ESM.xlsx

idiaru Angela (08:30:50) (in thread): > Seen@Mildred Anashiethat’s going to be 4 different experiments:thinking_face:. Curation using that Excel sheet is going to be tasking

Mildred Anashie (08:33:08) (in thread): > It was reported partly in the text you shared but I think those excel sheets can be curated once we can figure out increase and decrease > > Or should we just focus in the text?

Scholastica Urua (08:35:07) (in thread): > Hello@Mildred AnashieI agree there’s more than one experiment. But looking at the excel sheet its kinda confusing. I think the text will be easier to curate.

idiaru Angela (08:36:09) (in thread): > @Mildred AnashieI think the excel sheet is curatable but very tasking. At the bottom there is a well defined significance for each experiment. I think the tasking part would be going through each organism to determine if they are significant then curating them. > I’m a bit doubtful of using just text as they might have omitted some organisms especially if you consider the large number of organisms listed on the excel sheet

Mildred Anashie (08:37:07) (in thread): > The significance is easy > > The bolder texts are significant

Mildred Anashie (08:37:30) (in thread): > Very few of the taxas appear to be significant

Scholastica Urua (08:38:53) (in thread): > But how do you tell which is increased or decreased?

Mildred Anashie (08:38:58) (in thread): > Look at the P value and FDR column

idiaru Angela (08:39:06) (in thread): > True@Mildred Anashieusing the excel sheet would be the best method then

idiaru Angela (08:39:56) (in thread): > @Scholastica UruaI’m yet to see any pointers to that:thinking_face:

Mildred Anashie (08:43:53) (in thread): > So the only pointer I am assuming from here is, > > Most of the figures appear this way <0.001 and some appear this way 0.001 > > So I think the ones with the sign (<) are decreased and the ones without are increased

idiaru Angela (08:45:28) (in thread): > I agree with you. I think you’re on to it.@Mildred Anashie

Scholastica Urua (08:47:16) (in thread): > I also think reading the article in detail and comparing it with the supplementary table will provide more insight. While scanning through, I noticed there’s a mention of which is higher in which sample…

Mildred Anashie (08:52:57) (in thread): > For the experiments I can see > > for the feacal samples > > Day 0 vs Day 4 RNA later (significant Signatures) > Day 0 vs Day 4 FOBT card (No significant signatures) > FOBT vs RNAlater (Significant signatures) > > For the oral samples > Day 0 vs Day 4 Scope mouthwash(Significant signatures) > OMNIgene vs Scope mouthwash (Significant signatures)

Mildred Anashie (08:53:57) (in thread): > Let me try to do that@Scholastica Uruato see if it will correspond with the directionI’mproposing

Scholastica Urua (08:54:27) (in thread): > Well done@Mildred Anashie

Aananditaa (08:58:34): > Hii! I am facing some problems with the curation of this article:https://alzres.biomedcentral.com/articles/10.1186/s13195-024-01402-1I can’t seem to find the PMID I have downloaded the citation doc as well but I can’t find it there. Can someone please help me out?@C. Mirzayi (please do not tag this account)@Peace Sandy - Attachment (BioMed Central): Profiles of subgingival microbiomes and gingival crevicular metabolic signatures in patients with amnestic mild cognitive impairment and Alzheimer’s disease - Alzheimer’s Research & Therapy > Background The relationship between periodontitis and Alzheimer’s disease (AD) has attracted more attention recently, whereas profiles of subgingival microbiomes and gingival crevicular fluid (GCF) metabolic signatures in AD patients have rarely been characterized; thus, little evidence exists to support the oral-brain axis hypothesis. Therefore, our study aimed to characterize both the microbial community of subgingival plaque and the metabolomic profiles of GCF in patients with AD and amnestic mild cognitive impairment (aMCI) for the first time. Methods This was a cross-sectional study. Clinical examinations were performed on all participants. The microbial community of subgingival plaque and the metabolomic profiles of GCF were characterized using the 16S ribosomal RNA (rRNA) gene high-throughput sequencing and liquid chromatography linked to tandem mass spectrometry (LC–MS/MS) analysis, respectively. Results Thirty-two patients with AD, 32 patients with aMCI, and 32 cognitively normal people were enrolled. The severity of periodontitis was significantly increased in AD patients compared with aMCI patients and cognitively normal people. The 16S rRNA gene sequencing results showed that the relative abundances of 16 species in subgingival plaque were significantly correlated with cognitive function, and LC–MS/MS analysis identified a total of 165 differentially abundant metabolites in GCF. Moreover, multiomics Data Integration Analysis for Biomarker discovery using Latent cOmponents (DIABLO) analysis revealed that 19 differentially abundant metabolites were significantly correlated with Veillonella parvula, Dialister pneumosintes, Leptotrichia buccalis, Pseudoleptotrichia goodfellowii, and Actinomyces massiliensis, in which galactinol, sn-glycerol 3-phosphoethanolamine, D-mannitol, 1 h-indole-1-pentanoic acid, 3-(1-naphthalenylcarbonyl)- and L-iditol yielded satisfactory accuracy for the predictive diagnosis of AD progression. Conclusions This is the first combined subgingival microbiome and GCF metabolome study in patients with AD and aMCI, which revealed that periodontal microbial dysbiosis and metabolic disorders may be involved in the etiology and progression of AD, and the differential abundance of the microbiota and metabolites may be useful as potential markers for AD in the future.

Mildred Anashie (09:00:04) (in thread): > So the direction I was proposingdoesn’tseem to align with the text but I noticed the few taxas mentioned in text are also in the table > > Maybe one of our mentors can help us out here@Esther Afuape@Chioma Onyido@Peace SandyAre this tables curatable ? > I see the significance showed but wecan’tdeduce increased and decreased taxas:pray:

Scholastica Urua (09:01:46) (in thread): > This is the PMID 38373985

Mildred Anashie (09:01:54) (in thread): > Hi@AananditaaThis is your PMID38373985

Aananditaa (09:02:36) (in thread): > Thank you so much:blush:can you please tell where it was written so I can keep in mind from next time

Mildred Anashie (09:02:36) (in thread): > You can simply paste your articles name on Pubmed andyou’llget it therehttps://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 36 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Aananditaa (09:03:12) (in thread): > Ohh thank you so much!!@Mildred Anashie

Scholastica Urua (09:10:31): > Hello everyone, so I’m reviewing a fellow applicant’s work, I encountered this particular section. Please should these variables be curated as confounders? I recall Chloe discussing confounders extensively, but the presence of “adjusted” in this statement has given me pause, prompting me to seek clarification. > Thank you:pray:. - File (JPEG): Adjusted.JPG

ayesha khan (09:20:51) (in thread): > @Barakat Akinsikuyes thank you so much , its segatella copri

Peace Daniel (09:27:58) (in thread): > Was a linear regression conducted?

Scholastica Urua (09:31:50) (in thread): > Yes, yes it was@Peace Daniel. Thanks for the reminder:hugging_face:These are indeed confounders.

Chiemelie Carita Ndibe (09:54:42): > Hello mentor@Svetlana Ugarcina Perovic@Peace Sandy@C. Mirzayi (please do not tag this account), I want to to start a second contribution and sawBald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquariumon paper to curate. I want to confirm I can claim it and curate - Attachment: #312 Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium > Bald sea urchin disease shifts the surface microbiome on purple sea urchins in an aquarium – Chloe G Shaw – Pathogens and Disease
> https://academic.oup.com/femspd/article/doi/10.1093/femspd/ftad025/7275090

Barakat Akinsiku (10:00:28) (in thread): > @ayesha khanYou’re welcome. Well done

Barakat Akinsiku (10:02:33) (in thread): > @Chiemelie Carita NdibeHas anyone commented on the paper’s github for it to be assigned to them? If not you can comment under it and ask for it to be assigned to you. Afterwards you’ll see the assigned tag showing it has been assigned to you

Scholastica Urua (10:16:15) (in thread): > Hi@Chiemelie Carita Ndibeit doesn’t seem the paper has been assigned to anyone yet. I just checked. > But you have to comment under the issue preferably not here for the mentors to assign it to you.

Adenike Oladimeji-Kasumu (10:23:50) (in thread): > @Chiemelie Carita NdibeYou have to make a comment requesting the it to be assigned to you on GitHub as@Scholastica Uruaand@Barakat Akinsikuas said

Chiemelie Carita Ndibe (10:24:29) (in thread): > Thank you@Scholastica Urua, I already commented on the paper and tagged@Svetlana Ugarcina Perovic. Should I also tag the other mentors on Github

Adenike Oladimeji-Kasumu (10:26:06) (in thread): > You would soon be responded to. It will be assigned to you if no one has claimed it before you. So you can download the material and start going through it. Keep checking your email inbox to receive a response from any of the mentors.

Scholastica Urua (10:30:41) (in thread): > It’s the weekend, I believe the mentors will get to it as soon as possible.

Nana (11:04:29) (in thread): > When the term adjusted for is used with those variables age etc ..it points to confounders and it should be curated for

Blessing Laweh (11:41:14): > Hello Team! Hope everyone is well. > Please I have some questions, is there anybody available to help me, thank you:sob::heart_hands:

Aleru Divine (11:41:59) (in thread): > Sure thing@Blessing Lawehshoot!:hugging_face:

Joan C. Chukwuemeka (11:42:02) (in thread): > Okay…..?

Joan C. Chukwuemeka (11:42:31) (in thread): > almost sent “shoot”.. Lols@Aleru Divine

Aleru Divine (11:43:00) (in thread): > :sweat_smile:

idiaru Angela (11:44:45) (in thread): > Sure@Blessing Laweh

Ruth Bamgbose (11:44:48) (in thread): > Yeah..

Blessing Laweh (11:45:12) (in thread): > Ooh thank you@Aleru Divine@Joan C. ChukwuemekaI’m done curating a paper. I’ve editted the study based on review and I’d like to submit it as a contribution on Outreachy. How do I go about that? > > Also, I’d like to curate another paper. Can I also record this as a contribution on Outreachy? Or it’s just one contribution per project?

Blessing Laweh (11:45:58) (in thread): > And I’d have fired@Joan C. Chukwuemeka:wink:

Aleru Divine (11:46:36) (in thread): > This should helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711194995334309?thread_ts=1711194807.379159&channel=C04RATV9VCY&message_ts=1711194995.334309 - Attachment: Attachment > Hello @Chiemelie Carita Ndibe Here are steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > When recording the first contribution, the merged date refers to the date you submitted your contribution. > > -The URL is the link to the curation form: > https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc will serve as your Contribution URL.

Blessing Laweh (11:46:37) (in thread): > @idiaru Angelamy friendddddddd I finally finished ooo.:sob:thanks for your help

Aleru Divine (11:48:00) (in thread): > @Blessing Lawehyou can record any contribution you make on the outreachy website and that includes all the papers you curate.

Blessing Laweh (11:48:06) (in thread): > Trust you with the links@Aleru Divineyou is an Angel:smiling_face_with_tear::heart_hands:Thanks alot

Ruth Bamgbose (11:48:26) (in thread): > You can make as many contributions as you can

Joan C. Chukwuemeka (11:48:47) (in thread): > Go tohttps://www.outreachy.org/dashboard/you’d see the Bioconductor project and select record contribution. The link to your bugsigdb study is what you will fill into the URL section. > > And yes you can curate another available paper. All contributions can be recorded on Outreachy. - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Blessing Laweh (11:49:28) (in thread): > Thank you@Joan C. Chukwuemekathank you@Ruth Bamgbose:pray:

Blessing Laweh (11:50:28) (in thread): > @Aleru Divineso after I’ve submitted this one, if I make another contribución I can submit it for Outreachy, still under Microbiomes yeah?

idiaru Angela (11:51:46) (in thread): > Congratulations@Blessing Lawehfinally:sweat_smile:

idiaru Angela (11:52:38) (in thread): > Yes@Blessing Lawehall the contributions you make should be recorded on outreachy and you can make as many as you can

Mkpouto Shedrack (11:54:56): > Hello Team, hope everyone is doing great. I would appreciate reviews of my paper pleasehttps://bugsigdb.org/Study_985 - Attachment (BugSigDB): Exploring the Relevance between Gut Microbiota-Metabolites Profile and Chronic Kidney Disease with Distinct Pathogenic Factor - BugSigDB > The intimate correlation of chronic kidney disease (CKD) with structural alteration in gut microbiota or metabolite profile has been documented in a growing body of studies.

Aleru Divine (11:55:50) (in thread): > It’syour lucky day:sweat_smile:I’mas free as can be:hugging_face:Let me get on with it.

Blessing Laweh (11:57:21) (in thread): > Ahhhhhhh I didn’t know that. I thought we were to do like 1 contribution to 1 outreachy project each. (Haven’t done another one besides this:smiling_face_with_tear:) > > After your review and corrections I wanted to do more bec I enjoyed it haha No problem. Thanks for your response@idiaru Angela

Mkpouto Shedrack (11:59:25) (in thread): > Appreciate you Aleru, I have had lots of concerns with this study lol

Aleru Divine (12:00:45) (in thread): > I’lllet you know whenI’mdone:pray:

idiaru Angela (12:03:28) (in thread): > @Blessing Lawehthere’s still days left of the contribution period I believe you can still make quality contributions if you wish. Plus our mentors always advice us to put quality over quantity:grin:

idiaru Angela (12:04:13) (in thread): > I’ll also check it out@Mkpouto Shedrackwelldone

Blessing Laweh (12:05:11) (in thread): > Yeahhhhh right! That’s why I took my time on that paper. Needed to make sure it was accurate.  Thanks for pointing that out to me @Idiaru Angela

Chiemelie Carita Ndibe (12:31:39): > Thank you@C. Mirzayi (please do not tag this account)and@Svetlana Ugarcina Perovicfor sharing the recording.

Aleru Divine (12:59:19) (in thread): > Hey@Mkpouto ShedrackI have gone through your paper and I have the following observations: > 1. I noticed you added laboratory experiment as a study design. This is not a laboratory experiment I think it’s just case control. > 2. I couldn’t find any matched on factors. > 3. The correct statistical test is LEfSe.Here’swhy “Differential abundance of identified taxa between each group was synchronously assessed using the linear discriminant analysis (LDA) effect size (LEfSe) method with…” > 4. I also believe you’re supposed to curate 3 experiments. > The reason is from this excerpt > “In this study, a liquid chromatography coupled-mass spectrometry and long-read sequencing were applied to identify gut metabolites and microbiome with statistically-discriminative abundance in diabetic CKD patients (n = 39), hypertensive CKD patients (n = 26), or CKD patients without comorbidity (n = 40) compared to those of healthy participants (n = 60).” > > It is suggesting that healthy participants was compared to all the CKD sub groups. > > So you’ll have 3 experiments. > 1. D-CKD vs healthy > 2. H-CKD vs healthy > 3. NC-CKD vs healthy > Their sample sizes according to the paper are > diabetic CKD patients (n = 39), > hypertensive CKD patients (n = 26), > CKD patients without comorbidity (n = 40) > healthy participants (n = 60). > > For the various signatures, I believe figure 3 and 7 are curatable (figure 7 shows comparison between each group and also aligns with figure 3 which is more general) > > Incaseyoufind it hard to curate figure 7, the texts between table 3 and figure 7 should help with that.I really hope this helps.I’malso still available if you have any other questions or if thisisn’tclear enough.:sweat_smile:I’vegot nothing on my hands at the moment.So, please keep them coming.

idiaru Angela (13:13:24) (in thread): > @Aleru Divinecan you take a look at figure 7 again, I don’t think it is curatable.

Aleru Divine (13:15:58) (in thread): > @idiaru AngelaI said it is because of the text before it.I’mnot very sure but it is looking like it.Plusit’sthe only place they compared healthy participants against sub groups.:pleading_face:I may be wrong tho!

idiaru Angela (13:19:33) (in thread): > Looking at it. I don’t think it is. There’s no indication of which taxa is decreased or increased in any group. In the text tho, there is a little more information about differential abundance but it looks like one sub group wasn’t mentioned at all:thinking_face:. It means there might be experiment without signatures in this study

Aleru Divine (13:24:20) (in thread): > All of this made sense to me when I read the paper - File (PNG): IMG_8027

Aleru Divine (13:25:36) (in thread): > That’sthe reason:grimacing:I did have my doubts.And if you read the text and look at figure 7, I was able to differentiate between the groups.Justdon’tpay attention to the amino acids:face_with_peeking_eye:

idiaru Angela (13:29:18) (in thread): > I get you totally@Aleru Divinebut if it doesn’t indicate increase or decrease then I guess its not useful for curation. The text however should definitely be curated. Well done on the review

Aleru Divine (13:38:13) (in thread): > I sort of used figure 3 and the text to interpret it.:sweat_smile:

Nitya Singhal (13:43:36): > Hey, I have this one doubt while creating signatures, some NCBI is available as unclassified rather than the exact name. For example- this NCBI “Burkholderiaceae” is present as “Burkholderiaceae_unclassified.” So I wanna know if both are same ?@Chioma Onyido<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Peace Sandy

Peace Daniel (13:59:51) (in thread): > I don’tthinkthey’rethe same, it could be a specie of Burkholderiaceae thathasn’tbeen classified yet

Rahila-me (14:02:00) (in thread): > NO they are not the same

Mildred Anashie (14:07:40) (in thread): > @Scholastica Uruaand I went through this study for@Mkpouto ShedrackYou guys can go through this thread it’ll helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710747766480949 - Attachment: Attachment > Hello everyone, I hope you had a wonderful weekend. :hugging_face: > Please we’ll appreciate your thoughts on this :pray: > > @Mildred Anashie and I have been reviewing @Mkpouto Shedrack curation; https://bugsigdb.org/Study_985. However, we find ourselves at a crossroads regarding signatures to curate for each experiment. Here’s our current understanding: > > There are four experiments outlined: > > 1. Healthy vs CKD (all) (curatable result in Figure 3) > 2. Healthy vs H-CKD > 3. Healthy vs NC-CKD > 4. Healthy vs d-CKD > > We’ve encountered difficulty in identifying significant results for the other three experiments where CKD was separated into different groups. The article primarily references Figure 4 and other figures which do not appear to be curatable. We concluded that only Experiment 1 will have signatures, while the other experiments should still be curated but without signatures. > > Could you kindly review this and share your thoughts?

Mildred Anashie (14:08:47) (in thread): > @Mkpouto ShedrackDid you still encounter any challenges? > > We thought this was clear enough

Mildred Anashie (14:12:38) (in thread): > No they are not the samehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710164161349969?thread_ts=1710162083.404089&channel=C04RATV9VCY&message_ts=1710164161.349969This might help a bit - Attachment: Attachment > It’s a bit confusing most times and I see that the ID shows Unculture, Unclassified, unidentified and unknown Gammaproteobacteria > > What I understand is that taxas with unknown tags typically refer to taxa that have not been confidently identified or classified at the species level, “uncultured” or “unclassified” species often refer to taxa that have been identified but have not yet been successfully cultured or classified to a known taxonomic group > > I’m of the opinion that Most studies use term interchangeably, I think it mostly depends on context >
> I don’t know if this answers anything :woman-shrugging::skin-tone-5:

Scholastica Urua (14:17:35) (in thread): > Yeah, we did@Mildred Anashie

Scholastica Urua (14:18:59) (in thread): > No@Nitya Singhalthey are not the same thing

Aleru Divine (14:23:01) (in thread): > Where’sthe thread@Mildred Anashie:pray:

Scholastica Urua (14:24:41) (in thread): > Here’s the thread@Aleru Divine

Scholastica Urua (14:24:45) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710747766480949

Aleru Divine (14:25:26) (in thread): > Thank you@Scholastica Urua:hugging_face:

idiaru Angela (15:52:05) (in thread): > @Scholastica UruaThe rank for lachnospiraceae bacterium NK4A136 is species but it was recorded in the study as genus. That makes me think it might actually not be the same:thinking_face:

Abiola Salako (17:14:46) (in thread): > @Blessing Lawehwell done. Please don’t forget to prioritise quality over quantity. Wishing you the best on this curating journey:smiling_face_with_3_hearts:

Mkpouto Shedrack (17:22:42) (in thread): > Thank you so much for your observations@Aleru Divine, I really do appreciate points 1 and 3, for your 4th point, I followed recommendations earlier made while curating it so that explains my grouping them that way.

Mkpouto Shedrack (17:24:38) (in thread): > @Mildred AnashieI feel am done with the study so I decided to put it on here to get a final pair of eyes to catch some errors. Thank you for your insights.

Mkpouto Shedrack (17:25:25) (in thread): > Thanks everyone. Really do appreciate the feedback.

Abiola Salako (17:31:28) (in thread): > @Nitya SinghalWell done, they are not the same thing

Abiola Salako (17:32:50) (in thread): > Well done@Mkpouto Shedrackwill glance through it now.@Mkpouto ShedrackWell done, I believe most of the corrections have been done as I just finished looking through your study. Well done on your curation.

Adedoja Isaac (18:36:03) (in thread): > Just like everyone said, “Burkholderiaceae_unclassified” indicates a sequence belonging to the Burkholderiaceae family, but the exact species is unknown.

Akinbode Mariam (19:51:22): > Hello guys, Happy sunday. i would love reviews on my paper please .https://bugsigdb.org/Study_995 - Attachment (BugSigDB): Acupuncture inhibits neuroinflammation and gut microbial dysbiosis in a mouse model of Parkinson’s disease - BugSigDB > Growing evidences show that gut microbiota is associated with the pathogenesis of Parkinson’s disease (PD) and the gut-brain axis can be promising target for the development of the therapeutic strategies for PD.

Samreen Aftab (21:51:12): > Hello everyone, I’ve been facing really bad network issues, because of which I’ve not been able to work as much the last few days. I just wanted to know if more papers will be added in the next week?@Svetlana Ugarcina Perovic@Peace Sandy@C. Mirzayi (please do not tag this account)

2024-03-24

Abiola Salako (00:52:47) (in thread): > Thank you@Mildred Anashie@idiaru Angelafor your responses.

Samreen Aftab (01:18:04): > Hi everyone, can anyone review my paper? Here’s the link to my curationhttps://bugsigdb.org/Study_1007. Thank you - Attachment (BugSigDB): Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission - BugSigDB > Inflammatory bowel disease (IBD) is a chronic, relapsing, inflammatory disorder which comprises two main conditions: Crohn’s disease (CD) and ulcerative colitis (UC).

Peace Daniel (02:12:43) (in thread): > Hey,I’dreview and let you know:blush:

Nitya Singhal (02:44:53): > Please upload new papers to curate@Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido<@UBNSEMS3S>@Esther Afuape

Nitya Singhal (03:08:47): > What if the statistical test used in the paper is not mentioned in the list?

Nitya Singhal (03:17:50): > Does the highlighted portion show the abundance of taxons in responders?@Scholastica Urua@Aleru Divine - File (PNG): image.png

Nitya Singhal (03:18:08) (in thread): > @Aleru Divine

Aleru Divine (03:19:17) (in thread): > @Nitya Singhalyes it does.So these will be increased in responders.

Muqtadirat Yussuff (03:19:24) (in thread): > Yes it does

Aleru Divine (03:20:11) (in thread): > @Nitya Singhalcan you share a link to the article, let me take a look too.But if Idon’tfind it,it’sokay to leave it blank.

Muqtadirat Yussuff (03:20:33) (in thread): > Hi, link to your study please so we could check

Nitya Singhal (03:20:49) (in thread): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01677-w - Attachment (BioMed Central): Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer - Microbiome > Background Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis. In this unique study, we compared pre- to post-treatment salivary microbiome in patients with SCC by 16S rRNA gene sequencing and examined how microbiome changes correlated with the expression of an anti-microbial protein. Results Treatment of SCC was associated with a reduction in overall bacterial richness and diversity. There were significant changes in the microbial community structure, including a decrease in the abundance of Porphyromonaceae and Prevotellaceae and an increase in Lactobacillaceae. There were also significant changes in the microbial community structure before and after treatment with chemoradiotherapy, but not with surgery alone. In patients treated with chemoradiotherapy alone, several bacterial populations were differentially abundant between responders and non-responders before and after therapy. Microbiome changes were associated with a change in the expression of DMBT1, an anti-microbial protein in human saliva. Additionally, we found that salivary DMBT1, which increases after treatment, could serve as a post-treatment salivary biomarker that links to microbial changes. Specifically, post-treatment increases in human salivary DMBT1 correlated with increased abundance of Gemella spp., Pasteurellaceae spp., Lactobacillus spp., and Oribacterium spp. This is the first longitudinal study to investigate treatment-associated changes (chemoradiotherapy and surgery) in the oral microbiome in patients with SCC along with changes in expression of an anti-microbial protein in saliva. Conclusions The composition of the oral microbiota may predict treatment responses; salivary DMBT1 may have a role in modulating the oral microbiome in patients with SCC. Graphical Abstract After completion of treatment, 6 months after diagnosis, patients had a less diverse and less rich oral microbiome. Leptotrichia was a highly prevalent bacteria genus associated with disease. Expression of DMBT1 was higher after treatment and associated with microbiome changes, the most prominent genus being Gemella Video Abstract

Nitya Singhal (03:21:52) (in thread): > @Aleru Divine@Muqtadirat Yussuff

Aleru Divine (03:26:49) (in thread): > @Nitya Singhalthe statistical test was LEfSe. > Let me see if they specified the LDA - File (PNG): IMG_8029

Scholastica Urua (03:27:47) (in thread): > Yes, it does@Nitya Singhal

Nitya Singhal (03:28:21) (in thread): > Actually, there was another important test used in this named NMDS. i wanted to included it too.@Aleru Divine

Aleru Divine (03:28:50) (in thread): > Did that test for the differential abundance?

Muqtadirat Yussuff (03:28:58) (in thread): > Just checked and yes it does, was about to send the same snippet@Aleru Divinedid

Scholastica Urua (03:29:00) (in thread): > Was this test used for differential abundance?

Nitya Singhal (03:29:59) (in thread): > @Aleru Divine@Scholastica Urua - File (PNG): image.png

Scholastica Urua (03:31:39) (in thread): > Lemme check out fig 1b to be sure

Aleru Divine (03:33:16) (in thread): > @Nitya Singhalit seems NMDS was used for the analysis of beta-diversity.

Scholastica Urua (03:34:15) (in thread): > @Aleru Divineis right. Also Fig 1B is not curatable. So I’ll stick with LefSe@Nitya Singhal

Aleru Divine (03:34:43) (in thread): > That’scorrect@Scholastica Urua

Nitya Singhal (03:36:35) (in thread): > @Scholastica Uruawill we not use p-value from NMDS plots?

Aleru Divine (03:39:34) (in thread): > @Nitya Singhalour concern is usually the alpha diversity and this is beta diversity. So

Aleru Divine (03:40:33) (in thread): > Idon’tthink you should worry about that@Nitya Singhal

Scholastica Urua (03:40:45) (in thread): > What@Aleru Divinesaid

Nitya Singhal (03:40:49) (in thread): > but p-values aren’t mentioned anywhere else.

Nitya Singhal (03:41:31) (in thread): > please have a look - File (PNG): image.png - File (PNG): image.png

Aleru Divine (03:46:59) (in thread): > Take a look at the description of figure 1.There’smention of p values and adjusted p values.It’snot only NMDS.It is also found within text.

Abiola Salako (03:57:07) (in thread): > @Nitya Singhal, We only curate reports with differential abundance and alpha diversity index/indices.

Abiola Salako (03:58:03) (in thread): > Yes@Nitya Singhal

Aleru Divine (04:09:35): > Hi everyone,@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI found this study with a missing signature, I found the taxa to add and I’d like to add them.https://bugsigdb.org/Study_567 - Attachment (BugSigDB): Decreased dietary fiber intake and structural alteration of gut microbiota in patients with advanced colorectal adenoma - BugSigDB > Background: Accumulating evidence indicates that diet is one of the most important environmental factors involved in the progression from advanced colorectal adenoma (A-CRA) to colorectal cancer.

Nitya Singhal (04:14:24) (in thread): > Ok got you@Aleru Divine@Abiola Salako

Nitya Singhal (04:16:23) (in thread): > One more question… Is figure 7 curatable?@Aleru Divine@Scholastica Urua@Mildred Anashie

Aleru Divine (04:21:09) (in thread): > Figure 7 isn’t curatable > > Figure 3e, 4f and 5f are curatable.

Nitya Singhal (04:24:04) (in thread): > Can you review my curation?@Aleru DivineIt would be really nice of you.:blush::hugging_face:https://bugsigdb.org/Study_1016 - Attachment (BugSigDB): Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer - BugSigDB > BACKGROUND: Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis.

Aleru Divine (04:24:56) (in thread): > Sure thing@Nitya Singhalit’llbe my pleasure:hugging_face:

Aleru Divine (04:25:07) (in thread): > On it:+1::partying_face:

Nitya Singhal (04:25:41) (in thread): > Youu my friendddd:heart_eyes::star-struck:@Aleru Divine(sending virtual hugs)

Aleru Divine (04:26:01) (in thread): > :people_hugging:

Peace Daniel (06:03:55) (in thread): > Hey again:wave:I think your study is a cross-sectional observational study and not a case control (could be both but let me know your reasons why you chose a case control) > > You included G, F, S and O while curating your signatures. I believe they stand for genus, family, species and order respectively so you should search for Sutterella unclassified instead of G-Sutterella unclassifiedSo far, this is whatI’veobserved

Peace Daniel (06:05:58): > Happy Sunday everyone > > Not a curation question but hoping for a response here:wave:How do you cope with procrastination? Sometimes I find it difficult completing a task at hand if there’s no pressure

Muqtadirat Yussuff (06:08:40) (in thread): > Hi, you could try a second brain or a task tracker such as notion to keep you in check. Not gonna lie, you might still procrastinate things such as checking off the task or the task itself but slowly, you tend to get used to it and that’s progress, no matter how small it seems

Peace Daniel (06:13:15) (in thread): > Didn’tknow notion had this use,I’lltry a task tracker. Thank you:blush:

Peace Daniel (06:13:38) (in thread): > I could use an accountability partner tho:weary::purple_heart:

Samreen Aftab (06:15:17) (in thread): > Thank you@Peace Danielyou’re right about the study design, I corrected it. > Can you tell me why I should not include G, F, S. O in my signatures?

Samreen Aftab (06:18:21): > Hello everyone > How should I curate signatures like this? Should I search for G-Dorea uncl. or only Dorea uncl.? - File (PNG): image.png

Peace Daniel (06:18:45) (in thread): > Another observation,your workhasn’tbeen marked as completed.

Muqtadirat Yussuff (06:19:17) (in thread): > Depends on the field you need accountability for but yes, a partner would be really helpful. Good luck overcoming procrastination by the way

Samreen Aftab (06:19:24) (in thread): > yeah@Peace DanielI’ll do that in a while:slightly_smiling_face:are my experiments correct tho?

Peace Daniel (06:22:15) (in thread): > If you take a look at the rank,it’salready classified as a specie so instead just search dialister invisus and do the same for the others - File (JPEG): IMG_2355

Peace Daniel (06:23:02) (in thread): > I’dtake a look at your experiments and give you a feedback later tonight, my device is out of battery now:face_holding_back_tears:

Samreen Aftab (06:23:30) (in thread): > @Peace Danielokay thank you !

Peace Daniel (06:23:59) (in thread): > Thanks for the chat:hugging_face:

Aleru Divine (06:27:00) (in thread): > Hey@Nitya SinghalI’ve finished reviewing your curation. First of all, I’d acknowledge that there’s a lot of information on the paper and you tried to get them all.:clap::clap:I have some observations and they’re as follows: > 1. You added Welch’s t test as one of the statistical tests. It was used to adjust p-values. So just go with only LEfSe. > 2. There was MHT correction “Welch’s t test and Benjamini–Hochberg adjusted p values were used for ALDEx2 results.” > 3. Ididn’tfind any information on antibiotics exclusion (please check again) > 4. I noticed you had some missing data in experiments 2-4.You need to fill the data becausethey’rejust the same as experiment 1, no differences.I’mtalking about Lab analysis and statistical tests. > 5. The alpha diversity metrics were inverse Simpson(not faith) and richness. > 6. For signatures, signature 1 is always increase in abundance and signature 2 is always decrease in abundance.(From video tutorial). > For the signatures, here are my observations: > 1. For experiment 1, you had 4 signatures and I completely understand your confusion. It should have been just 2 that is the differential abundance between pre- and post-treatment saliva. The figure to curate from is figure 1F and not 1E.The differencial abundance is denoted by the red and blue colors. > 2. For experiment 2, you were correct with saying figure 3E(signature 1) but incorrect for 2E(signature 2) I believe this was a typographical error.The figure to curate is Figure 3E for both signatures and signature 1 is always increased while 2 is decreased in abundance. > 3. For experiment 3, the figure to curate is 2E and you should also have 2 signatures that is differential abundance before and after chemoradiotherapy. > 4. For experiment 4, you were absolutely correct to curate figure 4F but youdidn’tinclude all signatures and again, you started with decreased. > 5. For experiment 5, the figure to curate is figure 5F.(LEfSe analysis identifying the most differentially abundant OTUs between responders and non-responders after chemoradiotherapy.) although there was only increased abundance that was noted. > Hope this helps:pray:

Aleru Divine (06:32:20) (in thread): > @Samreen AftabI think G means Genus in this case.

Scholastica Urua (06:33:02) (in thread): > @Samreen AftabI think you should search for Dorea unclassified. G is specifying its rank which is genus

Aleru Divine (06:33:28) (in thread): > It looks like an unclassified Dorea specie. > > Dorea unclassified

Aleru Divine (06:40:11) (in thread): > Hey@Peace DanielI get you:sob:dealing with procrastination can be tricky, one thing that helps me is breaking down tasks into smaller, more manageable bits. It makes them feel less overwhelming and easier to tackle without needing too much pressure. Also, setting specific deadlines for myself even if they’re self-imposed keeps me on track. > > And:face_with_peeking_eye:I look forward to the satisfaction that comes with ticking off tasks from a list.

Peace Daniel (06:48:47) (in thread): > Oouu i love the last line:face_holding_back_tears::purple_heart:Thank you@Aleru Divine

idiaru Angela (07:03:28) (in thread): > Hey@Peace Daniel, for me also I give myself self imposed deadlines then create a reward system for finishing my task on or before the deadline. It works quite well for me. The reward could be something really small like talking a walk( because I love taking walks) , watching an episode of a series I like. Just anything to get my brain more excited to get the task done

idiaru Angela (07:03:57) (in thread): > Hey@Akinbode Mariamwould check it out and give you feedback. Well done

Svetlana Ugarcina Perovic (07:06:42) (in thread): > You could go to unfinished curations of your colleagues and support them, thanks. Team work is appreciated.

Svetlana Ugarcina Perovic (07:09:54) (in thread): > Oh, this is a GREAT question. Some time ago<@UBNSEMS3S>mentioned that she has been experiencing > > Productive procrastinationinvolves deliberately choosing productive activities that are not the most important or pressing. > and I have been experiencing it too!

Peace Daniel (07:12:58) (in thread): > That’s a great idea@idiaru AngelaI could try this too:purple_heart:

Peace Daniel (07:13:49) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic

Chioma Onyido (07:23:27) (in thread): > What tables?

idiaru Angela (07:25:36) (in thread): > @Chioma Onyidohttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711196846763069?thread_ts=1711106429.974329&cid=C04RATV9VCYThe one that was mentioned above. They were described to signify differential abundance in the study in this thread but its in form of excel sheet and we were wondering how to discern increased abundance from decreased abundance - Attachment: Attachment > https://static-content.springer.com/esm/art%3A10.1186%2Fs12866-021-02387-9/MediaObjects/12866_2021_2387_MOESM2_ESM.xlsx

Chioma Onyido (07:27:40) (in thread): > Okay I see 7 tables, which of them?

idiaru Angela (07:28:35) (in thread): > All of them ma’am:face_with_peeking_eye:. Each table was used to describe a different contrast

Amarachi Lewachi (07:32:42): > Hi,@Svetlana Ugarcina Perovic@Chioma OnyidoI completed my curation a while ago and it is still showing needs review. Is there something else I need to do? I have been awaiting feedback so I can make any corrections where necessary. Thank you. Here is the link.https://bugsigdb.org/Study_933 - Attachment (BugSigDB): Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis - BugSigDB > Background: > Infantile cholestasis (IC) is the most common hepatobiliary disease in infants, resulting in elevated direct bilirubin levels.Indeed, hepatointestinal circulation impacts bile acid and bilirubin metabolism.

Chioma Onyido (07:35:13) (in thread): > I would use the mean abundance. > For this expt here: RNAlater vs FOBT card > The first taxa had alowermean of 0.0136 in RNAlater and ahighermean of 0.0327 in FOBT card. > If RNAlater is group 1 and FOBT group 0, that means this taxa will be curated under the decreased signature for RNAlater. > I hope I got your question right. - File (JPEG): IMG_0330

Chioma Onyido (07:35:57) (in thread): > Second and third taxa with a higher mean of 0.5198 and .0045 in the RNAlater group will be curated under the increased signature. And so on… > Ohh boyyy, this table is quite lengthy, glad there are significant taxa (highlighted with asterisks).

Peace Daniel (07:37:33) (in thread): > You’d need to be patient as there are other studies that need reviews as well. Once it’s reviewed you’ll be notified via email and GitHub

Svetlana Ugarcina Perovic (07:38:34) (in thread): > @Amarachi Lewachihttps://github.com/waldronlab/BugSigDBcuration/issues/185you have to claim it for review here. - Attachment: #185 Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis > Alterations in gut microbiota and metabolite profiles in patients with infantile cholestasis - Jin et al - BMC
> https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-03115-1

idiaru Angela (07:39:46) (in thread): > Thank you so much for the clarification:saluting_face:. And thank you for your time@Chioma Onyido

Peace Daniel (07:39:47) (in thread): > I noticed youdidn’tcomment on GitHub thatyou’redone curating and would love a review, please do so

Amarachi Lewachi (07:40:08) (in thread): > Thank you@Svetlana Ugarcina Perovic

idiaru Angela (07:41:37): > Hi everyone@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy@Esther AfuapeI found a study with a missing NCBI ID clostridium_sensu_scrito_1. After a detective search I found numerous journals refer to the taxa as the true clostridim genus, including the journal belowhttps://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.001792-0May I proceed to edit the taxa as Clostridim genus with an NCBI ID of 1485 > Link to the study:https://bugsigdb.org/Study_518/Experiment_1/Signature_1 - Attachment (microbiologyresearch.org): Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I) > The species of Clostridium comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of Clostridium that form a distinct cluster in the 16S rRNA tree (cluster I) should be regarded as the true representatives of the genus Clostridium (i.e. Clostridium > sensu stricto). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of Clostridium cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other Clostridium species that are not part of this cluster grouped reliably with other species of clostridia in a number of well-resolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of Clostridium cluster I and are not found in any other bacteria. blastp searches on various proteins in the genomes of Clostridium tetani E88 and Clostridium perfringens SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of Clostridium cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus Clostridium > sensu stricto in more definitive terms. We have also identified a 7–9 aa conserved insert in the enzyme phosphoglycerate dehydrogenase that is uniquely found in the Clostridium thermocellum, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter tengcogensis and Caldicellulosiruptor saccharolyticus homologues, and is absent from all other bacteria. These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster. - Attachment (BugSigDB): Study 518/Experiment 1/Signature 1 > Source: Figure 3 Description: Patients with endometriosis demonstrated a significantly higher abundance of the following taxa compared to control patients. There…

Chioma Onyido (07:43:06) (in thread): > You’rewelcome!:raised_hands:

Chioma Onyido (07:44:57) (in thread): > Hello there, thank you for your work. > Could you also go through the talk page of unsolved/ resolved taxa to confirm ifit’snot already been reported?

idiaru Angela (07:46:19) (in thread): > @Chioma OnyidoI already did that. It has not been reported yet.

Scholastica Urua (07:51:08) (in thread): > Wow, thank you@Chioma Onyidofor clarifying this:pray:

Chioma Onyido (08:00:32) (in thread): > Confirmed. Nice detective work!:female-detective:Please go ahead and effect changes and also leave a note on the talk pagehttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_IDindicating that Clostridium sensu stricto has been solved as Clostridium genus, include your sources as well for reference purposes.Thank you! - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

idiaru Angela (08:02:28) (in thread): > Thank you@Chioma Onyido:blush::blush:

Mildred Anashie (08:47:59) (in thread): > Hi@Chioma OnyidoWell done@idiaru Angelafor your detective work:blush::hugging_face:A few weeks ago I was searching on clostridium senso stricto and shared what I found and I got this reply(see thread) > > Just sharing the thread for you to see the reply I got from@Esther Afuapeand also because clostridium senso stricto actually existed on the talk page and I can’t find it again

Mildred Anashie (08:50:20) (in thread): > Thank you@Chioma Onyidothis was confusing:hugging_face::yellow_heart:

Mildred Anashie (08:53:47) (in thread): > Well done on your review@Aleru DivineVery detailed:clap:

idiaru Angela (08:54:10) (in thread): > @Mildred Anashiethe thread:eyes:

Mildred Anashie (08:54:24) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1709833134786389 - Attachment: Attachment > Hello @Svetlana Ugarcina Perovic @Peace Sandy @Esther Afuape @Chioma Onyido > I found this pages with a similar missing NCBI ID Clostridium sensu stricto 1 > https://bugsigdb.org/Study_237 > Experiment 1 signature 1 and Experiment 3 signature 2 > https://bugsigdb.org/Study_767/Experiment_2/Signature_1 > Experiment 2 Signature 1 > > https://bugsigdb.org/Study_518/Experiment_1/Signature_1 > Experiment 1 signature 1 > > https://bugsigdb.org/Study_717/Experiment_4/Signature_1 > Experiment 4 Signature 1 > > Found this link https://www.midasfieldguide.org/guide/fieldguide/genus/clostridium_sensu_stricto_1 that shows the NCBI ID for the taxa as 1485 which is same as the ID for Clostridium > Found an information on google that seems to support this in my opinion, please help cross check this information and let me know if I can update it > Thank you!

Mildred Anashie (08:54:57) (in thread): > Sorry, I thought I added it@idiaru Angela

Scholastica Urua (08:56:36) (in thread): > Well done@Aleru Divine

idiaru Angela (08:57:58) (in thread): > @Mildred Anashie:thinking_face::thinking_face:

Mildred Anashie (09:08:54) (in thread): > My thoughts exactly > > Now I’m confused on if this applies to the studies I earlier identified (That’s if they still have missing NCBI taxas)

idiaru Angela (09:10:00) (in thread): > @Mildred AnashieI haven’t changed the other studies coz I didn’t identify them. But I definitely think it applies

idiaru Angela (09:13:08) (in thread): > @Akinbode MariamI’ve gone through the curation and everything checks out:+1:. Well done!

Mildred Anashie (09:14:33) (in thread): > @Chioma Onyido@Esther Afuapeis it okay to effect the change for the ones I earlier identified? > Also is there a reason why clostridium senso is no longer available on the talk page?:thinking_face:

Aleru Divine (09:15:26) (in thread): > Thanks@Mildred Anashie@Scholastica Urua

Chioma Onyido (09:48:30) (in thread): > I think that’s because it’s been resolved and edited by Angela. Yes I believe you should effect the changes you identified.

Mildred Anashie (09:55:05) (in thread): > Okay then…Thank you:pray:Although Angela said shedidn’tfind it before she effected the changethat’swhy I asked ifthere’sa reason it disappeared > > Would I need to leave a note about the changes I made?@Chioma Onyido

idiaru Angela (10:03:22) (in thread): > @Mildred AnashieI already left a note on the discussion page for missing NCBI IDs

Samreen Aftab (11:02:36): > The p value to be entered is the adjusted value after MHT correction or before?

idiaru Angela (11:03:06) (in thread): > Yes after MHT correction

Samreen Aftab (11:05:40): > In my studyhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9241752/should this table be curated? - File (PNG): image.png

Mildred Anashie (11:13:40) (in thread): > Did you curate the other tables showing differential abundance from the appendix? > > If you you did then I think this should be curated too

Samreen Aftab (11:19:14) (in thread): > @Mildred AnashieI’ve curated only this table, but I’m not sure about the rest because i dont know which experiments to put them under - File (PNG): image.png

idiaru Angela (11:19:44) (in thread): > I agree with@Mildred Anashieit’s should be curated

Samreen Aftab (11:33:47) (in thread): > @Mildred Anashie@idiaru Angelaalso do heatmaps need to be curated? If so , how to read these heatmaps? - File (PNG): image.png

idiaru Angela (11:34:39) (in thread): > @Samreen AftabI don’t think heat maps are curatable

Mildred Anashie (11:34:47) (in thread): > I’mstil going through the supplementals but I think you should curate Table 5 as well if youhaven’t@Samreen Aftab

Samreen Aftab (11:35:36) (in thread): > I’ve curated Table 5@Mildred Anashie, thank you. I’m just confused about the rest of the figures and tables

Mildred Anashie (11:37:18) (in thread): > I think heatmaps can be curated but there are just some that look almost impossible to interpret and its usually advisable to look for other sources > I think this is one of those ones thatisn’tcuratable > > Iwouldn’tcurate this@Samreen Aftab

Samreen Aftab (11:39:41) (in thread): > Thank you@Mildred AnashieAlso about appendix table 9, should I create a separate experiment to curate that table?

Mildred Anashie (11:43:01) (in thread): > I think you should if youdon’thave the experiment already > > So I think table 5 and 9 should be curatedBut I’munsure about table 7 but every other tabledoesn’tlook curatable to me@Samreen Aftab

Mildred Anashie (11:47:12) (in thread): > Errrmmmm > > I think the p value stated or the default 0.05(in cases where itwasn’texplicitly mentioned) is what should be recorded > > If we record the adjusted p value after MHT correction, what happens to studies that MHT correctionwasn’tdone?:thinking_face:Please I need clarity on this@Svetlana Ugarcina Perovic@Chioma Onyidoto be sureI’vebeen doing the right thing:pray:

idiaru Angela (11:51:06) (in thread): > @Mildred Anashiefrom the curation policy, it was mentioned that generally the mht-corrected list is the list curated in the experiment. That’s why I believe the p-value after mht correction if it was done should be recorded

idiaru Angela (12:04:15) (in thread): > I don’t think table 7 is curatable either

Mildred Anashie (12:08:26) (in thread): > Yea > > I get, but for the significant thresholdit’susually the p value set that should be recorded in my opinion > I think the MHT correction list is referring to a case where you have to record results or something like that:thinking_face:@Samreen Aftabis your question referring to the significant threshold?

idiaru Angela (12:13:14) (in thread): > In my opinion the MHT corrected significance threshold is what should be recorded:thinking_face:. Let’s wait for a reply from the mentors though

Peace Daniel (12:14:28) (in thread): > @Samreen Aftab@Mildred Anashie@Scholastica Urua@Aleru DivineI need a hand here:wave:Samreen is curating the supplementary material but I think those that were statistically significant in the suppl. are the highlighted ones and should be curated. Can someone please confirm this

Samreen Aftab (12:20:30) (in thread): > Yes@Mildred Anashie

Mildred Anashie (12:22:23) (in thread): > Looking at the supplemental tables not all the curatable tables have highlighted taxas soI’mthinking thatshouldn’tbe her basis for curation > > Others opinions might differ though@Peace Daniel

Peace Daniel (12:27:09) (in thread): > Well, I thoughtwe’reto curate statistically significant taxas. It looked to me like all abundant taxas were listed and significant ones were highlighted > > Would love to read other opinions tho

Scholastica Urua (12:31:16) (in thread): > @Peace DanielLooking at ‘Appendix Table 5’ which was used as the source, I don’t actually see any highlighted ones though. Although I haven’t gone through the article in detail… - File (JPEG): supp.JPG

Peace Daniel (12:33:04) (in thread): > Yes,you’dsee highlighted ones in other slides. The description underneath got me thinking@Scholastica Urua

Mildred Anashie (12:33:58) (in thread): > Each curatable table tagged differential abundance has statistically significant taxas reported > > She can use the direction column and P(FDR) to interpret increase and decrease in my opinion > > If you look you’d see that even tables that can’t be curated also have columns highlighted > > That’s why I think the basis for curating shouldn’t be the highlighted columns > > Except you are saying the tables that don’t have highlighted text are not curatable@Peace Daniel

Peace Daniel (12:40:16) (in thread): > I didn’t say that should be the basis Anashie, I’m just stating. tables that can be curated should have the highlighted columns since it was stated they are statistically significant. > > This is my own thought tho:wave:

Mildred Anashie (12:44:00) (in thread): > I understand your point@Peace DanielBut from my opinionit’sthe tables that show differential abundance that should be focused on

Mildred Anashie (14:13:27) (in thread): > Okay@Samreen AftabThe mentors will help on this though@idiaru Angelabut possibly you are right to record the adjusted p value for the threshold in cases where it is adjusted > > But I’ve always thoughtit’sthe P value we are to record on BugSigdb and then answer the follow up question, if the P value was adjusted or not hence the reason for the MHT (Yes/No) section@Chioma Onyido@Esther Afuape@Peace Sandy:pray:

Mildred Anashie (14:23:03) (in thread): > See this@idiaru AngelaIt says P value or FDR used for differential abundance > > Is this saying either:thinking_face: - File (JPEG): IMG_2841

idiaru Angela (14:24:50) (in thread): > My own interpretation would be FDR if present P value if FDR correction isn’t present@Mildred Anashie

Mildred Anashie (14:26:50) (in thread): > Okay that could be right > > Hopefully I can get clarity on this:confused:

Akinbode Mariam (16:27:11) (in thread): > Thank you so much@idiaru Angela

Modinat Ganiyu (18:54:35): > Hi everyone. Can anyone please review my paper? Here’s the link to my curationhttps://bugsigdb.org/Study_1059Thank you! - Attachment (BugSigDB): Effects of OsomeFood Clean Label plant-based meals on the gut microbiome - BugSigDB > BACKGROUND: Plant-based diets offer more beneficial microbes and can modulate gut microbiomes to improve human health.We evaluated the effects of the plant-based OsomeFood Clean Label meal range (‘AWE’ diet), on the human gut microbiome.

idiaru Angela (19:14:10) (in thread): > Would look through and give you feedback@Modinat Ganiyu

Abiola Salako (19:26:15) (in thread): > First of all, your experiment one was tagged ‘incomplete’@Modinat Ganiyukindly check it and adjust. The same thing goes for your third experiment.

Modinat Ganiyu (19:32:18) (in thread): > Okay thank you:heart:

Modinat Ganiyu (19:33:28) (in thread): > For now@Abiola Salakoplease ignore experiment 3 I’ll ask our mentors to delete it

idiaru Angela (20:02:26) (in thread): > @Modinat GaniyuWell done on the curation. These are some of my observations > 1. The group name having aws should be more defined. Anyone that comes across the study can’t tell what aws is > 2. I couldn’t find the area where experiment 1 was mentioned. If you don’t mind can you point me to it?

Modinat Ganiyu (20:12:02) (in thread): > Overweight participants and other weight group were mentioned in the paper many times that was why I considered it but their taxa wasn’t mentioned. Check this out - File (PNG): image.png - File (PNG): image.png

Modinat Ganiyu (20:13:34) (in thread): > They are subgroups under the second Experiment

idiaru Angela (20:15:17) (in thread): > But it didn’t say it was significant:thinking_face:. I think we only curate experiments without signatures if they are said to be statistically significant

Modinat Ganiyu (20:17:35) (in thread): > hmmm…that’s true. They are not statistically significant. This means I should delete that

Modinat Ganiyu (20:18:00) (in thread): > Please any more observation@idiaru Angela

idiaru Angela (20:18:20) (in thread): > No@Modinat GaniyuI think everything else is good. Well done

Modinat Ganiyu (20:18:59) (in thread): > Okay, thank you for your time and efforts@idiaru Angela

Precious Orakwe (20:29:24): > Good day everyone, I need a review on my paper. > Please@Svetlana Ugarcina Perovic@Muqtadirat Yussuff@Mildred Anashie@Scholastica Urua@Amanda Adoyihelp me review my paper. Here is the link:https://bugsigdb.org/Study_970/Experiment_1 - Attachment (BugSigDB): Study 970/Experiment 1 > …

Modinat Ganiyu (20:44:54) (in thread): > Just finished curating mine, let me check this out

Modinat Ganiyu (20:57:43) (in thread): > I observed your grouping was the other way round. Group 0 is supposed to be the control group while group 1 should be the exposed group. > Here, you have ‘melatonin-deficiency mice’ as the group 0 while ‘Mice with normal melatonin synthesis’ as group 1 > If you don’t mind, can you tell me why?

Nitya Singhal (22:26:47): > Good morning everyone. Wishing you and your family a very happy Holi from India. It is a festival of colors and joy celebrated by Hindus all over the world. So I hope that this Holi brings the color of joy and happiness to your life.:blush::partying_face:

Aleru Divine (22:33:06) (in thread): > Thank you Nitya! Happy Holi:heart_hands::sparkles:

Manisha Nair (23:32:37) (in thread): > @Nitya Singhalthanks a lot

Manisha Nair (23:32:58) (in thread): > @Scholastica Uruathanks for help

2024-03-25

Barakat Akinsiku (00:30:04) (in thread): > Happy Holi Nitya, wishing you a joyous festival:partying_face::partying_face:

Scholastica Urua (01:30:26) (in thread): > Happy Holi@Nitya Singhal, wishing you best:tada:

Samreen Aftab (01:54:09) (in thread): > Happy Holi:heart:@Nitya Singhal

Modinat Ganiyu (01:55:54): > Amazing Morning to you all:blush:Please@Svetlana Ugarcina Perovic@Peace Sandy@C. Mirzayi (please do not tag this account)@Chioma Onyido<@U1LCB8WEA>I‘d like to get Experiment 2 and Experiment 3 deleted. Thank you:pray:https://bugsigdb.org/Study_1059 - Attachment (BugSigDB): Effects of OsomeFood Clean Label plant-based meals on the gut microbiome - BugSigDB > BACKGROUND: Plant-based diets offer more beneficial microbes and can modulate gut microbiomes to improve human health.We evaluated the effects of the plant-based OsomeFood Clean Label meal range (’AWE’ diet), on the human gut microbiome.

Bolanle Wahab (02:01:47) (in thread): > Thank you!@Nitya SinghalHappy Holi:heart:

Ima-obong (Aimah) (02:27:21) (in thread): > Thank you and Happy Holi

Chioma Onyido (02:41:03) (in thread): > Deleted.

Victoria (Burah) Poromon (02:41:35): > Hello Everyone, Good morning and happy new week. > > I would like to make a suggestion, for people who still want to make study curation contributions. > > There are papers on GitHub that has been assigned since 2 weeks and 3 weeks ago. Buthaven’tbeen marked for review yet. (The ones with no “Needs review” tag from 2-3 weeks ago)I’dlike to suggest that we (1 or 2 persons) leave a comment on GitHub under those issues. Asking the original assignees ifthey’restill working on the curation. > > This way, if they were done and forgot to ask for a review, they can remember to do so. > Ifthey’restuck and they need help, they can also signify and collaborate on it. And, > If they’re simply no longer working on it, someone else can take it up.<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapePlease is this doable?

Scholastica Urua (02:41:40) (in thread): > Hello@Precious Orakwe, well done on your curation. Here’s a few things I’ve observed; > 1. I noticed that the condition field is not filled. I think the condition of interest here is ‘melatonin’ although I can’t seem to find it in the dropdown. I couldn’t also find a close term on EFO. Although I’ll need other opinions on this… > 2. I also noticed you included confounders. Please cross-check as I couldn’t find this information in the article. > > 3. Also, I couldn’t find a mention of LDA in the study. > > I’ll go through your curation in detail and let you know other details I find.

Mildred Anashie (02:43:12) (in thread): > Thank you@Nitya Singhal:yellow_heart:

Mildred Anashie (02:45:39) (in thread): > That sounds like a great idea@Victoria (Burah) Poromon@Svetlana Ugarcina Perovicencourages supporting and collaborating with othersso I’mthinking it should be allowed

Victoria (Burah) Poromon (02:47:59) (in thread): > Thank you!@Mildred Anashie

Scholastica Urua (02:55:57) (in thread): > This is a nice idea@Victoria (Burah) Poromon

Nana (02:58:07) (in thread): > This is fine

Nana (03:00:48): > @Svetlana Ugarcina Perovicgood morning and happy Monday. Some papers marked needs review as first curation has not been reviewed yet.?

Samreen Aftab (03:01:44): > https://bugsigdb.org/Study_1007Can anyone review this please? - Attachment (BugSigDB): Dysbiosis in the Gut Microbiota in Patients with Inflammatory Bowel Disease during Remission - BugSigDB > Inflammatory bowel disease (IBD) is a chronic, relapsing, inflammatory disorder which comprises two main conditions: Crohn’s disease (CD) and ulcerative colitis (UC).

Aleru Divine (03:11:40) (in thread): > Yeah@Victoria (Burah) Poromon, this sounds like a great idea.:hugging_face:

Ima-obong (Aimah) (03:21:21) (in thread): > Hello@Samreen Aftabwill get on it

Mildred Anashie (03:21:36): > Hello everyone > It’s a new week:partying_face:and this appears to be our last week of contribution:pensive:. > Just a friendly reminder that we should not forget to record our contributions on OutreachyHow has BugSigdb-ing been so far?:blush:Looking forward to what we will achieve together this week:raised_hands::blush:I also would like to appreciate our mentors for their patience, responsiveness to questions and encouragement > Thank you@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace Sandy@Levi Waldron:heart_hands:

Barakat Akinsiku (03:23:49) (in thread): > Thank you Mildred and thank you to all our mentors. BugSigdb-ing has been great and very insightful:blush:

Blessing Ene Anyebe (03:25:46) (in thread): > Thank you@Mildred Anashieand huge thank you to the mentors.:orange_heart:Happy new week!

Samreen Aftab (03:27:07) (in thread): > Great idea!@Victoria (Burah) Poromon

Aleru Divine (03:29:46) (in thread): > Thank you@Mildred Anashie:heart_hands:it has been amazing so far, many thanks toeveryone’ssupport and many many to the mentors.:heart::heart:I look forward to a productive last week of contributions:sparkles:

Ima-obong (Aimah) (03:31:55) (in thread): > It’s been an awesome experience bugsigdbing this past weeks..I really appreciate our mentors for being really helpful and thank you for always being available to help too@Mildred Anashie

Samreen Aftab (03:32:04): > Hello@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Esther AfuapeI noticed this issue on githubhttps://github.com/waldronlab/BugSigDBcuration/issues/145from a few weeks back, and I discovered that this study has not been even created yet on bugsigdb. Can I work on it? - Attachment: #145 Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares > Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares – Thomson P. et al. – Open Vet J > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805769/

Muqtadirat Yussuff (03:34:28) (in thread): > Can someone please share a PDF of the paper? It’s not opening on my end

Muqtadirat Yussuff (03:36:12) (in thread): > Yes, none of mine has been reviewed which has made me take a step back on curation and focus on reviewing other curations.

Peace Daniel (03:43:45) (in thread): > Happy new week, it has been amazing so far.I’vepushed myself beyond my limit andI’mamazed at what I can do when I set my heart to it. > Shout out to everyone for the great teamwork and patience. Appreciation to the mentors and co-mentors for always helping out:purple_heart:

Ima-obong (Aimah) (03:53:17) (in thread): > @Samreen AftabI have gone through your paper and From Fig 1, > Alpha diversity for Simpson is unchanged to me and not decreased cause even in the paper it was stated that “Simpson diversity appeared relatively stable across for healthy individuals and CD patients” but I’d love to hear your thoughts on why you think it’s decreased > > > I also noticed that your signature curations are from Appendix Table 5, I think you should also curate from Figure 3; which shows “Differential abundance analysis to detect differences in taxonomic groups between the different disease groups(UC patients,CD patients) and control. > Or is there a reason why you think the figure isn’t curatable? I’d love to hear them. > Thank you

Samreen Aftab (03:57:24) (in thread): > @Ima-obong (Aimah)I’m unsure which one you’re referring to since I put unchanged for Simpson diversity for HC vs CD patients - File (PNG): image.png

Blessing Laweh (03:57:57) (in thread): > Contributing to bugsigdb made me realise that my own little participation is for a greater good. When I go through an article and I realise how much work has already been done and for what reason it makes me thanks and optimistic for the future of medicine and science. > > I wish everyone a good, productive and stress-free week. Mentors and mentees alike:pray::heart_hands:

Flourish Ralph (03:58:13) (in thread): > Thank you mentors and everyone.It’sbeen an amazing learning experience.:heart_hands:

Ima-obong (Aimah) (03:58:59) (in thread): > Okay..that’s clear now..was looking at the first experiment… well-done:clap:

Blessing Laweh (04:01:04) (in thread): > Happy Holi@Nitya SinghalId love to experience the festival one day. I looks so fun! Enjoy your day:purple_heart:

Adedoja Isaac (04:01:19) (in thread): > Thank you@Mildred Anashieand oir mentors too. Happy new week.

Abiola Salako (04:07:02) (in thread): > Thank you@idiaru AngelaI slept off while looking through her article:joy:

Abiola Salako (04:08:49) (in thread): > Good suggestion!@Victoria (Burah) Poromon

Abiola Salako (04:14:52) (in thread): > It has been an amazing experience. Gratitude to our mentors@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy@Levi Waldron@C. Mirzayi (please do not tag this account)for their guidance and many thanks to my fellow contributors for their support@Aleru Divine@Mildred Anashie@Ima-obong (Aimah)@idiaru Angelaand every other person.

Peace Daniel (04:23:17): > Hello everyone, happy new week. > > I need a little help here please:wave:Do you think these are curatable? I’m finding it a bit difficult sourcing curatable taxas in my study as differential abundance wasn’t used. Here’s a linkhttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01733-7#Fig1 - Attachment (BioMed Central): Dysbiosis of saliva microbiome in patients with oral lichen planus - BMC Microbiology - File (JPEG): IMG_2358 - File (JPEG): IMG_2359

idiaru Angela (04:27:49) (in thread): > @Peace Danielgood morning. I think table 4 and 5 might be curatable using their mean values. I’ll attach a thread of one of our mentors giving an explanationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711280113553769?thread_ts=1711106429.974329&cid=C04RATV9VCY - Attachment: Attachment > I would use the mean abundance. > For this expt here: RNAlater vs FOBT card > The first taxa had a lower mean of 0.0136 in RNAlater and a higher mean of 0.0327 in FOBT card. > If RNAlater is group 1 and FOBT group 0, that means this taxa will be curated under the decreased signature for RNAlater. > I hope I got your question right.

Samreen Aftab (04:28:52) (in thread): > @Ima-obong (Aimah)which of these should be curated? - File (PNG): image.png - File (PNG): image.png

Aleru Divine (04:39:04) (in thread): > @Peace Danieltable 4 and 5 are curatable and a way to interpret it is stated in the description of the table. > > I’ve highlighted it. - File (PNG): IMG_8046 - File (PNG): IMG_8047

Peace Daniel (04:40:51) (in thread): > Thank you so much@Aleru Divine@idiaru AngelaThe explanation is also in the text, I just needed to be sure. Thanks again:hugging_face:

Peace Daniel (04:40:52) (in thread): > Thank you so much@Aleru Divine@idiaru AngelaThe explanation is also in the text, I just needed to be sure. Thanks again:hugging_face:

Aleru Divine (04:41:14) (in thread): > In my opinion, they are both curatable@Samreen Aftab

Abiola Salako (04:45:04) (in thread): > Yes@Samreen Aftabboth look curatable.

Scholastica Urua (04:45:07) (in thread): > Thank you mentors everyone for all your help so far. Its been an amazing journey.:hugging_face:

idiaru Angela (04:47:16) (in thread): > I agree@Samreen Aftabthey are both curatable

Samreen Aftab (04:48:16) (in thread): > But the phylum of dorea unclassified is firmicutes, so should I curate both dorea unclassified and firmicutes

Aleru Divine (04:49:17) (in thread): > Go with Dorea.It is more specific.

idiaru Angela (04:50:27) (in thread): > No just Dorea unclassified

idiaru Angela (04:50:52) (in thread): > You should probably curate just the organisms column

Svetlana Ugarcina Perovic (04:51:02) (in thread): > YES!

Ima-obong (Aimah) (04:51:20) (in thread): > @Samreen Aftabthough my emphasis was on the Fig3A, but I guess I’ll go with what others are suggesting…you can curate both

Svetlana Ugarcina Perovic (04:51:43): > Good morning:potted_plant:this isa true team work. Well done everyone, we are privileged to work with you.<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma Onyido@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711348895127679 - Attachment: Attachment > Hello Everyone, Good morning and happy new week. > > I would like to make a suggestion, for people who still want to make study curation contributions. > > There are papers on GitHub that has been assigned since 2 weeks and 3 weeks ago. But haven’t been marked for review yet. (The ones with no “Needs review” tag from 2-3 weeks ago) > > I’d like to suggest that we (1 or 2 persons) leave a comment on GitHub under those issues. Asking the original assignees if they’re still working on the curation. > > This way, if they were done and forgot to ask for a review, they can remember to do so. > If they’re stuck and they need help, they can also signify and collaborate on it. And, > If they’re simply no longer working on it, someone else can take it up. > > @UBNSEMS3S @Svetlana Ugarcina Perovic @Chioma Onyido @Peace Sandy @Esther Afuape > Please is this doable?

Victoria (Burah) Poromon (04:54:23) (in thread): > Thank you!@Svetlana Ugarcina Perovic

Scholastica Urua (04:55:07) (in thread): > @Muqtadirat Yussuffthis is the PDF - File (PDF): fimmu-13-900132.pdf

Svetlana Ugarcina Perovic (05:00:44) (in thread): > Do not worry. Every review process takes time. We are working on it.

Victoria (Burah) Poromon (05:02:41) (in thread): > Thank you@Svetlana Ugarcina PerovicWe enjoy working with the community too:blush:

Peace Daniel (05:08:50) (in thread): > This is a great idea@Victoria (Burah) Poromon

Habiba Saad (05:12:07): > hey there, i asked about this last week. kindly let me know if this is right so i can add it.@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape - Attachment: Attachment > hey there i have found the missing signature of erysipelotrichaceae UCG-003 by an alternative name of bacterium LF3 on midas field guide. is this correct? kindly guide me mentors @Svetlana Ugarcina Perovic @Peace Sandy

Ima-obong (Aimah) (05:16:52) (in thread): > Thank you@Abiola Salakofor always coming through:hugging_face::smiling_face_with_3_hearts:

Modinat Ganiyu (05:30:34) (in thread): > Thank you@Chioma Onyido

Oluwatomisin Omojokun (05:40:50): > Good morning BugsigDB team, > I hope this message finds you well. Just checking in to see how things are going with BugsigDB. Is there anything new or exciting happening with the project? > Wishing you a productive and successful day ahead! > Best regards, > Tomisin cares

Oluwatomisin Omojokun (05:45:44) (in thread): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (05:47:20) (in thread): > Good morning@Oluwatomisin Omojokunsending you my best:confetti_ball:.

Ima-obong (Aimah) (05:49:34) (in thread): > Good morning@Oluwatomisin Omojokun.. wishing you a great week ahead

Linda Uchenwoke (05:58:33) (in thread): > Good Morning@Oluwatomisin OmojokunI absolutely love my project topic and I’m enjoying curating the paper. Wishing you a pleasant week too.

Bolanle Wahab (06:04:35) (in thread): > Good morning@Oluwatomisin OmojokunThank you and have a nice day:heart:

Precious Orakwe (06:08:07) (in thread): > Good morning@Oluwatomisin Omojokunit has not been easy for me, I have been curating one paper for the past 12 days now, but I am happy that I now understand the process now, but its unfortunate that there are no more tasks to work on in GitHub. > Wishing you a pleasant week ahead.

Ima-obong (Aimah) (06:11:28) (in thread): > @Precious Orakwewell done, you can also check the GitHub page for papers that had been assigned to applicants for 3weeks now and doesn’t have the “needs review” tag on it, ask if they need help with the paper, and their progress on it too

Precious Orakwe (06:12:05) (in thread): > Thanks team for all your reviews. For the condition I knew it was endogenous melatonin but I couldn’t find it in the dropdown, that’s why I left it blank. > > I will go back and see if I can edit my work, will that be possible

Scholastica Urua (06:14:29) (in thread): > Has it been tagged for review yet@Precious Orakwe

Precious Orakwe (06:15:05) (in thread): > Where@Scholastica Urua, is it on Github?

Scholastica Urua (06:15:59) (in thread): > On GitHub, does it have the ‘need review’ tag?

Precious Orakwe (06:17:18) (in thread): > I don’t think so

Scholastica Urua (06:18:01) (in thread): > If it has not been tagged for review then you can still edit it.

Svetlana Ugarcina Perovic (06:18:49): > Reminder: If the GitHub issue with your curated paper is with tag****“needs review” ****that means now it’s in our hands under review and you are kindly asked to not make any changes while we are reviewing it.

Precious Orakwe (06:20:12) (in thread): > Ok, thanks, is there any task I can still work on while I wait for my paper to be reviewed

Scholastica Urua (06:21:18) (in thread): > While waiting for review, here is some ways you can help out with BugSigDB: > * Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > * Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID > * See other possible ways to help on the help page:https://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Precious Orakwe (06:22:35) (in thread): > No, it’s has not been tagged needs review - File (PNG): Screenshot_20240325-112118.png

Scholastica Urua (06:23:15) (in thread): > Also, you can browse through the GitHub page for issues that have been open for a while (that is unfinished curation not tagged for review) and offer to collaborate with the original assignee.

Precious Orakwe (06:25:34) (in thread): > Thanks @ima-obong

Precious Orakwe (06:26:10) (in thread): > Thanks

Blessing Laweh (06:31:20) (in thread): > I was just going to ask something related to this thanks for the heads-up:pray:

Oluwatomisin Omojokun (06:33:00) (in thread): > Duly noted

Blessing Laweh (06:33:27): > Hello Team. There’s currently no paper available to curate how else can I contribute to Bugsigdb??

Joan C. Chukwuemeka (06:34:29) (in thread): > @Blessing LawehCheck out the help pages athttps://bugsigdb.org/Help:Contents - Attachment (BugSigDB): Help:Contents > …

Aleru Divine (06:35:03) (in thread): > @Blessing Lawehyou can help with offering to review curations of fellow contributors.There’splenty above.

Joan C. Chukwuemeka (06:35:59) (in thread): > Hi@Aleru DivineGood Morning:slightly_smiling_face:

Aleru Divine (06:36:31) (in thread): > Good morning@Joan C. Chukwuemeka:hugging_face:

NWAKAEGO VINCENT (06:38:13) (in thread): > thanks everyone

Blessing Laweh (06:38:26) (in thread): > OK thank you@Aleru Divine@Joan C. Chukwuemeka:purple_heart:

Aleru Divine (06:39:05) (in thread): > Good morning@Blessing Laweh:sweat_smile:

Modinat Ganiyu (06:39:59) (in thread): > @Scholastica UruaThank you for being detailed. I also noticed the LDA and the confounders wasn’t mentioned in the paper but thought to revisit later before commenting on that. Your observations are valid, thank you for confirming my thoughts.@Precious OrakweWell done on the paper you curated. > Please kindly go through it to confirm these and make adjustments where necessary. Thank you:hugging_face:

EBERE ADEKOGBE (06:40:35) (in thread): > Good morning everyone:grinning:

Joan C. Chukwuemeka (06:41:06) (in thread): > Lol at:face_with_raised_eyebrow:@Blessing Lawehgreetings to you too

Blessing Laweh (06:41:35) (in thread): > Good morrrrrnnninggggggg@Aleru Divine:rolling_on_the_floor_laughing:OK so some fellow already have someone assistaning them with review…so maybe I’ll just go with Cleanup@Joan C. Chukwuemekasuggested. > > > For the cleanup, do I need permission before I cleanup a paper? Like those with missing NCBI?

Aleru Divine (06:41:49) (in thread): > :joy::sweat_smile:

Aleru Divine (06:42:26) (in thread): > Yes@Blessing Lawehyou’llhave to post it on the channel before you commence.

Blessing Laweh (06:43:03) (in thread): > OK cool. Thank you@Aleru DivineAnd good morningggggg@Joan C. Chukwuemeka:sob::heart_hands:

EBERE ADEKOGBE (06:53:43): > Hi,@Svetlana Ugarcina Perovic@Chioma OnyidoI completed my curation a while ago and it is still showing needs review. I have been awaiting feedback so I can make any corrections where necessary. Thank you. Here is the link.https://bugsigdb.org/Study_913 - Attachment (BugSigDB): - BugSigDB > …

Joan C. Chukwuemeka (06:55:34) (in thread): > @EBERE ADEKOGBESee thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711357244366759?thread_ts=1711350048.639329&cid=C04RATV9VCY - Attachment: Attachment > Do not worry. Every review process takes time. We are working on it.

Scholastica Urua (07:10:30): > Hello@Bolanle WahabI found one of your curation under pages with missing NCBI ID;https://bugsigdb.org/Study_1048/Experiment_2/Signature_1It has ‘actinobacteria’ highlighted orange. I think ‘Actinomycetota’ (201174) will be a good replacement. > Also ‘Bacillota’ (1239) may replace ‘firmicutes’. > > Please do check them out. - Attachment (BugSigDB): Study 1048/Experiment 2/Signature 1 > Source: text Description: they were observed at higher abundances following storage at 22°C for 64 h Abundance in Group 1: increased abundance in pig feces(P2… - File (JPEG): Actino.JPG

Bolanle Wahab (07:17:55) (in thread): > @Scholastica Uruaalright, thank you:heart:, will change them

Nana (07:44:12) (in thread): > Ok

Abiola Salako (08:08:00): > @Svetlana Ugarcina Perovic@Chioma Onyido@Esther AfuapeWell done to you all. I stumbled upon an issue on GitHub that was opened three weeks ago while searching for a collaboration opportunity. I noticed that the issue was initially assigned to someone, then reassigned to someone else without receiving the ‘Needs Review’ label. Upon investigating further, I found that the first assignee had already curated the study but didn’t notify you for review. > > Here’s the issue:https://github.com/waldronlab/BugSigDBcuration/issues/238The study curated:https://bugsigdb.org/Study_942. - Attachment (BugSigDB): Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke - BugSigDB > BACKGROUND: Integrative analysis approaches of metagenomics and metabolomics have been widely developed to understand the association between disease and the gut microbiome. - Attachment: #238 Alteration in gut mycobiota of patients with polycystic ovary syndrome > Alteration in gut mycobiota of patients with polycystic ovary syndrome – Ke Chen et al. – Microbiology Spectrum
> https://journals.asm.org/doi/10.1128/spectrum.02360-23

Amanda Adoyi (08:47:19): > Aloha people. Hope everyone’s good. Would love it if anyone’s got the time to spare for a good review of this work. Would especially love it if you could check out the alpha diversity measurement portion. Thank you so much in advance:slightly_smiling_face:https://bugsigdb.org/Study_1057 - Attachment (BugSigDB): Gut microbiome profiling of a rural and urban South African cohort reveals biomarkers of a population in lifestyle transition - BugSigDB > BACKGROUND: Comparisons of traditional hunter-gatherers and pre-agricultural communities in Africa with urban and suburban Western North American and European cohorts have clearly shown that diet, lifestyle and environment are associated with gut microbiome composition.

Amanda Adoyi (08:52:23): > While working on the above paper, I was forced to learn how to read volcano plots. Here is a guide if you come across one during your curation and don’t know howhttps://youtu.be/7aWAdw2jhj0?si=PWt83g2NccApGg0P - Attachment (YouTube): Volcano plots explained | How to interpret a volcano plot for DGE

Bolanle Wahab (09:11:45) (in thread): > Hi@Amanda AdoyiI looked through the alpha diversity portion of, there were results for both Shannon and Chao1 for lean and obese group (experiment 4) but you recorded just Shannon, is there a reason? Still looking through.

Bolanle Wahab (09:12:32) (in thread): > Thank you:heart:

Amanda Adoyi (09:14:44) (in thread): > @Bolanle Wahabto be very honest, I am still looking through which is why I pointed it out. Thanks for the direction you’ve pointed me in. I was hoping for such feedback.

Akinbode Mariam (09:22:17) (in thread): > Thank you@Mildred Anashieand our mentors@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)its been an amazing learning experience

Akinbode Mariam (09:23:42) (in thread): > it looks good from my side youre good to go

Svetlana Ugarcina Perovic (09:27:56) (in thread): > Many thanks for letting us know.

Bolanle Wahab (09:41:48) (in thread): > You’rewelcome:heart:@Amanda Adoyi

Abiola Salako (09:45:51) (in thread): > You’re most welcome:saluting_face:

EBERE ADEKOGBE (09:48:39) (in thread): > :ok_hand:ok thank you@Joan C. Chukwuemeka

Joan C. Chukwuemeka (09:49:28) (in thread): > You’re welcome@EBERE ADEKOGBE

Aleru Divine (09:54:16) (in thread): > This is so thoughtful of you@Amanda Adoyi. Thank you for sharing:heart:

Druscilla Nakanwagi (09:59:49): > Hello > I am filling in my final application > Are there community specific questions? > And what is the project timeline?

Svetlana Ugarcina Perovic (10:00:34) (in thread): > <@UBNSEMS3S>could you please answer on this. Thanks!

Peace Daniel (10:11:10) (in thread): > Thanks for asking@Druscilla NakanwagiI also had it in mind to ask about the project timeline as well@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)Is it fine to draft a rough sketch for the timeline based on the task we want to accomplish?

NWAKAEGO VINCENT (10:14:10) (in thread): > can you help me check if i am doing the right thing@Chioma Onyido@Scholastica Urua@idiaru Angela@Mildred Anashiehttps://bugsigdb.org/Study_1056 - Attachment (BugSigDB): Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts - BugSigDB > BACKGROUND: To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities.

idiaru Angela (10:14:50) (in thread): > Sure@NWAKAEGO VINCENTwhat exactly do you want to check

NWAKAEGO VINCENT (10:15:58) (in thread): > the study i createdhttps://bugsigdb.org/Study_1056

Mildred Anashie (10:20:03) (in thread): > Okay > > I can@NWAKAEGO VINCENT

Scholastica Urua (10:20:41) (in thread): > Okay, I will@NWAKAEGO VINCENT

idiaru Angela (10:24:02) (in thread): > @NWAKAEGO VINCENTI see you’ve only curated the first experiment. I think you’re on the right track. I have 2 notes though > 1. You can make the group names a bit more explanatory. That way someone who views your curation can know what the groups are without having to go to the article > 2. You should use ncbi taxonomy browser to match the taxa to their respective ncbi Id, that way they stop showing in red. You can search the taxa herehttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi > Then input the taxa ID in the space for signature. Only if it can’t be found should you leave it as is. Well done@NWAKAEGO VINCENT - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

NWAKAEGO VINCENT (10:26:26) (in thread): > thank you@idiaru Angelai will make the changes right away

Mildred Anashie (10:33:10) (in thread): > Yea > > You are on track for the experiment you have entered and Angela’s suggestion for the signature section is exactly what should be done > > Well done:+1:

Scholastica Urua (10:37:08) (in thread): > Hello@NWAKAEGO VINCENTI agree with@idiaru Angelaand@Mildred Anashie. Well done on your curation.

NWAKAEGO VINCENT (10:38:15) (in thread): > thank you ladies@Mildred Anashie@Scholastica Urua

Scholastica Urua (10:39:01) (in thread): > @NWAKAEGO VINCENTPlease check out this my recent post. It has some of your highlighted taxa.https://community-bioc.slack.com/archives/C04RATV9VCY/p1711365030194369 - Attachment: Attachment > Hello @Bolanle Wahab > I found one of your curation under pages with missing NCBI ID; > https://bugsigdb.org/Study_1048/Experiment_2/Signature_1 > It has ‘actinobacteria’ highlighted orange. I think ‘Actinomycetota’ (201174) will be a good replacement. > Also ‘Bacillota’ (1239) may replace ‘firmicutes’. > > Please do check them out.

NWAKAEGO VINCENT (10:40:09) (in thread): > alright , thanks

Blessing Ene Anyebe (10:55:26): > Hello everyone, how’s your day and curation assistance going?:new_moon_with_face:I was looking through the BugSigDB studies to find a way to contribute and I noticed that the curations would benefit from aLast review datefeature. > > It has theRevision editorsfeature but it would also benefit from the last review date feature. This would be a code contribution and maybe out of scope for us but I thought to point it out. > If this is considered and implemented, I think it would help future contributors. > > Thanks guys.:orange_heart:

Victoria (Burah) Poromon (10:55:49) (in thread): > Thank you for asking.@Druscilla Nakanwagi

Joan C. Chukwuemeka (11:00:44) (in thread): > @Blessing Ene AnyebeIf you hover on the “i” icon at the top right of reviewed papers, i think it shows the reviewer and review date.

Blessing Ene Anyebe (11:02:03) (in thread): > Oh that’s great then. I only feel it will be better on the main page. > > Thank you for pointing out@Joan C. Chukwuemeka

Scholastica Urua (11:06:00) (in thread): > @Blessing Ene AnyebeIf you also click on ‘History’, you’ll see theRevision history.

Blessing Ene Anyebe (11:07:14) (in thread): > I checked that@Scholastica UruaI’mnot sure it carries the date.

Joan C. Chukwuemeka (11:07:38) (in thread): > You’re welcome@Blessing Ene Anyebe - File (PNG): image.png

Mildred Anashie (11:08:00) (in thread): > @Blessing Ene AnyebeThe history carries the date the page was created

Blessing Ene Anyebe (11:08:25) (in thread): > Super. Thank you guys so much

Scholastica Urua (11:08:41) (in thread): > Yes, it carries the date and the name(s) of the revised editor.

Joan C. Chukwuemeka (11:08:43) (in thread): > for revision history: - File (PNG): image.png - File (PNG): image.png

ayesha khan (11:43:40): > how do u help in cleanups ?

idiaru Angela (11:49:30) (in thread): > @ayesha khanyou can start herehttps://bugsigdb.org/Help:Cleanup#Links_to_lists_of_pagesRemember to post what you want to do here and get a confirmation from the mentors before changing anything. - Attachment (BugSigDB): Help:Cleanup

Linda Uchenwoke (12:49:49): > Hello Team, What happens if you mistakenly add the same experiment twice, with one marked as incomplete and the other marked as complete?

Aleru Divine (12:50:29) (in thread): > @Linda Uchenwokeyou can request for one to be deleted.

Mildred Anashie (12:50:39) (in thread): > If you have other experiments to add you can just edit it > > Or ask the mentors to delete the one added by mistake

idiaru Angela (12:51:10) (in thread): > @Linda Uchenwokeif you have another experiment to add to the study you can simply edit it however if you don’t you can tag the mentors with a link of the experiment to be deleted

Linda Uchenwoke (12:53:08) (in thread): > Thank youu@Mildred Anashie@Aleru Divineand@idiaru Angela

Linda Uchenwoke (13:01:09) (in thread): > Hello@Chioma Onyido@Esther Afuape@Svetlana Ugarcina PerovicPlease delete the experiment 2 in this studyhttps://bugsigdb.org/Study_1066 - Attachment (BugSigDB): - BugSigDB > …

Precious Orakwe (13:20:25) (in thread): > Good Evening@Svetlana Ugarcina Perovictrust you are doing well. > > The most fun part is finding the problem and providing a solution to solving it, the less fun part is not knowing what and where to start curating from.

Svetlana Ugarcina Perovic (13:40:32) (in thread): > Deleted.

Linda Uchenwoke (14:10:17) (in thread): > Thank you!@Svetlana Ugarcina Perovic

Linda Uchenwoke (14:19:42): > Can more than 2 signatures be added to one study?

idiaru Angela (14:20:44) (in thread): > Are you asking more than one experiment @Linda@Linda Uchenwokenot signature?

Mildred Anashie (14:21:07) (in thread): > You can have only two signatures per experiment > > Both increased and decreased@Linda Uchenwokeif this s what you are asking about

Oluwatomisin Omojokun (14:21:58) (in thread): > Yes, you can have more than two experiment but not sure about signature

Linda Uchenwoke (14:27:07) (in thread): > I have numerous figures at various levels with various taxons, and I want to ensure that each relevant aspect is appropriately represented. What should I do?@idiaru Angela@Mildred Anashie@Oluwatomisin Omojokun

Mildred Anashie (14:28:11) (in thread): > You record only taxas that are said to be differentially abundant@Linda UchenwokeLook out for those

Linda Uchenwoke (14:29:51) (in thread): > All of the ones I want to record are differentially abudant@Mildred Anashie

idiaru Angela (14:29:54) (in thread): > Can you send the figures for proper clarification? The usual rule is if the figures contain the same contrast (I.e the same group 1 and 0) then they are combined into one experiment but if they contain different contrasts then you can simply separate that into 2 experiments or even more > To understand better you can look out for a reviewd study that has multiple experiments and study the curation . > Remember that relative abundance is not curated in BugSigDB

Linda Uchenwoke (14:30:28) (in thread): > Can I share link to my study@idiaru Angela?

idiaru Angela (14:30:38) (in thread): > Yes@Linda Uchenwoke

Linda Uchenwoke (14:32:10) (in thread): > https://bugsigdb.org/Study_1066@idiaru Angela - Attachment (BugSigDB): Alteration in gut mycobiota of patients with polycystic ovary syndrome - BugSigDB > Polycystic ovary syndrome (PCOS) is a serious disease characterized by high androgen, insulin resistance (IR), hyperglycemia, and obesity, leading to infertility.The gut mycobiota has been reported to evolve in metabolic diseases including obesity, hyperglycemia, and fatty liver.

Linda Uchenwoke (14:33:12) (in thread): > Seen?@idiaru Angela

idiaru Angela (14:33:38) (in thread): > Yes@Linda UchenwokeI’m going to look through the article now.

Linda Uchenwoke (14:34:12) (in thread): > Okay, Thank you. Will be waiting for your reply.

idiaru Angela (14:39:58) (in thread): > Deviating a bit from your original question I saw you stated the matched on as ethnic group but it actually appears to be age. See the excerpt from your article “In the current study, we recruited 17 PCOS patients and 17 age-matched healthy controls for community structure and functional analysis of the gut mycobiota.” > For your original question, it appears you’ll only have one experiment. FIG 3,4,5 show the differential abundance at the different taxa levels for the same contrast. So they are to be curated in the same experiment. All the increased taxa are curated in one signature and all decreased taxa are curated in signature 2@Linda Uchenwoke

UBNSEMS3S (14:40:49) (in thread): > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > * Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > * Fixing curation issues when possible. As presented on this page:https://bugsigdb.org/Help:Contents#TODO_for_reviewers > * The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > * Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > * The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline.Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project. - Attachment (BugSigDB): Help:Contents > …

Peace Daniel (14:42:17) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Victoria (Burah) Poromon (14:43:11) (in thread): > Thank you<@UBNSEMS3S>

Abiola Salako (14:43:31) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Druscilla Nakanwagi (14:43:49) (in thread): > Thank you<@UBNSEMS3S>

Iman Ngwepe-Ntshibida (14:45:39) (in thread): > Thank you for the clarity@C. Mirzayi (please do not tag this account)

Linda Uchenwoke (14:47:31) (in thread): > @idiaru AngelaThis was in the main article, age wan’t even mentioned. Should I still take out ethinic group? - File (PNG): Screenshot 2024-03-25 at 19.44.42.png

UBNSEMS3S (14:48:20) (in thread): > I see the source of the confusion. That’s not matching on ethnicity, that’s excluding everyone not of that ethnicity which is a bit different.

Linda Uchenwoke (14:49:20) (in thread): > All of them are of Chinese ancestry<@UBNSEMS3S>

UBNSEMS3S (14:49:34) (in thread): > Right. That’s not matching.

idiaru Angela (14:50:14) (in thread): > It was stated in the introduction part of your article@Linda Uchenwoke - File (JPEG): Screenshot_20240325_194942_Chrome.jpg

Mildred Anashie (14:50:32) (in thread): > @Linda UchenwokeI think you should curate Fig 7b instead > > You have just one experiment and it says that LEfSe was used to identify the taxas that were enriched > > And Yes they were matched on just age - File (PNG): IMG_2855

Linda Uchenwoke (14:53:34) (in thread): > @idiaru AngelaYes, I can see the age match which appeared when I added the pubID. Should I remove the ethnic group match?

Mildred Anashie (14:54:07) (in thread): > Yes replace the ethnic group with age

idiaru Angela (14:54:20) (in thread): > @Linda Uchenwoketo identify matched on factors it is usually stated clearly. You can simply use the search option on your pdf reader and search the word “match”. If the words matched on wasn’t used it isn’t matching.

Linda Uchenwoke (14:54:29) (in thread): > How please?<@UBNSEMS3S>

idiaru Angela (14:54:42) (in thread): > Yes@Linda Uchenwokeremove the ethnic group

idiaru Angela (14:55:23) (in thread): > Are you asking how to remove the ethnic group@Linda Uchenwoke?

Mildred Anashie (14:57:07) (in thread): > What<@UBNSEMS3S>is saying is that “Matched on” is different from exclusion and inclusion criteria > > It is usually clearly stated that the participants were matched on in your paper it says “age” > And whereit’snot stated you leave it blank(do not enter anything for “matched on”@Linda Uchenwoke

idiaru Angela (14:59:39) (in thread): > And yes@Linda Uchenwokefigure 7 looks easier to curate. It’s a combination of Fig 3,4,5.

Iman Ngwepe-Ntshibida (15:03:40): > Hey beautiful people, some help please…in the paper that i am given we have 4 groups, my problem is how they are grouped initially i thought of grouping like this AM together with the AM EVs and FE together with FE EVs, however the signatures(differential abundant) present in the additional file, table 8 seem to group these 4 differently.https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01694-9#MOESM1 - Attachment (BioMed Central): Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles - Microbiome > Background Reports regarding the presence of bacteria in the fetal environment remain limited and controversial. Recently, extracellular vesicles secreted by the human gut microbiota have emerged as a novel mechanism for host-microbiota interaction. We aimed to investigate the presence of bacterial extracellular vesicles in the fetal environment during healthy pregnancies and determine whether extracellular vesicles derived from the gut microbiota can cross biological barriers to reach the fetus. Results Bacterial extracellular vesicles were detectable in the amniotic fluid of healthy pregnant women, exhibiting similarities to extracellular vesicles found in the maternal gut microbiota. In pregnant mice, extracellular vesicles derived from human maternal gut microbiota were found to reach the intra-amniotic space. Conclusions Our findings reveal maternal microbiota-derived extracellular vesicles as an interaction mechanism between the maternal microbiota and fetus, potentially playing a pivotal role in priming the prenatal immune system for gut colonization after birth. Video Abstract

Linda Uchenwoke (15:05:38) (in thread): > Thank you so much:orange_heart:@idiaru Angela@Mildred Anashieand<@UBNSEMS3S>

Mildred Anashie (15:10:45) (in thread): > Hi@Iman Ngwepe-NtshibidaI think you have about 6 experiments but significant signatures for just 4:thinking_face: - File (JPEG): IMG_2857 - File (JPEG): IMG_2856

Linda Uchenwoke (15:11:13) (in thread): > Is my statistical test correct?@idiaru Angela@Mildred Anashie

Mildred Anashie (15:12:45) (in thread): > I think it is LEfSe@Linda UchenwokeJudging from the Fig 7 and the highlighted text in image attached here - File (PNG): IMG_2855

idiaru Angela (15:16:57) (in thread): > Actually@Linda Uchenwokethere’s a difference between Fig 3,4,5 and figure 7. The difference is the fact that they were gotten using 2 different statistical tests. So you’re not wrong in your original curation. I think this highlight from the curation policy should guide you on how to g about curating the signatures - File (JPEG): Screenshot_20240325_201404_Chrome.jpg

Aleru Divine (15:19:37) (in thread): > @Iman Ngwepe-NtshibidaI agree with@Mildred Anashie, although you have 4 groups, there was a pairwise comparison according to table 6.Soyou’llcurate 6 experiments.Amongst these 6 experiments, only 4 showed significant differences in the taxa.That is why you have table 8 giving differential abundance for only 4 comparisons.Excluding AM vs FE_EV and > AM_EV vs FE

Mildred Anashie (15:20:35) (in thread): > @Iman Ngwepe-NtshibidaI hope@Aleru Divineexplanation is clear

Iman Ngwepe-Ntshibida (15:24:00) (in thread): > @Mildred Anashieyes I get@Aleru Divineexplanation. In that case I guess some experiments won’t have signatures ? Because we can’t use the rel.abundance ?

Mildred Anashie (15:24:48) (in thread): > Yes the ones that differential abundance wasn’t reported for won’t have signatures@Iman Ngwepe-Ntshibida

Barakat Akinsiku (15:25:03) (in thread): > Yes@Iman Ngwepe-Ntshibidalike Mildred and Aleru explained you’ll have 6 experiments out of which two will have no signatures

Aleru Divine (15:25:46) (in thread): > That’scorrect@Iman Ngwepe-Ntshibida

Linda Uchenwoke (15:26:36) (in thread): > Could you please provide a clearer explanation? I didn’t fully understand your conclusion.@idiaru Angela

Iman Ngwepe-Ntshibida (15:26:52) (in thread): > @Aleru Divine@Mildred Anashie@Barakat AkinsikuI appreciate your help, many thanks.:slightly_smiling_face:

Linda Uchenwoke (15:32:30) (in thread): > @Chioma Onyido@Esther Afuape@Aleru DivinePlease look at my curation’s statistical test.

idiaru Angela (15:33:19) (in thread): > @Linda Uchenwokefrom your article, 2 different tests for differential abundance were carried out the Mann Whitney and the Lefse test. Following the curation policy in this kind of situation if they are largely overlapping (which they are in this case) use the test that has the larger number of signatures. > Did I manage to answer your question?:sweat_smile:

idiaru Angela (15:35:07) (in thread): > The results from the Mann Whitney are in figure 3,4,5 while those from Lefse are in figure 7

Scholastica Urua (15:40:11): > Hello everyone, please I need some help reviewing this curation I and@Muqtadirat Yussuffare working on;https://bugsigdb.org/Study_974.:pray:I’m looking forward to your feedback…:hugging_face: - Attachment (BugSigDB): The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer - BugSigDB > Microbiota can influence the occurrence, development, and therapeutic response of a wide variety of cancer types by modulating immune responses to tumors.Recent studies have demonstrated the existence of intratumor bacteria inside ovarian cancer (OV).

Mildred Anashie (15:40:44) (in thread): > @Aleru Divinewhat do you think about the statistical test for this study > > I think 3,4 and 5 is showing Fecal microbial community composition > > Angela and I seem to have different views, I’d really like another opinion on thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711391530277689?thread_ts=1711390782.792099&channel=C04RATV9VCY&message_ts=1711391530.277689 - Attachment: Attachment > https://bugsigdb.org/Study_1066 @idiaru Angela

Scholastica Urua (15:42:46) (in thread): > Also, please what’s your take on the Sequencing type and Sequencing platform?:thinking_face:

Svetlana Ugarcina Perovic (15:47:16) (in thread): > @Sidra Khanhere is answer to your question

Aleru Divine (15:48:52) (in thread): > @Linda Uchenwokeyou kinda had 2 different tests > > LEfSe and Mann-Whitney > LDA > 4 > > I’d say LEfSe was the test because the paper states explicitly that it was used to identify the different taxa enriched in each group,

Scholastica Urua (15:48:55) (in thread): > Thank you<@UBNSEMS3S>

Mildred Anashie (15:49:21) (in thread): > I’ll check this out soon@Scholastica Urua

Aleru Divine (15:49:25) (in thread): > @Mildred AnashieI was looking at it andhere’swhat I think:face_with_open_eyes_and_hand_over_mouth::point_up:

idiaru Angela (15:49:52) (in thread): > @Scholastica Uruathe sequencing platform appears to be Illumina > “ILLUMINACLIP:TruSeq2-PE.fa:2:30:10 SLIDINGWINDOW:4:20 MINLEN:35. By using Kraken2”

Aleru Divine (15:51:35) (in thread): > That’scorrect@Mildred AnashieMann-Whitney identified the microbial composition and LEfSe identified their differential abundance.

Scholastica Urua (15:53:47) (in thread): > Thank you so much@idiaru Angela:hugging_face:This is helpfull

Linda Uchenwoke (15:57:49) (in thread): > Lefse highlights the most mentioned taxas(the ones in the keywords) while Mann Whitney has 3,4 and 5. They are almost on the same scale so I don’t know which to prioritise.@Aleru Divine

Aleru Divine (15:58:33) (in thread): > Well done@Scholastica Urua

Aleru Divine (15:59:33) (in thread): > It’sLEfSe in this case@Linda UchenwokeMann-Whitney identified the microbial composition and LEfSe identified their differential abundance.

idiaru Angela (16:05:58) (in thread): > I still disagree@Aleru Divine. The statement I highlighted describes the relative abundance between the two groups and not just microbial composition - File (JPEG): Screenshot_20240325_210401_Chrome.jpg

idiaru Angela (16:06:32) (in thread): > Though I do agree you should curate the results from Lefse. It appears to have more signifant taxa.@Linda Uchenwoke

Linda Uchenwoke (16:07:50) (in thread): > @Chioma Onyido@Esther Afuape@Svetlana Ugarcina PerovicPlease help me out:pray:

idiaru Angela (16:08:21) (in thread): > Some taxa do appear to be different in the two tests though if I look at it more closely. I’d advice you call the attention to the mentors to get a solid confirmation

Scholastica Urua (16:08:34) (in thread): > Thank you@Aleru Divine

Aleru Divine (16:09:47) (in thread): > They talked about Mann-Whitney a lot up there and then just below, they stated that > > “To identify the different taxa enriched in each group, linear discriminant analysis (LDA) effect size (LEfSe) was performed [LDA score (log 10) >4].” > > That makes me think LEfSe was used for the differential abundance testing and not Mann-W.

idiaru Angela (16:11:18) (in thread): > But we know that 2 statistical tests can be used. The use of one test doesn’t automatically disqualify the use of the other@Aleru Divine

Aleru Divine (16:11:50) (in thread): > Correct:white_check_mark:

Mildred Anashie (16:16:10) (in thread): > Well done@Scholastica Uruaand@Muqtadirat YussuffThe sequencing platform appears to be Illimina while the type should be left blank in my opinion because they mentioned that the limitation to the study was that they didn’t verify their results using WMS or PCR and there was no mention of 16s either - File (JPEG): IMG_2860

Scholastica Urua (16:19:57) (in thread): > I thought so too but needed a second opinion. Thank you so much for your help as always@Mildred Anashie. This is really helpful.:pray:What do you think about the rest of the curation?

Chioma Onyido (16:28:52) (in thread): > Everybody’s answer is reasonable.:white_check_mark:Sometimes researchers conduct different statistical test for significant taxa because they want to compare the taxa between the statistical tests used. > In cases where the statistical test produces completely different results, then both can be curated in bugsigdb as different experiments (see curation policy), > But in cases where the statistical test produces overlapping results, then the stat test that reports the larger number of taxa should be reported (again, curation policy) > > Now I would’ve gone with Mann-Whitney results because they reported taxa on the phylum, family and genus level, in fact with about 30 genera. But after taking a closer look, I confirmed that only 2 were significant (those with asterisks *), so I moved to Lefse (figure 7). > > I looked at Lefse and confirmed that all the significant taxa identified in Mann-Whitney were shown in the Lefse results (and more)! With the family, phylum and genus level clearly showing. > SoI’mgoing with only Lefse.:white_check_mark:

Chioma Onyido (16:31:18) (in thread): > Bottomline: I know it’s stated that we only curate differential abundance on bugsigdb but in some cases (like fig 3b, 4b and 5b), these relative abundance figures clearly shows the significant differences between the groups, not just the taxa each group contains (as seen in 3a, 4a and 5a).Mann-Whitney results (Fig 3b, 4b and 5b) are curatable) but since they overlap significantly with the Lefse results which has larger signatures, I would curate just Lefse to avoid redundancy. > I hope this helps. Great team work here honestly!:clap:

Mildred Anashie (16:32:58) (in thread): > Thank you so much@Chioma OnyidoI really appreciate your explanations and clarification on this:pray::hugging_face:

idiaru Angela (16:33:38) (in thread): > Thank you@Chioma Onyidoyou really always come through with the detailed explanations:heart_hands:

Aleru Divine (16:34:34) (in thread): > Thank you for the clear explanation@Chioma Onyidoyou rock!:heart_hands:

Linda Uchenwoke (16:35:30) (in thread): > Thank you for the detailed explanation@Chioma OnyidoI really appreciate:orange_heart:

Abiola Salako (16:49:57) (in thread): > Well done@Scholastica Uruaand@Muqtadirat Yussuff

Mildred Anashie (16:58:03) (in thread): > I think the curation is nicely done > > Well done again@Scholastica Urua@Muqtadirat Yussuff:clap:

Scholastica Urua (16:59:30) (in thread): > Thank you@Mildred Anashiefor taking the time to review our curation:orange_heart:

Mkpouto Shedrack (17:00:29) (in thread): > Went through it and it’s nicely done

Ruth Bamgbose (17:04:04) (in thread): > Thank you<@UBNSEMS3S>

Adenike Oladimeji-Kasumu (17:04:38) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Chioma Onyido (17:39:25) (in thread): > You’rewelcome!

Ruth Bamgbose (17:43:28): > Hello everyone, please I need some help finding the condition for this curation. > > So the study is focused on ‘To generate hypotheses on how changes to the gut microbiota by iron adversely affect development, and to determine whether the form of iron influences microbiota outcomes’ , > > so I selected ‘Abnormality of iron homeostasis’ as condition since I understood that iron homeostasis is the control of iron balance, transport and storage in the body, and abnormality will include changes in this. And Since the study pertains to changes induced by different forms of iron supplementation,and the levels which they affect the gut microbiota and metabolism, > I feel this is the best option.https://bugsigdb.org/Study_999What do you think? - Attachment (BugSigDB): Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood - BugSigDB > The gut microbiota is implicated in the adverse developmental outcomes of postnatal iron supplementation.

Scholastica Urua (17:57:48) (in thread): > I think ‘Abnormality of iron homeostasis’ is a close enough term in my opinion.@Ruth Bamgbose

Abiola Salako (18:00:01) (in thread): > @Ruth BamgboseI agree with what@Scholastica Uruasaid.

idiaru Angela (18:24:07) (in thread): > Searched a bit but I don’t think I saw a closer term@Ruth Bamgbose:thinking_face:

Peace Daniel (18:27:31): > Hello everyone > > From this statement “Although a previous publication from our group shows that granzyme B-deficient CD4+ T cells are partially responsible for this phenotype, in this report we present data demonstrating that the microbiota, in particular members of the order Turicibacterales, have an important role in conferring resistance. Mice deficient in Turicibacter sanguinis have increased susceptibility to severe disease. However, when these mice are co-housed with resistant mice, or colonized with T. sanguinis, susceptibility to severe infection is reduced. “Can I conclude turicibacterales is the same as turicibacter sanguinis?Link to the full articlehttps://pubmed.ncbi.nlm.nih.gov/37163036/ - Attachment (PubMed): Turicibacterales protect mice from severe Citrobacter rodentium infection - PubMed

idiaru Angela (18:30:31) (in thread): > While Turicibacterales is an order T. Sanguinis is a species. They aren’t the same as they don’t have the same rank

Mildred Anashie (18:30:39) (in thread): > I’mnot sure you should conclude because Turicibacter sanguinis is a specific type of bacteria within the broader classification of Turicibacterales.@Peace Daniel

Peace Daniel (18:36:04) (in thread): > Okay@idiaru Angela@Mildred Anashie

Nitya Singhal (22:32:30) (in thread): > Hey@Scholastica Urua, I believe the sequencing platforms are RT-qPCR and Illumina. Also, the sequencing type is WMS( whole metagenome sequencing). Attached are the supporting screenshots. Hope, it helps.:heart: - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Nitya Singhal (22:44:45) (in thread): > Hey@Iman Ngwepe-Ntshibida, sorry for late response but yes I completely agree with@Aleru Divineand@Mildred AnashieEarlier it seemed that there are 4 groups but when I went through supplementary tables, it was clearly mentioned that 6 groups are there.

Nitya Singhal (22:46:54): > Hey@Svetlana Ugarcina PerovicKindly delete the following signatures- > sig 1 and 2 of exp 1 > sig 1 and 2 of exp 3https://bugsigdb.org/Study_1016 - Attachment (BugSigDB): Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer - BugSigDB > BACKGROUND: Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis.

Nitya Singhal (22:48:38): > Please review my curation. > I have made the changes you suggested me@Aleru Divine(Svetlana ma’am will delete the signatures 1 and 2 of exp 1 and 3 so ignore them)https://bugsigdb.org/Study_1016 - Attachment (BugSigDB): Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer - BugSigDB > BACKGROUND: Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis.

Nitya Singhal (22:49:14): > Also, if anyone wants my assistance in reviewing their paper then I am absolutely free.

Nitya Singhal (23:34:07) (in thread): > @Chioma Onyido@Peace Sandy<@UBNSEMS3S>

2024-03-26

Aleru Divine (01:01:10) (in thread): > Hi@Nitya Singhal, good morning.I’llcheck this one more time.

Nitya Singhal (01:13:04) (in thread): > good morning@Aleru Divine:blush:

Ruth Bamgbose (01:37:59) (in thread): > Alright , thank you all@Scholastica Urua@Abiola Salako@idiaru Angela

Barakat Akinsiku (02:38:29): > Good morning BugSigDBiers, hope we’re all keeping well today? Wishing everyone a bright and glorious day!:sparkles::sparkles:

Nitya Singhal (02:39:41) (in thread): > Good morning@Barakat AkinsikuHave a great day ahead.

idiaru Angela (02:40:19) (in thread): > Hey@Nitya Singhalwould also go through and give feedback

Joan C. Chukwuemeka (02:40:38) (in thread): > Good morning to you too@Barakat Akinsiku

Chioma Onyido (02:41:41) (in thread): > Deleted.

Nitya Singhal (02:43:07) (in thread): > Hey,@Chioma OnyidoCan’t signatures 3 and 4 be named as 1 and 2?

Peace Daniel (02:47:18) (in thread): > Good morning, I feel excited about it:woman-cartwheeling:

Nitya Singhal (02:47:50) (in thread): > Sure@idiaru AngelaI would love that:smile:

Nitya Singhal (02:52:35): > Good morning,@Svetlana Ugarcina Perovicma’am. I wanted to know something about recording the contribution on Outreachy. We have to describe our contribution, so I wanted to know what would be expected from us in that description. I am not sure if I shall explain what I learnt from the curation or what it was about.

Barakat Akinsiku (03:03:49) (in thread): > Hi@Nitya SinghalI think you can just describe what your contribution was about ie the name of the study and the curation steps you took

Ima-obong (Aimah) (03:17:49) (in thread): > @Nitya SinghalI agree with@Barakat Akinsiku, input the name of the study and how you curated it.

Ima-obong (Aimah) (03:18:21) (in thread): > Hello.. wishing you an awesome day too

Mildred Anashie (03:19:34) (in thread): > Hello@Barakat AkinsikuDoing quite well, Thank you:heart_hands:

Ima-obong (Aimah) (03:20:24) (in thread): > Though I also I get confused about what link to submit…is it the link to the GitHub issue or the actual bugsigdb study link?

Peace Daniel (03:25:52) (in thread): > Hello@Amanda Adoyihaven’tbeen seeing from you in awhile:wave:

Scholastica Urua (03:38:06) (in thread): > Hello@Barakat Akinsikudoing quite well. Hope you’re doing well yourself?

Linda Uchenwoke (03:40:47) (in thread): > @Chioma OnyidoGood morning. Since I’m using LEFse as my test. should i take out the 0.05 signifinance threshold i recorded for the Mann-Whitney results?

Scholastica Urua (03:41:17) (in thread): > @Ima-obong (Aimah)We are to submit the link to the curation itself. Something like this;https://bugsigdb.org/Study_—

Ima-obong (Aimah) (03:46:25) (in thread): > Thanks@Scholastica Urua

Abiola Salako (03:47:51) (in thread): > Thank you@Barakat Akinsiku

Rahila-me (04:04:36): > Hello@Svetlana Ugarcina PerovicGood morning, i just wanted to ask is it that some of us will not have one curation reviewed even if it is the first one so we could record a merge date on the outreachy website? just a concerned fellow wandering

Barakat Akinsiku (04:08:03) (in thread): > Hi@Ima-obong (Aimah)yes, Scholastica’s right

Linda Uchenwoke (04:20:08) (in thread): > @Aleru DivineWhat do you think?

Aleru Divine (04:26:35) (in thread): > @Linda Uchenwoketheydidn’treally state the threshold for LEfSe.But I’d go with 0.05 since it was the one mentioned
> > Also<@UBNSEMS3S>said thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1705071980989609?thread_ts=1705067917.442009&cid=C04RATV9VCY - Attachment: Attachment > If they don’t state a p-value threshold, then we can assume it’s .05.

Svetlana Ugarcina Perovic (04:27:49) (in thread): > No worries at all if it’s not reviewed. It’s important only to claim it for review i.e. to get the tag “needs review”.

Linda Uchenwoke (04:44:37) (in thread): > I’ll leave it at 0.05 then. Thank you so much,@Aleru Divine! Also, if this isn’t too much to ask, could you take a glance at my work before I submit it?

Rahila-me (04:45:09) (in thread): > okey, my has that tag. just wanted to put my merge date if i see my score

Aleru Divine (04:46:48) (in thread): > Sure thing,:blush:I am currently reviewing a study. I will review yours as soon as I am done with this and get back to you.:hugging_face:

Linda Uchenwoke (04:49:36) (in thread): > Alright, I’ll be waiting. Thank you:hugging_face:

idiaru Angela (05:31:04) (in thread): > @Nitya Singhalsee this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710324730127549?thread_ts=1710311151.944309&cid=C04RATV9VCY - Attachment: Attachment > This is because page history is an important part of the wiki, and renaming a page would make it complicated to represent that history. Also note that deleted pages are not truly gone, if you navigate to that page in the future, you will still see links to the deleted material.

Victoria (Burah) Poromon (06:18:00) (in thread): > Hi@Rahila-meI think your merged date can be the day “needs review” tag was added on your GitHub issue. Since ithasn’tbeen reviewed yet.

Rahila-me (06:33:35) (in thread): > @Victoria (Burah) Poromonthanks

Nitya Singhal (06:38:45) (in thread): > Hey@Aleru Divine@idiaru Angeladid you review the curation?

Praise Agbetuyi (06:39:31) (in thread): > @Barakat AkinsikuThank you and I wish you the same

idiaru Angela (06:45:13) (in thread): > Hey@Nitya Singhalstill on it. Would get back to you in 2 hours

Nitya Singhal (06:55:37): > Hey, if anyone wants my assistance in reviewing their paper then I am available.

Svetlana Ugarcina Perovic (07:10:28): > Hello everyone, hope you are doing well. > > Just wanted to reassure you to not worry (or contact us) aboutpending reviews: We are working diligently to get you all feedback, with our corrections if needed. > > We appreciate your patience as we continue to review. We have been overwhelmed by the amount of interest we’ve had and the productivity of all of you. You are all truly amazing and, once we have to make a decision, it is going to be incredibly difficult, but we will ensure that you are all considered fairly!<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic

Mildred Anashie (07:33:12) (in thread): > Hi@Nitya Singhalcan you help me review this?https://bugsigdb.org/Study_1060Still curating though due to the number of experiments - Attachment (BugSigDB): Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe - BugSigDB > BACKGROUND: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood.

Nitya Singhal (07:35:40) (in thread): > yeah sure@Mildred Anashie

Nitya Singhal (07:36:06) (in thread): > give me some time. I’ll get back to you:blush::heart:

Chioma Onyido (07:36:31) (in thread): > This message is for anyone not sure about whichmerge date to enter when recording contributions on Outreachy. > > Pending when your curation will be reviewed and graded by the mentors, ifyou’renot sure what merge date to enterwhen you’refilling out your contribution on Outreachy, you can enter the date when the “needs review” label was attached to your study on GitHub. > I thinkthat’llfly for now@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape<@UBNSEMS3S>See thread for ref…https://community-bioc.slack.com/archives/C04RATV9VCY/p1711448280247749?thread_ts=1711440276.544779&channel=C04RATV9VCY&message_ts=1711448280.247749

Mildred Anashie (07:38:17) (in thread): > Thank you so much@Svetlana Ugarcina Perovicand@Chioma Onyido:hugging_face:

Oluwatomisin Omojokun (07:42:54) (in thread): > @Svetlana Ugarcina Perovic, Thank you for much for all you do during this contribution stage.

Mildred Anashie (07:44:05): > Hello everyone > > Hi@Chioma Onyido@Esther Afuape@Peace SandyI’m currently curating this studyhttps://bugsigdb.org/Study_1060The paper is a population based study, the participants were divided into population and subsistence methods/patterns > > They’re results for all the comparisons done in the supplemental tables 4,5,6 and 7. > > My issue is in identifying the appropriate condition for the experiments done on subsistence methods (I used socioeconomic status, is there something that can properly replace this)? > > For the experiments done on population,Hope I am right to use “Population” as the condition. > > Also anyone willing to help me review this, especially the location and the Group 1 description for the experiments:pray:This is also me giving shoutout to@Aleru Divinefor the curation she did that had about 45 experiments:raised_hands::raised_hands:this is not up to that but……:joy::laughing: - Attachment (BugSigDB): Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe - BugSigDB > BACKGROUND: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood.

Mildred Anashie (07:44:25) (in thread): > Sure > Thank you:pray:

Abiola Salako (07:44:32) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@Chioma Onyido

Peace Daniel (07:45:58) (in thread): > I’d take a look at the location and description for you

Adenike Oladimeji-Kasumu (07:46:18) (in thread): > Thank you@Svetlana Ugarcina Perovicand@Chioma Onyidofor this information and for your support as well:hugging_face:

Mildred Anashie (07:46:45) (in thread): > Thank you@Peace Daniel

Peace Daniel (07:47:40) (in thread): > Wow these are a lot, well done@Mildred Anashie@Aleru Divine

idiaru Angela (07:48:23) (in thread): > Hey@Nitya Singhalwell done on the curation good job. > I noticed that for experiment 1, you didn’t add the significance threshold but it can be found in the description for Fig 1. And the source for Experiment 1 signatures are actually Fig 1G not F > 2. For Experiment 5 the significance threshold is also supposed to be 0.05 not 0.006. Got this from the description of the figure > 3. For the description of your signature sources, I noticed you kept using the term relative abundance. I think its best to use differential abundance as that’s what you curated. > Those are my observations for now. I’ll go over it again later for another perspective:slightly_smiling_face:

Oluwatomisin Omojokun (07:49:02) (in thread): > The study i am also curating has a lot of experiment for curation. Welldone@Mildred Anashie@Aleru Divine

Joan C. Chukwuemeka (07:49:19) (in thread): > nice one@Aleru Divine.

idiaru Angela (07:50:34) (in thread): > Well done@Mildred Anashie

Nitya Singhal (07:50:51) (in thread): > 1G is for p-values and not differential abundance so I guess 1F has to be the source. Please tell me if I am wrong:sweat_smile:

Scholastica Urua (07:53:16) (in thread): > Well done@Mildred Anashie

idiaru Angela (07:53:32) (in thread): > Sorry@Nitya Singhal1F is the correct source

Aleru Divine (07:59:59) (in thread): > Oh I feel ya@Mildred AnashieWell done:raised_hands::heart_hands:@Bolanle Wahabknock knock:face_holding_back_tears:We have another sister study:face_with_peeking_eye:

Bolanle Wahab (08:05:43) (in thread): > @Aleru Divine:joy::joy:Welcome to the club@Mildred Anashie, weldone:clap::clap:

Mildred Anashie (08:10:36) (in thread): > Now I knowthere’smore like this:joy:Please guys I need help with the condition, location and Group description > > Thank you:pray:

Joan C. Chukwuemeka (08:12:01) (in thread): > okay@Mildred Anashie, taking a look

Joan C. Chukwuemeka (08:14:14) (in thread): > @Mildred AnashieI think condition should beoral microbiome measurementEFO:0801229 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Praise Agbetuyi (08:17:33): > Hello everyone, I hope your day is going as planned. Can I choose Illumina as the platform for sequencing if the one mentioned in my paper is HiSeq since it is developed and manufactured by Illumina?

Joan C. Chukwuemeka (08:18:08) (in thread): > @Mildred Anashiesee snapshots of excerpts from the paper - File (PNG): image.png - File (PNG): image.png

Mildred Anashie (08:19:03) (in thread): > Thank you so much@Joan C. Chukwuemeka:pray:This is really helpful I was sure the condition I usedwasn’tright

Joan C. Chukwuemeka (08:19:29) (in thread): > @Praise Agbetuyican you share the study link please?

Joan C. Chukwuemeka (08:20:28) (in thread): > You’re welcome@Mildred AnashieGlad to help

Aleru Divine (08:23:46) (in thread): > Hi@Nitya Singhalyou did a great job on this:hugging_face:I just have two a tiny addition to what@idiaru Angelahad pointed out. > 1. for signature 2 in experiment 5, you used figure 5E. Idon’tthink that is curatable as it is the relative abundances of the families. > 2. I found the taxonomy ID’s for both“ Leptotrichaceae” and “Lactobacillaceae” so you will replace them so they will no longer be highlighted as red. > For Leptotrichaceae the ID is 1129771 > For Lactobacillaceae the ID is 33958 > > You can confirm here and use this link for future searches.https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=33958&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (08:23:53) (in thread): > @Joan C. ChukwuemekaSaliva samples were gotten from Angola and Zimbabwe populations and the study was conducted and published in Portugal from what I read > > I’m thinking I should have used Angola and Zimbabwe instead of Portugal > > This is the help I need for the location

Precious Orakwe (08:24:47): > Good day@Svetlana Ugarcina Perovic, i want to start my final application, please is there any project time line for the internship

idiaru Angela (08:25:28) (in thread): > I think Angola and Zimbabwe should be used@Mildred Anashiefrom the curation policy, the location is where the participants were recruited from.

Ruth Bamgbose (08:25:59) (in thread): > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Praise Agbetuyi (08:26:27): > Hey guys, I noticed something helpful while curating. Reading the paper online on the original site is much easier than going through the downloaded version. > I had trouble finding details in the downloaded copy, but the online version made it almost instant and even revealed more information. Also, when working on a downloaded paper, you can use the search function to help narrow down your search. > > Just thought I’d share these tips with you all! Hope your evening is going well. Just wanted to say hi:blush::orange_heart:

Peace Daniel (08:27:04) (in thread): > Yes you should use Angola and Zimbabwe, I just read that the saliva samples was collected in both Angola and Zimbabwe respectively

Praise Agbetuyi (08:27:16) (in thread): > https://bugsigdb.org/Study_1071 - Attachment (BugSigDB): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BugSigDB > Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life.The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies.

Joan C. Chukwuemeka (08:29:01) (in thread): > For location, the sampled ethnic groups from southwestern Angola and Zimbabwe, so the location of each experiment, should be where the ethnic group being compared is located. > > for example: Experiment one will be Angola, if both ethnic groups are from Angola. > However, if they made comparison between an ethnic group in Angola and one in Zimbabwe, then both location will be inputted for that specific experiment. you can actually use more that one location. > > PS: That’s quite a curation you have there, Well done - File (PNG): image.png

NWAKAEGO VINCENT (08:30:14): > hello everyone , I am done curating this paper and will appreciate your reviewhttps://bugsigdb.org/Study_1056 - Attachment (BugSigDB): Comparison of fecal and oral collection methods for studies of the human microbiota in two Iranian cohorts - BugSigDB > BACKGROUND: To initiate fecal and oral collections in prospective cohort studies for microbial analyses, it is essential to understand how field conditions and geographic differences may impact microbial communities.

Precious Orakwe (08:31:36) (in thread): > thanks@Ruth Bamgbose

Nitya Singhal (08:31:51) (in thread): > Hey, so shall I delete signature 2 of exp 5?@Aleru Divine

Mildred Anashie (08:32:12) (in thread): > I get@Joan C. Chukwuemekabut they mixed the comparisons > Comparing both Angola and Zimbabwe populations and only one population is from Zimbabwe > > Let me explain better > The group that is Zimbabwe is Tshwa and it was compared with almost all the Angola populations > > See Supplemental Table 4 and 5

Peace Daniel (08:32:23) (in thread): > I feel downloading the paper is much more easier (different strokes for different people)because I can easily highlight documents with different colors and also add notes to it, you can also search keywords quickly. > > Whichever helps get the work done tho:clap::purple_heart:

Aleru Divine (08:32:24) (in thread): > Yes@Praise AgbetuyiI thinkit’sIllumina.Illumina has both MiSeq and HiSeq.

idiaru Angela (08:32:25) (in thread): > Hey@NWAKAEGO VINCENTwill review and give you feedback. Well done

Joan C. Chukwuemeka (08:32:37) (in thread): > For group description, if its not available in the paper, I think you could do google search about them. > My current curation did a comparison on social groups of macaques, without plain info on them, so researched it online and got the info.

Joan C. Chukwuemeka (08:33:04) (in thread): > you can input both location then@Mildred Anashie

Praise Agbetuyi (08:34:03) (in thread): > Awesome,@NWAKAEGO VINCENT. Well done

Peace Daniel (08:34:28) (in thread): > What@Joan C. Chukwuemekasays is reasonable Anashie

Joan C. Chukwuemeka (08:34:30) (in thread): > Thanks a lot<@UBNSEMS3S>

Aleru Divine (08:34:35) (in thread): > Yeah I think it’s okay to delete it. > > Figure 5f didn’t identify any for NR

Praise Agbetuyi (08:34:43) (in thread): > Okay. Thank you@Joan C. Chukwuemekaand@Aleru Divine

Svetlana Ugarcina Perovic (08:34:48) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711361929093659 - Attachment: Attachment > Reminder: > If the GitHub issue with your curated paper is with tag “needs review” that means now it’s in our hands under review and you are kindly asked to not make any changes while we are reviewing it.

Scholastica Urua (08:35:22) (in thread): > Nice observations@Joan C. Chukwuemeka:+1:

Mildred Anashie (08:35:37) (in thread): > Yea I searched and what I have for group description is browsed and combined with the little information in the paper > > Thank you so much@Joan C. Chukwuemeka@Peace Daniel@idiaru Angela

Svetlana Ugarcina Perovic (08:36:07) (in thread): > @NWAKAEGO VINCENTyou just claimed it to us for review.Please do not edit anything more, while it is under review by our team.

Peace Daniel (08:36:56) (in thread): > The description for group 1 looks fine to me as well@Mildred AnashieWell done:thumbsup:

Svetlana Ugarcina Perovic (08:37:15) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/325 - File (PNG): Screenshot 2024-03-26 at 13.37.02.png

Joan C. Chukwuemeka (08:38:36) (in thread): > Yes, It’s Illumina

idiaru Angela (08:38:53) (in thread): > Oh you were right:sweat_smile:. Just signature 2

Precious Orakwe (08:39:48) (in thread): > well done@NWAKAEGO VINCENT

Svetlana Ugarcina Perovic (08:40:53) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710419862129939 - Attachment: Attachment > IMPORTANT: when the GitHub issue with your curation is claimed for review and got a label “needs review” any edits from this point are not allowed.

Nitya Singhal (08:42:28): > @Svetlana Ugarcina PerovicI just want u to delete 2nd signature of experiment 5. My friends told me that 2nd signature is not necessary. Could you delete it? > > I just got to know about no changes after “needs review”@Peace Sandy@Chioma Onyidohttps://bugsigdb.org/Study_1016 - Attachment (BugSigDB): Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer - BugSigDB > BACKGROUND: Oral squamous cell carcinoma (SCC) is associated with oral microbial dysbiosis.

Svetlana Ugarcina Perovic (08:43:29) (in thread): > Your curation is under reviewhttps://github.com/waldronlab/BugSigDBcuration/issues/307Please see the message above. - Attachment: #307 Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer > Salivary microbiome changes distinguish response to chemoradiotherapy in patients with oral cancer – Marcell Costa de Medeiros – Microbiome
> https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01677-w

Praise Agbetuyi (08:43:43) (in thread): > Yeah,@Peace Daniel, thanks for sharing your perspective! Everyone indeed has their preferred way of working, and identifying the approach that suits us best and helps us get the work done efficiently is essential. Happy curating!:blush::orange_heart:

Nitya Singhal (08:45:17) (in thread): > I apologise for the same but I wasn’t aware about this “no changes after marked as needs review”@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (08:50:46): > Hello everyone and mentors@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma OnyidoI need clarity please. > On the ‘Record contribution’ site, my second contribution appears as Contribution #1 and my first contribution (the general questionnaire) appears as Contribution #2. > I hope this would not affect my final application.

Svetlana Ugarcina Perovic (08:52:21) (in thread): > This is not a problem.

Adenike Oladimeji-Kasumu (08:52:54) (in thread): > Alright then. Thank you@Svetlana Ugarcina Perovicfor the clarification.

Aleru Divine (08:54:08) (in thread): > Thank you@Svetlana Ugarcina PerovicI must say, I was a bit concerned.

Aleru Divine (08:56:45) (in thread): > Thank you so much@Svetlana Ugarcina Perovicand@Chioma Onyido:blush:

Bolanle Wahab (08:57:56) (in thread): > I noticed this too > Thanks@Adenike Oladimeji-Kasumufor bringing it up and@Svetlana Ugarcina Perovicfor clarifying

Scholastica Urua (09:03:29) (in thread): > I noticed it too@Adenike Oladimeji-Kasumu. Thanks for asking

Aleru Divine (09:14:49) (in thread): > Hi@Linda Uchenwokewell done on your curation. You did a really great job:blush:For your signatures, I noticed you only curated the genus.I understand the description is “Different microbial genera were identified by LEfSe” but I think genera in this case refers to the taxonomic hierarchy in general and that comprises of all the hierarchy present. SoI’dsuggest you curate all.Also, consider the ones identified by the cladogram.

Nitya Singhal (09:15:39) (in thread): > Sincere apologies and kind request@Svetlana Ugarcina Perovicma’am

Blessing Ene Anyebe (09:22:07) (in thread): > Thank you@Adenike Oladimeji-Kasumu:orange_heart:

Aleru Divine (09:24:22) (in thread): > Forgive me@Adenike Oladimeji-Kasumuthank you for asking this:heart:

Bolanle Wahab (09:57:04): > Hi everyone@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Chioma Onyido@Esther AfuapeI have asked this question before and someone pointed me to a thread where@Chioma Onyidosaid ifthere’sno actual body site for host specie,itshouldn’tbe curated. > In this case, they experimented on Sewage andthereare differential Abundance results too, should I curate it without host specie and body site or leave it? > Thank you.

Amanda Adoyi (09:59:52) (in thread): > @Peace DanielI’m good and around:slightly_smiling_face:Thanksss

Scholastica Urua (10:00:26) (in thread): > @Bolanle Wahabdo you think this could work for the body site you are refering to?https://www.ebi.ac.uk/ols4/ontologies/envo/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FENVO_00002018 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Joan C. Chukwuemeka (10:00:43) (in thread): > @Bolanle Wahabwhat’s the study link?

Bolanle Wahab (10:03:10) (in thread): > @Scholastica UruaI don’t think so,it’sactually a study observing storage conditions of biological specimen and pig feces and sewage were used for the experiments

Bolanle Wahab (10:03:25) (in thread): > @Joan C. Chukwuemekahttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8510183/ - Attachment (PubMed Central (PMC)): Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns > Storage of biological specimens is crucial in the life and medical sciences. Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses. …

Scholastica Urua (10:05:51) (in thread): > Okay@Bolanle Wahablet me check out the article

Chioma Onyido (10:14:04) (in thread): > Uhm…Genera is plural for genus.:eyes:

Aleru Divine (10:19:23) (in thread): > @Chioma Onyidogenera can also be said to be a class of things or a group like a classification system.I think theywould’vejust listed out the genus if they meant for the genus only.But I see species, family, order and class in the list.

Mildred Anashie (10:22:29) (in thread): > I agree with Chioma@Aleru Divinethat genera is plural for genus > > But Idon’tknow if that means the curator should curate only the genus listed in the figure

Mildred Anashie (10:25:17) (in thread): > Doing a little research@Aleru Divine@Chioma OnyidoI also found this:thinking_face: - File (JPEG): IMG_2880

Aleru Divine (10:26:02) (in thread): > @Mildred AnashieI know it’s the plural but I know in class they sometimes referred to taxonomy as genera. And you see they listed other taxonomy groups.That’smy concern.

Bolanle Wahab (10:26:56) (in thread): > I’d really like a response please:pray:If I and@Aleru Divinehave to curate 288 experiments:joy_cat:,we’dlike them to be accurate.Thank you

Aleru Divine (10:27:03) (in thread): > Exactly@Mildred Anashie

Aleru Divine (10:27:56) (in thread): > :face_holding_back_tears:Help!!!@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape

Scholastica Urua (10:31:36) (in thread): > @Bolanle WahabI think ‘feces’ is one body site since pig feces was used. But I’m still going through the article to understand it. 288 is a lot, well done guys.

Chioma Onyido (10:33:27) (in thread): > The Genera statement is not about if she should curate all levels (I think she should). it’s about genera definition specifically. Mildred’s screenshot is generally speaking. But I’m not a microbiologist… so.:sweat_smile:

Bolanle Wahab (10:33:42) (in thread): > @Scholastica UruaYes, it is for Pig, but they are separate experiments,we’retrying to figure out the one for sewage > Thank you very much:heart:

Aleru Divine (10:39:08) (in thread): > The sewage samples were from sewage and not a host. > > There’s this statement from@Chioma Onyidohttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710968937518219?thread_ts=1710951789.235799&channel=C04RATV9VCY&message_ts=1710968937.518219That is whywe’reconfused:pleading_face:Hi@Chioma Onyidoplease help. - Attachment: Attachment > Hi @idiaru Angela Good question! > I presented a similar paper in the past where sig taxa results were reported for different environments, I remember that they compared household to work environment. > > If it’s not from an actual body site of the host species, then it should take be curated. See curation policy for host species.

Aleru Divine (10:39:56) (in thread): > @Chioma Onyidoplease help out here:sleepy::face_holding_back_tears::pray:https://community-bioc.slack.com/archives/C04RATV9VCY/p1711461424433369 - Attachment: Attachment > Hi everyone > @C. Mirzayi (please do not tag this account) @Svetlana Ugarcina Perovic @Chioma Onyido @Esther Afuape > I have asked this question before and someone pointed me to a thread where @Chioma Onyido said if there’s no actual body site for host specie, it shouldn’t be curated. > In this case, they experimented on Sewage and there are differential Abundance results too, should I curate it without host specie and body site or leave it? > Thank you.

Aleru Divine (10:40:20) (in thread): > :face_with_open_eyes_and_hand_over_mouth:

Aleru Divine (10:41:07) (in thread): > Yes!She’styping:partying_face::partying_face::hugging_face:

Chioma Onyido (10:46:05) (in thread): > I thinkyou’veall done right by curating the taxa from the host- pig. > As for sewage, I know you really want to,:sweat_smile:but I still think itshouldn’tbe curated because Sewage is not a host, annddd…it’sdefinitely not abodysite. We only curate host species in bugsigdb. > > But…ifyou’renot fully convinced yet, you could wait and present it during the office hour on Thursday,there’llbe an opportunity to ask the mentors directly andwe’llget more insights. > Maybeyou’llbe allowed to curate it and leave a note on thestudy’stalk page.:woman-shrugging:

Bolanle Wahab (10:48:49) (in thread): > @Chioma Onyidoyou caught me:joy:, I want to butI won’t,we’dwait till Thursday,thank youuu:heart:

Aleru Divine (10:50:26) (in thread): > Thank you so much@Chioma Onyido:pray:

idiaru Angela (10:50:38) (in thread): > Thank you@Chioma Onyido

Scholastica Urua (10:51:10) (in thread): > Thank you@Chioma Onyido:hugging_face:

Oluwatomisin Omojokun (10:53:20) (in thread): > YES@Praise Agbetuyi

Oluwatomisin Omojokun (10:57:42) (in thread): > Thanks,@Praise Agbetuyi, I prefer the downloaded PDF to the online version of the articles.

Oluwatomisin Omojokun (11:00:07) (in thread): > Thanks@Svetlana Ugarcina Perovicfor the clarification. well done

Oluwatomisin Omojokun (11:02:53) (in thread): > Thank you@Chioma Onyido

Scholastica Urua (11:09:53) (in thread): > Please when you fill out the final application and submit, can you go back to edit it before the last day of submission?

Bolanle Wahab (11:14:09) (in thread): > @Scholastica Uruayes you can, it’s there - File (JPEG): IMG_9744

Scholastica Urua (11:14:55) (in thread): > Thank you@Bolanle Wahab:pray:

Faith Ifeoluwa Alexander (11:23:24): > Hello Everyone. > > I was away last week cuz I had to attend to my Baby’s health. He was really fussy as he is in his teething stage. He is better and I am back now.@Mildred Anashiewere you the one that commented under my issue on GitHub?

idiaru Angela (11:24:22) (in thread): > Hi@Faith Ifeoluwa Alexanderglad to know your baby is better:blush:

Faith Ifeoluwa Alexander (11:25:27) (in thread): > Thank you@idiaru Angela

Mildred Anashie (11:25:51) (in thread): > I’mnot sure I wasHaven’tcommented under any issue yet > Still working on my assigned issue > > My GitHub username is @MyleeeA > > Sorry about yourbaby’shealth@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (11:26:26) (in thread): > Yes, it was you. That was the name I saw.

Faith Ifeoluwa Alexander (11:27:04) (in thread): > Oh sorry, it wasn’t you.

Linda Uchenwoke (11:27:20) (in thread): > Hello@Aleru Divine, thanks for the review. Your last statement is a bit unclear. Are you suggesting that I add all the microbial genera listed in Fig 7 to my signatures?

Faith Ifeoluwa Alexander (11:28:01) (in thread): > It was @Imalovee

Rahila-me (11:28:42) (in thread): > @Faith Ifeoluwa Alexanderhope you gays are fine, welcome back

Faith Ifeoluwa Alexander (11:29:46) (in thread): > He is still fussy but he is better now.

idiaru Angela (11:30:01) (in thread): > @Linda Uchenwokefrom yesterday’s discussion, I suppose that would be the case. All the taxa in Fig 7 lefse results should be curated

idiaru Angela (11:31:01) (in thread): > @Ima-obong (Aimah)is the person you might be looking for

Linda Uchenwoke (11:31:24) (in thread): > Ohh alrightt. Genera is the plural form for Genus so I was so confused. Thanks for the clarification@idiaru Angela

idiaru Angela (11:32:13) (in thread): > Yeah@Linda Uchenwokethat’s what@Aleru Divinewas trying to clarify earlier. You’re welcome

Faith Ifeoluwa Alexander (11:34:13) (in thread): > Okay. Thank you@idiaru Angela.

Scholastica Urua (11:34:57) (in thread): > Welcome back@Faith Ifeoluwa AlexanderSending you and your baby my best

Faith Ifeoluwa Alexander (11:35:43): > @Ima-obong (Aimah)I got your message. I had a few corrections to make on my paper but I have not been able to get to it which is why I haven’t commented on my issue yet.

Joan C. Chukwuemeka (11:36:11) (in thread): > Welcome back@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (11:36:34) (in thread): > Thank you so much everyone.

Ima-obong (Aimah) (11:40:44) (in thread): > @Faith Ifeoluwa Alexanderhello…good to know everything is going on well with you. > > You’re doing well

Faith Ifeoluwa Alexander (11:42:48): > Hello once again Everyone. > > How do I make the description of Group 1 of my experiments less vague? > > Any ideas pls?

idiaru Angela (11:44:57) (in thread): > Hey@Faith Ifeoluwa Alexanderyou can get an idea from the authors description of the group. Usually authors give a brief description of each group that is used in the study

Faith Ifeoluwa Alexander (11:47:30) (in thread): > Not description of Contribution. It’s description of an experiment.

Eniola Adebayo (11:47:43) (in thread): > Welcome back@Faith Ifeoluwa Alexander

Ima-obong (Aimah) (11:48:31) (in thread): > I agree with@idiaru Angelaand since group 1 is the diseased group, describing it with the name of the disease being studied works too

Scholastica Urua (11:49:46) (in thread): > @idiaru Angelais right@Faith Ifeoluwa Alexanderyou can also provide a link to your study so we can check for the description.

Faith Ifeoluwa Alexander (11:49:49) (in thread): > @Ima-obong (Aimah)only the name of the disease?

Faith Ifeoluwa Alexander (11:50:07) (in thread): > Okay. Let me do that@Scholastica Urua

idiaru Angela (11:50:52) (in thread): > Not only the name of the disease. You can also add diagnostic criteria or any other explanatory information that the authors gave about the group 1.

Faith Ifeoluwa Alexander (11:51:03) (in thread): > bugsigdb.org/Study_971

Ima-obong (Aimah) (11:51:45) (in thread): > Something like ” group 1; people living with Parkinson disease”

Scholastica Urua (11:54:48) (in thread): > Going through your curation, I don’t think your group 1 definition is vague. Please@idiaru Angelacan you confirm this:pray:

Faith Ifeoluwa Alexander (11:55:34) (in thread): > Okay. Do you think it’s descriptive enough?

idiaru Angela (11:57:42) (in thread): > @Scholastica UruaI think it’s actually precise. If she wanted to give a better definition she could say “parkinson disease patients diagnosed according to the UK Society Brain Bank Clinical Diagnostic Center” . I think either description still works - File (JPEG): Screenshot_20240326_165456_Samsung Internet.jpg

Scholastica Urua (11:58:53) (in thread): > That’s right@idiaru Angela

Faith Ifeoluwa Alexander (12:00:09) (in thread): > Okay. Thank you so much. I would just leave it the way it is then.

Scholastica Urua (12:00:35) (in thread): > @Faith Ifeoluwa AlexanderI noticed your Group 1 sample size for experiment 4 is not specified. I don’t know if its deliberate, just thought to point it out… - File (JPEG): size.JPG

Faith Ifeoluwa Alexander (12:01:46) (in thread): > Okay@Scholastica UruaI will check it.

Faith Ifeoluwa Alexander (12:09:09) (in thread): > @Scholastica Uruait was not reported in the paper. Only Calprotection negative and positive patients were reported. The size per gender was not reported.

Faith Ifeoluwa Alexander (12:10:05) (in thread): > Patients with elevated or normal levels were not specified.

Scholastica Urua (12:12:33) (in thread): > Okay, I guess it can be left blank if not specified. Well done on your curation@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (12:13:16) (in thread): > Okay. Thank you so much@Scholastica Urua.

Samreen Aftab (12:15:24): > Hello everyone! How’s your day going?:blush:I’m incredibly grateful for the opportunity to work with such amazing people under the guidance of our mentors. As an engineering undergrad, this project was initially quite challenging for me to grasp, but it turned out to be an incredible learning experience, especially in the field of microbiology! > This was my first time contributing to open source, and I thoroughly enjoyed it. It was both fun and educational!

Faith Ifeoluwa Alexander (12:16:21) (in thread): > It’s been an interesting journey I must say. It sharpened my ability to pay attention to details.

Barakat Akinsiku (12:17:25) (in thread): > That’s great to hear@Samreen AftabWell done!

Barakat Akinsiku (12:19:19) (in thread): > Welcome back@Faith Ifeoluwa AlexanderHope you and baby are keeping well now

idiaru Angela (12:21:16) (in thread): > Honestly I’ve learnt so much BugSigDB-ing. From learning what sequencing of genes means, the different statistical test, and conducting a literature review. In 3 weeks I’ve sharpened different skills and learnt some more. It’s been quite the journey:blush:

Linda Uchenwoke (12:40:34) (in thread): > @Aleru Divine@Mildred AnashieI’ve added all specific taxa. Good to go now?

Aleru Divine (12:41:14) (in thread): > Yes:raised_hands:@Linda Uchenwoke

Linda Uchenwoke (12:43:50) (in thread): > One more question, Is MHT correction true? I’m a bit unsure@Aleru Divine

Aleru Divine (12:46:23) (in thread): > Yes it is

Linda Uchenwoke (12:49:10) (in thread): > Thank you so much for the review, I really appreciate:orange_heart:@Aleru Divine

Blessing Ene Anyebe (13:11:38) (in thread): > Sorry about yourbaby’shealth. I wish your baby quick recovery.:orange_heart:Welcome back@Faith Ifeoluwa Alexander:sparkles:

Faith Ifeoluwa Alexander (13:12:31) (in thread): > Yes, we are@Barakat Akinsiku. Thank you so much.

Faith Ifeoluwa Alexander (13:13:33) (in thread): > Thank you so much@Blessing Ene Anyebe.

Eniola Adebayo (13:14:55) (in thread): > That’sgood to hear:clap:@Samreen Aftab

Faith Ifeoluwa Alexander (13:35:41): > Pls, what does it mean when my signature sections are showing Lua error????

Faith Ifeoluwa Alexander (13:35:54): > Any remedy???

Mildred Anashie (13:36:51) (in thread): > Can you share an image of what you mean?

idiaru Angela (13:37:09) (in thread): > I haven’t seen anyone talk of this error yet:thinking_face:

Faith Ifeoluwa Alexander (13:37:33) (in thread): - File (JPEG): IMG_20240326_183712.jpg

Faith Ifeoluwa Alexander (13:38:02) (in thread): > I only edited my source to add Text to the Table 2.

idiaru Angela (13:38:44) (in thread): > I suggest you tag the mentors to this

Mildred Anashie (13:39:27) (in thread): > Haven’tcome across this before@Faith Ifeoluwa Alexander@Chioma Onyido@Svetlana Ugarcina Perovic@Esther AfuapePlease help out here:pray:

Faith Ifeoluwa Alexander (13:39:49) (in thread): > @Svetlana Ugarcina Perovic@Esther Afuapepls what does Lua Error mean in my signature when I just edited my source to add Text???

Peace Daniel (13:42:28) (in thread): > I’venot come across this before but try to refresh the page and if the error persistsyou’dneed to wait for the mentors@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (13:43:23) (in thread): > I have refreshed the page. I want to submit if for review when I noticed it.

Peace Daniel (13:45:07) (in thread): > Oh, sorry about that.Let’swait for the mentors

Joan C. Chukwuemeka (13:54:31) (in thread): > @Faith Ifeoluwa Alexanderhere’s further info on that. Yet to decipher the implication:thinking_face: - File (PNG): image.png

Joan C. Chukwuemeka (13:55:46) (in thread): > what i saw online about it:This error message suggests that the Lua script running on your web page or server has exceeded a predefined limit for the number of “expensive” function calls. Expensive function calls are those that consume a significant amount of resources such as CPU time or memory. If you’re unable to resolve the issue on your own, consider reaching out to the developer community for Lua or the specific framework/library you’re using.

Faith Ifeoluwa Alexander (13:57:29) (in thread): > All I did was to edit my source & that is when this came up.

Esther Afuape (13:57:40) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

Abiola Salako (14:00:21) (in thread): > Thank you@Chioma Onyido

Abiola Salako (14:03:27) (in thread): > That’s good to know@Samreen Aftab

Joan C. Chukwuemeka (14:05:30) (in thread): > Lua is a lightweight scripting language that’s used in various applications, including MediaWiki, the software that powers Wikipedia and other wikis. In MediaWiki, Lua allows customizing the wiki’s appearance and functionality through extensions and gadgets. > Here’s how to interpret the error message: > * Lua error:This indicates that an error occurred within the Lua script. > * Too many expensive function calls:This means that the script is making too many calls to functions that take a long time to execute. This can slow down the script’s performance. > The backtrace included in the error message provides more specific information about where the error originated: > * The error originated from a function namedgetExpensiveData. > * Line 209 of the filemw.title.lua. > * ThereviewButtonfunction within theModule:Signaturemodule (lines 9 and 113). > * Line 518 of the filemw.lua > @Faith Ifeoluwa AlexanderThis is likely a backend resolution. Mentors have been tagged. Let’s wait:thinking_face:

Faith Ifeoluwa Alexander (14:08:16) (in thread): > Okay. Thank you so much. I have been panicking cuz I put a lot of work into that curation.

Mildred Anashie (14:20:02) (in thread): > Thank you@Joan C. Chukwuemekafor your researchIt’sinsightful

Barakat Akinsiku (14:26:03) (in thread): > I just learned something new. Thanks@Joan C. Chukwuemeka

Chioma Onyido (14:31:18) (in thread): > Don’t be worried,we’venotified the mentors. it’ll be resolved soon.@Faith Ifeoluwa Alexander

Faith Ifeoluwa Alexander (14:33:19) (in thread): > Okay. Thank you so much@Chioma Onyido

U1LCB8WEA (14:35:52) (in thread): > I’ve made a bug report athttps://github.com/waldronlab/BugSigDB/issues/224. Is it correct that there are so many experiments in this one study? It’s a real outlier, I’ve never seen so many experiments! - Attachment: #224 Lua error: too many expensive function calls > See https://bugsigdb.org/Study_971 - e.g. Experiment 12. I note that the error doesn’t occur when navigating directly to https://bugsigdb.org/Study_971/Experiment_12. Note - this is an extremely large number of experiments for a study, and and might not be worth supporting so many experiments if it would reduce performance on the rest of the site. > > image

Faith Ifeoluwa Alexander (14:39:44) (in thread): > Yes, it is correct<@U1LCB8WEA>. The experiments were conducted across the various groups reported in the study.

Faith Ifeoluwa Alexander (14:42:16) (in thread): > <@U1LCB8WEA>do I need to do anything about the study? Or should I attach the link to the literature I curated here?

Joan C. Chukwuemeka (14:58:33): > <!here>The study I’m co-curating with@Ikeh Darlington Ikehathttps://bugsigdb.org/Study_911is up for peer review. Do notify us of any observation/correction please. thanks. > > Also while trying to resolve the NCBI Taxa ID in the study, I encountered some naming convention for which I’m seeking clarity: > > Anaerostignum was reported in the paper but I Saw Anaerotignum (Taxonomy ID: 2039240 ) - could “Anaerostignum” be a typo? > > Secondly Can these replacements/resolutions suffice with a review note added to record the originally reported taxa for the following:? > 1. “Lachnospiraceae bacterium 10-1(Taxonomy ID: 1235800 - under unclassified Lachnospiraceae) for Lachnospiraceae UCG-010 > 2. unclassified Bacteroidales (Taxonomy ID: 185291) for Unclassified Bacteroidales RF16 group > 3. unclassified Kiritimatiellales (Taxonomy ID: 2202730) for unclassified Kiritimatiellae WCHB-1-41 > 4. uncultured Eubacteriales bacterium (Taxonomy ID: 172733 & has uncultured Clostridiales bacterium as homotypic sunonym) for**** unclassified**Clostridiales bacterium > <@U1LCB8WEA><@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapekindly assist:pray: - Attachment (BugSigDB): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - BugSigDB > BACKGROUND: During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism.

Faith Ifeoluwa Alexander (15:22:19) (in thread): > <@U1LCB8WEA>@Svetlana Ugarcina Perovic@Esther Afuape@Chioma OnyidoCan I still go ahead to submit the paper for review or hold on till the bug is resolved?

Peace Daniel (15:26:46) (in thread): > I’dhave a look,well done:clap:

Scholastica Urua (15:41:34) (in thread): > Well done@Joan C. Chukwuemekaand@Ikeh Darlington Ikeh

Mildred Anashie (16:05:04) (in thread): > Well done on your curation@Joan C. Chukwuemekaand@Ikeh Darlington Ikeh:clap:

Scholastica Urua (16:26:41) (in thread): > I just conducted a Google search and observed that some articles use the terms “Anaerostignum” and “Anaerotignum” interchangeably. However, I cannot confirm whether they refer to the same entity. I am eager to hear the insights of mentors on this. - File (JPEG): spp..JPG

Joan C. Chukwuemeka (16:29:25) (in thread): > Yea.. Thanks@Scholastica Urua. > The snapshot seems to infer Anaerostignum as a Genus for Anaerotignum, but Anaerostignum is not on NCBI, Anaerotignum is a Genus in NCBI, hence why I was considering it as a feasible replacement.:thinking_face:

Abiola Salako (16:48:18) (in thread): > @Joan C. ChukwuemekaIt’s possible that this could be a viable substitute for Anaerostignum. Sometimes, these discrepancies occur simply due to spelling errors or variations in taxonomy. > > Let’s seek our mentor’s view as@Scholastica Uruasuggested.

Svetlana Ugarcina Perovic (17:36:41) (in thread): > When I am not sure about nomenclature i.e. bacterium name I go (beside NCBI) to check it out herehttps://lpsn.dsmz.de/

Svetlana Ugarcina Perovic (17:37:45) (in thread): > Also, a quick search through papershttps://www.microbiologyresearch.org/content/journal/ijsemwhere new species/genera are described - Attachment (microbiologyresearch.org): International Journal of Systematic and Evolutionary Microbiology > Official publication of the ICSP and the BAM division of the IUMS.International Journal of Systematic and Evolutionary Microbiology (previously International Journal of Systematic Bacteriology) is the journal of record for publication of novel microbial taxa and the official publication of the International Committee on Systematics of Prokaryotes and the Bacteriology and Applied Microbiology Division of the International Union of Microbiological Societies. See full journal scope.Instructions for authors for International Journal of Systematic and Evolutionary Microbiology can be found here.Editorial BoardEditor-in-Chief: Professor Martha E Trujillo, University of Salamanca, SpainMore The ICSP is pleased to announce the publication of the 2022 revision of the International Code of Nomenclature of Prokaryotes

Svetlana Ugarcina Perovic (17:39:34) (in thread): > It seems indeed that AnaeroStignum is a typo. You could leave this in a note and recorded it as Anaerotignum.

Abiola Salako (17:46:25) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the clarification

Mildred Anashie (17:57:25) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:raised_hands:

Joan C. Chukwuemeka (18:12:46) (in thread): > Thank you@Svetlana Ugarcina Perovic

Faith Ifeoluwa Alexander (18:40:50) (in thread): > Pls, how do you leave a note for issues like this?

Faith Ifeoluwa Alexander (18:43:02): > @Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape<@UBNSEMS3S>do I still put my paper up for review or wait till the bug is resolved? I don’t know what I need to do. > > Your responses will be appreciated. Thank you so much.

Melissa Aidée (20:14:36): > Hi everyone, hope you’re all doing well this week! :)

U1LCB8WEA (21:17:58) (in thread): > Idon’tthink you need to worry about the bug. At leastthere’sa workaround in the meantime so we can see the signatures one experiment at a time.

2024-03-27

Nitya Singhal (00:29:18): > Good morning everyone! Wishing you a great day ahead:blush:

Nitya Singhal (00:30:16) (in thread): > Hey@Mildred AnashieI believe the location shall be Angola and Zimbabwe

Scholastica Urua (00:57:44) (in thread): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (01:03:16) (in thread): > Hello@Faith Ifeoluwa Alexanderone way to leave a note is through the talk page. This will guide you on creating a talk page;https://community-bioc.slack.com/archives/C04RATV9VCY/p1710233489795919?thread_ts=1710232358.053269&cid=C04RATV9VCY - Attachment: Attachment > Steps on creating a ‘Talk’ page; > 1. Open your curation > 2. Click on the three dots above (Image 1) > 3. Click on ‘Discussion’ (Image 2) > 4. A talk page will be created were you can write up your discussion. > 5. When done, scroll down to save page. > Hope this helps. > PS: I’m using this study as a sample, I’m not making any edits to it.

Scholastica Urua (01:06:16) (in thread): > Hello@Melissa AidéeI am. Hope you’re doing well too.

Scholastica Urua (01:06:47) (in thread): > Thank you@Nitya Singhal, wishing you same:hugging_face:

Abiola Salako (01:20:11) (in thread): > Morning@Nitya Singhal. Thank you.

Abiola Salako (01:21:01) (in thread): > @Melissa AidéeYes, I am. Thank you.

Mildred Anashie (01:26:33) (in thread): > Thank you@Nitya Singhal:blush:

Mildred Anashie (01:27:15) (in thread): > Hi@Melissa AidéeDoing well, Thank you

Mildred Anashie (01:29:52): > @fetlework gubena aragePlease see thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

fetlework gubena arage (01:35:24): > @Mildred AnashieThank you so much

idiaru Angela (02:42:51) (in thread): > Have a great day too@Nitya Singhal

Peace Daniel (02:47:37) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711502278231649?thread_ts=1711474541.599179&channel=C04RATV9VCY&message_ts=1711502278.231649 - Attachment: Attachment > I don’t think you need to worry about the bug. At least there’s a workaround in the meantime so we can see the signatures one experiment at a time.

Ikeh Darlington Ikeh (03:21:24) (in thread): > Thanks everyone for your contributions, you have cleared a lot of doubts with your contributions, and we appreciate them.@Svetlana Ugarcina Perovicthank you so much for confirming the typo errors. Actually, there are a few other typos in the paper, not necessary on taxa, so I figured that would be a typo too, we will leave notes where each typo seen in the paper affects curation data. Thank you all.:pray:

Akinbode Mariam (03:21:25) (in thread): > Good morning@Nitya Singhal

Amanda Adoyi (03:26:34): > Good morning people and ciao. I got a 2-part question: > I need to know; can a heterotypic synonym always be used as a synonym for a taxon even if they represent different levels of classification? > > can one ignore the NA genus when curating?@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape

idiaru Angela (03:27:57) (in thread): > Good morning@Amanda Adoyifor question 1, I’m pretty sure if they are different levels of classification they can’t be used interchangeablly. They have to be same rank.

Amanda Adoyi (03:28:41) (in thread): > Thank you@idiaru Angela

Joan C. Chukwuemeka (03:30:41) (in thread): > @Amanda Adoyisee thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1698959648751439?thread_ts=1697819021.342109&cid=C04RATV9VCY - Attachment: Attachment > Heterotypic synonyms have been generally fine.

Mildred Anashie (03:30:46) (in thread): > Good morning@Amanda AdoyiI don’t think they should be used if they are different levels of classification > > For the NA genusI’mwondering if it was just reported as NA or with an additional name

Joan C. Chukwuemeka (03:32:24) (in thread): > Here’s also an excerpt fromInternational Journal of Systematic and Evolutionary Microbiology[2] publication - Attachment (microbiologyresearch.org): International Code of Nomenclature of Prokaryotes. Prokaryotic Code (2022 Revision) > Microbiology Society journals contain high-quality research papers and topical review articles. We are a not-for-profit publisher and we support and invest in the microbiology community, to the benefit of everyone. This supports our principal goal to develop, expand and strengthen the networks available to our members so that they can generate new knowledge about microbes and ensure that it is shared with other communities. - File (PNG): image.png

Bolanle Wahab (03:32:49) (in thread): > @Amanda AdoyiI don’t think NA should be ignored because it could mean unclassified or unidentified taxa

Amanda Adoyi (03:33:00) (in thread): > Now…part 2…if the taxon is not clearly identified or known, hence ‘NA’ shall I just walk by?@Mildred Anashiethe family has been identified but the genus is recorded as ‘NA’ so unknown perhaps. I cannot just record the family; it isn’t specific as other members of said family also exist.

Amanda Adoyi (03:33:16) (in thread): > Thank you@Bolanle Wahabhol’ up I read that wrong. You’re saying it shouldn’t be ignored. So ‘unknown’ should be put in its place?

Joan C. Chukwuemeka (03:33:56) (in thread): > @Ikeh Darlington Ikehfor any other suspected Taxa typo, it will be best to first check in here with the mentors before proceeding.

Aleru Divine (03:34:42) (in thread): > Hi@Melissa Aidée,I’mdoing very well. Thank you! I hope you are too.

Aleru Divine (03:35:20) (in thread): > Good morning and thank you@Nitya Singhaland everyone:heart:Have a great dayy’all:heart_hands::hugging_face:

Mildred Anashie (03:35:36) (in thread): > Okay I understand your question better > > But recording NAdoesn’tseem to really identify anything in my opinion > Responses from the mentors will clarify that for you though@Amanda Adoyi

Amanda Adoyi (03:36:58) (in thread): > @Mildred AnashieI think I share this opinion. I need clarity.

Bolanle Wahab (03:40:24) (in thread): > @Amanda AdoyiI think ‘unknown’ could work but yeah our mentors would clarify

Scholastica Urua (03:40:37): > Hello everyone, hope we are doing well today? > Please I have question.@Muqtadirat Yussuffand I are at a cross road about the study design on this curation we are working. I think its cross sectional because they were no healthy control but@Muqtadirat Yussuffthinks its case control. So we are seeking your opinions please.:pray:See excerpt from the study; > > “The RNA-sequencing data and clinical and survival data of 373 patients with OV in The Cancer Genome Atlas (TCGA) were collected and downloaded. According to the knowledge-based functional gene expression signatures (Fges), OV was classified into two subtypes, termed immune enriched and immune-deficient subtypes. The immune-enriched subtype, which had higher immune infiltration enriched with CD81 T cells and the M1 type of macrophages (M1) and higher tumor mutational burden, exhibited a better prognosis.”https://bugsigdb.org/Study_974 - Attachment (BugSigDB): The Interaction between Intratumoral Microbiome and Immunity Is Related to the Prognosis of Ovarian Cancer - BugSigDB > Microbiota can influence the occurrence, development, and therapeutic response of a wide variety of cancer types by modulating immune responses to tumors.Recent studies have demonstrated the existence of intratumor bacteria inside ovarian cancer (OV).

Amanda Adoyi (03:40:54) (in thread): > Thanks@Joan C. ChukwuemekaI’ll check it out

Joan C. Chukwuemeka (03:41:59) (in thread): > @Amanda Adoyion the NA, I agree with@Mildred Anashie, however can you provide a view of how it was reported on the paper with NA?

Amanda Adoyi (03:45:42) (in thread): > @Joan C. ChukwuemekaIt appears like this. Using this in conjunction with the volcano plot one can identify the taxa. Some however are ‘NA’ and while they may seem important, there are no faces to them. - File (PNG): Screenshot (132).png

Muqtadirat Yussuff (03:46:50) (in thread): > And I went with case control because cross sectional is used for determining prevalence while case control is for studying comparisons. We’d like your thoughts on this, thank you.

Ikeh Darlington Ikeh (03:48:25) (in thread): > Sure@Joan C. Chukwuemeka. But there are some that are very obvious, like the one I shared with you in Figure 5, which we don’t need to bug the mentors about them.

Blessing Ene Anyebe (03:48:31) (in thread): > Hello@Melissa AidéeI am doing well. How do you do as well?

Muqtadirat Yussuff (03:49:43) (in thread): > It’s fine, thank you:joy:

Bolanle Wahab (03:53:37) (in thread): > @Amanda Adoyithis shows they represent something, they have phyla and data values, just not identified, I don’t think you should ignore it in my opinion.

Aleru Divine (03:56:09) (in thread): > @Scholastica Urua@Muqtadirat Yussuffthis is a cross-sectional observational study in my opinion. > > They divided OV patients into 2 sub groups or subtypes and they kind of like observed or should I say studied the tumor micro environment. > > In a case-control, there is usually the group of cases, which are the ones who have the outcome of interest and a control.But here, in your study, they were interested in the outcome of both subtypes.Does this make sense? - File (JPEG): IMG_8068

Amanda Adoyi (03:56:30) (in thread): > Perhaps to be on the safe side I should mark them as unknown. Of course they have values but are they important to the signatures if they can’t be identified? Lolz. Headache. > > Even if I do identify them, I’ll have to decide if ‘unclassified’ or ‘unknown’ is appropriate.

Joan C. Chukwuemeka (03:58:59) (in thread): > @Amanda AdoyiI seem to see a trend in the table - it’s as though the “NA” genus appear just for firmicutes, is that the case when you check the full table?

Oluwatomisin Omojokun (03:58:59) (in thread): > Hi@Melissa Aidée, I am doing great. Thanks > hope you are good too

Mildred Anashie (04:00:19) (in thread): > @Joan C. Chukwuemekayea it looks that way from what she shared > > But some of the Firmicutes are identified however:thinking_face:

Amanda Adoyi (04:01:30) (in thread): > @Joan C. ChukwuemekaOh no. This is just a cross section of one table. It appears for proteobacteria and bacteroidetes as well. You’re damn observant tho.

Scholastica Urua (04:01:41) (in thread): > Yes, it does make sense@Aleru DivineThank you so much for your input:pray:

Joan C. Chukwuemeka (04:03:56) (in thread): > Yea, I see that@Mildred Anashie. My thought is that perhaps certain firmicutes, proteobacteria and bacteroidetes could not be identified up to genus level, then that taxon level may be reported with a side note you know. > > The authors should have perhaps also provided more insight on what NA means Though:thinking_face:Well, I’d also love to know the mentors advice on resolving this:crossed_fingers:

Scholastica Urua (04:06:00) (in thread): > @Muqtadirat YussuffI checked and the issue has not yet been tagged for review, should we go ahead and change it to cross sectional?

Amanda Adoyi (04:06:38) (in thread): > The authors simply identified them as ‘unclassified genera’

Muqtadirat Yussuff (04:06:43) (in thread): > Thank you@Aleru Divine

Muqtadirat Yussuff (04:07:13) (in thread): > Yeah@Scholastica Urua, I’ll edit the discussion page

Scholastica Urua (04:07:33) (in thread): > Okay, it’s nice working with you:hugging_face:

Amanda Adoyi (04:07:39) (in thread): > I think that while I wait for the mentors I’ll simply curate them as ’unclassfied * insert phylum *’

Mildred Anashie (04:08:25) (in thread): > Your idea also makes sense@Amanda AdoyiIt could work for now

Oluwatomisin Omojokun (04:08:55) (in thread): > The study design described in your text is a retrospective observational study design. In this study, the researchers collected data from existing sources without intervening or manipulating any variables.

Muqtadirat Yussuff (04:09:14) (in thread): > And you too, thank you so much for your help@Scholastica Urua

Scholastica Urua (04:11:21) (in thread): > Thank you so much for your input@Oluwatomisin OmojokunBut there’s no “retrospective” study design on BugSigDB:thinking_face:

Joan C. Chukwuemeka (04:11:42) (in thread): > @Amanda Adoyi,your idea may work, however, what are the two numeric tables point for? some NA have positive score, some have negative score for the first column:thinking_face:. Having some reservation if that depicts the direction - increase/decrease?

Amanda Adoyi (04:13:12) (in thread): > Yes@Joan C. ChukwuemekaThat’s for the volcano plot. I’ll show you. It does depict differential abundance relative to cohort. - File (PNG): Screenshot (133).png

Joan C. Chukwuemeka (04:15:56) (in thread): > So negative is decreased, positive score is increased abundance. by implication the unclassified phylum will appear in both by the current Idea. > > Alright@Amanda Adoyi. Well done. > We all await further info from the mentors

Amanda Adoyi (04:17:14) (in thread): > It could appear in both. Basically the researchers just couldn’t tell what genera they were.

Joan C. Chukwuemeka (04:17:35) (in thread): > Yea, sure thing@Amanda Adoyi

Amanda Adoyi (04:17:48) (in thread): > Thanks@Joan C. ChukwuemekaYep. We do.

Mildred Anashie (04:23:11) (in thread): > The study has a retrospective nature but I thinkit’sa cross sectional study design > > I agree with@Scholastica Uruaand@Aleru Divine

Bolanle Wahab (04:34:50): > Good day@Svetlana Ugarcina Perovic@Chioma Onyido@Esther AfuapePlease I’d like to delete signature 3 in experiment 33https://bugsigdb.org/Study_1048Thank you

Peace Sandy (04:42:23) (in thread): > Deleted:white_check_mark:

Bolanle Wahab (04:46:45) (in thread): > Thank you@Peace Sandy

Chiemelie Carita Ndibe (05:22:08): > hello@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Peace Sandy@Scholastica Urua

Chiemelie Carita Ndibe (05:24:58): > Hello@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Peace Sandy@Scholastica Urua, I am trying to add a study with the DOI citation but the information is not populating. How can I resolve that?

Mildred Anashie (05:25:40) (in thread): > Use thestudy’sPMID@Chiemelie Carita Ndibe

Scholastica Urua (05:28:18) (in thread): > Hello@Chiemelie Carita Ndibelike Mildred said, please use the PMID.

Chiemelie Carita Ndibe (05:29:00) (in thread): > I cannot find the PMID, can you help me with where it is located in the paper?

Scholastica Urua (05:29:10) (in thread): > If you can’t find the PMID on your paper, you can copy the name, paste and search it onpubmed.ncbi.nlm.nih.govYou’ll see it then. I hope this is helpful

Scholastica Urua (05:30:19) (in thread): > You can also drop the link to your paper so we help you check.

Chiemelie Carita Ndibe (05:32:25) (in thread): > Thank you@Scholastica Urua

Faith Ifeoluwa Alexander (05:32:56) (in thread): > Okay. Thank you so much.

Faith Ifeoluwa Alexander (05:33:34) (in thread): > Thank you@Peace Daniel.

Faith Ifeoluwa Alexander (05:39:26) (in thread): > Hope you have been able to resolve that@Chiemelie Carita Ndibe.

Faith Ifeoluwa Alexander (05:43:19) (in thread): > I agree with@Aleru Divine. The absence of Healthy controls cancels it out as Case-control study.

Faith Ifeoluwa Alexander (05:44:10) (in thread): > Good Morning! I am. Thank you. I hope you are too.

Chiemelie Carita Ndibe (05:44:40): > hello@Scholastica Urua, In the experiment, there are three groups, the diseased, recovered and healthy. How do I categorise them in the Group 0 and 1. Should I just take the diseased and the control which are like the major experimental concern?

Scholastica Urua (05:45:40) (in thread): > Please can you drop a link to the curation? It’ll better inform my answer. Thank you:blush:

Chiemelie Carita Ndibe (05:46:40) (in thread): > Alright ,https://academic.oup.com/femspd/article/doi/10.1093/femspd/ftad025/7275090

Aleru Divine (05:47:04) (in thread): > @Chiemelie Carita NdibeIt depends on the paper to be honest, you could compare > Diseased and Healthy. > Recovered and Healthy > Recovered and Diseased > > Can you share you paper please. That would clear it.

Flourish Ralph (05:52:25) (in thread): > Thank you<@UBNSEMS3S>

Aleru Divine (05:56:32) (in thread): > @Chiemelie Carita Ndibethat’showI’ddo it:point_up:Healthy(0) vs Diseased(1) > Healthy(0) vs Recovered(1) > Recovered(0) vs Diseased(1)

idiaru Angela (05:56:47) (in thread): > From the article, I think you’d have the 3 experiments that Aleru listed above. They seem to have compared all 3 groups@Chiemelie Carita Ndibe

Faith Ifeoluwa Alexander (05:57:36) (in thread): > Thank you@Scholastica Urua. So is this different from the discussion page for missing Taxas?

Scholastica Urua (06:04:05) (in thread): > @Aleru Divineand@idiaru Angelaare right. I have seen 3 experiments and the comparison mentioned here; - File (JPEG): IMG_20240327_110158_005.jpg

Iman Ngwepe-Ntshibida (06:04:32): > Good day.@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)may you please signature 2 for experiment 1, 2 and 5 in this studyhttps://bugsigdb.org/Study_1055 - Attachment (BugSigDB): Maternal microbiota communicates with the fetus through microbiota-derived extracellular vesicles - BugSigDB > BACKGROUND: Reports regarding the presence of bacteria in the fetal environment remain limited and controversial.Recently, extracellular vesicles secreted by the human gut microbiota have emerged as a novel mechanism for host-microbiota interaction.

Scholastica Urua (06:05:34) (in thread): > Yes, it is different@Faith Ifeoluwa Alexander

Mildred Anashie (06:06:05) (in thread): > Yesit’sdifferent@Faith Ifeoluwa AlexanderWhat@Scholastica Uruais trying to show is how to open a discussion for a particular study in thestudy’sdiscussion/talk page

Scholastica Urua (06:11:26) (in thread): > There’s also another way to make a note especially when it pertains to changing a taxa@Faith Ifeoluwa Alexander; > 1. Click on the + sign near the taxa of interest > 2. Include a note of what the study originally reported eg.****“Study originally reported xyz”**** > 3. Save for review - File (JPEG): Note 1.JPG - File (JPEG): Note 2.JPG

Svetlana Ugarcina Perovic (06:15:49) (in thread): > Deleted.

Iman Ngwepe-Ntshibida (06:17:10) (in thread): > @Svetlana Ugarcina PerovicThank you

Peace Daniel (06:20:28): > Hi@Scholastica UruaIf you’ve not yet claimed study 333 for review, Ithink sex can be used as gender in your controlled confounders

Faith Ifeoluwa Alexander (06:23:26) (in thread): > I agree with@Aleru Divine. I just read it in your paper now.

Scholastica Urua (06:34:42) (in thread): > Hi@Peace Daniel, thank you for bringing this to my attention. This was an incomplete study I was interested in completing. Unfortunately, when I began the experiment, it started with ‘Experiment 2’ instead of ‘Experiment 1’. I notified the mentors about the issue and was awaiting feedback. I did eventually get feedback on it. However, before receiving the feedback,@Oluwatomisin Omojokunhad proceeded with the study. I believe this will be beneficial for her.

Peace Daniel (06:36:44) (in thread): > Okay noted@Oluwatomisin Omojokun

Barakat Akinsiku (06:41:16) (in thread): > Hi@Chiemelie Carita Ndibeif the information is not populating after entering the DOI you can input them manually ie set to manual and add authors name, abstract etc

Svetlana Ugarcina Perovic (06:45:29): > Good morning:rocket:YOU ARE DOING AMAZING TEAM WORKin finalizing still open GitHub issues. > > IMPORTANT: The deadline for final applications isApril 2, 2024 at 4pm UTC.Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline. > > GOOD NEWS: Applicants who submit a final application will be able to continue recording and editing their contributions to your project. They can record contributions until the intern announcement on May 1, 2024 at 4pm UTC.Applicants who have not submitted a final application will not be able to record or edit their contributions.<@U1LCB8WEA><@UBNSEMS3S>@Peace Sandy@Esther Afuape@Chioma Onyido@Svetlana Ugarcina Perovic

Peace Sandy (06:47:07) (in thread): > @Chiemelie Carita Ndibeset to manual and enter the details manually

Oluwatomisin Omojokun (06:47:17) (in thread): > Thanks for the info@Svetlana Ugarcina Perovic

Mildred Anashie (06:48:39) (in thread): > Thank you for this information:blush:@Svetlana Ugarcina Perovic

Peace Daniel (06:50:56) (in thread): > Good morningand thanks for the reminder:hugging_face:

Samreen Aftab (06:51:21) (in thread): > Wow that’s great news. I was heartbroken after I messed up the signatures while curating my first paper, but this just gives me more time to learn and contribute:slightly_smiling_face:

Blessing Ene Anyebe (06:52:03): > Hello everyone, good BugSigDB-ing day to you.:hugging_face:So@Praise Agbetuyiand I are curating a study. > Here is the study::https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02125-1This is our curation so far:https://bugsigdb.org/Study_1071So we recorded that our curatable differentially abundance is in Figure 4c. > > > > Our struggle is we are unsure if the experiment should have signatures, and we would appreciate a third eye. - Attachment (BioMed Central): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BMC Microbiology > Background Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease. Results We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the Dialister. The relative abundance of Phascolarctobacterium and Dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved. - Attachment (BugSigDB): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BugSigDB > Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life.The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. - File (PNG): image (2).png

Scholastica Urua (06:52:27) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the good news:relaxed:. > A wonderful morning to you

Aleru Divine (06:53:39) (in thread): > Amazing!:star-struck:thanks@Svetlana Ugarcina Perovicfor the information.

Peace Daniel (06:55:54) (in thread): > The fig you attached have signatures in green and red

idiaru Angela (06:56:22) (in thread): > The experiment should definitely have signatures. FIG 4f is curatable@Blessing Ene Anyebe

Mildred Anashie (06:56:24) (in thread): > I see results for 2 experiments > 1. psoriasis vulgaris (PV) and pustular psoriasis (PP) (Fig4f) > 2. psoriasis (P) and Healthy/Normal control (N) (Fig 2f) > There might be more

Blessing Ene Anyebe (06:58:11) (in thread): > @Praise AgbetuyiI told you 4f is curatable:sweat_smile:Thank you@idiaru Angela:orange_heart:

Blessing Ene Anyebe (06:58:29) (in thread): > Thank you so much@Mildred Anashie:orange_heart:

Amanda Adoyi (07:04:39) (in thread): > @Svetlana Ugarcina PerovicThis is good news because I was afraid I’d have to rush through my curation.

Mildred Anashie (07:05:10) (in thread): > You are welcome@Blessing Ene Anyebe

Praise Agbetuyi (07:13:42) (in thread): > Thank you@Peace Daniel@idiaru Angelaand@Mildred Anashie. > > > Three responses makes it a nice rythm with the 3rd eye we requested for.@Blessing Ene Anyebe, I guess we can hit the ground flying:grin:

Ima-obong (Aimah) (07:14:55) (in thread): > This is great news…thank you@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (07:17:24) (in thread): > Thank you for this@Svetlana Ugarcina PerovicI also urge everyone to check their emails for the recent mail that was sent about the final application.

Barakat Akinsiku (07:21:44) (in thread): > Thank you@Svetlana Ugarcina Perovic

Chiemelie Carita Ndibe (07:25:33) (in thread): > Thank you for your responses@Aleru Divine@idiaru Angelaand@Scholastica UruaDo I add extra experiments with the “duplicate signature” button, I also want to confirm that I will be adding only experiments with significant alpha diversity

Praise Agbetuyi (07:25:46) (in thread): > Also, a follow up question. > > Could someone help look at the significance threshold, we noticed there was another value (0.05) in the paper, aside 0.01

Faith Ifeoluwa Alexander (07:25:53) (in thread): > I also saw the groups@Mildred Anashiepointed out. But like she said try to search through the article, there could be more.

Praise Agbetuyi (07:27:41) (in thread): > Wow. > > Great news!! > > > Thank you for the information.

Chiemelie Carita Ndibe (07:28:08) (in thread): > Thank you@Faith Ifeoluwa Alexander@Barakat Akinsikuand@Peace Sandy, I have resolved the challenge:grin:

Scholastica Urua (07:28:31) (in thread): > You can add a new experiment using either theDuplicate this Experimentbutton or theAdd a new Experiment button at the top.

Mildred Anashie (07:28:41) (in thread): > I think you should use 0.05 > > 0.05, 0.01 and 0.001 was used to show significance@Praise Agbetuyi

idiaru Angela (07:29:02) (in thread): > @Chiemelie Carita Ndibeit’s best you add experiments using the add a new experiment button that’s right at the top of the study page. You can add experiments that don’t have significant alpha diversity if they have differentially abundant taxa. However if there is no differentially abundant taxa add only experiments with significant alpha diversity. - File (JPEG): Screenshot_20240327_122815_Samsung Internet.jpg

Faith Ifeoluwa Alexander (07:30:20) (in thread): > I would say 0.05. I think the other p values were used to make comparisons between groups represented in the study.

Chiemelie Carita Ndibe (07:31:47) (in thread): > Thanks a lot,@Scholastica Uruaand@idiaru Angela. I appreciate:pray:

idiaru Angela (07:32:04) (in thread): > @Praise Agbetuyiit’s best to record the highest significance threshold used by the authors. In this case 0.05 works best

Scholastica Urua (07:32:37) (in thread): > @idiaru AngelaJust answered the second question. In addition, alpha diversity will recorded as unchanged in the case where they have differentially abundant taxa.

Praise Agbetuyi (07:33:05) (in thread): > I am doing great:blush:Hope it’s been a beautiful week for you@Melissa Aidéetoo?

Iman Ngwepe-Ntshibida (07:38:18) (in thread): > Awesome news. Thanks

Iman Ngwepe-Ntshibida (07:45:20): > Hey all, can someone point me to where I can get information about the internship project timeline for the final application.

Peace Daniel (07:47:30) (in thread): > https://www.outreachy.org/outreachy-june-2024-internship-round/communities/bioconductor/#microbiome-study-curation - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Peace Daniel (07:48:02) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Scholastica Urua (07:48:04) (in thread): > @Iman Ngwepe-Ntshibidahttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&cid=C04RATV9VCY - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Iman Ngwepe-Ntshibida (07:50:27) (in thread): > @Peace Danieland@Scholastica Uruathank you:blush:

Praise Agbetuyi (08:12:33) (in thread): > Okay. > > Thank you@Mildred Anashie@Faith Ifeoluwa Alexander@idiaru Angela

Samreen Aftab (08:36:49): > If anyone wants help in curating a paper, let me know, I’m free

Bolanle Wahab (08:44:19) (in thread): > Thank you so much:partying_face:@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (09:03:56) (in thread): > Good day@Svetlana Ugarcina PerovicThanks a lot for this.

Barakat Akinsiku (09:26:17) (in thread): > Same here. Welldone@Samreen Aftab

Abiola Salako (09:50:00) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:29:25): > REMINDER: We have our team meeting and office hoursat 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. > > Please double check the meeting time with your local time using this link:https://www.timeanddate.com/worldclock/converter.html?iso=20240328T130000&p1=179&p2=5805

Blessing Ene Anyebe (10:29:59) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic:orange_heart::orange_heart:

Aleru Divine (10:31:18) (in thread): > Got it! Thank you for the reminder@Svetlana Ugarcina Perovic:pray:

Mildred Anashie (10:33:10) (in thread): > Thank you for the reminder:pray:Looking forward to the meeting@Svetlana Ugarcina Perovic

Barakat Akinsiku (10:39:22) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (10:40:02) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic.:pray:

Oluwatomisin Omojokun (10:49:59) (in thread): > Thanks for the reminder@Svetlana Ugarcina Perovic

Scholastica Urua (10:50:06) (in thread): > Thank you@Svetlana Ugarcina Perovic. Looking forward to it as always.

Abiola Salako (10:58:52) (in thread): > Thank you@Svetlana Ugarcina PerovicLooking forward to it .

Linda Uchenwoke (11:09:58) (in thread): > Thank you for the info!@Svetlana Ugarcina Perovic

Evelyn Mary Attah (11:12:17): > good day @everyone, my curation is yet to be reviewed, do I make a final contribution on outreachy page or wait till it’s reviewed first?

idiaru Angela (11:14:32) (in thread): > @Evelyn Mary Attahsee this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711452991192939?thread_ts=1711451428.212249&cid=C04RATV9VCY - Attachment: Attachment > This message is for anyone not sure about which merge date to enter when recording contributions on Outreachy. > > Pending when your curation will be reviewed and graded by the mentors, if you’re not sure what merge date to enter when you’re filling out your contribution on Outreachy, you can enter the date when the “needs review” label was attached to your study on GitHub. > I think that’ll fly for now @Svetlana Ugarcina Perovic @Peace Sandy @Esther Afuape @UBNSEMS3S > > See thread for ref… > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711448280247749?thread_ts=1711440276.544779&channel=C04RATV9VCY&message_ts=1711448280.247749

idiaru Angela (11:15:24) (in thread): > Thank you@Svetlana Ugarcina Perovic. Looking forward to it.

Barakat Akinsiku (11:17:40) (in thread): > @Evelyn Mary Attahyou can make your contributions using the day you claimed your study for review as the merge date

Mildred Anashie (11:17:55) (in thread): > You can go ahead and make your final applicationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711451428212249 - Attachment: Attachment > Hello everyone, hope you are doing well. > > Just wanted to reassure you to not worry (or contact us) about pending reviews: We are working diligently to get you all feedback, with our corrections if needed. > > We appreciate your patience as we continue to review. We have been overwhelmed by the amount of interest we’ve had and the productivity of all of you. You are all truly amazing and, once we have to make a decision, it is going to be incredibly difficult, but we will ensure that you are all considered fairly! > > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Svetlana Ugarcina Perovic

Aleru Divine (12:02:50) (in thread): > @Evelyn Mary Attahyou can go ahead and make a final contribution. And also, we can edit our contributions.https://community-bioc.slack.com/archives/C04RATV9VCY/p1711536329162399 - Attachment: Attachment > Good morning :rocket: YOU ARE DOING AMAZING TEAM WORK in finalizing still open GitHub issues. > > IMPORTANT: The deadline for final applications is April 2, 2024 at 4pm UTC. Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline. > > GOOD NEWS: Applicants who submit a final application will be able to continue recording and editing their contributions to your project. They can record contributions until the intern announcement on May 1, 2024 at 4pm UTC. Applicants who have not submitted a final application will not be able to record or edit their contributions. > > @U1LCB8WEA @UBNSEMS3S @Peace Sandy @Esther Afuape @Chioma Onyido @Svetlana Ugarcina Perovic

ayesha khan (12:39:28) (in thread): > Thank you@Svetlana Ugarcina Perovic, looking forward to it

Joan C. Chukwuemeka (13:03:39): > Good evening<@U1LCB8WEA>@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Peace Sandy@Esther Afuape@Chioma OnyidoI found this studyhttps://bugsigdb.org/Study_379/Experiment_2under Fix improper value section (https://bugsigdb.org/Property:Processing_error) > > one of the flagged value is****“Oral health” among the confounders . I went through the publication and found that”Oral health was assessed by tooth loss”Would it be correct to replace”Oral health” with****“number of teeth measurement”****which is listed in the allowed values for Confounders controlled for? - Attachment (BugSigDB): Study 379/Experiment 2 > … - Attachment (BugSigDB): Property:Processing error

Ima-obong (Aimah) (13:14:59) (in thread): > Anticipating it ..thank you@Svetlana Ugarcina Perovic

Scholastica Urua (13:58:14) (in thread): > Well done@Joan C. ChukwuemekaHello<@U1LCB8WEA>@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI also found this experiment with******‘height’******which is one of the confounders flagged. Can I change it to******‘body height******’ which is an accepted value?https://bugsigdb.org/Study_144/Experiment_3#_ERR5f5e6d8d0ed87b8ccf2ac863778d40ef

Nitya Singhal (14:04:39): > > Hello everyone. I just wanted to know if there can be more than one statistical tests.@Oluwatomisin Omojokunand I were curating a paper that had more than 1 test involved. So please help us with the same.

idiaru Angela (14:06:03) (in thread): > Yes@Nitya SinghalMore than one statistical test can be used to test for differential abundance

Joan C. Chukwuemeka (14:06:07) (in thread): > @Nitya SinghalVarious tests may be carried out, but the statistical test used for differential abundance testing is the one to be curated. > Could you share your study link.

Nitya Singhal (14:06:23) (in thread): > https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-02001-4#Fig3

Nitya Singhal (14:07:20) (in thread): > @idiaru Angelaand@Joan C. Chukwuemekahave contrasting opinions.:sweat_smile:

idiaru Angela (14:09:29) (in thread): > @Nitya Singhalsee this thread. We recently had a discussion about a paper that used 2 statistical tests for differential abundance testing@Chioma Onyidohelped us shed more light into why that happenshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711398532483669?thread_ts=1711390782.792099&cid=C04RATV9VCY - Attachment: Attachment > Everybody’s answer is reasonable. :white_check_mark:
> Sometimes researchers conduct different statistical test for significant taxa because they want to compare the taxa between the statistical tests used. > In cases where the statistical test produces completely different results, then both can be curated in bugsigdb as different experiments (see curation policy), > But in cases where the statistical test produces overlapping results, then the stat test that reports the larger number of taxa should be reported (again, curation policy) > > Now I would’ve gone with Mann-Whitney results because they reported taxa on the phylum, family and genus level, in fact with about 30 genera. But after taking a closer look, I confirmed that only 2 were significant (those with asterisks *), so I moved to Lefse (figure 7). > > I looked at Lefse and confirmed that all the significant taxa identified in Mann-Whitney were shown in the Lefse results (and more)! With the family, phylum and genus level clearly showing. > So I’m going with only Lefse. :white_check_mark:

Joan C. Chukwuemeka (14:09:57) (in thread): > Here’s an excerpt from the study”Differential abundance was evaluated using the plugin ******ANCOM******* , which considers the compositional changes associated with treatment. Finally, LEfSE analysis was performed per standard practices to determine which populations were enriched by treatment using LDA, which is inversely related to ANCOM data****Meaning- ANCOM and LEfSe analyses were used sequentially to evaluate differential abundance in the dataset. ANCOM was likely used to identify general compositional changes associated with treatment, whileLEfSe***analysis, employing LDA, was used to determine which specific microbial populations were enriched or depleted by treatment. > So I believe LEfSe should be of choice here - File (PNG): image.png

idiaru Angela (14:12:10) (in thread): > It appears in addition to ANCOM, they also used Lefse@Nitya Singhal

Mildred Anashie (14:13:12) (in thread): > Yes you can have two statistical tests and in this paper I think you have ANCOM and LEfSe@Nitya Singhal

Scholastica Urua (14:14:16) (in thread): > @Nitya Singhalyour paper also use Lefse in addition to ANCOM and it has a curatable fig.

Nitya Singhal (14:16:28) (in thread): > Ok thank you everyone:smile:

Nitya Singhal (14:17:20) (in thread): > so all these tests here will not be used? - File (PNG): image.png

Joan C. Chukwuemeka (14:18:28) (in thread): > @Nitya SinghalAnother excerpt showing LEfSE used in preference for microbial difference analysis - File (PNG): image.png

Nitya Singhal (14:19:02) (in thread): > sorry wrong link

Nitya Singhal (14:19:40) (in thread): > https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-02021-0#Sec23 - Attachment (BioMed Central): Gut microbiota: effect of pubertal status - BMC Microbiology > Background The make-up of gut microbiota at different puberty stages has not been reported. This cross-sectional study analyzed the bio-diversity of gut microbiota at different puberty stages. Result The subjects (aged 5–15 years) were divided into non-pubertal (n = 42, male%: 66.7%) or pubertal groups (n = 47, male%:44.68); in both groups, Firmicutes, Bacteroidetes and Proteobacteria were the dominant phylum. There was no difference of alpha- and beta-diversity among disparate puberty stages. Non-pubertal subjects had members of the order Clostridiales, family Clostridiaceae, genus Coprobacillus which were significantly more prevalent than puberty subjects. Also, the pubertal subjects had members of class Betaproteobacteria, order Burkholderiales which were significantly more prevalent than the non-pubertal subjects. Their relative abundance was independent of BMI-Z. In the pubertal subjects, the abundance of genus Adlercreutzia, Ruminococcus, Dorea, Clostridium and Parabacteroides was associated with the level of testosterone. Conclusions This is the first report of the diversity of gut microbiota at different puberty stages. The various species of gut microbiota changed gradually associated with puberty stages. Differences in gut microflora at different pubertal status may be related to androgen levels.

Nitya Singhal (14:20:25) (in thread): > this one I was talking about@Mildred Anashie@Joan C. Chukwuemeka@Scholastica Urua@idiaru Angela

Joan C. Chukwuemeka (14:21:46) (in thread): > Alright@Nitya Singhal, It’s still Lefse - File (PNG): image.png

Nitya Singhal (14:22:18) (in thread): > what about these? - File (PNG): image.png

Scholastica Urua (14:22:25) (in thread): > Lefse is also used here - File (JPEG): nn.JPG

Nitya Singhal (14:22:53) (in thread): > I agree on using LEfSE but what about the rest?

Mildred Anashie (14:23:02) (in thread): > LEfSe is the test > You record only the test used for differential abundance@Nitya Singhal

Nitya Singhal (14:23:23) (in thread): > Ok so rest of the tests won’t be considered?

Scholastica Urua (14:23:48) (in thread): > All the others were used to statistically calculate the clinical characteristics. So they’ll not be curated.

Joan C. Chukwuemeka (14:23:52) (in thread): > Yes@Nitya Singhal

Mildred Anashie (14:23:58) (in thread): > Yes therewon’t@Nitya SinghalBugSigdb is interested in only the test used for differential abundance

Nitya Singhal (14:24:42) (in thread): > Thank you so much, everyone.. Your inputs are always appreciated.

Joan C. Chukwuemeka (14:25:32) (in thread): > You’re welcome@Nitya Singhal

Nitya Singhal (14:27:10): > Hey, I wanna confess something. > This platform showed how women empower women from all across the world. This makes me love this work culture a lot more. Thank you so much@Svetlana Ugarcina Perovicfor bringing us all together under one umbrella. Knowing women all across the world is blissful. May this healthy environment prevail. > Sending lots of love to all the women reading this.:blush::heart:

Leenaa Al-Amin (15:32:47): > hello@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy, I want to collaborate with@Linda Uchenwokeon my studyhttps://bugsigdb.org/Study_998, please how do collaborations work, is she allowed to add experiments to the curation? - Attachment (BugSigDB): Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain - BugSigDB > A link between the gut microbiome and Parkinson’s disease (PD) has been intensively studied, and more than 100 differential genera were identified across the studies.However, the predominant genera contributing to PD remain poorly understood.

Isoken Ibizugbe (15:36:20) (in thread): > Thanks guys, as the numerous can be quite confusing

Svetlana Ugarcina Perovic (16:20:36) (in thread): > This made my day! Thank YOU.

Svetlana Ugarcina Perovic (16:24:39) (in thread): > Leenaa, you are the main curator i.e. responsible for your assigned curation, and your advisor/co-curator is Linda. You are discussing with Linda what you are going to edit and/or add in your curation.

Svetlana Ugarcina Perovic (16:27:09) (in thread): > @Joan C. Chukwuemeka@Scholastica Uruaplease do the corrections, thanks!

Leenaa Al-Amin (16:36:54) (in thread): > Alright, thank you for the clarification!

Faith Ifeoluwa Alexander (16:58:03): > Hello Good Evening everyone. Hope we had a productive day.@Scholastica UruaI just got on my Laptop to try out what you suggested about clicking on the + sign near the taxa but it took me to the review page. So what do you suggest I do?

Faith Ifeoluwa Alexander (17:01:02) (in thread): > Never mind@Scholastica Urua. I have gotten a hang of it now. Thanks.

Joan C. Chukwuemeka (18:11:17) (in thread): > Alright:+1:

Melissa Aidée (20:46:50) (in thread): > I am doing fine you guys, thank you! ^^

Melissa Aidée (23:17:58) (in thread): > Hello again everyone, I have a question. My article says it used ITS and 16S, but I can only enter one of them on the Experiment page. Does anyone know how I could proceed?

2024-03-28

Scholastica Urua (00:29:44) (in thread): > Okay Svet, thank you

Scholastica Urua (00:31:05) (in thread): > Okay@Faith Ifeoluwa Alexander, well done

Mildred Anashie (00:48:12) (in thread): > I think you have to Enter the one used for differential abundance for the experiment you are recording > > Also from a study I curated, I picked that ITS is used for fungal species identification and taxonomic classification and 16S is used for bacterial and archaea identification and taxonomic classification > > “By utilizing both ITS and 16S rRNA sequencing, researchers can comprehensively analyze both fungal and bacterial components of microbiome samples, providing a more holistic understanding of microbial communities and their interactions in various environments”. > > In the study I curated results, were given for both fungal microbiome and bacterial microbiome, what I did was record the significant experiments and signatures with their respective sequencing types > I hope this is clear@Melissa AidéeAlso Idon’tknow if I did the right thing (paper is yet to be reviewed) but I followed my paper and recorded information based on the paper. This is the link to the study I’m talking abouthttps://bugsigdb.org/Study_1022@Chioma Onyido@Esther Afuape<@UBNSEMS3S>can you help out here please:pray: - Attachment (BugSigDB): White-nose syndrome restructures bat skin microbiomes - BugSigDB > Inherent complexities in the composition of microbiomes can often preclude investigations of microbe-associated diseases.Instead of single organisms being associated with disease, community characteristics may be more relevant.

Isoken Ibizugbe (00:56:04) (in thread): > About this same experiment, there are contrasted groups with no LDA diagram or the relative abundance of bacteria taxa. Do we still create experiments for them - File (JPEG): IMG_3166 - File (JPEG): IMG_3165

Scholastica Urua (01:00:02) (in thread): > Hello@Melissa Aidée, like@Mildred Anashiesaid, the one with the differential abundance should be used. But I think if results are different for each of them, they can be curated as two separate experiments. > I hope this is right.

Aleru Divine (01:01:40) (in thread): > Yesthat’sright@Scholastica Uruaand@Mildred Anashie

Aleru Divine (01:01:45) (in thread): > Well done

idiaru Angela (01:11:25) (in thread): > No@Isoken Ibizugbe. They have no significant Alpha diversity or differential taxa.

Mildred Anashie (01:11:38) (in thread): > For the first image we do not curate Principal Cordinates analysis (PCoA) on BugSigdb > > For the second image it looks like you might have experiments without significant signatures butwe’llhave to confirm if the experiments were significant or not before recording > > Also we are looking out for differential abundance and not generally relative abundance (although relative abundance between groups can be curated)@Isoken Ibizugbecan I see Table S4?

Mildred Anashie (01:25:48) (in thread): > @Isoken IbizugbeI think you you have about 7eperiments going through table s4 (see the image showing alpha diversity) with the alpha diversity indices mentioned to be unchanged > > Also a lot of those experiments do not have significant signatures so you record without signatures (See this)https://community-bioc.slack.com/archives/C04RATV9VCY/p1710277923151239?thread_ts=1710265890.754799&channel=C04RATV9VCY&message_ts=1710277923.151239 - Attachment: Attachment > Yeah you can curate an experiment with no signatures if there was no significant results. - File (JPEG): IMG_2940 - File (JPEG): IMG_2939 - File (JPEG): IMG_2937

Mildred Anashie (01:37:29): > Hi@Chioma Onyido@Svetlana Ugarcina Perovic@Esther AfuapeHi everyone:wave:I was going through the pages with missing NCBI ID and I found this studyhttps://bugsigdb.org/Study_837The study has been reviewed so I’m not sure the curator is still working on it and I think most of the taxas are appearing in orange because of the way they were entered (correct me if I’m wrong) > The taxas were entered with their rank (g,c,o etc) > A few of those taxas have NCBI IDs and I’ll like to effect the change with your permission if that’s okay, Thank you:pray:Also for anyone that missed the message about our weekly office hourhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711549765482209 - Attachment: Attachment > REMINDER: We have our team meeting and office hours at 9 AM EDT tomorrow at https://us02web.zoom.us/j/2737200499. > > Please double check the meeting time with your local time using this link: https://www.timeanddate.com/worldclock/converter.html?iso=20240328T130000&p1=179&p2=5805 - File (JPEG): IMG_2942

idiaru Angela (01:38:43) (in thread): > Hey@Mildred Anashiejust as a means of clarificationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710357317003159?thread_ts=1710356210.762269&cid=C04RATV9VCYSee this thread where we were asked not to curate experiments if they don’t have significant alpha diversity measure or differential taxa. I’m pretty sure same was said in a previous office hour we’ve had. This is a bit confusing - Attachment: Attachment > No you were right. B, D and E should not be curated because they are not significant.

Scholastica Urua (01:56:13): > Good morning@Chioma Onyido@Esther Afuape@Peace Sandy. > Please help delete experiments from this study;https://bugsigdb.org/Study_1070Thank you:pray: - Attachment (BugSigDB): Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension - BugSigDB > The mycobiome is an essential constituent of the human microbiome and is associated with various diseases.However, the role of oral and gut fungi in hypertension (HTN) remains largely unexplored.

Scholastica Urua (01:58:27) (in thread): > Experiments 1 to 10 please:pray:. > There’s been a miscommunication with the original curator and we’ll like start over. So sorry for the inconvenience

Mildred Anashie (02:19:36) (in thread): > Please read Further you’ll see that the B,D and E was asked to be recorded as No difference which equals unchanged because generally “No difference in Alpha diversity is unchanged” reason I said she should curate as unchanged@idiaru AngelaMore clarification would be helpful though

Chioma Onyido (02:21:27) (in thread): > Hmmm could you share with me the reason?

idiaru Angela (02:21:39) (in thread): > I think applies when there’s differential taxa. Would love to clarify at the office hour later today@Mildred Anashie

Scholastica Urua (02:22:34) (in thread): > I’ve edited my initial post@Chioma Onyido:pray:. Was collaborating with@eneje promiseon the project but now they’ll prefer to make the edit their selves since its their second curation. So they asked if we could kindly start over.

Mildred Anashie (02:26:14) (in thread): > Okay that would be best:thumbsup:

Mildred Anashie (02:50:14) (in thread): > Please when asking you should share the screenshots to enable us know if the S4 should be curated or not@idiaru Angela

Peace Daniel (03:03:12) (in thread): > Hi Anashie, it looks like that as well. Do confirm by checking the source in the article while you await the mentors response. > Well done

Mildred Anashie (03:04:27) (in thread): > I have done that,that’show I confirmed the rank was added along side the taxa

Peace Daniel (03:11:53) (in thread): > Great:clap:

Samreen Aftab (03:23:13): > Hello everyone, most of the signatures are in orange in this curation. Is the way I entered the taxa correct or is there some other way I should enter them? - File (PNG): image.png

Scholastica Urua (03:25:10) (in thread): > @Samreen Aftabthe unclassified should be before the other names. You can also use the NCBI taxonomy site (https://www.ncbi.nlm.nih.gov/taxonomy) to confirm the signatures.

Aleru Divine (03:25:25) (in thread): > Hi@Samreen Aftab, you can search then and find their tax IDs from the taxonomy browser.That way theywon’tbe highlighted as BugSigDB would recognize the IDs > > Link to taxonomy browser:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Samreen Aftab (03:27:14) (in thread): > @Aleru Divine@Scholastica UruaI searched for all the taxas (for example: Lachnospiraceae unclassified) on NCBI but found the NCBI Ids of only a few. For the rest, there’s no NCBI ID for the unclassfied taxa

Scholastica Urua (03:28:36) (in thread): > The first highlighted signature is available on NCBI asunclassified Lachnospiraceae; - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (JPEG): eg.JPG

Scholastica Urua (03:29:09) (in thread): > Let me check for the rest@Samreen Aftab

Samreen Aftab (03:31:04) (in thread): > Oh okay, the unclassified should have been before the names. Thank you@Scholastica Urua:sweat_smile:I’ll fix them

Aleru Divine (03:31:05) (in thread): > @Samreen Aftabsome of these are even already in the BugSigDB database.Start with “unclassified… - File (JPEG): IMG_8076

Scholastica Urua (03:32:51) (in thread): > You’re welcome@Samreen Aftab

Chioma Onyido (03:34:36) (in thread): > Deleted.

Scholastica Urua (03:35:19) (in thread): > Thank you so much:pray:

Linda Uchenwoke (03:43:15) (in thread): > @Aleru Divine@Mildred AnashieI think the study design isn’t accurate. What study design do you think it is? I’m thinking Cross-Sectional Study

Aleru Divine (03:43:58) (in thread): > Let me have a look at it.

Mildred Anashie (03:47:51) (in thread): > It’s a Meta analysis@Linda UchenwokeThey were conducting a systematic review of other studies and they also used data gotten from other studies

Mildred Anashie (03:50:15) (in thread): > @Samreen Aftabyoucanalso search on Uniprot > Google search can also help you

Aleru Divine (03:52:59) (in thread): > @Linda Uchenwokethis is a meta analysis study. > This text from the materials and methods confirms it > > Additionally, figure 1 and table 1 gives additional information on all the “INCLUDED STUDIES” - File (JPEG): IMG_8079

Mildred Anashie (03:54:27) (in thread): > Also see this@Linda Uchenwoke - File (JPEG): IMG_2947

Linda Uchenwoke (04:03:18) (in thread): > Did you see the no-meta analysis was performed in the image you sent? I think that was what confused me@Mildred Anashie

Linda Uchenwoke (04:03:58) (in thread): > Thank youu@Aleru Divine@Mildred Anashie

Mildred Anashie (04:04:21) (in thread): > I think that is saying no meta analysis was conducted for blood@Linda Uchenwoke

Joan C. Chukwuemeka (04:24:51): > Good morning<!here>So I discovered somethings today while fixing values flagged as improper values: > * The section of “confounders controlled for” seems to be case sensitive based on the allowed values list - in a particular study, “helicobacter pylori” was flagged, and updating it to “Helicobacter pylori” cleared off the flagging. > * Using two separate words together in the same section can also cause a flag - in another study, “chemotherapy and acute lymphoblastic leukemia” was flagged, and updating it to “chemotherapy”, “acute lymphoblastic leukemia” cleared off the flagging.:nerd_face: > Hoping this helps when we curate studies were confounders are controlled for.:crossed_fingers:Happy BugSigDB-ing:seedling:and don’t forget the office hour today:hugging_face:

Linda Uchenwoke (04:44:57) (in thread): > In the experiment for the feces samples two types of sequencing were done, whole meta genome shotgun and 16S. I think we should go with 16s because the study conducted a comprehensive search using keywords related to microbiota analysis, such as “Parkinson’s disease,” “blood,” “brain,” “gut,” and “feces.” It specifically mentions the use of “16S rRNA” as one of the keywords, indicating the focus on microbial community analysis using 16S rRNA sequencing. > > what do you think@Mildred Anashie

Mildred Anashie (04:46:44) (in thread): > @Linda Uchenwokeyou have studied the paper better than me > > SoI’mgoing with your thoughts too:blush:althoughI’llstill glance through

Linda Uchenwoke (04:47:40) (in thread): > what do you think?@Aleru Divine

Linda Uchenwoke (04:48:11) (in thread): > I don’t want Leenaa and I to make any mistakes at all:sweat_smile:

Aleru Divine (04:48:15) (in thread): > I’llhave to go through the paper@Linda Uchenwoke

Aleru Divine (04:48:34) (in thread): > Going through it now.

Linda Uchenwoke (04:50:01) (in thread): > Okayy, will be waiting.

eneje promise (04:55:06) (in thread): > @Chioma OnyidoThank you

Aleru Divine (05:05:18) (in thread): > @Linda UchenwokeHere is an excerpt > “Recent Shotgun metagenomic data (PRJNA433459) (Qian et al., 2020), which were re-analyzed with Kraken2 in this study, were further used to verify the results obtained from 16S rRNA. For each RNA-Seq dataset, all reads were classified with Kraken2 using…” > > > Also I see “Using shotgun metagenomics data (PRJNA433459), we found that 377 genera were significantly different between PD patients and controls (P < 0.05, Supplementary Data 7), with 251 genera depleted and 126 enriched in PD, respectively.” > > They have table 6,7 and 8 all providing shotgun Metagenomics data on the significantly different bacteria taxa between control and PD.While I think they may have used shotgun to verify results from 16S, you can compare the results from both and see if there were any new observations from shotgun.Then you would record a new experiment.But if thereisn’t,you’lljust go with 16S because it does seem like shotgun was used for further verification.

Samreen Aftab (05:20:33): > Can anyone help me curating this paper? It has no figure which can be curated. I cannot find any statistical test for differential abundance testing. Also there’s only one group for the experiment.:sweat_smile:https://pubmed.ncbi.nlm.nih.gov/36650865/ - Attachment (PubMed): Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares - PubMed > These findings contribute to the knowledge of microbes’ presence in the uterus, while future studies are required to demonstrate the role of these microorganisms in health and disease.

Aleru Divine (05:21:01) (in thread): > Let me have a look@Samreen Aftab:sweat_smile:

idiaru Angela (05:30:18) (in thread): > Hey@Samreen AftabI looked through and I couldn’t find alpha diversity measures or differential abundance. Just relative abundance:thinking_face:

Linda Uchenwoke (05:31:05) (in thread): > Yess@Aleru DivineI saw the excerpt on shotgun. While shotgun metagenomics was used for verification and to provide additional insights, the primary focus and conclusions were derived from 16S rRNA sequencing data. Thank you for the review.

Aleru Divine (05:33:15) (in thread): > @Samreen AftabI don’t see anything on differential abundance testing. All I see mentioned is relative abundance. > > I don’t see any supplemental resources either:grimacing:

Samreen Aftab (05:34:29) (in thread): > Yeah, and there is only one group. I’m very confused since there isn’t much to record for this paper

idiaru Angela (05:34:41) (in thread): > I don’t think this paper is curatable. I think you should draw the attention of the mentors to know what to do@Samreen Aftab

Ima-obong (Aimah) (05:37:14) (in thread): > This is really helpful..thank you@Joan C. Chukwuemeka

Aleru Divine (05:38:02) (in thread): > I agree about drawing the attention of the mentors@idiaru Angela

Samreen Aftab (05:41:14): > @Chioma Onyido@Esther Afuape@Peace Sandyhttps://pubmed.ncbi.nlm.nih.gov/36650865/Is this paper curatable? There are no signatures which can be curated, and overall there isn’t much information to record. - Attachment (PubMed): Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares - PubMed > These findings contribute to the knowledge of microbes’ presence in the uterus, while future studies are required to demonstrate the role of these microorganisms in health and disease.

Ima-obong (Aimah) (05:47:37) (in thread): > @Samreen AftabMaybe the mentors can give you a link to the actual journal where the paper was listed like the “Microbiology Spectrum Journal(American Society for Microbiology)” cause most papers opened on the PubMed site are always brief summary of the actual paper.@Chioma Onyido@Svetlana Ugarcina Perovic

idiaru Angela (05:50:13) (in thread): > @Ima-obong (Aimah)pubmed already links the full article.

Leenaa Al-Amin (05:52:55) (in thread): > hello@Aleru Divine, according to this, although the 16S data was used to identify the Blautia genus as being depleted in PD patients it was shotgun metagenomics data that showed the specific species on further analysis - File (JPEG): IMG_4801

Aleru Divine (05:54:12) (in thread): > @Linda Uchenwokecome look at this.

Ima-obong (Aimah) (05:55:06) (in thread): > @idiaru AngelaI’m aware of that .. > just that I once had a paper like this on PubMed, but searched the full name on Google and it opened on a particular journal with the full pdf and supplemental material. > I Experienced this when I wanted to work on curations with no experiments > The mentors will know best though

Aishat Ijiyode (05:58:49) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic

Aishat Ijiyode (06:01:51) (in thread): > Thank you for the information@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (06:11:02) (in thread): > You’re welcome@Ima-obong (Aimah)

Leenaa Al-Amin (06:12:21) (in thread): > @Aleru Divinewhat I did was put down the signatures for the differentially abundant genera and species from all the meta analysis into one experiment for the feces samples, although Ididn’tcurate the Blautia genus because I curated the specific species - File (JPEG): IMG_4804 - File (JPEG): IMG_4805 - File (JPEG): IMG_4803 - File (JPEG): IMG_4807

Aleru Divine (06:14:58) (in thread): > Don’tyou think it should be 2 different experiments, and in the case of shotgun, curating the species identified.

Aleru Divine (06:19:26): > Hello@Levi Waldron@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI would like to report this error message in my study page.“Lua error: too many expensive function calls” > > Signatures 1 and 2 in experiment 126 > Signature 1 in experiment 127 > > The signatures above reported the error message and I still have more to curate.I believeI’dhave to wait till this is sorted out.Thank you so much! > > Link to study:https://bugsigdb.org/Study_1048 - File (JPEG): IMG_8082 - File (JPEG): IMG_8081

Leenaa Al-Amin (06:34:03) (in thread): > The challenge I have with creating another experimentfor the shotgun dataisthat the only information I have about it is the species that were enriched and depleted as well as the Project ID, the details of the study where the data is gotten from are not stated clearly in this paper in the way the 16S data is stated - File (JPEG): IMG_4808 - File (JPEG): IMG_4800

Aleru Divine (06:38:56) (in thread): > Thenit’sokay to create one experiment with 16S and add the species from shotgun asyou’vedone.16S was majorly used.I believe this is okay.

Naomi Ibe (06:42:36): > Hello,there’s seems to be an issue with adding signatures this morning, after adding a study and attempting to add a signature, it freezes and brings up this blank page - File (PNG): Screenshot_20240328-114116.png

Mildred Anashie (06:42:43) (in thread): > Yes going through this 16s was mentioned more

Mildred Anashie (06:43:37) (in thread): > It might be your connection thoughI haven’ttried this morning

Linda Uchenwoke (06:44:59) (in thread): > I could be wrong but the area the highlighted text is from does not specifically address the concept of differential abundance in fecal samples alone. Instead, it discusses the differences in microbial genera between Parkinson’s disease (PD) patients and controls across various sample types (feces, blood, and brain) using different analytical methods. I think that is why it’s confusing. > > Both Greengenes and SILVA are databases commonly used in 16S rRNA gene sequencing analysis. Greengenes analysis identified 32 significantly different genera between PD patients and controls, with 9 depleted and 23 enriched in PD. > SILVA analysis found 23 significantly altered genera in PD patients compared to controls. > > Shotgun metagenomics data analysis revealed 377 significantly different genera between PD patients and controls in fecal samples. > > If we are comparing the taxonomic diversity provided by 16S rRNA gene sequencing and shotgun metagenomic sequencing, shotgun metagenomics would typically yield more taxa and a broader representation of microbial communities especially for differential abundance analysis. I think we can ask the mentors for more clarity.

Naomi Ibe (06:45:17) (in thread): > @Mildred Anashieyea it just started working right now and stopped again:smiling_face_with_tear:

Linda Uchenwoke (06:46:30) (in thread): > What do you think?@Leenaa Al-Amin@Aleru Divine@Mildred Anashie

Praise Agbetuyi (06:47:53) (in thread): > Than k you for the remimder

Praise Agbetuyi (06:48:01) (in thread): > Looking forward to it

Joan C. Chukwuemeka (06:50:31) (in thread): > The study is just about exploring the bacterial communities in the uteruses of Chilean purebred mares, a breed with a long history in South America’s equine industry. By analyzing DNA from uterine samples, they sought to understand the types of bacteria present and their potential functions during estrus, a key reproductive stage. > > I think that’s why it’s just relative abundance that was recorded.:blush:

Aleru Divine (06:51:39) (in thread): > What you said makes sense@Linda Uchenwoke

Svetlana Ugarcina Perovic (06:54:51) (in thread): > This study is not curatable, you are right! Thank you for notification.

Joan C. Chukwuemeka (06:57:38): > Good day all, > For the study in the snapshot, I’m thinking that based on the allowed values in confounders controlled for, “diet” should be a fitting replacement for both daily consumption of pickled vegetables and daily consumption of fresh fruits. What do you think? can I update it to that?:blush:@Chioma Onyido<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic@Esther Afuape@Peace Sandy - File (PNG): image.png

Leenaa Al-Amin (07:01:52) (in thread): > I curated the experiments for the blood and the brain samples separately, since both the 16S and shotgun metagenomic data was used for the feces sample experiment I curated the Blautia species identified from the shotgun metagenomics data leaving out the Blautia genus as well as the other genera found using the 16S data, however I did not curate the 251 genera depleted and 126 enriched in PD found from the shotgun metagenomics data asit’squite extensive, I’m starting to think a better option would be to curate the 16S data and leave out shotgun metagenomics data used to verify, and I’ll just curate the Blautia genus without adding the specific species. What do you guys think@Linda Uchenwoke@Aleru Divine

Mildred Anashie (07:02:01) (in thread): > Yes the mentors will guide us better@Linda Uchenwoke

Svetlana Ugarcina Perovic (07:02:14) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/145 - Attachment: #145 Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares > Characterization of microbial communities and predicted metabolic pathways in the uterus of healthy mares – Thomson P. et al. – Open Vet J > > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9805769/

Svetlana Ugarcina Perovic (07:02:28) (in thread): > Issue closed. Thank you!

Leenaa Al-Amin (07:03:46) (in thread): > @Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeplease could you guide us better:pray:

Svetlana Ugarcina Perovic (07:09:15) (in thread): > Please bring up your questions/doubts to today’s meeting. Thanks!

Leenaa Al-Amin (07:12:56) (in thread): > Alright!

Svetlana Ugarcina Perovic (07:13:32) (in thread): > Your very productive activities in a collaboration mode made my morning. See you at the team meeting today - Attachment: #95 Office Hours > Welcome, Outreachy applicants! > > My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Svetlana (pronouns: she/her) on the BugSigDB project and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on our GitHub repo: #94 > > Also, between now and Monday, April 1st, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participate or observe these meetings as well as ask questions. > > These meetings are scheduled for:
> Thursday March 7, 9-10 AM ET* (Zoom Link TBA)
> *Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240307T140000&p1=179 > > Thursday March 14, 9-10 AM ET (https://us02web.zoom.us/j/2737200499)
> Thursday March 21, 9-10 AM ET (https://us02web.zoom.us/j/2737200499)
> Thursday March 28, 9-10 AM ET (https://us02web.zoom.us/j/2737200499) > > Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20240314T130000&p1=179
> PLEASE NOTE: this is an hour earlier for some countries due to daylight savings time! > > We are happy to meet with you on a different day or time upon request. Thank you!

Svetlana Ugarcina Perovic (07:16:24) (in thread): > https://github.com/waldronlab/BugSigDB/issues/224 - Attachment: #224 Lua error: too many expensive function calls > See https://bugsigdb.org/Study_971 - e.g. Experiment 12. I note that the error doesn’t occur when navigating directly to https://bugsigdb.org/Study_971/Experiment_12. Note - this is an extremely large number of experiments for a study, and and might not be worth supporting so many experiments if it would reduce performance on the rest of the site. > > image

Svetlana Ugarcina Perovic (07:17:15) (in thread): > You can comment in the open github issue above that you are facing the same problem. Thanks!

Aleru Divine (07:17:49) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:blush:

Ikeh Darlington Ikeh (07:24:14) (in thread): > No love for the men!? please share some love our way too, we need it too. Thanks… > > Well, on behalf of all the men, we are also sending our love to the women.:love_letter::heart::heartpulse:

Aleru Divine (07:25:33) (in thread): > Here’ssome love for all the men:heart::heart::heart::sweat_smile:@Ikeh Darlington Ikeh:hugging_face:

Peace Daniel (07:26:08) (in thread): > :sweat_smile:Extra love for the men:heart::heart::heart::heart:

Svetlana Ugarcina Perovic (07:27:00) (in thread): > @Nitya Singhalhighlighted female power (agree!) and I highly appreciate applicants’ power and whole Bioconductor community! - Attachment (X (formerly Twitter)): Svetlana U. Perović (@svetlana_up) on X > @outreachy This made my day! > > A big thanks to @LeviWaldron1 and @nsegata and whole #Bioconductor community who are holding this :umbrella: with me!!

Praise Agbetuyi (07:30:06) (in thread): > Yes, it is very helpful. Thank you@Joan C. Chukwuemeka

Ikeh Darlington Ikeh (07:31:49) (in thread): > @Svetlana Ugarcina PerovicThank you, much love from here to all the applicants, wish us all the best as this round comes close to conclusion. Happy Easter Holidays to all the Christians in here.:heart::hugging_face::clap::poultry_leg::falafel:

Praise Agbetuyi (07:37:06) (in thread): > So sweet,@Nitya Singhal. Thank you. Here is also more love to all the curators in the house.

Amanda Adoyi (07:42:29): > Aloha and Guten tag. Is there a template to follow for the Outreachy internship project timeline?

idiaru Angela (07:45:19) (in thread): > Aloha@Amanda Adoyisee herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&cid=C04RATV9VCY - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Amanda Adoyi (07:45:36) (in thread): > Thank you

Nitya Singhal (07:52:24) (in thread): > That is such a beautiful thread. Thank you@Svetlana Ugarcina Perovicma’am for posting it on X. I feel blessed:blush:

Nitya Singhal (07:58:14) (in thread): > Hey@Ikeh Darlington Ikeh, > Like Yin and Yan are complementary, so do women and men exist co-dependently. Hence, I do send love for men, too, and thank them for believing in young female leaders of this organization, and, instead of pushing them down, you let them lead the world.:blush::heart:

Scholastica Urua (08:08:17) (in thread): > Happy Easter holidays to you too@Ikeh Darlington Ikeh:sparkling_heart::hugging_face:

Oluwatomisin Omojokun (08:09:34) (in thread): > Good afternoon teammates, please kindly review. I and@Nitya Singhalwork on the curation studyhttps://bugsigdb.org/Study_1068Thank you all - Attachment (BugSigDB): The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota - BugSigDB > BACKGROUND: Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry.

Oluwatomisin Omojokun (08:13:55) (in thread): > @Ikeh Darlington Ikehsending you:heart::smiling_face_with_3_hearts:. > To all the amazing beautiful ladies here. i appreciate you.:heart::heart::heart::heart_eyes::smiling_face_with_3_hearts:Much love from Tomisin

Joan C. Chukwuemeka (08:14:16) (in thread): > Still hoping to get feedback on this:pray:

Isoken Ibizugbe (08:25:54): > Can someone help with reading this. I thought increased is positive and decreased is negative - File (JPEG): nn.JPG

Mildred Anashie (08:27:57) (in thread): > I’m guessing your group 1 is Puberty. > > The taxas in green are the taxas increased in puberty and those in red (increased in non-puberty) are decreased in puberty@Isoken Ibizugbe

Peace Daniel (08:28:09) (in thread): > The Taxas in green are increased in puberty, that means they’ll be decreased in non-puberty and viceversa > > I.e burkholderiales increased abundance in puberty and decreased in non-puberty > While Clostridiaceae increased in non-puberty and decreased in puberty

Nitya Singhal (08:29:09) (in thread): > But i found this in a study and it says a little opposite. - File (PNG): image.png

Nitya Singhal (08:30:30) (in thread): > @Mildred Anashie@Peace Daniel

Mildred Anashie (08:32:04) (in thread): > In my opinion this is specific to the study > > There’s a study I curated and the researchers tagged the increased group as negative and the decrease as positive@Nitya SinghalAlso can you share the full figure?

Peace Daniel (08:32:05) (in thread): > Can you share the fig attached to this img@Nitya SinghalYes I also thinkit’sspecific to the study and sharing the img would help

Isoken Ibizugbe (08:35:06) (in thread): > This is it - File (PNG): IMG_3171

Peace Daniel (08:35:52) (in thread): > @Isoken Ibizugbewe’veresponded to your question. Please check the message I and@Mildred Anashiedropped

Isoken Ibizugbe (08:37:03) (in thread): > I thought u said to share the full image

Peace Daniel (08:39:46) (in thread): > No I was referring to@Nitya Singhal

Nitya Singhal (08:42:25): > @Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido<@UBNSEMS3S>Kindly delete signature 1 of experiment 3 for this studyhttps://bugsigdb.org/Study_1068

Aleru Divine (08:49:07) (in thread): > @Isoken IbizugbeI assume your group 1 is puberty, so your increased group would be the taxa listed in puberty(green) and your decreased group would be non puberty(red).

Isoken Ibizugbe (08:49:26) (in thread): > Yes it is

Esther Afuape (08:54:49) (in thread): > Deleted:white_check_mark:

Joan C. Chukwuemeka (09:01:44): > <!here>It’s time for the Office hour:blush:. Do join in

Leenaa Al-Amin (09:02:24) (in thread): > please can you share the link:pray:

Naomi Ibe (09:02:41) (in thread): > Please can you share the link if you have it?

Oluwatomisin Omojokun (09:04:15) (in thread): > REMINDER: We have our team meeting and office hoursat 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. > > Please double check the meeting time with your local time using this link:https://www.timeanddate.com/worldclock/converter.html?iso=20240328T130000&p1=179&p2=5805 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Naomi Ibe (09:04:58) (in thread): > Thank you

Isoken Ibizugbe (09:10:16) (in thread): > So should we record the other experiments without signatures?

Abiola Salako (09:12:30) (in thread): > I agree with@Aleru Divine

Amanda Adoyi (09:45:47): > Aloha previous Outreachy applicants…I want to know if the Outreachy timeline should be some kind of table with possible tasks on possible dates. eg: “2nd May - 15th May - Review curations” etc.@Esther Afuape@Chioma Onyido@Peace Sandy…

Leenaa Al-Amin (10:02:17): > hello@C. Mirzayi (please do not tag this account), here’s the link to the paper I mentioned during the office hourhttps://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.875101/fullhttps://bugsigdb.org/Study_998. Also, I forgot to mention, the sequencing type used for the brain samples is “RNA-Seq” and it’s not among the dropdown options - Attachment (Frontiers): Frontiers | Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain > A link between the gut microbiome and Parkinson’s disease (PD) has been intensively studied, and more than 100 differential genera were identified across the… - Attachment (BugSigDB): Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain - BugSigDB > A link between the gut microbiome and Parkinson’s disease (PD) has been intensively studied, and more than 100 differential genera were identified across the studies.However, the predominant genera contributing to PD remain poorly understood.

Scholastica Urua (10:02:29): > Hello@Nana:wave:Can we jump on a call concerning recording the final contribution so I guide you through.

Bolanle Wahab (10:03:37): > Big thanks,<@UBNSEMS3S>and@Svetlana Ugarcina Perovic, for the awesome office hours session!Feeling relieved knowing@Aleru Divineand I were on track with our study curation. Your clarification on the sewage samples was a lifesaver - we were totally lost there.:pray:And seriously, thanks for the tip on focusing just on experiments with signatures. That’s a huge weight off our shoulders - bye bye to 72 experiments!:sweat_smile:Thank you everyone!:pray::heart:

Nana (10:03:48): > Sure@Scholastica Urua

Oluwatomisin Omojokun (10:03:59) (in thread): > yes, I need clarification

Peace Daniel (10:03:59): > Hi@C. Mirzayi (please do not tag this account)I wanted to ask this question but time was out.It’ssimilar to what Joan said and I want to know if its fine to notify you on adding new variables for matched on and confounders

Scholastica Urua (10:04:05) (in thread): > Hello@Amanda AdoyiI think it can be any format you personally choose.

Amanda Adoyi (10:04:42) (in thread): > Thank you

Mildred Anashie (10:05:16) (in thread): > I think this works, in my opinion the format can be either table or not:smile:

Aleru Divine (10:06:00) (in thread): > Thank you so much for the session<@UBNSEMS3S>and@Svetlana Ugarcina Perovic:hugging_face:

Amanda Adoyi (10:06:03): > I am realizing that not all papers are curatable and that honestly gives me a headache.

Mildred Anashie (10:06:20) (in thread): > Well done@Bolanle Wahaband@Aleru Divine:heart_hands:

Abiola Salako (10:06:32) (in thread): > Well done@Bolanle Wahaband@Aleru Divine

Mildred Anashie (10:07:22) (in thread): > Hi@Chioma Onyido@Svetlana Ugarcina Perovic@Esther AfuapeShould I go ahead with this?:pray:

Amarachi Lewachi (10:07:37) (in thread): > Same to be honest because how to we tell that a paper is not curatable?

Mildred Anashie (10:08:03) (in thread): > So I asked during the office hour and the response I got was you could orcouldn’tIt’sgoing to be up to you@Isoken Ibizugbe

Amanda Adoyi (10:08:12) (in thread): > Aye…

Peace Daniel (10:08:23) (in thread): > Checking for diversity and differential abundance butthat’d be after reading the whole thing:see_no_evil::sweat_smile:

Scholastica Urua (10:09:12) (in thread): > okay@Oluwatomisin Omojokun

Amanda Adoyi (10:11:02) (in thread): > Even then some papers are not so clear. Like the 144 experiments. I would have started questioning at experiment 12 because wth…why do those even exist? lolz > > Some papers…are just too much.

Peace Daniel (10:12:03) (in thread): > Ngl…that’sa lot of work

Scholastica Urua (10:12:17) (in thread): > I just invited you to the call@Oluwatomisin Omojokun

Amanda Adoyi (10:21:26) (in thread): > @Peace Danielhonestly

Scholastica Urua (10:22:01) (in thread): > @Nanasee this link for the timeline;https://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&cid=C04RATV9VCY - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Rahila-me (10:27:16) (in thread): > @Scholastica UruaThanks a lot for the clarification

Oluwatomisin Omojokun (10:49:38) (in thread): > Thanks for the clarification@Scholastica Urua@Rahila-me

Oluwatomisin Omojokun (10:54:16): > Good day everyone > Please kindly help in reviewing a study by@Oluwatomisin Omojokunand@Nitya Singhalhttps://bugsigdb.org/Study_1068 - Attachment (BugSigDB): The biological effects of microencapsulated organic acids and botanicals induces tissue-specific and dose-dependent changes to the Gallus gallus microbiota - BugSigDB > BACKGROUND: Microencapsulated organic acids and botanicals have the potential to develop into important tools for the poultry industry.

Esther Afuape (10:55:03) (in thread): > Yea please

Mildred Anashie (10:56:34) (in thread): > Okay > > Thank you@Esther Afuape:hugging_face:

Nana (11:10:36): > @Peace Sandyplease I need clarification on this one: When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project. How do we calculate this timeline

Peace Sandy (11:12:46) (in thread): > Hi@Nanathe timeline can be calculated in weeks, the duration of the internship is 12 weeks, so you can structure your goals to fit the timeline which is 12 weeks

Peace Daniel (11:13:05) (in thread): > Hey there, would love to give you a review:hugging_face:

Nana (11:22:42) (in thread): > Ok..thanks

Ima-obong (Aimah) (11:42:40) (in thread): > Hello,@Oluwatomisin OmojokunI’ve just gone through your curation and experiments 1 - 3 have no recorded signatures..which I believe shouldn’t be curated. > > I also went through the paper and truly, these experiments have no differentially abundant signatures. > > For experiment four, the signatures curated are sourced form Figure 4, but checking that figure,it seems as though that figure accounts for relative abundance and not differential abundance.. > As this was stated in the paper > ” The NTC exhibited an increase in LDA of Aerococcaceae etc population relative to the 300g/MT group which corresponds to a decrease in relative abundance, > > Meanwhile relative to 300g/MT, the 500g/MT treatment group had a lower LDA in clostridiaceae etc which translates to increase in relative abundance”…… > > What do you think?

Nitya Singhal (12:06:31) (in thread): > I was also confused about it because in my previous curations I was told to curate differential abundance and not relative so I guess if that is the case then the signatures can’t be added.@Svetlana Ugarcina Perovic@Chioma Onyido<@UBNSEMS3S>what are your opinions?

Peace Daniel (12:08:40) (in thread): > You didn’t include a condition > (I think you should search for effects of Microencapsulated organic acids and effects of botanicals) as it seems this was studied > > Differential abundance was evaluated using the plugin ANCOM

Peace Daniel (12:09:06) (in thread): > Finally, LEfSE analysis was performed per standard practices [65] to determine which populations were enriched by treatment using LDA, which is inversely related to ANCOM data

Peace Daniel (12:09:19) (in thread): > From your article@Nitya Singhal

Ima-obong (Aimah) (12:09:48) (in thread): > @Nitya Singhalyou’re correct and aslo, I think it’s figure 3 that actually has signatures that are differentially abundant in it

Nitya Singhal (12:10:47) (in thread): > @Peace Daniel, actually that condition name is not available. We tried searching for the closest name but couldn’t find any.

Peace Daniel (12:11:42) (in thread): > I’dgive it a look onceI’mdone reviewing your paper

Nitya Singhal (12:14:59) (in thread): > You are right that ANCOM is used for evaluating differential abundance so Fig 3 will help but me and@Oluwatomisin Omojokun, were confused about how to curate it, like which one increased and which decreased. The text provided in the paper talks about relative abundance mostly.

Ima-obong (Aimah) (12:15:15) (in thread): > @Nitya Singhalwhat are you going to do with experiments 1-3 as they have no signatures..me thinks those Experiments shouldn’t be added..Watcha say?

Nitya Singhal (12:17:04) (in thread): > I’ll discuss it with@Oluwatomisin Omojokunfirst and probably gonna drop the experiments with no signatures. However, the experiments that do have signatures are of relative abundance so we need to think about it from the beginning.:sweat_smile:

Peace Daniel (12:17:12) (in thread): > From what I’ve read; > It seems analysis was done based on treatment and location( this had significant alpha diversity) > > In the ileum, there was no difference in treatment by organ. > > Pairwise differences between the treatment groups was instead performed by LEfSE, which is an independent analysis but provides species differences, which was considered significant if the LDA > +/− 2 and Q < 0.05 at the family level. > > However, there were dose-dependent responses observed in the jejunum at the family level

Peace Daniel (12:17:43) (in thread): > I’mstill reading to understand how the ANCOM should be read@Nitya Singhal

Ima-obong (Aimah) (12:18:26) (in thread): > Alright@Nitya Singhal

Nitya Singhal (12:20:38) (in thread): > Yup, I went through all the information@Peace Daniel, and they have performed experiments on 2 body sites, so we had double of similar experiments.

Peace Daniel (12:23:21) (in thread): > Okay

Precious Orakwe (12:27:37): > Good day@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account), please is there any sample or pattern for writing the project timeline on outreachy?

Peace Daniel (12:34:28) (in thread): > According to my understanding and statements from the article > Lactobacillaceae decreased in NTC and increased in 300g/Mt > I.e (NTC vs 300g/Mt) > > Lactobacillaceae decreased in 300g/Mt and increased in 500g/Mt > > So we have a comparison between 3 groups and the charts are compared between the two groups simultaneously > > Another example > Enterobacteriaceae decreased in NTC and increased in the 300 g/MT > But > > Enterobacteriaceae increased in NTC and decreased in the 500 g/MT

Praise Agbetuyi (12:34:32) (in thread): > Oh, I missed the call. Please, is there a recording or summary you could share, I also need clarification on making the final contribution,@Scholastica Urua

Peace Daniel (12:34:56) (in thread): > I can have a meet with you if you still need more explanation@Nitya Singhal

Nitya Singhal (12:37:22) (in thread): > Yes, we knew this and included it in our signatures.

Peace Daniel (12:38:02) (in thread): > Ican’tfind these in your curation tho

Nitya Singhal (12:38:51) (in thread): > We talked about Enterobacteriaceae specifically. Didn’t you find it?

Peace Daniel (12:39:07) (in thread): > I’mreferring to fig 3 which was ANCOM and not lefse

Peace Daniel (12:39:17) (in thread): > Youdidn’tcurate fig 3 I suppose

Nitya Singhal (12:39:53) (in thread): > Ya not from fig 3

Nitya Singhal (12:39:57) (in thread): > but we did consider that

Peace Daniel (12:40:09) (in thread): > AndI don’tthink fig 4 is curable as it was relative abundance

Peace Daniel (12:41:15) (in thread): > Hello, check thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Nitya Singhal (12:44:17) (in thread): > ok we’ll go through this

Melissa Aidée (12:44:41) (in thread): > I’ll check it, thank you very much!!

Abiola Salako (12:47:35) (in thread): > @Precious Orakwekindly go through what@Peace Danielshared above.

Scholastica Urua (12:48:00) (in thread): > Hello@Praise Agbetuyiwe were talking about how to navigate the outreachy website to fill the final application.

Ima-obong (Aimah) (12:48:47) (in thread): > My question though is; can we arrange the timeline in this manner: Week 1- Week6; review of curated papers.. > Week7-Week10; curation of research papers etc. > > Or do we mix them up? E.g. Week1 review curated papers > Week 2 curate research papers ..till the last week

Scholastica Urua (12:48:57) (in thread): > No, there’s no recording of the call. But if you are having challenges I’ll like to help wherever I can. I’m available for another call, just lemme know.

Ifeyinwa Ohondu (12:53:07) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Abiola Salako (12:54:58) (in thread): > @Ima-obong (Aimah)I think your timeline should be based on your personal decision and workload perception. Design it the way that feels right for you or what do you think?

Ima-obong (Aimah) (12:57:48) (in thread): > Thanks@Abiola Salako..just that these things can be a bit confusing…do they also expect a little write-up alongside it or just straight up timeline?…these are the issues:face_with_hand_over_mouth:Guess I’ll do as you said.. follow my lead.

Mildred Anashie (13:00:21) (in thread): > Yea@Ima-obong (Aimah)I guessyou’dwrite based on your personal decision like@Abiola Salakosaid > > It’s your timeline:blush:

Ima-obong (Aimah) (13:01:39) (in thread): > Alright then:smiling_face_with_3_hearts:

Nitya Singhal (13:19:59): > Kindly delete the experiment 2 of the study-https://bugsigdb.org/Study_1075 - Attachment (BugSigDB): Gut microbiota: effect of pubertal status - BugSigDB > BACKGROUND: The make-up of gut microbiota at different puberty stages has not been reported.This cross-sectional study analyzed the bio-diversity of gut microbiota at different puberty stages.RESULT: The subjects (aged 5-15 years) were divided into non-pubertal (n = 42, male%: 66.

Nitya Singhal (13:20:33) (in thread): > @Svetlana Ugarcina Perovic@Peace Sandy@Chioma Onyido<@UBNSEMS3S>@Esther Afuape

Praise Agbetuyi (13:23:34): > Hello everyone, Please for this study,@Blessing Ene Anyebeand I are curating, and I am thinking we use PP as group 1 instead of PV. I need your view, please. - File (PNG): image.png

Sidra Khan (13:24:24): > Hello everyone, I hope you all are doing great. I need some help reviewing this curation I and@Scholastica Uruaare working on this studyhttps://bugsigdb.org/Study_1044. > I’m looking forward to your feedback and insights. - Attachment (BugSigDB): The Airway Microbiota Signatures of Infection and Rejection in Lung Transplant Recipients - BugSigDB > Infection and rejection are the two most common complications after lung transplantation (LT) and are associated with increased morbidity and mortality.We aimed to examine the association between the airway microbiota and infection and rejection in lung transplant recipients (LTRs).

Peace Daniel (13:24:25): > Hello@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma OnyidoIn this curationhttps://bugsigdb.org/Study_412/Experiment_2These were controlled for > “age, alcohol drinking, ethnic group, smoking behavior, cannabis use, homelessness in past six months, number of receptive anal intercourse acts in past month (RAI),number of anal sex partners in past six months, indicator for RAI in past the past seven days, indicator for a positive sexually transmitted infection (STI) test, use of antibiotics in the past month, type of anti-retroviral therapy, pre-exposure prophylaxis, cocaine use” > > My questions: > 1. Can I replace “number of receptive anal intercourse acts in past month (RAI)” with “Anal intercourse” > 2. “use of antibiotics in the past month” with “Antibiotics > ?? - Attachment (BugSigDB): Study 412/Experiment 2 > …

Peace Daniel (13:25:02) (in thread): > Would take a look

Aleru Divine (13:25:22) (in thread): > Can you share the link to the paper please

Chioma Onyido (13:29:32) (in thread): > Deleted.

Peace Daniel (13:30:14) (in thread): > This should be ithttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02125-1 - Attachment (BioMed Central): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BMC Microbiology > Background Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease. Results We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the Dialister. The relative abundance of Phascolarctobacterium and Dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.

Praise Agbetuyi (13:31:04) (in thread): > 10.1186/s12866-021-02125-1 - Attachment (BioMed Central): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BMC Microbiology > Background Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life. The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies. Our objective was to identify differences in the fecal microbial composition of patients with psoriasis compared with healthy individuals to unravel the microbiota profiling in this autoimmune disease. Results We collected fecal samples from 30 psoriasis patients and 30 healthy controls, sequenced them by 16S rRNA high-throughput sequencing, and identified the gut microbial composition using bioinformatic analyses including Quantitative Insights into Microbial Ecology (QIIME) and Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). Our results showed that different relative abundance of certain bacterial taxa between psoriasis patients and healthy individuals, including Faecalibacterium and Megamonas, were increased in patients with psoriasis. It’s also implicated that many cytokines act as main effect molecules in the pathology of psoriasis. We selected the inflammation-related indicators that were abnormal in psoriasis patients and found the microbiome variations were associated with the level of them, especially interleukin-2 receptor showed a positive relationship with Phascolarctobacterium and a negative relationship with the Dialister. The relative abundance of Phascolarctobacterium and Dialister can be regard as predictors of psoriasis activity. The correlation analysis based on microbiota and Inflammation-related indicators showed that microbiota dysbiosis might induce an abnormal immune response in psoriasis. Conclusions We concluded that the gut microbiome composition in psoriasis patients has been altered markedly and provides evidence to understand the relationship between gut microbiota and psoriasis. More mechanistic experiments are needed to determine whether the differences observed in gut microbiota are the cause or consequences of psoriasis and whether the relationship between gut microbiota and cytokines was involved.

Mildred Anashie (13:31:42) (in thread): > Could you share why?@Praise AgbetuyiAlthough I think you might be right > PP can be group 1 because carrying out a little research I saw that PP is more severe and less common

Aleru Divine (13:32:19) (in thread): > Hi@Peace DanielI agree strongly with using “antibiotics”.I also agree with using Anal intercourse in place of receptive anal intercourse.Anal intercourse is a more general term, but I believe it conveys the idea and it iswhat’savailable:thinking_face:

Praise Agbetuyi (13:32:30) (in thread): > This is the link to the curation too.https://bugsigdb.org/Study_1071 - Attachment (BugSigDB): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BugSigDB > Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life.The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies.

Peace Daniel (13:33:05) (in thread): > Yes, awaiting a go ahead from the mentors

Scholastica Urua (13:33:52) (in thread): > I think your grouping is alright@Praise Agbetuyifrom your curation. > You curated Group 0 as Healthy Control

Aleru Divine (13:35:06) (in thread): > You’recorrect@Praise AgbetuyiPP is often more severe than PV.:thumbsup:

Mildred Anashie (13:35:25) (in thread): > I don’tknow if this could mean anything but it seems to say that PV is similar to the healthy control - File (JPEG): IMG_2972

Aleru Divine (13:35:48) (in thread): > Alright

Praise Agbetuyi (13:36:09) (in thread): > But this part got me thinking - File (PNG): image.png

Peace Daniel (13:36:54) (in thread): > I was just about typing what@Mildred Anashieposted about the healthy controls

Aleru Divine (13:36:56) (in thread): > Thatdoesn’tmatter@Praise Agbetuyi

Scholastica Urua (13:36:57) (in thread): > I’ve not been able to check out the article itself though. Poor network:disappointed_relieved:

Mildred Anashie (13:37:37) (in thread): > Thatdoesn’treally show which group is case and control in my opinion@Praise AgbetuyiI’lljust advice you use the PP and be consistent if you have other experiments

Peace Daniel (13:38:11) (in thread): > PP should be group 1 IMO

Scholastica Urua (13:39:38) (in thread): > Thank you@Peace Daniel. We’ll appreciate your review.

Faith Ifeoluwa Alexander (13:40:43): > Good Evening Everyone. Hope we all had a great day & our curations are going smoothly. > > I am currently submitting my second contribution on the Outreachy website. Pls, is it the URL to my study curation that I am to submit or the link to the article I curated?

Aleru Divine (13:41:26) (in thread): > The link to your study curation on BugSigDB@Faith Ifeoluwa Alexander

Scholastica Urua (13:41:26) (in thread): > @Faith Ifeoluwa Alexanderit’s the URL to the BugSigDB curation you’re submitting

Praise Agbetuyi (13:41:53) (in thread): > Ohh, okay. Thank you@Peace Daniel@Mildred Anashie@Scholastica Urua@Aleru Divine

Faith Ifeoluwa Alexander (13:41:58) (in thread): > Okay. Thank you so much.

Mildred Anashie (13:42:45) (in thread): > Exactly what they said@Faith Ifeoluwa Alexander

Blessing Ene Anyebe (13:46:57) (in thread): > Thank you guys so much:orange_heart::orange_heart:

Isoken Ibizugbe (14:05:17): > Can someone please help reviewhttps://bugsigdb.org/Study_1075

UBNSEMS3S (14:28:51): > Today’s office hours recording. Thank you all who attended! - File (MPEG 4 Video): video1476115684.mp4

idiaru Angela (14:31:36) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Scholastica Urua (14:33:09) (in thread): > Thank you<@UBNSEMS3S>

Faith Ifeoluwa Alexander (14:34:18) (in thread): > Pls, I have hit another obstacle. How do I submit a final application after recording my contributions?

Blessing Ene Anyebe (14:34:35) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Faith Ifeoluwa Alexander (14:34:40) (in thread): > I don’t know how to navigate this section.

Faith Ifeoluwa Alexander (14:35:11) (in thread): > Thank you<@UBNSEMS3S>

UBNSEMS3S (14:40:27) (in thread): > Please flag for review on Github and we will get to it as soon as we can.

UBNSEMS3S (14:40:57) (in thread): > Yes sounds good to me.

Aleru Divine (14:42:00) (in thread): > Thank you so much<@UBNSEMS3S>

Faith Ifeoluwa Alexander (14:51:18): > Please I need help in submitting my final application. Anybody who is available should pls help me out. I don’t know how to move forward.

Scholastica Urua (15:01:35) (in thread): > Hello@Faith Ifeoluwa AlexanderHow can I help?

Faith Ifeoluwa Alexander (15:03:46) (in thread): > Thank you. Do I click on this green icon that says “Apply for this project” to go ahead? - File (JPEG): Screenshot_20240328-200256.jpg

Scholastica Urua (15:05:29) (in thread): > Yes, that’s right. > And when you are done, you click submit. Also note that you can still edit the final application after submission until the last day. Which is 2nd of April

Faith Ifeoluwa Alexander (15:06:27) (in thread): > Oh, Okay. Thank you for the heads-up. I appreciate it.

Faith Ifeoluwa Alexander (15:08:00) (in thread): > How do I fill in the past experience section?

Scholastica Urua (15:08:00) (in thread): > Happy to help Faith.

Faith Ifeoluwa Alexander (15:08:13) (in thread): > This is my first time on Open Source.

Ikeh Darlington Ikeh (15:08:44) (in thread): > Alsodon’tforget to record all your contributions,even the ones involving taxa resolution on studies curated by others.

Scholastica Urua (15:09:36) (in thread): > For the past experience, I think you can include none since this is your first time. This is my first time too, so I just recordedNonein that field. > > Hope this is okay?@Chioma Onyido@Esther Afuape@Peace Sandy

Faith Ifeoluwa Alexander (15:12:01) (in thread): > Oh,@Ikeh Darlington Ikeh. If I get you right, I am to include my interactions with everyone in the community.

Ikeh Darlington Ikeh (15:13:56) (in thread): > Thank you:pray:@C. Mirzayi (please do not tag this account), I was looking out for this.

Peace Daniel (15:33:24) (in thread): > Okay, thank you<@UBNSEMS3S>

Adenike Oladimeji-Kasumu (15:42:27) (in thread): > Thank you for sharing@C. Mirzayi (please do not tag this account)

Leenaa Al-Amin (15:56:57) (in thread): > hello@C. Mirzayi (please do not tag this account)so sorry to bother you, I just wanted to remind you about this:sweat_smile:

Amanda Adoyi (16:12:14) (in thread): > Please@Ikeh Darlington Ikehyou’d need to explain a bit more on that.

Peace Daniel (16:33:58): > Hello again:blush:<@UBNSEMS3S>@Svetlana Ugarcina PerovicIn study 833, herehttps://bugsigdb.org/Study_833This statement “Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety > After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety,” > > My questions; > 1. can “Anxiety” be replaced with “anxiety disorder “ which is available on BugSigdb > ? > 2. Can I replace “country “ with “geographic area”? > https://bugsigdb.org/Study_844 - Attachment (BugSigDB): Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes - BugSigDB > BACKGROUND: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify.

UBNSEMS3S (16:40:32) (in thread): > Yes and yes

Peace Daniel (16:41:11) (in thread): > Thank you

Amanda Adoyi (16:54:16): > Please I’d like to know; > “Developing a BugSigDB dashboard and other resources to help promote BugSigDB to researchers.” comes off as something that may be tricky to allocate a timeline to. I imagine dashboard development would require some significant time, like a typical development project would…depending on the scale. ‘Other resources’ here entails what sorts of resources?<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape

Abiola Salako (17:32:30) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Manisha Nair (22:52:52): > Can anyone please help me identify the decreasing group of signatures. Also, is the statistical test I’ve mentioned correct? If yes, what is the significance threshold. Curated Study:https://bugsigdb.org/Study_1010Link:https://journals.asm.org/doi/10.1128/spectrum.05273-22 - Attachment (BugSigDB): The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age - BugSigDB > The World Health Organization recommends untargeted iron supplementation for women of reproductive age (WRA) in countries where anemia prevalence is greater than 40%, such as Cambodia.Iron supplements, however, often have poor bioavailability, so the majority remains unabsorbed in the colon.

2024-03-29

Chimdimma Nwachukwu (00:41:08): > Hi everyone, please can someone help me with the first task to be done?

Adenike Oladimeji-Kasumu (00:50:48) (in thread): > Hello@Manisha NairWell done:+1:In my opinion, the statistical tests you mentioned are correct although I could not determine what the significance threshold is. > Then the source of your signatures in my opinion are kind of hard to curate. I applaud you for taking out information from the Caption to explain the graphs though. I checked your supplementary material and found another graph (figure S5) yet doesn’t look curatable to me. > Let’s wait for another look from any of our colleagues or mentors. - File (JPEG): IMG_20240329_054303_898.jpg

Adenike Oladimeji-Kasumu (00:53:03) (in thread): > Plus, I want to add that Alpha Diversity was mentioned in your paper but it’s not in your curation. Specifically, Richness, Evenness, Shannon and Faith. - File (JPEG): IMG_20240329_050932_634.jpg

Adenike Oladimeji-Kasumu (00:58:54) (in thread): > Hello@Chimdimma NwachukwuI’m not sure what you mean by first task though. Have you recorded any contribution here before now? I am asking because the Bioconductor project had been closed for new entry.

Scholastica Urua (01:29:42) (in thread): > Hello@Manisha Nairwell done on your curation. > In addition to what@Adenike Oladimeji-Kasumuhas highlighted, I noticed a few things; > > There is no information about ‘matched-on’ in the article. I’m guessing you got yours from Table 1. If so, I wouldn’t record that because the study did not specifically mention they were matched on those factors. > > I’m also thinking ‘influence of inflammation’ should be a confounder because of this excerpt from page 2.:thinking_face: - File (PNG): image.png

Manisha Nair (01:34:40) (in thread): > @Adenike Oladimeji-KasumuBut it’s not mentioned whether Shannon, richness and other factors are increasing or decreasing. Which option should I choose?

Aleru Divine (02:23:48) (in thread): > Hi@Chimdimma NwachukwuI also have the same question.Have you recorded any contribution?

Faith Ifeoluwa Alexander (02:25:16): > Good Morning everyone. Hope we had a restful night. > > Pls, I want to know if weekends should be included in our timelines or if that is left to us to decide.

Faith Ifeoluwa Alexander (02:27:06) (in thread): > Hello@Chimdimma Nwachukwu, are you referring to the first contribution for the Bugsigdb project?

Faith Ifeoluwa Alexander (02:28:48) (in thread): > I also have a question as regards this. > > Isn’t this a technical task that will require some technical knowledge and skills?

Ima-obong (Aimah) (02:30:46) (in thread): > @Manisha Nairregarding changes in alpha diversity, here is what I found in your paper; > > The change in four different alpha diversity metrics between weeks 0 and 12 were examined for each trial arm, as depicted in Fig. 2. After P-value correction,**** we found no*****significant differences in alpha diversity***change between placebo and either trial arm.

Ima-obong (Aimah) (02:30:58) (in thread): > Check for this in Fig 2

Mildred Anashie (02:31:11) (in thread): > @Adenike Oladimeji-KasumuFigure S5 isn’t curatable to me as well@Manisha Nairthe indices are said to be unchanged also I do not see any significance there so I agree that there are unchanged > > I think your signature sources are correct because differential abundance wasn’t mentioned anywhere else asides Fig 4 and 5 > > > For the statistical test this is an excerpt from your paper “These samples were then examined for differential microbial abundance using four separate tools: ALDEx2, Corncob, MaAsLin2, and ANCOM-II”. I’m wondering if all four test should be entered > > I see you have 3 experiments > Baseline and week 12 for the three trails > > P value can be 0.05 (The default p value) - File (PNG): IMG_2981

Ima-obong (Aimah) (02:32:47) (in thread): > So from fig2, the alpha diversity metrics stated(evenness, richness, faith and Shanon) are unchanged

Mildred Anashie (02:35:30) (in thread): > I’mnot sure if it should be included or not but we are expected to work for 30hours a week I think you should set the timeline based on your personal schedule/decision:woman-shrugging:@Faith Ifeoluwa Alexander

Peace Daniel (02:35:40) (in thread): > Good morning,Idon’tthink weekends should be included

Peace Daniel (02:36:21) (in thread): > You can always fit the 30 hours during the weekday in my opinion@Faith Ifeoluwa Alexander

Peace Daniel (02:45:04) (in thread): > Hello again, could you inform me why you chose cross sectional as your study design? We seem to have an event-free participants samples were collected from which seems like a control to me > > > Besides this, the curation looks fine to me. > Well done@Sidra Khan@Scholastica Urua

Manisha Nair (02:51:39) (in thread): > @Ima-obong (Aimah)@Mildred Anashiethank you so much for the help. It cleared some of my doubts:relaxed:But, I still can’t figure out the decreasing group of signatures in all 3 experiments. Can anyone please help.

Mildred Anashie (02:54:28) (in thread): > It’sa bithard to tell actually but the fig description showed this@Manisha Nair - File (PNG): IMG_2991

Manisha Nair (02:56:47) (in thread): > @Mildred Anashieit’s difficult to understand the figure even after reading the description:smiling_face_with_tear::smiling_face_with_tear:

Aleru Divine (03:00:13) (in thread): > We’re expected to work 30hours a week@Faith Ifeoluwa Alexander.If the 30 hoursdoesn’tfit in the weekdays.Maybe you can extend to the weekends.That’smore of a personal decisionI’dsay.But at the end of the day, 30hours a week is expected of us.

Mildred Anashie (03:04:26) (in thread): > Yea:smiling_face_with_tear:Very few are clear, I can see Weisella decreased in placebo, Enterococcus is increased in Ferrous sulphate and Escherichia-shigella is decreased in Ferrous sulphate but increased in Ferrous bisglycinate > These are the few I can deduce from that@Manisha Nair

Faith Ifeoluwa Alexander (03:05:35) (in thread): > Okay. Thank you everyone. I was including dates so I wanted to know if I should include weekends.

Scholastica Urua (03:06:45) (in thread): > I noticed that too@Manisha Nair. Deciphering the figure is a bit difficult.

Ima-obong (Aimah) (03:10:34) (in thread): > The figure is a bit difficult to read, I can’t even differentiate the orange from the red lines..well done@Manisha Nair, you can follow@Mildred Anashie’s lead on that.

Manisha Nair (03:15:37) (in thread): > @Scholastica UruaShould I mention ‘age’ in the ‘matched on’ field as the study mentions women between the ages of 18-45 participated in the study? Also, inflammation is not present in the ‘co founders controlled for’ section. Should I just avoid it? - File (PNG): Screenshot (420).png - File (PNG): Screenshot (421).png

Mildred Anashie (03:18:36) (in thread): > You do not avoid inflammation, you record that way > You can also look for a closely related term that can replace that@Manisha NairAlso itdidn’tstate that age was a confounder,that’sthe inclusion criteria

Scholastica Urua (03:19:53) (in thread): > I think the age should not be recorded for matched-on. It has to be stated that they wereage-matched or matched-on agefor it to be recorded.@Manisha Nair

Manisha Nair (03:21:02) (in thread): > @Mildred Anashie@Scholastica UruaThanks for making it clear for me. I understood.

Scholastica Urua (03:21:26) (in thread): > Also, like@Mildred Anashiementioned, look for closely related term for the confounder. But if you can’t find it, it can be recorded that way rather than avoiding it.

Adenike Oladimeji-Kasumu (03:34:41) (in thread): > @Manisha NairYes, it says that the alpha diversity was unchanged in the paper. You can confirm it. > Also,@Mildred Anashieyes, Figure S5 doesn’t look curatable to me. I just sighted it so she could also check as well… When I went through the paper, I saw that Its kind of hard to tell about the signature abundance from the figures

Abiola Salako (03:44:47) (in thread): > Thank you@Aleru Divine@Mildred Anashie@Peace Danielfor your responses.

Joan C. Chukwuemeka (03:47:08) (in thread): > Good morning all, nice inputs here@Manisha NairOn statistical test, the figure you used as source ,mentioned that“Microbiome differential abundance tool *******CornCob******* identified 3 genera” So out the 4 mentioned, the appropriate one of choice should be the one that identified the differentially abundant genera -******CornCob******* So there is noCornCobin BugSigDB. However, I followed the referenced article in your paper at no. 57 [https://doi.org/10.1038/s41467-022-28034-z] , which referenced yet another paper (no. 10) [https://www.nature.com/articles/s41467-022-28034-z#ref-CR10] that provided context on what*****CornCob******* ***** ****is about.CornCobmeans******count regression for correlated observations******with the beta-binomial, This suggests it models read counts (counts of how many times a specific organism’s sequence was detected) using the beta-binomial distribution, which is suitable for proportions within groups. > > For BugSidDB curation,beta-binomial regressionshould be the statistical test, > > I am still trying to decipher the interpretation of the figure though:thinking_face:They said:Colors were used to indicate direction of change with red indicating increase and blue indicating decrease. - Attachment (Nature): Microbiome differential abundance methods produce different results across 38 datasets > Nature Communications - Many microbiome differential abundance methods are available, but it lacks systematic comparison among them. Here, the authors compare the performance of 14 differential… - File (PNG): image.png

Joan C. Chukwuemeka (04:17:15) (in thread): > Eureka!:grin:I think I get it now@Manisha Nairincreased abundance in Ferrous bisglycinate group vs PlaceboEnterobacteriaceaeWeissellaEscherichia-Shigelladecreased abundance in Ferrous bisglycinate group vs placeboEnterococcusincreased abundance in ferrous sulfate group vs PlaceboEnterococcusWeisselladecreased abundance in ferrous sulfate group vs placeboEnterobacteriaceaeEscherichia-ShigellaSo, I think you are supposed to have just 2 experiments: > 1. Ferrous bisglycinate group(group 1) vs Placebo (group 0) > 2. Ferrous sulfate group(group 1) vs placebo (group 0). > Don’t think they were comparing the two case/exposed groups:******Ferrous bisglycinate group vs Ferrous sulfate group.******:thinking_face:

Mildred Anashie (04:22:13) (in thread): > @Joan C. Chukwuemekasamples were collected at 2 timepoints and they were testing the effect of the trial at those time points > > Baseline and week 12 and results are presented that way in my opinion > > I think it should 3 experiments > Baseline vs Week12 for placebo > Baseline vs week 12 for ferrous sulphate > Baseline vs week 12 for ferrous bisglycinate

Adenike Oladimeji-Kasumu (04:24:07) (in thread): > I also think there are 3 experiments as@Mildred Anashiehas listed

Joan C. Chukwuemeka (04:28:33) (in thread): > @Mildred AnashieThey evaluated change between week 0 and week 12. like asking Was there any change from what was seen in week 0 and in week 12? > Example, for Enterobacteriaceae, the answer is in fig 5 description: FIG 5The relative abundance of Enterobacteriaceae showed a small but significant increase***** following the 12-week trial****** with ferrous bisglycinate. *Do you get? > > This suggests that there was a change in the abundance of Enterobacteriaceae between week 0 (before the trial/baseline) and week 12 (after the trial).

Mildred Anashie (04:35:01) (in thread): > I think it’s clearer from the alpha diversity figure,I didn’tlook at that > > The experiments are between the trials and not the time points, you are correct@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:36:23) (in thread): > Alright:+1:@Mildred Anashie

Leenaa Al-Amin (05:05:57): > Good morning@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeand everyone , I have some signatures in my curation without IDs, I’ve searched NCBI and UNIPROT amd was only able to find that of “WAL_1855D” as an unclassified Sporobacterium species, however I’m not sure if I should curate the signature as Sporobacterium sp. WAL 1855D or as the genus Sporobacterium because the table in my paper is referring to genera - File (JPEG): IMG_4810 - File (JPEG): IMG_4813 - File (PNG): IMG_4815

Esther Afuape (05:06:46) (in thread): > Did you check the discussion page? This has been resolved

Leenaa Al-Amin (05:11:27) (in thread): > @Esther AfuapeI just checked thank you:sweat_smile:, so do I curate it as the species or the genera because my paper is dealing with abundant genera

Esther Afuape (05:13:32) (in thread): > Did you find an ID for the genus?

Leenaa Al-Amin (05:17:54) (in thread): > yes I saw the sporobacterium genus ID on NCBI - File (JPEG): IMG_4816

Leenaa Al-Amin (05:18:30) (in thread): > also do I leave the other signatures whose IDs Icouldn’tfind as it is ?

Barakat Akinsiku (05:26:11) (in thread): > Hi@Leenaa Al-Aminyes. It’s okay to leave signatures of IDs you couldn’t find. Hopefully someday they’d be resolved as well

Esther Afuape (05:31:21) (in thread): > Yes leave the ones youcouldn’tfind.WAL is a species of Sporobacterium so curating just Sporobacterium seems too vague.

Manisha Nair (05:31:29) (in thread): > @Joan C. ChukwuemekaYour explanation is really helpful. Thank you so much. I really appreciate it. > I’ve made the required changes. Can you please review it. I’ll request moderators to delete the third experiment.

Joan C. Chukwuemeka (05:35:49) (in thread): > Alright@Manisha NairGlad to help. > > I’d review it and get back to you. Well done.:+1:

Scholastica Urua (05:36:00) (in thread): > Hello@Leenaa Al-Amin, I think you should curateSporobacterium sp. WAL 1855Dinstead of just Sporobacterium. - File (JPEG): WAL.JPG

Manisha Nair (05:43:03): > @Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyPlease delete experiment 3 and it’s signatures from the following study.https://bugsigdb.org/Study_1010 - Attachment (BugSigDB): The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age - BugSigDB > The World Health Organization recommends untargeted iron supplementation for women of reproductive age (WRA) in countries where anemia prevalence is greater than 40%, such as Cambodia.Iron supplements, however, often have poor bioavailability, so the majority remains unabsorbed in the colon.

NWAKAEGO VINCENT (06:22:42) (in thread): > thank you for the recording

Leenaa Al-Amin (06:28:20) (in thread): > alright, thank you all

Flourish Ralph (06:30:06) (in thread): > @Aleru Divineare we also meant to include the hours per weekday/day? > Like Monday - 6 hours?

Aleru Divine (06:35:26) (in thread): > Idon’tknow about that@Flourish Ralph

Flourish Ralph (06:49:15) (in thread): > Okay, thank you

Chioma Onyido (07:02:45) (in thread): > Deleted.

Nana (07:09:16) (in thread): > @Chioma Onyidoif an experiment talked about a case and control, and later now talked generally about the two groups but not as a case or control but both at different time point where the microbiome is increasing at point A and this type of geneus at point B and then this one at point C. What will you put as group 0 and group 1? Will it be the same thing but the different time point?

Peace Daniel (07:12:11): > Hello everyone, it seems BugSigdb is currently under maintenance so there’s no need to fret if you come across it:hugging_face:Wishingy’alla happy Good Friday as well:purple_heart:

Peace Daniel (07:15:34): > Hello<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeWhile trying to resolve processing errors in study 604, link: https://bugsigdb.org/Study_604 > > These variables were confounders: > age, alcohol use, body mass index, sex, geography, loss of 10 lbs in past year, gastrointestinal discomfort on day of stool collection, constipation in past 3 months, fruits or vegetables daily, stool sample travel time, stool sample travel time > > My questions; > 1. can I replace “geography” with “geographic area” as “geographic site” was mentioned in the article > 2. “constipation in past 3 months” with “constipation” > > 3. “alcohol use” with “alcohol drinking”

Esther Afuape (07:19:28) (in thread): > Constipation and alcohol drinking are fine…is the definition of geographic area related to the geographic site mentioned in the paper?

Peace Daniel (07:21:36) (in thread): > Okay thanks, I’ll confirm this once BugSigdb is up again@Esther Afuape

idiaru Angela (07:23:11) (in thread): > Hi@Chioma OnyidoI’ve already submitted this paper for review but in yesterday’s office hour, chloe said we could curate environmental samples. I’d like to know If it’s possible for me to add the missing experiments to this study before it is reviewed. Thank you.

Mildred Anashie (07:27:17) (in thread): > Yea@Peace DanielI noticed itwasn’tresponding and was showing error when I tried to edit signatures

Peace Daniel (07:32:46) (in thread): > It’sworking fine now@Mildred Anashie

Mildred Anashie (07:33:17) (in thread): > OkayI’lltry again, thank you:pray:

Peace Daniel (07:34:41) (in thread): > Yes the geography mentioned was (Seattle, Atlanta and Albany) all in USA and same location of thesubjects recorded in the study@Esther Afuape

Blessing Ene Anyebe (07:52:10): > Hello everyone, for the Christians from around the world, happy Good Friday to you.:orange_heart:I would love your thoughts on this: How do you determine the LDA score? (Most studies I have seen it is usually not stated.) > > In this study@Praise Agbetuyiand I are curating it says “LefSe analysis was performed to identify differentially abundant taxa, which are highlighted on the phylogenetic tree in cladogram format and for which theLDA scores are shown.” > > In this case how is the LDA score determined? > > Thank you everyone. - File (PNG): image.png

Mildred Anashie (07:54:44) (in thread): > Hi@Blessing Ene AnyebeHappy Good Friday to you too:hugging_face:You can use the default if itisn’tstated > See thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1709738784493999?thread_ts=1709738367.253199&channel=C04RATV9VCY&message_ts=1709738784.493999 - Attachment: Attachment > The default LDA value is 2.00 in LefSe. For p value they stated: “P values < 0.05 were considered statistically significant.”

Peace Daniel (07:55:48) (in thread): > Yes, the default is 2.00

Blessing Ene Anyebe (07:56:01) (in thread): > You’re awesome@Mildred AnashieThank you:orange_heart:

Mildred Anashie (07:56:46) (in thread): > Thank you and You are welcome:hugging_face:@Blessing Ene Anyebe

Aleru Divine (08:00:01) (in thread): > Happy Good Friday to you too:hugging_face:

Aleru Divine (08:00:55) (in thread): > Thank you Peace:hugging_face:Happy Good Friday to you too.BugSigDB works fine now:blush:

Blessing Ene Anyebe (08:01:03) (in thread): > Happy Good Friday@Aleru Divine:orange_heart:

Peace Daniel (08:02:52) (in thread): > Yes,it’sfine now

Scholastica Urua (08:33:25) (in thread): > Hello@Peace DanielThank you for your feedback. > We didn’t go with case-control because all participants were lung transplant recipients (LTRs). They were just grouped differently. Although there is clinically stable (event-free) participants in the study, they were not really healthy control from my opinion. > > What do you think of this?

Peace Daniel (08:38:58) (in thread): > Alright, this makes sense as well@Scholastica Urua

Kelechi Madubuko (08:49:00) (in thread): > Thank you<@UBNSEMS3S>

Joan C. Chukwuemeka (08:51:10) (in thread): > @Manisha Naircondition is what is contrasted between groups. In this case,nutritional supplement exposure measurementhttp://www.ebi.ac.uk/efo/EFO_0600066is more related. Though still searching EFO for one possibly specific to iron - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Linda Uchenwoke (09:28:57) (in thread): > Hello<@UBNSEMS3S>Please help us:pray:

Joan C. Chukwuemeka (09:43:26) (in thread): > Signature description can be:Description:Differentially abundant bacterial Taxa in the Ferrous bisglycinate group compared to the Placebo group. > > makes it less vague.

Esther Afuape (09:56:23) (in thread): > You can go ahead then

Blessing Ene Anyebe (10:10:22) (in thread): > Thank you@C. Mirzayi (please do not tag this account):rocket:

Oluwatomisin Omojokun (10:11:43) (in thread): > Happy good friday everyone:heart:

USLACKBOT (10:19:58): > This message was deleted.

Esther Afuape (10:28:05) (in thread): > The groups compared always make up the group 1 and 0. You can add the time point for it to be well described.Group A at timepoint 1 vs group B at timepoint 1

Sidra Khan (11:03:07) (in thread): > Hi@Peace Daniel, thanks for the review. I second@Scholastica Uruaon this question. Also, it is mentioned in the study, below is the screenshot you can check - File (PNG): image.png

Peace Daniel (11:18:02) (in thread): > Okay, thank you@Esther Afuape

Peace Daniel (11:18:48) (in thread): > This is a confirmation,thanks for sharing@Sidra Khan

Svetlana Ugarcina Perovic (11:34:09): > It’s Friday – we did it! Another amazing BugSigDB week!And, happy Easter weekend to those who celebrate :hatching_chick:<@U1LCB8WEA><@UBNSEMS3S>@Peace Sandy@Esther Afuape@Chioma Onyido@Svetlana Ugarcina Perovic

Peace Daniel (11:34:55) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy Easter:hatching_chick:

Mildred Anashie (11:35:26) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy weekend to you and all the mentors:hugging_face:

Blessing Ene Anyebe (11:35:35) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy Easter:orange_heart::orange_heart::orange_heart:

Svetlana Ugarcina Perovic (11:36:56) (in thread): > @idiaru Angelado not worry, curation of environmental samples is optional. If you are really into adding soil signatures, go ahead :)

Rahila-me (11:39:29) (in thread): > Happy BugSigDB week! to everyone and Easter celebration

Adedoja Isaac (11:44:05) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (11:58:06) (in thread): > Thanks@Svetlana Ugarcina PerovicHappy Good Friday everyone:seedling:

Barakat Akinsiku (12:08:43) (in thread): > Thank you@Svetlana Ugarcina Perovicand Happy Good Friday and Easter to everyone:partying_face::partying_face:

idiaru Angela (12:12:35) (in thread): > Thank you@Svetlana Ugarcina Perovic. I’ll just let it be then not to cause any confusion.

Leenaa Al-Amin (12:21:37): > hello@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuapeand everyone . In the meta-analysis I’m curating, the sequencing type for the brian samples is “RNA-Seq” whichisn’tan option in the drop-down - File (JPEG): IMG_4800

Aleru Divine (12:26:06) (in thread): > Yay! Thank you@Svetlana Ugarcina PerovicHappy Easter to everyone celebrating:hugging_face:

Scholastica Urua (12:46:22) (in thread): > Hello@Leenaa Al-AminI can see 16S sequencing type too. I think this thread will be helpful to you since you are curating a meta analysis.:hugging_face:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710237489267499?thread_ts=1710228540.842369&cid=C04RATV9VCY - Attachment: Attachment > What I would probably do in the case of meta-analysis where there isn’t a consistent answer, would be just to leave that field blank since none of the ones under discussion here are mandatory. But honestly all of the solutions already proposed here are reasonable! :sweat_smile: In any case, discussion like this what you’ve pointed out @Scholastica Urua should definitely go on the “Discussion” page for this study, so it will be available to anyone wondering in the future why you made the choice you did.

Bolanle Wahab (13:12:34) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy Easter everyone:partying_face::heart:

Leenaa Al-Amin (14:25:02) (in thread): > Thank you@Scholastica Urua, just to be clear, I should leave it that field blank as well as state my reason for doing so on the discussion page for the study?

Aleru Divine (14:27:35): > Hi@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma OnyidoPlease I would like to delete signature 2 in the experiment 1 of this study.https://bugsigdb.org/Study_879Thank you so much! - Attachment (BugSigDB): Oral lesion and microbiome diversity in COVID-19 hospitalized patients - BugSigDB > INTRODUCTION: The oral cavity is an important site for the entry and multiplication of respiratory viruses, and the immune system and oral microbiome act as antiviral barriers.Data regarding oral microbiome and COVID-19 is scarce.

Scholastica Urua (14:34:55) (in thread): > I think you should capture all the information possible. Then still leave a note to explain the once you couldn’t capture.

Samreen Aftab (14:49:13): > Hello everyone > The sequencing type here is PCR right? - File (PNG): image.png

Mildred Anashie (14:54:05) (in thread): > What I see here is 18s, V6-V7 regions > > Not sure if this is right:thinking_face:@Samreen Aftab

Samreen Aftab (14:55:04) (in thread): > Yeah I noticed that too@Mildred Anashiebut that is not in the drop-down:crying_cat_face:

Mildred Anashie (14:56:25) (in thread): > Yea itisn’tDon’tknow if this can be curated or we are missing something:face_with_diagonal_mouth:

Samreen Aftab (14:57:32) (in thread): > <@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma OnyidoCan you help a bit here please ?

Samreen Aftab (14:58:34) (in thread): > @Mildred AnashieAnother quick query. The statistical test is for the beta diversity right? I got a little confused:sweat_smile:

Mildred Anashie (14:59:32) (in thread): > I’mnot sure I understand@Samreen Aftab

Samreen Aftab (15:02:25) (in thread): > Here, the statistical test is PERMANOVA right?@Mildred Anashie - File (PNG): image.png

Samreen Aftab (15:04:47): > Can anyone give this paper a read? I can’t find any figures/tables to curate:smiling_face_with_tear:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8602383/@Aleru Divine@Mildred Anashie@Scholastica Urua - Attachment (PubMed Central (PMC)): Association between Parkinson’s disease and the faecal eukaryotic microbiota > Parkinson’s disease (PD) is one of the most common neurodegenerative disease, and is so far not considered curable. PD patients suffer from several motor and non-motor symptoms, including gastrointestinal dysfunctions and alterations of the enteric …

Mildred Anashie (15:05:35) (in thread): > No PERMONOVA is for beta diversity like you pointed out > > We record the statistical test used for differential abundance > > The statistical test is Wilcoxon-Mann-Whitney test > > See this excerpt “To find significant differences in feature counts between PD and controls, a two-sided Wilcoxon-Mann-Whitney test for…”

Samreen Aftab (15:06:33) (in thread): > Ah okay, thank you@Mildred Anashie

Scholastica Urua (15:06:41) (in thread): > Will do that now@Samreen Aftab

Mildred Anashie (15:07:00) (in thread): > I’lltake a look@Samreen Aftab

Aleru Divine (15:09:30) (in thread): > I will take a look@Samreen Aftab

Mildred Anashie (15:11:40) (in thread): > So I see Table 1 showing taxas that differed significantly between PD and controls but I’m still trying to understand the table@Aleru Divine@Scholastica UruaAnd thereisn’tmuch information in text:face_with_diagonal_mouth:

Scholastica Urua (15:13:21) (in thread): > Fig 2a is showing alpha diversity between Control vs PD. So that’s curable. Still checking out the table@Mildred Anashie - File (PNG): Screenshot_20240329-201206.png

Aleru Divine (15:13:34) (in thread): > I’mtrying to make sense of it@Mildred Anashie:sweat_smile::cold_sweat:

Mildred Anashie (15:14:56) (in thread): > Yea@Scholastica Uruathat’ll help us know the comparison that was done

Samreen Aftab (15:16:48) (in thread): > yes@Scholastica UruaIt seems like i have to record only the experiment without any signatures, but is that okay?

Scholastica Urua (15:17:48) (in thread): > Yes, it’s okay to have an experiment without signatures (if there’s none).

Mildred Anashie (15:18:44) (in thread): > It’sokay to record an experiment without signatures@Samreen Aftabbut I thinkthere’san information in that table if we can decipher it > > I hopeI’mright:smile:

idiaru Angela (15:19:02) (in thread): > It seems you can decipher table 1 using the mean values@Samreen AftabIf you check below each taxa, the mean value for pd and control is shown using the mean, you’d know which was increased and decreased in the PD and control group

idiaru Angela (15:20:50) (in thread): > For instance , in the first taxa, the mean is higher in PD than it is in control. It means the taxa increased in PD. I guess this table is quite similar to one@Chioma Onyidohelped us decipher a while back - File (JPEG): Screenshot_20240329_201938_Samsung Internet.jpg

Mildred Anashie (15:21:01) (in thread): > Guys see this…:thinking_face: - File (JPEG): IMG_3009

idiaru Angela (15:22:04) (in thread): > @Mildred Anashiethe image you sent definitely refers to differential abundance from table 1.

Aleru Divine (15:22:29) (in thread): > Oh this makes sense@Mildred Anashie

Mildred Anashie (15:23:33) (in thread): > Yea my thoughts exactly@Aleru Divine@idiaru Angela

idiaru Angela (15:23:39) (in thread): > Table 1 is deciphered using the mean. If you use the mean to solve the differential abundance, it correlates with what is in the text@Mildred Anashiesent.@Samreen Aftab

Scholastica Urua (15:24:00) (in thread): > This is more understandable and is also referencing table 1@Mildred Anashie

Mildred Anashie (15:26:13) (in thread): > @Samreen AftabI hope the text, table 1 and@idiaru Angelaexplanation on the mean helps you understand differential abundance for the experiment > > Also I think you have just one experiment > And the Statistical test is stated under the table andit’sMann Whitney-Wilcoxon

Scholastica Urua (15:27:23) (in thread): > Also guys, did you notice it uses 18S sequencing (V6 - V7)? > Which is not available on BugSigDB.

Mildred Anashie (15:28:10) (in thread): > Yea@Scholastica UruaWe were discussing that herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711738153074479 - Attachment: Attachment > Hello everyone > The sequencing type here is PCR right?

idiaru Angela (15:28:49) (in thread): > Yeah@Scholastica Urua. Maybe it might be added to the options:thinking_face:

Scholastica Urua (15:31:15) (in thread): > I just went through the thread now@Mildred Anashie. Noticed there was no conclusion on how to proceed…

Scholastica Urua (15:32:02) (in thread): > I guess we’ll have to lookout for the mentors response on that.

Aleru Divine (15:32:34) (in thread): > 18S rRNA, definitely the first time I’m seeing this.

Samreen Aftab (15:38:25) (in thread): > Thank you guys for the help!:hugging_face::face_holding_back_tears:

idiaru Angela (15:39:57) (in thread): > You’re welcome!

Peace Daniel (16:05:04): > Hello again<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Peace Sandy@Esther Afuape@Chioma OnyidoFinal question for the day:hugging_face: > 1. In this study, here:https://bugsigdb.org/Study_530 > Confounders controlled for: > age, body mass index, race, sex, alcohol consumption, total energy intake, disease status at the first follow-up and sequencing batch, oral health statusQuestions: > * Can I replace “alcohol consumption” with “alcohol drinking” > > * “Oral health status” with “oral hygiene” > 2. In another study, here:https://bugsigdb.org/Study_815Confounders controlled for: > diet, symptoms, mode of delivery, age at visit, Probiotics use in the first year of life > > Questions: > * can I replace “mode of delivery” with “mode of birth” > * “age at visit” with “age” - Attachment (BugSigDB): Longitudinal disease-associated gut microbiome differences in infants with food protein-induced allergic proctocolitis - BugSigDB > BACKGROUND: Complex interactions between the gut microbiome and immune cells in infancy are thought to be part of the pathogenesis for the marked rise in pediatric allergic diseases, particularly food allergies.

Mildred Anashie (16:07:19): > I think age can replace age at visit@Peace DanielWell done:+1:

Aleru Divine (16:08:50) (in thread): > Hi@Peace DanielI agree with > Alcohol consumption > Mode of birth > Age:hugging_face:I’ll be on the lookout for response from the mentors:eyes:

Peace Daniel (16:12:32) (in thread): > Oral health status is a bit tricky but the study was based on cigarette smoking and oral microbiota, so I think it might suffice:thinking_face:

Leenaa Al-Amin (16:17:02) (in thread): > @Scholastica Uruaplease where do I leave the note, I’m not familiar with how to do that, the only discussion page I know of is that of missing ncbi ids:sweat_smile:

Scholastica Urua (16:17:47) (in thread): > You’ll leave the note on the talk page.

Aleru Divine (16:19:13) (in thread): > Yeah,it’sa bit tricky.:grimacing:“Oral health status” sort of refers to the overall condition of the oral cavity of an individual, on the other hand, “oral hygiene” specifically refers to the practices and behaviors involved in maintaining oral health. > > Does the study mention anything on oral hygiene practices? > > Let me have a look.

Scholastica Urua (16:19:41) (in thread): > This will guide you on creating a talk page@Leenaa Al-Aminhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710233489795919?thread_ts=1710232358.053269&cid=C04RATV9VCY - Attachment: Attachment > Steps on creating a ‘Talk’ page; > 1. Open your curation > 2. Click on the three dots above (Image 1) > 3. Click on ‘Discussion’ (Image 2) > 4. A talk page will be created were you can write up your discussion. > 5. When done, scroll down to save page. > Hope this helps. > PS: I’m using this study as a sample, I’m not making any edits to it.

Leenaa Al-Amin (16:21:19) (in thread): > thank you so much@Scholastica Urua:pray:

Scholastica Urua (16:21:49) (in thread): > You’re welcome@Leenaa Al-Amin

Samreen Aftab (16:22:33): > Hello again everyone, can anyone please review this curation? > I have two questions here: > 1. The sequencing type here is 18S, however it is not in the drop-down of bugsigdb. > 2. There was no mention of Lefse in the paper, so should I input the default value of LDA or should I just leave it blank? > Thank you.https://bugsigdb.org/Study_992 - Attachment (BugSigDB): Association between Parkinson’s disease and the faecal eukaryotic microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disease, and is so far not considered curable.PD patients suffer from several motor and non-motor symptoms, including gastrointestinal dysfunctions and alterations of the enteric nervous system.

Aleru Divine (16:23:38) (in thread): > @Samreen Aftabif no mention of LEfSe, then leave out filling the LDA.I have no idea on what to do regarding your first question:pleading_face:

Peace Daniel (16:25:33) (in thread): > That’sa first,you’llneed to wait for the mentors regarding your first question:smiling_face_with_tear:

Peace Daniel (16:25:52) (in thread): > Please do@Aleru Divine

idiaru Angela (16:29:31) (in thread): > @Samreen Aftabit’s the sequencing type that you need clarification on. You mentioned statistical test instead

Samreen Aftab (16:34:07) (in thread): > you’re correct. I apologize for the error@idiaru Angela

Scholastica Urua (16:41:07) (in thread): > LDA score is only applicable for LeFse@Samreen Aftab. We already discussed your first question in the previous post. I think we’ll have to wait for the mentors concerning that.:disappointed_relieved:

Aleru Divine (17:05:56) (in thread): > Ican’tseem to find the full text:sleepy:

Peace Daniel (17:19:18) (in thread): > Here@Aleru Divinehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6913090/ - Attachment (PubMed Central (PMC)): Cigarette smoking and oral microbiota in low-income and African-American populations > Cigarette smoking is a common risk factor for diseases and cancers. Oral microbiota is also associated with diseases and cancers. However, little is known about the impact of cigarette smoking on the oral microbiota, especially among ethnic minority populations.We …

Chioma Onyido (18:04:39) (in thread): > In my past curation experiences, I’ve encountered a similar situation, but ITS instead. > > Typically when ITS is used, it’s for fungal studies. > 16S sequencing is commonly used for prokaryotes. > 18S sequencing on the other hand is used for sequencingeukaryotes. > How to curate this is what I’m not sure of since there’s no drop down option specifically for 18S in bugsigdb, you can go ahead with the rest of the curation pending when the mentors respond. You’ve to be patient too, replies might come in a bit slow due to the Easter holidays.@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>a likkle help here please. - Attachment (cd-genomics.com): Eukaryotic 18S rRNA Sequencing - CD Genomics > Our eukaryotic 18S rRNA sequencing service aims to reveal the eukaryotic diversity, evolutionary relationship of eukaryotes, and the correlation between eukaryotes and the environment.

Peace Daniel (18:46:41) (in thread): > @Chioma Onyidodo you think oral hygiene would suffice in this case pls?

Mildred Anashie (19:53:14) (in thread): > See this@Melissa Aidéehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711749879265819?thread_ts=1711739087.953669&cid=C04RATV9VCY - Attachment: Attachment > In my past curation experiences, I’ve encountered a similar situation, but ITS instead. > > Typically when ITS is used, it’s for fungal studies. > 16S sequencing is commonly used for prokaryotes. > 18S sequencing on the other hand is used for sequencing eukaryotes. > How to curate this is what I’m not sure of since there’s no drop down option specifically for 18S in bugsigdb, you can go ahead with the rest of the curation pending when the mentors respond. You’ve to be patient too, replies might come in a bit slow due to the Easter holidays. > @Svetlana Ugarcina Perovic @U1LCB8WEA @UBNSEMS3S a likkle help here please.

Mildred Anashie (19:53:50) (in thread): > Thank you@Chioma Onyido:hugging_face:

Aleru Divine (21:06:01) (in thread): > Thanks for sharing the paper@Peace Daniel

2024-03-30

Samreen Aftab (00:01:24) (in thread): > Thank you@Mildred Anashie@Chioma Onyido:blush:

Scholastica Urua (00:27:55) (in thread): > Thank you@Chioma Onyido

Scholastica Urua (00:45:52): > Hello@Svetlana Ugarcina Perovic,@Chioma Onyido,@Esther Afuape,@Peace Sandyand everyone, happy weekend.:hugging_face:Please when similar taxa are documented to be increased or decreased how should that be curated? Like in this case:point_down: - File (JPEG): similar.JPG

Samreen Aftab (00:46:46): > Good morning everyone, if you’re working on a paper, and need any help, please let me know. I’m free now and would be happy to collaborate!:blush:

Samreen Aftab (01:01:56) (in thread): > I think you should curate them separately.@Scholastica Urua

Scholastica Urua (01:19:31) (in thread): > Yeah, but I don’t think one name can come up twice in the same group when you are entering them on BugSigDB. I don’t know if I’m making sense.:disappointed_relieved:

Samreen Aftab (01:23:31) (in thread): > Are you recording the signatures like OTU294|Parabacteroides or just Parabacteroides? > If it’s the latter, I think you should record it as one signature.@Scholastica Urua

Adenike Oladimeji-Kasumu (02:20:15) (in thread): > I’m seeing something like this for the first time. I’ll be looking forward to other contributions on how these signatures should be curated. > It would have been so simple if they were distinct species. > Well done@Scholastica Urua

Adenike Oladimeji-Kasumu (02:22:48): > Happy weekend everyone:tada:I trust that we’re all doing well. > I am also free to help with reviews and I am opening to collaborative curation.

Scholastica Urua (02:34:07) (in thread): > @Samreen AftabI’m just recording ‘Parabacteroides’ without the OTU…

Scholastica Urua (02:35:27) (in thread): > Happy weekend@Adenike Oladimeji-Kasumu:hugging_face:

idiaru Angela (02:41:20) (in thread): > Hey@Scholastica Uruain a previous thread that I’ll try to find, I believe we were asked to curate them as they appear. So one taxa can appear in both increase and decrease groups

Joan C. Chukwuemeka (02:41:35) (in thread): > 18s rRNA sequencing… that’s quite interesting and different from the popular ones we see. > > Was quite curious why they may choose that over, perhaps 16s.:thinking_face:… Checked out the difference between the two: here’s what I found:point_down:Both 18S rRNA and 16S rRNA sequencing are techniques used to analyze ribosomal RNA (rRNA) genes for the purpose of identifying and classifying organisms within a sample. However, they target different types of organisms based on the kind of rRNA present:18S rRNA sequencing: Targets eukaryotes. It analyzes the 18S rRNA gene found in the small subunit of eukaryotic ribosomes. This is useful for studying the diversity of fungi, protists, and other complex organisms in a sample.16S rRNA sequencing:******Targets prokaryotes (bacteria and archaea)******. It analyzes the 16S rRNA gene found in the small subunit of prokaryotic ribosomes. This is the gold standard technique for studying bacterial communities in various environments like soil, gut microbiome, or oceans. > > Although It’s weekend, I believe we’d hear from the mentors on how this can be captured/curated into BugSigDB, once they are available.<@U1LCB8WEA>@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma Onyido

Samreen Aftab (02:45:53) (in thread): > @Scholastica Uruathen I don’t think you have any other option except recording them as one signature. > I am looking forward to inputs from our mentors and fellow contributors tho.

idiaru Angela (02:46:26) (in thread): > Here@Scholastica Uruahttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710517426265079?thread_ts=1710516856.042729&cid=C04RATV9VCY - Attachment: Attachment > Yes it’s possible. I’ve come across this and we had a discussion with @Svetlana Ugarcina Perovic a while ago about why this is. Let me look for the thread, should be among my saved items…

Mildred Anashie (02:52:07) (in thread): > Happy weekend@Adenike Oladimeji-Kasumu:blush:

Abiola Salako (02:52:48) (in thread): > Well done@Adenike Oladimeji-Kasumu

Samreen Aftab (02:53:11) (in thread): > @idiaru AngelaI don’t think she’s asking about a signature in two contrasting groups. I think she’s asking how similar taxa should be recorded like OTU294 and OTU293 Parabacteroides:thinking_face:

Samreen Aftab (02:53:43) (in thread): > Happy weekend@Adenike Oladimeji-Kasumu. Enjoy your day!

Mildred Anashie (02:54:33) (in thread): > You might have to record just one@Scholastica UruaCan you check text if the taxas were mentioned that way in text?This might seem like different strains:thinking_face:

idiaru Angela (02:55:30) (in thread): > Oh true@Samreen Aftab. I still do believe they would be recorded as 1:thinking_face:. Since the OTU number aren’t being recorded. There’s no way to differentiate them

Samreen Aftab (02:56:14) (in thread): > Yes@idiaru AngelaI believe so too.

Abiola Salako (02:56:54) (in thread): > Thank you@Chioma Onyido

Adenike Oladimeji-Kasumu (03:02:55) (in thread): > Thank you for sharing that@idiaru AngelaI definitely missed that thread. I didn’t know it was possible

Scholastica Urua (03:07:06) (in thread): > Thank you for the thread@idiaru Angela:pray:@Mildred Anashiethere’s a supplementary material but it’s also recorded that way. And this is not the only one, there’s a couple of them like this in the study. > > What I did was to record as 1 but include a note on the talk page. Thought to share here for more opinions.

idiaru Angela (03:10:08) (in thread): > I think what you did is good enough@Scholastica Urua:+1:

Mildred Anashie (03:12:43) (in thread): > That’s okay@Scholastica UruaThere’s this study I’m editing Missing NCBI taxas and I saw this (Image) The curator curated including the rank since the same taxas were reported and there are no NCBI IDs for themIf it was specified, Genus or Family like this I think it’d have been easier to curate bothBut what you’ve done so far is okay - File (JPEG): IMG_3026

Scholastica Urua (03:13:27) (in thread): > Thank you@Mildred Anashieand@idiaru Angela:pray:

Abiola Salako (03:20:15) (in thread): > @Scholastica UruaI want to believe you’re on the right track. Welldone

Abiola Salako (03:31:22): > Morning everyone. > Trust we all are doing well. > I just want you to know that I am open to any collaborative opportunity. Thank you:bouquet:

Scholastica Urua (03:33:38) (in thread): > This is the curation, I’m collaborating with@Hamza Hajion it. Although we are still working on it, we’ll really appreciate peer-review.:hugging_face:https://bugsigdb.org/Study_978

Scholastica Urua (03:34:09) (in thread): > Good morning@Abiola Salako

Abiola Salako (03:41:48) (in thread): > @Scholastica Uruathere’s an ID for Prevotella 1-8 I don’t know if that can suffice here and then you leave a note stating it was 2 that was mentioned or you leave it like that or wait for other people’s input before proceeding. - File (JPEG): Screenshot_20240330_083620_Slack.jpg

Scholastica Urua (03:52:41) (in thread): > Thank you@Abiola Salako. Will look into it.

Amarachi Lewachi (04:05:19) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic. Goodluck to all applicants.

Praise Agbetuyi (04:53:25) (in thread): > I am doing fine. Thank you. > > Happy weekend@Adenike Oladimeji-Kasumu

Praise Agbetuyi (04:55:55) (in thread): > Happy weekend:blush:

Praise Agbetuyi (04:57:12) (in thread): > Good morning and happy weekend@Abiola SalakoNoted.

Amarachi Lewachi (05:13:18): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@C. Mirzayi (please do not tag this account). As part of the outreachy final application, we are required to provide an internship project timeline. Kindly provide this information. Thank you

idiaru Angela (05:14:06) (in thread): > Here@Amarachi Lewachihttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&cid=C04RATV9VCY - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Amarachi Lewachi (05:16:11) (in thread): > Thank you so much@idiaru Angela

Aleru Divine (05:18:36): > Good morning and happy weekend everyone, I’d like to get reviews and opinions on this study I just finished curating:pray:Thank you in anticipationhttps://bugsigdb.org/Study_879 - Attachment (BugSigDB): Oral lesion and microbiome diversity in COVID-19 hospitalized patients - BugSigDB > INTRODUCTION: The oral cavity is an important site for the entry and multiplication of respiratory viruses, and the immune system and oral microbiome act as antiviral barriers.Data regarding oral microbiome and COVID-19 is scarce.

idiaru Angela (05:24:55) (in thread): > Would look through and give you feedback

Aleru Divine (05:32:15) (in thread): > Thank you so much@idiaru Angela

ayesha khan (05:36:37): > Hello everyone .Hope you are doing well . Just wanted you to know that I open for any help .Thank You

ayesha khan (05:51:16): > Also since we are almost near the end of contribution phase , I wanted to thank all the fellow contributors and@Svetlana Ugarcina Perovicfor being so kind and helpful throughout. This was my first time contributing to an opensource community but you guys were so helpful throughout , even to dumbest questions of mine . It was truly a learning experience . This community has taught me much more than just curating studies:smile:.@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape<@UBNSEMS3S>I truly appreciate you and your work .Hoping to keep contributing to this community .:crossed_fingers:

Mildred Anashie (06:01:08) (in thread): > Yea I agree@ayesha khanAll the mentors have been truly amazing and helpful:hugging_face:

Ima-obong (Aimah) (06:04:25) (in thread): > @ayesha khan..it’s really been an awesome experience for me too.. the mentors have really been super helpful.

idiaru Angela (07:03:19) (in thread): > Hey@Aleru Divinewell done on this curation. Seems a bit confusing since the differential abundance results were not in tables but in the text. I have one observation though. I think making the source of the signatures more specific would be great. That way anybody who comes across the curation can easily identify the source of the signature rather than searching the entire text for it > A source like “paragraph 2 under discussion text” might work better

Aleru Divine (07:05:15) (in thread): > Thank you so much for going through this for me@idiaru AngelaI really appreciate it:heart:You suggestion makes so much sense.I will update the descriptions to be more specific.Thank you so much:pray:

idiaru Angela (07:09:11) (in thread): > Also for the condition for Experiment 1 are you sure it is to have 2 conditions:thinking_face:. Seems to me like oral lesions as the condition is good enough since both groups already have Covid 19@Aleru Divine

idiaru Angela (07:10:17) (in thread): > For Experiment 2 I have same observation. The contrast there seems to be disease severity rather than Covid 19

Aleru Divine (07:10:49) (in thread): > I was also thinking about that.:sweat_smile:I will just leave oral lesions then. Thanks again

Aleru Divine (07:11:25) (in thread): > That would mean changing for all of them.

idiaru Angela (07:13:32) (in thread): > Yes@Aleru DivineI can’t remember the curation now, but in one of the reviewed studies, it was mentioned that the condition should be what was contrasted. If the 2 groups being contrasted have the same disease then it is no longer the condition. > I’m not sure if you get what I’m trying to say:sweat_smile:For instance, in one of the experiments, oxygen therapy is what is contrasted between the two groups of patients who have covid 19

Aleru Divine (07:21:05) (in thread): > I understand.:sweat_smile::hugging_face:

idiaru Angela (07:21:09) (in thread): > Also@Aleru DivineI think you should review the data transformation. I’m of the opinion that it is relative abundances rather than raw counts even tho Deseq2 was used for statistical analysis

Aleru Divine (07:24:59) (in thread): > The study mentions reads were obtained though@idiaru Angela. > Why do you suggest relative abundance?

idiaru Angela (07:28:15) (in thread): > “The fastQ files obtained were processed and analyzed using QIIME 2 (Quantitative Insights Into Microbial Ecology version 2020.11). Sequences such as primes, barcode and chemeric reads were removed using the DADA2 software package enclosed in QIIME2 (BOLYEN et al., 2019). The parameters used included amplicons of 260 bp with an average Phred score of 30 or higher, resulting in the generation of amplicon sequence variants (ASVs). The taxonomy was constructed by inserting the sequences into Silva using the q2-fragment-insertion plugin, which utilizes the SATé-enabled phylogenetic placement (SEPP) method” > The mention of the generation of ASVs:thinking_face:.

Aleru Divine (07:33:18) (in thread): > Okay? but also, “3368 ASVs were detected in the samples based on the rarefied readings.”

idiaru Angela (07:44:53) (in thread): > But it mentions nothing about counting the data:thinking_face:

Modinat Ganiyu (08:15:45) (in thread): > @ayesha khanThis community has been super helpful all through. I’ve connected with lovely people and even made friends:blush:that we’ll continue to relate after this contribution phase. As for the mentors, they’re so patient, kind and understanding:heart:I want to say a very big thanks to our mentors and all contributors for being so accommodating and bringing calmness to the atmosphere. I Love you all:heart::hugging_face:

Ajayi Mercy (08:37:43): > Hey there, everyone! Hope you’re all having a good day. I was wondering if anyone could lend a hand with my second contribution. I’d really appreciate it!:blush:here is the linkhttps://journals.asm.org/doi/10.1128/spectrum.02974-23

Peace Daniel (08:38:13) (in thread): > Hey there,I’dbe happy to help

Joan C. Chukwuemeka (08:40:05) (in thread): > Hi@Ajayi Mercy, you can drop your question or area where you need help?

Ajayi Mercy (08:40:33) (in thread): > @Peace Danielthank you I have shared the link

Peace Daniel (08:41:19) (in thread): > Okay, will take a look now

Aleru Divine (08:43:34) (in thread): > Thanks for deleting this:hugging_face::pray:@Chioma Onyido

Aleru Divine (08:45:04) (in thread): > I thought reads were like counts:sob:help!

Scholastica Urua (08:45:23): > Hello everyone,@Hamza Hajiand I completed this curation and its ready for peer review. Really looking forward to your feedback. Thank you for your help:pray:https://bugsigdb.org/Study_978 - Attachment (BugSigDB): The Gut Microbiome Is Associated with Clinical Response to Anti-PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer - BugSigDB > We report on a comprehensive analysis of the gut microbiomes of patients with gastrointestinal (GI) cancer receiving anti-PD-1/PD-L1 treatment.

Ajayi Mercy (08:45:46) (in thread): > @Joan C. Chukwuemekaokay thanks

Joan C. Chukwuemeka (08:48:57) (in thread): > Here’s a link to the curation policy - it will also guide you on the curationhttps://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > …

Ajayi Mercy (08:49:36) (in thread): > @Joan C. Chukwuemekathanks so much

Joan C. Chukwuemeka (08:57:34) (in thread): > You’re welcome@Ajayi Mercy:blush:

idiaru Angela (09:48:03) (in thread): > I think we should throw the question open to the house and get more feedback

Adenike Oladimeji-Kasumu (09:51:59) (in thread): > @Ajayi Mercyif there are any specific questions you need answers to, I’ll be happy to help.

Mildred Anashie (10:40:38) (in thread): > Going through your paper now > > Have you started the curation? > Are you stuck on a particular aspect?@Ajayi Mercy

Abiola Salako (10:51:48) (in thread): > @Ajayi Mercy, where and when do you want us to come in?

Bolanle Wahab (12:22:40): > Hi@Chioma Onyido@Esther Afuape@Peace SandyCould you please delete experiment 2 and it’s signature, thank youhttps://bugsigdb.org/Study_912 - Attachment (BugSigDB): Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics - BugSigDB > BACKGROUND: The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited.

Rahila-me (12:37:13): > Is this same thing as Antibiotics exclusion:receiving no medication for allergic diseases in the 2 months prior to sampling.

Aleru Divine (12:37:58) (in thread): > No itisn’t@Rahila-me

Mildred Anashie (12:38:11) (in thread): > I’mnot sure it is > > In my opinion Antibiotics should be clearly stated@Rahila-me

idiaru Angela (12:38:55) (in thread): > No it isn’t

Bolanle Wahab (12:39:56) (in thread): > @Rahila-meno itisn’t,I think it has been addressed during one of your office meetings

Rahila-me (12:48:16) (in thread): > ok.. Thanks guys:ok_hand:

Ikeh Darlington Ikeh (13:13:39) (in thread): > Sorry I’m late here. If you reviewed some existing curations, like resolving taxa conflicts or you added more signatures, You can record it as a contributions you made to BugSigDB. That’s what I meant in a nutshell. Just paste the link to the curation you edited.

Peace Daniel (14:46:30): > Hello@Peace Sandy@Esther Afuape@Chioma Onyido@Svetlana Ugarcina Perovic<@UBNSEMS3S>While trying to resolve processing errors, I came across study 840 which didn’t have a PMID initially but I tried searching for one (didn’tfind it), I noticed the curator added matched on and confounders but going through the article I couldn’t find this > > I also noticed, one experiment was recorded when I can see 2 or probably more. > Is it okay to work on this curation (it was completed in 2023) and post it after for a review?

Esther Afuape (14:50:36) (in thread): > Yes you can

Peace Daniel (14:52:57) (in thread): > Okay, thank you

Faith Ifeoluwa Alexander (14:58:30): > Good Evening everyone and Happy Easter to everyone celebrating. Happy Weekend to everyone as well. > > Pls, I noticed the timeline for the internship is from May 2nd to August 23rd which exceeds the 12 weeks we are directed to work for. > > My question is this, for the extra 3 weeks on the timeline, what are the activities expected of us?@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma OnyidoThank you for your anticipated response.

Faith Ifeoluwa Alexander (14:59:53): > Additionally, how do I collaborate with another contributor to work together on a curation? > I have seen a lot of people working together on a curation and I want to know how I can do that.

Aleru Divine (14:59:59) (in thread): > @Faith Ifeoluwa Alexanderinternship starts from 27th May I believe.

Faith Ifeoluwa Alexander (15:02:46) (in thread): > But<@UBNSEMS3S>response to a question about timeline stated May 2th.

Faith Ifeoluwa Alexander (15:03:06) (in thread): > So that was why I asked.

Peace Daniel (15:03:29) (in thread): > You can ask someone to be a co-collaborator, this means the person can edit your curation. > > I suppose this is how it works:thinking_face:

Faith Ifeoluwa Alexander (15:05:24) (in thread): > @Peace Danielis that how you got a co-collaborator?

Peace Daniel (15:07:33) (in thread): > Oh, Ididn’trequest for one. > I only share for peer reviews

Aleru Divine (15:09:00) (in thread): > Must have been a mistake.

Scholastica Urua (15:19:59) (in thread): > That would be a mistake@Faith Ifeoluwa Alexander. So your timeline will start on the 27th.

Scholastica Urua (15:22:11) (in thread): > @Faith Ifeoluwa Alexanderyou can also check GitHub for issues that have not been marked for review. Then ask offer to work with the curator to complete their project.

Faith Ifeoluwa Alexander (15:26:26) (in thread): > Okay. I will do that. Thank you@Scholastica Urua. One more question do I send a DM to the curator to ask to work with them?

Scholastica Urua (15:27:21) (in thread): > You can comment under the issue and wait for their reply.

Faith Ifeoluwa Alexander (15:27:25) (in thread): > Oh, Okay. Thank you. I will go & correct it now.

Faith Ifeoluwa Alexander (15:27:42) (in thread): > Okay.

Peace Daniel (15:28:58): > Hello@Esther Afuape@Peace Sandy@Chioma OnyidoIn this study, link:https://bugsigdb.org/Study_831These were added as matched on factors: > Epidemiological data included age, sex, height, weight, and relevant comorbidities including a Charlson Comorbidities Index (CCI). > > Question: > Is it okay to replace “height” and “weight” with “body height” and “body weight” respectively? > > And also, > Confounders controlled for: > antibiotic, timepoint, ventilation > > Question: > Would “time” be a suitable replacement for “timepoint” ? - Attachment (BugSigDB): Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort - BugSigDB > BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms.

Scholastica Urua (15:33:24) (in thread): > Well done@Peace Daniel:raised_hands:I think body height and body weight should work. Let’s wait for a mentor’s reply though…

Peace Daniel (15:34:29) (in thread): > Thank you@Scholastica Urua

Svetlana Ugarcina Perovic (15:45:12) (in thread): > No, it is not the same.

Svetlana Ugarcina Perovic (15:46:17) (in thread): > Deleted.

Mildred Anashie (15:49:23) (in thread): > Yea > > I agree, body height and body weight should be okay > > Also I think time could work but amentor’s confirmationwould be betterWell done@Peace Daniel

Peace Daniel (15:57:36) (in thread): > Thank you@Mildred Anashie

Svetlana Ugarcina Perovic (16:03:38) (in thread): > Leave it blank and make a note. CORRECTION: I just added 18S so now you should see it in the drop-down.

Svetlana Ugarcina Perovic (16:13:19) (in thread): > Leave it blank and make a note. CORRECTION: I just added 18S so now you should see it in the drop-down.

Bolanle Wahab (17:30:16) (in thread): > Thank you@Svetlana Ugarcina Perovic

Praise Agbetuyi (18:32:07): > Hello everyone,@Blessing Ene Anyebeand I have finalized our curation:tada:, and will like to request for peer review. > > We truly appreciate and anticipate your valuable insights. Thank you for your constant support:pray::heart_hands:https://bugsigdb.org/Study_1071 - Attachment (BugSigDB): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BugSigDB > Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life.The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies.

Manisha Nair (21:35:26) (in thread): > @Joan C. ChukwuemekaWhen I try typing in the condition field, there is no such option as “nutritional supplement exposure measurement”. > I’ve added**”environmental exposure measurement” ****in the condition field as******nutritional supplement exposure measurement ****falls under the category of******environmental exposure measurement**********.****

2024-03-31

Barakat Akinsiku (02:04:05): > Goodmorning BugSigDBiers and Happy Easter to everyone celebrating:partying_face::partying_face::hatching_chick:Wish you all a lovely celebration:hugging_face::blush:

Scholastica Urua (02:08:57) (in thread): > Good morning@Barakat AkinsikuWish you same:boom:

Peace Daniel (02:16:40) (in thread): > Good morning,Thank you

Mildred Anashie (02:42:49) (in thread): > Thank you@Barakat AkinsikuSame to you:dizzy:

Peace Daniel (03:29:04) (in thread): > @Svetlana Ugarcina Perovicis this okay please?

Svetlana Ugarcina Perovic (05:11:14) (in thread): > @Peace DanielPlease check in the paper if this is actually correct:Matched on age, sex, height, weight, Charlson Comorbidities Index (CCI)Confounders controlled for antibiotic, timepoint, ventilation > ?

Svetlana Ugarcina Perovic (05:12:12) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710354753168349?thread_ts=1710354713.297979&cid=C04RATV9VCY - Attachment: Attachment > If they didn’t state any clearly (usually using words like “adjusted for” or “controlled for”) they probably didn’t control for any confounders. Controlling for confounders is fairly uncommon in microbiome research currently.

Svetlana Ugarcina Perovic (05:14:41) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698694042973379?thread_ts=1698664068.335649&cid=C04RATV9VCY - Attachment: Attachment > > However, in her study, is it safe to say they were matched on age and gender? > Unless they explicitly say that they matched on age and gender, then no we cannot safely conclude that. Even if they do an analysis to show that there was no stat. sig. difference in age and gender between cases and controls that is not the same thing as matching. Matching has to be something that is specifically and deliberately done prior to data analysis. > > Typically. There are ways to do matching during data analysis but I think of the 100s of papers we’ve curated I’ve seen exactly 1 do so.

Peace Daniel (05:18:06) (in thread): > Okay@Svetlana Ugarcina PerovicI was skeptical about it earlier but since it was reviewed Ididn’tmention it,I’llcheck the paper again

Manisha Nair (05:21:27) (in thread): - File (JPEG): IMG20240331144548.jpg

Peace Daniel (05:30:06) (in thread): > Good day@Esther Afuape@Svetlana Ugarcina PerovicI have an update on this study. I searched for this study on GitHub to see if I could find any supplemental material and I realized it was initially assigned to someone and@Aleru Divinehave now completed the study here and asked for a reviewhttps://bugsigdb.org/Study_879This means study 840 is a duplicate and can be deletedhttps://bugsigdb.org/Study_840GitHub issuehttps://github.com/waldronlab/BugSigDBcuration/issues/68Thank you andwell done@Aleru Divine - Attachment: #68 Oral lesion and microbiome diversity in COVID-19 hospitalized patients > Costa S, Fonseca JVDS, Scaccia N, et al. Oral lesion and microbiome diversity in COVID-19 hospitalized patients.. Authorea Preprints; 2023. DOI: 10.22541/au.169511765.50376146/v1. > > Preprint available here: https://www.authorea.com/users/666162/articles/667143-oral-lesion-and-microbiome-diversity-in-covid-19-hospitalized-patients

Svetlana Ugarcina Perovic (05:36:53) (in thread): > Deleted. Thanks!

Aleru Divine (05:39:29) (in thread): > Oh!:hugging_face:Thank you@Peace Daniel

Peace Daniel (06:21:11) (in thread): > Hello@Svetlana Ugarcina PerovicI’ve searched the article with these keywords “matched”, “matched on”, “adjusted for” and “controlled for” but nothing came up. Only the statement below had a result for “matched” > > “To evaluate whether COVID-19 patients presented a signature in their fecal microbiota, we compared their microbiota to non-COVID-19 control patients with ventilatory support in ICU. Nineteen non-COVID-19 ICU patients (control/pneumonia group) were compared with ten COVID-19 ICU patients (COVID-19 group) at day 0 and day 7, the timepointsmatchedfor the comparison.” > > This statement was related to Fig 4 which showed the “timeline of sampling” > > I also looked out for linear or regression model so I don’t think these are actual confounders or matched on factors, could you please confirm this?

Svetlana Ugarcina Perovic (06:24:44) (in thread): > Correct@Peace DanielWell done! > “Matched on” and “Confounders controlled for” inputs deleted.

Peace Daniel (06:27:59) (in thread): > Thank you@Svetlana Ugarcina Perovic

Blessing Ene Anyebe (06:29:21) (in thread): > Thank you@Barakat Akinsiku:orange_heart:

Peace Daniel (06:40:56) (in thread): > One more thing@Svetlana Ugarcina PerovicBoth experiments 1 and two had matched on and confounders, you have deleted that for experiment 1. I tried deleting these for experiment 2 but I don’t have access to

Mildred Anashie (06:43:35) (in thread): > Well done:clap:@Peace DanielYes we do not have access to delete, I think@Svetlana Ugarcina Perovicwill delete the one left once the message is seen

Peace Daniel (06:44:45) (in thread): > Alright, thank you@Mildred Anashie

Svetlana Ugarcina Perovic (07:21:49) (in thread): > Deleted. Thanks!

Evelyn Mary Attah (09:01:57): > Good day@Svetlana Ugarcina Perovicare there community-specific questions? Kindly assist me with this. Thank you

Mildred Anashie (09:03:57) (in thread): > Good day@Evelyn Mary Attahhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Joan C. Chukwuemeka (09:09:53) (in thread): > @Manisha Nairoh…I see:thinking_face:. Alright, If I see a better option, I’d revert to you

Praise Agbetuyi (11:28:49) (in thread): > Also, Kindly note that the internship begins on the 27th of May and not the 2nd of May.

Praise Agbetuyi (11:29:34) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711825110859019 - Attachment: Attachment > Good Evening everyone and Happy Easter to everyone celebrating. Happy Weekend to everyone as well. > > Pls, I noticed the timeline for the internship is from May 2nd to August 23rd which exceeds the 12 weeks we are directed to work for. > > My question is this, for the extra 3 weeks on the timeline, what are the activities expected of us? @Svetlana Ugarcina Perovic @UBNSEMS3S @Esther Afuape @Peace Sandy @Chioma Onyido > > Thank you for your anticipated response.

Praise Agbetuyi (11:35:43) (in thread): > Thank you<@UBNSEMS3S>

Praise Agbetuyi (12:46:18): > Hello everyone!:blush:I hope our day has been going on fine. I’ve been enjoying my experience in this BugSigDB community, and it’s made me realize how valuable community is to progress and life. Thank you@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape<@UBNSEMS3S>@everyone > > I have a suggestion that prospective interns, even at the contribution stage, should carry out a task on sharing their experiences, knowledge, or progress on social media using a designated hashtag and create a short post highlighting features, uses, and links to BugSigDB. > > I know some persons are doing this on a personal level already, but If it can be incorporated, such that at the contribution stage, all participants engage in this during the contribution stage, it can complement the publicity activity on ground already.

Oluwatomisin Omojokun (13:17:50): > Happy Easter celebration my Bugsigdb community. Thank you for being amazing peoples. I have learnt a lot within the space of one month. From the depth of my heart i say Thank you all, especially@Svetlana Ugarcina Perovic@Esther Afuape@C. Mirzayi (please do not tag this account)@Peace Sandy. > Tomisin cares:heart_eyes::heart:

Oluwatomisin Omojokun (13:18:57) (in thread): > Thank you@Barakat Akinsiku

2024-04-01

Joan C. Chukwuemeka (02:17:26): > Good morning all,:blush:<!here>Happy New month. Wishing everyone a fulfilling month ahead.:seedling:Welcome to another BugSigDB-ing week:nerd_face:Remember, Final application submission deadline is tomorrow, April 2nd 2024. > All the best:+1:

Peace Daniel (02:43:39) (in thread): > Good morning and a happy new month to you too. > > Thanks for the reminder!

Scholastica Urua (02:48:14) (in thread): > Good morning@Joan C. ChukwuemekaHappy new month to you too:hugging_face:

Blessing Ene Anyebe (02:54:09) (in thread): > Happy new month@Joan C. Chukwuemeka:orange_heart::orange_heart::orange_heart:

Blessing Ene Anyebe (02:59:28): > Good morning everyone! > It has been truly amazing being part of this community.:hugging_face:One thing that really stood out for me is how everyone here embodied a healthy and supportive competition. It’s almost hard to believe that there’s a competition because everyone showed true grace and team-work. > > It’s amazing to see and I love that I’m a part of such environment. However it goes for all of us, you are all amazing (Our mentors and contributors) and it’s a privilege working with you all this past month. > > Happy new month people and welcome to my birthday month.:partying_face::new_moon_with_face::orange_heart::sparkles:

Manisha Nair (03:14:38) (in thread): > Sure, and again thanks a lot for helping me@Joan C. Chukwuemeka

Peace Daniel (03:27:10) (in thread): > Good morning, this is my birth month as well.:dancer:

Precious Orakwe (03:35:46) (in thread): > Happy new month

idiaru Angela (03:36:46) (in thread): > Happy new month@Blessing Ene Anyebeand happy birthday in advance

Flourish Ralph (03:44:10) (in thread): > Happy new month and happy birthday in advance!:tada::hugging_face:

Blessing Ene Anyebe (03:44:40) (in thread): > Thank you beautiful women:orange_heart::orange_heart:

Blessing Ene Anyebe (03:45:29) (in thread): > @Peace Daniel:hugging_face::hugging_face:Happy birthday in-advance:orange_heart:

Scholastica Urua (03:50:40) (in thread): > Happy new month and happy birthday in advance@Blessing Ene Anyebe:tada::hugging_face:

Aleru Divine (03:50:58) (in thread): > Good morning@Joan C. Chukwuemekaand a happy new month to you too:heart::hugging_face:

Aleru Divine (03:52:02) (in thread): > Happy new month@Blessing Ene Anyebeand a happy birthday in advance to you and@Peace Daniel:partying_face::heart::hugging_face:

idiaru Angela (03:52:38): > Good morning and Happy New Month@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyI noticed that these two studies have the same PMID and are curations of the same article. I believe one should be deleted. Thankshttps://bugsigdb.org/Study_991 - Attachment (BugSigDB): Association between Parkinson’s disease and the faecal eukaryotic microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disease, and is so far not considered curable.PD patients suffer from several motor and non-motor symptoms, including gastrointestinal dysfunctions and alterations of the enteric nervous system. - Attachment (BugSigDB): Association between Parkinson’s disease and the faecal eukaryotic microbiota - BugSigDB > Parkinson’s disease (PD) is one of the most common neurodegenerative disease, and is so far not considered curable.PD patients suffer from several motor and non-motor symptoms, including gastrointestinal dysfunctions and alterations of the enteric nervous system.

Blessing Ene Anyebe (03:58:35) (in thread): > Thank you@Scholastica Uruaand@Aleru Divine:hugging_face::orange_heart:happy new month:hugging_face::sparkles:

Ajayi Mercy (04:09:22): > Good morning everyone and happy new month! I got this error message while trying to save my experiment “You do not have permission to edit this page, for the following reason: > The action you have requested is limited to users in the group”

idiaru Angela (04:10:53) (in thread): > Good morning@Ajayi Mercydo you have an account and are you logged in on the current browser you’re using?

Peace Daniel (04:17:45) (in thread): > Thank you@Aleru Divine@Blessing Ene AnyebeHappy birthday in advance:orange_heart:

Ajayi Mercy (04:18:17) (in thread): > yes, I do I have sorted it out I tried to log in again. it’s fine now thanks

Peace Daniel (04:20:11) (in thread): > Hello@idiaru AngelaWhile this is true, I noticed both studies was started in 2024 and is most likely close to completion by@Samreen Aftabwhile the other belongs to a present outreachy applicant as well > I think@Oluwatomisin Omojokunand@Samreen Aftabshould complete the other one and ask for a review so the one she created can be deleted > > It seems@Oluwatomisin Omojokunstudy is the most recent

idiaru Angela (04:24:11) (in thread): > Hi@Peace Daniel. It was already assigned to@Samreen Aftaband she has already started to work on it. Either way one has to be deleted since they are duplicates.

Peace Daniel (04:25:05) (in thread): > Yes, most likely the second one

Raihanat Adewuyi (04:26:07) (in thread): > Thanks you for the clarification@C. Mirzayi (please do not tag this account)

Mildred Anashie (04:41:34) (in thread): > Thank you@Joan C. ChukwuemekaHappy new month to you:heart:

Joan C. Chukwuemeka (04:48:48) (in thread): > You’re welcome@Manisha Nair

Ima-obong (Aimah) (04:51:18) (in thread): > Happy new month@Blessing Ene Anyebeand a Happy birthday in advance. It’s been nice working with you.

Ima-obong (Aimah) (04:52:49) (in thread): > A happy new month to you@Joan C. Chukwuemeka. Thank you for all your support here.

Ima-obong (Aimah) (04:58:11) (in thread): > @Praise Agbetuyithis is actually a nice one, cause I had noticed that contributors in other communities were making social media posts on LinkedIn, though theirs were tasks specific contents…but then, > it’s still a great idea for contributors to use their handles and talk about BugSigDb community and the amazing work going on here.

Mildred Anashie (05:02:02) (in thread): > Hi@Manisha NairJust to understand, is there a reason why you are not using “iron supplementation” or “supplementation” as the condition?:thinking_face:

Manisha Nair (05:08:56) (in thread): > @Mildred AnashieSuch an option is not available. I tried looking in the Ontology Lookup Service but couldn’t find it.

Peace Daniel (05:12:22): > Hello and happy new month/week@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyStudy 1023 is a duplicate of study 1024, I think the curator originally started with 1023 but didn’t input the PMID and lost it so he/she created study 1024. > > I have added the PMID to study 1024 which looks like the current study the curator is working on and 1023 can be deleted > > > Linkshttps://bugsigdb.org/Study_1023https://bugsigdb.org/Study_1024 - Attachment (BugSigDB): Gut Microbiota is Altered in Patients with Alzheimer’s Disease - BugSigDB > … - Attachment (BugSigDB): Gut Microbiota is Altered in Patients with Alzheimer’s Disease - BugSigDB > Previous studies suggest that gut microbiota is associated with neuropsychiatric disorders, such as Parkinson’s disease, amyotrophic lateral sclerosis, and depression.

Mildred Anashie (05:17:50) (in thread): > In my opinion “Response to dietary supplementation” should work for this > > Or “Response to Iron supplementation” > But there are both unavailable on BugSigdb@Manisha Nair

Mildred Anashie (05:20:40) (in thread): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyThe curator said of this articlehttps://bugsigdb.org/Study_1010used “Environmental exposure measurement” as the conditionI’masking this question becauseI’mskeptical about that being the right condition to suffice > > Could I be wrong? > Also what do you suggest best fits? > > Thank you for your responses:blush: - Attachment (BugSigDB): The Effect of Oral Iron Supplementation on Gut Microbial Composition: a Secondary Analysis of a Double-Blind, Randomized Controlled Trial among Cambodian Women of Reproductive Age - BugSigDB > The World Health Organization recommends untargeted iron supplementation for women of reproductive age (WRA) in countries where anemia prevalence is greater than 40%, such as Cambodia.Iron supplements, however, often have poor bioavailability, so the majority remains unabsorbed in the colon.

Manisha Nair (05:23:14) (in thread): > @Mildred AnashieI tried searching a lot. Couldn’t find any appropriate ones.:disappointed:

Abiola Salako (05:29:51) (in thread): > Thank you for the reminder@Joan C. Chukwuemeka

Abiola Salako (05:30:30) (in thread): > Thank you@Blessing Ene Anyebe

Scholastica Urua (06:19:00): > Hello everyone, and a happy new month of April to you all! It’s been an incredible journey collaborating with each and every one of you here. I want to express my heartfelt gratitude for all your assistance. A special thank you goes out to our mentors for the invaluable work they do; it truly cannot be easy.:gratitude-thank-you::heart_hands:<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy, could I kindly request clarification on the following matter:pray:? I’ve been collaborating with@Welile Dlaminion a curation project. We’ve observed that signatures are reported using two different statistical tests [LEfSe and Mann-Whitney (Wilcoxon)], and they appear to overlap (image 1 and 2). Consequently, I’ve curated them as one experiment. While considering adding a note on the talk page, I stumbled upon this particular note in image 3. > > Could you please take a look at the article:https://bugsigdb.org/Study_894? > > Thank you in anticipation.:hugging_face: - Attachment (BugSigDB): Alterations in the Gut Microbiota and Metabolomics of Seafarers after a Six-Month Sea Voyage - BugSigDB > Maintaining the health of seafarers is a difficult task during long-term voyages.Little is known about the corresponding changes in the gut microbiome-host interaction.This study recruited 30 seafarers undertaking a 6-month voyage and analyzed their gut microbiota using 16S rRNA gene sequencing. - File (JPEG): image 2.JPG - File (JPEG): image 1.JPG - File (JPEG): image 3.JPG

Scholastica Urua (06:31:57) (in thread): > Also, does the condition -seasonal gut microbiome measurementwork well for the study?:pray:https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0007753 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Joan C. Chukwuemeka (06:50:08) (in thread): > Happy new month@Blessing Ene Anyebe, happy birthday in advance to you and@Peace Daniel

Joan C. Chukwuemeka (06:53:37) (in thread): > @Mildred Anashiewe’re still in search of an appropriate condition. here’s why she went for the current one, pending when a more closer and appropriate one is gotten:https://community-bioc.slack.com/archives/C04RATV9VCY/p1711848926638759?thread_ts=1711680772.913259&cid=C04RATV9VCYhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711876887783549?thread_ts=1711680772.913259&cid=C04RATV9VCYSo far in EFO, the term with iron, in terms of supplementation is “dietary heme iron intake measurement”, but the supplement in the study is not heme iron, hence why it wasn’t of choice. If you do find a more closer term, do let us know. Thanks. - Attachment: Attachment > @Joan C. Chukwuemeka When I try typing in the condition field, there is no such option as”nutritional supplement exposure measurement”. > > I’ve added “environmental exposure measurement” in the condition field as nutritional supplement exposure measurement falls under the category of environmental exposure measurement. - Attachment: Attachment

Welile Dlamini (07:03:12) (in thread): > Hello everyone, Wishing everyone a prosperous month, thank you to our fantastic mentors who guide us daily really appreaciate<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy, great question at@Scholastica Urua

Blessing Ene Anyebe (07:11:09) (in thread): > Thank you@Ima-obong (Aimah):hugging_face:It is lovely working with you as well:orange_heart:

Mildred Anashie (07:28:33) (in thread): > Is this an incomplete study you are trying to complete?@Scholastica Urua

Scholastica Urua (07:29:25) (in thread): > No, it’s not. It’s a new project@Mildred Anashie

Mildred Anashie (07:43:59) (in thread): > Okay@Scholastica UruaI went through the article and saw what you highlighted and shared andI’mof the opinion that the Fig 1d is showing differential abundanceI’munsure why<@UBNSEMS3S>said they are no differential abundance results > > Maybethere’ssomething we are missing:thinking_face:Waiting for responses though:hand_with_index_and_middle_fingers_crossed:

Scholastica Urua (07:44:56) (in thread): > Thank you@Mildred Anashie:pray:

Aleru Divine (08:51:17) (in thread): > @Scholastica Urua@Welile Dlaminiwell done on your curation. I just went through the study > > I think both wilcoxon and LEfSe were used for differential abundance testing and they are actually overlapping. So I believe you’ve done the right thing curating them as 1 experiment. You can use both as the statistical tests and leave a note as you’ve mentioned. > > I also think seasonal gut microbiome works for the study.@Mildred AnashieI join you to wait for other responses:sweat_smile:

Mildred Anashie (08:54:15) (in thread): > Happynew month:smiling_face_with_3_hearts:Happy Birthday in advance to you and@Peace Daniel:confetti_ball:

Scholastica Urua (08:54:45) (in thread): > Thank you for your contribution@Aleru Divine

Svetlana Ugarcina Perovic (09:35:34) (in thread): > Thanks! I will check it out with the curators!

Svetlana Ugarcina Perovic (09:38:12) (in thread): > @Samreen Aftab@Oluwatomisin Omojokunplease seehttps://github.com/waldronlab/BugSigDBcuration/issues/223 - Attachment: #223 Association between Parkinson’s disease and the faecal eukaryotic microbiota > Association between Parkinson’s disease and the faecal eukaryotic microbiota - Weis et al. - NPJ Parkinsons Disease
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8602383/

Svetlana Ugarcina Perovic (09:39:31) (in thread): > Deleted, thank you!

Svetlana Ugarcina Perovic (09:41:41) (in thread): > Agree, good job!

Scholastica Urua (09:43:13) (in thread): > Thank you@Svetlana Ugarcina Perovic. Can I go ahead and change the note?

Svetlana Ugarcina Perovic (09:43:35) (in thread): > Please do.

Svetlana Ugarcina Perovic (09:49:15): > :good_luck:**** Dear applicants, good luck with your final application!****And, do not worry aboutpending reviews: We are working diligently to get you all feedback. > > We appreciate your patience as we continue to review. We have been overwhelmed by the amount of interest we’ve had and the productivity of all of you. YOU ARE ALL TRULY AMAZING and,once we have to make a decision, it is going to be incredibly difficult, but we will ensure that you are all considered fairly!<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic

Abiola Salako (09:50:14): > Thank you so much for all you do@Svetlana Ugarcina PerovicWe’re grateful.

Svetlana Ugarcina Perovic (09:52:01) (in thread): > I personally admire how you quickly created an incredibly supportive and collaborative and productive! environment. Thank YOU for all your work and lessons I learnt from you!

Mildred Anashie (09:56:01) (in thread): > Thank you so much@Svetlana Ugarcina PerovicThe encouragement from you and the other mentors was really helpful and for me it played a significant role in my learning:heart_hands::heart:I’m also really grateful to fellow applicants for their support:heart_hands::heart:

Scholastica Urua (10:02:16) (in thread): > Thank you for your support@Svetlana Ugarcina Perovic. It’s been amazing collaborating with everyone here.:sparkling_heart:

Faith Ifeoluwa Alexander (10:03:44) (in thread): > Thank you@Svetlana Ugarcina Perovic. You have been really helpful. It’s been an interesting journey so far I must say.

Peace Daniel (10:03:51) (in thread): > Thank you so muchI’velearnt a lot and will continue to do so:heart:

Scholastica Urua (10:05:31) (in thread): > @Svetlana Ugarcina PerovicPlease when recording previously ‘incomplete studies’ as a contribution, will it be okay to include tomorrow’s date as the merged date or we should leave it blank?

idiaru Angela (10:07:46) (in thread): > Thank you@Svetlana Ugarcina Perovic. It’s been an absolute pleasure working with you and all the other contributors.

Mildred Anashie (10:08:44) (in thread): > I’mthinking it should be submitted for review to the mentors, probably here on this channel and then you tag the mentors to itThat’sif the issue is not on GitHub for you to leave a comment@Scholastica Urua:thinking_face:

Faith Ifeoluwa Alexander (10:11:22) (in thread): > I am not sure about filling out tomorrow as the merged date, however, let’s wait to hear from the mentors@Scholastica Urua

Desire Oluwarotimi (10:12:17) (in thread): > It’s been a great run. > > Thank you.@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)<@U1LCB8WEA>And to all my colleagues as well, Thank you.:saluting_face:

Peace Daniel (10:13:18) (in thread): > Yes,you’dneed to notify them here if the issue is not open on GitHub

Faith Ifeoluwa Alexander (10:14:27) (in thread): > Happy New Month & Happy Birthday to you in advance.@Blessing Ene Anyebe

Scholastica Urua (10:16:16) (in thread): > Thank you everyone:hugging_face:.

Faith Ifeoluwa Alexander (10:18:23) (in thread): > Going through your curation, I found a taxa in red in the first Signature of the second Experiment, hope you noticed that.

Samreen Aftab (10:21:23) (in thread): > Thank you for pointing it out. I created the study a few days back, but I was not able to mark it for review since it said I didn’t have permission to do so. I was about to ask here about it, but it slipped out of my mind.@Peace Daniel@idiaru Angela@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (10:23:46) (in thread): > Thanks a lot@Svetlana Ugarcina Perovic. > > And<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandyfor being such supportive mentors.Grazie mille:pray:Muchas gracias:heart:

Peace Daniel (10:25:03) (in thread): > That’strue@Samreen AftabI just checked,let’swait for@Svetlana Ugarcina Perovicregarding this

Svetlana Ugarcina Perovic (10:27:40) (in thread): > Solved:https://bugsigdb.org/Study_991deleted.@Samreen Aftabyou should claim your curation for review in the corresponding GitHub issue (not on BugSigDB platform). Also pay attention that you left “incomplete” fields in your curation.

Samreen Aftab (10:29:15) (in thread): > Yes@Svetlana Ugarcina Perovicthat’s what I said earlier, when I try to edit my experiment to make it “needs review”, it says I don’t have permission to do so.

Svetlana Ugarcina Perovic (10:31:55) (in thread): > @Samreen Aftabthis screenshot might help you to understand better the protocol. - File (PNG): Screenshot 2024-04-01 at 16.31.08.png

Peace Daniel (10:34:31) (in thread): > @Samreen AftabI just marked one of your experiments as complete, “needs review” > > Check to be sureyou’relogged in

Samreen Aftab (10:36:18) (in thread): > Ah yeah, I’m sorry. You’re right, thank you@Peace Daniel

Aleru Divine (10:47:08) (in thread): > Thank you so much for all your support@Svetlana Ugarcina Perovicthis has been an amazing journey everyone:heart:

Barakat Akinsiku (10:49:15) (in thread): > Thank you@Svetlana Ugarcina Perovicand everyone. It’s truly been an incredible journey

Svetlana Ugarcina Perovic (11:02:15) (in thread): > Thank you@Peace Daniel

Raihanat Adewuyi (11:27:03) (in thread): > Thank you@Svetlana Ugarcina Perovicfor all your support.. It’s been amazing collaborating with everyone here.. And thanks guys for the support.

Blessing Ene Anyebe (11:29:11) (in thread): > Thank you@Svetlana Ugarcina PerovicYou’re amazing to work with. Thank you for your patience and thank you to all our mentors!:orange_heart::hugging_face:

Welile Dlamini (11:39:22) (in thread): > thank you@Svetlana Ugarcina Perovic@Aleru Divine

Nana (11:44:20) (in thread): > Thank you for always showing up for us. We love you@Svetlana Ugarcina Perovic:heart::heart:

Sneha Singh (12:35:37) (in thread): > That’sa great idea!

Sneha Singh (12:37:00): > Hello everyone! Can someone please guide me for what should I write in this section? - File (PNG): IMG_2384

Aleru Divine (12:38:09) (in thread): > Hi@Sneha Singhthis should helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Mildred Anashie (12:38:10) (in thread): > Hihttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Sneha Singh (12:43:08) (in thread): > Thank you:heart:

Mildred Anashie (12:45:13): > Hello everyone > I’m working on completing this study along side@Desire Oluwarotimiand@Barakat AkinsikuI have a very quick question:grin:Can someone help me with this? > I am unsure if this figure 3 should be curated (Image and link to study attached) > > The significant threshold is unclear, we really want to be sure it wasn’t clearly stated before using 0.05Also can ANCOM replace ANCOM BC for statistical tests?@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy:pray:http://dx.doi.org/10.1186/s40168-023-01671-2 - Attachment (BioMed Central): A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs - Microbiome > Background Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention is modulation of the composition of gut microbiota, and in fact, probiotic treatment has been proposed and tried in human atopic dermatitis (AD) patients. Since dogs are currently receiving intensive medical care, this will be the same option for dogs, while evidence of gut dysbiosis in cAD is still missing, although skin microbial profiling in cAD has been conducted in several studies. Therefore, we conducted a comprehensive analysis of both gut and skin microbiota in cAD in one specific cAD-predisposed breed, Shiba Inu. Additionally, we evaluated the impact of commonly used medical management on cAD (Janus kinase; JAK inhibitor, oclacitinib) on the gut and skin microbiota. Furthermore, we genotyped the Shiba Inu dogs according to the mitochondrial DNA haplogroup and assessed its association with the composition of the gut microbiota. Results Staphylococcus was the most predominant bacterial genus observed in the skin; Escherichia/Shigella and Clostridium sensu stricto were highly abundant in the gut of cAD-affected dogs. In the gut microbiota, Fusobacteria and Megamonas were highly abundant in healthy dogs but significantly reduced in cAD-affected dogs. The abundance of these bacterial taxa was positively correlated with the effect of the treatment and state of the disease. Oclacitinib treatment on cAD-affected dogs shifted the composition of microbiota towards that in healthy dogs, and the latter brought it much closer to healthy microbiota, particularly in the gut. Additionally, even within the same dog breed, the mtDNA haplogroup varied, and there was an association between the mtDNA haplogroup and microbial composition in the gut and skin. Conclusions Dysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota. Video Abstract - File (PNG): staphylococcus.PNG

Faith Ifeoluwa Alexander (12:45:20) (in thread): > Simply put, just describe how you will carry out each task using the timeline given. > > For instance, you can write it this way: Week 1 to Week 2: Review of article etc.

Peace Daniel (12:51:22) (in thread): > From this article I read, it seems ANCOM BC is more thorough than ANCOMhttps://forum.qiime2.org/t/interpreting-ancom-and-ancom-bc-results/28494/6I think it could but we’d need a confirmation from the mentors (using ANCOM for ANCOM BC) - Attachment (QIIME 2 Forum): Interpreting ANCOM and ANCOM-BC results > Hi @Linda_Abenaim, To add on to @gregcaporaso’s excellent advice, I think its worth considering a couple possibilties. There aren’t differences at phylum level. This wouldn’t suprise me. Members of hte same phyla can have very little in common and still be grouped together. For example, humans, sharks, and lancet worms are all part of the same phylum (phylum chordata) but beyond having spinal cords and bilateral symmetry, there isn’t much we share from an ecological perspective! Pat Schloss …

Aleru Divine (12:51:32) (in thread): > Hi@Mildred AnashieI looked at this study before:sweat_smile:I believe the figure can be curated. See this text just before figure 3, > > “In 9 of the 12 skin sites, the abundance of S. pseudintermedius was significantly higher in cAD-affected dogs not receiving medical treatment (cADpre) than in healthy dogs” > > It gives a hint of how we can interpret the figures.I also think that ANCOM can be used as ANCOM-BC is not among the drop down

Scholastica Urua (12:54:02) (in thread): > @Mildred AnashieI think ANCOM can replace ANCOM BC for statistical test since ANCOM is available on BugSigDB but we’ll have to confirm with the mentors.

Mildred Anashie (12:55:45) (in thread): > Okay@Aleru DivineSee this,I’mnot sure what it’s saying - File (JPEG): IMG_3127

Mildred Anashie (12:56:48) (in thread): > Thank you@Scholastica Uruaand@Peace Daniel:heart:

Scholastica Urua (12:57:34) (in thread): > I also think fig 3 could be curated. It showing different spp that were abundant in contrasting groups.

Mildred Anashie (12:58:52) (in thread): > Okay@Scholastica UruaI really needed to be sure so we don’t end up curating about 36 experiments that we shouldn’t have > I started curating because I’m of the opinion it’s curatable, but some statements are unclear to me

Desire Oluwarotimi (12:58:54) (in thread): > @Scholastica UruaBut the supplementary material mentioned it to be mean relative abundance and not differential abundance

Aleru Divine (13:00:59) (in thread): > @Mildred Anashiethis is talking about 0.2331, 0.1221 and 0.2889 I believe.Can you read through to the end of the sentence

Mildred Anashie (13:10:34) (in thread): > @Aleru Divinedid you open Figure S7 and S8 that the text seem to be referencing? > That was really confusing > > But I’m thinking instead of figure 3, Table S7 should be curated@Desire Oluwarotimi:thinking_face:

Aleru Divine (13:12:46) (in thread): > I am unable to access the supplement file:cold_sweat:Can you share a screenshot?

Mildred Anashie (13:13:47) (in thread): > For the Figures?@Aleru Divine

Scholastica Urua (13:13:54) (in thread): > I thought it was just me@Aleru Divine. It keeps downloading empty files. Although I’ve been able to download the Supp. table

Aleru Divine (13:13:59) (in thread): > Yeah

Peace Daniel (13:14:12) (in thread): > In my opinion@Mildred AnashieI don’tthink fig 3 should be curated > > Your article made an explicit use of the word “differential abundance” which I could see in the suppl

Desire Oluwarotimi (13:17:00) (in thread): > @Peace DanielThat’s the same thing I think. > > But on the other hand, that information seems to be too vital. The reason I think so is that there’s no other place in the paper aside Figure 3 where all 12 skin sites were involved. > It’s either 4 out of 12 or something else.

Mildred Anashie (13:17:12) (in thread): > This is S7@Aleru DivineThis is the link to the tableshttps://static-content.springer.com/esm/art%3A10.1186%2Fs40168-023-01671-2/MediaObjects/40168_2023_1671_MOESM15_ESM.xlsx - File (JPEG): IMG_3128

Desire Oluwarotimi (13:17:57) (in thread): > @Mildred AnashieI agree to leaning more to the supplementary materials as well. It’s obviously more detailed.

Bolanle Wahab (13:18:35) (in thread): > Thank you so much@Svetlana Ugarcina Perovicit’sbeen a pleasure:heart::heart:

Scholastica Urua (13:20:00) (in thread): > From the little comparison I’ve been able to make, I think fig 3 and table S7 has similar information. And table S7 is a summary ofdifferentially abundant Staphylococcus spp. between dog groups which looks curatable to me.:woman-shrugging:

Peace Daniel (13:21:04) (in thread): > Well@Desire OluwarotimiI still think it doesn’t matter, we can always record experiments with significant alpha diversity but no signatures. > > There was barely any information relating fig 3 to differential abundance

Desire Oluwarotimi (13:21:37) (in thread): > @Scholastica UruaIt looks curatable. I agree to that. > > I’m asking if you’d curate mean relative abundance results. Because that exactly what that figure contains.

Peace Daniel (13:21:44) (in thread): > So why not curate only s7?? > > > Oh wow@Desire Oluwarotimi:sweat_smile:

Aleru Divine (13:22:05) (in thread): > @Mildred Anashiethe text also specifically says figure S7 f-h and I think only their p-values are insignificant.Does that make sense?:grimacing:

Desire Oluwarotimi (13:23:34) (in thread): > Both S7 and Fig 3 do not contain differential results but they are curatable quite alright. > > I want to be sure you guys are aware of that.@Peace Daniel@Scholastica Urua

Mildred Anashie (13:23:56) (in thread): > Let me understand you@Aleru DivineYou are saying Fig 3 should be curated regardless?

Peace Daniel (13:24:57) (in thread): > @Desire OluwarotimiI don’tagree

Mildred Anashie (13:25:07) (in thread): > @Desire OluwarotimiI think Figure S7 contains information for differential abundance but Table S7 doeshttps://static-content.springer.com/esm/art%3A10.1186%2Fs40168-023-01671-2/MediaObjects/40168_2023_1671_MOESM15_ESM.xlsxWhat do you think?

Scholastica Urua (13:27:56) (in thread): > I was actually referring toTable S7@Mildred AnashieI think it does contain information for differential abundance.

Desire Oluwarotimi (13:30:14) (in thread): > I see what you all are referring to now. > > S6 is the one with mean relative abundance. > S7 is the one with differential abundance.@Peace Daniel@Scholastica Urua@Mildred Anashie

Aleru Divine (13:33:06) (in thread): > Table S7 is curatable@Mildred Anashieand I believeit’sthe same as figure 3

Aleru Divine (13:34:40) (in thread): > Both can be curated(they are the same) even the text referenced both.

Mildred Anashie (13:38:09) (in thread): > Okay, Thank you everyone@Aleru DivineDo you think S. pseudintermedius is increasing in Adpre or healthy:thinking_face:And is anyone able to find information on the significant threshold?

Aleru Divine (13:39:52) (in thread): > See this text just before figure 3,“In 9 of the 12 skin sites, the abundance of S. pseudintermedius was significantly higher in cAD-affected dogs not receiving medical treatment (cADpre) than in healthy dogs”

Aleru Divine (13:45:25) (in thread): > P < 0.05@Mildred Anashie

Mildred Anashie (13:48:16) (in thread): > Could you share how you found that?@Aleru DivineI was of the opinion that it is p< 0.05 but then I didn’t see it clearly stated and this alpha diversity figure confused me > You would see significance at 0.11:thinking_face: - File (JPEG): Fig.S2a-f

Aleru Divine (13:51:28) (in thread): > Okay, nowthat’sconfusing.Ididn’tsee the figure.Here’sanother text.I hopeI’minterpreting it correctly > > “Figure S2. For alpha diversity, Shannon indices were compared between four groups: healthy dogs (Healthy), cAD-affected dogs without medical treatment (cADpre), cADpre dogs that received 2 weeks of oclacitinib treatment (cADpost), and cAD-affected dogs already on oclacitinib treatment (cADtreat). The comparisons were made in 12 skin sites: abdomen (a), axilla (b), cubital flexor (c), flank (d), front paw (e), hind paw (f), inguinal area (g), medial pinnae (h), palmar metacarpal (i), perilabial area (j), perineum (k) and ventral tail (l). Asterisks (*) indicate p-values showing significant correlations (p< 0.05) are presented.”

Desire Oluwarotimi (13:53:04) (in thread): > They had quite a number of p values and that makes everything super confusing.

Mildred Anashie (13:53:19) (in thread): > Now they are writing something else and showing something else because what I shared is the S2 file:thinking_face:@Aleru Divine

Desire Oluwarotimi (13:53:57) (in thread): > Each plot in that S2 file has a p value.:joy:

Aleru Divine (13:54:04) (in thread): > I am so confused:cold_sweat:

Mildred Anashie (13:55:02) (in thread): > I guess we’d go for p<0.05 > But how would the significance for the ones showing significance above 0.1 be interpreted:thinking_face:@Desire Oluwarotimithe P values above each plot is showing the significance for the comparison ifI’msaying it right

Aleru Divine (13:58:28) (in thread): > Yeah,that’scorrect@Mildred Anashiebut I think these are the corrected p values

Samreen Aftab (13:58:40): > Hello guys, is this table curatable? (by looking at the mean abundance) - File (PNG): image.png

Desire Oluwarotimi (14:00:02) (in thread): > Yes, I think that’s exactly what it is supposed to be.@Mildred Anashiei

idiaru Angela (14:01:34) (in thread): > I actually believe it could be:thinking_face:. Using the mean abundance. But from the description above the table, it seems the differential abundance that was calculated using the Kruskal-Wallis test is better suited for the curation of this experiment@Samreen Aftab

Mildred Anashie (14:02:04) (in thread): > So in your opinion@Aleru Divine0.05 is still correct

Aleru Divine (14:05:40) (in thread): > Yeah, I would go with that

Aleru Divine (14:28:03) (in thread): > This looks like it can be curated.But for more context, could you share the link to the paper please.@Samreen Aftab

U1LCB8WEA (14:31:20) (in thread): > Looks like it to me too, based on the abundance ratio and FDR. As a bonus, you can paste taxids into the signature box and save having to type names! If you sort by ratio you should be able to group together all the taxa by increased or decreased in cases.

Barakat Akinsiku (14:33:01) (in thread): > Interesting takes. Thank you everyone for your input:blush:

Aleru Divine (14:33:55) (in thread): > Thank you so much for the confirmation@Levi Waldron

idiaru Angela (14:34:51) (in thread): > Thank you for the clarification@Levi Waldron

Barakat Akinsiku (14:43:32) (in thread): > Lol, fancy having the taxon ids:grinning:

idiaru Angela (14:46:28) (in thread): > If only all authors did same:sweat_smile:@Barakat Akinsiku

Barakat Akinsiku (14:49:01) (in thread): > I know right:smile:@idiaru Angela

Aleru Divine (15:06:53) (in thread): > I know:sweat_smile::sweat_smile::face_with_open_eyes_and_hand_over_mouth:

Joan C. Chukwuemeka (15:33:26) (in thread): > Thanks<@U1LCB8WEA>

Scholastica Urua (15:36:58) (in thread): > Thank you<@U1LCB8WEA>

Svetlana Ugarcina Perovic (15:40:09) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710967674258869?thread_ts=1710957842.557139&cid=C04RATV9VCY - Attachment: Attachment > ANCOM-BC uses a linear model. In this case, just curate it as ANCOM.

Mildred Anashie (15:41:07) (in thread): > Thanks alot@Svetlana Ugarcina Perovicdefinitely saving this thread:hugging_face:

Mildred Anashie (16:18:04): > Hello everyone > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy<@UBNSEMS3S>@Scholastica Uruaand I worked on completing this incomplete study from “Incomplete Pages” under the “Todo for reviewers”https://bugsigdb.org/Study_672The study is now ready for review and we would really like to get feedback on this > Also can this be recorded as a contribution? > What can we use as a merge date? > > Thank you:pray: - Attachment (BugSigDB): Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial - BugSigDB > The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health.

Aananditaa (17:01:39): > Hi! I have a doubt regarding the project timeline which we have to fill during final application can anyone please suggest where I can find more about it

Svetlana Ugarcina Perovic (17:03:08) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&cid=C04RATV9VCY - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Svetlana Ugarcina Perovic (17:04:40) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711898929582889?thread_ts=1711890117.924109&cid=C04RATV9VCY - Attachment: Attachment > Also, Kindly note that the internship begins on the 27th of May and not the 2nd of May.

Sneha Suman (17:10:13): > Hii! > I have tried to curate the study as per my knowledge, I would like to request the mentors to review it. Thank you for you efforts:pray:! - Attachment (BugSigDB): Dysbiosis of skin microbiome and gut microbiome in melanoma progression - BugSigDB > BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy.Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy.

Svetlana Ugarcina Perovic (17:12:39) (in thread): > Noted. Thank you.

Aananditaa (17:52:12) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

2024-04-02

Glorious Katushabe (03:17:09): > Good morning team, I am recording my contribution and I am wondering which URL to post as its requested in the section

Mildred Anashie (03:18:37) (in thread): > Good morning@Glorious KatushabeIf you are recording a study you curated on BugSigdbYou’llinclude the link to the curation, copy and paste where URL is required

Scholastica Urua (03:22:42) (in thread): > Hello@Glorious Katushabe, the link to your curation will be recorded as the URL. It’ll be something like this;https://bugsigdb.org/Study_…

Glorious Katushabe (03:25:21) (in thread): > Thank you@Mildred Anashieand@Scholastica Urua. how about for the first curation form where answered questions with annotated article? i could not locate my URL

Scholastica Urua (03:26:09) (in thread): > For the first curation, you’ll include a link to the form…

Scholastica Urua (03:27:46) (in thread): > This link;https://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDcDon’t worry if the link opens up an empty form. The mentors already have what they need once you’ve submitted the filled form. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Mildred Anashie (03:28:49) (in thread): > Thank you@Scholastica UruaI was looking for that

Glorious Katushabe (03:30:39) (in thread): > Thank you, this is so helpful@Scholastica Urua

Svetlana Ugarcina Perovic (03:32:35): > :tulip:**** Good luck with your final application!****

Blessing Ene Anyebe (03:33:06) (in thread): > Thank you@Svetlana Ugarcina Perovicthank you:hugging_face::partying_face::orange_heart:

Mildred Anashie (03:33:18) (in thread): > Thank you@Svetlana Ugarcina Perovic:hugging_face::hugging_face::hugging_face:

Scholastica Urua (03:33:25) (in thread): > Thank you@Svetlana Ugarcina Perovic:hugging_face:

Samreen Aftab (03:33:39) (in thread): > Thank you!@Svetlana Ugarcina PerovicIt’s been an amazing journey working with all of you!

Peace Daniel (03:41:45) (in thread): > Thank you@Svetlana Ugarcina PerovicGood luck everyone:blush:

Victoria (Burah) Poromon (03:44:37) (in thread): > Thank you!@Svetlana Ugarcina Perovic:blush:

Abiola Salako (03:48:21) (in thread): > Thank you@Svetlana Ugarcina Perovic

Oluwatomisin Omojokun (03:52:28) (in thread): > What is the merge date for the first linkhttps://cunysph.az1.qualtrics.com/jfe/form/SV_6uloQhkJtX2zsDc

Oluwatomisin Omojokun (03:53:28) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (03:53:32) (in thread): > The date you finished should work for merge date for the first task@Oluwatomisin Omojokun

Oluwatomisin Omojokun (03:53:56) (in thread): > Thanks@Mildred Anashie

NWAKAEGO VINCENT (03:54:19) (in thread): > Thank you

Adenike Oladimeji-Kasumu (04:05:32) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (04:34:37) (in thread): > Thank you so much@Svetlana Ugarcina Perovicand Good luck everyone:heart_hands:

Bolanle Wahab (04:49:01) (in thread): > Thank you so much@Svetlana Ugarcina PerovicAll the best everyone:heart:

Adedoja Isaac (04:52:29) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kelechi Madubuko (05:03:35) (in thread): > Thank you@Svetlana Ugarcina PerovicGood luck to us:muscle:

Kelechi Madubuko (05:09:27) (in thread): > Thank you@Svetlana Ugarcina Perovicfor your time and efforts so far. I’ve learnt quite a lot from the mentors and co-contributors within such a short space. Thanks again everyone

Akinbode Mariam (05:15:05) (in thread): > Thank you@Svetlana Ugarcina Perovic

Manisha Nair (05:17:14) (in thread): > Thank you@Svetlana Ugarcina Perovic

Barakat Akinsiku (06:26:32) (in thread): > Thank you@Svetlana Ugarcina Perovicand Goodluck everyone:heart:

Rahila-me (06:30:48): > So guys, once your dashboard is showing update your application it means you have done the final application?..Good luck all

Eniola Adebayo (06:31:04) (in thread): > Thankyou@Svetlana Ugarcina Perovic

Faith Ifeoluwa Alexander (06:34:11) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (06:50:12) (in thread): > Thanks@Svetlana Ugarcina Perovic

Ima-obong (Aimah) (07:53:04) (in thread): > Thank you@Svetlana Ugarcina Perovic, wishing us all the best outcome.

Joan C. Chukwuemeka (11:45:36): > Hello everyone:wave:,<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>@Esther Afuape@Chioma Onyido@Peace SandyI found this studyhttps://bugsigdb.org/Study_837listed under Pages_with_missing_NCBI_ID. > > The initial curator recorded the taxa with the alphabet prefix that is indicative of each taxon level, which is how it appeared in the paper. For the signature_1 in Experiment_3,* Eubacterium coprostanoligenes was reported as genus and family, like g_Eubacterium_coprostanoligenes, & f_Eubacterium_coprostanoligenes. However, there isEubacterium coprostanoligenes in NCBI withTaxonomy ID: 290054, which is a species taxon level. To resolve it, will be right then to capture: > g_Eubacterium_coprostanoligenes (the genus level) asEubacterium (Taxonomy ID: 1730, rank - genus)* and > f_Eubacterium_coprostanoligenes(the family level) asEubacteriaceae (Taxonomy ID: 186806, rank - family)? perhaps with a review note?:thinking_face: > (Pic 1 - NCBI, Pic 2- research paper, Pic 3 - BugsigDB curation) - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Mildred Anashie (11:49:19) (in thread): > @Joan C. Chukwuemekawell done:clap:I asked for permission earlier to work on this but I realized that the ones in the paper are of different ranks. i.e Genus and Family while the ID was showing species just as you pointed out and that’s why I left it and I think that’s why the initial curator curated them that way indicating the ranks > > It’s same for the other unresolved taxas appearing in orangehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711604249194549 - Attachment: Attachment > Hi @Chioma Onyido @Svetlana Ugarcina Perovic @Esther Afuape > Hi everyone :wave: > I was going through the pages with missing NCBI ID and I found this study https://bugsigdb.org/Study_837 > The study has been reviewed so I’m not sure the curator is still working on it and I think most of the taxas are appearing in orange because of the way they were entered (correct me if I’m wrong) > The taxas were entered with their rank (g,c,o etc) > A few of those taxas have NCBI IDs and I’ll like to effect the change with your permission if that’s okay, Thank you :pray::skin-tone-5: > > Also for anyone that missed the message about our weekly office hour > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711549765482209

UBNSEMS3S (11:52:50) (in thread): > As Mildred mentioned, Eubacterium coprostanoligenes group doesn’t appear to be quite the same thing as what you’ve identified.

Joan C. Chukwuemeka (11:55:26) (in thread): > Alright<@UBNSEMS3S>, My thoughts is that one of the species is in the genus level of Eubacterium coprostanoligenes,Eubacteriumand the other in its family level, which isEubacteriaceae. That’s why I had such consideration. > Are the alphabet prefix not indicative of the taxon level?:thinking_face:

Nitya Singhal (12:32:28): > Hey,<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>@Esther Afuape@Chioma Onyido@Peace SandySince it says that we can continue recording the contributions so can we still contribute and curate papers?

Aleru Divine (12:35:07) (in thread): > Yesthat’scorrect@Nitya Singhal

Blessing Ene Anyebe (12:36:40): > I think we can no longer update our final application!:sweat_smile:

Mildred Anashie (12:48:14) (in thread): > Yes we can continue@Nitya Singhal:blush:

Mildred Anashie (12:48:59) (in thread): > Yes wecan’t🫨@Blessing Ene Anyebe

Peace Daniel (13:12:52) (in thread): > Yes

Joan C. Chukwuemeka (13:15:45) (in thread): > @Mildred Anashiethe slack chat conversation you sent, showed the permission was granted to you.. still not quite cleared on this:thinking_face:

Mildred Anashie (13:18:38) (in thread): > Yes@Joan C. ChukwuemekaI was granted permission to resolve it but after doing further research and going through the paper I understood better why the initial curator did the curation that way > > It was because the taxas were of different ranks and it was clearly indicated in the paper, Icouldn’tsolve it the way I had initially thought tothat’swhy I left it the way it was

Joan C. Chukwuemeka (13:24:01) (in thread): > Then we are on the same page. > > My question points to the finding that based on Taxonomic lineage, the speciesEubacterium coprostanoligenesis under the genusEubacteriumand familyEubacteriaceae.Doesn’t the g_ and F_ prefix denote genus and family respectively? > If so, won’t the corresponding genus and family forEubacterium coprostanoligenes be a fit? > <@UBNSEMS3S>* *

Joan C. Chukwuemeka (13:30:23) (in thread): > I know there can be different species under one genus and different genus under a family, hence why I thought that if it’s affirmed that it can be edited that way, a review note will be added too. > > Would really love clarity on this?:thinking_face:.

Mildred Anashie (13:30:56) (in thread): > Yes g_ and f_ denotes genus and family > I get what you are saying, which is to replace g_Eubacterium coprostanoligenes with Eubacterium and f_Eubacterium coprostanoligenes with Eubacteriaceae > > ButI’munsure if that will work > > The mentors can guide better on this@Joan C. Chukwuemeka

Mildred Anashie (13:33:16) (in thread): > Also this might be a lot different from the Eubacterium genus and Eubacteriaceae Family > > Because the other taxas reported in their ranks also share the same problem so I was of the opinion to leave it the way the initial curator did

Peace Daniel (13:34:13) (in thread): > @Joan C. Chukwuemekai think if it were the same genus it would’ve been given a synonym to indicateit’ssimilarity

Joan C. Chukwuemeka (13:38:18) (in thread): > Yea@Mildred Anashie, some taxas are unresolvable currently, and can be resolved in the near future as scientific research evolves… > > The researchers here gave us a hint of the taxon level they identified up to with the prefix. > I trust this would be sorted one day > Fingers crossed:crossed_fingers::relaxed:.

Joan C. Chukwuemeka (13:40:24) (in thread): > @Peace DanielI’m not sure I understand your assertion:thinking_face:?

Scholastica Urua (13:56:49) (in thread): > @Nitya Singhalyes, you can still curate papers. It just can’t be recorded on outreachy anymore.

Peace Daniel (14:12:49) (in thread): > I don’t think they can be replaced as they seem to be two different genus, if they were the same it would be linked to a homotypic/heterotypic synonym on NCBI

Joan C. Chukwuemeka (14:31:14) (in thread): > @Peace DanielI think you misunderstood the question/conversation… > Perhaps read through again…https://community-bioc.slack.com/archives/C04RATV9VCY/p1712078641526969?thread_ts=1712072736.028109&cid=C04RATV9VCY - Attachment: Attachment > Then we are on the same page. > > My question points to the finding that based on Taxonomic lineage, the species Eubacterium coprostanoligenes is under the genus Eubacterium and family Eubacteriaceae. > > Doesn’t the g_ and F_ prefix denote genus and family respectively? > If so, won’t the corresponding genus and family for _Eubacterium coprostanoligenes be a fit? > @UBNSEMS3S_

Peace Daniel (14:35:20) (in thread): > Not quite sure where the misunderstanding lies@Joan C. ChukwuemekaFrom the images you shared, one is a genus (the article) and the one you found on NCBI (is a specie) > I’m saying it’s not the same, or was this not your question? > > In simpler terms, they could be different families, genus and species so it’s best to leave as it is for now

Samreen Aftab (15:20:26): > Hello everyone > I made a mistake in my final application, I think I accidentally checked the box which confirmed if my time commitments have changed. Is there any way I can change it please?:smiling_face_with_tear:<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy - File (PNG): image.png

Blessing Ene Anyebe (15:23:22) (in thread): > Ouch:sneezing_face:

Peace Daniel (15:26:01) (in thread): > I’mnot sure the mentors can assist with this@Samreen Aftab

Svetlana Ugarcina Perovic (15:27:06) (in thread): > Please do contact the outreachy support.

Abiola Salako (15:53:03) (in thread): > Yes, we can@Nitya Singhal

Abiola Salako (15:53:45) (in thread): > Yes we can’t@Blessing Ene Anyebe

Joan C. Chukwuemeka (16:16:26) (in thread): > That wasn’t my Question@Peace DanielHowever, It’s already sorted

Esther Afuape (16:23:19) (in thread): > @Joan C. Chukwuemekasimply curating them as genus Eubacterium and family Eubacteriaceae is too vague. What is present in the paper is specific.It’sa specific group. Seeing Eubacterium or Eubacteriaceae in the curation is a far reach from what the actual group is.

Mildred Anashie (16:27:32) (in thread): > Thank you for the explanation and clarification@Esther Afuape:blush:

2024-04-03

Oluwatomisin Omojokun (01:05:12) (in thread): > You can keep checking your email for this - File (PNG): Screenshot (25).png

Samreen Aftab (01:08:18) (in thread): > Thank you everyone:pleading_face:

Desire Oluwarotimi (02:49:19): > Good morning everyone. > > I woke up to some of my study’s signatures like this. Any help?? - File (PNG): Screenshot 2024-04-03 at 07.43.15.png

Scholastica Urua (02:55:25) (in thread): > Good morning@Desire OluwarotimiPlease see this thread;https://community-bioc.slack.com/archives/C04RATV9VCY/p1711621166939199?thread_ts=1711621166.939199&cid=C04RATV9VCY - Attachment: Attachment > Hello @Levi Waldron @Svetlana Ugarcina Perovic @UBNSEMS3S @Chioma Onyido @Peace Sandy @Esther Afuape > > I would like to report this error message in my study page. > > “Lua error: too many expensive function calls” > > Signatures 1 and 2 in experiment 126 > Signature 1 in experiment 127 > > The signatures above reported the error message and I still have more to curate. I believe I’d have to wait till this is sorted out. > > Thank you so much! > > Link to study: https://bugsigdb.org/Study_1048

Scholastica Urua (02:57:02) (in thread): > …and this. Hope this helpshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711502278231649?thread_ts=1711474541.599179&cid=C04RATV9VCY - Attachment: Attachment > I don’t think you need to worry about the bug. At least there’s a workaround in the meantime so we can see the signatures one experiment at a time.

Desire Oluwarotimi (03:01:37) (in thread): > Thank you@Scholastica Urua

Mildred Anashie (03:04:53) (in thread): > Yea@Desire OluwarotimiI faced the same too and informed the mentors in the issue on GitHub once I was done curating the paper

Desire Oluwarotimi (03:06:40) (in thread): > Yeah, I guess we’ll have to do the same when we are done.@Mildred Anashie

Mildred Anashie (03:07:49) (in thread): > Alright thenWell done:clap:

Barakat Akinsiku (04:29:33) (in thread): > Just noticed it too. Goodmorning everyone

Mildred Anashie (04:30:08) (in thread): > Good morning@Barakat Akinsiku

Barakat Akinsiku (04:31:31) (in thread): > Hi@Mildred AnashieGood morning:hugging_face:

Scholastica Urua (04:33:02) (in thread): > Good morning@Barakat Akinsiku

Abiola Salako (04:51:12) (in thread): > Good morning@Barakat Akinsiku

Barakat Akinsiku (05:19:06) (in thread): > Good morning@Scholastica Urua@Abiola Salako:hugging_face::hugging_face:

Ikeh Darlington Ikeh (06:35:56): > Is anyone else missing the activities and messages from this community like me?

Mildred Anashie (06:36:43) (in thread): > I’mnot sure I understand you@Ikeh Darlington Ikeh:thinking_face:

Scholastica Urua (06:52:45) (in thread): > I think he’s saying messages are not popping up like before:smile:@Mildred Anashie

Aleru Divine (06:53:17) (in thread): > @Mildred Anashieis think I understand what he means:sweat_smile:I kinda miss it too@Ikeh Darlington Ikeh

Mildred Anashie (06:53:56) (in thread): > Righttttt@Aleru Divineand@Scholastica Urua:joy:Yea, I miss it too@Ikeh Darlington Ikeh

Scholastica Urua (06:54:36) (in thread): > Same here:sweat_smile:

Abiola Salako (07:23:28) (in thread): > Yes I do@Ikeh Darlington Ikeh:grinning:

Peace Daniel (07:41:41) (in thread): > Yh,it’s gettingquiet here

Faith Ifeoluwa Alexander (10:07:25) (in thread): > Good Afternoon@Desire OluwarotimiI experienced it. Just report it & it will be dealt with. It’s a system bug & it usually clears off when reported.

Joan C. Chukwuemeka (10:46:33) (in thread): > Yea…:relaxed::relaxed:No fresh open issues to curate for now… > NCBI Detective work and other help content to-dos for now:hugging_face:

Oluwatomisin Omojokun (12:06:50) (in thread): > Same here

Joan C. Chukwuemeka (12:34:03): > Good day all<@UBNSEMS3S><@U1LCB8WEA>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI noticed some studies that have experiments still appear listed under the help category of Studies that have no Experiments (https://bugsigdb.org/Help:Cleanup#Studies_that_have_no_Experiments) An example is this -https://bugsigdb.org/Study_991What could be the reason?:thinking_face: - Attachment (BugSigDB): Help:Cleanup - Attachment (BugSigDB): Dysbiosis of skin microbiome and gut microbiome in melanoma progression - BugSigDB > BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy.Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. - File (PNG): image.png

Aleru Divine (12:56:34): > Hello and good evening everyone!@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Peace Sandy@Chioma Onyido@Esther AfuapeI found some published papers that has not been curated in BugSigDB yet and I read through them and I believe they can be curated.Here are some links: > 1. https://journals.asm.org/doi/10.1128/spectrum.00055-21 > 2. https://onlinelibrary.wiley.com/doi/full/10.1002/advs.202205058 > I wanted to ask if I can go ahead to curate them.Thank you so much!

Peace Daniel (12:59:34) (in thread): > That’sa great find@Aleru DivineI also have one like this,I’dprobably plug it in once you get your response:clap:

Aleru Divine (13:00:26) (in thread): > Okay@Peace Daniel:hand_with_index_and_middle_fingers_crossed:

Mildred Anashie (13:00:54) (in thread): > Well done@Aleru DivineThis papers look curatable to me too > I can assist if you get the go ahead and you do need help with any:blush:

Aleru Divine (13:02:30) (in thread): > Sure thing@Mildred Anashie:hugging_face:

Peace Daniel (13:11:44) (in thread): > Or I might just do it now, saves response time:blush:Hello@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA>I found this published paper I believe is good to curate, may I go ahead with it?https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166687/

Svetlana Ugarcina Perovic (13:15:12) (in thread): > @Peace Danielplease seehttps://github.com/waldronlab/BugSigDBcuration/issues/204#issuecomment-2035145792Our priority is to close currently open/wip issues, before opening new ones, thank you!

Joan C. Chukwuemeka (13:17:11) (in thread): > @Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA>@Esther Afuape@Chioma Onyido@Peace SandyI think studies 1029 to Study 1043 (https://bugsigdb.org/Study_1029-https://bugsigdb.org/Study_1043) listed under studies without experiment” needs to be deleted. > > Reason: They all have same doi/url that links to the same research paper which was finally curate athttps://bugsigdb.org/Study_1044

Peace Daniel (13:18:00) (in thread): > Yes@Svetlana Ugarcina PerovicI just saw it,I’llstart working on it:purple_heart:

Mildred Anashie (13:18:08) (in thread): > @Svetlana Ugarcina Peroviccan we try to complete some of the studies that do not have the ‘needs review’ tag on GitHub?

Svetlana Ugarcina Perovic (13:19:22) (in thread): > Yes please, but in agreement with the assigned person.

Mildred Anashie (13:19:51) (in thread): > Okay > > Thank you:pray:@Svetlana Ugarcina Perovic

Aleru Divine (13:20:02) (in thread): > @Svetlana Ugarcina PerovicI currently do not have any issues to work on:pleading_face:is there any issue I can work on at the moment please?

Mildred Anashie (13:21:03) (in thread): > I think we can go through the GitHub repo@Aleru Divineand assist in finishing incomplete curation > But in agreement with the assigned person

Joan C. Chukwuemeka (13:21:18) (in thread): > @Svetlana Ugarcina PerovicPlease could you help with this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1712164631909619?thread_ts=1712162043.385739&cid=C04RATV9VCY - Attachment: Attachment > @Svetlana Ugarcina Perovic @UBNSEMS3S @U1LCB8WEA @Esther Afuape @Chioma Onyido @Peace Sandy I think studies 1029 to Study 1043 (https://bugsigdb.org/Study_1029 - https://bugsigdb.org/Study_1043) listed under studies without experiment” needs to be deleted. > > Reason: They all have same doi/url that links to the same research paper which was finally curate at https://bugsigdb.org/Study_1044

Svetlana Ugarcina Perovic (13:22:24) (in thread): > Also, you could go trough the issues with label:reviewed and according to the feedback/scoring correct the curation in bugsigdb (if it’s not already corrected). cc@Aleru Divine

Aleru Divine (13:23:01) (in thread): > Okay@Mildred Anashie:thumbsup:

Aleru Divine (13:23:44) (in thread): > Got it@Svetlana Ugarcina PerovicThank you so much:pray:

Svetlana Ugarcina Perovic (13:25:12) (in thread): > Deleted. Thank you!

Joan C. Chukwuemeka (13:28:05) (in thread): > Alright. Thanks a lot@Svetlana Ugarcina Perovic. > Still discovering more, will drop them here too, once I’m done.

Joan C. Chukwuemeka (14:41:43) (in thread): > @Svetlana Ugarcina PerovicHere are other studies listed under******“studies without experiment” ****that***** *****needs to be deleted.Study_1021(empty study)Study_1025 (curated athttps://bugsigdb.org/Study_970)Study_1017(already exists in bugsigdb - info athttps://github.com/waldronlab/BugSigDBcuration/issues/287)Study_1013(curated athttps://bugsigdb.org/Study_1024)Study_1011(DOI returns error)Study_962, Study_963, &Study_964 (curated athttps://bugsigdb.org/Study_965)Study_937, Study_938, Study_939, Study_940 &**** Study_943(have same doi/url that links to the same research paper &was curated athttps://bugsigdb.org/Study_941)Study_936(empty study)Study_916(curation ongoing athttps://bugsigdb.org/Study_917)Study_915(curated athttps://bugsigdb.org/Study_902)Study_901 (DOI returns error)Study_898 (paper was’nt curatable-info athttps://github.com/waldronlab/BugSigDBcuration/issues/144)Study_893(curated athttps://bugsigdb.org/Study_864)Study_890(curated athttps://bugsigdb.org/Study_891)Study_889(closed issue -https://github.com/waldronlab/BugSigDBcuration/issues/162)Study_878 &** Study_888**- no doi

Peace Daniel (15:21:16): > Hi everyone@Ajayi Mercyreached out to me and requested we collaborate on this study together. Study 840, herehttps://bugsigdb.org/Study_840I have a few questions that needs clarification and would appreciate your inputs > > Questions: > Can the selected condition (BugSigdb) be a suitable find for “skin microbiome” which was originally studied > > From the text and fig 6, I could see both Wilcoxon(used for CLR) and ANOVA were used for differential abundance, is this right? > > I’d love to curate fig 2c for alpha diversity measures of the 5 social groups, although from the text I read there was no significant difference. What do you think about it? > > And also what’s your thoughts on fig 5c? > > I anticipate your responses :) - Attachment (BugSigDB): Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques - BugSigDB > While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates-important animal models for translational biomedical research.

idiaru Angela (16:05:58) (in thread): > Hey@Peace DanielI’m not sure if the current condition is perfect but if there’s no other fit I guess it might work > For curating figure 2c, that would be at your perogative since there was no significant difference for all groups except 1 of them. > From the text and figure 6, I see no indication that ANOVA was used for differential abundance, just wilcoxon > This excerpt under the heading “data analysis” talks about differential abundance > “To identify potential significant differences between phyla across different social groups and across different sampling periods, we used Kruskal-Wallis (KW) (52) or Wilcoxon signed rank (53) tests in the R package ggpubr (v 0.4.0).”

Svetlana Ugarcina Perovic (16:07:32) (in thread): > ALL deleted. Thank you!

Peace Daniel (16:07:41) (in thread): > @idiaru AngelaTo more fully understand differentially abundant taxa, we compared ASV features between sampling periods (2013 versus 2015), using the program ALDEx2 (q2-aldex2) (71 – 73). These were chosen for comparison because they showed a significant difference in pairwise alpha diversity using Faith’s PD calculations. The subset of samples collected during both sampling periods (n = 75) were filtered from the clustered and batch adjusted feature table of non-rarefied counts. Significance was calculated using Welch’s t-test and Wilcoxon test on CLR transformed counts. Benjamini–Hochberg (BH) corrected values were calculated for each feature

idiaru Angela (16:08:37) (in thread): > @Peace Danielfrom the above I see no where in which ANOVA was used for differential abundance

Peace Daniel (16:09:21) (in thread): > ALDEx2 is ANOVA

idiaru Angela (16:13:47) (in thread): > ALDEx2 was used to analyse the compositional data while there was the application of Welch’s t-test and Wilcoxon test on CLR transformed counts to assess significance@Peace Daniel

Peace Daniel (16:17:17) (in thread): > Can you point me to this

idiaru Angela (16:20:57) (in thread): > From the above excerpt you sent in the thread, Welch’s t-test and wilconxon test was used for differential abundance

Peace Daniel (16:34:59) (in thread): > On CLR transformed counts**, if you take a look at fig 6. There’s a volcano plot and a violin plot. > I think Wilcoxon was used for confirmation

Peace Daniel (16:42:43) (in thread): > @Mildred Anashie@Aleru Divine@Scholastica UruaWhat do you think please?

idiaru Angela (16:50:12) (in thread): > The volcano plots are simply a representation of the results gotten from the statistical tests in my opinion. While ALDEx2 was used to the compositional data (abundance of the microbial data) , welch t-tests and wilcoxon was used to get the “statistically significant” abundance of the composition between two groups@Peace DanielIn my opinion, the entire figure 6 was gotten using just one statistical test

Aleru Divine (16:53:20) (in thread): > Hi@Peace Danielgoing through the study and I don’t think “abnormality of the skin” is suitable, since they did not study any abnormalities but the skin itself. > > I was thinking this would be more appropriate > Seehttps://www.ebi.ac.uk/ols4/ontologies/uberon/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FUBERON_0002097Let me check your other questions - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Peace Daniel (16:58:27) (in thread): > Hm, considering the axillae was sampled…does the body really fit?@Aleru DivineI’dwork with this tho, till any further updates

Aleru Divine (17:01:33) (in thread): > Figure 2c shows significant difference between F and V. You can curate the others as unchanged > Yeah, go ahead and curate for all. > > I think figure 5C is Shannon, according to the description but for non-core taxa. See the description.

Peace Daniel (17:01:54) (in thread): > Yea exactly > > That means the non-coretaxa would be another experiment right?

Aleru Divine (17:02:19) (in thread): > Let me check your second concern

Aleru Divine (17:16:44) (in thread): > This was a bit tricky, butIagree with@idiaru Angela“Significance was calculated using Welch’s t-test and Wilcoxon test”

Peace Daniel (17:20:42) (in thread): > Is this for the sampling periods bcz this is the only one with differential abundance ?@Aleru DivineAnd what do you think about the mention of CLR transformation counts?

Joan C. Chukwuemeka (17:25:10) (in thread): > Alright. Thanks@Svetlana Ugarcina PerovicI think this bunch of studies were as a result of some persons not remembering the link to their study, so they just create a new one. > > So, for current and Future curators/contributors it will be nice to take note of the link of any new study we create, and where we forget, going through our browser history can help too. This, I believe, will prevent such re-occurrence.:blush:

Mildred Anashie (17:35:38) (in thread): > Still going through the paper@Peace DanielBut I see (see image) > > I’m thinking we might have a case of two statistical tests for the comparison done on sampling period > Wilcoxon was used for between groups comparisons but the ALDEx2 seems to be a confirmatory test done for differential abundance > For the comparisons done on the social groups your test will be Wilcoxon in my opinion because that’s what was used for between groups comparisons > > PS: I believe we curate between group relative abundance > > > And 5c seems to show another experiment > CLR transformation counts in my opinion is saying your Data transformation is Centered Log ratio but they say “We calculated CLR-transformed relative abundances” soI’m notsure if this is saying CLR was applied to relative abundance and if only CLR should be recorded - File (PNG): IMG_3195 - File (PNG): IMG_3194

Peace Daniel (17:38:53) (in thread): > Thank you@Mildred AnashieYes I know Wilcoxon was used for social groups, the confusion was that for the sampling periods

Peace Daniel (17:40:31) (in thread): > Could you explain a bit more on the group relative abundance or point me to it? SeemsI’mmissing something

Aleru Divine (17:42:11) (in thread): > Center log ratio was used to transform relative abundances.(If that makes sense).Here “To identify potential significant differences between phyla across different social groups and across different sampling periods, we used Kruskal-Wallis (KW) (52) or Wilcoxon signed rank (53) tests in the R package ggpubr (v 0.4.0).” > > Further confirms Wilcoxon

Mildred Anashie (17:43:37) (in thread): > One of the images shared said pairwise comparisons between social groups and between sampling period > > This was mentioned under the heading “Relative abundance”

Peace Daniel (17:43:55) (in thread): > But the figure I curated shows both ANOVA and Wilcoxon. > If it were to be Wilcoxon alone it means Iwouldn’tcurate the volcano plot andthat’dbe incomplete@Aleru Divine

Peace Daniel (17:44:22) (in thread): > Would take a look, thanks@Mildred Anashie

Mildred Anashie (17:45:47) (in thread): > @Aleru Divineyou are saying curating relative abundance is okay?

Aleru Divine (17:47:23) (in thread): > The excerpt I sharedwasn’tjust referring to relative abundance I think.Even if it was under it@Mildred Anashie

Aleru Divine (17:51:21) (in thread): > ANOVA? Idon’tsee any mention of ANOVA@Peace Daniel

Peace Daniel (17:56:28) (in thread): > This is ANOVA or am I mistaken? - File (PNG): IMG_2407

Aleru Divine (18:01:01) (in thread): > ANOVA-like, not ANOVA. Although I may be wrong.

Mildred Anashie (18:05:45) (in thread): > I’mthinking you should curate just Wilcoxon:thinking_face:I might be wrong though like@Aleru Divinesaid:joy:

Peace Daniel (18:06:19) (in thread): > In this term, ANOVA is a close representation, > I also read it incorporates data like Kruskal walis and Anova

Peace Daniel (18:07:47) (in thread): > Ohhh:joy::joy::sob:This has been a lot of work,that’sfine then > Thanks a lot@idiaru Angela@Aleru Divine@Mildred Anashie:pray::purple_heart:

Aleru Divine (18:11:59) (in thread): > You can raise this tomorrow during office hours@Peace Daniel:pray:I’minvested in knowingwhat’scorrect.

Mildred Anashie (18:12:48) (in thread): > Great suggestion@Aleru Divine

Peace Daniel (18:18:25) (in thread): > Oh, I thoughtthere’dbe no more office hours > > Thanks for the suggestion@Aleru Divine

Aleru Divine (18:31:50) (in thread): > I hope there is:pleading_face:

idiaru Angela (18:32:48) (in thread): > Me too:face_holding_back_tears:@Aleru Divine

Mildred Anashie (18:33:30) (in thread): > We would find out in a few hours:hand_with_index_and_middle_fingers_crossed:

Abiola Salako (18:35:55) (in thread): > Well done, Ladies:bouquet:The energy you all gleamed:raised_hands:@idiaru Angela@Aleru Divine@Mildred Anashie

2024-04-04

Scholastica Urua (00:35:11) (in thread): > Such an engaging thread. Well done@Peace Daniel@idiaru Angela@Mildred Anashie@Aleru Divine:hugging_face:

Joan C. Chukwuemeka (02:58:49) (in thread): > Good morning@Peace Daniel, Here’s my view on your questions > > Questions: > 1. Can the selected condition (BugSigdb) be a suitable find for “skin microbiome” which was originally studied > ******I think “skin microbiome measurement” should be a better fit. EFO:0801228 ****http://www.ebi.ac.uk/efo/EFO_0801228Q2.***** *****From the text and fig 6, I could see both Wilcoxon(used for CLR) and ANOVA were used for differential abundance, is this right?******Statistical test for differential abundance I see is Wilcoxon test.*********Excerpts 1:*****To identify potential significant differences between phyla across different social groups and across different sampling periods, we used Kruskal-Wallis (KW) (52) or Wilcoxon signed rank (53) tests in the R package ggpubr.********2nd Excerpt********: For comparisons across social groups, an overall P-value is shown on each plot and was calculated using a Kruskal-Wallis test. Pairwise comparisons between social groups were calculated using Wilcoxon tests. For sampling period, differences between the 2013 and 2015 seasons were calculated using Wilcoxon tests.********“Comparison across group********”is likely relative abundance, which Kruskal-Wallis test was used whereas “******Comparison between groups”****, which is differential abundance, Wilcoxon test was used. > > Q3. I’d love to curate fig 2c for alpha diversity measures of the 5 social groups, although from the text I read there was no significant difference. What do you think about it?:thinking_face:***** fig 2c for alpha diversity measures of the 5 social groups seems workable, however, I’d try to revert to you on this later. Trying to understand the comparisons that were made, which will define the experiments, so we don’t end up with many experiments with unchanged alpha diversity and maybe no signature.*****Q4. And also what’s your thoughts on fig 5c?******On figure 5c, the Non-Core Shannon’s Diversity measures the diversity of the transient or less abundant bacteria on the skin surface of the monkeys. **** - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Nitya Singhal (03:01:54) (in thread): > @Scholastica Urua@Svetlana Ugarcina Perovic, but outreachy still allows us to record the contribution.

Scholastica Urua (03:06:03) (in thread): > Hello@Nitya Singhal, the ‘Record your contribution’ link in outreachy has been discontinued for now. So we can’t record new contributions.

Nitya Singhal (03:06:35) (in thread): > It is available to me though@Scholastica Urua

Joan C. Chukwuemeka (03:11:30) (in thread): > @Peace DanielI noticed that both my suggestion for the condition and that of@Aleru Divineis not available in BugSigDB drop down. > I wish we could use EFO code in the condition section, the way we do in the signature section with NCBI ID:thinking_face:@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandycould help out here please.

Mildred Anashie (03:20:12) (in thread): > Yes@Nitya SinghalI noticed you can still record contributions, although Ihaven’tbecauseI’muncertain if I should > > And I thinkthat’swhat I understood from this messagehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711536329162399@Svetlana Ugarcina Peroviccould you please clarify:pray: - Attachment: Attachment > Good morning :rocket: YOU ARE DOING AMAZING TEAM WORK in finalizing still open GitHub issues. > > IMPORTANT: The deadline for final applications is April 2, 2024 at 4pm UTC. Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline. > > GOOD NEWS: Applicants who submit a final application will be able to continue recording and editing their contributions to your project. They can record contributions until the intern announcement on May 1, 2024 at 4pm UTC. Applicants who have not submitted a final application will not be able to record or edit their contributions. > > @U1LCB8WEA @UBNSEMS3S @Peace Sandy @Esther Afuape @Chioma Onyido @Svetlana Ugarcina Perovic

Peace Daniel (03:21:11) (in thread): > Yes@Joan C. ChukwuemekaThanks for your input, did you read why I think ALDEx2 should be included with Wilcoxon tho?

Nitya Singhal (03:21:22) (in thread): > but will they be considered?@Mildred Anashie@Svetlana Ugarcina Perovic

Scholastica Urua (03:21:34) (in thread): > @Nitya SinghalI think we are not suppose to record anymore though.

Aleru Divine (03:21:58) (in thread): > Yeah,there’sstill the “record contributions” button.@Nitya Singhal@Scholastica Urua@Mildred Anashie

Peace Daniel (03:22:30) (in thread): > Check out fig 6 which I curated, the volcano plot has more signatures and those in the violin plot is also included in the volcano plot which makes the volcano plot more concise. > > The volcano plot was done with ALDEx2@Joan C. Chukwuemeka

Nitya Singhal (03:27:45) (in thread): > but will they be considered for further evaluation?@Aleru Divine

Aleru Divine (03:28:46) (in thread): > I have no idea about that:sweat_smile:

Mildred Anashie (03:28:58) (in thread): > @Nitya SinghalI’munsure if there would be considered

Nitya Singhal (03:34:56): > Good afternoon from India. Please help me out with this query dear mentors@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido<@UBNSEMS3S>@Peace Sandy@Ikeh Darlington IkehThere is an option to record contributions on the website of Outreachy even after the deadline has passed. So will my contributions recorded after 2nd April be considered for the evaluation of the result that is to be declared on 1st of May? > Please help me out with this. Thank you:heartpulse:

Mildred Anashie (03:38:46) (in thread): > Today is Thursday and I think this question can be asked during the office hour (If we have office hours today)<@UBNSEMS3S>@Svetlana Ugarcina Peroviccould you please give information on the office hour?:pray::pray:

Joan C. Chukwuemeka (04:07:38) (in thread): > Yes@Peace DanielI did see the ALDEx2 part you mentioned. I still think the calculation in itself was with Wilcoxon.. like@Aleru Divineand@Mildred Anashiepointed out. > > However, we’d hopefully get more clarification from the mentors.

Aleru Divine (05:04:19) (in thread): > Me too@Joan C. Chukwuemeka

Svetlana Ugarcina Perovic (06:40:43): > Hello hello, we are evaluating your final application. > That said, there’s no need for additional recordings in outreachy. You are encouraged to continue working in BugSigDB where your activity is automatically recorded. Thank you!!We have our team meeting as usual at 9 AM EDT. See you! https://us02web.zoom.us/j/2737200499)<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma Onyido

Aleru Divine (06:42:29) (in thread): > Thank you so much@Svetlana Ugarcina PerovicI’mlooking forward to the meeting:partying_face::partying_face:

Bolanle Wahab (06:44:22) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:heart:

Mildred Anashie (06:46:18) (in thread): > Thanks a lot@Svetlana Ugarcina Perovic:pray::blush:

idiaru Angela (06:50:55) (in thread): > Thank you@Svetlana Ugarcina Perovic:heart_hands:

Peace Daniel (06:58:59) (in thread): > Thank you@Svetlana Ugarcina Perovic

Abiola Salako (07:14:07) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (07:26:41) (in thread): > Thanks a lot@Svetlana Ugarcina Perovicfor the update.:relaxed:

Praise Agbetuyi (07:36:33) (in thread): > Okay. Well noted. Thank you@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (07:52:02) (in thread): > Good day@Svetlana Ugarcina Perovic, > Please delete these as well: > * Study 947- curated athttps://bugsigdb.org/Study_949 > > * Study 1030 > * Study 1031 > * Study 1032 > * Study 1033 > * Study 1034 > * Study 1035 > * Study 1036 > * Study 1037 > * Study 1038 > * Study 1039 > * Study 1040 > * Study 1041 > * Study 1042 > (Study_1030 to Study 1042, all have same doi/url that links to the same research paper which was finally curated athttps://bugsigdb.org/Study_1044) > * Study_1050 (empty study) > > * Study_1072 - being curated athttps://bugsigdb.org/Study_1073 - Attachment (BugSigDB): Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host - BugSigDB > BACKGROUND: Intestinal helminths are extremely prevalent among humans and animals.In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry. - Attachment (BugSigDB): - BugSigDB > … - Attachment (BugSigDB): - BugSigDB > … - Attachment (BugSigDB): - BugSigDB > … - Attachment (BugSigDB): - BugSigDB > …

Svetlana Ugarcina Perovic (07:58:19) (in thread): > ALL deleted. Thanks!

Eniola Adebayo (08:10:44) (in thread): > Thankyou@Svetlana Ugarcina Perovic

Scholastica Urua (08:19:55) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aishat Ijiyode (09:23:29) (in thread): > Thank you@Svetlana Ugarcina Perovic

EBERE ADEKOGBE (09:36:37) (in thread): > Thank you@Svetlana Ugarcina Perovic

UBNSEMS3S (09:46:06): > Thank you all for attending. Just to emphasize, we are working on your providing feedback and scores on your curations. We want to give everyone a thorough review. We appreciate your patience.

idiaru Angela (09:46:53) (in thread): > Thank you for your time@C. Mirzayi (please do not tag this account)

Joan C. Chukwuemeka (09:48:26) (in thread): > Thank you<@UBNSEMS3S>.

Desire Oluwarotimi (09:48:52) (in thread): > Thank you very much<@UBNSEMS3S>

Aleru Divine (09:49:10) (in thread): > Thank you so much for the office hours session<@UBNSEMS3S>:hugging_face:

Peace Daniel (09:49:42) (in thread): > Thank you

Joan C. Chukwuemeka (09:52:13) (in thread): > > <@UBNSEMS3S>Please on finding a new microbiome-related research paper, do we open it as an issue first on GitHub before curation?:thinking_face:

Ima-obong (Aimah) (09:55:17) (in thread): > Thank you<@UBNSEMS3S>

Praise Agbetuyi (10:00:16) (in thread): > Thank you<@UBNSEMS3S>

Abiola Salako (10:05:23) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Raihanat Adewuyi (10:12:32) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Adegboye Rukayat (10:19:36) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Adegboye Rukayat (10:22:29): > Good day everyone, trust you all have a great day. Please a quick question, if the location of the subject is not defined in the paper should I leave it blank?

Blessing Ene Anyebe (10:24:58) (in thread): > Thank you so much@C. Mirzayi (please do not tag this account)Please would the recording be shared?

Peace Daniel (10:25:36) (in thread): > Check the location of the researchers, by their school or hospital

idiaru Angela (10:27:00) (in thread): > “If no location is mentioned in the article, look at the affiliation of the first and last authors of the paper for their location” > This is an excerpt from the curation policy. The location of the authors can help you determine what you should curate for that

Peace Daniel (10:30:27) (in thread): > You can also share your paper so we take a second look:hugging_face:

Adegboye Rukayat (10:36:44) (in thread): > Alright thank you, I will do that

idiaru Angela (10:37:54): > Hi and good day@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapePlease I’d like experiment 15, it’s signatures and experiment 16 of this study deleted. They are duplicates of already added experiments. Thank youhttps://bugsigdb.org/Study_1074 - Attachment (BugSigDB): Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection - BugSigDB > Long-term effect of Direct-acting antivirals (DAAs) on gut microbiota, short-chain fatty acids (SCFAs) and microbial translocation in patients with hepatitis C virus (HCV) infection who achieve sustained virological response (SVR) were limited.

Scholastica Urua (11:19:13) (in thread): > Thank you<@UBNSEMS3S>

Aleru Divine (13:17:44): > Hello@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI’dlike to delete experiments 2 and 3 from this study.Thank you so much! > > Link:https://bugsigdb.org/Study_920 - Attachment (BugSigDB): Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans - BugSigDB > Nutrition has broad impacts on all physiological processes.However, how nutrition affects human immunity remains largely unknown.

Esther Afuape (13:20:07) (in thread): > Deleted.

Aleru Divine (13:20:35) (in thread): > Thank you so much:blush:

2024-04-05

Svetlana Ugarcina Perovic (04:01:44) (in thread): > Deleted.

Svetlana Ugarcina Perovic (04:45:53): > :tulip:Happy Friday! We will be off Slack in the next days, focusing on reviewing your contribution work. Thanks!

Joan C. Chukwuemeka (04:47:43) (in thread): > Happy Friday too@Svetlana Ugarcina Perovic. Thanks for the update. Well done with the work. Would miss you here tho…:hugging_face:

Aleru Divine (04:48:32) (in thread): > Happy Friday to you too@Svetlana Ugarcina PerovicThanks for the update.

Desire Oluwarotimi (04:48:36) (in thread): > Happy Friday@Svetlana Ugarcina PerovicWelldone and thank you for the heads up.

idiaru Angela (04:57:37) (in thread): > Happy Friday:cherry_blossom:Thank you for the update@Svetlana Ugarcina Perovic

Peace Daniel (04:57:47) (in thread): > Happy Friday, thank you:purple_heart:

idiaru Angela (04:57:54) (in thread): > Thank you!!

Peace Daniel (04:59:34) (in thread): > Happy Fridayto y’alltoo:purple_heart:@Joan C. Chukwuemeka@Aleru Divine@Desire Oluwarotimi@idiaru Angela

Scholastica Urua (05:22:37) (in thread): > Happy Friday@Svetlana Ugarcina PerovicWell done to all the mentors and thank you for your hard work:pray:

Barakat Akinsiku (05:43:24) (in thread): > Happy Friday@Svetlana Ugarcina Perovicthank you for all you do

Kelechi Madubuko (07:11:12) (in thread): > Happy Friday!@Svetlana Ugarcina Perovicwe’ll miss your updates here. Can’t wait for you guys to get back on

Oluwatomisin Omojokun (07:16:25) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Oluwatomisin Omojokun (07:17:57) (in thread): > Happy friday@Svetlana Ugarcina Perovic. Thanks

Adenike Oladimeji-Kasumu (07:42:07) (in thread): > Happy Friday@Svetlana Ugarcina Perovicand everyone. I appreciate all your support here.

Samreen Aftab (09:50:22) (in thread): > Thanks for the update@Svetlana Ugarcina Perovic

Blessing Laweh (13:02:54) (in thread): > Thank you and weldone:clap::clap:

2024-04-06

Scholastica Urua (04:02:18): > Hello everyone, happy weekend!:hugging_face:@idiaru Angelaand I have been collaborating to complete this curation, and we would greatly appreciate a peer review before the final submission. > > Also, we are still a bit unsure about the study design. > > Thank you all in anticipation:pray:https://bugsigdb.org/Study_1074 - Attachment (BugSigDB): Long-term benefit of DAAs on gut dysbiosis and microbial translocation in HCV-infected patients with and without HIV coinfection - BugSigDB > Long-term effect of Direct-acting antivirals (DAAs) on gut microbiota, short-chain fatty acids (SCFAs) and microbial translocation in patients with hepatitis C virus (HCV) infection who achieve sustained virological response (SVR) were limited.

idiaru Angela (04:23:01) (in thread): > Hello everyone. Would really appreciate the peer reviews. Thank you!

Peace Daniel (05:07:43) (in thread): > Well done@idiaru Angela@Scholastica UruaI’llgive the study design a check

idiaru Angela (05:08:11) (in thread): > Thank you@Peace Daniel

Peace Daniel (05:16:31) (in thread): > Your study design looks fine to me, plus > “A longitudinal study of 50 patients with HCV “

Peace Daniel (05:38:18): > Hello everyone and happy weekendhttps://journals.asm.org/doi/10.1128/spectrum.02974-23#SuF1I’d love to curate fig 4B as it’s similar to fig 2B which I curated, what are your thoughts on this for differential abundance?

idiaru Angela (05:40:12) (in thread): > Thank you@Peace Daniel

Aleru Divine (05:49:31) (in thread): > Hi@Peace Danielyeah I see what you’re saying. And I think it can be used for differential abundance becauseit’sshowing the difference in abundance between 2 groups(2013 and 2015).

Aleru Divine (05:52:58) (in thread): > I agree with@Peace Danielon the study design.It’scorrect.Well done guys! I’ll give it a review

Peace Daniel (05:54:26) (in thread): > Thanks for the confirmation

idiaru Angela (05:57:00) (in thread): > Hey I definitely think Fig 4B is curatable. you should calculate the P values given to ensure that the taxa is indeed significant and curatable@Peace Daniel

Peace Daniel (05:57:31) (in thread): > Yes it is, thanks@idiaru Angela

idiaru Angela (05:57:37) (in thread): > Thank you@Aleru DivineAwaiting your feedback:hugging_face:

Aleru Divine (07:45:04) (in thread): > I’mgoing through this study and my head is all over the place guys:sleepy:

idiaru Angela (07:47:28) (in thread): > It’s a very confusing one:sweat_smile:@Aleru Divine. There are many groups in this study

Aleru Divine (07:50:21) (in thread): > I can see that:sob:

Scholastica Urua (08:03:20) (in thread): > Thank you@Peace Danieland@Aleru Divine. > Yes, the study is pretty confusing:disappointed_relieved:

Aleru Divine (08:10:35): > Hi everyone, I hope you all are having a great weekend:hugging_face:I have a question from the paper I’m curating. So from the paper, they took samples from hospital sewage. My question is, is it okay to use humans as host species? Since the sewage is from a hospital. > > I have another option and that is to leave it blank. > > I’d really appreciate your feedback:pray:.

idiaru Angela (08:14:21) (in thread): > Hi@Aleru DivineI would say leave it blank and add it to the discussion page. This is because the sewage from hospitals might also include other medical and environmental wastes thrown away using the drainage.

Aleru Divine (08:19:10) (in thread): > This makes a lot of sense@idiaru Angelathank you so much.I’llleave it blank.

Mildred Anashie (08:21:44) (in thread): > Yea@idiaru AngelaI agree with this suggestion

Joan C. Chukwuemeka (08:33:33) (in thread): > @Aleru DivineSewage is an environmental sample, so it’s best left blank. The Condition or group description I believe will communicate the source of the sample.

Abiola Salako (09:42:02) (in thread): > Yes@Aleru DivineIT’s BETTER LEFT BLANK

Svetlana Ugarcina Perovic (10:27:01) (in thread): > Agree.

Peace Daniel (13:10:18): > Hello everyone, > > I’m done curating this study 840, herehttps://bugsigdb.org/Study_840This curation was originally started by@Ajayi Mercybut she requested I collaborate with her on it. I’d love to get a peer review on it please. Thank you so much:pray::purple_heart: - Attachment (BugSigDB): Yearly variation coupled with social interactions shape the skin microbiome in free-ranging rhesus macaques - BugSigDB > While skin microbes are known to mediate human health and disease, there has been minimal research on the interactions between skin microbiota, social behavior, and year-to-year effects in non-human primates-important animal models for translational biomedical research.

Peace Daniel (13:13:15) (in thread): > Now that my schedule is a bit clear, I’ll give your study a review:hugging_face:@Scholastica Urua@idiaru Angela

Scholastica Urua (13:19:57) (in thread): > Well done@Peace DanielI’ll take a look.

Ajayi Mercy (19:12:48): > @Peace Danielthank you so much for agreeing to collaborate with me on this. Your effort is commendable. Thank you once again

2024-04-07

Mildred Anashie (01:30:18) (in thread): > I briefly went through it and it was a bit confusingto figure out > > Well done@Peace Danieland@Ajayi Mercy:clap:I’llalso take a look at this

Peace Daniel (05:02:44) (in thread): > @Scholastica Urua@Mildred AnashieI’mstill not very much satisfied with the condition, please let me know if you have any close options:pray::purple_heart:

Scholastica Urua (05:22:36) (in thread): > @Peace DanielI was thinkingskin microbiome measurement might be a closer term because the researchers analyzed skin microbes from 78 rhesus macaques…http://www.ebi.ac.uk/efo/EFO_0801228Abnormality of skin morphologytends to be a more broader term as it may include skin cancer, any abnormal skin structure etc… > > What’s your take on this@Mildred Anashie? - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Mildred Anashie (06:56:09) (in thread): > Yea@Scholastica UruaI see that they are analyzing the variations and effect of the skin microbiome of monkeys observed longitudinally (different sampling periods) and their interactions with other monkeys in similar social behaviors > > I agree with you

Peace Daniel (07:13:07) (in thread): > Alright then, noted thanks

Peace Daniel (07:15:37) (in thread): > The issue with this condition you mentioned@Scholastica Uruais thatit’snot on BugSigdb > > Could you please narrow your searchto what’son BugSigdb as I noticed some conditions on EFOcan’tbe found in BugSigdb

Scholastica Urua (07:24:55) (in thread): > Okay@Peace Daniel. I’ll check for closer terms available on BugSigDB.

idiaru Angela (09:25:03): > Hello and good day@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI’d like signatures 3 and 4 deleted from experiment 1 in this study. Thank you so muchhttps://bugsigdb.org/Study_991 - Attachment (BugSigDB): Dysbiosis of skin microbiome and gut microbiome in melanoma progression - BugSigDB > BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy.Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy.

Scholastica Urua (12:31:57) (in thread): > Hello@Peace Danielso the closest condition I could find that’s also available on BugSigDB ismicrobiome measurement. Although this does not specifically mention the skin, I think the body site curated already covers that. > > Personally, this terms seems to better fit thanAbnormality of skin morphology. What do you think?https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0007882 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Mildred Anashie (12:35:48): > Hi everyone and Happy Sunday:relaxed::hugging_face:I have a quick question from this paper I’m curating > > This LDA scores were mentioned 1.8 and 4.2 for two different experiments andI’mthinking they can’t be entered this way on BugSigdb > > I’m wondering what would be most appropriate > 2 for the first and 4 for the second or just use 2 the default LDA score for both:thinking_face:I’m unsure:neutral_face::face_with_diagonal_mouth:Anticipating your responses, Thank you:pray:

Peace Daniel (12:46:25) (in thread): > I think 2 and 4 are rounded figures but I hope the mentors clarify this

idiaru Angela (13:22:16) (in thread): > This is something interesting:thinking_face:

Scholastica Urua (13:27:41) (in thread): > For quality sake, I think we have to wait for the mentors to clarify this.@Mildred AnashieI think while waiting for their response, you can leave it blank and maybe include a note:thinking_face:

Aleru Divine (14:04:10) (in thread): > Idon’tknow ifI’mcorrect but I think you can just curate the LDA scores as mentioned.@Mildred AnashieI think they can be entered that way.Using rounded figures seems kinda wrong to me:grimacing:And yes we wait for confirmation from the mentors:sweat_smile:

Aleru Divine (14:09:13) (in thread): > Now that I think about it, LDA scores are usually represented as LDA > 3 or 4. That would mean greater than the value mentioned and so using a rounded figure might be actually be correct > > OMG! Idon’tknow:sob::cold_sweat:

Peace Daniel (14:12:07) (in thread): > I just tried it, you can actually enter it as 1.8 and 4.2 on BugSigdb, but a clarification would be better@Mildred Anashie

Aleru Divine (14:13:01) (in thread): > Okay guys I found a reviewed study that used LDA > 3.5 and I think this confirms@Mildred Anashiecan go on with curating the scores given in the paper.For reference,here’sthe link to the paper:sweat_smile:https://bugsigdb.org/Study_623 - Attachment (BugSigDB): Fusobacterium nucleatum Promotes Chemoresistance to Colorectal Cancer by Modulating Autophagy - BugSigDB > Gut microbiota are linked to chronic inflammation and carcinogenesis.Chemotherapy failure is the major cause of recurrence and poor prognosis in colorectal cancer patients.Here, we investigated the contribution of gut microbiota to chemoresistance in patients with colorectal cancer.

Aleru Divine (14:13:52) (in thread): > *victory dance:dancer::sob:

Scholastica Urua (14:14:03) (in thread): > Well done@Aleru Divine

Peace Daniel (14:14:13) (in thread): > Alright, thank you@Scholastica Urua

Aleru Divine (14:14:26) (in thread): > Thank you@Scholastica Urua:hugging_face:

Mildred Anashie (14:17:33) (in thread): > Thank you guys:smiling_face_with_3_hearts::smiling_face_with_3_hearts::smiling_face_with_3_hearts:

Nana (14:23:01) (in thread): > Wow..this is very interesting..we keep learning everyday

Mildred Anashie (14:29:19) (in thread): > Yea@NanaSpecial thanks@Aleru Divine:heart:

Desire Oluwarotimi (14:43:42): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI’d love to delete the following signatures from my study. > Signature 2 of Experiment 1 > Signature 1 of Experiment 23 > Signature 2 of Experiment 25 > Signature 1 of Experiment 26https://bugsigdb.org/Study_1049 - Attachment (BugSigDB): A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs - BugSigDB > BACKGROUND: Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life.

Svetlana Ugarcina Perovic (15:39:38) (in thread): > Deleted.

Svetlana Ugarcina Perovic (15:41:49) (in thread): > Deleted.

idiaru Angela (15:44:42) (in thread): > Thank you!

idiaru Angela (17:13:41): > Hi everyone.https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5The excerpt below is from this article. I’m a bit confused on the statistical test used for differential abundance based on this statement > “The linear discriminant analysis (LDA) with effect size (LefSe) algorithm [186] in Galaxy modulehttp://huttenhower.sph.harvard.edu/galaxy/was used to detect features with significant differential abundance between different biological categories of samples based on the factorial Kruskal–Wallis test and the pairwise Wilcoxon test to identify taxa with significant differential relative abundances at genus level with alpha values of 0.05 and a threshold value of 3.0 on the logarithmic LDA scores for discriminative features (p < 0.05 and LDA score/effect-size threshold = 3).” > In this case, what would be the statistical test. Thank you for your responses - Attachment (BioMed Central): Dysbiosis of skin microbiome and gut microbiome in melanoma progression - BMC Microbiology > Background The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression. Results Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier. Conclusion The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.

Aleru Divine (17:36:27) (in thread): > Hi@idiaru Angelathis is a bit tricky:thinking_face:It looks like LEfSe was based on Kruskal Wallis and Wilcoxon.That would mean they initially used bothKruskal Wallis and Wilcoxonto access/test for the differently abundance.And LEfSe focused on identifying taxa with significant differential relative abundances at genus level. > > I’d say all 3 tests:cold_sweat:

idiaru Angela (17:39:16) (in thread): > Right@Aleru DivineI was thinking in the same direction too! Wanted opinions to ensure I was doing the right thing

Aleru Divine (18:07:12) (in thread): > Yeah,:thumbsup:let’ssee other opinions

Scholastica Urua (18:09:36) (in thread): > Hi@idiaru Angelalike@Aleru Divinesaid LefSe was based on both Kruskal Wallis and Wilcoxon. Though the Kruskal Wallis seems to be more focused of alpha diversity. Also, the curatable signatures are presented as LefSe results so I would go for LefSe as the statistical test. > My opinion though…

Joan C. Chukwuemeka (18:10:54) (in thread): > Based on little research in the context provided, LEfSe combines the statistical rigor of the factorial Kruskal-Wallis test and the pairwise Wilcoxon test with linear discriminant analysis (LDA) to assess the effect size of each differentially abundant feature. > > LEFSe leverages the results from Kruskal-Wallis and Wilcoxon tests: > > Kruskal-Wallis test identifies if there’s an overall difference in abundance between categories. > > Wilcoxon test helps pinpoint which categories differ from each other. > > LEFSe goes beyond just identifying differences: It incorporates an effect size measure along with statistical significance. The effect size indicates the strength of the difference in abundance between categories for a particular taxon. > > LEFSe uses LDA scores which represent the contribution of each taxon to the overall differences observed between categories. > > In this context, LEFSe uses the information from Kruskal-Wallis (overall difference) and Wilcoxon (pairwise differences) to identify taxa at the genus level that are statistically significantly different in abundance between biological categories, while also considering the strength of those differences through the LDA scores. > > By considering both statistical significance and effect size, LEFSe helps researchers focus on the most discriminative features (taxa) that contribute the most to the observed differences between biological categories. > > I’d go with LEFSe, since it’s the one that was used to determine the increase/decrease abundance.

idiaru Angela (18:17:02) (in thread): > Thank you@Scholastica Urua@Joan C. Chukwuemeka. Your responses sheds more light to my problem.

Aleru Divine (18:22:18) (in thread): > This makes more sense now@Scholastica Urua@Joan C. Chukwuemeka:thumbsup:

Victoria (Burah) Poromon (18:38:47) (in thread): > Insightful thread!:sweat_smile:Cuz personally, anytime I see a specified LDA score my first choice is always Lefse:weary:Because of the curation policy.

Scholastica Urua (18:39:56): > Hello everyone, the image below is an excerpt were I’m curating signatures from. So I’m curating the lowest taxonomic unit mentioned but in situations like these highlighted ones where the lowest taxonomic unit is just presented as****‘s_’,****would it be correct to curate the given genus? or curate the genus and attachedspfor exampleRummeliibacillus sp. in place of g_Rummeliibacillus;s_? > > Thank you as I look forward to your responses.:pray:This is the link to the article for more context;https://pubmed.ncbi.nlm.nih.gov/35076270/ - Attachment (PubMed): Parkinson’s Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats - PubMed > Parkinson’s disease (PD) is known to be associated with altered gastrointestinal function and microbiota composition. To date, the effect of PD medication on the gastrointestinal function and microbiota, at the site of drug absorption, the small intestine, has not been studied, although it may repre … - File (JPEG): sp.JPG

idiaru Angela (18:42:48) (in thread): > Right! I tend to do same@Victoria (Burah) Poromon

Victoria (Burah) Poromon (18:44:28) (in thread): > I’mnot sure, butI’dsay to curate the given genus.

idiaru Angela (18:45:45) (in thread): > I’d say curating the genus that was specified would do. The s just as a - in front of it. Not really giving a lower taxonomic representation.@Scholastica Urua

Scholastica Urua (18:46:53) (in thread): > Thank you@Victoria (Burah) Poromonand@idiaru Angela

2024-04-08

Desire Oluwarotimi (02:34:10) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (02:36:36) (in thread): > Yea > > I agree with them > Curating the ones that the specieswasn’tmentioned seems more appropriate > Well done:+1:

Aleru Divine (02:53:34) (in thread): > Yeah I’ll go with curating the genus too.Well done guys.

Scholastica Urua (03:01:17) (in thread): > Thank you@Mildred Anashieand@Aleru Divine

Raihanat Adewuyi (04:34:00) (in thread): > I will also go with curating the genus that was specified.@Scholastica Urua

NWAKAEGO VINCENT (11:07:34): > can someone help with the link to fix missing taxons pls

Mildred Anashie (11:10:10) (in thread): > https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgiI’mguessing this is what you are looking for? - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

idiaru Angela (11:10:49) (in thread): > https://bugsigdb.org/Category:Pages_with_missing_NCBI_IDHi@NWAKAEGO VINCENT - Attachment (BugSigDB): Category:Pages with missing NCBI ID

NWAKAEGO VINCENT (11:15:38) (in thread): > thank you ladies

Adenike Oladimeji-Kasumu (11:31:04): > Hello everyone:hugging_face:I trust our day is going well. > Please I need help with these taxons: > 1. I can’t find ruminococcus2, can I curate as ruminococcus sp? > 2. Is “Enterobacteriaceae bacteria” the same as “Enterobacteriaceae bacterium”? (Seeing that it’s only a singular and plural difference) > 3. I have “g_Eschrichia_shigella” also as a part of my signatures. How do I curate that? As I cannot find “Eschrichia shigella” in NCBI > 4. Please help me find the NCBI taxon ID for “Enterobacteriales”. I’ve been checking but I can’t find it > Please help.

NWAKAEGO VINCENT (11:39:57): > 4.Enterobacteralesfor Enterobacteriales”. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Aleru Divine (11:42:50) (in thread): > Hi@Adenike Oladimeji-KasumuI think number 2 is the same.For the others, you can just curate as seen.Although Idon’tthink Escherichia shigella is an organism.Escherichia is a different genus > Shigella is also a different genus.Enterobacteriales might be a typographical error as I found 91347-for Enterobacterales( without an i).

idiaru Angela (11:44:23) (in thread): > For 1, if they are not the same rank then you can’t curate Ruminococcus sp in place > 2. I would think those are the same > For 4@NWAKAEGO VINCENTfound the taxa ID for you in the channel

Adenike Oladimeji-Kasumu (11:45:49) (in thread): > Thank you@Aleru Divine. Exactly for Eschrichia Shigella o:rolling_on_the_floor_laughing:but I just need a second opinion. But it is written as “Eschrichia” not “Eschrichia”. Do you think it could be a typo error too?

Aleru Divine (11:46:17) (in thread): > Yeah, it could be:sweat_smile:

Adenike Oladimeji-Kasumu (11:48:08) (in thread): > Thank you@NWAKAEGO VINCENTSo it could just be a typo error as@Aleru Divinepointed out

idiaru Angela (11:48:40) (in thread): > For escherichia_shigella I think there’s a note on that taxa on the discussion page for missing ncbi taxa IDs. Might help@Adenike Oladimeji-Kasumu

Adenike Oladimeji-Kasumu (11:49:26) (in thread): > Alright@idiaru Angela. I’ll look for it. Thank you

Adenike Oladimeji-Kasumu (11:50:47) (in thread): > Then, please I remember someone asked about “Ruminococcaceae UCG_002” one time. > Can anyone remember the resolve? Because it cannot be found on the NCBI list as well

Mildred Anashie (12:03:29) (in thread): > I’ve come across Escherichia/shigella sp. a couple of times but I’m not sure how to curate as a genushttps://www.uniprot.org/taxonomy/1940338

Adenike Oladimeji-Kasumu (12:25:19) (in thread): > Wow!!!@Mildred AnashieThank you for this

Joan C. Chukwuemeka (13:09:01) (in thread): > @Adenike Oladimeji-Kasumuthis snapshot is for Escherichia/shigella. > > It’s possible not to see a taxa yet in NCBI or uniprot, in which case you curate as seen in the article/paper. > Taxonomic research and classification is an evolving science, so one that is not resolved today, the likes of “ruminococcus2”, will likely be resolved in the near future.:seedling: - File (PNG): image.png

Adenike Oladimeji-Kasumu (13:15:34) (in thread): > Yes. Thank you@Joan C. ChukwuemekaI’ve been able to resolve for Escherichia/shigella. And I curated ruminococcus so in place of ruminococcus2. > I’m left with Ruminococcaceae UCG_002. Thats what I’m looking for

Mildred Anashie (13:23:06) (in thread): > I think just as Joan saidyou’dhave to leave Ruminococcaceae UCG_002 just the way it is

Adenike Oladimeji-Kasumu (13:25:32) (in thread): > Yes@Mildred Anashiethat’s the way to go

Joan C. Chukwuemeka (13:58:32) (in thread): > Alright@Adenike Oladimeji-Kasumu. However, for ruminococcus, I think it will be helpful if you also add a review note that it was originally reported as “ruminococcus 2”, should anything change later.:slightly_smiling_face:UCG means “******uncultured genus******”, however the numbering at the end, is what makes us curate it as seen most times especially when there are more than one of them, like having Ruminococcaceae UCG_002 and then Ruminococcaceae UCG_005 in the same place > > Hoping for a resolution in nearest future:seedling:

Adenike Oladimeji-Kasumu (14:03:59) (in thread): > Sure@Joan C. ChukwuemekaThank you:blush:

2024-04-09

Peace Daniel (02:54:20): > Good day all and a happy Tuesday to you! > > In this studyI’mcurating, this image fig 3 attached was related to differential abundance in the text, more precisely underidentification of taxa that differed between patients treated with and without entacaponeLink here:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9022099/My questions are these; > * Do y’allagree this image is curatable? > * Can someone confirm fig 2 is not curatable as I see relative abundance > * Also what do you think about the second image, I found it in the supplementals and there was no supporting information - Attachment (PubMed Central (PMC)): A Pilot Study Exploring the Association of Entacapone, Gut Microbiota, and the Subsequent Side Effects in Patients With Parkinson’s Disease > Entacapone, one of the most common drugs distributed among patients with Parkinson’s disease, is a peripherally acting catechol-O-methyltransferase (COMT) inhibitor that is used in addition to levodopa to control symptoms. However, there have … - File (JPEG): IMG_2428 - File (JPEG): IMG_2429

Peace Daniel (02:57:13) (in thread): > Also, does this confirm the statistical test to be Fisher and Wilcoxon? > > “The identification of significantly different phylum and genus between PD_LE and PD_L was performed using t-test. Variable comparison between the two groups were conducted by Fisher’s exact test and Wilcoxon rank sum test.” > > Lastly, does this mean much?:thinking_face:“ANCOM was also conducted for sensitivity analysis”

Aleru Divine (03:28:36) (in thread): > Hi@Peace Daniel, good morning.Figure 3 does represent differential abundance and reading through the description, it looks like this was what differed after the treatment of entacapone.So I’m guess the ones in the positive direction would be increased and the ones directed in the negative (-) direction would be the decreased.Idon’tthink figure 2 is curatable.And also the supplemental figure:thinking_face:

Aleru Divine (03:33:05) (in thread): > I found this for the statistical analysis in the statistical analyses and 16s rRNA sequence data section.“The identification of significantly different phylum and genus between PD_LE and PD_L was performed using t-test.” > I like to think t-test was used for differential abundance test.Because even figure 3 shows significant phylum and genus.

Mildred Anashie (03:34:35) (in thread): > I agree that differential abundance was mentioned but the issue is,I can’tsee in what group what taxa was increased or decreased (Am I missing something:thinking_face:) > > Ican’tseem to open the supplemental tables could you share them here?

Scholastica Urua (03:35:45) (in thread): > Good morning@Peace Danielfig 3 is curatable. I think the ones with the negative log values would be decreased while the positive would be increased. I don’t think fig 2 is curatable.

Peace Daniel (03:39:09) (in thread): > Thank you@Scholastica Urua@Aleru Divine@Mildred AnashieWe all agree on fig 3 and 2…and noted on the statistical test@Aleru Divine

Peace Daniel (03:40:51) (in thread): > Is this supposed to mean MHT correction? - File (JPEG): IMG_2430

Scholastica Urua (03:41:13) (in thread): > Yes@Peace DanielFalse Discovery Rate meaning yes to MHT

Mildred Anashie (03:42:33) (in thread): > You are welcome, I get the groups nowIt’sjust one experiment and one group is the control and the other case group > > also that additional image is not curatable@Peace DanielYes FDR can imply MHT correction

Peace Daniel (03:42:49) (in thread): > This study is so strange, I have to confirm everything:smiling_face_with_tear:

Peace Daniel (03:43:24) (in thread): > Yes@Mildred AnashieIt’s just one experiment with information scattered everywhere I need a lens:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Mildred Anashie (03:43:28) (in thread): > Some studies are like that@Peace Daniel:relaxed:

Aleru Divine (03:43:55) (in thread): > Yeahthat’sMHT correction

Aleru Divine (03:44:45) (in thread): > I feel ya@Peace Daniel:sweat_smile:

Peace Daniel (03:53:13) (in thread): > You’reright@Aleru Divinethey clearly wrote phylum here:sweat_smile:

Peace Daniel (05:42:40): > Hello all, > > I got this mail and wanted to share with y’all incase you’d be interested in attending toohttps://campaign-statistics.com/link_click/PvQhsoonWr_NOXRy/ec2fdeececcfa7f70e1aa141c63a05af - Attachment (events.ringcentral.com): Microbiome-VIF n.28 - Apr 17 | RingCentral Events > MVIF event: bite-sized microbiome meeting - File (JPEG): IMG_2432

Blessing Ene Anyebe (05:53:09) (in thread): > Yes, Welldone@Peace Danielfor re-sharing.:orange_heart:

Aleru Divine (06:06:29) (in thread): > Thanks for sharing Peace.I also received the email:partying_face:looking forward to it

Scholastica Urua (06:12:07) (in thread): > Thanks for sharing@Peace Daniel

Barakat Akinsiku (06:35:28) (in thread): > Thank you for sharing@Peace Daniel

idiaru Angela (06:49:09): > Hi Good morning everyone,@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy@C. Mirzayi (please do not tag this account)in this study I’m curating, there are differential organisms that were recorded that are not microbiome, for example “Triticum aestivum”. Should I also record such organisms since they have NCBI IDs or should they be ignored. > Thanks

idiaru Angela (06:49:32) (in thread): > Thanks@Peace Daniel

Mildred Anashie (06:53:10) (in thread): > This was mentioned with organisms showing differential abundance between groups?:thinking_face:

idiaru Angela (06:53:50) (in thread): > Yes@Mildred Anashie. They were included along with other microbiome

Mildred Anashie (06:55:19) (in thread): > Pretty uncertain of what step you should take:face_with_raised_eyebrow:@idiaru AngelaWaiting for the mentors insights on this:hand_with_index_and_middle_fingers_crossed:

Scholastica Urua (06:57:50) (in thread): > Haven’t come across this before@idiaru AngelaLooking forward to the answer though.

Peace Daniel (07:11:24) (in thread): > Hey@idiaru Angeladoing a google search, Triticum aestivum is wheat. I don’t think this should be recorded

Peace Daniel (07:12:11) (in thread): > Y’allare welcome:purple_heart:

idiaru Angela (07:12:31) (in thread): > Yeah@Peace DanielI checked and saw it was wheat, that’s why I wanted to confirm before leaving it out of the curation

Barakat Akinsiku (07:18:35) (in thread): > @idiaru Angelasince it’s wheat it shouldn’t be part of a microbiome curation but let’s see what the mentors say

Aleru Divine (07:21:21) (in thread): > This is quite interesting@idiaru Angela. Maybe there was common wheat in the sample analyzed.:sweat_smile:However it got there.

idiaru Angela (07:30:54) (in thread): > Yeah, it’s a laboratory experiment on skin microbiome so its very plausible@Aleru Divine

idiaru Angela (07:31:52) (in thread): > @Barakat Akinsiku@Peace DanielThought about leaving them out also. I’d just like a confirmation from the mentors before I do so. Thank you!

Joan C. Chukwuemeka (07:40:16) (in thread): > @idiaru Angelathat’s quite interesting. do you mind sharing the paper link?

idiaru Angela (07:42:49) (in thread): > Here@Joan C. Chukwuemekahttps://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02458-5The figures that contain these organisms are supplementary figure 5 and 6 - Attachment (BioMed Central): Dysbiosis of skin microbiome and gut microbiome in melanoma progression - BMC Microbiology > Background The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy. Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy. However, the role of the skin microbiome has not been well explored in the skin tumour microenvironment and the link between the gut microbiome and skin microbiome has not been investigated in melanoma progression. Therefore, the aim of the present study was to examine associations between dysbiosis in the skin and gut microbiome and the melanoma growth using MeLiM porcine model of melanoma progression and spontaneous regression. Results Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets. The bacterial composition of samples was analysed by high throughput sequencing of the V4-V5 region of the 16S rRNA gene. A significant difference in microbiome diversity and richness between melanoma tissue and healthy skin and between the faecal microbiome of MeLiM piglets and control piglets were observed. Both Principal Coordinate Analysis and Non-metric multidimensional scaling revealed dissimilarities between different bacterial communities. Linear discriminant analysis effect size at the genus level determined different potential biomarkers in multiple bacterial communities. Lactobacillus, Clostridium sensu stricto 1 and Corynebacterium 1 were the most discriminately higher genera in the healthy skin microbiome, while Fusobacterium, Trueperella, Staphylococcus, Streptococcus and Bacteroides were discriminately abundant in melanoma tissue microbiome. Bacteroides, Fusobacterium and Escherichia-Shigella were associated with the faecal microbiota of MeLiM piglets. Potential functional pathways analysis based on the KEGG database indicated significant differences in the predicted profile metabolisms between the healthy skin microbiome and melanoma tissue microbiome. The faecal microbiome of MeLiM piglets was enriched by genes related to membrane transports pathways allowing for the increase of intestinal permeability and alteration of the intestinal mucosal barrier. Conclusion The associations between melanoma progression and dysbiosis in the skin microbiome as well as dysbiosis in the gut microbiome were identified. Results provide promising information for further studies on the local skin and gut microbiome involvement in melanoma progression and may support the development of new therapeutic approaches.

Scholastica Urua (07:49:02): > Hello everyone, compliment of the day. > Please when alpha diversity is presented in this format what will be the right measure to document? Richness or chao or both? - File (PNG): Screenshot_20240409-114422.png

Scholastica Urua (07:49:36) (in thread): > Study link:https://bugsigdb.org/Study_925 - Attachment (BugSigDB): Parkinson’s Disease Medication Alters Small Intestinal Motility and Microbiota Composition in Healthy Rats - BugSigDB > Parkinson’s disease (PD) is known to be associated with altered gastrointestinal function and microbiota composition.

Aleru Divine (07:52:28) (in thread): > Itwill be Chao1@Scholastica UruaChao1 is the abundance-based estimator of species richness.

Victoria (Burah) Poromon (07:54:59) (in thread): > I’drecord only chao1 too > Because it was used to estimate the richness.

Peace Daniel (07:55:42) (in thread): > Agreed@Scholastica Urua

Scholastica Urua (07:56:22) (in thread): > Thank you guys:pray:

Barakat Akinsiku (08:00:00) (in thread): > @Scholastica Uruachao1 is more robust as it takes into account abundance and predicts true species richness so is a better record

Scholastica Urua (08:05:13) (in thread): > This makes sense. Thank you@Barakat Akinsiku

Joan C. Chukwuemeka (08:14:37) (in thread): > Alright, here’s what I found from brief online research:******Wheat-based ingredients like wheat germ oil, wheat protein, or wheat extract are commonly used in skincare and cosmetic formulations *****due to their emollient, moisturizing, and nourishing properties. When applied to the skin, these products may leave residues or interact with the skin’s microbiome in various ways, *******though direct colonization by wheat organisms is unlikely. Melanoma is a type skin cancer******From the figures, the organism was increased in abundance in both Melanoma tissue and melanoma surface.My thought is,***** Although direct colonization by wheat organisms is unlikely, ******If the study subjects use *******Wheat-based skincare and cosmetic formulations, *****maybe as part of therapeutic measure for the *******Melanoma, which is a type skin cancer*******, or just for the benefits of the product, prior to the sample collection, there may be a possibility of the formulation residues which are left to harbor the organism which the researchers here detected from the tissue and surface of the melanoma. *I think you may need to curate it with the rest. > However, I hope to hear the mentors thought on this too.:seedling:

Joan C. Chukwuemeka (08:24:28) (in thread): > I see the study was on Piglets, right?@idiaru Angela”Parallel analysis of cutaneous microbiota and faecal microbiota of the same individuals was performed in 8 to 12 weeks old MeLiM piglets.” > > If so, the use of cosmetics won’t be applicable then.:thinking_face:

idiaru Angela (08:33:08) (in thread): > Yes@Joan C. ChukwuemekaThe study was on Piglets. Cosmetics can’t be used on piglets?:thinking_face:

Joan C. Chukwuemeka (08:42:21) (in thread): > I dived in further on the possibility of “Triticum aestivum” in piglet skin microbiome study in relation to melanoma. My finding:Possible Explanations: > 1. Misidentification:There’s a possibility of misidentification during the sequencing process. Sequencing analyzes DNA, and sometimes there can be errors in assigning the DNA sequence to a specific organism. > 2. Contamination:Contamination during sample collection or processing could have introduced wheat DNA. This is less likely if the study followed proper protocols for handling biological samples. > 3. Unexpected Finding:It’s also possible that this is a novel finding requiring further investigation. Perhaps wheat particles containing DNA landed on the piglets’ skin and were captured during sample collection. However, this wouldn’t necessarily mean wheat plays a role in melanoma development. > Wheat, however, is a food source and wouldn’t be expected to be alive on the skin surface. so, could it be a result from the faecal sample recorded for the skin?:thinking_face:hmmm..Ok…let’s wait for the mentors.:smile::smile:

Scholastica Urua (08:46:28) (in thread): > Hello everyone, I have just completed this curation and need a second opinion on a few details. > > Can you please help confirm the statistical test asLefse and data transformation asraw counts. Thank you:pray:

Victoria (Burah) Poromon (08:52:38) (in thread): > Hi@Scholastica UruaI’ll take a look too > But I think generally the data transformation for Lefse is relative abundance > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1699808143495129?thread_ts=1699704087.950319&channel=C04RATV9VCY&message_ts=1699808143.495129 - Attachment: Attachment > Oh wow > Could you correct this list please? @Levi Waldron > > ANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance

Scholastica Urua (08:56:14) (in thread): > My thoughts exactly@Victoria (Burah) Poromonbut the use of relative abundance is not really clear in this study.

Peace Daniel (09:06:26) (in thread): > I think it’s raw counts as it was mentioned under data analysis in the article. Relative abundances is usually explicitly stated with accompanying figures but (this might be new)@Scholastica Urua

Victoria (Burah) Poromon (09:11:35) (in thread): > Okay@Scholastica UruaI saw a part of the study that said “Richness and diversity were estimated on the raw OTU counts table using phyloseq” soI’dbe confused a bit if I were you too:sweat_smile:If I was the one curating, i thinkI’dgo forrelative abundance, because of the statistical test that was used. > > ButI’dlove more clarity on this too. Cuz my opinion can be wrong.

Scholastica Urua (09:41:46) (in thread): > Yeah, that part is a bit confusing@Victoria (Burah) Poromon

Desire Oluwarotimi (10:28:07): > Hello everyone. I hope we are all doing great. > > I need help determining the sample sizes for the contrast groups (EMR and WT) in this study.https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9127079/ - Attachment (PubMed Central (PMC)): Gut Microbiota Dysbiosis Induced by Decreasing Endogenous Melatonin Mediates the Pathogenesis of Alzheimer’s Disease and Obesity > Lifestyle choices, external environment, aging, and other factors influence the synthesis of melatonin. Although the physiological functions of melatonin have been widely studied in relation to specific organs, the systemic effects of endogenous melatonin …

Mildred Anashie (10:34:43): > Hello everyone I’m a bit confused on what signatures are increasing and decreasing in the groups from this table >
> > MPTP (grp 1) VS control and MPTP+Acu (grp 0) > MPTP+Acu (grp 1) VS control and MPTP (grp 0) > > And if this grouping would be correct following the table our if it should be this way instead following table and this excerpt > > MPTP (grp 1) VS control (grp 0) > MPTP+Acu (grp 1) VS control (grp 0) > > > “Genus-level analyses showed a clear distinction between the gut microbiota of the Control and MPTP groups. A total of 44 genera were identified and differed significantly among the three groups (Table S1; p< 0.05, Dunn’s post hoc test following Kruskal–Wallis one-way ANOVA). Of these genera, 26 were significantly different between the Control and MPTP groups (Table S1; adjusted p < 0.05); 16 genera in the MPTP group were enriched, but 10 genera were depleted compared to the Control group. The acupuncture treatment significantly reversed the changes in the relative abundance of the 18 genera, which was similar to those in the Control group (Fig. 5A and B). Additionally, genera Bacteroides and Parabacteroides did not differ between the MPTP and Control groups, but decreased in the MPTP + Acu group compared to the MPTP group (Fig. 5C, Table S1).” > > I hope my question is clear and thanks in anticipation for your responses - File (JPEG): IMG_3648

idiaru Angela (10:37:14) (in thread): > @Scholastica UruaLooking at the paragraph tagged data analysis. I think relative abundance was used in this study for the data transformation.

Aleru Divine (10:41:38) (in thread): > Hi Mildred, in my opinion your grouping should be based on severity.MPTP(1) vs control(0) > MPTP + Acu(1) vs control(0) > And a third > MPTP + Acu(1) vs MPTP(0)

Scholastica Urua (10:42:04) (in thread): > Are you referring to this section@idiaru Angela? - File (JPEG): Data analysis.JPG

idiaru Angela (10:44:50) (in thread): > Hi@Desire OluwarotimiThis was the only information on sample sizes I could find from the article > “Serum melatonin level in Aanat−/− and wild-type (WT) mice (n =10). (B) Blood glucose level using the glucose tolerance test (GTT) (n = 7). (C) Blood glucose level using the insulin tolerance test (ITT) (n = 7). (D) Hematoxylin and eosin staining of the mouse brain (1000 μm), skin (50 μm), liver (50 μm), lungs (50 μm), and testis (50 μm) (n = 3-5)”

Desire Oluwarotimi (10:51:12) (in thread): > I saw that as well and I think there are still a few other information in this same format in the paper. > > I don’t think it fits.

Desire Oluwarotimi (10:57:03) (in thread): > Hey Mildred. I’m not quite sure but here is what I think concerning the increased and decreased signatures. > > Take the third for example (Aestuariispira) when comparing control and MPTP, I think it’s increased for MPTP given the value of their first integers. Just the higher integer in my opinion. > We could as well say that MPTP was increased when compared with control for the first ten genus taxa. > > Let’s see what others suggest.

Scholastica Urua (10:58:36) (in thread): > Hello Mildred, I’m also leaning towards@Aleru Divinegrouping based on this supplementary table.

Aleru Divine (11:01:30) (in thread): > Yep, I agree with that@Desire Oluwarotimiuse the SD values to determine the increased and decreased. That would be the higher value = increased…@Mildred Anashie

Aleru Divine (11:03:49) (in thread): > @idiaru Angelathere are other samples sizes in the paper:cold_sweat:hence the confusion.

idiaru Angela (11:05:48) (in thread): > Hey@Mildred AnashieIf I were to interprete this table, the groupings would be > Control vs MPTP > Control vs MPTP +Acu > Then MPTP vs MPTP + Acu > The increase and decrease in significance can be deduced by comparing the mean + SD between the two groups that you are comparing > Those denoted with an * in the MPTP column are significant for comparison 1 > Those with # on column MPTP + Acu are significant for comparison 2 > While Those with a * in column MPTP+ Acu are significant for comparison 3 > That’s how I’d interprete this table in my opinion

Mildred Anashie (11:07:54) (in thread): > I can’t see them mention the sample size > > Sinceit’s alaboratory experiment,itshouldn’tbe guessed > I think leaving it blank is the right option except otherwise@Desire Oluwarotimi

idiaru Angela (11:09:17) (in thread): > Yeaah@Scholastica Urua

idiaru Angela (11:17:48) (in thread): > Ohhh. I see@Aleru Divine

Mildred Anashie (11:17:49) (in thread): > I’m not quite clear on the taxas increasing and decreasing based on the mean value and SD > > Could this mean those with mean values and SD above 0 are increased and those from Zero and below are decreased?:thinking_face:@idiaru AngelaAlso the control groupdoesn’tshow significance does this imply only one signature across all experiments?

idiaru Angela (11:24:13) (in thread): > On using the mean + SD to determine increase or decrease, take the 3rd taxa for instance that has mean 0.0005 in the control compared to 5.0881 in the MPTP group, we could say that taxa is increased in the MPTP group because it has a higher mean, same reasoning for the first 2 taxa on the table and extended to the entire table. > Basically if the mean is higher in the group 1 then it is increased, if it is higher in the group 0 then it is decreased

Mildred Anashie (11:27:03) (in thread): > Okay > > I see what you are saying now > Still using the 3rd one it is showing decrease in the MPTP+Acu but increase in the MPTP > Right?

Desire Oluwarotimi (11:28:56) (in thread): > Yes Mildred. You are correct.

Desire Oluwarotimi (11:29:38) (in thread): > Can@idiaru Angelaexplain a bit better how those asterisks and hash symbols come into play please?

Chioma Onyido (11:30:52) (in thread): > For you@Mildred AnashieYes only one signature across expts. - File (JPEG): IMG_0702

Mildred Anashie (11:32:51) (in thread): > The asterisk is showing significance for the MPTP group and hash is showing significance for the MPTP + Acu group@Desire OluwarotimiI believe there’s a third experiment as pointed out from the text I shared and from the observations of others and the asterisks in the MPTP + Acu group will be showing significance for the MPTP + Acu vs MPTP group@Chioma Onyidois this right? > > Following this then the comparisons would be > > MPTP + Acu vs control > MPTP vs control > MPTP + Acu vs MPTP > > and so > MPTP vs Control and MPTP+Acu > MPTP + Acu vs Control and MPTPshouldn’tbe right:thinking_face:

idiaru Angela (11:35:37) (in thread): > Yes@Mildred Anashiebut that particular taxa is not significant for the MPTP vs MPTP + Acu comparison

Chioma Onyido (11:36:42) (in thread): > I’m not sure why the description says that the genera in bold are the significant ones. But other taxa are significant too (reading from the p values)..

idiaru Angela (11:36:43) (in thread): > @Desire OluwarotimiNot all the taxa on the table are significant for all 3 groups so I believe the * and # symbols were placed there to help differentiate which of the taxas are significant for each comparison made

idiaru Angela (11:38:26) (in thread): > Hi@Chioma Onyidothank you > They mentioned that those in bold are significant for the control vs MPTP group. Those taxa in bold are the taxa that have an * in the MPTP column. So I believe the other significant taxa with p values < than 0.05 are significant but only for the other comparisons.

Chioma Onyido (11:39:20) (in thread): > > @Desire OluwarotimiNot all the taxa on the table are significant for all 3 groups so I believe the * and # symbols were placed there to help differentiate which of the taxas are significant for each comparison made > I’m curious how you were able to read it this way? Is this indicated somewhere within text maybe I missed it.

Mildred Anashie (11:44:50) (in thread): > Itwasn’treally mentioned in text@Chioma Onyidobut this was my initial confusion because if we use just the taxas in bold then wewouldn’tbe properly interpreting the table since other taxas not in bold also show significance based on the * and # > Unless we are ignoring those symbols:thinking_face:

idiaru Angela (11:46:15) (in thread): > From the text that@Mildred Anashiedropped, they indicated that 26 genera were statistically different in the MTPT vs control comparison, going to the table, I noticed that those 26 genera were identified by an * in the MPTP column, so I assumed the # that was denoted in the MTPT + Acu column would also denote the differentially abundant taxa in the control vs MPTP + Acu comparison.

Mildred Anashie (11:47:05) (in thread): > Can youconfirm the grouping@Chioma OnyidoFollowing the table and textthen the comparisons would beMPTP + Acu vs controlMPTP vs controlMPTP + Acu vs MPTPand soMPTP vs Control and MPTP+AcuMPTP + Acu vs Control and MPTP shouldn’t be right:thinking_face:

Chioma Onyido (11:49:11) (in thread): > Agreed! What about the rep symbol for significant taxa between MPTP vs MPTP+Acu@idiaru Angela

Chioma Onyido (11:51:22) (in thread): > Yousaid“While those with a * in column MPTP+Acu are sig for comparison 3” > > How?:eyes:

Mildred Anashie (11:51:45) (in thread): > @idiaru Angelaactually pointed me to that and it made sense to me > > I suspected three comparisons anddidn’tsee the * in the MPTP + Acu group showing significance as well

Chioma Onyido (11:53:31) (in thread): > Parabacteroides and Bacteroides are sig between MPTP vs MPTP+Acu, Bacteroides does have a star but Parabacteorides has no star. > Explain…:sneezing_face: - File (JPEG): IMG_0703

idiaru Angela (11:57:19) (in thread): > @Chioma Onyidookay now I’m also confused. Seems I might have been wrong with that interpretation

Scholastica Urua (11:58:39) (in thread): > I’m thinking signatures in the 3rd experiment will be determined using the mean + SD. Let’s takeMarvinbryantiafor example, it’s increased in MPTP. WhileGracilibacteris increased in MPTP+Acu:woman-shrugging:

idiaru Angela (12:00:04) (in thread): > @Scholastica Uruathe question would then be, are all the taxa on the table differently abundant for the MPTP vs MPTP + Acu comparison?

Scholastica Urua (12:02:26) (in thread): > Initially, I was thinking only those with the both the * and # symbols but looking at it again, that might not be right:disappointed_relieved:

idiaru Angela (12:03:33) (in thread): > Right!@Scholastica Uruathought that might be it too

Mildred Anashie (12:04:11) (in thread): > I’mthinking that might have been an error because Parabacteroides wasn’t also shown in the Figure 5c that they referenced:thinking_face:And the Bacteroides is decreasing in the table and figure for MPTP + Acu group > > Could this be correct@Chioma Onyido(Just speculating)

Aleru Divine (12:04:18) (in thread): > That’s right,@Scholastica Uruabecause they said the genera in bold are those showing significant difference between Control and MPTP groups.But still not everything in bold has the symbols.

idiaru Angela (12:06:05) (in thread): > @Aleru Divineeverything in bold has the * symbol

Chioma Onyido (12:08:06) (in thread): > Every suggestion makes sense to me but I’m still doubting this 3rd comparison. > > Here’s something I found under the figure description of Fig. 5: > Fig. 5.Effects of acupuncture on changes in the relative abundance of the gut microbial community at the genus level in MPTP-induced PD mice. (A) The relative abundance of 18 selected bacterial genera. *******p < 0.05, p < 0.01 vs. Control*****; *******#p < 0.05, ##p < 0.01 vs. MPTP group********; results are mean ± standard deviation by one-way ANOVA.Which means that the # and ## you see in the MPTP+Acu group is for the comparison with MPTP, i.e. MPTP vs MPTP+Acu experiment. > To me, it makes sense why only the MPTP+Acu group carried the # symbol because that’s the focus of the study:to understand how acupuncture alters the gut microbiome of PD miceWhile the * and ** you see in both MPTP and MPTP+Acu groups are for comparisons with controls. > > Does this make sense?

Aleru Divine (12:08:18) (in thread): > @idiaru Angelathere I mistakenly looked at the control because I zoomed in:tired_face:

Aleru Divine (12:09:49) (in thread): > Okay@Chioma Onyidolooking at the table now, this makes so much sense.

Scholastica Urua (12:10:39) (in thread): > Thank you@idiaru Angela

Mildred Anashie (12:10:45) (in thread): > The Fig 5 description seems incomplete in my opinion:cry:@Chioma Onyido

Chioma Onyido (12:11:06) (in thread): > So let’s do a quick example, > > for Bacteroides which has both * and # symbols in the MPTP+Acu column will be curated for both MPTP+Acu vs MPTP and MPTP+Acu vs Control experiments.

Chioma Onyido (12:11:52) (in thread): > How do you mean@Mildred Anashie

Mildred Anashie (12:12:34) (in thread): > They explained just A leaving out B and C@Chioma Onyido

Aleru Divine (12:13:32) (in thread): > That explains this concern “Parabacteroides and Bacteroides are sig between MPTP vs MPTP+Acu, Bacteroides does have a star but Parabacteorides has no star.” > > Parabacteroides has no star and will only be curated for when comparing MPTP+Acu with the MPTP group:grimacing:right?@Chioma Onyido

Aleru Divine (12:14:48) (in thread): > Okay I completely understand now, thank you@Chioma Onyido

Mildred Anashie (12:14:58) (in thread): > From your explanation above@Chioma Onyidothis would mean those with the * will be used to curate the comparisons done with the controls and the MPTP comparisons would be curated using the #:thinking_face:

Chioma Onyido (12:15:12) (in thread): > Both Bacteroides and Parabacteroides will be curated for MPTP+Acu vs MPTP experiment. > They both have #@Aleru Divine

idiaru Angela (12:15:15) (in thread): > @Chioma Onyidoit makes sense now. Thank you!

Chioma Onyido (12:15:43) (in thread): > * and **** is only for comparing MPTP or MPTP+AcuVS controls.

Chioma Onyido (12:18:39) (in thread): > > They explained just A leaving out B and C@Chioma Onyido > They did say 18 selected genera, I counted it andit’s19. I assumed it’s a typo.Should’vebeen 19 selected genera*

Scholastica Urua (12:18:41) (in thread): > I actually understand this a lot better now. Thanks@Chioma Onyido

Mildred Anashie (12:24:38) (in thread): > Thank you so much@Chioma Onyido@idiaru Angela@Aleru Divine@Scholastica Urua@Desire OluwarotimiI’m truly grateful for the help and clarity:blush::blush:Just for clarity sake, since Parabacteroides was mentioned in text as being significantly decreased I’d have to record it even though it wasn’t reported with a hash symbol

Chioma Onyido (12:28:27) (in thread): > Parabacteroides was recorded with a hash symbol. Double hash for that matter.:sweat_smile: - File (JPEG): IMG_0706

Mildred Anashie (12:29:31) (in thread): > That’strue > > Scratch that:woman-facepalming::joy:

Mildred Anashie (12:29:50) (in thread): > Thanks a lot for your time:pray:

Chioma Onyido (12:31:24) (in thread): > Hehe, no worries! I enjoyed the discussion. > Thanks a bunch for taking on this task.:blush:You all are great team players.:100:

idiaru Angela (12:32:13) (in thread): > Recounted and it was indeed 18:grin:

Mildred Anashie (12:32:33) (in thread): > It’san absolute pleasure@Chioma OnyidoIt’s been insightful and the learning has been worth it:relaxed::hugging_face:

idiaru Angela (12:33:24) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1712659749797419?thread_ts=1712659749.797419&cid=C04RATV9VCYHi@Chioma Onyidocan I please get help here:sneezing_face: - Attachment: Attachment > Hi Good morning everyone, > @Svetlana Ugarcina Perovic @Chioma Onyido @Esther Afuape @Peace Sandy @C. Mirzayi (please do not tag this account) in this study I’m curating, there are differential organisms that were recorded that are not microbiome, for example “Triticum aestivum”. Should I also record such organisms since they have NCBI IDs or should they be ignored. > Thanks

Peace Daniel (13:51:42) (in thread): > :joy:you ran@Chioma Onyido

Peace Daniel (13:52:23) (in thread): > A nice read@Chioma Onyido@Mildred Anashie@idiaru Angela@Aleru Divine

idiaru Angela (13:59:44) (in thread): > Some problems deserve:sneezing_face::joy:@Peace Daniel

Chioma Onyido (15:10:05) (in thread): > Interesting…haven’t seen this one before. Not sure why wheat was among the identified taxa, could be one of the reasons from Joan’s findings. > Hi@Svetlana Ugarcina Perovic<@UBNSEMS3S>a little help here pleaseee

idiaru Angela (15:46:22) (in thread): > They identified 2 different species of wheat and added them to the differential abundance results

Svetlana Ugarcina Perovic (16:02:36) (in thread): > HINT: “The V4-V5 region of the bacterial 16S rRNA gene was amplified to prepare amplicons from the extracted DNA using the primer pair: BactB-F (GGATTAGATACCCTGGTAGT) and BactB-R (CACGACACGAGCTGACG).”

idiaru Angela (16:23:44) (in thread): > Got it!@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (16:28:26) (in thread): > https://www.ncbi.nlm.nih.gov/gene?Db=gene&Cmd=DetailsSearch&Term=803115

Aishat Ijiyode (18:01:02) (in thread): > Thanks for sharing@Peace Daniel

Joan C. Chukwuemeka (18:34:26) (in thread): > Not sure I quite understand the hint. Are you curating it then@idiaru Angela?

2024-04-10

Oluwatomisin Omojokun (00:06:37) (in thread): > I think she will curate it regarding the link sent by@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (02:53:44) (in thread): > Ok, let’s not going into sequencing details, just common sense:slightly_smiling_face:The study methodology is amplification and sequencing ofbacterialgene (16S rRNA gene).Triticum aestivumisplant. Thus, it should not be recorded asbacterial signature.

Joan C. Chukwuemeka (02:55:21) (in thread): > Alright. Thanks a lot@Svetlana Ugarcina PerovicIt’s much clearer now. > > Wonder how it got recorded alongside other ones… Perhaps an error from the researchers.:relaxed:

Svetlana Ugarcina Perovic (02:57:47): > Inspired by your:ear_of_rice:discussion from yesterday:ear_of_rice:here goes some light reading material for your Tuesday morning: > > SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare?https://link.springer.com/article/10.1186/s12864-017-3501-4 - Attachment (SpringerLink): SILVA, RDP, Greengenes, NCBI and OTT — how do these taxonomies compare? - BMC Genomics > Background A key step in microbiome sequencing analysis is read assignment to taxonomic units. This is often performed using one of four taxonomic classifications, namely SILVA, RDP, Greengenes or NCBI. It is unclear how similar these are and how to compare analysis results that are based on different taxonomies. Results We provide a method and software for mapping taxonomic entities from one taxonomy onto another. We use it to compare the four taxonomies and the Open Tree of life Taxonomy (OTT). Conclusions While we find that SILVA, RDP and Greengenes map well into NCBI, and all four map well into the OTT, mapping the two larger taxonomies on to the smaller ones is problematic.

Svetlana Ugarcina Perovic (03:02:13): > See you next week at MVIF! If you attended the last one (hope you enjoyed it), could you share with me your impressions, what was good what was to improve? Thanks - Attachment: Attachment > Hello all, > > I got this mail and wanted to share with y’all incase you’d be interested in attending too > > https://campaign-statistics.com/link_click/PvQhsoonWr_NOXRy/ec2fdeececcfa7f70e1aa141c63a05af

Peace Daniel (03:07:09) (in thread): > Thanks for the clarification@Svetlana Ugarcina Perovic

Aleru Divine (03:13:54) (in thread): > Thanks for the clarification@Svetlana Ugarcina Perovic:sweat_smile:

Mildred Anashie (03:17:58) (in thread): > Thank you@Svetlana Ugarcina PerovicSee you next week:hugging_face:What stood out for me was the question and answer sessions because it gave more insights into the researchers work and methodology

Mildred Anashie (03:19:13) (in thread): > Thanks for Clarifying@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (03:20:29) (in thread): > Yes, I also like Q&As!

Peace Daniel (03:20:54) (in thread): > It was a new experience for me, learning about latest research and learning new terminologyI’venot heard about before. > I loved the Q and A section and this short talk on “Achieving pan-microbiome biological insights via the dbBact knowledge base”It’sjust inspiring seeing how much time and effort is put into researching and sharing with many other people > > Thank you and see you next week:hugging_face:@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (03:23:13) (in thread): > Btw, recordings of previous MVIFs are available herehttps://www.youtube.com/@MicrobiomeVIF/playlistsSoon the last one will be up as well! - Attachment (YouTube): Microbiome Virtual International Forum > Microbiome Virtual International Conference (MVIF) is a recurring bite-sized alternative to multi-day microbiome conference: > Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference! > > Every month there is an event, with a great speaker from the microbiome field and 3 selected talks and many research highlights! > Follow the event live… > But if you miss it… in this channel you will find the videos of the events!

Peace Daniel (03:25:39) (in thread): > That’s so kind of you@Svetlana Ugarcina Perovicsubscribed:blush:

idiaru Angela (03:29:28) (in thread): > Thank you@Svetlana Ugarcina Perovic

idiaru Angela (03:37:35) (in thread): > Thank you!

Scholastica Urua (03:38:46) (in thread): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (03:43:07) (in thread): > Thank you@Svetlana Ugarcina PerovicI enjoyed the last session. What stood out for me was hearing and learning new terminologies for the first time. Had to check some terms out to fully grasp what was discussed:sweat_smile:but it was a good one. The Q & A was very insightful. > > Looking forward to the next.:hugging_face:

Aleru Divine (03:46:50) (in thread): > This you so much for sharing this article@Svetlana Ugarcina Perovic.It is so comprehensive and enlightening:pleading_face:

Svetlana Ugarcina Perovic (03:49:23): > Ok, one more good read to share with you:books:one of my favourites. YourTriticumdiscussion and critical reading made me a very proud mentor. Good job!Common/emerging myths and misconceptions in the human microbiome field, and explains why they are likely incorrect:https://www.nature.com/articles/s41564-023-01426-7 - Attachment (Nature): Human microbiome myths and misconceptions > Nature Microbiology - Walker and Hoyles highlight selected myths and misconceptions in the human microbiota literature.

Aleru Divine (03:55:02) (in thread): > Looking forward to it@Svetlana Ugarcina Perovicand thank you for sharing the recordings. > > What stood out for me was how detailed the speakers were while they were presenting. Even going further to make some suggestions from the results.The sessions were very interesting and informative. > > It was truly an honor to be a part of it.

idiaru Angela (04:01:23) (in thread): > This article is unfortunately closed access:face_holding_back_tears:

Aleru Divine (04:02:26) (in thread): > Exploring myths and misconceptions? Oh count me in:sweat_smile::hugging_face:I’m genuinely excited to read this article! > > Thank you for sharing@Svetlana Ugarcina Perovic

Aleru Divine (04:04:47) (in thread): > @idiaru AngelaI checked pubmed and it is also closed access.:cold_sweat::sob:

idiaru Angela (04:05:47): > Good morning@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace SandyPlease I’d like to delete signature 2 from experiment 5, it was wrongly curated. Thank youhttps://bugsigdb.org/Study_991 - Attachment (BugSigDB): Dysbiosis of skin microbiome and gut microbiome in melanoma progression - BugSigDB > BACKGROUND: The microbiome alterations are associated with cancer growth and may influence the immune system and response to therapy.Particularly, the gut microbiome has been recently shown to modulate response to melanoma immunotherapy.

Svetlana Ugarcina Perovic (04:08:07) (in thread): > ahh, just a sec please

Svetlana Ugarcina Perovic (04:09:35) (in thread): > Deleted.

idiaru Angela (04:16:04) (in thread): > Thank you!

Svetlana Ugarcina Perovic (04:22:22) (in thread): > Here you gohttps://t.co/9dZUxlg8Nk

Peace Daniel (04:24:34) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:pray::heart:

idiaru Angela (04:29:57) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

Aleru Divine (04:31:21) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (04:42:06) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

Joan C. Chukwuemeka (05:34:52) (in thread): > Thanks for sharing these resources@Svetlana Ugarcina Perovic.:seedling:

Rahila-me (06:20:36) (in thread): > Thank you very much for sharing@Svetlana Ugarcina Perovic. It was an eye opner

Rahila-me (06:20:41) (in thread): > opener

Rahila-me (06:22:02) (in thread): > The last session was cool, looking forward to the upcoming one@Svetlana Ugarcina Perovic

Rahila-me (06:22:54) (in thread): > ok..Thanks for sharing@Svetlana Ugarcina Perovic

Oluwatomisin Omojokun (07:03:31) (in thread): > Looking forward to the next one. The last one was interesting. Thanks@Svetlana Ugarcina Perovic

Barakat Akinsiku (07:38:36) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (07:39:07) (in thread): > Yea… Quite an enlightening read@Aleru Divine. > My key takeaways: > * Most Papers I have reviewed seem to use SILVA. > * Not all the taxonomies have nodes up to species level and intermediate rank( sub-, super-, infra-) > * As OTT is the largest of the five taxonomies (SILVA,RDP, Greengenes,NCBI, &OTT), and all other taxonomies map well on it, It will be helpful If it had a sequence database associated with it -:that will likely make OTT the reference taxonomy of choice.:seedling:I was already thinking of how OTT will be useful in resolving the taxa with missing NCBI IDs on BugSigDB:nerd_face: > In the meantime, we’d keep using the NCBI taxonomy as a common framework when comparing analyses performed on different taxonomic classifications.:blush:Thanks@Svetlana Ugarcina Perovic

Barakat Akinsiku (07:56:39) (in thread): > I enjoyed learning about new research the speakers were working on and the discoveries they made. The Q and A sessions were also pretty enlightening. Thank you for the video recordings@Svetlana Ugarcina Perovic

Scholastica Urua (08:15:40): > Hello everyone, hope your day is going well… > > Hello@Chioma OnyidoRegarding Experiment 1, it appears that in the original study, certain signatures in the control group were labeled as Other9, Other10, Other11, Other61, etc. I am uncertain about the curation process for these signatures.@Roderick Mominhas provided a list of these signatures on thetalk page. > > Additionally, concerning Table 2, which utilizes the Kruskal-Wallis test, it should be treated as a separate experiment like you mentioned. I noticed it also includes an LDA score, indicating that LEfSe might have been employed. My question pertains to whether these groupings are appropriate and how we ascertain the increased and decreased taxa: > > 1. Control vs WBL > 2. Control vs WBH > 3. WBL vs WBH > > Could you please clarify these points for me? Thank you in anticipation.:pray:Study link:https://bugsigdb.org/Study_886 - Attachment (BugSigDB): Talk:Study 886 > Author of Discussion: JimFlashy/Roderick Momin Date Created: 7th March 2024 Last Modified: 21th March 2024… - Attachment (BugSigDB): Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome - BugSigDB > The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. - File (JPEG): Table 2.JPG

Mildred Anashie (08:20:23) (in thread): > Hi@Scholastica UruaIhaven’tgone through the study but looking at the image you shared,I’mthinking towards using the Mean and SD for each comparison:thinking_face:

Scholastica Urua (08:23:48) (in thread): > I’m thinking in that direction too@Mildred Anashie. Seems similar to what was discussed yesterday but need to be sure before creating those experiments.

idiaru Angela (08:27:52) (in thread): > There’s also the consideration that Lefse uses a one against all approach. If the statistical test used here is Lefse then it would be a one against all curation. There’s also the fact that the authors didn’t distinguish which taxa was differentially abundant between each comparison group unlike the one that was discussed yesterday. > If Lefse was used then that would make sense

Mildred Anashie (08:31:21) (in thread): > Yea@idiaru AngelaItwasn’tshown which taxa is differentially abundant across all > > But the superscript a and b seems to be showing significance in the control groupI’mwondering ifthat’llapply to all:thinking_face:

Scholastica Urua (08:33:29) (in thread): > @idiaru Angelaif we are to go with theone against all approach, the groupings will be different from the ones I suggested like in this post you sent me earlier;https://community-bioc.slack.com/archives/C04RATV9VCY/p1687877254481389?thread_ts=1687872680.081639&cid=C04RATV9VCY - Attachment: Attachment > The default for LEfSe is one against all I believe so I would curate this as: > 1. Non-constipation PD (group 1) vs. constipation PD AND controls (group 0) > a. Curate blue bars as increased > 2. Constipation PD (group 1) vs. non-constipation PD AND controls (group 0) > a. Curate red bars as increased > 3. Non-constipation AND constipation PD vs. controls (group 0) > a. Curate green bars as decreased

idiaru Angela (08:34:47) (in thread): > @Mildred Anashiethe subscript shows the strength if the significance according to that description

idiaru Angela (08:35:02) (in thread): > Yess@Scholastica Urua:thinking_face:

Scholastica Urua (08:44:50) (in thread): > So now I’m conflicted on the groupings as well:disappointed_relieved:

Mildred Anashie (08:58:19) (in thread): > Which is indicating significance@idiaru Angela@Scholastica Uruafrom the table description I think your groupings would be control vs WBL and control vs WBH > > It says “All OTUs had a significantly different abundance when comparing uninfected control to either worm burden low (WBL) or worm burden high (WBH) groups”I’mnot certain the last experiment which is WBL vs WBH should be curated

Scholastica Urua (09:14:54) (in thread): > I see your point@Mildred Anashie

Scholastica Urua (09:21:55) (in thread): > If we are using the mean + SD to curate the signatures that means the 10th taxa (527874) will be increased while the first taxa (547854) will be decreased inControl vs WBLright?

Aleru Divine (09:22:58) (in thread): > I do agree with@Mildred Anashie, from the description it is looking like only comparison with the control group had significant differences in the abundance.I’llgo through the study to see if it mentions comparing the worm burden groups.

idiaru Angela (09:25:23) (in thread): > Yes@Scholastica Urua. That’s correct

Aleru Divine (09:28:32) (in thread): > Yeah that is correct@Scholastica UruaThe standard deviation measures how concentrated the data are around the mean; the more concentrated, the smaller the standard deviation. > > So the higher number = decreased > Lower number = increased

Scholastica Urua (09:31:33) (in thread): > There’s also the case of Prevotella appearing a couple of times in the same group:thinking_face:

Aleru Divine (09:36:55) (in thread): > I thought they all have different IDs

Chioma Onyido (09:37:04) (in thread): > I would curate it once and maybe put a note with the OTU IDs.

Mildred Anashie (09:38:35) (in thread): > @Scholastica Uruathat was my concern too but@Chioma Onyidohas clarified that > > Thank you:blush:

Scholastica Urua (09:38:48) (in thread): > Yes, they all have different IDs@Aleru DivineNoted@Chioma OnyidoThank you

Aleru Divine (09:42:04) (in thread): > Thanks@Chioma Onyido:sweat_smile:@Scholastica UruaI thoughtthey’dbe different with the IDs

Chioma Onyido (09:42:37) (in thread): > Thank YOU for taking on this task.:pray:

Chioma Onyido (09:43:56) (in thread): > > I thought they’d be different with the IDs > Yes if onlythere’ssomewhere within text or a supp file where they indicated the species of the diff IDs. There is actually a supp file but we were unable to access it.

Chioma Onyido (09:46:34) (in thread): > There’s also the option of curatingPrevotella spp.. because could be different species.@Svetlana Ugarcina Perovicplease what’s the best way to go about this?:pray:

Aleru Divine (09:53:40) (in thread): > You guys!!! I was looking at the table:sob::sob::sob:I just opened the paper and saw the LEfSe results.:woman-facepalming:

Scholastica Urua (09:54:34) (in thread): > @Chioma OnyidoIf I understand you correctly that means curatingPrevotellafor one andPrevotella spp. as another… > It appears more than twice in a group so….:disappointed_relieved:

idiaru Angela (09:54:41) (in thread): > @Aleru Divine:eyes:

Mildred Anashie (09:55:30) (in thread): > The LEfSe results are for different experiments that have already been curated ifI’mright@Aleru Divine

Scholastica Urua (09:55:41) (in thread): > @Aleru DivineI think those have been curated as experiments 1 and 2 already

Aleru Divine (09:56:15) (in thread): > I may be lost.So you are referring to the table?

Scholastica Urua (09:56:40) (in thread): > Yes, I’m referring to Table 2 as additional experiments.

Aleru Divine (09:58:59) (in thread): > Okay@Scholastica Urua:sweat_smile:ThinkI’mback on track.

Aleru Divine (10:00:54) (in thread): > @Scholastica Uruahow about the first idea of curating one and then leaving a note.

Aleru Divine (10:01:20) (in thread): > Thanks everyone for bringing me back:sweat_smile::hugging_face:

Scholastica Urua (10:05:50) (in thread): > @Aleru DivineI’ll curate it that way while waiting for response from@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:08:41) (in thread): > That’s another Svetlana:wink:

Svetlana Ugarcina Perovic (10:09:53) (in thread): > I believe@Chioma Onyidoprovided an answer in the corresponding GitHub issue, right?

Scholastica Urua (10:10:09) (in thread): > Oh my, I have edited it:sweat_smile:

Svetlana Ugarcina Perovic (10:11:52) (in thread): > ah, I see above an open question@Chioma Onyidook let me check

Svetlana Ugarcina Perovic (10:12:59) (in thread): > yes, correct, as@Chioma Onyidosaid “curatingPrevotella spp.. because could be different species.”

Svetlana Ugarcina Perovic (10:14:18) (in thread): > and@Scholastica Uruasaid “There’s also the case of Prevotella appearing a couple of times in the same group:thinking_face:”

Svetlana Ugarcina Perovic (10:14:53) (in thread): > thus, follow your common sense and curate it just like you discussed it here

idiaru Angela (10:21:25) (in thread): > Thank you@Svetlana Ugarcina Perovic

Scholastica Urua (10:21:32) (in thread): > Thank you@Svetlana Ugarcina Perovicfor clarifying:pray:

Scholastica Urua (10:22:06) (in thread): > Thank you everyone for your contributions:hugging_face:

Aleru Divine (10:24:14) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (10:36:05): > Hello everyone:hugging_face:I’m working on completing this studyhttp://bugsigdb.org/Study_876I have a few (many:sweat_smile:) questions > 1. Is fig 3a and 3d (complete data set shown in Table S3, Tab 3-7) curatable? Also what does the nine countries imply based on location of subjects? It said that they combined the microbiome of MSM of publicly available metagenomic datasets covering this regions. page 3 > 2. What would be the sample sizes for the experiments grouped based on sexual practices? Table S4 (Table S1 shows the clinical data though) > 3. Table S2 is showing significant differential abundance of the Prevotella and S. Copri species in kSGBs (Known species-level genome bins) and the uSGBs (unknown Species-level genome bins) in the MSM and Non MSM group with sample size shown for the kSGBs and uSGBs. Should this be curated and what would be the sample size? The original sample size given for MSM and Non MSM? Page 3 and Figure 2 is on page 5 > 4. How do I tell increase and decrease in Table S2 and S3? > 5. Should the Alpha diversity that didn’t reach statistical significance be curated as unchanged or left out of the curation since the authors said Alpha diversity was not generally associated with sexual practices (Under Sexual practices associated with the change of gut microbiome of MSM towards Non westernization) page 5. See Figure S4 for alpha diversity. > Link to pdfhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC10982974/bin/mmc7.pdfThank you in anticipation:pray: - Attachment (BugSigDB): Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices - BugSigDB > The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained.Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM.

Peace Daniel (11:00:31) (in thread): > Would go through your article now

USLACKBOT (11:00:37): > This message was deleted.

Mildred Anashie (11:02:08) (in thread): > Check 3d and “To further compare the MSM microbiota….

idiaru Angela (11:09:26) (in thread): > Seen it@Mildred AnashieFig 3d looks a bit difficult to interprete:thinking_face:.. but Fg 3A looks curatable

Mildred Anashie (11:10:06) (in thread): > 3d results is shown properly in Table S3

idiaru Angela (11:12:44) (in thread): > Opened that supplemental but I’m not sure how it can be curated either:thinking_face:

Peace Daniel (11:20:38) (in thread): > Does 3A not show relative abundance or am I missing something ?@idiaru Angela@Mildred Anashie

idiaru Angela (11:23:19) (in thread): > @Peace Danielit shows relative abundance between the different 4 groups in a whiskers plot with the significance denoted. That’s differential abundance

Peace Daniel (11:24:10) (in thread): > Okay just checked the caption, 3A is curatable

Aleru Divine (11:25:20) (in thread): > Figure 3A is can be curated@Mildred Anashie@Peace Danielit is showing the differential abundance.You can see the description.About figure 3d:grimacing:I don’tthink it is.

Peace Daniel (11:29:23) (in thread): > I don’t think 3d is curatable and how to read it > Regarding table s2 > “Prevotellaceae members significantly enriched in MSM relative to non-MSM, related to fig 2” > Fig 2C caption says “Log2-transformed abundances of Prevotellaceae members with a minimum abundance of 0.1 at 90th percentile in all subjects. S. copri complex clades are highlighted in red, and uSGBs are denoted in blue. Asterisk signs indicate species differentially enriched in MSM relative to non-MSM.”

Mildred Anashie (11:31:45) (in thread): > Is Table S3 curatable? > > What 3d is saying is explicitly shown in S3 in my opinion

Aleru Divine (11:35:55) (in thread): > For this table S2, I believe it is about the significantly enriched in MSM relative to non-MSM, so I think it only has the increased group.And yes the sample sizes should be the original sample size of MSM and Non-MSM.Which is 84 and 24

Mildred Anashie (11:36:19) (in thread): > @Peace Danielyou are saying I should follow Fig2C to interpret S2?:thinking_face:

Peace Daniel (11:40:33) (in thread): > Yes@Mildred Anashie@Aleru DivineI noticed some tables have just the increased group

Aleru Divine (11:40:56) (in thread): > @Mildred Anashiethe tables in table S3 can be curated.From table 3 - 7. > > The reason I think so is because of the description.Here’sand excerpt > “Species enriched in MSM individuals relative to the Westernized (Tab 3). > Species enriched in MSM individuals relative to the non-Westernized (Tab 4). > Species enriched in the Westernized populations compared to MSM individuals (Tab 5). > Species enriched in the non-Westernized populations compared to MSM individuals (Tab 6). Species differentially abundant in MSM and non-MSM samples (Tab 7).”

Peace Daniel (11:41:02) (in thread): > @Mildred Anashieit was stated in your paper, so I think you should

Peace Daniel (11:43:02) (in thread): > That’strue@Aleru Divinebutthey’requite a lot and how to read the significant taxas is another issue

Mildred Anashie (11:43:28) (in thread): > I agree@Aleru Divinethat the S3 should be curated my concern is the fact that the data was from 9 countries/regions and what taxas are increasing and decreasing from those

Aleru Divine (11:54:10) (in thread): > @Mildred AnashieYeah I see:thinking_face:but Idon’tknow if the regions matter.Because beneath the figure, I think they still grouped them into Wes, urban and non-Wes.Andthey’realready grouped in the description.With each table eitherincreasing or decreasingDon’tknow ifwe’reon the same page.

idiaru Angela (11:56:32) (in thread): > I agree with you@Aleru Divine. They don’t seem to be grouped according to country

Aleru Divine (11:57:37) (in thread): > @Peace DanielI agree with you.@Mildred Anashiethey’rea lot of signatures and we need to only identify the ones that are significant.I feel like it is somewhere in the text:thinking_face:

Mildred Anashie (12:00:22) (in thread): > I think I understand you@Aleru DivineCould this mean there are two experiments and the four tables are showing taxas increasing in either of the groups?:thinking_face:

Aleru Divine (12:02:30) (in thread): > Yeah:+1:that’scorrect@Mildred Anashiethat’swhat the description says too

Peace Daniel (12:08:16) (in thread): > Yes I see 2 experiments showing increase for either groups too

Peace Daniel (12:08:49) (in thread): > I’mbattling with network issues rn so I keep refreshing

Peace Daniel (12:09:50) (in thread): > I think all questions have been answered save for sample size right@Mildred Anashie?

idiaru Angela (12:10:45) (in thread): > I believe if there was alpha diversity done between two groups, it should be curated as unchanged regardless of their statistical association

Mildred Anashie (12:11:38) (in thread): > Also would it mean all the taxas are significant in Table S3?

Aleru Divine (12:12:30) (in thread): > That’sthe partI’mtrying to figure out right now.Although I think some are repeated@Mildred Anashie

Aleru Divine (12:17:04) (in thread): > @Mildred AnashieI think this will help.“The False Discovery Rates (FDRs) were estimated by Fisher’s exact test corrected for multiple hypotheses using Bonferroni method. FDRs lower than 0.05 were considered significant.” > > It is part of the description of table S3

Rahila-me (12:47:18): > Hello everyone, > Is it possible for a curation not to have a condition. > 2. how possible can i curate for this KO_Magnum in this excel sheet

Mildred Anashie (12:47:49) (in thread): > In that case very few are actually significantThanks a lot@Aleru DivineIt was becoming confusingCan you confirm that Victivallis_vadensis is significant and Lentisphaeria_bacterium|t__SGB9153 isn’t:thinking_face:So I can proceed:pray:

Scholastica Urua (12:48:46) (in thread): > Hello@Rahila-mecan you share your article for better understanding:pray:

Peace Daniel (12:48:49) (in thread): > Hi@Rahila-meplease share the link to your article

Aleru Divine (12:50:14) (in thread): > Alright, what table is this?

Mildred Anashie (12:50:45) (in thread): > Tab 3 > 191 and 193 I think

Rahila-me (12:51:17) (in thread): > ok:https://www.nature.com/articles/s41598-019-43280-w - Attachment (Nature): Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota > Scientific Reports - Characterization of microbial communities in the chicken oviduct and the origin of chicken embryo gut microbiota

Aleru Divine (12:54:06) (in thread): > The FDR value of Victivalis_vadensis is 0.0100…yeah it is less than 0.05.Yes this is significant > > And Lentisphaeria_bacterium|t__SGB9153 is not > > Confirmed!:+1:

Scholastica Urua (13:02:53) (in thread): > From the article, the study aimed to characterize the microbial community in the chicken reproductive tract and determine the origin of the chicken embryo gut microbiota. > > I thinkMicrobiome measurementwill be suited for the condition. Let’s see other opinions@Rahila-mehttp://www.ebi.ac.uk/efo/EFO_0007882 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Scholastica Urua (13:03:19) (in thread): > I don’t seem to get your other question clearly:thinking_face:

Aleru Divine (13:04:42) (in thread): > I agree with you on that@Scholastica UruaI think the study aims to understand the origin of the gut microbiota in chicken embryos. So microbiome measurement is a good fit@Rahila-me

Kelechi Madubuko (13:13:16) (in thread): > It was such an insightful session.. I look forward to attending next week’s session

Aleru Divine (13:21:09) (in thread): > @Scholastica Uruashe wants to know if she can curate the signatures.

Aleru Divine (13:23:33) (in thread): > @Rahila-me, it seems curatable to me, you can use the mean value to identify increases and decreased. But it is a lot.:cold_sweat:Additionally, table s2 and s3 can also be curated. Alpha diversity measures for the groups are in figure S3. > > I will be checking the paper to get additional information because it is a lot. I only see mean values, no information on p values and whether or not they are all significant.

Scholastica Urua (13:25:51) (in thread): > Let me go through the article

Mildred Anashie (13:26:20) (in thread): > Exactly@Aleru Divineit’s a bit confusing as significance and p valueisn’tstated

Mildred Anashie (13:28:36) (in thread): > Ican’tsee alpha diversity in Figure 3@Aleru DivineI’mseeing relative abundance and correlation:thinking_face:

Aleru Divine (13:29:58) (in thread): > S3 > The first supplemental file@Mildred Anashie

Rahila-me (13:36:43) (in thread): > @Aleru DivineThe only curatable table is this one ooh,@Mildred AnashieExactly my point: it’s a bit confusing as significance and p value isn’t stated, > but i will give it my best

Rahila-me (13:37:34) (in thread): > Thank you all, I appreciate all your responses@Scholastica Urua@Aleru Divine@Mildred Anashie

Joan C. Chukwuemeka (14:01:43) (in thread): > @Rahila-methe table seems to point towards relative abundance, have you checked figure 2? - File (PNG): image.png

Joan C. Chukwuemeka (14:14:35) (in thread): > See this too@Rahila-me******“The relative taxa abundance of the groups is presented as a mean % value”.******So, I don’t think the table is to be curated for differential abundance:point_down:******Differential abundance analysis by Analysis of Composition of Microbiomes (ANCOM) was used to identify significantly and differentially abundant genera in each sampling location****** - File (PNG): image.png - File (PNG): image.png

Mildred Anashie (14:23:08) (in thread): > I’m leaning towards your opinion@Joan C. ChukwuemekaAlthough the tables are showing relative abundance in each of the groups which seems to me as between group comparisons:thinking_face:

Joan C. Chukwuemeka (14:50:43) (in thread): > @Mildred AnashieThe paper specified that it was relative abundance.******“The relative taxa abundance of the groups is presented as a mean % value”.******and ANCOM (shown in FIG 2) was used for differential abundance:******Differential abundance analysis by Analysis of Composition of Microbiomes (ANCOM) was used to identify significantly and differentially abundant genera in each sampling location******

Joan C. Chukwuemeka (15:00:22) (in thread): > For condition:******animal reproductive system cell ******EFO:0002962**seems to be closer to the study aim based on the experiment contrast:thinking_face:http://www.ebi.ac.uk/efo/EFO_0002962 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

idiaru Angela (15:03:10) (in thread): > This table definitely look like they are pointing towards relative abundance rather then differential abundance

Rahila-me (16:12:41) (in thread): > @Joan C. ChukwuemekaSure:ok_hand:

2024-04-11

Svetlana Ugarcina Perovic (03:26:38): > Good morning :potted_plant:two points to share today: > 1. Right now we are focused onclosing open issues: > We encourage you to check in the GitHub issues: > * if there are still not curated papers – contact the assigned applicant and collaborate in curating; > * if reviewed issues are corrected in BugSigDB (green label: Reviewed) – if they are still not corrected you can make correction based on our feedback and/or support the assigned curator to correct their curation. > 2. Today, we have our team meeting and office hours at 9 AM EDT athttps://us02web.zoom.us/j/2737200499. > > See you:wave:<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape@Svetlana Ugarcina Perovic

Desire Oluwarotimi (03:28:24) (in thread): > Thank you@Svetlana Ugarcina PerovicSee you.

Joan C. Chukwuemeka (03:36:49) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thanks for the update:seedling:. See you at the Office hour:hugging_face:

Aleru Divine (03:41:02) (in thread): > Good morning and thank you@Svetlana Ugarcina PerovicLooking forward to the office hours as always:blush:

Victoria (Burah) Poromon (03:49:01) (in thread): > Thank you@Svetlana Ugarcina Perovic

idiaru Angela (03:53:19) (in thread): > Good morning@Svetlana Ugarcina Perovic. Anticipating the office hour as always.

Glorious Katushabe (04:25:06) (in thread): > Thank you@Svetlana Ugarcina Peroviclooking forward to the meeting

Scholastica Urua (04:33:25) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thank you for the update. > Looking forward to the office hour.

Rahila-me (04:42:00) (in thread): > Good morning@Svetlana Ugarcina Perovic, Thank you for the heads-uo

Barakat Akinsiku (04:49:23) (in thread): > Thank you for the update@Svetlana Ugarcina Perovic

Nana (05:57:34) (in thread): > @Svetlana Ugarcina Perovicthank you for the update

Roderick Momin (07:36:49): > Prevotella copri (Segatella copri) is shown to both increase and decrease in terms of relative abundance in Table 2 for mystudy. 2 instances show it increasing and 1 decreasing. What is the correct way to include this in the signature list? Add to both increase and decrease?

idiaru Angela (07:39:19) (in thread): > Yes@Roderick MominIt should be added to both signatures > See this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710517652414799?thread_ts=1710516856.042729&cid=C04RATV9VCY - Attachment: Attachment > Ohh got it! > > “Different bacterial strains may have different biological properties due to the different genes: > for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98%” > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639

Mildred Anashie (07:40:47) (in thread): > Yes@Roderick Mominit’s possible for a signature to increase and decrease just like what@idiaru Angelashared > > So you add to both

Roderick Momin (07:42:30) (in thread): > Warm regards.

Rahila-me (09:17:28): > Is the meeting still on, i am unable to join

UBNSEMS3S (09:20:08): > It is. I see you joining and I’m letting you in. Not sure what’s wrong.

Nana (09:27:11): > I have been able to join

Aleru Divine (09:47:32): > Hi<@UBNSEMS3S>, thank you so much for the office hours session today. > Here’s the link to the paper I shared during office hours. The one with asomewhat differentrepresentation of the differential abundance. > > Link:https://journals.asm.org/doi/10.1128/spectrum.01437-23 - File (PNG): Screenshot 2024-04-11 at 14.36.55.png

Victoria (Burah) Poromon (09:54:41): > Hello, Good day everyone. > Hi<@UBNSEMS3S>I was going to ask my question during the office hour, but I had a hard time joining the meeting on my pc. So Iwouldn’thave been able to share my screen. > > I want to know the appropriate group to use as my group 0 for this study. > > Alpha diversity wasn’t done for the Food samples, so if that is my group 0, what’s the best way to interpret the alpha diversity for 1100 hours (pre-fed group)? > > Thank you… I’ll also leave the link to the paper here:https://journals.asm.org/doi/10.1128/aem.02479-18#F1 - File (JPEG): 88403e76-2998-426a-8035-453a1ad473e4 - File (JPEG): 7013df58-d84c-4849-835b-1816c38b6534

UBNSEMS3S (09:57:51) (in thread): > When you have a longitudinal/time based study like this usually the group 0 will be the earliest time point.

Victoria (Burah) Poromon (09:58:50) (in thread): > Oh okay okay I get it now > Thank you so much!

Svetlana Ugarcina Perovic (17:42:35) (in thread): > Here is a summary why we are not opening new issues andwe are focused on closing open issueshttps://docs.google.com/spreadsheets/d/1DncuBI_CrAoRURlictxCoOeQiRVnxqaIl7hU3zAmksQ/edit?usp=sharingFeel free to contribute to red highlighted tasks:heart: - File (Google Sheets): reviewed_firstcurations_april2024

2024-04-12

Svetlana Ugarcina Perovic (02:52:52): > Good morning! A random Friday Question for you: - File (PNG): Screenshot 2024-04-12 at 08.51.32.png

Joan C. Chukwuemeka (03:00:06): > Good morning everyone,<!here>It was quite interesting to find thatunidentifiedtaxa is taken into consideration in NCBI Taxonomy database. > > One of its heterotypic synonym is “other”.:seedling:Thought to share, especially for those, who like me, didn’t know before.:nerd_face:Have a fulfilling Friday.:hugging_face: - File (PNG): image.png

idiaru Angela (03:04:09) (in thread): > Coffee please:coffee:

Scholastica Urua (03:26:24) (in thread): > Definitely tea!:teapot::smile:

Mildred Anashie (03:26:44) (in thread): > Quite interesting@Joan C. ChukwuemekaThank you

Scholastica Urua (03:27:41) (in thread): > Wow, thanks for sharing@Joan C. Chukwuemeka

Oluwatomisin Omojokun (03:27:55) (in thread): > Coffee:+1:

Mildred Anashie (03:28:44) (in thread): > Can I say both?:coffee::teapot::sweat_smile:Because it really depends:upside_down_face::woman-cartwheeling:

Peace Daniel (03:28:45) (in thread): > Coffee always:face_with_hand_over_mouth:

Joan C. Chukwuemeka (03:29:05) (in thread): > Tea, Please:grinning::hugging_face:

Peace Daniel (03:30:32) (in thread): > Thanks for sharing@Joan C. Chukwuemeka

Glorious Katushabe (04:46:51) (in thread): > Tea always:tea:

Svetlana Ugarcina Perovic (05:08:17) (in thread): > :yellow_heart:Thank you for covering all the pending curation!We are working on pending reviews:wink:<@U1LCB8WEA><@UBNSEMS3S>@Peace Sandy@Esther Afuape@Chioma Onyido@Svetlana Ugarcina Perovic

Aleru Divine (05:09:03) (in thread): > Wow:open_mouth:Thanks for sharing@Joan C. Chukwuemeka

Rahila-me (05:11:22): > @Scholastica Uruahi, lets collaborate,

Scholastica Urua (05:12:57) (in thread): > Hello@Rahila-me

Rahila-me (05:14:10) (in thread): > hi

Rahila-me (05:16:35) (in thread): > So we read it through and starts right

Scholastica Urua (05:18:27) (in thread): > Yes, I’ll be in your DM:hugging_face:

Raihanat Adewuyi (05:26:00) (in thread): > Tea always

Blessing Ene Anyebe (05:46:18) (in thread): > @Mildred AnashieI am with you on that! Both really, depending on mood.:sweat_smile:

Barakat Akinsiku (05:51:52) (in thread): > Tea girl here:grinning:

Barakat Akinsiku (06:12:15) (in thread): > Interesting, thanks for sharing@Joan C. Chukwuemeka

Precious Orakwe (07:06:18): > @MyleeeA a new curation was assigned to us to finalize on GitHub, please dm me so that we can work together. Thank you.

Mildred Anashie (07:06:45) (in thread): > Okay@Precious Orakwe

Victoria (Burah) Poromon (07:06:58) (in thread): > Coffee in the morning > Tea at night:sweat_smile:

Blessing Ene Anyebe (07:08:14) (in thread): > @Victoria (Burah) PoromonLovely insertion! I thinkI’lladopt:partying_face::hugging_face::fire:

Victoria (Burah) Poromon (07:11:39) (in thread): > Yes please:relieved::joy:@Blessing Ene AnyebeCoffee to stay alert during the day > And Lemon or Green tea at night:relieved:

Abiola Salako (07:54:37) (in thread): > Thanks for sharing@Joan C. Chukwuemeka

Abiola Salako (07:57:13) (in thread): > TEA ALWAYS:blush:

Ima-obong (Aimah) (08:28:39) (in thread): > Coffee:coffee:

Kelechi Madubuko (08:35:32) (in thread): > Green tea by 7:15am.. coffee by 11am.. green tea again by 7:15pm. My personal routine

U1LCB8WEA (08:49:29) (in thread): > coffeeeee (and sometimes tea too):sweat_smile:

Peace Daniel (09:08:58): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeI’d love Signature 3 of Experiment 1 to be deleted in this study pleasehttps://bugsigdb.org/Study_924 - Attachment (BugSigDB): Dysbiosis of gut microbiota in a selected population of Parkinson’s patients - BugSigDB > INTRODUCTION: In recent years the hypothesis that gut microbiota associates with Parkinson’s disease (PD) has gained importance, although it has not been possible to define a specific microbiota composition as a predictive biomarker of this disease.

Svetlana Ugarcina Perovic (09:09:41) (in thread): > Deleted.

Peace Daniel (09:15:23) (in thread): > Thank you

Aleru Divine (10:52:41) (in thread): > Coffee for me:hugging_face:

Chiemelie Carita Ndibe (23:02:58): > hello@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Peace Sandy@Chioma Onyido. I am curating a study but the condition “bald sea urchin disease” is not listed in bugsigdb or OLS. How do I go about it

2024-04-13

Aleru Divine (02:11:10) (in thread): > Hi@Chiemelie Carita Ndibe, I saw this from your study. > > I think you can go with bacterial infection or bacterial disease (available in BugSigDB) in this case.https://www.ebi.ac.uk/ols4/search?q=bacterial+infection&ontology=efo - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions - File (PNG): IMG_8163

Aleru Divine (02:14:01): > Good morning everyone and happy weekend:sparkles::heart_hands:@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeI’d like to delete experiments 4 and 5 with their signatures from this study. Thank you so much - Attachment (BugSigDB): Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis - BugSigDB > Coronavirus disease 2019 (COVID-19) severity has been associated with alterations of the gut microbiota.However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive.

Barakat Akinsiku (03:29:20): > Hi everyone, good morning and hope we’re having a great start to the weekend:blush::sparkles:I’ve just completed this study and would love a peer reviewhttps://bugsigdb.org/Study_949Also, I was unable to find the taxon ids of these signatures on NCBI taxonomy database and Uniprot and would appreciate any detective help: > Prevotellaceae NK3B31 group > Coriobacteriaceae UCG-002 > Prevotellaceae UCG-001 > > Thank you all and enjoy the rest of your day - Attachment (BugSigDB): Guts within guts: the microbiome of the intestinal helminth parasite Ascaris suum is derived but distinct from its host - BugSigDB > BACKGROUND: Intestinal helminths are extremely prevalent among humans and animals.In particular, intestinal roundworms affect more than 1 billion people around the globe and are a major issue in animal husbandry.

Svetlana Ugarcina Perovic (03:33:55) (in thread): > Deleted.

Mildred Anashie (03:37:09) (in thread): > Well done on your curation@Barakat Akinsiku:clap:For the taxas they seem as though they are yet to be resolved (No IDs for them yet), butI’llstill check if I can come across anything

Aleru Divine (03:48:03) (in thread): > Thank you so much:blush:

Barakat Akinsiku (03:53:09) (in thread): > Okay@Mildred AnashieThank you:blush:

idiaru Angela (04:26:30): > Good morning everyone, > I have a number of questions for this particular study I’m curating. Link belowhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC5665539/1. I can’t seem to find the sequencing platform, I think it was not included but I’d love your thoughts on that > 2.Do you agree the sequencing type is PCR > 3.The statistical test used was the wilcoxon ranked test, but the transformation seems to be raw counts rather than relative abundances, I’d like other opinions on this > 4. In table 2 attached below, the results reference a previous study that was conducted. I want to confirm if that should be ignored. > 5.In the curation of table 2, should the “subgroup” or “group” attached to the species be curated as seen or should I just curate the species and leave a note. Thank you for your responses. - Attachment (PubMed Central (PMC)): Progression of Parkinson’s disease is associated with gut dysbiosis: Two-year follow-up study > We previously reported gut dysbiosis in patients with Parkinson’s disease (PD).The aim of this study is to examine whether gut dysbiosis correlates with the progression of PD.We examined changes in gut microbiota and demographic features in 2 …

idiaru Angela (04:56:54) (in thread): > Well done@Barakat Akinsiku:clap:

Aleru Divine (04:57:22) (in thread): > Good morning@idiaru Angela, I have gone through the study and paper and here’s what I think. > 1. The sequencing platform I believe is qRT-PCR (“Bacterial counts by rRNA-targeted quantitative reverse-transcription PCR (qRT-PCR)”). > 2. I agree with PCR. > 3. I also agree with raw counts. See this thread and the input by@Levi Waldronhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1699808242225429?thread_ts=1699704087.950319&channel=C04RATV9VCY&message_ts=1699808242.225429 > 4. I don’t think you should ignore Table 2 because it looks that the only table comparing years 0 and 2. And according to the aim, methods and patients information, I think it is the perfect table to curate. > 5. Finally, I think you should curate as seen:thinking_face: - Attachment: Attachment > That looks right, but any of those listed as relative abundance could also have an additional transformation applied :sweat_smile:

Peace Daniel (05:05:04) (in thread): > Well done@Barakat AkinsikuWould take a look at your study

Joan C. Chukwuemeka (05:06:48) (in thread): > I agree with@Aleru Divinein most points. > * Sequencing type is PCR > * Data transformation is raw counts > * Most times referenced studies gives more insight into the current one, so I’d not ignore it. > * Taxa should be Curated as seen, however, if you can get the full genera name for the species, I believe that should be fine. E.g. if you haveS.aureusreported, curatingStaphylococcus aureuswill be better and less vague, as long as you confirm that’s the genera been referred to/abbreviated. And you may not see NCBI ID for some of such abbreviated ones if left as it is. > * Sequencing platform -RT-qPCR

idiaru Angela (05:14:04) (in thread): > Thank you very much@Aleru Divinefor 4, yes I was going to curate that table My doubt arises from the description where a and b was used to denote taxa that was differentially abundant between parkinson disease patients and controls in a previous work done by other authors that is not directly related to the current study. Do you still think that I should curate that?

Joan C. Chukwuemeka (05:15:47) (in thread): > Please can you reshare the table..not showing from here

idiaru Angela (05:15:53) (in thread): > @Joan C. Chukwuemekathank you so much. For the taxa, my main question was that the suffix group and subgroup was attached to the species so for instance should I record “Staphylococcus aureus subgroup” which doesnt have ncbi id or should I record “Staphylococcus aureus” and leave a note about the suffix

idiaru Angela (05:16:27) (in thread): > @Joan C. Chukwuemeka@Aleru DivineThis is the table in question - File (JPEG): Screenshot_20240412_233844_WPS Office.jpg

Aleru Divine (05:17:04) (in thread): > I don’t think it matters@idiaru AngelaI thinkit’sjust a reference.:thinking_face:

Joan C. Chukwuemeka (05:19:57) (in thread): > Oh that.. for the ones with “group” suffix, I think its likely okay to curate the Genus/species and add a review note, sounds like a reference to that group of species. > However the ones with “sub group” suffix may be referring to a strain and may have to be Curated as such, as strains are taxa level below the species.:thinking_face:

idiaru Angela (05:39:38) (in thread): > Thank you so much@Aleru Divine@Joan C. Chukwuemeka:blush:. Very helpful

Barakat Akinsiku (06:08:59) (in thread): > Thank you@Peace Danieland@idiaru Angela

Scholastica Urua (06:45:27) (in thread): > Hello@Barakat Akinsikuwell done on your curation. I think following should work for some of the taxa with unresolved NCBI ID: > 1. uncultured Coriobacteriaceae bacterium for Coriobacteriaceae UCG-002 > 2. uncultured Prevotellaceae bacterium for Prevotellaceae UCG-001 > Then leave a note of what was originally reported using the green bubble. > > This is courtesy of the review I got from@Esther Afuape;https://github.com/waldronlab/BugSigDBcuration/issues/233#issuecomment-2045908526Also, refer to the discussion page to see how Erysipelotrichaceae_ucg_003 and Ruminococcaceae UCG-014 were resolved. > My thoughts though, I might not be totally right… - Attachment: Comment on #233 The Gut Microbiome Is Associated with Clinical Response to Anti–PD-1/PD-L1 Immunotherapy in Gastrointestinal Cancer > Thank you @Scholarpat please curate the ruminococcacea_UCG as uncultured oscillospiraceae bacterium as it has been resolved on the discussion page. Don’t worry about the rank. Do the same for lachnospiraceae_UCG using uncultured lachnospiraceae bacterium. please don’t forget to leave a note of what was originally reported using the green bubble.

Abiola Salako (07:09:19) (in thread): > Thanks for sharing@Scholastica Urua

Peace Daniel (07:16:45) (in thread): > I’mwondering if the numbers attached do not connote something@Scholastica UruaUCG 001,…UCG 002

Peace Daniel (07:17:16) (in thread): > It’squite different from UCG in my opinion

Scholastica Urua (07:18:57) (in thread): > @Peace Danielif you check the study in the issue I quoted and also on the discussion page they had different numbers attached to them not just UCG…

Peace Daniel (07:21:58) (in thread): > Uhm, okay

Barakat Akinsiku (07:23:59) (in thread): > Thanks so much@Scholastica Urua. This is quite helpful

Scholastica Urua (07:24:39) (in thread): > The mentors may have a different opinion though. Just thought to share:blush:You’re welcome@Barakat Akinsiku:hugging_face:

Mildred Anashie (10:14:35): > Hello everyone > > I have a quick question, Can inflammatory bowel disease replace Chronic inflammatory bowel disease for Matched on factors? > > The chronic inflammatory bowel disease is being flagged (Not on the list of allowed values) > > Thank you:pray:

Scholastica Urua (10:23:09) (in thread): > @Mildred AnashieFrom my opinion, I think it can since Inflammatory bowel disease (IBD) is an umbrella term for chronic inflammatory conditions of the digestive tract. So, technically, “Chronic inflammatory bowel disease” is another way of referring to IBD. They are not separate conditions but rather different ways of describing the same group of diseases. > > But the mentors have to weigh in on this to be sure.

idiaru Angela (10:24:03) (in thread): > Yes@Mildred AnashieI agree with scholastica.

Joan C. Chukwuemeka (10:28:35) (in thread): > Yes@Mildred AnashieI think it’s a close fit

Mildred Anashie (10:49:23) (in thread): > Thanks a lot:blush:Needed other thoughts before I enter it that way

Aleru Divine (11:01:15) (in thread): > Yeah I agree too. Great job guys:sweat_smile:

Precious Orakwe (11:56:16): > Good day everyone > > Please I have a little question, how does one know that a paper has more than one experiment, and must it be only 2 signatures that a paper has. > > Thank you

Victoria (Burah) Poromon (12:11:04) (in thread): > Hi@Precious OrakweOne way to know if your paper has more than one experiment is if the study has more than 1 contrast groups > > And for the signatures, it is mostly just two (increased & decreased)

Victoria (Burah) Poromon (12:13:57): > Hello@Peace Sandy,@Svetlana Ugarcina Perovic,<@UBNSEMS3S>,@Chioma Onyido,@Esther AfuapePlease I’d like to delete signature 3 from experiment 3 in this study:https://bugsigdb.org/Study_864Thank you so much. - Attachment (BugSigDB): Feeding Rapidly Alters Microbiome Composition and Gene Transcription in the Clownfish Gut - BugSigDB > Diet is a major determinant of intestinal microbiome composition.While studies have evaluated microbiome responses to diet variation, less is understood about how the act of feeding influences the microbiome, independent of diet type.

Aleru Divine (12:16:55) (in thread): > I agree with @victoria, contrast groups determine how manyexperiments you’llhave in your study.Also there might be some contrast groups without alpha diversities or signatures(no need to record that as an experiment).Signatures are usually increased and decreased abundance.

idiaru Angela (12:20:19) (in thread): > Hi@Precious Orakwea paper has more than one experiment depending of the number of contrast groups that the paper compares. For instance, if a paper that is evaluating the condition parkinson’s disease, compares parkison’s disease patients and healthy controls, that would be one experiment (one contrast group). If the paper also compares parkinsons disease patients with severe disease to those with mild parkinsons disease and that comparison has differential abundance results or alpha diversity results, that would be another experiment with condition “disease severity” and so on depending on the number of contrast that the authors made and have results for. > For your second question, each experiment usually has 2 signatures, one signature for increased taxa in the group1 and the second one for decrease taxa in the group 1. In some cases, If there is only increase or decrease, then the experiment (contrast) would only have one signature.

Mildred Anashie (12:50:59) (in thread): > Hi@Precious OrakweI agree with all their commentsYou’llhave to read through the paper to identify the comparisons made and that makes up the experiments

Precious Orakwe (12:58:38) (in thread): > Thanks everyone for your answers, am grateful

Precious Orakwe (13:01:48) (in thread): > @Mildred AnashieI sent you a DM for a while now about the paper we were asked to curate, you have not given me feedback concerning it. Please reply the message so that we can submit the paper for review. > Thank you

Chiemelie Carita Ndibe (13:05:04): > hello@Oluwatomisin Omojokun. I wanted to add an experiment and noticed you are already working on the bald sea urchin disease paper. Can I still work on it.

Blessing Laweh (13:11:03): > Knock knock. Hello anyone here:eye::lips::eye:I need help with some corrections please, thank you

Mildred Anashie (13:16:05) (in thread): > @Precious OrakweI’mnot sure I understand what you mean by a while because we have worked on the paper together,I’vefinished my part and I can see you have done yours as well > > Based on my observations and what we agreed to do everything is okay > > Although I’m still trying to be surethere’sno experiment here becauseit’sfocused on relative abundance, if so then we actually have just one experiment and it can be sent for review > > “Intestinal microbial compositions of different PD stages differed significantly > We divided patient group into two subgroups according to disease stages, to learn if there were bacterial indicators that changed consistently with the development of PD pathology. > Patients with Hoehn and Yahr (H&Y) stage ranging from > 1-2.5 were included in the mild PD (MPD) group, while patients with H& Y stage ranging from 3-5 were included in the severe PD (SPD) group. There were no statistically significant differences among MPD, SPD and control groups in terms of age, gender and BMI, however, the unified Parkinson’s disease rating scale (UPDRS) scores of the MPD group were significantly lower than that of the SPD group, which proved our assumption (Table S2 in Supporting Information). > At the genus level, only two bacterial genera changed consistently with the development of PD pathology. The relative abundance of Faecalibacterium was 5.14% in control group, reduced to 3.17% in MPD group, and remarkably decreased to 1.22% in SPD group (P-0.048). The relative abundance of Megasphaera was 0.04% in controlgroup, increased to 2.52% in MPD group, and substantially increased to 5.50% in SPD group (P=0.003) (Figure 5). When the two untreated PD samples were removed from the analysis, the significant differences were maintained for genera Faecalibacterium (P=0.038) and Megasphaera (P=0.004), suggesting that though medication was likely having an effect, disease stage was still significantly impacting gut microbiota in PD. These data indicate that gut microbiota of different disease stages may differ as PD pathology progresses.” > > Can someone help me confirm that weshouldn’tcurate this? - File (JPEG): IMG_3688

Mildred Anashie (13:17:09) (in thread): > Hi@Blessing LawehWhat corrections?

Aleru Divine (13:20:16) (in thread): > I believe this is can be curated as it is comparing the relative abundances of 3 groups. This represents the differential abundance@Mildred Anashie

Aleru Divine (13:20:55) (in thread): > Hey@Blessing Laweh, shoot:eyes:

Blessing Laweh (13:25:24) (in thread): > Hello@Mildred Anashie@Aleru Divinelongtime…so in confused on how to do these corrections. So far I’ve only been able to correct the richness - File (JPEG): Screenshot_20240413-182414_Slack.jpg - File (JPEG): Screenshot_20240413-182111_Gallery.jpg

Mildred Anashie (13:25:35) (in thread): > I’m thinking it’s comparing the relative abundance of the taxas among the groups and not between the groups:thinking_face:@Aleru Divine

Blessing Laweh (13:26:57) (in thread): > Like in those part I had zero point, I’m to correct them too in the study I curated right? I don’t understand how to go about it

Mildred Anashie (13:28:14) (in thread): > I’lljust type and share following whatI’mreading > > So from the image “There is no matching in the study is saying that you should remove what you entered for “Matched on”. > Simply means participants/subjects were not matched on any factors@Blessing Laweh

Aleru Divine (13:28:27) (in thread): > Among/between.But think about it,you’llstill compare between two groups in an experiment right?:eyes:

Mildred Anashie (13:29:46) (in thread): > Did you read the text attached?

Aleru Divine (13:32:04) (in thread): > It looks like your study has no matched on factors but you included it.It appears you curated experiments and signatures from other figures except 3C and 4D.According to the feedback,they’reirrelevant.Also check your sequencing details carefully,you’remissing something/something is wrong.

Mildred Anashie (13:34:05) (in thread): > Yes you are to correct them andit’sstated in the corrections shared, like the statistical test and sequencing etc. > > For the sequencing details and statistical test,you’llhave to read through your paper to identify what sequencing was done and record it (It’susually stated in the paper) > For statistical test you should look out for the test that was used for the differential abundance (Differential abundant results is what will be recorded for your signatures and it saysit’sin Fig 3D and 4C)

Aleru Divine (13:35:31) (in thread): > Yes, I did. “Comparison of relative abundance of Faecalibacterium and Megasphaera in > groups of different disease stages.” > > But at the end of the day, you’ll compare > HC vs MPD > HC vs SPD… > > So I feel like it can be curated. I may be wrong regardless:grimacing:

Mildred Anashie (13:37:52) (in thread): > I’m talking about this…:grimacing:@Aleru Divine“Intestinal microbial compositions of different PD stages differed significantlyWe divided patient group into two subgroups according to disease stages, to learn if there were bacterial indicators that changed consistently with the development of PD pathology.Patients with Hoehn and Yahr (H&Y) stage ranging from1-2.5 were included in the mild PD (MPD) group, while patients with H& Y stage ranging from 3-5 were included in the severe PD (SPD) group. There were no statistically significant differences among MPD, SPD and control groups in terms of age, gender and BMI, however, the unified Parkinson’s disease rating scale (UPDRS) scores of the MPD group were significantly lower than that of the SPD group, which proved our assumption (Table S2 in Supporting Information).At the genus level, only two bacterial genera changed consistently with the development of PD pathology. The relative abundance of Faecalibacterium was 5.14% in control group, reduced to 3.17% in MPD group, and remarkably decreased to 1.22% in SPD group (P-0.048). The relative abundance of Megasphaera was 0.04% in controlgroup, increased to 2.52% in MPD group, and substantially increased to 5.50% in SPD group (P=0.003) (Figure 5). When the two untreated PD samples were removed from the analysis, the significant differences were maintained for genera Faecalibacterium (P=0.038) and Megasphaera (P=0.004), suggesting that though medication was likely having an effect, disease stage was still significantly impacting gut microbiota in PD. These data indicate that gut microbiota of different disease stages may differ as PD pathology progresses.”

Aleru Divine (13:39:10) (in thread): > Okay let me go through this

Blessing Laweh (13:40:07) (in thread): > Thank you@Aleru Divine@Mildred Anashiebut in the paper it states the experiment was matched on age, body mass index, comorbidity and smoking status for each experiment…

Mildred Anashie (13:41:54) (in thread): > Can you share your paper?It might help, I thinkit’susually the participants that are matched and not the experiment:thinking_face:@Blessing Laweh

Aleru Divine (13:42:35) (in thread): > From here “At the genus level, only two bacterial genera changed consistently with the development of PD pathology. The relative abundance of Faecalibacterium was 5.14% in control group, reduced to 3.17% in MPD group, and remarkably decreased to 1.22% in SPD group (P-0.048). The relative abundance of Megasphaera was 0.04% in controlgroup, increased to 2.52% in MPD group, and substantially increased to 5.50% in SPD group (P=0.003) (Figure 5).” I think this can be said to be differential abundance. > > Additionally, the end statement “These data indicate that gut microbiota of different disease stages may differ as PD pathology progresses.” > > What do you think?

Aleru Divine (13:44:04) (in thread): > That’sright@Mildred Anashieonly participants are matched on factors.Please share the paper@Blessing Laweh:pray:

Blessing Laweh (13:46:07) (in thread): > https://journals.asm.org/doi/10.1128/spectrum.01901-21Here@Mildred Anashie@Aleru Divinethank you

Mildred Anashie (13:48:56) (in thread): > I can see it from your perspective > > I read this to be saying Faecalinacterium decreased in this and also decreased in this. > > I can’t see a direct comparison saying this compared to this or this compared to this > It appears to be comparison done across all the groups simultaneously:thinking_face:@Aleru DivineI hopeI’mnot confused here:face_with_peeking_eye::woman-facepalming:

Aleru Divine (13:49:56) (in thread): > Ididn’tfind any matched on factors.I searched the keyword “match/matched”. > > What page did you find this?

Aleru Divine (13:51:40) (in thread): > Reduced to 3.17 in MPD compared to 5.14 in control.That’sthe way I kinda interpreted it.:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Mildred Anashie (13:54:16) (in thread): > Same here@Aleru Divine….I only saw the inclusion criteria for the participants > > “A total of 53 participants, comprising 8 in the healthy control group (HCG; 3 males, 5 females), 12 in the untreated pulmonary TB group (UTG; 5 males, 7 females), 15 in the treated pulmonary TB group (TTG; 9 males, 6 females), 11 in the cured pulmonary TB group (CTG; 3 males, 8 females), and 7 in the lung cancer patient group (LCG; 5 males, 2 females) were recruited in the present study. The characteristics of the enrolled participants are shown in Table S1. The mean ages of the HCG, UTG, TTG, and CTG were 30.0, 34.6, 37.5, and 29.9 years, respectively. The LCG exhibited the greatest mean age at 58.7. None of the participants in the UTG, the CTG, and the HCG had comorbidities. Two patients in the TTG had diabetes or kidney stones, while three patients in the LCG had either diabetes or hypertension. All participants had no history of smoking. Individuals in the TTG had received anti-TB treatment for 2 weeks to 2.5 months, while individuals in the CTG had received anti-TB treatment for longer than 6 months. All five cohorts exhibited similar average body mass index (BMI).” > > I’m thinking you got that from here@Blessing Laweh

Aleru Divine (13:55:52) (in thread): > Yeah, thesearen’tmatched on factors@Blessing Laweh

Mildred Anashie (13:56:10) (in thread): > Also you can just Ctrl + F and type Matched,it’llhelp you know ifthere’smatching done or not > > Usually they would say They were matched on…@Blessing Laweh

Blessing Laweh (14:01:55) (in thread): > Istg I read it somewhere that said participants were matched on…or was it compared?? Please give me a minute to find it out.

Mildred Anashie (14:02:38) (in thread): > Also i think your statistical test is LEfSe. > > see this “Taxonomical biomarkers of each sample group were analyzed using the LEfSe package 1.0 (format_input.py -c 1 -u 2 -o 1000000; run_lefse.py -l 4; plot_res.py –dpi 600 –format pdf) with an LDA score of 4 and aPvalue of <0.05 (55).”

Mildred Anashie (14:06:27) (in thread): > Its also clearly stated that they did Metagenomic sequencing (WMS on BugSigDB) on Illumina….. > > Metagenome sequencing. > > “The above extracted DNA samples were used for metagenome sequencing by Guangzhou Sagene Biotech Co., Ltd. (Guangzhou, China). One microgram of total DNA per sample was used as an input material for sequencing library construction using a NexteraXT DNA sample preparation kit (Illumina, CA, USA). Prepared genomic DNA from HeLa cells was used as negative control 2 (NC2) to identify the possible contamination during sequencing library construction. After quality assessment, the library preparations were sequenced on an Illumina NovaSeq 6000 platform, and paired-end raw reads were generated with a read length of 150 bp.”

Blessing Laweh (14:10:30) (in thread): > I didn’t find any part of the study that specifically said “matched on”. What I did was record what the participants were compared on…my mistake, I’ll correct that. Thanks for pointing that out.

Blessing Laweh (14:17:45) (in thread): > For the statistical test, I included it as LEfSe in experiment 1 but did not in the other 3 experiments.:woman-facepalming:I’ll correct that too, thanks@Mildred Anashie

Blessing Laweh (14:24:40) (in thread): > One of the correction says Fig 3C and 4D are only curatable hence the other experiments are irrelevant…however, I created experiments based on the fact that the the experiments had the HCG compared to 3 other groups…I don’t know if you understand me

Blessing Laweh (14:25:40) (in thread): > If you don’t mind taking a look at my the study I curated to better understand, here’s the linkhttps://bugsigdb.org/Study_988 - Attachment (BugSigDB): Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing - BugSigDB > The microbiota plays an important role in human health and disease development.The lung microbiota profile in pulmonary tuberculosis (TB) patients and the > effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively.

idiaru Angela (14:30:49) (in thread): > I think you might be right on track@Mildred Anashie:sweat_smile:

idiaru Angela (14:38:42) (in thread): > While the HCG was compared to other groups, only 3C and 4D shows differential abundance. 3B for instance shows relative abundance which isn’t curated in BugsigDB

idiaru Angela (14:39:34) (in thread): > Same thing for 4B. In each experiment you should only curate the differential abundance, which in this study is shown by the lefse bars like in 4D. Relative abundance should not be curated. If a comparison was done and doesn’t have differential abundance results then you should not curate any signatures for that.

Aleru Divine (14:41:55) (in thread): > Some of the sources you stated are not curatable. (They represent the relative abundance). The only curatable sources are 3C and 4D. > > I see comparisons between > HCG, LTG and UTG in figure 3C > > And, 4D is between UTG and TTG. But only taxa for UTG was listed. > I also see alpha diversity measures (4a) for UTG, TTG, and CTG

Blessing Laweh (16:04:10) (in thread): > Hello@idiaru Angelathanks for your input.
> > So what in getting now is I am not to curate any study with relative abundance that’s why the other experiments are irrelevant right?

Blessing Laweh (16:04:52) (in thread): > Sorry for the slow response. Slack keeps hanging on my phone.

Mildred Anashie (16:05:54) (in thread): > Not any study, experiments that show relative abundance > Although relative abundance between groups is differential abundance > > I hope this makes sense:blush:@Blessing Laweh

Blessing Laweh (16:07:33) (in thread): > It doesn’t@Mildred Anashie:sweat_smile::sob:

Mildred Anashie (16:11:39) (in thread): > I hope this helpshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697468494614279?thread_ts=1697450304.857849&channel=C04RATV9VCY&message_ts=1697468494.614279 - Attachment: Attachment > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

Aleru Divine (16:14:33) (in thread): > And this@Blessing Lawehhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549 - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

idiaru Angela (16:24:34) (in thread): > So yes, any experiment curated with 4B,3B is not relevant to BugSigDB

Blessing Laweh (16:31:02) (in thread): > You guys are the best. Thanks a lot for your time and explanation@Mildred Anashie@Aleru Divine@idiaru AngelaI understand it to an extent but would understand it better when I go through the paper, my curation and your explanations again. > > Thanks alot for your help. I’d let you guys know how it goes. Have a good night/timezone:heart_hands:

idiaru Angela (16:44:41) (in thread): > Goodluck@Blessing Laweh:sweat_smile:

Aleru Divine (16:47:34) (in thread): > Have a great night@Blessing Lawehand@Mildred Anashieand@idiaru Angela:heart_hands:

Mildred Anashie (16:48:20) (in thread): > Yes Goodluck@Blessing LawehAnd you too@Aleru Divine:blush:

2024-04-14

Svetlana Ugarcina Perovic (11:13:17) (in thread): > Deleted.

Victoria (Burah) Poromon (11:34:44) (in thread): > Thank you so much

2024-04-15

Peace Daniel (03:12:26): > Happy new week y’all:hugging_face:I just want to put it out, if you need help with making corrections or a curation, please feel free to reach out to me. > I’m very much available:purple_heart:

Scholastica Urua (03:13:10) (in thread): > Good morning Peace

Mildred Anashie (03:42:28) (in thread): > Happy new week@Peace Daniel:hugging_face:

Peace Daniel (03:46:24) (in thread): > Good morning@Scholastica Urua

Peace Daniel (03:46:34) (in thread): > Thank you@Mildred Anashie

Ruth Bamgbose (04:38:47): > Hello,@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy<@UBNSEMS3S>Please delete signature 1 of experiment 2 and signature 3 of experiment 3 of this studyhttps://bugsigdb.org/Study_917Thank you. - Attachment (BugSigDB): Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe - BugSigDB > BACKGROUND: The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH).

Mildred Anashie (04:45:40): > Happy new week everyone:blush::hugging_face:Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy<@UBNSEMS3S>PleaseI’lllike to delete Signature 3 ofExperiment7 inthis study, it was entered in errorhttps://bugsigdb.org/Study_876Thank you. - Attachment (BugSigDB): Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices - BugSigDB > The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained.Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM.

Peace Daniel (04:49:58) (in thread): > Just a side note@Mildred AnashieWhy not use antibiotic and ethnic group for these confounders in your study antibiotic use, ethnicity?

Mildred Anashie (04:54:07) (in thread): > Thank you Peace:blush:I was actually thinking of using the ethnic group for ethnicity justwasn’tcertain > Now I think about it, antibiotic can work for antibiotic use > > Thank you again

Mildred Anashie (04:55:14) (in thread): > You can help change them@Peace DanielIf youdon’tmind > Since you said you were less busy:blush:

Peace Daniel (05:01:39) (in thread): > Sure,that’sso kind of you@Mildred Anashie

Ruth Bamgbose (05:47:31) (in thread): > Hi@Peace Daniel, can you help review this studyhttps://bugsigdb.org/Study_917@Scholastica Uruayou also offered on GitHub,can you also help review the study? - Attachment (BugSigDB): Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe - BugSigDB > BACKGROUND: The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH).

Peace Daniel (05:52:20) (in thread): > Yes, I will:hugging_face:@Ruth Bamgbose

Scholastica Urua (05:59:46) (in thread): > I will@Ruth Bamgbose

Ruth Bamgbose (06:00:30) (in thread): > Thank youu@Peace Daniel@Scholastica Urua

Aleru Divine (08:37:11) (in thread): > Happy New week@Peace Daniel:hugging_face::sparkles:

Oluwatomisin Omojokun (10:33:35): > Good afternoon, Please kindly help us review this study by bolanleW and mehttps://bugsigdb.org/Study_912

Peace Daniel (10:34:44) (in thread): > Good afternoon,I’dlove to give a review:hugging_face:

Peace Daniel (11:03:04) (in thread): > @Ruth Bamgbose@Scholastica UruaI’mwondering if this is actually a cross sectional study due to this statement, varying time points and the presence of healthy controls in the study > > “This allowed us to account for the compositional nature of microbiome data, control for location and viral control with ART as potential confounders, and account for the longitudinal study design.”

Peace Daniel (11:04:53) (in thread): > Also the statistical test > > “To determine genera that significantly differed in abundance across cohorts, we used ANCOM-BC” > > “Differential abundance of genera relative to healthy controls. A Using ANCOM-BC, significant differential log-fold changes between microbes were calculated relative to healthy controls using only baseline values.”

Peace Daniel (11:10:53) (in thread): > Hi@Oluwatomisin OmojokunI don’tthink there was controlling for confounders in this study as I searched with these keywords “controlled, adjusted, confounder” but if you feel i missed it please point me to it

Peace Daniel (11:12:47) (in thread): > No lda score tooThere’sa MHT correction, try searching FDR

Oluwatomisin Omojokun (13:59:29) (in thread): > Thanks,@Peace Daniel, i will cross-check

Ruth Bamgbose (16:24:02) (in thread): > Yeah for that , if you look at this text > > “To understand which genera significantly differed between cohorts, we used ANCOM-BC2 [41, 42], a dif- ferential abundance (DA) analysis package for com- positional microbiome data that allows for regression modeling to control for potential confounding fac- tors. Specifically, we determined which genera differed between HC and the ART-experienced or ART-naïve cohorts in models that also included the effect of time, viral load, and location to control for confounders. “ > > The way I understand it is, ANCOM BC was used to analyse differential abundance with regression models and the models were specifically used to control for potential confounding factors such as time, viral load, and location and to identify which genera differed significantly between the cohorts. It also stated that for two different models were used to analyse baseline values and values and two time points.

Ruth Bamgbose (16:32:09) (in thread): > And for the study thanks for pointing that out. I can’t believe i skipped that during my edits. You’re right, its aTime series or longitudinal observational study @Peace Daniel**** ****

Peace Daniel (16:37:23) (in thread): > Oh, I could be wrong@Ruth Bamgbose

Mildred Anashie (17:13:09) (in thread): > I might agree with@Peace DanielThe paper says ANCOM BC was used for differential abundance > > Linear regression was used to stratify by location and viral load. > > We curate the statistical test for differential abundance > > This is my opinion@Ruth Bamgbose

2024-04-16

Scholastica Urua (01:50:38) (in thread): > Hello@Ruth Bamgbose, > > I have reviewed the study and have a few observations to share: > > 1. The study design appears to be a time series/longitudinal observational study, which I agree with. > > 2. It seems that ANCOM-BC was used as the statistical test for differential abundance, and linear regression was utilized to measure various variables, including alpha diversity, and to control for potential confounding factors, among other things. > > 3. I noticed that in experiments 1 and 3, only location and viral load were documented as confounders, with time being omitted. I couldn’t find any explanation for this in the article. I might have missed something but it might be worthwhile to revisit this part. > > 4. The study mentionsFDR-adjusted p-valuesin several instances, indicating adherence to multiple hypothesis testing correction (******Yes******to MHT; you documented******No******. > > 5. Regarding one of the curated signatures, clostridium_sensu_stricto_1, it has been resolved to the Clostridium genus with the NCBI ID OF1485(you can also refer to the discussion page for further details). > > Overall, the study has been well curated. Well done - File (JPEG): FDR.JPG - File (JPEG): Cofounders.JPG

Ruth Bamgbose (02:09:52) (in thread): > For number 3,it’sbecause of this > “ The model used also evaluated the effect of location and viral outcome. A zero means that there is no significant difference in the genus between cohorts. B Similar to A, however both timepoints were included > in the model; therefore, time was added to the model, and we controlled for dependence between samples belonging to the same patient”.The way it is stated here is that time was added in the second model.

Ruth Bamgbose (02:11:24) (in thread): > Thanks so much for the review@Peace Daniel@Mildred Anashie@Scholastica Urua. Also what are your GitHub usernames so I can mention you?

Scholastica Urua (03:15:53) (in thread): > I’m @Scholarpat on GitHub:hugging_face:

Mildred Anashie (03:16:50) (in thread): > @MyleeeA

Peace Daniel (04:17:52) (in thread): > You’rewelcome@Ruth BamgboseI’m@fiddyhamma and do let me know if you need any assistance later on:purple_heart:

Rahila-me (05:14:02): > <!here>, Good morning All:good_luck::bioc:

Mildred Anashie (05:38:09) (in thread): > Good morning@Rahila-me

idiaru Angela (05:43:54) (in thread): > Good morning@Rahila-me

Peace Daniel (06:17:17) (in thread): > Hey, good morning

Peace Daniel (06:46:09) (in thread): > And also, the location controlled as a confounder in your study…could it be the location where the samples was taken?@Ruth BamgboseIm wondering if geographic area could be a good replacement

Mildred Anashie (06:54:09) (in thread): > @Peace DanielI saw mention of Rural and Urban > I thinkthat’sthe location they referred to

Peace Daniel (06:58:26) (in thread): > Okay, location is a better fit as she used then@Mildred Anashie

Barakat Akinsiku (07:08:34) (in thread): > Good morning@Rahila-me:blush:

Scholastica Urua (07:33:53) (in thread): > Good morning@Rahila-me

Victoria (Burah) Poromon (08:06:08): > Good day everyone > So I found two websites that can be used to find bacteria taxonomy. > I thought it will be nice to share it here > 1. https://lpsn.dsmz.de/ > 2. https://bacdive.dsmz.de/ - Attachment (bacdive.dsmz.de): BacDive | The Bacterial Diversity Metadatabase > The Bacterial Diversity Metadatabase provides strain-linked information about bacterial and archaeal biodiversity.

idiaru Angela (08:08:27) (in thread): > Thank you Victoria

Mildred Anashie (08:10:23) (in thread): > Thank you so much Victoria for sharing > Gone through them and they are very useful, it provides the NCBI ID along side:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Victoria (Burah) Poromon (08:17:39) (in thread): > @Mildred AnashieYes it does! > LPSN also provides the gender of the bacteria:sweat_smile:

Barakat Akinsiku (08:24:40) (in thread): > Thank you for sharing@Victoria (Burah) Poromon

Svetlana Ugarcina Perovic (08:49:07) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711489001147419?thread_ts=1711479513.033609&cid=C04RATV9VCY - Attachment: Attachment > When I am not sure about nomenclature i.e. bacterium name I go (beside NCBI) to check it out here https://lpsn.dsmz.de/

Mkpouto Shedrack (08:52:16) (in thread): > Thanks for sharing@Victoria (Burah) Poromon, This is very useful.

Victoria (Burah) Poromon (08:53:18) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (08:58:50) (in thread): > Thank you for sharing this@Victoria (Burah) Poromon:heart:

Victoria (Burah) Poromon (11:01:20): > Hello@Svetlana Ugarcina Perovic,@Peace Sandy,@Chioma Onyido,@Esther AfuapePlease I’d like to delete Experiment 4 and its signature from this study.https://bugsigdb.org/Study_988Thank you. - Attachment (BugSigDB): Insights into the Unique Lung Microbiota Profile of Pulmonary Tuberculosis Patients Using Metagenomic Next-Generation Sequencing - BugSigDB > The microbiota plays an important role in human health and disease development.The lung microbiota profile in pulmonary tuberculosis (TB) patients and the > effects of anti-TB treatment on the profile need to be determined thoroughly and comprehensively.

Svetlana Ugarcina Perovic (11:32:49) (in thread): > Deleted.

Victoria (Burah) Poromon (11:35:40) (in thread): > Thank you.

Oluwatomisin Omojokun (11:44:41) (in thread): > Thanks@Victoria (Burah) Poromonand@Svetlana Ugarcina Perovic

Samreen Aftab (16:47:23): > Hello everyone, since my college exams are this month, I’ve been really busy with my academics and unfortunately I’ve not found any time to work upon curations in the last 15 days. I was assigned a paper to curate and while I’ve gone through the paper, I don’t think I’ll find time this month to curate it all by myself (there are a lot of signatures to curate). I would like to collaborate with someone to finish this paper. Thank you.https://pubmed.ncbi.nlm.nih.gov/28195358/ - Attachment (PubMed): Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome - PubMed > PD is accompanied by dysbiosis of gut microbiome. Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways, and demonstrate independent effects of PD medications on the microbiome. The findings provide new leads and testable hypothe …

Aleru Divine (16:48:31) (in thread): > Hi@Samreen Aftab, best of luck in your coming exams:four_leaf_clover:I’m open to collaborate with you on this.:blush:

Samreen Aftab (16:49:12) (in thread): > Okay@Aleru Divinedm me

Mildred Anashie (16:49:49) (in thread): > Hi@Samreen AftabSuccess in your upcoming exams:blush:Currently working on one now, would have definitely loved to

Samreen Aftab (16:51:20) (in thread): > thank you@Mildred Anashieit’s been a stressful month:smiling_face_with_tear:

Peace Daniel (17:05:57) (in thread): > Hi@Samreen AftabWish you the best in your upcoming exams:purple_heart:@Aleru Divinedo let me know if you need an extra hand:face_with_hand_over_mouth:

Joan C. Chukwuemeka (17:44:24) (in thread): > All the best in your exams@Samreen Aftab

2024-04-17

Scholastica Urua (04:07:16) (in thread): > Wishing you the best of luck in your exams@Samreen Aftab

Abiola Salako (05:26:53) (in thread): > @Samreen Aftabwishing you the very best in your exams

Abiola Salako (05:28:11) (in thread): > Thank you for sharing@Victoria (Burah) Poromon

idiaru Angela (06:10:05) (in thread): > Best of luck in your college exams@Samreen Aftab

Svetlana Ugarcina Perovic (06:30:45) (in thread): > @Samreen AftabTHANK you for taking care of your curation!Reaching out for help is an important skill.

Svetlana Ugarcina Perovic (06:31:37) (in thread): > And YOU have that skill! I wish you all the best for your exams!

Svetlana Ugarcina Perovic (06:31:55) (in thread): > :bouquet:

Samreen Aftab (06:53:54) (in thread): > Thank you!@Svetlana Ugarcina Perovic:heart:

Samreen Aftab (06:54:09) (in thread): > Thank you everyone for your kind wishes:blush:

Barakat Akinsiku (06:58:25) (in thread): > All the best in your exams:hugging_face:@Samreen Aftab

NWAKAEGO VINCENT (07:38:36) (in thread): > I wish you all the best in your exam@Samreen Aftab

Svetlana Ugarcina Perovic (08:27:30): > Tomorrow instead of our regular team meeting we would like to invite to join us at another amazing MVIFhttps://www.microbiome-vif.org/en-USSee you tomorrow at MVIF!<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

idiaru Angela (08:28:54) (in thread): > Looking forward to the forum:blush:

Abiola Salako (08:42:07) (in thread): > Looking forward to it.

Peace Daniel (08:51:09) (in thread): > Looking forward to it:dancer:

Rahila-me (08:56:11) (in thread): > Looking forward to it:bioc:

Joan C. Chukwuemeka (08:57:54) (in thread): > Thanks for the Update@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (09:51:08): > Since finalizing previous curations is under control (THANKS TO YOU), I have added somepapers to curate. > * feel free to claim a paper for curation from the GitHub issue that you did not open (that’s a catch:slightly_smiling_face:) > > * feel free to open a GitHub issue with a paper to curate that will be available for other curator (not for yourself). You can leave a comment why you chose that particular paper. Do not forget to check if it is already curated. > Curate, collaborate, communicate, and ENJOY!

idiaru Angela (09:51:58) (in thread): > Oh nice! Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (09:52:27) (in thread): > I knew that you will like it@idiaru Angela

Peace Daniel (09:53:23) (in thread): > This is a great idea, thank you@Svetlana Ugarcina Perovic

Aleru Divine (09:54:42) (in thread): > Thanks for the update@Svetlana Ugarcina Perovic:star-struck:

Oluwatomisin Omojokun (09:55:08) (in thread): > Thanks @svetlana_up

idiaru Angela (09:56:59) (in thread): > Yes I do like it very much:joy::blush:. Thank you

Aleru Divine (09:58:53) (in thread): > Yoo-hoo!:sparkles:looking forward to it:star-struck:

Oluwatomisin Omojokun (09:59:45) (in thread): > noted@Svetlana Ugarcina Perovic

Peace Daniel (10:03:19) (in thread): > I hope I did it correctly:face_with_hand_over_mouth:I found this paper a while ago andI’msharing it here if anyone would like to curate it:hugging_face:https://github.com/waldronlab/BugSigDBcuration/issues/352 - Attachment: #352 Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients > Characterization of oral bacterial and fungal microbiome in recovered COVID-19 patients Nana Wei
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10166687/

Joan C. Chukwuemeka (10:15:29) (in thread): > Oh…Thanks a lot@Svetlana Ugarcina Perovic

Nana (11:09:43) (in thread): > Noted@Svetlana Ugarcina Perovic:dancer:

Nana (11:11:04) (in thread): > @Svetlana Ugarcina Perovicthanks for the information

Barakat Akinsiku (11:11:12) (in thread): > Oh nice, thank you@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (11:34:29) (in thread): > Great! Thank you@Svetlana Ugarcina Perovic

Aleru Divine (11:42:17): > Hey everyone! Just wanted to let you know that I opened two new issues with papers to curate, in case anyone’s interested.:hugging_face:You can find them here: > * Issue 357 > * Issue 355 > And there are more issues open too, so feel free to take a look if you’ve got some free time! > > Happy BugSigDB-ing!:sparkles:

Rahila-me (12:02:22) (in thread): > Lovely@Svetlana Ugarcina Perovic

Rahila-me (12:03:29): > <!here>they are new issues on Github, feel free to request for them.

idiaru Angela (13:58:38): > Hey everyone:blush:. I also opened a couple new issues on guthub. Please request them for curation if you’re interested in curating them. > Happy BugSigDB-ing > * https://github.com/waldronlab/BugSigDBcuration/issues/354 > * https://github.com/waldronlab/BugSigDBcuration/issues/353

Scholastica Urua (14:15:44) (in thread): > Nice, thank you@Svetlana Ugarcina Perovic

Scholastica Urua (14:48:40) (in thread): > Noted, looking forward to this@Svetlana Ugarcina Perovic

Mildred Anashie (14:58:42) (in thread): > This sounds great, Well done everyone for all the hard work:clap::heart:…..Thank you@Svetlana Ugarcina Perovic:blush:The last line:hugging_face::hugging_face::hugging_face:(curate, collaborate, communicate and enjoy):grin::ok_hand:

Joan C. Chukwuemeka (15:17:12): > Hello<!here>I’ve added two new issues for curation. Do request for them if interested::hugging_face: > * Issue_361 > * Issue_362 > Happy BugSigDB-ing:seedling:CC:@Svetlana Ugarcina Perovic@Levi Waldron<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape - Attachment: #361 The Vaginal Microbiome is Associated with Endometrial Cancer Grade and Histology - Attachment: #362 Differences in the microbial profiles of early stage endometrial cancers between Black and White women.

Isoken Ibizugbe (15:56:25) (in thread): > Where do you find papers to create issues with

idiaru Angela (16:07:24) (in thread): > Hi@Isoken IbizugbeUsually I go to PubMed, link below and search for articles that include keywords that I’m interested in. For instance “microbiome” “parkinson disease” Then I look through the article to confirm that they are curatable by checking if they have alpha diversity results or differential abundance results. > Finally, if I confirm the paper is curatable, I get the PMID of the paper and search on BigSigDB to confirm that it has not been curated before I open it as a new issue. As a confirmation, I also search the title of the paper incase it wasn’t populated with the PMID.https://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

idiaru Angela (16:07:56) (in thread): > There’s a thread that also explains this process much better but I can’t seem to find it:sleepy:

2024-04-18

Isoken Ibizugbe (01:26:49) (in thread): > Thanks

Faith Ifeoluwa Alexander (03:06:38) (in thread): > Hello@idiaru Angelajust a clarification pls. > > Is this a curation that we would collaborate on?

Mildred Anashie (03:22:49): > Good morning everyoneHi@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy<@UBNSEMS3S>Please I’ll like to delete Signature 3 of Experiment14 and Signature 2 of Experiment 9in this study, it was entered in errorhttps://bugsigdb.org/Study_876Thank you.:pray: - Attachment (BugSigDB): Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices - BugSigDB > The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained.Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM.

Svetlana Ugarcina Perovic (03:39:00) (in thread): > Deleted.

idiaru Angela (03:48:04) (in thread): > Hi@Faith Ifeoluwa Alexander. Good morning > They are new issues that you can curate yourself or collaborate with others to do. > As I opened these 2 issues I can’t work on them. But I can request to be assigned to the other issues co contributors have openedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1713361868432089?thread_ts=1713361868.432089&cid=C04RATV9VCY - Attachment: Attachment > Since finalizing previous curations is under control (THANKS TO YOU), I have added some papers to curate. > > • feel free to claim a paper for curation from the GitHub issue that you did not open (that’s a catch :slightly_smiling_face: ) > • feel free to open a GitHub issue with a paper to curate that will be available for other curator (not for yourself). You can leave a comment why you chose that particular paper. Do not forget to check if it is already curated. > Curate, collaborate, communicate, and ENJOY!

Mildred Anashie (03:48:28) (in thread): > Thank you:pray:

Faith Ifeoluwa Alexander (03:48:40) (in thread): > Okay. Thank you.

Svetlana Ugarcina Perovic (03:50:39) (in thread): > See you today at MVIF!:wave:

Barakat Akinsiku (03:53:49) (in thread): > Looking forward to it

Nana (03:58:21) (in thread): > Ok@Svetlana Ugarcina Perovic:dancer:

Aleru Divine (04:03:57): > Good morning everyone!@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther AfuapeFrom the study@Abiola Salakoand I are curating, we have a few questions and we’d appreciate your feedback:pray:The questions are: > 1. Regarding the experimental condition, do we curate irritable bowel syndrome (IBS) since the study assessed IBS-like symptoms and the abundances of bacterial taxa in faecal samples were compared between IBS+ and IBS- PD patients. Or should we go with Parkinson’s disease(PD). We are leaning towards IBS:thinking_face: > 2. Regarding the grouping, we considered using IBS+ as group 1 and IBS- as group 0 instead of PD and healthy controls again because of the differential abundance results. > 3. If we are using IBS+ and IBS- as contrast groups that would rule out the matched-on factor because only controls were matched for sex and age. Here is an excerpt “This casecontrol study compared patients with a diagnosis of PD according to the Queen Square Brain Bank criteria with control subjects frequency matched for sex and age (5 years) without any signs of parkinsonism or potential premotor symptoms.” > 4. There is also a bit a confusion on the variables to curate as confounders controlled for. > The reason is, firstly, “Covariates were selected based on differential prevalence in PD and control groups (Table 1) …and in the final model with resolved hyperthyroidism and hypercholesterolaemia as potential confounders”. > > They study also stated that “(ii) a multivariate model including IBS status and potential confounders. As confounders, the variables that had differences in prevalence between IBS+ and IBS PD patients were selected (Table 3: hypothyroidism, lactose intolerance, gender, body mass index, dopamine agonist use and Jankovic tremor score).” > > The study also stated again “None of the potential confounders showed a statistically significant association with the taxa of interest (adjusted P value >0.1 for all confounders and all three taxa).” > > And finally, “Using a liberal threshold of P < 0.1 for identifying potential confounders, only lactose intolerance and the use of thyroxin and dopamine agonist were differentially distributed between the groups. Thus they were added as confounders in the model.” > > We would really love additional opinions:pray:I was thinking of going with these as confounders “hypothyroidism, lactose intolerance, gender, body mass index, dopamine agonist use and Jankovic tremor score” as the study stated that they were selected as a result of their differences in prevalence between IBS+ and IBS PD. > > Link to article:Download article.pdfSupplementary file.docx

idiaru Angela (04:11:17) (in thread): > Hi@Aleru Divine@Abiola SalakoGood morning and weldone > For the condition I would also go with IBS since they were contrasting the groups on IBS and both of the groups has PD > For the matching I’m of the opinion that it still applies. From the excerpt you sent, it seems the control group isn’t healthy controls but rather IBS - PD patients serve as the control group > > > For the question on co founders I believe only the last statement applies. While they tested for a number of cofounders, only those that showed significant associations were added to the model. So I would go with lactose intolerance and the use of thyroxine and dopamine as the cofounders since they were later added to the model. > Well done guys

Aleru Divine (04:15:40) (in thread): > Thank you so much for your feedback@idiaru Angela, yes there are healthy controls in the study different from the PD patientswho were later separated into IBS+ and IBS-

idiaru Angela (04:18:06) (in thread): > Okayy@Aleru Divinethen I don’t think the matching would apply then. Just for the comparison between PD and healthy controls would it apply

Aleru Divine (04:18:44) (in thread): > Thank you:pray:@idiaru Angela

idiaru Angela (04:19:50) (in thread): > For 2 , I think your grouping is perfect:ok_hand:

Mildred Anashie (04:24:56) (in thread): > Hello@Aleru DivineThe condition is IBS in my opinion > > For the confounders I agree with Angela > > Only lactose intolerance and the use of thyroxin and dopamine agonist applies > > Also your grouping should be IBS+ and IBS- like you pointed out > > Well done:+1:

Aleru Divine (04:26:49) (in thread): > Thank you for the confirmation@Mildred Anashie

Bolanle Wahab (04:31:03): > Good morning@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther AfuapeIn this studyhttps://bugsigdb.org/Study_1048I keep getting this “lua error: too many expensive function calls” when adding signatures , at first it goes after a while but it has refused to go now, should I keep adding the signatures? - Attachment (BugSigDB): Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns - BugSigDB > Storage of biological specimens is crucial in the life and medical sciences.Storage conditions for samples can be different for a number of reasons, and it is unclear what effect this can have on the inferred microbiome composition in metagenomics analyses.

Svetlana Ugarcina Perovic (04:33:42) (in thread): > Please report your bug herehttps://github.com/waldronlab/BugSigDB/issues/224 - Attachment: #224 Lua error: too many expensive function calls > See https://bugsigdb.org/Study_971 - e.g. Experiment 12. I note that the error doesn’t occur when navigating directly to https://bugsigdb.org/Study_971/Experiment_12. Note - this is an extremely large number of experiments for a study, and and might not be worth supporting so many experiments if it would reduce performance on the rest of the site. > > image

Bolanle Wahab (04:38:48) (in thread): > Okay! > Thank you@Svetlana Ugarcina Perovic:heart:

Victoria (Burah) Poromon (06:15:56) (in thread): > Well done!@Aleru DivineAnd I agree with@Mildred Anashieon the confounders

Victoria (Burah) Poromon (06:19:02): > Hi everyone, Happy Thursday! > I have a not-so-work-related question for everyone. I’m hoping we can learn new tricks and ideas from each other:face_with_peeking_eye:Balancing work and personal life can be tasking sometimes. So it’s not abnormal that we can feel mentally stressed and tired. > > Question: How do you cope with burnout from work??? > > I’ll share mine in the thread.

Victoria (Burah) Poromon (06:19:54) (in thread): > For me, One of the things I do is I turn things I love doing into incentives. For example, I love to watch kdrama and read a book in my free time > So I make them incentives and reward myself with an episode of kdrama after working:sweat_smile:

idiaru Angela (06:21:50) (in thread): > Hey@Victoria (Burah) PoromonI also do watch kdramas too:sweat_smile::blush:. My most preferred go to is sleeping though. I would sleep for a relatively long time.

Aleru Divine (06:21:52) (in thread): > Thank you@Victoria (Burah) Poromon

Victoria (Burah) Poromon (06:23:02) (in thread): > Right!@idiaru AngelaNothing beats a good nap:face_with_hand_over_mouth:

Barakat Akinsiku (06:27:38) (in thread): > This is interesting. Yes incentives work@Victoria (Burah) Poromon. Another tip is the 20/20 rule or taking a short 5 minute break once you’ve observed you’re not really assimilating or focused on the task at hand

Aleru Divine (06:30:48) (in thread): > @Victoria (Burah) Poromonincentives adds an extra layer of motivation to get through the workday:hugging_face:and I am heavy on taking short naps too@idiaru Angela:sweat_smile:Taking a break, taking a walk to nowhere sometimes:sweat_smile:just getting my mind off work generally is how I cope with it

Victoria (Burah) Poromon (06:31:19) (in thread): > Yes yes yes@Barakat AkinsikuThis also helps with keeping your physical body active:yellow_heart:Great tip!

Victoria (Burah) Poromon (06:33:34) (in thread): > @Aleru DivineGreat!:relieved:

Scholastica Urua (06:34:01) (in thread): > Firstly, I’ve learned to set realistic goals for myself. Pushing too hard and trying to achieve too much in a short time can really take a toll on me. > > I’ve also found that defining specific times for work and leisure activities is crucial. Admittedly, it’s been quite challenging lately:face_holding_back_tears:, but I’m making an effort. There are days when I give myself permission to completely unplug from work. > > Sometimes, I indulge in watching movies (one of my favorite pastimes:sweat_smile:). I also take long naps when I’m mentally stressed to recharge. It’s amazing how much better I feel after taking that time for myself.

Bolanle Wahab (06:37:59) (in thread): > @Victoria (Burah) PoromonI used to use incentives but I started overdoing it:sweat_smile:I’d find myself watching more episodes than I intended to so I stopped and used most of my mornings and early afternoon for work cause I realized I’m more productive at that time before engaging in other activities of the day.

Victoria (Burah) Poromon (06:39:10) (in thread): > Great thinking@Scholastica UruaIt can get overwhelming sometimes butyou’redoing great:yellow_heart:Good job on giving yourself credit!:face_with_hand_over_mouth::face_with_hand_over_mouth:

Victoria (Burah) Poromon (06:42:55) (in thread): > @Bolanle WahabThis is definitely one of the cons of this method:joy:It’s hard to stick to an episode sometimes:weary:

Peace Daniel (06:45:52) (in thread): > Food, delicious food and then I sleep:smiling_face_with_smiling_eyes_and_hand_covering_mouth::joy:@Victoria (Burah) Poromon

Aleru Divine (06:48:22) (in thread): > Fooooooood@Peace Daniel:pleading_face::face_with_hand_over_mouth:

Victoria (Burah) Poromon (06:48:23) (in thread): > Wow dear@Peace DanielA certified foodie:joy::joy:

Peace Daniel (06:52:20) (in thread): > Yes@Aleru Divine@Victoria (Burah) PoromonSometimeswe’rejust a bit hungry lol:face_holding_back_tears:

Mildred Anashie (06:58:29) (in thread): > Sleep and watch movies with a bit of food:joy::joy:

Joan C. Chukwuemeka (06:59:38) (in thread): > For me, I pace myself as I work..5-10minutes break in-between. I also try to stick to my mental schedule/plan for each day.. makes it harder for me to get burned out or stressed, once that is done.

Joan C. Chukwuemeka (07:00:02): > Good morning all,@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther AfuapeIn theStudyI’m completing its curation with@Glorious Katushabe, The contrast was between ferrous sulfate (FS) iron supplemented or ferrous bis-glycinate chelate (FC) iron supplemented pups(pre-weaned rats) & Young adult rats and > vehicle control-supplemented (CON) pups/young adult rats (YA). > The previous curator selected “******Abnormality of iron homeostasis”******, which is not appropriate. > > So far in EFO, the term with iron, in terms of supplementation is “******dietary heme iron intake measurement*******”, but the supplement in the study is not heme iron but ferrous sulfate and ferrous bis-glycinate chelate. > The closest term on EFO isnutritional supplement exposure measurement, however it’s not available on BugSigDB.Will it be okay for us to curate**** *****environmental exposure measurement******, ****whichnutritional supplement exposure measurement fallsunder? - Attachment (BugSigDB): Gut Microbiome Alterations following Postnatal Iron Supplementation Depend on Iron Form and Persist into Adulthood - BugSigDB > The gut microbiota is implicated in the adverse developmental outcomes of postnatal iron supplementation. - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions - File (PNG): image.png

Victoria (Burah) Poromon (07:03:24) (in thread): > @Joan C. ChukwuemekaInteresting! > Is your mental schedule/plan the same as aTodo’slist or daily deliverables?

Victoria (Burah) Poromon (07:05:47) (in thread): > @Mildred AnashieAre you sureit’sjust “a bit of food”?:joy:Don’tbe shy, this is a safe space:relieved:

Bolanle Wahab (07:16:12) (in thread): > @Victoria (Burah) Poromonyesss:sob:

Peace Daniel (07:16:52) (in thread): > It’sa lot of food@Mildred Anashie@Victoria (Burah) PoromonI can feel it,we’retwinning:dancer:

Mildred Anashie (07:18:47) (in thread): > Okay okay > > I’ve been caught:face_with_peeking_eye::melting_face:@Victoria (Burah) Poromon@Peace DanielAs a sweet tooth just add cookies/chocolates and a slice of cake:face_holding_back_tears:

Peace Daniel (07:28:56) (in thread): > You’vesaid it all@Mildred Anashie

Joan C. Chukwuemeka (07:30:00): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace SandyPlease help deleteExperiment 7andExperiment 8of thisStudywith their signatures. > It may have been entered in error by the previous curator. - Attachment (BugSigDB): Study 999/Experiment 7 > … - Attachment (BugSigDB): Study 999/Experiment 8 > …

Mildred Anashie (07:30:46) (in thread): > This is a very tricky one@Joan C. ChukwuemekaBut I think what you are suggesting fits, but the mentors can guide better

Joan C. Chukwuemeka (07:41:12) (in thread): > Yea@Mildred Anashie. Awaiting their response

Joan C. Chukwuemeka (07:52:16) (in thread): > Yea@Victoria (Burah) Poromonis kind of similar, but a flexible one. Prioritizing an Early wake-up time, means I do things at my pace with no need for rush, which is most times the source of stress - (so much to do in a short time).

Victoria (Burah) Poromon (07:56:25) (in thread): > @Joan C. ChukwuemekaGreat tip! > Thanks for sharing.

Scholastica Urua (08:12:30) (in thread): > I agree with@Mildred Anashieit’s a tricky one. Here for the answer though:crossed_fingers:

Barakat Akinsiku (08:16:16) (in thread): > Lol at food@Peace DanielBe careful not to stress-eat though:smile:Seriously an indulgent food reward is not bad every once in a while

Rahila-me (08:22:07): > Good afternoon@Svetlana Ugarcina Perovic@Chioma OnyidoPlease help me delete Signature 2 of Experiment 5 of this curation:https://bugsigdb.org/Study_943

UBNSEMS3S (08:57:21): > As a reminder, there is no BugSigDB meeting today. Instead I encourage you all to attend MVIFhttps://www.microbiome-vif.org/en-USIt’s free! - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Mildred Anashie (08:58:19) (in thread): > Thank you<@UBNSEMS3S>Waiting for the live stream to start:hugging_face:

Scholastica Urua (09:00:00) (in thread): > Thank you<@UBNSEMS3S>

idiaru Angela (09:00:22) (in thread): > Thank you

Aleru Divine (09:10:09) (in thread): > Thanks<@UBNSEMS3S>I’m tuned in:grinning_face_with_star_eyes:

Svetlana Ugarcina Perovic (09:23:00) (in thread): > Deleted.

Svetlana Ugarcina Perovic (09:23:13) (in thread): > Deleted!

Joan C. Chukwuemeka (10:00:38) (in thread): > Thank You@Svetlana Ugarcina Perovic

Peace Daniel (10:01:16) (in thread): > I understand why there are fewer experiments on fungal microbiomes study (skin) thanks to that question asked

Joan C. Chukwuemeka (11:49:21) (in thread): > The sessions were quite Insightful. Looking forward to the next MVIF:hugging_face:

Scholastica Urua (12:47:17): > Hello everyone, I’ve added a couple of new issues on GitHub. Please do check them out.:blush: > * 367 > * 368 > * 369

Nana (12:48:30) (in thread): > @Joan C. Chukwuemekayeah it was very insightful

Rahila-me (13:42:03) (in thread): > Seen, Thanks

Rahila-me (13:42:52) (in thread): > It was lovely to be there

Joan C. Chukwuemeka (13:47:52) (in thread): > Still looking forward to hearing from you on this please:pray:@Svetlana Ugarcina Perovic<@UBNSEMS3S>

UBNSEMS3S (14:57:29) (in thread): > Wait if something is in the ontology it should be usable so nutritional supplement exposure measurement should work.

Peace Daniel (15:00:55) (in thread): > Sometimesit’snot<@UBNSEMS3S>I’vehad this issue of finding something in the ontology butcan’tuse it in BugSigdb

UBNSEMS3S (15:01:01) (in thread): > Weird.

Mildred Anashie (15:02:37) (in thread): > YeaI’veexperienced same@Peace Daniel

UBNSEMS3S (15:09:32) (in thread): > Environmental exposure assessment is so vague. What about just iron or iron biomarker measurement? Neither is quite right but they’re better than environmental exposure I think.

Peace Daniel (15:13:46) (in thread): > Iron biomarker measurement seem fine to me and is available on BugSigdb@Joan C. Chukwuemeka<@UBNSEMS3S>

Joan C. Chukwuemeka (15:52:22) (in thread): > Okay<@UBNSEMS3S>, What of******dietary heme iron intake measurement********“**which is a form of iron intake measurement, though not “heme” iron was given:thinking_face:in the study? iron biomarker measurement refers to some measurement of protein/molecule - File (PNG): image.png

Joan C. Chukwuemeka (16:10:01) (in thread): > :thinking_face::shrug: - File (PNG): image.png

Mkpouto Shedrack (17:56:22) (in thread): > Good luck with your exams@Samreen AftabHope you’ve found someone to collaborate with?!.

Mkpouto Shedrack (18:10:24) (in thread): > @Svetlana Ugarcina PerovicMissed this because I didn’t know the exact time to join, hope it was all it was planned to be.

2024-04-19

Peace Daniel (02:47:19) (in thread): > Good morning@Joan C. ChukwuemekaCorrect me if I’m wrong but according to what I researched and understand, ferrous sulphate seems to be a non-heme iron. If this was what was contrasted, I feel as though dietary iron measurement or something of this sort suits better

Joan C. Chukwuemeka (03:00:02): > Good morning<!here>I’ve added new issues for curation. Do request for them if interested::hugging_face: > * Issue_370 > * Issue_371 > * Issue_372 > * Issue_373 > Happy BugSigDB-ing:seedling:CC:@Svetlana Ugarcina Perovic@Levi Waldron<@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape

Joan C. Chukwuemeka (03:02:09) (in thread): > Good morning@Peace DanielYea,That was stated. > Currently, there’s nothing on BugSigDB drop down that’s quite correct/matches the type of Iron used in the study, hence, I was trying to clarify from the mentors If “******dietary heme iron intake measurement********”which is refers to a form of iron intake measurement, would be of better choice over “******iron biomarker measurement”, **which refers to* measurement of some molecule e.g. protein or metabolite which is used as a measure of iron metabolism*CC:@Glorious Katushabe - Attachment: Attachment > Okay @UBNSEMS3S, What of **dietary heme iron intake measurement*“* which is a form of iron intake measurement, though not”heme” iron was given :thinking_face:in the study? iron biomarker measurement refers to some measurement of protein/molecule

Peace Daniel (03:07:21) (in thread): > Yes, I get you.@Joan C. ChukwuemekaI was wondering if this form of iron intakedoesn’tactually mean a form of heme iron intake per the conditions name. WhatI’mtrying to clarify is if this conditionwouldn’tbe mistaken as a form of heme iron was supplemented rather than non-heme

Bolanle Wahab (03:43:19): > Good morning everyone > Please I’d like your reviews on the curation@Oluwatomisin Omojokunand I worked on especially the signatures in experiment 2, 5 and 6. > Figure 7 and supplementary material 3 had differential abundance results of the experiments but I curated results from figure 7, I just need to be sure I curated everything. > Thank you.https://bugsigdb.org/Study_912 - Attachment (BugSigDB): Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics - BugSigDB > BACKGROUND: The importance of the gut microbiota for physiological processes in mammals is well established, but the knowledge of their functional roles in fish is still limited.

USLACKBOT (03:46:54): > This message was deleted.

Joan C. Chukwuemeka (04:00:16) (in thread): > @Rahila-meI tried searching for just that signature, for Experiment 4 (https://bugsigdb.org/Study_943/Experiment_4/Signature_1), and it came up, But no curator/revision editor name. See attached Image. Could it have been sent for deletion before?:thinking_face: - Attachment (BugSigDB): Study 943/Experiment 4/Signature 1 > Source: FIG 3 (A1) Description: The LEfSe analysis was performed among three groups and found that compared with inflammatory depression group and Non-inflammatory… - File (JPEG): IMG_20240419_085538.jpg

Rahila-me (04:08:31) (in thread): > @Joan C. Chukwuemekait was never sent for deletion but it took long to load when i saved it, maybe that’s why.

Joan C. Chukwuemeka (04:15:25) (in thread): > Okay@Rahila-me, not to worry, I believe the mentors will have a fix for it.:pray:

idiaru Angela (04:16:26) (in thread): > Hey@Rahila-meI had this problem yesterday. I think there’s a bug. It resolved though when I edited and resaved it.

Joan C. Chukwuemeka (04:18:22) (in thread): > Oh.. okay. Nice to know@idiaru Angela:+1:@Rahila-meyou could follow the link for just the signatures that I shared and try to edit, as@idiaru Angeladid.

Rahila-me (04:29:40) (in thread): > @Joan C. Chukwuemeka@idiaru Angelayea, it must be a bug, it works now, i have my signature 1 back, Thanks to you both

Joan C. Chukwuemeka (04:30:00) (in thread): > Glad it did…:smiley:

Peace Daniel (04:48:38) (in thread): > Well done on your curation@Bolanle WahabI would give your study another review:blush:

Victoria (Burah) Poromon (06:30:41) (in thread): > Well done! > I’ll also take a look at it

Svetlana Ugarcina Perovic (06:57:38) (in thread): > @Mkpouto Shedrackrecordings will be available soonhttps://www.youtube.com/channel/UCJ345jOp6hOnzP0Ja2-hw6A - Attachment (YouTube): Microbiome Virtual International Forum > Microbiome Virtual International Conference (MVIF) is a recurring bite-sized alternative to multi-day microbiome conference: > Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference! > > Every month there is an event, with a great speaker from the microbiome field and 3 selected talks and many research highlights! > Follow the event live… > But if you miss it… in this channel you will find the videos of the events!

Scholastica Urua (07:40:20) (in thread): > Thank you@Svetlana Ugarcina Perovic

Bolanle Wahab (07:48:19) (in thread): > Thank you:heart:@Peace Daniel@Victoria (Burah) Poromon

Svetlana Ugarcina Perovic (08:04:48) (in thread): > Such an important question! And I do not have an answer, although I really like yours. Let me think…

Aleru Divine (08:07:37) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:hugging_face:

Svetlana Ugarcina Perovic (08:18:40): > Hmmm, but what I know is that I really like my Fridays. I keep them meeting-free and usually doing something special, cooking for my family and friends, trying something new (e.g. checking out a new local cafe) etc.Happy Friday ALL!

Mildred Anashie (08:19:47) (in thread): > Sounds great….Happy Friday:blush:

Rahila-me (08:27:35) (in thread): > @Svetlana Ugarcina Perovicnice, happy Friday too

Aleru Divine (08:40:34) (in thread): > This is a really cool@Svetlana Ugarcina Perovic, happy Friday to you too and everyone:hugging_face:

idiaru Angela (08:42:32) (in thread): > Happy Friday too:blush:@Svetlana Ugarcina Perovic

Peace Daniel (09:07:19) (in thread): > This is beautiful,happy Friday, happy weekend:blush:

Joan C. Chukwuemeka (09:12:44) (in thread): > This is lovely@Svetlana Ugarcina Perovic, making time for Family and friends is quite essential.:smiling_face_with_3_hearts:Happy Friday to you too and everyone here

Glorious Katushabe (09:20:23) (in thread): > Happy Friday too@Svetlana Ugarcina Perovicand everyone here

Scholastica Urua (09:47:08) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:hugging_face:

Victoria (Burah) Poromon (10:01:14) (in thread): > Fridays also come with a relaxing feeling:face_exhaling::face_exhaling:Petition to add it to the weekends:joy::joy:Happy Friday Everyone!:hugging_face:

Victoria (Burah) Poromon (10:37:06) (in thread): > Hi@Bolanle Wahabwell done on your curation. > I’ve gone through it and these are what i noticed: > 1. You can changeRuminicoccaceae to* Oscillospiraceae*In experiment 5. Also, I believe that section is a little case sensitive,aliivibriois correct but capitalise the first letter. > 2. As for if you curated everything,I’mstill looking at the table. But i noticedit’sshowing relative abundance and not differential. Same as Figure 7. > 3. Please take a look at supplementary material 4, that looks like differential abundance.

Barakat Akinsiku (10:39:48) (in thread): > Happy Friday@Svetlana Ugarcina Perovicand everyone

Victoria (Burah) Poromon (10:54:51): > Hi everyone > I just finished curating a study > > I’d really appreciate reviews on it. > Specific areas: > 1. Alpha diversity result > 2. The body site > 3. Signature 2 in experiment 2, do you think I should delete that? Or leave it? I’m conflicted a bit, ifit’sneeded in the curation or not. > Thank you so much.https://bugsigdb.org/Study_940 - Attachment (BugSigDB): Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients - BugSigDB > The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19).However, the oral fungal microbiota in COVID-19 remains unclear.This article aims to characterize the oral mycobiome in COVID-19 and recovered patients.

Mildred Anashie (10:57:03) (in thread): > Well done on your curation@Victoria (Burah) PoromonI’lltake a look

Victoria (Burah) Poromon (10:58:13) (in thread): > Thank you so much@Mildred Anashie

Mildred Anashie (11:11:31) (in thread): > I’mthinking Surface of tongue is a much better fit to Mucosa of the tongue:thinking_face:@Victoria (Burah) Poromon

Victoria (Burah) Poromon (11:12:05) (in thread): > Okay > Let me see if that works

Victoria (Burah) Poromon (11:13:05) (in thread): > It does! > Thank you@Mildred Anashie

Bolanle Wahab (11:30:29) (in thread): > @Victoria (Burah) PoromonThank you so much, one of the mentors suggested I used figure 7, and it was clearthat’swhy I used it and aliivibriowasn’tin the dropdown atall

Victoria (Burah) Poromon (11:34:27) (in thread): > Oh okay, I see. > About aliivibrio,I’msaying you should change it to “Aliivibrio” check it out.If you don’t find it then just use the ID: 511678

Bolanle Wahab (11:42:00) (in thread): > Most of the time, the signature just comes up regardless butI’dtry this , thank you:heart:

Victoria (Burah) Poromon (11:43:01) (in thread): > Okay then:heart::heart:You’rewelcome

Peace Daniel (11:50:50) (in thread): > Well done on your curation@Victoria (Burah) Poromon

Mildred Anashie (11:53:55) (in thread): > Soyou might have more than 2 experiments but without signatures though because I can see significant alpha diversity results, still trying to figure them outI’mthinking if this is confirmed then they should all be recorded@Victoria (Burah) Poromon

Aleru Divine (11:54:45) (in thread): > Hi@Victoria (Burah) Poromon, well done on your curation.:hugging_face:Your alpha diversity measures are correctly curated.:+1:Surface of the tongue is perfect:+1:

Peace Daniel (11:56:20) (in thread): > For your experiment 2, I’m not sure Covid 19 should be group 0 > But the signatures look fine

Aleru Divine (11:58:15) (in thread): > @victoria, figure 4 is missing 1 experiment which is control vs post covid-19 > > I see significant results in the alpha diversity measures.

Peace Daniel (11:58:54) (in thread): > There should be 3 experiments from whatI’veseen so far

Mildred Anashie (12:00:49) (in thread): > Also the alpha diversity results in Figure 3 a and b is showing significant resultsShouldn’tthose be curated?:thinking_face:Idon’tsee differential abundance though

Victoria (Burah) Poromon (12:02:38) (in thread): > @Aleru DivineSo that means I need to add a new experiment right? > Because I believe the study did a contrast between covid-19 group and post-covid group

idiaru Angela (12:03:06) (in thread): > Hey@Victoria (Burah) Poromonwelldone on this curation > As regards the curation of the figure below, I think it might be better to take a one against all approach in the curation of this figure. See Chloe explain how such figures should best be curatedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1687877254481389?thread_ts=1687872680.081639&cid=C04RATV9VCY - Attachment: Attachment > The default for LEfSe is one against all I believe so I would curate this as: > 1. Non-constipation PD (group 1) vs. constipation PD AND controls (group 0) > a. Curate blue bars as increased > 2. Constipation PD (group 1) vs. non-constipation PD AND controls (group 0) > a. Curate red bars as increased > 3. Non-constipation AND constipation PD vs. controls (group 0) > a. Curate green bars as decreased - File (JPEG): Screenshot_20240419_165858_Samsung Internet.jpg

Mildred Anashie (12:04:31) (in thread): > If you look at the lines above the alpha diversity resultsyou’llsee the comparisons done and it shows significant alpha diversity for the control and post Covid 19@Victoria (Burah) Poromon

Victoria (Burah) Poromon (12:04:48) (in thread): > @Mildred AnashieI saw that too, and Ididn’tcurate it since itwon’thave signatures. > Do you think I should curate it still?

idiaru Angela (12:05:07) (in thread): > This means that you’d have 3 experiments@Victoria (Burah) PoromonControl vs Covid 19 and post Covid > Control and Covid 19 vs Post covid > Control and post covid vs Covid 19

idiaru Angela (12:05:55) (in thread): > Yes@Victoria (Burah) Poromonall experiments with significant alpha diversity should be curated even though they have no signatures

Mildred Anashie (12:06:18) (in thread): > I’mthinking since their alpha diversities are showing significance they should be curated > > If they were unchanged then they could be left out in my opinion@Victoria (Burah) Poromon

Aleru Divine (12:06:52) (in thread): > @Victoria (Burah) Poromonyou already compared covid vs post covid.Add one more comparing control vs post covid.

Peace Daniel (12:09:22) (in thread): > Hi@Bolanle WahabI mentioned to@Oluwatomisin OmojokunIdidn’tsee any confounders in this study earlier, could you point me to it?

Victoria (Burah) Poromon (12:12:05) (in thread): > Okay > Thank you all so much!@idiaru Angela,@Mildred Anashie,@Aleru Divine,@Peace DanielI’ll have another look at this. > > I think I alsodidn’tcurate some groups because the study showed no difference in alpha diversity. > I’ll read it through again to be very sure. > > Thank you all again!

Aleru Divine (12:15:08) (in thread): > For figure 3,@Mildred Anashieand@Victoria (Burah) Poromonplease ignore control vs covid because it’s the same everywhere. > > Only curate > control vs SC and > covid-19 vs SC > > There are significant alpha diversity results in this case. > > About the differential abundance, see this excerpt “Moreover, the abundance of differential oral fungi in the SC group was basically consistent with that of the COVID-19 group, but significantly different from the control group (Figure 3h) (Table S15, Supporting Information).” > Maybe table S15 will have data on the differential abundance between SC and Control.

Peace Daniel (12:15:19) (in thread): > @Victoria (Burah) PoromonAlways remember group 0 should be closest to the control, I.e the one with less severity in the comparison

Peace Daniel (12:17:50) (in thread): > Once again, well done on your curation. > My only area of conflict is the confounders > > And the signatures@Victoria (Burah) Poromonpointed out

Mildred Anashie (12:18:49) (in thread): > The issue is the supplementary information does not show Figure S15@Aleru Divine

Aleru Divine (12:21:57) (in thread): > It’s a table S15@Mildred Anashie:sweat_smile:I’msorry.And the table does not seem like it can be curated > Please check it out@Mildred Anashie@idiaru Angela@Peace Daniel@Victoria (Burah) Poromon:sleepy:.

Mildred Anashie (12:22:46) (in thread): > YesI’veseen it:joy::joy::smiling_face_with_3_hearts:@Aleru Divine

Peace Daniel (12:24:47) (in thread): > Agreed@Aleru Divine

Peace Daniel (12:25:44) (in thread): > Is it my eyes or how many pages are in this supplemental ??:flushed:

Aleru Divine (12:26:09) (in thread): > It’s not your eyes:sleepy::tired_face:🫨🫨🫨🫨🫨:sob:

Victoria (Burah) Poromon (12:26:31) (in thread): > A lot of pages:joy::joy::joy::joy:

Mildred Anashie (12:26:45) (in thread): > There are a lot:joy:

Victoria (Burah) Poromon (12:27:01) (in thread): > I almost cried trying to scroll down:joy::joy:

Peace Daniel (12:27:11) (in thread): > Wow, we keep seeing new things. > I was surprised cuz seriously??

Peace Daniel (12:28:01) (in thread): > Well done on your curation again@Victoria (Burah) PoromonYour study is the motivation I needed to start mine:man-cartwheeling::smiling_face_with_smiling_eyes_and_hand_covering_mouth:

idiaru Angela (12:45:02) (in thread): > Took a good look at s15 and it definitely isn’t curatable. Over 200 pages of tables though:sneezing_face:

Aleru Divine (12:52:35) (in thread): > :sleepy:also the grouping,I don’tsee anything on SC, just different controls I think.

idiaru Angela (13:01:54) (in thread): > Exactly@Aleru Divine

Victoria (Burah) Poromon (13:23:34) (in thread): > @idiaru AngelarightIt’seven 551 pages > > Theydidn’tspare any detail:sweat_smile:

idiaru Angela (13:33:25) (in thread): > Well done@Victoria (Burah) Poromon:raised_hands:

Victoria (Burah) Poromon (13:43:54) (in thread): > Thank you so much everyone for your input > Really appreciate it. > > AndI’veread the paper again. The explanation after figure 3 states the reason for the alpha diversity analysis between covid-19, sc, post-covid-19 and scr. > > So according to the study, “The fungal community distribution between covid-19 and Sc’s as well as post-covid-19 and Scr’s, was observed with no significant difference” > > They went ahead to say they speculate that Sc’s could be judged as Covid-19. > > I think this also clarifies the number of experiments I should have right? > Which is 3

idiaru Angela (14:08:13) (in thread): > Yeah@Victoria (Burah) Poromongood work

Bolanle Wahab (16:49:10) (in thread): > @Peace DanielI also found out thereweren’tany and forgot to remove them. > Thank you:heart:

Peace Daniel (17:08:11) (in thread): > That’s fine.You’rewelcome@Bolanle Wahab

Peace Daniel (17:28:05): > Good day all, I have some questions regarding study 892https://bugsigdb.org/Study_892@Oluwatomisin Omojokunrequested we make corrections togetherI feel as though fig 2A has statistical significance but I’d like to confirmFor Signatures in fig3:bacillus (decreased)Clostridium (increased)Peptoclostridium (decreased)Turicibacter(increased)I’d like to confirm this too and the groupsthey were increased/decreased inas I can’t clearly see the greens and orange - Attachment (BugSigDB): PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation - BugSigDB > BACKGROUND: The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals.

Peace Daniel (17:29:18) (in thread): > On a second thought,I’mwondering if bacillus and Turicibacter were significant with the description in the image

2024-04-20

Scholastica Urua (02:15:11) (in thread): > Hello@Peace Danielyou’re right, fig 2A is statistically significant so I think it’s curatable; > QIN vs QXL > MIN vs QXL > > For fig 3A however, I can’t figure out which is green or orange in the image yet:worried:. If I do, will let you know…

Peace Daniel (02:16:47) (in thread): > Thank you@Scholastica Uruathese are the groups I had in mind as well > > The image is not very clear,it’sjust the big and small circles that are quite visible

Scholastica Urua (02:18:06) (in thread): > Yeah, I noticed. The image is not very clear.

Aleru Divine (07:33:26): > Hello everyone and Happy Weekend! > > I am currently curating this studyhttps://www.spandidos-publications.com/10.3892/ol.2024.14368and I need your opinion on the signatures. > I know that Figure 4 can be curated but I want to be sure that Figure 5 can also be curated (The figures have correlations too). > > This excerpt also confirms that I should curate it. But I need your opinion:pray:“A species composition heatmap was then used to discover the changed phyla between LM group and NLM.” > > Thank you so much! - Attachment (spandidos-publications.com): Fusobacteria alterations are associated with colorectal cancer liver metastasis and a poor prognosis > Liver metastasis is a major cause of mortality in patients with advanced stages of colorectal cancer (CRC). The gut microbiota has been demonstrated to influence the progression of liver diseases, potentially providing novel perspectives for diagnosis, treatment and research. However, the gut microbial characteristics in CRC with liver metastasis (LM) and with no liver metastasis (NLM) have not yet been fully established. In the present study, high‑throughput 16S RNA sequencing technology was employed, in order to examine the gut microbial richness and composition in patients with CRC with LM or NLM. A discovery cohort (cohort 2; LM=18; NLM=36) and a validation cohort (cohort 3; LM=13; NLM=41) were established using fresh feces. In addition, primary carcinoma tissue samples were also analyzed (LM=8 and NLM=10) as a supplementary discovery cohort (cohort 1). The findings of the present study indicated that the intestinal microbiota richness and diversity were increased in the LM group as compared to the NLM group. A significant difference was observed in species composition between the LM and NLM group. In the two discovery cohorts with two different samples, the dominant phyla were consistent, but varied at lower taxonomic levels. Phylum Fusobacteria presented consistent and significant enrichment in LM group in both discovery cohorts. Furthermore, with the application of a random forest model and receiver operator characteristic curve analysis, Fusobacteria was identified as a potential biomarker for LM. Moreover, Fusobacteria was also a poor prognosis factor for survival. Importantly, the findings were reconfirmed in the validation cohort. On the whole, the findings of the present study demonstrated that CRC with LM and NLM exhibit distinct gut microbiota characteristics. Fusobacteria detection thus has potential for use in predicting LM and a poor prognosis of patients with CRC.

Aleru Divine (07:36:49) (in thread): > I curated the condition as > “Metastatic colorectal cancer” and not just “colorectal cancer” > > The reason is, even though the condition being studied here is indeed colorectal cancer (CRC), there is a specific focus on its metastatic aspect to the liver. > > Is this okay?:pray:

idiaru Angela (07:37:27) (in thread): > I’m not sure how to determine increase and decrease from Fig 5. How can you do that@Aleru Divine:thinking_face:

Aleru Divine (07:39:39) (in thread): > @idiaru Angela:sweat_smile:I used the colors - File (JPEG): IMG_8223

Mildred Anashie (07:41:09) (in thread): > So I think it should be curated@Aleru DivineIf you look at the top of D for example you will see that both groups are represented (LM as purple and NLM as Red) > > So you can also see the increase and decrease taxas for each group using the color codes

idiaru Angela (07:43:24) (in thread): > I see now. Thanks@Aleru Divine@Mildred AnashieFor the condition I think its close enough. There is no condition that explicitly states liver metastasis

Mildred Anashie (07:43:34) (in thread): > Increase will be those under LM represented in I think green:sweat_smile:and the decrease will be those represented in the gold like color and it’s same for the NLM in my opinion

Aleru Divine (07:50:51) (in thread): > The abundance of some taxa represented in both figures is the same. For example, Proteobacteria in cohort 1 is decreased while Bacteroidetes is increased for LM in both figures.:hugging_face:Thank you so much@idiaru Angela@Mildred Anashie:people_hugging::heart:

Mildred Anashie (07:56:55) (in thread): > You are welcome:hugging_face:I think since they are different cohorts it’s okay to curate that way

Barakat Akinsiku (09:20:35) (in thread): > Yeah@Aleru DivineI think Metastatic colorectal cancer is a good term for the condition

Aleru Divine (09:28:45) (in thread): > Thank you@Barakat Akinsiku:heart:

Barakat Akinsiku (09:51:02): > Hi everyone, good afternoon and hope we’re having a great day:blush:I just completed this study and would love peer reviewshttps://bugsigdb.org/Study_947Also for Experiment 2 Signature 1, I inputed Anaerovorocaceae in place of Mogibacteriaceae following the given synonym here(not homotypic but heterotypic)https://lpsn.dsmz.de/family/mogibacteriaceaeI hope this is in order - Attachment (BugSigDB): Social isolation induces intestinal barrier disorder and imbalances gut microbiota in mice - BugSigDB > Social isolation, a known stressor, can have detrimental effects on both physical and mental health. - File (PDF): social isolation mice.pdf

idiaru Angela (10:07:48) (in thread): > Hi@Barakat AkinsikuHeterotypic synonyms are in order too. I’ll give the study a look and give feedback

Mildred Anashie (10:08:14) (in thread): > Yes@Barakat AkinsikuHeterotypic synonyms work just fine > Well done:clap:

Barakat Akinsiku (10:21:54) (in thread): > Thank you@idiaru Angela@Mildred Anashie

Peace Daniel (10:41:51) (in thread): > Well done@Barakat AkinsikuI’ll take a look at your study > > Looks good to me,well done:purple_heart:

Barakat Akinsiku (11:19:20) (in thread): > Thank you:hugging_face:@Peace Daniel

Blessing Ene Anyebe (11:55:37) (in thread): > Such a lovely thread! Beautiful to read guys.:hugging_face::orange_heart:One thing I also usethat’snot mentioned is changing my scenery. > > Once everything is getting too hazy and stressful I either take a short trip or change my work environment for period of time. > > Nature works well for me. > * Going to the park with my laptop to work, > * going to a public diner or cafe. > That change gets me in the grove back again. > > I also do fun activities. (Hangout with friends. games, and so on)

Scholastica Urua (13:57:05) (in thread): > Well done on your curation@Barakat AkinsikuHeterotopic synonyms are also fine.

Svetlana Ugarcina Perovic (16:00:20) (in thread): > This study was reviewed and corrected. FYI, 3A is indeed a very challenging figure, but from the figure caption it seems you can focus just on the taxa with asterisks, then the color of bubbles. For example, there are a couple of greenPeptoclostridium, which are recorded asPeptoclostridium spp.increased in leaf-eating seasons. On the other hand, a genus likeErysipelotrichales, which has asterisks but no colors, doesn’t seem curateable because you don’t know which condition they’re increased in.

Peace Daniel (16:05:58) (in thread): > Yes,that’strue@Svetlana Ugarcina PerovicThe image is not very clear too and the colors used are not good contrasts soit’sharder to understand. > > Initially, I thought the bigger the circle the more the abundance but there are smaller bubbles inside too

2024-04-21

Mildred Anashie (07:34:02): > Hi everyone > > Happy Sunday:blush:Ijust finished curating this study and I’ll appreciate your reviews > Especially for the condition and the number of experiments (found just one and I thinkthat’sall there is but I need other eyes to confirm this)https://bugsigdb.org/Study_1025Thank you in anticipation:hugging_face: - Attachment (BugSigDB): Effects of alcohol on the composition and metabolism of the intestinal microbiota among people with HIV: a cross-sectional study - BugSigDB > OBJECTIVES: Alcohol consumption is not uncommon among people with HIV (PWH) and may exacerbate HIV-induced intestinal damage, and further lead to dysbiosis and increased intestinal permeability.

Aleru Divine (07:46:52) (in thread): > Hi@Mildred Anashiewell done on your curation.:clap:I agree with the number of experiment you’ve curated. > > For the condition, the study aimed to determine the changes in the faecal microbiota and its association with alcohol consumption in HIV-infected patients not necessarily measuring alcohol consumption. So “gut microbiome measurement” is a more suitable condition in my opinion.https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0007874I’dlike to also know what others think. - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Mildred Anashie (07:51:53) (in thread): > Thank you@Aleru DivineWhat they did was to determine how the composition of the gut microbiota is altered in HIV-Infected individuals who consume alcohol compared to those who do not > > This was the basis for the condition I choose:thinking_face:

Aleru Divine (07:53:53) (in thread): > Okay. I just thought sinceit’schanges in gut Microbiota,it’dbe gut microbiome measurement.But I do get your point.

idiaru Angela (07:56:04) (in thread): > For the condition@Mildred AnashieI definitely agree with what you’ve picked. Alcohol consumption is the differential measurement between the two groups

Mildred Anashie (07:57:38) (in thread): > I totally understand why you thought so@Aleru DivineIt was confusing for me before I finally decided on picking that and I still needed others opinions to be as accurate as possible

Mildred Anashie (07:58:02) (in thread): > Thanks a lot@Aleru Divine@idiaru Angela:heart:

Aleru Divine (07:59:04) (in thread): > Thank you@idiaru Angela,@Mildred Anashiethank you:heart:It can be a lot confusing sometimes.:sleepy:

Scholastica Urua (07:59:17) (in thread): > Hello@Mildred Anashieyou are right about the number of experiment, its just one. > Also the study is contrasting drinking status soAlcohol consumption measurementis a suitable condition. > Well done on your curation

idiaru Angela (08:01:28) (in thread): > I also only identified one experiment. Welldone on this curation@Mildred Anashie

idiaru Angela (08:16:38) (in thread): > Hey@Barakat Akinsiku. Well done on this curation. Sorry this feedback is coming a little later After going through the study I made an observation, Lefse by principle doesn’t control for cofounders so I don’t think sex can be a cofounder controlled for.

Scholastica Urua (08:19:52) (in thread): > That’s@idiaru AngelaLEfSe doesn’t so I don’t think there should be confounders in the curation.

Mildred Anashie (08:30:11) (in thread): > I agree@idiaru AngelaIdidn’tcome across that while scanning through

Victoria (Burah) Poromon (09:26:11) (in thread): > Well done@Mildred AnashieI think the condition you entered is perfect too.

2024-04-22

Svetlana Ugarcina Perovic (05:03:11): > Good morning:potted_plant:all your messages answered:white_check_mark:please do ping me if I missed one or two:upside_down_face:Have a good week and keep up the good BugSigDB-ing!

idiaru Angela (05:05:13) (in thread): > Good morning@Svetlana Ugarcina Perovic. Have a great week too:cherry_blossom:. > Happy BugSigDB-ing everyone:saluting_face:

Aleru Divine (05:15:06) (in thread): > Good morning and thank you@Svetlana Ugarcina Perovic:pray:Wishing you and everyone a good week:sparkles:Happy BugSigDB-ing@idiaru Angela:hugging_face:and everyone!

Mildred Anashie (05:40:24) (in thread): > Good morning@Svetlana Ugarcina PerovicHave a great week too:hugging_face:

Scholastica Urua (05:43:44) (in thread): > Good morning@Svetlana Ugarcina PerovicWishing everyone a happy new week:heartpulse:

Joan C. Chukwuemeka (05:44:37) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thanks for all you do. Have a great week ahead too.

Nana (06:05:38) (in thread): > Good morning@Svetlana Ugarcina PerovicHappy BugSigDB-ing everyone

Joan C. Chukwuemeka (06:11:03): > Good morning all,<!here>Trust our week is on to a good start:blush:So I co-curated thisstudywith@Ikeh Darlington Ikehwhich went well. However, we received author’s feedback that will require adjustment to the curation. > Below is one of the feedback received. > > Author's feedback: > > > 1. Perhaps it is a constraint you have in the way of coding data into the portal but the ANCOM-BC approach was performed with AGE as covariate, not categorical variable (like the Alpha diversity analyses), the plot Fig 4A shows the +-1SD against the mean just to visualize results. > > > My Thoughts: > > > * ******AGE as covariate & Not categorical variable (like the Alpha diversity analyses)******: I know that a covariate is a variable that can influence the outcome you’re measuring, but isn’t the main focus of the study. In this case, they considered the age (AGE) of the macaques as a covariate. In my understanding,******This means they statistically accounted for the potential influence of age on the bacteria abundance when comparing the different groups, and not as a categorical variable with distinct groups (e.g., young vs. old). ****So the experiment/contrasts we curated based on the age will need to be adjusted. > Secondly, It will likely not be curated with the figures we used before, ’cause as they also pointed out,******“the plot Fig 4A shows the +-1SD against the mean just to visualize results.” ****That is just to show how the changes interacted with age.:thinking_face:The challenge is, I’m yet to decipher what the contrasts groups will now be? Thinking If It was between Rich and lean Seasons, and what would form the source of the signatures based on these, cause the ones on the paper for Rich vs Lean Seasons are relative abundances?:thinking_face:Please I’d appreciate our views and help with this. > Link to theStudy - Attachment (BugSigDB): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - BugSigDB > BACKGROUND: During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. - Attachment (BioMed Central): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - Microbiome > Background During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored. Results In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age. Conclusions In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract

Joan C. Chukwuemeka (07:09:44) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy@Aleru Divine@Mildred AnashieHelp needed here Please:pray:

Mildred Anashie (07:19:08) (in thread): > I’lltake a look at this soon@Joan C. ChukwuemekaWell done on your curation

Rahila-me (07:46:17): > @fetlework gubena arageHello good morning, A review has been made on your work that needs some corrections, I would love to collaborate with you on that. Let me know if you need help. Thank you.@Svetlana Ugarcina Perovic

idiaru Angela (08:17:43) (in thread): > Hey@Joan C. Chukwuemeka. Looking at the article, I believe the author might be referring to age being a covariate, so in the definition of groups the mean age should not be included as each group wasn’t contrasted based on that. > This would mean that the current curation is correct but the group would be defined with Early Pre-G amplified with age vs Earlg Pre-GC weakened with age. > It seems experiment expressed in Fig 4A was testing if the effects of Early Pre-GC changed with increasing age or not

Joan C. Chukwuemeka (08:36:22) (in thread): > @idiaru AngelaEarly Pre-G amplified with age vs Early Pre-GC weakened with age?:thinking_face:Note that there are 3 different possible interaction types with age written in the article- it either amplifies with age, is attenuated/decreased with age, or reversed with age. > > When you say Early Pre-GC weakened with age, i’m not clear on that? > And what would form the source of the signatures? - File (PNG): image.png

Joan C. Chukwuemeka (08:46:12) (in thread): > Here’s a case example interpretation of Figure 4a from the paper > 1. Colored bars indicate the effect direction(blue = positive, yellow = negative) of an increase in 1 SD of specific predictors (Early-preGC = 59.3 ng/g; Late-preGC = 67.0 ng/g; PostGC = 52.7 ng/g) estimated at the mean value of age (mean = 4.7 years), and at the mean value of all the other predictors. > 2. Red and black lines indicate the effect estimated at the mean plus 1 SD (red = 7.1 years) and at the mean minus 1 SD (black = 2.3) of age. > > * Case example:Panel A 1st taxon from the right: when subjects are 4.7 years old (mean age),the abundance of Bifidobacterium experiences a 2.3 log-folddecrease with an increase in maternal GCs during the early gestation of 59 ng/g (1SD).When the subjects are 2.3 years old(mean age-1SD), the same increase in maternal GCs is associated with an 0.12 log foldincrease in Bifidobacterium abundance (black whisker). Finally,when the subjects are 7.1 years old(mean age + 1 SD), the same increase in maternal GCs is associated with a 4.6 log-folddecrease in the abundance (red whisker). When the bar is not plotted, the effect of the same increase in maternal GCs at the mean age is 0. > * Taxa showing the black head (estimates at 2.3 years) further from 0 than the red head (estimates at 7.1 years) show an effect that is reduced with age. - File (PNG): image.png

idiaru Angela (08:49:14) (in thread): > “Out of a total of 319 genera analyzed, 23.2% (74) were significantly affected by maternal GCs during early gestation moderated by age (Early-preGCAge). The effect of a 1 SD increase in Early-preGC on differential abundance amplified with Age in 14.1% of the genera (positive: 4.7%; negative 9.4%), decreased with Age in 0%, and reversed in 9.1%. Late prenatal maternal GCs moderated by age (Late-preGCAge) had a similar effect on microbial composition in terms of the number of genera significantly affected (84 out of 319, 26.3%). However, the effect of an increase of 1 SD of Late-preGC amplified with Age in only 1.6% of genera (positive: 0.6%; negative 1%), reduced in 3.8% (positive: 1.0%; negative: 2.8%), and reversed in as many as 20.9% of genera. A total of 85 out of 319 genera (26.6%) were affected by postnatal maternal GC moderated by age (PostGC*Age). The effect of PostGC amplified with Age in 1.9% of genera (positive: 0.3%; negative: 1.6%), weakened with Age in 4.1% (positive: 2.5%; negative: 1.6%) and mainly reversed with age in 20.6% of genera ” > > From this excerpt that refers to the results in Fig 4, I see what you’re saying@Joan C. Chukwuemeka. The issue would now be how to categorise amplified, reduced/decreased, weakened, reversed into groups 0 and group 1.

Joan C. Chukwuemeka (08:52:43) (in thread): > Yes@idiaru AngelaLike now, ForBifidobacterium, Exposure to Increased maternal GCs during the early gestation (Early-preGC), its abundance decreased with age.

idiaru Angela (09:04:02) (in thread): > @Joan C. ChukwuemekaI would say group 0 = weakened, reduced/decreased, reversed with age > while group 1 = amplified with Age. > But I would like other opinions on this

Aleru Divine (11:07:58) (in thread): > Hi@Joan C. Chukwuemeka, well done on your curation. > I will go through the study, your concerns, and the discussion here and then get back to you.:pray:My apologies for taking so long, I have had quite the day.

Mildred Anashie (11:23:10) (in thread): > So this has been really confusing and I’m grateful for the comments I’ve read so far@idiaru Angeladid you see Table 3? > > Idon’tthink the grouping should be based on weakened, amplified, reduced or reversed > > Still trying to figure out the comparisons > I apologize this is taking long@Joan C. Chukwuemeka

Scholastica Urua (11:27:56) (in thread): > This is quite a curation. Well done@Joan C. Chukwuemeka:+1:I’ll take a look…

idiaru Angela (11:30:48) (in thread): > Yes@Mildred AnashieI just looked at table 3, I don’t think it’s contrary to what I suggested

Mildred Anashie (11:39:24) (in thread): > I’m of the opinion that if it is that way then the differential abundant taxas won’t be represented:thinking_face:I’m thinking it should be > Early-preGC vs Age > PostGC vs Age > LateGC vs Age > Offspring GC vs Age > > And we would have the 2.3, 4.7 and 7.1 represented > Does this make sense? > Would the differential abundance be represented using this contrasts?@Joan C. Chukwuemeka

Joan C. Chukwuemeka (11:39:44) (in thread): > I quite understand@Mildred Anashie. Getting a comparison outside the Age interaction is the challenge. I know it’s likely, but deciphering the signature source..

Joan C. Chukwuemeka (11:40:34) (in thread): > They said Age was treated as a covariate.:thinking_face:

Mildred Anashie (11:47:17) (in thread): > Yea@Joan C. ChukwuemekaBut I’m thinking they were checking > For example, the levels of glucocorticoids during early gestation (Early-preGC) and how it interacts with the age of the macaques > > > And they did some sort of linear modeling > > I might not be communicating properly how I’m understanding this though:face_with_peeking_eye:

idiaru Angela (11:57:17) (in thread): > @Mildred Anashieyeah they did some sort of linear modelling with age as covariate. Specifically for Fig 4 tho, what I’m thinking is that they know that maternal GCs affects the microbiome of offsprings, sl they set out to measure how these changes were affected with increasing age of the macaques:thinking_face:

Mildred Anashie (12:13:22) (in thread): > Are we saying the same thing@idiaru Angela:thinking_face:

Joan C. Chukwuemeka (12:20:03) (in thread): > I was thinking perhaps the OffspringGc can be used as a reference but there was no contrast between it and maternal GCs (EarlypreGC, LatepreGC and PostGC).:thinking_face:

Joan C. Chukwuemeka (12:22:49) (in thread): > A covariate is more like a confounder sort of.. which according to them Age was

Mildred Anashie (12:37:09): > Hello<!here>…. I was assigned thisstudyand I’m having issues getting all the Supplementals they keep referring to Figure S1, Table S3, Table S4 and so on but what I can find is just Table S1 and Table S2……Just sharing this here incase anyone has a way around this, Thank you in Anticipation:hugging_face: - Attachment (PubMed Central (PMC)): Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19 > Bacterial-viral interactions in saliva have been associated with morbidity and mortality for respiratory viruses such as influenza and SARS-CoV. However, such transkingdom relationships during SARS-CoV-2 infection are currently unknown. Here, we aimed …

idiaru Angela (12:44:32) (in thread): > It seems only Table S1 and S2 are availablein the supplemental file. Tried downloading it from other journals but got the exact same file in 3 different journals only containing Table S1 and S2

Joan C. Chukwuemeka (12:45:41) (in thread): > Yea@idiaru Angelasame here

Mildred Anashie (12:53:13) (in thread): > Okay > > Thank you,I’lllikely work with what is available then

Joan C. Chukwuemeka (13:08:32) (in thread): > All statistical analysis and table and figure generation were performed using R version 3.6.1, and R Markdown files detailing all statistical analyses and visualizations are available in a public GitHub repository (https://github.com/mka2136/covid19_saliva_microbiome).So, got this from the repo@Mildred Anashiemaybe check it out - File (Excel Spreadsheet): DESeq2_combined.xlsx - File (Excel Spreadsheet): metadata.xlsx

Aleru Divine (13:46:12) (in thread): > Hey everyone, well done on the inputs so far, this is indeed a confusing one:sweat_smile:I think the contrast groups should be the ages denoted as black and red. This means we’ll focus on comparing offspring at 2.3 years old (mean age minus 1 standard deviation) and 7.1 years old (mean age plus 1 standard deviation). > > Using the excerpt below as an example, > “Case example: Panel A 1st taxon from the right: when subjects are 4.7 years old (mean age), the abundance of Bifidobacterium experiences a 2.3 log-fold decrease with an increase in maternal GCs during the early gestation of 59 ng/g (1SD). When the subjects are 2.3 years old (mean age-1SD), the same increase in maternal GCs is associated with an 0.12 log fold increase in Bifidobacterium abundance (black whisker). Finally, when the subjects are 7.1 years old (mean age + 1 SD), the same increase in maternal GCs is associated with a 4.6 log-fold decrease in the abundance (red whisker). When the bar is not plotted, the effect of the same increase in maternal GCs at the mean age is 0. Taxa showing the black head (estimates at 2.3 years) further from 0 than the red head (estimates at 7.1 years) show an effect that is reduced with age” > > The excerpt explains how the abundance of Bifidobacterium changes in response to increased maternal glucocorticoids (GCs) during early gestation at different ages of offspring. I think that the contrast groups would be Offspring at 2.3 years old (younger group-black) experiencing increased/decreased maternal GCs during early gestation and the offspring at 7.1 years old (older offspring-red) experiencing increased/decreased maternal GCs during early gestation. > > The case example shared in the paper compares the abundance of Bifidobacterium in these two contrast groups, and we can observe how the effect of increased maternal GCs during early gestation differs between younger and older offspring. > > This is what I think, but then yellow indicates the negative direction which naturally means a decrease in maternal GCs unless I am missing something or there was a slight mistake. > > Does this make any sense?:grimacing:

idiaru Angela (14:02:03) (in thread): > Yes it does indeed@Aleru Divinebut I think that’s what Joan already curated previously, but the author says the age is a covariate and not the categorical variable:thinking_face:

Scholastica Urua (14:45:33) (in thread): > What your saying does make sense@Aleru DivineI looked at the article and it was pretty confusing:disappointed_relieved:. Well done you guys

Aleru Divine (14:49:38) (in thread): > Okay@idiaru Angela:thumbsup:So, from theauthor’sfeedback, “the plot Fig 4A shows the +-1SD against the mean just to visualize results.” I think thatwould leave us with with the positive and negative maternal glucocorticoid levels/direction as the contrasting groups.Considering the age is not a variable.

idiaru Angela (15:25:28) (in thread): > Makes a lot of sense@Aleru Divine:saluting_face:

Aleru Divine (16:17:02) (in thread): > Yeah@idiaru Angela, waiting on other opinions though.

Joan C. Chukwuemeka (16:30:54) (in thread): > Yea@Aleru Divinethat’s like what we initially did. However, the feedback that Age is a covariate seems to point in another direction without Age in the comparison. > > Thanks for your input though..

2024-04-23

Joan C. Chukwuemeka (05:10:57) (in thread): > Good morning all, still trying to get this done.@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovicplease I need your help here

Svetlana Ugarcina Perovic (06:04:48) (in thread): > Email sent. Sharing it with you to see how we are contacting and requesting the supplementary material. - File (PNG): Screenshot 2024-04-23 at 12.03.40.png

Svetlana Ugarcina Perovic (06:09:23) (in thread): > @Joan C. Chukwuemekaleave it as it is curated with the note from the author.

idiaru Angela (06:10:31) (in thread): > Thank you@Svetlana Ugarcina Perovic. This is a useful template for future use:blush:

Svetlana Ugarcina Perovic (06:11:30) (in thread): > Also made the other 2 points noted as the author advised “to update”.

Svetlana Ugarcina Perovic (06:12:50) (in thread): > This is a very challenging task. Good work! And good discussion! What we are curating is the content from the paper. Do remember that. If it is not clear, then it is not clear:slightly_smiling_face:

Joan C. Chukwuemeka (06:32:00) (in thread): > Alright, Thanks a lot@Svetlana Ugarcina Perovic. Quiet a relief:gratitude-asl:

Joan C. Chukwuemeka (06:55:26) (in thread): > Thanks a lot@Svetlana Ugarcina Perovic. > Saving This for when the need arises.:blush:

Svetlana Ugarcina Perovic (06:59:21) (in thread): > Here is a template that you can edit for your purposehttps://bugsigdb.org/Requests - Attachment (BugSigDB): Requests > …

Aleru Divine (07:02:36) (in thread): > Thank you for clearing this up:pray:@Svetlana Ugarcina Perovic@Joan C. ChukwuemekaI feel ya:sweat_smile:

Mildred Anashie (07:04:24) (in thread): > Thanks alot@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (07:05:21) (in thread): > Thank you so much@Svetlana Ugarcina PerovicI’mgrateful:relaxed::hugging_face:

Aleru Divine (07:07:23) (in thread): > @Mildred Anashie:flushed:I put this up for curation. I didn’t download and check the supplemental file. I genuinely apologize for this. > > Thank you so much@Svetlana Ugarcina Perovicfor requesting the missing supplemental materials and sharing the template.:pray:It sure will come in handy.

Mildred Anashie (07:09:41) (in thread): > It’stotally fine@Aleru Divine:hugging_face:I think some papers are like that with incomplete supplementals,let’shope we get a positive response from the Authors:hand_with_index_and_middle_fingers_crossed:

Aleru Divine (07:32:07): > Good day everyone! I hope you all are having a great day. > I recently completed this study with@Samreen Aftaband we would appreciate it if you gave it a peer review. > > Link to study:https://bugsigdb.org/Study_905Thank you so much! - Attachment (BugSigDB): Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome - BugSigDB > BACKGROUND: There is mounting evidence for a connection between the gut and Parkinson’s disease (PD).Dysbiosis of gut microbiota could explain several features of PD.

idiaru Angela (08:14:23) (in thread): > Well done@Samreen Aftab@Aleru Divine. Would give it a review

Barakat Akinsiku (08:17:29) (in thread): > Thank you for sharing the template@Svetlana Ugarcina Perovic

Mildred Anashie (08:44:05) (in thread): > Well done@Aleru Divine@Samreen Aftab:clap:

Scholastica Urua (08:51:13) (in thread): > Well done@Aleru Divine@Samreen Aftab:+1:

Svetlana Ugarcina Perovic (09:16:47) (in thread): > @Aleru Divine@Mildred Anashieno worries! If I would be the author of incomplete suppl. material I would be happy to be informed about it. Probably they are not aware of it. So, I’m very optimistic in getting response soon.

Nana (09:37:10) (in thread): > Well done to you too

Rahila-me (09:37:43) (in thread): > Aiit, i will check it out

Joan C. Chukwuemeka (10:18:35) (in thread): > Well done on the curation@Aleru DivineIs Parkinson disease status not among the confounders based on the excerpt below?:thinking_face: - File (PNG): image.png

Barakat Akinsiku (10:24:38) (in thread): > Well done on your curation@Aleru Divineand@Samreen Aftab

idiaru Angela (10:47:20) (in thread): > Hey@Aleru Divine. Well done! > Looking at the signatures of Experiment 1 and 2, they seem to be the same thing. So my suggestion is, why not include them into 1 signature since they have the same group 0 and add to the group 1 definition of Experiment 1 to include that of Experiment 2 instead of having 2 signatures in the same study that are exactly same:thinking_face:

Aleru Divine (10:57:55) (in thread): > Thanks everyone:blush:

Aleru Divine (10:59:47) (in thread): > @Joan C. ChukwuemekaI did see that, but while I was curating the signatures, the description of the table was just a bit different. > > Here is the excerpt “(B) All PD vs. controls adjusted for sex, age, geographic site, dietary fruit/vegetable, and transit time, tested using GLM > (C) Patients who were not on COMT inhibitors or anticholinergic drugs (AC) vs. controls, adjusted for sex, age, geographic site, dietary fruit/vegetable, and transit time, tested using GLM”

Aleru Divine (11:02:14) (in thread): > @idiaru AngelaI’lldo that and leave a note.I was actually concerned about it.Thank you:pray:

idiaru Angela (11:03:36) (in thread): > You’re welcome!:blush:@Aleru Divine

Aleru Divine (11:05:09) (in thread): > @idiaru Angelawhat about the samples size?It’snot the same for both.

idiaru Angela (11:09:25) (in thread): > @Aleru DivineCan there be 2 sample sizes?:thinking_face:The sample size for group 0 is same > The only difference would then be the sample size for group 1 > Or would it be better left as 2 experiments:thinking_face:For me, I think I would add the definition of group 1a and 1b being PD patients Excluding COMT & AC users, then add the sample sizes for both and then leave a note? > I’m not sure if that’s a perfect solution though

Aleru Divine (11:11:46) (in thread): > I don’t think there can be 2 sample sizes.Nowthere’sthe confusion.

Aleru Divine (11:18:57) (in thread): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandyplease help:pray:In this study that I and@Samreen Aftabcurated, the signatures are the same for both experiment 1 and 2.A good suggestion was curating as one experiment and leaving a note regarding the group names but another confusion is in the sample sizes.For the experiment 1, > Group 1 name: Parkinson’s Disease Patients > Group 1 sample size: 197For the experiment2,Group 1 name: Parkinson’s Disease Patients(Excluding COMT & AC users)Group 1 sample size: 141 > > Since they have the same signatures, do I curate as one experiment, add a note on thediscussions page and request to delete the second one.Or do I leave it as separate experiment?

Joan C. Chukwuemeka (11:35:20) (in thread): > I think leaving as two experiments is okay. The researchers hypothesized that Parkinson’s disease and Parkinson’s disease medications have distinct signatures of the gut microbiome. > > So the result shows otherwise, which was part of their conclusion:******“********……Results coalesce divergent findings of prior studies, reveal altered abundance of several taxa, nominate functional pathways,******* and demonstrate independent effects of PD medications on the microbiome.”*****In essence, the study showed that medications used to treat PD might have separate impacts on the gut microbiome, independent of the disease itself.

Aleru Divine (11:41:19) (in thread): > Thanks@Joan C. Chukwuemekabecause of this emphasis, I curated as 2 experiments.

Joan C. Chukwuemeka (11:42:46) (in thread): > I also think it will be helpful if COMT is written in full in the curation, -catechol-O-methyltransferase (COMT)

Aleru Divine (11:43:59) (in thread): > Fixing that.Thank you:pray::blush:

Joan C. Chukwuemeka (11:44:23) (in thread): > You’re welcome:relaxed:

2024-04-24

Scholastica Urua (04:57:46): > Good morning everyone, hope you’re all doing fine. I just completed thisstudyand would greatly appreciate peer review. > > My specific areas of concern include the condition and statistical test(s) for each experiments. > > Looking forward to your feedback. Thank you in anticipation:pray:. - Attachment (BugSigDB): Intestinal microbiota influences clinical outcome and side effects of early breast cancer treatment - BugSigDB > The prognosis of early breast cancer (BC) relies on cell autonomous and immune parameters.The impact of the intestinal microbiome on clinical outcome has not yet been evaluated.

Peace Daniel (04:59:24) (in thread): > Well done on you curation,I’lltake a look

idiaru Angela (05:01:51) (in thread): > Good morning Scholastica. Well done. Would give it a review

Peace Daniel (05:22:20) (in thread): > This is a lot, well done@Scholastica UruaI think the condition is fine > So far, I’ve observed both PLS-DA and Lefse were used.In some cases lefse was used for pathways which wedon’tcurate and PLS-DA for differentially abundant species > Have you reported the lua error you encountered?

Scholastica Urua (05:23:32) (in thread): > Thank you@Peace Daniel. Yes, I’ve submitted a report on GitHub concerning the error message.

Peace Daniel (05:25:33) (in thread): > Your study says its longitudinal, did you observe this? > > Experimental tumor model and treatments > Mice: All animal experiments were carried out in compliance with French and European laws and regulations.

Peace Daniel (05:26:56) (in thread): > I think you have both human and animal experiments in your study@Scholastica Urua

Scholastica Urua (05:28:23) (in thread): > In some of the experiments, like exp. 17 for example they were measuring the effect of CT. If patients had neurotoxicity after CT or not. That’s why I’m concerned about the condition.

Peace Daniel (05:28:53) (in thread): > I’llcheck that again@Scholastica Urua

Scholastica Urua (05:30:17) (in thread): > Yes@Peace Danielthere’s both human and mice experiment. Just the last experiment made use of mice. This was actually a concern. I was wondering if it should be documented under one curation or not since the last experiment is a laboratory exp.:thinking_face:

idiaru Angela (05:32:46) (in thread): > Hey@Scholastica UruaI’m not sure Fig 1 B and E point to differential abundance from this description of the figure > “Variable importance plot (VIP) scores were obtained within partial least square discriminant analysis by segregating stage I (orange) from stage II-III (blue), describing the most discriminant species in descending order of importance before (B; pre-CT-A, n = 56) and after E; post-CT, D, n = 34) adjuvant chemotherapy (only bacteria with prevalence >2.5% were taking into account” > > Also for the condition for Experiment that compares patients with breast cancer at different stages, would “disease staging” not be a good fit?

Aleru Divine (05:33:16) (in thread): > Well done on your curation@Scholastica UruaI will give it a look.

Peace Daniel (05:33:58) (in thread): > @Scholastica UruaWhen I curated something similar, my study design was both case-control and laboratory experiment > Then I added laboratory experiment to the group name that belonged to the laboratory experiment > > For instance, ex 17 > Group name: CT patients with ct(laboratory experiment)

idiaru Angela (05:35:59) (in thread): > Hey@Scholastica UruaThen for Experiments comparing before and after chemotherapy “response to treatment” seems like a good fit

Peace Daniel (05:36:40) (in thread): > Ex 17, fig 4B you curated@Scholastica Urua“neurotoxicity evaluated 12 months after CT” > > I think you’re right to curate this condition differently from breast cancer

Peace Daniel (05:37:03) (in thread): > That’sa better option@idiaru Angela

Scholastica Urua (05:38:03) (in thread): > @idiaru AngelaI think disease staging will be a better fit. Thank you. > For Fig. 1B and E are you saying it shouldn’t be curated?

Peace Daniel (05:39:17) (in thread): > Disease staging?:thinking_face:

Scholastica Urua (05:39:50) (in thread): > @Peace DanielI think a curation is suppose to have just one study design. Or can there be more than one?:thinking_face:

Aleru Divine (05:40:07) (in thread): > I agree,@Peace Danieland@idiaru Angelathere are kinda different conditions in this case.

Peace Daniel (05:42:43) (in thread): > https://bugsigdb.org/Study_927@Scholastica Urua

Aleru Divine (05:42:45) (in thread): > @Peace Danielstaging a disease means determining how much within the body it has spread.I think it is a good fit.At least close enough.:grimacing:

idiaru Angela (05:43:58) (in thread): > Yeah@Peace Danielthe efo definition is “The stage or progression of a disease in an organism. Includes pathological staging of cancers and other disease progression.”

Peace Daniel (05:45:11) (in thread): > Okay noted@Aleru Divine@idiaru Angela

Scholastica Urua (05:45:52) (in thread): > You’re right@idiaru Angela. Disease staging fits well for that experiments…

Peace Daniel (05:46:25) (in thread): > What do you think about fig1b ?@Aleru Divine

Aleru Divine (05:47:43) (in thread): > Checking it out@Peace Daniel

idiaru Angela (05:47:46) (in thread): > @Scholastica UruaI think the highlights of discussion on how many study design there can be is that it’s possible that there can be 2 study designs but it’s not usually common > Then for figure 1B and E I don’t think they show differential abundance:thinking_face:

Scholastica Urua (05:51:23) (in thread): > Okay@idiaru Angela, thanks. What are your thoughts about the supplementary figures. Because most of them are described in a similar way?

Peace Daniel (05:51:39) (in thread): > we utilized a supervised analysis (Partial Least Squares Discriminant Analysis (PLS-DA) to explore the variance between the groups at baseline and post-CT > > I do thinkit’sdifferential abundance tho@idiaru Angela

Scholastica Urua (05:52:33) (in thread): > I do think so as well@Peace Danielbecause they were contrasting two groups…

Aleru Divine (05:56:18) (in thread): > I think it is the differential abundance too.@Peace Daniel@idiaru Angela@Scholastica Urua

idiaru Angela (05:57:06) (in thread): > I see what you’re saying@Scholastica UruaYou’re right to curate it

Scholastica Urua (05:57:13) (in thread): > So I was thinkingthiscould better replace disease staging as its more specific to tumor. What are your thoughts? - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Aleru Divine (05:59:38) (in thread): > From this excerpt “Variable importance plot (VIP) scores were obtained within partial least square discriminant analysis by segregating stage I (orange) from stage II-III (blue), describing the most discriminant species in descending order of importance before (B; pre-CT-A, n = 56) and after E; post-CT, D, n = 34) adjuvant chemotherapy (only bacteria with prevalence >2.5% were taking into account).” > > Emphasis on discriminant species which would mean differentiating species and would also imply “differential abundance”

Peace Daniel (06:01:59) (in thread): > Exactly@Aleru Divinevariance also means differences

Peace Daniel (06:03:42) (in thread): > I think the definition of disease staging is better to me@Scholastica Urua

Scholastica Urua (06:09:57) (in thread): > Thank you@Peace Daniel@idiaru Angela@Aleru Divine. You all have been most helpful.:hugging_face:Do let me know if you come across any other information of interest.:pray:

Peace Daniel (06:10:43) (in thread): > You’rewelcome:heart:@Scholastica Urua

idiaru Angela (06:12:07) (in thread): > Would do@Scholastica Urua

Aleru Divine (07:39:18) (in thread): > You’re welcome:heart:@Scholastica Urua

Adenike Oladimeji-Kasumu (08:07:27): > Good day everyone. I trust you are all doing well. Please can someone help me find the PMID of this document? I have tried inputting the information manually and its still not populating.https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0005826#amendment-0 - Attachment (journals.plos.org): The microbiome in urogenital schistosomiasis and induced bladder pathologies > Author summary The human microbiome comprises bacteria (plus viruses, fungi and archeae) inhabiting different sites of the body. They do not specifically cause diseases, but their presence, absence or population influence body functions. We therefore examined such organisms found along the urinary tract, in persons living in a rural community in Nigeria who considered themselves healthy, were infected with the parasite Schistosoma haematobium or had developed bladder complications along with the parasite infection. We found that these groups shared a large portion of the microbiome, but there were microbial species unique to infected persons and those with bladder complication. Some of these were capable of inducing inflammation and could offer less protection to the host. We also predicted pathways that are affected by the difference in the microbiome.

idiaru Angela (08:11:28) (in thread): > 28793309 > Here@Adenike Oladimeji-Kasumu

idiaru Angela (08:12:50) (in thread): > If you have any trouble finding the pmid in future just search the topic of the research work herehttps://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Adenike Oladimeji-Kasumu (08:13:15) (in thread): > Thank you so much@idiaru AngelaPlease Sis show me a screenshot of where you saw it.:smile:been looking for it throughout yesterday:woman-facepalming:

idiaru Angela (08:13:53) (in thread): > You’re welcome@Adenike Oladimeji-Kasumu:blush:

Svetlana Ugarcina Perovic (08:18:36) (in thread): > https://pubmed.ncbi.nlm.nih.gov/28793309/ - Attachment (PubMed): The microbiome in urogenital schistosomiasis and induced bladder pathologies - PubMed > The urinary microbiome is a factor to be considered in developing biomarkers, diagnostic tools, and new treatment for urogenital schistosomiasis and induced bladder pathologies.

Svetlana Ugarcina Perovic (08:19:25) (in thread): > @Adenike Oladimeji-Kasumuunder the title

Adenike Oladimeji-Kasumu (08:19:33) (in thread): > Thank you so much@Svetlana Ugarcina PerovicI do not know how I forgot that there is such a link.:blush:

Joan C. Chukwuemeka (12:13:06): > Good evening all<!here>I’m working on curating thisStudy, however, the curatable information I can spot so far are alpha diversities, no differentially abundant microbes. A part of the text (in the screenshot) seemed to suggest certain taxa groups as different, however the figure source (2nd screenshot) is about relative abundance. It seemed they showed more of differential metabolites. > > Although, they stated this within the discussion section******,“we observed that the major differential species belonged to the phyla Proteobacteria, Bacteroidetes, Cyanobacteria, and Firmicutes.”, ****Not able see within main text the contrast groups where they were significant. > > The phrase:point_right:“******Among these, Bacteroidetes, Cyanobacteria, and Firmicutes had very low relative abundance in the C group, which increased significantly with increasing PM2.5 concentration, especially in the H group.” ******seems to be a comparison between C group and H group,******* However, *******the figure source (2nd screenshot) is about relative abundance, so I think its a relative abundance comparison not differential.:thinking_face:(Groups:control group (C), Low concentration PM2.5 exposure group (L), medium concentration PM2.5 exposure group (M), and High concentration PM2.5 exposure group (H).)Please can anyone spot any clear record of differentially abundant taxa in the study?*****PS:*Identified contrast group based on alpha diversity metrics done::point_down: > 1. Low Vs Control > 2. Medium Vs Control > 3. High Vs Control > 4. ?Low Vs Medium? > 5. ?Low Vs High? > 6. ?Medium Vs High?** - File (PNG): image.png - File (PNG): image.png

idiaru Angela (12:33:57) (in thread): > Hey@Joan C. ChukwuemekaI just checked and confirmed that the study only has relative abundance results and significant alpha diversity results. But no differential abundance well presented in the paper. > I opened this issue so I apologise about this:pray:

Scholastica Urua (12:46:46) (in thread): > Hello@Joan C. ChukwuemekaI just checked the study and I only noticed relative abundance. Also noticed that the alpha diversity in some of the contrasting groups are significant which I think is curatable. But that’ll mean the curation will not have any signature at all…

Scholastica Urua (12:56:54) (in thread): > I came across these reviewedcurations without any signature at all. This may be a similar case…https://bugsigdb.org/Study_306https://bugsigdb.org/Study_843 - Attachment (BugSigDB): Microbiome and diversity indices during blood stem cells transplantation - new perspectives? - BugSigDB > OBJECTIVE: The human body is colonized by bacteria, fungi and viruses.Resident commensal bacteria are a fundamental line of resistance to colonization by exogenous microbes. - Attachment (BugSigDB): Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition - BugSigDB > Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome.

idiaru Angela (13:33:34) (in thread): > Ohh interesting@Scholastica Urua

Joan C. Chukwuemeka (13:42:10) (in thread): > Alright… Thanks for your input@idiaru Angela@Scholastica Urua:gratitude-asl:

Aleru Divine (15:04:26) (in thread): > Hi@Joan C. Chukwuemeka, I agree, there are significant alpha diversity measures reported in the paper and only relative abundance was presented. (Thiscan’tbe curated).There is no record of differentially abundant taxa. So no signatures.

UBNSEMS3S (16:52:51): > Hi everyone, > > Just a reminder that we have our team meeting at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. Looking forward to seeing you there.

Joan C. Chukwuemeka (16:55:27) (in thread): > Thanks for the update<@UBNSEMS3S>looking forward to it too:blush:

Scholastica Urua (17:00:55) (in thread): > Thank you<@UBNSEMS3S>. Looking forward to it:hugging_face:

Aleru Divine (17:12:27) (in thread): > Thanks for the reminder<@UBNSEMS3S>. > Looking forward to it, as always:blush:

idiaru Angela (17:32:52) (in thread): > Look forward to it. Thank you@C. Mirzayi (please do not tag this account)

Nana (18:21:46) (in thread): > <@UBNSEMS3S>thanks looking forward to it

2024-04-25

Barakat Akinsiku (02:58:01) (in thread): > Thank you<@UBNSEMS3S>

Mildred Anashie (03:18:36) (in thread): > Thanks for the update<@UBNSEMS3S>

Oluwatomisin Omojokun (04:12:20) (in thread): > noted@C. Mirzayi (please do not tag this account)

Kelechi Madubuko (08:04:27) (in thread): > Less than 1hr left.. let the countdown begin

Svetlana Ugarcina Perovic (08:42:00): > Just to say Hello Hello!I am on holidays April 25 and 26, May 1 (:it:public holidays). Please do ask today Chloe for any points where our doubts/discussions are still open and/or not enough clarified. Thanks!

idiaru Angela (08:43:37) (in thread): > Would do. Have a great holiday!@Svetlana Ugarcina Perovic

Mildred Anashie (08:45:12) (in thread): > Thanks for informing us > Do have a great holiday@Svetlana Ugarcina Perovic:blush:

Joan C. Chukwuemeka (08:46:14) (in thread): > Alright@Svetlana Ugarcina Perovic. Do Enjoy your Holidays:relaxed:

Scholastica Urua (08:46:14) (in thread): > Thank you. > Have a great holiday@Svetlana Ugarcina Perovic:blush:

Aleru Divine (08:51:00) (in thread): > Noted! > Have a great holiday!:hugging_face:@Svetlana Ugarcina Perovic

Barakat Akinsiku (09:01:30) (in thread): > Enjoy your holiday!@Svetlana Ugarcina Perovic

Peace Daniel (09:01:45) (in thread): > Noted, have a great holiday@Svetlana Ugarcina Perovic

Nana (09:20:11): > Please has the meeting ended, I was logged out

Mildred Anashie (09:20:48) (in thread): > Yes it has ended > > It was a short meeting today

Barakat Akinsiku (09:21:12) (in thread): > Yes@Nanathere weren’t much questions so we ended early

Nana (09:21:24) (in thread): > Ok..thank you

Nana (09:22:15) (in thread): > Aiit@Svetlana Ugarcina Perovicenjoy your holidays

UBNSEMS3S (09:22:48): > We had a short meeting today but it was still nice to hear from you all. Please post any questions here on Slack and I’ll be happy to answer.

Mildred Anashie (09:23:23) (in thread): > Thank you so much<@UBNSEMS3S>

idiaru Angela (09:23:31) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

Joan C. Chukwuemeka (09:23:58) (in thread): > Thanks<@UBNSEMS3S>for the office hour. > Here’s the link to the study to be deletedhttps://bugsigdb.org/Study_1037Thanks. (edited) - Attachment (BugSigDB): PM2.5 exposure perturbs lung microbiome and its metabolic profile in mice - BugSigDB > Fine particulate matter (PM2.5) have become a major public health concern because of their adverse effects on health.Lungs are considered the primary organ affected by PM2.5.In order to understand the mechanism underlying PM2.

Aleru Divine (09:24:35) (in thread): > Thank you so much<@UBNSEMS3S>

Scholastica Urua (09:24:40) (in thread): > Thank you<@UBNSEMS3S>

Barakat Akinsiku (09:31:37) (in thread): > Thank you@C. Mirzayi (please do not tag this account)

UBNSEMS3S (09:33:06) (in thread): > @Joan C. ChukwuemekaDeleted.

Joan C. Chukwuemeka (09:37:13) (in thread): > Thank you<@UBNSEMS3S>

Nana (10:34:30) (in thread): > @C. Mirzayi (please do not tag this account)okay..thank you for having us

idiaru Angela (12:51:13): > Hello everyone,@C. Mirzayi (please do not tag this account)In this study I’m curating (link below) I have questions about the statistical test used specifically for table 2https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771587/It was mentioned that Lefse was used to determine differential abundance under the methods. Then in the results it was mentioned that the Mann–Whitney U test was used to determine Table 3. > My question is then that is it safe to assume that table 2 was determined using the Mann-Whitney U test ? - Attachment (PubMed Central (PMC)): Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma > Altered gut microbiota has been connected to hepatocellular carcinoma (HCC) occurrence and advancement. This study was conducted to identify a gut microbiota signature in differentiating between viral-related HCC (Viral-HCC) and non-hepatitis B-, non-hepatitis … - File (JPEG): Screenshot_20240425_173825_Chrome.jpg

Mildred Anashie (12:53:34) (in thread): > @idiaru AngelaYou can have different statistical tests for different experiments > > You would be right to say Mann Whitney U was used for the Table 3 if it shows differential abundance for an experiment andit’s statedthat way

idiaru Angela (12:55:37) (in thread): > The question I was asking is the statistical test for table 2, if I could assume that table 2 and 3 were gotten using the same statistical test@Mildred AnashieWhile it was stated in the results that Mann-Whitney was used for table 3, nothing was specifically stated for table 2.

Aleru Divine (13:00:20) (in thread): > @idiaru Angela, no test was specified for table 2 although it is not looking like the typical LEfSe figure. I’d assume table 2 and 3 results were gotten using the statistical test. The format for table 2 and 3 are the same.:thinking_face:

Aleru Divine (13:00:53) (in thread): > But wearen’tsupposed to assume.

Mildred Anashie (13:01:33) (in thread): > I thinkit’sfor relative abundance andit’sreferring to the Supplemental Figure > > “Among the genera of the top 50 relative abundance (Supplemental Fig. S2), we identified 16 genera that were significantly different between Viral- and NBNC-HCC (Mann–Whitney U test, p < 0.05). Compared to Viral-HCC, 11 genera, i.e., Faecalibacterium, Agathobacter, Prevotella, Coprococcus, Subdoligranulum, Ruminococcus gauvreauii group, Lachnospiraceae ND3007 group, Erysipelotrichaceae UCG-003, CAG-56, Holdemanella, and Lachnospiraceae UCG-004, were reduced in NBNC-HCC, while 5 genera, including Bacteroides, Streptococcus, Ruminococcus gnavus group, Parabacteroides, and Erysipelatoclostridium, were found to be enriched (Table 3).”

Mildred Anashie (13:02:30) (in thread): > I think you should curate Fig 4 for that experiment instead of Table3:thinking_face:@idiaru Angela

idiaru Angela (13:04:31) (in thread): > Hi@Mildred Anashiethis excerpt still refers to differential abundance:thinking_face:.

idiaru Angela (13:05:17) (in thread): > Yeah@Aleru Divinethey follow the exact same format for presentation of the result. So I don’t know if it is safe to assume the statistical test are the same

Peace Daniel (13:08:36) (in thread): > Hi@idiaru AngelaI think it was Mann Whitney, take a look at this > > Among the genera of the top 50 relative abundance (Supplemental Fig. S2), we identified 16 genera that were significantly different between Viral- and NBNC-HCC (Mann–Whitney U test, p < 0.05) > > Also signatures in table 2 are similar to the supplemental S2

Aleru Divine (13:08:57) (in thread): > From the image (screenshot) you shared, I think you should use LEfSe for all. They’d have talked about Mann-Whitney if it was used for statistical test in that section.@idiaru Angela

Peace Daniel (13:09:58) (in thread): > @Aleru Divinetable 2 and 3 definitely don’t look like lefse

Peace Daniel (13:09:59) (in thread): > @Aleru Divinetable 2 and 3 definitelydoesn’tlook like lefse

Aleru Divine (13:11:53) (in thread): > Yes it doesn’t, but then this excerpt > “Taxonomies with significant abundance across various groupings were identified by linear discriminant analysis effect size (LEfSe) (Segata et al. 2011), which were conducted in Galaxy (https://huttenhower.sph.harvard.edu/galaxy/) using LDA scores > 2 and p < 0.05 was applied as a cutoff value.”

Peace Daniel (13:12:46) (in thread): > Still same article@Aleru DivineAmong the genera of the top 50 relative abundance (Supplemental Fig. S2), we identified 16 genera that were significantly different between Viral- and NBNC-HCC (Mann–Whitney U test, p < 0.05)

idiaru Angela (13:13:42) (in thread): > Under the results where Table 3 was referenced, they stated that it was gotten through the Mann Whitney test though@Aleru Divine

Aleru Divine (13:14:49) (in thread): > I was leaning towards mann-Whitney. But then here’s what they had to say about Mann-Whitney again - File (JPEG): IMG_8247

Aleru Divine (13:16:14) (in thread): > MaybeI’mthinking too much!@Peace Daniel@idiaru AngelaThe tabledoesn’tlook like a typical LEfSe table.It looks like table 3 which they said Mann-Whitney was used to identify.So naturallyit’slooking more like Mann-Whitney.I’m just taking everything into account.

UBNSEMS3S (13:16:27) (in thread): > Table 2 looks like Mann-Whitney to me. The main indicator is that they report medians. LEfSe would report LDA scores typically.

Peace Daniel (13:16:43) (in thread): > I understand you@Aleru Divine

UBNSEMS3S (13:17:36) (in thread): > This is a good example though of the importance of being very clear about which statistical test was used for each result. Ambiguity like this can be frustrating.

Peace Daniel (13:18:05) (in thread): > @idiaru Angelathe answers here > > Thank you for clarifying<@UBNSEMS3S>

Aleru Divine (13:18:06) (in thread): > Phew! Thanks for this clarification<@UBNSEMS3S>

idiaru Angela (13:20:16) (in thread): > Thank you@C. Mirzayi (please do not tag this account):clap:

Rahila-me (15:26:21) (in thread): > <@UBNSEMS3S>Thanks for hosting

NWAKAEGO VINCENT (17:51:04) (in thread): > Alright, thanks@Svetlana Ugarcina Perovic

U1LCB8WEA (21:22:41): > Could folks try out this staging of an upgraded site and let me know if it seems to be working?https://admin:bugsiwiki@bugsigdb-staging.wikiworks.com/

U1LCB8WEA (21:23:19) (in thread): > (It’sa sandbox so any edits there will be lost)

2024-04-26

Peace Daniel (02:28:20) (in thread): > Hello@Levi WaldronI tried searching for a signature, the response time was very slow but the result was fine. > I couldn’t login with my already existing details on BugSigdb > I explored Add a study page, seems fine too > Help and random pages work just fine too > Curation policy page is still incomplete, the table for study design

Aleru Divine (03:13:03) (in thread): > Good morning@Levi Waldron, The site works alright, it is also responsive just like BugSigDB.I tried requesting an account, since I couldn’t login with my account and that didn’t work. I am guessing that is intended.I searched random pages and that works perfectly.I also tried searching for a signature like@Peace Danieland it took too long to respond.TheHelp:Contentpage took a little too long to respond,I’mnot sure if that is because of my internetconnection because it seems to be working fine this morning.But the other pages on the TODO for reviewers section responded quite alright.

Peace Daniel (03:24:30) (in thread): > The help page might be your internet@Aleru Divineas it wasn’t that slow in mine

Rahila-me (03:38:12) (in thread): > ok

Joan C. Chukwuemeka (03:39:43) (in thread): > Good morning<@U1LCB8WEA>The wiki web page is responsive and pages on the header tab (Add a study, recent changes, random page, help, page tools(…)) works fine too

Barakat Akinsiku (03:40:40) (in thread): > Yes@Peace Danieleverything worked well from my end including the help pages and signature search so it must be a function of Aleru’s internet. All pages are responsive and I had no issues with webpages loading at snail speed

Joan C. Chukwuemeka (03:45:38) (in thread): > Signature search responded well, wasn’t slow from here - File (PNG): image.png - File (PNG): image.png

Aleru Divine (03:48:12) (in thread): > It is my internet connection then:sleepy:I will check it out again.Thanks everyone:people_hugging:

Joan C. Chukwuemeka (03:58:15) (in thread): > So, yea I was able to Log in successfully, however that was after I logged out from the other link. So, from my end, web content updates is what I think is yet to be completed.:gratitude-asl:@Peace Daniel@Aleru Divinedoes the screenshot below capture the error response you got on trying to log in? - File (PNG): image.png

Peace Daniel (03:59:21) (in thread): > Nope, it kept throwing a wrong username or password@Joan C. ChukwuemekaProbably an internet connection issue@Barakat Akinsiku

Peace Daniel (04:00:25) (in thread): > I’ll try to login in a private tab@Joan C. ChukwuemekaStill the same lol

Aleru Divine (04:02:38) (in thread): > Same with me@Peace Daniel. It said and is still saying “incorrect username or password entered”@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:03:17) (in thread): > @Peace DanielMaybe recheck you log in details and ensure you’re not logged in on the other bugsigdb link. > > “Session hijack error” is a pointer that one can’t be using same log in details at once in 2 different similar sites

Peace Daniel (04:04:34) (in thread): > I have my details saved on my phone soI’mnot quite sure@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:07:51) (in thread): > Well, Mine worked though.@Peace Daniel@Aleru DivineIf you’re logged out from the otherbugsigdb.orglink and you’re not able to log in on this one with same details, maybe try clearing your browser cache. - File (PNG): image.png

Aleru Divine (04:08:59) (in thread): > Let me try that@Joan C. Chukwuemeka

Aleru Divine (04:13:45) (in thread): > Stillisn’tworking for me@Joan C. Chukwuemeka:pleading_face:

Peace Daniel (04:14:33) (in thread): > Was waiting on your feedback@Aleru DivineWere you able to login?@Barakat Akinsiku

Joan C. Chukwuemeka (04:15:10) (in thread): > wow:thinking_face:. Perhaps, let others try.

idiaru Angela (04:42:03) (in thread): > Search is fine on my end, and all the pages look okay. I’m also unable to log in though

Joan C. Chukwuemeka (04:43:18) (in thread): > @idiaru Angelawhat was the error you got?

idiaru Angela (04:45:08) (in thread): > Incorrect username/ password

Joan C. Chukwuemeka (04:46:37) (in thread): > Oh.. okay.?.:thinking_face:. > Well, Like@Levi Waldronsaid, it’s a sandbox, i believe it will be sorted, esp when the main link is finalized:raised_hands:

idiaru Angela (04:57:54) (in thread): > Yeahh

Peace Daniel (04:58:07) (in thread): > That makes 3 of us@idiaru Angela

Barakat Akinsiku (04:59:27) (in thread): > @Peace DanielI just tried it now and incorrect username or password too. I guess it will all be sorted soon

Peace Daniel (05:00:09) (in thread): > Yes, it will@Barakat Akinsiku

idiaru Angela (05:02:38) (in thread): > Right@Peace Daniel

Scholastica Urua (07:33:21) (in thread): > I just tried logging in and also got incorrect username or password. Tried requesting an account and got an error message as well.

Aleru Divine (08:36:45) (in thread): > I and a few others had the same experience too@Scholastica Urua

Joan C. Chukwuemeka (12:33:54): > Good evening all<!here>, > In thestudyi’mcurating, the microbial signatures that are differentially abundant were presented in tables, 2 of which are shown in the images below with the footnote/description included.<@UBNSEMS3S>Please, I want to know if my below interpretation of the table is correct: > * If adjusted p-value is less than the significance level, 0.05 (i.e statistically significant), and the beta coefficient (coef) is positive, that suggests an increase in abundance. > * If adjusted p-value is less than the significance level, i.e 0.05 (i.e statistically significant), and the beta coefficient (coef) is negative, it suggests a decrease in abundance > so for Table S2(1st Image insert),******Anaerococcus******isincreased in abundancein premenopausal post-treatment group compared to the healthy controls, while******Parabacteroides******* isdecreased in abundancein premenopausal post-treatment group compared to the healthy controls. > > For Table 2(2nd Image insert),*****Arcanobacterium ****isincreased in abundancein postmenopausal pre-treatment group compared to the healthy controls, while******Gardnerella ****isdecreased in abundancein postmenopausal pre-treatment group compared to the healthy controls. - Attachment (PubMed): Increased diversity of a cervical microbiome associates with cervical cancer - PubMed > The cervical microbiome (CM) is a complex ecosystem that can change in response to gynecological cancers. We aimed to evaluate changes in the CM of patients who underwent chemoradiation (CRT) therapy for locally advanced cervical cancer. Before and after CRT, cervical swab samples were collected fro … - Attachment (BugSigDB): Increased diversity of a cervical microbiome associates with cervical cancer - BugSigDB > The cervical microbiome (CM) is a complex ecosystem that can change in response to gynecological cancers.We aimed to evaluate changes in the CM of patients who underwent chemoradiation (CRT) therapy for locally advanced cervical cancer. - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

UBNSEMS3S (12:48:25) (in thread): > That sounds right to me.

Joan C. Chukwuemeka (12:50:34) (in thread): > Okay. Thanks a lot<@UBNSEMS3S>:blush:

Peace Daniel (12:52:52) (in thread): > Taking notes and saved for later:blush:

Mildred Anashie (13:08:56) (in thread): > I was able to login just fine also every other thing is working just fine from my end

Mildred Anashie (13:09:58) (in thread): > Honestly@Peace DanielI went through this and was a bit confused had to start reading the paper before I saw Chloe’s response

Scholastica Urua (13:11:42): > Hello<@UBNSEMS3S>please can I be assignedthis issueto curate? > Thank you very much! - Attachment: #384 Diet changes due to urbanization in South Africa are linked to microbiome and metabolome signatures of Westernization and colorectal cancer > https://www.nature.com/articles/s41467-024-46265-0 > > Adding this for curation because it doesn’t exist on BugSigdb and I believe it should be curated

Mildred Anashie (13:18:51) (in thread): > I also commented on an issue on GitHub awaiting to be assigned the issue<@UBNSEMS3S>

Peace Daniel (13:36:08) (in thread): > Yes@Mildred AnashieThis is new to me

Aleru Divine (13:59:45) (in thread): > @Mildred Anashie@Peace Danielthat makes 3 of us.I’mglad this has been answered.Thank you<@UBNSEMS3S>and@Joan C. Chukwuemeka:pray:

UBNSEMS3S (15:50:15) (in thread): > Assigned.

UBNSEMS3S (15:51:50): > I think I’m caught up on Github issue assignments but please let me know if I missed any.

2024-04-27

Rahila-me (02:33:22) (in thread): > I have tried/tested out a couple things , and everything works fine. They are in order

Peace Daniel (10:25:43): > Hello<@UBNSEMS3S>@Peace Sandy@Esther Afuape@Chioma OnyidoI’d like Signature 2 of experiment 13 to be deleted please, it got duplicated somehowhttps://bugsigdb.org/Study_962 - Attachment (BugSigDB): Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs - BugSigDB > BACKGROUND: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide.New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD.

2024-04-28

Peace Daniel (09:06:39): > Good day all and happy Sunday, > > I just finished curating this paper and would love reviews. Most specific areas would be the condition and group size > > The only mention of size was here > “At sampling days 0, 7 and 14dpw, three random freshly voided faecal samples from three pigs per treatment pen were collected and pooled…” > > My thought is, there could be several pens in a farm andit’snot right to use 3 as the sizeI’dlove to hear fromy’alltho:wave::purple_heart:https://bugsigdb.org/Study_962 - Attachment (BugSigDB): Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs - BugSigDB > BACKGROUND: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide.New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD.

idiaru Angela (09:08:51) (in thread): > Well done@Peace Danielwould give it a look

Peace Daniel (09:11:50) (in thread): > Thank you@idiaru Angela

idiaru Angela (11:39:50) (in thread): > Hey@Peace Danielwelldone on this curation > I noticed that this study has samples from 2 locations I.e France and ireland which was used for the global analysis. > “To ensure a balanced statistical arrangement, diarrhoea samples were not included as part of the global analysis, nor when studying differences among sampling time points.” > > For the sample size I agree with leaving it blank, there’s no information on how many pens are in the farm. > > For the condition, for Experiments that compare different sampling time, e.g 0dpw and 7dpw I think “sampling time point” would be a good fit > Then with the experiments comparing diarrhea and feces at same time point I think “abnormal sample” would be a good fit since diarrhea is the abnormal sample of feces

Peace Daniel (11:46:35) (in thread): > But the study was done to determine the effect of antimicrobial use in post weaning diarrhoea > > Sampling time, treatment or consistency were factors

Peace Daniel (11:46:53) (in thread): > Can you point me to where you saw France in the study?

idiaru Angela (13:10:08) (in thread): > Yeah@Peace Danieli was talking specifically for the experiments under the same treatment group where the difference betwee both group is the sample time or fecal consistency. > > I got this excerpt from the methods > “Farms A, B and C used the control diet + 250 mg/Kg of sulphadiazine and 50 mg/Kg of trimethoprim as Sulfoprim 15% (Univet Limited, Ireland), while on farm D the control diet was supplemented with 400 mg/Kg of amoxicillin as Stabox 5% (Virbac, France).”

Peace Daniel (13:13:52) (in thread): > Oh, this is where the supplement was produced I think

Peace Daniel (13:16:21) (in thread): > So all groups are treatments but they were subdivided based on factors, hence, 0_dpw, 7pw are all treatments at this time period when the sample was taken > > “the present study was designed to compare the effects of in-feed antibiotics (Ab) and therapeutic doses of zinc oxide (Zn) with non-medicated animals (Ct) on the development of the post-weaning microbiota on four commercial pig farms. “

Peace Daniel (13:17:56) (in thread): > They used factors to further understand how these antimicrobials affected the weaned pigs based on several factors

Peace Daniel (13:26:28) (in thread): > I just confirmedit’sthe location these antibiotics were made

idiaru Angela (13:28:11) (in thread): > There seems to be global data involved:thinking_face:which led me to believe there was more than one country involved. > For the second one I’m not sure I understand you. Each experiment condition should be chosen based on its unique contrast. If the two contrasting groups have different time points but are on the same treatment, then effect of antimicrobial would not be a good fit anymore since the difference between the 2 groups is the sampling time point not the treatment given.

idiaru Angela (13:28:39) (in thread): > Okay@Peace Danielnoted:+1::blush:

Peace Daniel (13:29:32) (in thread): > Piglets treated with antibiotics Global data set involves both consistency and Day post weaning (dpw) factors

Peace Daniel (13:35:54) (in thread): > I think I get you@idiaru AngelaThank you

idiaru Angela (13:36:56) (in thread): > Good job@Peace Daniel. This curation looks tasking:blush:

Peace Daniel (13:39:30) (in thread): > Yea it was, thank you

Aleru Divine (16:58:26) (in thread): > Well done on your curation@Peace Danieland well done on the review@idiaru Angela

2024-04-29

Scholastica Urua (01:57:59) (in thread): > Well done@Peace Danieland@idiaru Angela:+1:

Joan C. Chukwuemeka (03:01:46) (in thread): > Well done on the curation@Peace Daniel. Study looks quite interesting at a glance. I’d review and revert with my view/feedback on it.

Joan C. Chukwuemeka (03:04:28): > Good morning all:wave:, > It’s another new week, so I’m wishing everyone a fulfilling week ahead. > Happy new Week and Happy BugSigDB-ing:seedling:

idiaru Angela (03:33:14) (in thread): > Have a great week@Joan C. Chukwuemekaand Happy BugSigDB-ing

Aleru Divine (03:40:00) (in thread): > Happy new week@Joan C. Chukwuemekaand everyone:sparkles:

Mildred Anashie (03:41:12) (in thread): > Happy new week@Joan C. Chukwuemekaand everyone > > And Happy BugSigdb-ing:hugging_face:

Scholastica Urua (04:10:59) (in thread): > Good morning@Joan C. ChukwuemekaHappy new week everyone:hugging_face:

Adenike Oladimeji-Kasumu (04:24:11) (in thread): > Happy new week@Joan C. Chukwuemekaand everyone:bouquet:

Svetlana Ugarcina Perovic (04:33:17): > Good morning :tulip:Contribution period is almost coming to an end. Thanks to your work, this period has been**** an enormous growth of the BugSigDB!****Only 2 issues are still pending; can we close them by May 1? :) > > [https://github.com/waldronlab/BugSigDBcuration/issues/290](https://github.com/waldronlab/BugSigDBcuration/issues/290)[https://github.com/waldronlab/BugSigDBcuration/issues/297](https://github.com/waldronlab/BugSigDBcuration/issues/297) > > <@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace Sandy@Svetlana Ugarcina Perovic

idiaru Angela (04:38:17) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thank you for your great mentorship during the contribution period. Would collaborate to finish up the curations:blush:

Mildred Anashie (04:48:42) (in thread): > Good morning@Svetlana Ugarcina Perovic:coffee:Thank you so much, just like Angela I would collaborate to finish up the curations:hugging_face:

Bolanle Wahab (04:58:21) (in thread): > Good morning@Svetlana Ugarcina Perovichttps://github.com/waldronlab/BugSigDBcuration/issues/121has been corrected and ready for review. - Attachment: #121 Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics > Exploring gut microbiota in adult Atlantic salmon (Salmo salar L.): Associations with gut health and dietary prebiotics – Jie Wang et al. – Animal Microbiome 2023 > > https://animalmicrobiome.biomedcentral.com/articles/10.1186/s42523-023-00269-1

Bolanle Wahab (05:00:20) (in thread): > @Svetlana Ugarcina Perovichttps://github.com/waldronlab/BugSigDBcuration/issues/297I have reported this several times but a new error comes up every time, the recent one is “ the time allocated for running scripts has expired” - Attachment: #297 Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns > Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns – Casper Sahl Poulsen – Microbiology Spectrum
> https://journals.asm.org/doi/10.1128/spectrum.01387-21

Svetlana Ugarcina Perovic (05:04:11) (in thread): > <@U1LCB8WEA>could you please help with these bugs:arrow_up:Thanks!

Svetlana Ugarcina Perovic (05:04:46) (in thread): > Thanks@Bolanle Wahabfor the updates!

Mildred Anashie (05:12:06): > Happy Mondayall > > Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy:blush:I have a few questions in this study I’m curating,https://pubmed.ncbi.nlm.nih.gov/37409975/I have identified a few experiments with signaturesWhat’s confusing to me is that they collected samples from precancer patients, cancer patients (subdivided into Early stage cancer- T1, T2 and Late stage cancer- T3, T4) and adjacent tumor tissue specimens (AT).So I can see experiments as Early stage and Late stage cancer with differential abundance whereas the alpha diversity was done based on the subdivision earlier mentioned which are theT1, T2, T3, T4Would this mean I’d record the significant alpha diversity’s without signatures and create another experiment as Early-stage and Late-stage (with no alpha diversity indices)?.:thinking_face:Also another experiment exists as Pre cancer and cancer (with no alpha diversity for this). Would recording without alpha diversity be right?Cancer in this case represents all the cancer groups (T1, T2, T3, T4) in my opinion. > > I alsocan’tfind the sample size for the TT group (Tumor Tissue) hopefully someone can come across it:hand_with_index_and_middle_fingers_crossed:I added the sample size for T1 and T2 to get sample size for Early stage and did same for Late stage.I’mthinking on doing same for Cancer adding (T1, T2, T3, T4), would this be right?Lastly it says Peripheral blood and tissue samples were collected. The body site for the cancer patients I used Arterial blood (as peripheral blood is unavailable:thinking_face:) and still unsure of what can best fit the experiments done using Tissue specimens.Considering going with Mouth for all experiments as samples were collected from participants with oral squamous cell carcinoma:thinking_face:I would really appreciate help with this, Thank you:pray:Happy BugSigdb-ing to everyone:raised_hands::hugging_face: - Attachment (PubMed): Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma - PubMed > Characterization of the oral microbiota profile through various studies has shown an association between the microbiome and oral cancer; however, stage-specific determinants of dynamic changes in microbial communities of oral cancer remain elusive. Additionally, the influence of the intratumoral mic …

Mildred Anashie (05:28:06) (in thread): > Does this mean anything?:thinking_face:Its like the only place where I saw TT mentioned - File (PNG): TT mentioned.PNG

idiaru Angela (06:02:02) (in thread): > Hey@Mildred Anashiewell done. Saw this for the sample size for tissue sample. Image below > > For the curation of experiments, I would say those with alpha diversity and no signatures should be curated. Then the experiments with signatures but no alpha diversity should be curated. I think its best to curate with the groups the authors used for the analysis. > For the sample sizes for the early and late stage, agree with your calculations > > From the article, I don’t think blood was used in the analysis for microbial composition, it seems it was used in the analysis for the immune cells so I don’t think it should be curated for body site. - File (JPEG): Screenshot_20240429_105732_Chrome.jpg

Mildred Anashie (06:03:53) (in thread): > Thank you so much@idiaru Angelafor your feedback > > AT is a different group from TT:smiling_face_with_tear:

idiaru Angela (06:04:21) (in thread): > Ohhh > Let me look through again

idiaru Angela (06:10:15) (in thread): > @Mildred Anashielook at this excerpt - File (JPEG): Screenshot_20240429_110855_Chrome.jpg

Scholastica Urua (06:13:28) (in thread): > Hello@Mildred Anashiefor the sample sizes for T1 to T4, I agree with your calculations.

Mildred Anashie (06:15:57) (in thread): > I actually saw this but this is like the number of samples collected from the subjects that had cancerous lesions and the Adjacent Tumor > > Unless this means that all the subjects had tissue tumor excluding those stated to be adjacent control (AT-20)@idiaru Angela:thinking_face:

idiaru Angela (06:19:47) (in thread): > Doesn’t cancerous lesions refer to tissue tumors in this case? > And the adjoining areas here refer to the normal tissues adjacent to the tumors

Mildred Anashie (06:23:40) (in thread): > It’spossible the study might be using them interchangeably

Aleru Divine (07:17:24) (in thread): > Thank you@Svetlana Ugarcina Perovicthe contribution period has been amazing so far, thanks to you and the other mentors:pray::heart:

Scholastica Urua (07:18:33) (in thread): > I think you’re right@idiaru Angela

Aleru Divine (07:26:07) (in thread): > Hi@Mildred Anashie@idiaru Angelawell done.I’lltake a look too:hugging_face:

Aleru Divine (12:01:09) (in thread): > Is this all clear now?@Mildred Anashie

Mildred Anashie (12:01:56) (in thread): > Please do share your thoughts:blush:

Aleru Divine (12:31:41) (in thread): > Okay@Mildred AnashieFirst of all, well done:clap::sparkles:.You already figured it out.Since alpha diversity measurements were performed on samples subdivided into T1, T2, T3, and T4 (representing different stages of cancer), you should record significant alpha diversity results accordingly.
> You can go ahead and create separate experiments for the Early-stage and Late-stage cancers group as I see signatures. > > For the experiment comparing Pre-cancer and Cancer groups, I agree that cancer represents all the cancer stages (T1, T2, T3, T4), it is okay to record the experiment without alpha diversity since it wasn’t stated. but I see that signatures were stated in figures 2 and 3, so yeah. > > Adding the sample sizes of (T1 and T2) and (T3 and T4) to get the sample size for the early stage and late stage is a really smart idea. I think doing the same for (T1, T2, T3, and T4) to represent the cancer group is okay too. Well done! > > Let me carefully go through the body site concern.:sweat_smile:

Mildred Anashie (12:33:43) (in thread): > Thank you so much@Aleru Divine:blush:Fingers crossed for the body site, stillhaven’tfigured that out yet

Aleru Divine (13:14:10) (in thread): > @Mildred Anashieonly tissue samples were used for microbial analysis.And I think that the tissue samples collected from both cancerous lesions and adjoining normal areas would likely be obtained from the oral cavity. > Reason is oral squamous cell carcinoma occurs in the oral cavity. > > “adjoining normal areas” refers to the tissue surrounding the cancerous lesion that are normal.

Mildred Anashie (13:28:50) (in thread): > So what do you suggest? > > Mouth? > Started with mouth tho because it made sense to me

Aleru Divine (14:19:17) (in thread): > There is no “tumor tissue” or “tissue” on the drop-down. But I do see the oral cavity. it is the same as the mouth though. > They both go.

Scholastica Urua (15:01:53) (in thread): > Thank you@Svetlana Ugarcina Perovic. You and your fellow mentors have been more than amazing:heart_eyes_cat:. It’s been so wonderful working with everyone in this community.:sparkling_heart:

Mildred Anashie (15:39:06) (in thread): > Okay > > Thanks alot@Aleru Divine:hugging_face:

Joan C. Chukwuemeka (15:56:24) (in thread): > @Peace DanielThis is quite a study you have here. Well, here are my thoughts. > * For condition - I think****“response to diet”****is a closer fit for the* contrast involving the treatments and for thecontrast involving the faecal consistency, as dietary treatment was also considered. Then for thecontrast involving the day post weaning-Sampling time is okay (Antimicrobial agent refers to A substance that kills or slows the growth of microorganisms, including bacteria, viruses, fungi and protozoans). > Global Analysis/dataset implies -all sample/dataset, so I think you need to adjust your naming of the groups and its description: > * Identified contrast:(16 experiments :face_with_peeking_eye:****)**** > Day post weaning (0, 7 or 14dpw) - 3 experiments > * Day 0 post weaning (0dpw) Vs 7days Post weaning(7dpw) > Shannon -Decreased > Richness -Decreased > Pielou-Decreased > Simpson-Decreased > Chao1 - unchanged > * Day 0 post weaning(0dpw) Vs 14days Post weaning(14dpw) > Shannon - Decreased > Richness - Decreased > Pielou -Decreased > Simpson-Decreased > Chao1-Decreased > * 7 days post weaning (7dpw) Vs 14days Post weaning(14dpw) > Shannon -Decreased > Richness -Decreased > Pielou-Decreased > Simpson-Decreased > Chao1-Decreasedtreatment (Ct, Ab or Zn) - 3 experiments > * Non-medicated piglets (Ct) Vs Antibiotics (Ab)medicated piglets > Shannon -Unchanged > Richness-Unchanged > Pielou-Unchanged > Simpson-Unchanged > Chao1-Unchangedfigure 5a-pink coloured taxa as increased abundance > * Non-medicated piglets (Ct) Vs Zinc oxide (ZnO)medicated piglets > Shannon -unchanged > Richness-Unchanged > Pielou-Unchanged > Simpson-Unchanged > Chao1-Unchangedfigure 5a-orange coloured taxa as increased abundance > * Non-medicated piglets (Ct) Vs Antibiotics (Ab)medicated and Zinc oxide (ZnO) medicated piglets (group 1) > Shannon -unchanged > Richness-unchanged > Pielou-Unchanged > Simpson-Unchanged > Chao1-Unchangedfigure 5a-blue coloured taxa as decreased abundancefaecal consistency (normal or diarrhoea) - 4 experiments > * Diarrheic-faeces_Antibiotics (Ab)medicated piglets(0dpw) Vs Normal-faeces_Antibiotics (Ab)medicated piglets(0dpw) > figure S3A-Pink coloured taxa as increased abundance(1 Taxa) > * Diarrheic-faeces_Non-medicated piglets(7dpw) vs Normal-faeces_Non-medicated piglets(7dpw) > Simpson-decreased > Chao1-decreasedfigure 5E-blue coloured taxa as increased abundance > * Diarrheic-faeces_Antibiotics (Ab)medicated piglets(7dpw) Vs Normal-faeces_Antibiotics (Ab)medicated piglets(7dpw) > Simpson-unchanged > Chao1-unchangedfigure 5E-Pink coloured taxa as increased abundance > * Diarrheic-faeces_Zinc oxide (ZnO) medicated piglets (7dpw) Vs Normal-faeces_Zinc oxide (ZnO) medicated piglets (7dpw) > Simpson-unchanged > Chao1-unchangedfigure 5E-orange coloured taxa as increased abundanceTreatment based on day post weaning-6 experiments > * Non-medicated piglets (Ct)(7dpw) Vs Antibiotics (Ab)medicated piglets(7dpw) > -No alpha diversity metricfigure 5C-pink coloured taxa as increased abundance > * Non-medicated piglets (Ct)(7dpw) Vs Zinc oxide (ZnO)medicated piglets(7dpw) > -No alpha diversity metricfigure 5C-orange coloured taxa as increased abundance > * Non-medicated piglets (Ct) (7dpw)Vs Antibiotics (Ab)medicated and Zinc oxide (ZnO) medicated piglets (7dpw)(group 1) > -No alpha diversity metricfigure 5c-blue coloured taxa as decreased abundance > * Non-medicated piglets (Ct)(14dpw) Vs Antibiotics (Ab)medicated piglets(14dpw) > -No alpha diversity metricfigure 5D-pink coloured taxa as increased abundance > * Non-medicated piglets (Ct)(14dpw)Vs Zinc oxide (ZnO)medicated piglets(14dpw) > -No alpha diversity metricfigure 5D-orange coloured taxa as increased abundance > * Non-medicated piglets (Ct) (14dpw)Vs Antibiotics (Ab)medicated and Zinc oxide (ZnO) medicated piglets(14dpw)(group 1) > -No alpha diversity metricfigure 5D -blue coloured taxa as decreased abundance > > would still need to recheck again though:smiley:

2024-04-30

Peace Daniel (01:28:51) (in thread): > Fig 5A is global data set and I curated that@Joan C. Chukwuemeka“Analysis of the global dataset (Fig. 5A and B)” > Pink, blue and orange represents CT,AB and Zn > > > Ididn’trecord for treatment alone because the alpha diversity was unchanged andyou’remixing the groups up, take a look at it again. Regards the condition,I’mnot quite sure response to diet is suitable for a dietary treatment focused on antimicrobials

Peace Daniel (01:34:25) (in thread): > I don’t agree with your alpha diversity for diarrhoea vs Faecal Ab and Zn 7 as well > > Finally, we compared the alpha diversity in normal and diarrhoea faecal samples collected at 7dpw. At species level, diarrhoeic faeces showed lower diversity for Chao1 and Simpson indexes only in the Ct group > Diarrhoeic samples collected from animals in the Ab medicated-feed group also showed higher diversity than non-diarrhoeic animals, but only for Shannon and Simpson indexes, and these differences were smaller

Peace Daniel (01:45:54) (in thread): > The groups with taxas are global data set and consistency@Joan C. ChukwuemekaYou should read it again please

Joan C. Chukwuemeka (02:00:01): > Hello everyone<!here>I’d appreciate our views/feedback on thestudyi’mcurating. > > The study aimed to evaluate******changes in the cervical microbiome (CM)********** ****of patients who******underwent chemoradiation (CRT) therapy******for locally advanced cervical cancer. > They separated the women into two age groups: premenopausal (still having periods) and postmenopausal (no longer having periods). They also had healthy women (HPV negative) in each age group for comparison.******Before and after chemoradiation CRT******, cervical swab samples were collected from 16 patients with squamous cell carcinoma of the cervix, and 30 healthy women. > Area of concern: > 1. For contrast that were between healthy controls and pre-treatment ( before******chemoradiation******) or post-treatment(after******chemoradiation)******for either age groups (Experiments 1 to 4) I chose******Vaginal (cervical) microbiome measurement ****asCondition, while and for the other contrasts between before and after******chemoradiation, ****I chose “******Response to radiation”. ****I’m thinking perhaps all should be “******Response to radiation” . ****What do you think? > 2. Can you spot record of alpha diversity metrics for the post treatment vs healthy controls contrast. Its signatures are recorded in Supplementary Table S2. > 3. Is relative abundance correct as the data transformation? - Attachment (Frontiers): Frontiers | Increased diversity of a cervical microbiome associates with cervical cancer > The cervical microbiome (CM) is a complex ecosystem that can change in response to gynecological cancers. We aimed to evaluate changes in the CM of patients … - Attachment (BugSigDB): Increased diversity of a cervical microbiome associates with cervical cancer - BugSigDB > The cervical microbiome (CM) is a complex ecosystem that can change in response to gynecological cancers.We aimed to evaluate changes in the CM of patients who underwent chemoradiation (CRT) therapy for locally advanced cervical cancer.

Joan C. Chukwuemeka (03:15:33) (in thread): > @Peace DanielAlright. > > There were alpha diversity for both species level and functional level: for Figure 1, only 1A and 1B were for species level, while for Supplementary Figure 1-1A,1B and 1E were for species level. The others were for Functional levels, which is not the curation focus on BugSigDB. And the reason I suggested the curation for the treatment alone is that it shows it was done but was unchanged as against not being done. > > Perhaps a second look is needed. Well done.

Peace Daniel (03:18:28) (in thread): > Yh I get your reasoning on alpha diversity for treatment@Joan C. ChukwuemekaThis is why I didn’t curate it tho, and no signatures > “The treatment did not affect diversity at species level”

Joan C. Chukwuemeka (03:25:21) (in thread): > Hi@Mildred AnashieI think You’ve got it right. The contrasts I identified are like you said. I think It’s possible to have Experiments without alpha diversity measures. Here are the contrasts I identified.Precancer(n=15) Vs Stage-3 cancer (T3)(n=15) > Chao 1 - Increased > Shannon -unchangedStage-1 cancer (T1)(n=15) Vs Stage-3 cancer (T3)(n=15)Chao 1 - Increased > Shannon -unchangedStage-2 cancer (T2)(n=15) Vs Stage-4 cancer (T4)(n=15)Chao 1 - Increased > Shannon - unchangedStage-3 cancer (T3)(n=15) Vs Stage-4 cancer (T4)(n=15)Chao 1 - decreased > Shannon - decreasedPrecancer (n=15) Vs Cancer(n =60)No alpha diversity but differential signatures - Figure 2B, 2C, 3A Supplementary figures: 2D, 3DEarly stage cancer(T1&T2) (n=30) Vs Late stage cancer(T3&T4) (n =30) > No alpha diversity but differential signatures are available in Figure 2D, 3B; Supplementary figures: 2A, 3EPrecancer (n=15) Vs Late stage Cancer(n =30) > signatures- figures 3B2Adjacent Tumor Tissue (AT) (n=20)Vs Precancer stage(n=15)signatures - Supplementary figures: 2C, 3B, 3DAdjacent Tumor Tissue (AT)(n=20) Vs Tumor Tissue (TT)Chao 1 - unchanged > Shannon - unchanged > signatures - Supplementary figures: 2B,3A, 3C > > The sample size of most of the groups are actually in Table 1, with the exception of AT which was mentioned within text. > > There was no clear mention of sample size for TT, however, I don’t know if it will be right to infer it as the same with AT, since they mentioned it as “counterpart” to AT.:thinking_face:Or perhaps to leave it blank

Mildred Anashie (03:28:02) (in thread): > Well done on your curation@Joan C. Chukwuemeka:clap:I’lltake a look at this

Peace Daniel (03:37:32) (in thread): > Hi@Joan C. ChukwuemekaWell done on your curation > I agree with you on relative abundance > For your second question take a look at fig 5B > > “Comparison of the non-parametric Shannon indices for healthy controls and patients before treatment. (A) and for patients before and after treatment, and at 3/6 months post-treatment (C) Chao index- comparison in healthy controls and patients before treatment (B) and in patients before and after treatment, and at 3/6 months post-treatment (D).”

Peace Daniel (03:48:03) (in thread): > From fig 5 C and D you have: > Pre treatment > Post treatment and > 3 months post treatment@Joan C. Chukwuemeka

Aleru Divine (04:05:28) (in thread): > Good morning@Joan C. Chukwuemeka! Well done on your curation. > I agree with relative abundance as data transformation. > > Alpha diversity measures are in figure 5. > > See this excerpt, > “We aimed to evaluate changes in the CM of patients who underwent chemoradiation (CRT)”I think“vaginal microbiome measurement”and“response to chemotherapy”are both good choicesfor the condition,none is wrong in my opinion.

Joan C. Chukwuemeka (04:05:36) (in thread): > @Peace DanielThis is what is shown in Figure 5:5A - Shannon diversityfor Premenopause & postmenopause:contrast -pre-treatment Vs healthy Controls 5B -Chao1 index for Premenopause & postmenopause:contrast -pre-treatment Vs healthy Controls 5C -Chao1 indexforPre-treatment vs Post-treatment andPre-treatment vs 3 months post treatment5D - Shannon diversityforPre-treatment vs Post-treatmentandPre-treatment vs 3 months post treatmentThe question**** ****is**** ****If there’s any record of alpha diversity metrics for thePost treatment vs healthy controlscontrast in the study? It’s not in Figure 5. - File (PNG): image.png

Aleru Divine (04:07:10) (in thread): > Yikes!There’snone@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:07:16) (in thread): > Yea, thanks@Aleru DivineI’m actually particular aboutPost treatment vs healthy controls contrast

Joan C. Chukwuemeka (04:07:56) (in thread): > Alright@Aleru Divine:+1:

Peace Daniel (04:08:10) (in thread): > Oh,there’snone@Joan C. ChukwuemekaMy apologies I mixed it up

Mildred Anashie (04:08:11) (in thread): > Idon’tsee alpha diversity for post treatment and healthy controls@Joan C. ChukwuemekaI guess youwouldrecord without alpha diversity

Joan C. Chukwuemeka (04:10:04) (in thread): > Thanks everyone. > Do you think I should go with both conditions or 1?:thinking_face:@Aleru Divine

Mildred Anashie (04:10:46) (in thread): > Response to chemotherapy or chemoradiation works fine in my opinion > > If they are available on BugSigdb tho@Joan C. Chukwuemeka

Joan C. Chukwuemeka (04:11:33) (in thread): > Yes, There’s “response to radiation”@Mildred Anashie

Aleru Divine (04:11:43) (in thread): > Just one:sweat_smile:

idiaru Angela (04:11:59) (in thread): > Hi@Joan C. ChukwuemekaFor the data transformation, I also agree with it being relative abundances > > For the condition, for the experiments between healthy and post treatment, I believe response to radiation is a better fit, since the microbiome measurement was done after radiation therapy > > I didn’t spot the specific Alpha-diversity you’re checking for > Well done!

Joan C. Chukwuemeka (04:13:38) (in thread): > Alright. Thank for the help everyone.:pray:Much appreciated.:gratitude-asl:

Adenike Oladimeji-Kasumu (06:47:46): > Hello everyone, I trust we are all having a productive week. Please I would like peer reviews on my recent curation. Below is the link and the link to the Paper.https://bugsigdb.org/Study_1035.https://journals.plos.org/plosntds/article?id=10.1371/journal.pntd.0005826. Thank you. - Attachment (BugSigDB): The microbiome in urogenital schistosomiasis and induced bladder pathologies - BugSigDB > BACKGROUND: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. - Attachment (journals.plos.org): The microbiome in urogenital schistosomiasis and induced bladder pathologies > Author summary The human microbiome comprises bacteria (plus viruses, fungi and archeae) inhabiting different sites of the body. They do not specifically cause diseases, but their presence, absence or population influence body functions. We therefore examined such organisms found along the urinary tract, in persons living in a rural community in Nigeria who considered themselves healthy, were infected with the parasite Schistosoma haematobium or had developed bladder complications along with the parasite infection. We found that these groups shared a large portion of the microbiome, but there were microbial species unique to infected persons and those with bladder complication. Some of these were capable of inducing inflammation and could offer less protection to the host. We also predicted pathways that are affected by the difference in the microbiome.

idiaru Angela (06:53:02) (in thread): > Well done@Adenike Oladimeji-KasumuWould give it a review

Peace Daniel (06:59:56) (in thread): > Well done@Adenike Oladimeji-KasumuI’dtake a look

Adenike Oladimeji-Kasumu (07:04:52) (in thread): > Thank you@idiaru Angelaand@Peace Daniel.

Joan C. Chukwuemeka (07:31:43) (in thread): > Well done:+1:@Adenike Oladimeji-Kasumuwould check it out.

Peace Daniel (07:35:32) (in thread): > @Adenike Oladimeji-Kasumu > 1. I didn’t find any matched on factor, what was stated was: > “Furthermore, gender and age influenced taxa abundance independent of infection or bladder pathology” > > 2. This excerpt seems to talk about confounders but with only this information, I’d love your input too@idiaru Angela“ While some of these criteria may indeed be due to urogenital schistosomiasis, it was necessary to prevent confounders and ambiguity. Samples suspected of urinary tract infection (positive nitrites, positive leukocyte esterase and ≥ 5wbc/high power field) were removed from further analysis” > > 3. I think your group names can be more concise with this and table 1 > “comprising (a) the Advanced group, having infection and bladder pathologies, (b) Bladder pathology-only group, (c) infection-only (detected by microscopy or PCR), and (d) controls (no infection or pathology). For microbiome abundance analysis, we also grouped all samples into two—infected and non-infected.” > > Fig6 and 5 doesn’t look like lefse > “Mann-Whitney test (or non-parametric White’s test [35] in STAMP) was used to test for significant differences between two groups. “ > > I think fig 7 is curatable which is lefse

Adenike Oladimeji-Kasumu (08:14:04) (in thread): > @Peace Danielwow! I will take a second look at this. I appreciate you

Peace Daniel (08:17:16) (in thread): > You’rewelcome@Adenike Oladimeji-KasumuPlease feel free to let me know whatever you disagree with, I could be wrong:blush:

idiaru Angela (08:20:33) (in thread): > Yeah I agree with your observation about the cofounders@Peace DanielFurther more Lefse and Mann-Whitney test cannot do that. > I’m yet to give the study a comprehensive review though

Adenike Oladimeji-Kasumu (08:23:38) (in thread): > Yeah, I did not record cofounders in my curation.

Peace Daniel (08:25:18) (in thread): > Alright waiting for yours@idiaru AngelaI think they wanted to prevent confounders but did not actually control for it. So if itwasn’tcontrolled for lefse and Mann Whitney are valid statistical tests@Adenike Oladimeji-Kasumuyes, I just shared an observation

idiaru Angela (09:02:17) (in thread): > @Adenike Oladimeji-Kasumuwell done on this curation. > 1. I believe the study design for this study should be case control not cross sectional observational. This is because the study divided participants based on if they had cases or not (control) > 2. I also didn’t find any information that directly states the subjects were matched on any parameter. > 3. For the signatures, I believe 5A should also be curated > 4. For the alpha diversity, I believe they should be unchanged. From the description of Fig 3, “Comparison of microbiome diversity indices (A) between urogenital schistosomiasis infection and controls, (B) in different states of urogenital schistosomiasis and controls, and (C) among age groups. Dark band represent mean diversity index, circles represent outliers. The differences in diversity were not significant (p>0.05) except in C(p = 0.038)” the differences were not statistically significant so should be unchanged > 5. Figure 5 and 6 do seem like Lefse results to me, but are not bar plots

Peace Daniel (09:04:27) (in thread): > It’shere:grin:I thought so as well regarding the study design but this was stated in the study@idiaru AngelaSeventy participants from Eggua, southwestern Nigeria provided morning urine samples and were screened for urogenital schistosomiasis infection and bladder pathologies in a cross-sectional study.

Peace Daniel (09:27:59) (in thread): > Also check this link out@idiaru Angela@Adenike Oladimeji-KasumuI think this clarifies the logFC use in Mann Whitney testhttps://microucph.github.io/amplicon_data_analysis/html/da.html

idiaru Angela (09:32:38) (in thread): > Yeah@Peace Daniel:grin::blush:. > For the study design, there’s a thread where it was said that sometimes authors might mislabel their own study design. And in this case, the participants were selected based on the exposure of interest

Peace Daniel (09:34:12) (in thread): > There’sthis too,it’squite confusing > > Differential abundance was measured with LogFC, the log2 of the number of times the OTUs belonging to a genus (or family) are more numerous in one group relative to the other.

Peace Daniel (09:34:42) (in thread): > Oh really@idiaru AngelaIt’smost likely a case control then

idiaru Angela (09:36:05) (in thread): > The link you sent is pretty informative@Peace Daniel:thinking_face:. I guess they weren’t clear enough on the statistical test used:sneezing_face:

Peace Daniel (09:37:29) (in thread): > I just feel like itwasn’tlefse given as fig 7 was presented in the study@idiaru Angela

Mildred Anashie (09:42:52) (in thread): > Well done on your curation@Adenike Oladimeji-KasumuI think 5a should be curated along side 5b > It appears one is showing Family and the other genus but for the same experiment > > Also I found this (Check image) > Does it mean anything?:thinking_face:Idon’tthink LEfSe was the statistical test used - File (PNG): IMG_4449

Adenike Oladimeji-Kasumu (09:45:24) (in thread): > Exactly@Peace DanielI also chose Case Control but edited it after reading that statement.@idiaru AngelaI didn’t curate 5A because it is Phylum level, I instead curated 5B. Same experiment but genus level. > For the Alpha diversity, that is noted. But it says that there was higher number of OTU detected in infected, pathology and Advanced cases respectively in each case. See attached picture to help Analyse the context please. > Yes, that’s what I deduced. That figures 5 and 6 are also Lefse results. But since@Peace Danielcalled my attention to Figure 7. What do you think? Note that figure 7 comprises different taxa levels. I believe that I have curated these microbes in the first experiment (Infected vs Non-infected). - File (JPEG): IMG_20240430_142436.jpg

Peace Daniel (09:46:05) (in thread): > Does this test exist in bugsigdb@Mildred Anashie?

Mildred Anashie (09:46:26) (in thread): > Yes EdgeR is on BugSigdb@Peace Daniel

Peace Daniel (09:47:00) (in thread): > Then this should be it I suppose@Mildred Anashie

Adenike Oladimeji-Kasumu (09:47:07) (in thread): > @Mildred Anashiethank you. > I saw that statement too but it isn’t really clear to me.

Peace Daniel (09:47:37) (in thread): > Oh@Adenike Oladimeji-KasumuI think you can curate it because another statistical test was used > > What do you think about fig 7@Mildred Anashie

Adenike Oladimeji-Kasumu (09:49:20) (in thread): > @Mildred AnashieMy assumption was to curate for the lowest taxa level, that’s why I didn’t curate 5A. So are you implying that there should be 3 signatures in that experiment?

idiaru Angela (09:49:24) (in thread): > I think 5A should be curated in the same experiments. For Fig 7, I believe the organisms have already been captured by the first statistical test

Mildred Anashie (09:50:24) (in thread): > No@Adenike Oladimeji-KasumuNot three signatures, include the increase and decrease based on the 2 signatures for the experiment you have curated already > > This is my opinion

idiaru Angela (09:51:01) (in thread): > @Adenike Oladimeji-Kasumuonly 2 signatures in the expriment, still curated as increase or decrease. In the curation policy, it is states that all taxa should be curated regardless of their taxa level. So Fig 5A is curated exactly as figc5B was

Peace Daniel (09:51:39) (in thread): > A different test was used so I feel it can be curated@idiaru Angela

Adenike Oladimeji-Kasumu (09:51:43) (in thread): > Okay… If I get you right, I should just as add them to the signatures I already have. Right?

idiaru Angela (09:52:08) (in thread): > Yes@Adenike Oladimeji-Kasumu

Peace Daniel (09:53:14) (in thread): > Found it@Adenike Oladimeji-Kasumu@idiaru AngelaThis is a review from@Chioma OnyidoSometimes, researchers do different stat tests for diff abundance analysis and then compare the results produced by these tests. In this case, Wilcoxon and LEfSe were both used and the results were different. When this happens, they should be curated as separate experiments in bugsigdb (see curation policy).

Mildred Anashie (09:53:24) (in thread): > Figure 7 is quite confusing@Peace Danielandthat’sbecauseit’sa different statistical test that was used

idiaru Angela (09:53:46) (in thread): > @Peace Danielsee this excerpt from the curation policy - File (JPEG): Screenshot_20240430_145256_Chrome.jpg

Peace Daniel (09:54:08) (in thread): > Okay, confirmed@idiaru Angela:grin:

Adenike Oladimeji-Kasumu (09:54:33) (in thread): > What I’m not understanding now is which one has the different statistical test (EdgeR)?

idiaru Angela (09:54:33) (in thread): > @Peace Danielonly if they report separate taxa should they be curated separately.

Mildred Anashie (09:54:47) (in thread): > I think you are both saying the same thing@Peace Danieland@idiaru AngelaWe need to cross check the taxas to confirm if it should be curated or not

Mildred Anashie (09:55:24) (in thread): > @Adenike Oladimeji-Kasumuit appears Fig 7 has a different statistical test from the other experiments

Peace Daniel (09:55:38) (in thread): > Yea I got it, it says different:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Adenike Oladimeji-Kasumu (09:56:12) (in thread): > @Mildred AnashieAlright… I get now

Peace Daniel (09:57:26) (in thread): > Agreed@Mildred Anashie

Joan C. Chukwuemeka (10:00:11) (in thread): > @Adenike Oladimeji-Kasumuhere are my views: > * There are no matched-on factors > * Antibiotic exclusion - recent use of Antibiotics > * For the contrast: urogenital schistosomiasis (infected) Vs non-infected (Experiment 3) > > > Group 0 name should beNon-infectednothealthy controlsGroup 0 sample size - 24(it differs from the control(n=13) used in the other contrasts. It was an additional grouping specifically for microbiome analysis. (Excerpt:We identified four major groups of participants based on the status of infection and bladder pathology (Table 1), comprising (a) the Advanced group, having infection and bladder pathologies,(b) Bladder pathology-only group, (c) infection-only (detected by microscopy or PCR), and (d) controls (no infection or pathology).******For microbiome abundance analysis, we also grouped all samples into two - infected and non-infected.************Signature source - Figures 5A, 5B and 7****** > > * Alpha diversity measure is only******Inverse Simpson. ****No richness measure, the mention of richness was only an explanation that Inverse Simpson takes both OTU richness and relative abundance into account. and it was “unchanged” for all the comparisons. > * For Statistical test: > > > All experiment - Mann-Whitney test was used to test for significant differences between two groups.For Experiment 3-urogenital schistosomiasis****(infected) Vs non-infected- Additional Statistical test - LEfSe for figure 7** - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png - File (PNG): image.png

Peace Daniel (10:00:36) (in thread): > They’re are not the same signatures people@Mildred Anashie@idiaru AngelaSome similarities yh but differences in sphingobacterium and xenorhabdus from whatI’vechecked so far

Peace Daniel (10:08:57) (in thread): > Didy’allsee it too:face_holding_back_tears:@Mildred Anashie@idiaru Angela

Joan C. Chukwuemeka (10:12:24) (in thread): > @Adenike Oladimeji-Kasumuyou may need to check the supporting information on the web version, which is a supplementary material. There’s an additional contrast/experiment-Figure S2Bpersons with urogenital schistosomiasis infection without bladder pathology ******(infection-only) ******and pathology without schistosomiasis infection******* (pathology-only)***** - File (PNG): image.png

Joan C. Chukwuemeka (10:12:50) (in thread): > I don’t think Edge R is the Statistical test

idiaru Angela (10:17:01) (in thread): > I see the differences@Peace Daniel

Mildred Anashie (10:23:22) (in thread): > @Joan C. Chukwuemekawhat do you think is the statistical test? > > Yea@Peace Daniel

Joan C. Chukwuemeka (10:24:53) (in thread): > @Mildred Anashie**** For Statistical test > > All experiment - Mann-Whitney test was used to test for significant differences between two groups. > For Experiment 3-urogenital schistosomiasis(infected) Vs non-infected- Additional Statistical test - LEfSe for figure 7

Joan C. Chukwuemeka (10:25:01) (in thread): > However, Based on the curation policy excerpt you shared@idiaru Angelaand what is in the study, there are quite a few similarities.

Peace Daniel (10:26:19) (in thread): > @Joan C. Chukwuemekaalso thinkit’sMann Whitney as well, this could be the time to tag the mentors@Adenike Oladimeji-Kasumu

Joan C. Chukwuemeka (10:26:22) (in thread): - File (PNG): image.png

Adenike Oladimeji-Kasumu (10:27:43) (in thread): > Hummm…. I need to go all over these messages to avoid being overwhelmed.:blush:Thank you so much@Joan C. Chukwuemekaand everyone

Joan C. Chukwuemeka (10:30:09) (in thread): > LEfSe result is only applicable in experiment 3 as i stated earlier - File (PNG): image.png

idiaru Angela (10:30:53) (in thread): > I agree with Mann-Whitney being the statistical test for alll except Fig 7

Joan C. Chukwuemeka (10:39:54) (in thread): > @Adenike Oladimeji-KasumuIt’s alright, no need to be overwhelmed. > Basics are: > * Study design - cross sectional or case control:thinking_face: > * There are no matched-on factors > * Antibiotic exclusion - recent use of Antibiotics > * For the contrast: urogenital schistosomiasis (infected) Vs non-infected (Experiment 3) > > > Group 0 name should beNon-infectednothealthy controls > > > Group 0 sample size - 24(it differs from the control(n=13) > > > ******Signature source - Figures 5A, 5B and 7****** > > * Alpha diversity measure is only******Inverse Simpson******and it was “unchanged” for all the comparisons. > * There’s an additional contrast/experiment-Figure S2B - persons with urogenital schistosomiasis infection without bladder pathology ******(infection-only) ******and pathology without schistosomiasis infection******* (pathology-only)***** > * For Statistical test: > > > All experiment - Mann-Whitney test was used to test for significant differences between two groups. > For Experiment 3-urogenital schistosomiasis****(infected) Vs non-infected- Additional Statistical test - LEfSe for figure 7**

Peace Daniel (11:55:06) (in thread): > Fig 6 is also curatable@Adenike Oladimeji-KasumuWell done for putting it together@Joan C. Chukwuemeka

Adenike Oladimeji-Kasumu (18:26:48) (in thread): > Thank you so much everyone for helping me with this. I appreciate all your effort. I have corrected all necessary part of the curation.

2024-05-01

Peace Daniel (01:08:44) (in thread): > Well done@Adenike Oladimeji-Kasumubut I think you mixed the conclusion for fig 7 which was similar to fig 5A and B.You’reto curate it separately as an experiment since fig 5 was Mann Whitney,itcan’tbe merged with fig 7

Mildred Anashie (02:15:16): > Happy NewMonthEveryone:rocket:Happy BugSigdb-ing too:hugging_face:Let’s do more inMay:rocket::clinking_glasses:

Scholastica Urua (02:35:58) (in thread): > Happy new month of May everyone:hugging_face:

Peace Daniel (02:50:38) (in thread): > Happy new month@Mildred Anashie@Scholastica Urua

idiaru Angela (03:06:48) (in thread): > Happy new month@Mildred Anashieand everyone

Joan C. Chukwuemeka (03:10:14) (in thread): > Thanks@Mildred AnashieHappy new month to you too and everyone

Aleru Divine (03:43:23) (in thread): > Thank you@Mildred Anashie:heart::people_hugging:Happy New month to you and to everyone:heart::sparkles::rocket:

Glorious Katushabe (04:44:19) (in thread): > Thank you@Mildred Anashieenjoy the new Month

Nana (04:50:02): > Happy workers day all. Good morning all

Rahila-me (04:52:23) (in thread): > @Mildred AnashieTo You too

Rahila-me (04:52:39) (in thread): > Same here@Nana

Aleru Divine (05:42:04): > Good morning everyone, and a Happy new month:sparkles:<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace SandyPleaseI’dlike to delete signature 1 in experiment 10 of this study. I was reviewing my study and realized I made a mistake:pray:https://bugsigdb.org/Study_1043 - Attachment (BugSigDB): Alteration in Oral Microbiome Among Men Who Have Sex With Men With Acute and Chronic HIV Infection on Antiretroviral Therapy - BugSigDB > Despite the antiretroviral therapy (ART), human immunodeficiency virus (HIV)-related oral disease remains a common problem for people living with HIV (PLWH).

Svetlana Ugarcina Perovic (05:50:45) (in thread): > Deleted.

Aleru Divine (05:53:08) (in thread): > Thank you so much:pray:

Svetlana Ugarcina Perovic (06:58:56): > Before TOMORROW’s official Outreachy announcement,we would like to CONGRATULATE to ALL OF YOU on your outstanding achievementduring Outreachy**** ****contribution period! Hope you improved your open source/open science skills and learned new ones, and hope you got even more motivated to continue working in the open source community.Tomorrow we will not have our weekly team meeting.Instead you can schedule a 1-1 meeting with me herehttps://cal.com/svetlana-up/mvifand discuss your open source/open science plans. I am happy to hear your ideas and support your career growth. > > Once again,thank you ALL for your GREAT work!Your mentors<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (07:01:52): > Thanks a lot@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape<@U1LCB8WEA>@Chioma Onyido@Peace Sandyfor your support all through. You all are Amazing.:gratitude-asl:

idiaru Angela (07:02:33) (in thread): > To the mentors, thank you all so much for the opportunity to participate in this wonderful community. It has been a superb experience so far and I have learnt so much. Thank you!@Peace Sandy@Esther Afuape@Chioma Onyido@C. Mirzayi (please do not tag this account)@Levi Waldron@Svetlana Ugarcina Perovic

Mildred Anashie (07:06:50) (in thread): > Thank you so much@Svetlana Ugarcina Perovicyou and all the mentors have made this experience very wonderful and totally worthwhile:hugging_face:I appreciate you all@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Peace Sandy<@UBNSEMS3S>@Levi Waldron

Mildred Anashie (07:10:01): > Hello everyone > > I’m done curating this study and I’ll really appreciate review before I submit for review from the Mentorshttps://bugsigdb.org/Study_1041My concern is in the fact that I see they mentioned Matched on and I went with a Cross sectional not case control study design but looking at the groups again I’m thinking some experiments appear to be case control especially those with signatures:thinking_face:So I’m wondering if this is a case of two study designs and I know I’m to go with the primary study design and I’m unsure which to settle for > Case control or Cross sectional observational not case control > > I was going to confirm during the office hour tomorrow but since they wouldn’t be one:white_frowning_face:I’ll really appreciate inputs and help with this - Attachment (BugSigDB): Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma - BugSigDB > Characterization of the oral microbiota profile through various studies has shown an association between the microbiome and oral cancer; however, stage-specific determinants of dynamic changes in microbial communities of oral cancer remain elusive.

Aleru Divine (07:12:52) (in thread): > Thank you so much:hugging_face:@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Chioma Onyido@Peace Sandy@Esther Afuape! > > This journey has been truly incredible. My open-source and communication skills have improved immensely. > > I’m super grateful to this community, the mentors, and my fellow applicants for making this journey so amazing. Thank you all from the bottom of my heart!:heart:

idiaru Angela (07:15:52) (in thread): > Well done@Mildred Anashiewould give it a look

Peace Daniel (07:18:01) (in thread): > Thank you so much for your support and this beautiful experience@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Chioma Onyido@Peace Sandy@Esther AfuapeTo my fellow contributors,y’allmade this journey so amazing and worthwhile. Thank you:pray::heart:

Peace Daniel (07:19:08) (in thread): > Well done@Mildred AnashieI’lltake a look

Flourish Ralph (07:22:31) (in thread): > Thank you mentors and my fellow contributors,it’sbeen a blast!:sparkles::sparkles:

Scholastica Urua (07:36:35) (in thread): > Thank you@Svetlana Ugarcina Perovicfor all your support.:smiling_face_with_3_hearts:Really grateful to all the mentors for their mentorship. Thank you<@UBNSEMS3S><@U1LCB8WEA>@Chioma Onyido@Peace Sandy@Esther Afuape. > > It was a real nice experience contributing on BugSigDB with fellow applicants. Thank you for making my open source experience fun:hugging_face:

Peace Daniel (07:40:30) (in thread): > As it was ethically not possible to include healthy subjects, we started our analysis with precancer samples; hence, the bacterial signature identified is specific to cancer stages compared with that of precancer samples. > > Finally, we had an unavailability of longitudinal samples. In our cross-sectional sample sets, we tried to match the subjects based on their age, sex, risk factor status, and ethnicity > > Youdidn’tcurate any healthy controls nor did I see any experiments for them, it should be a cross-sectional study@Mildred Anashie

Scholastica Urua (07:43:29) (in thread): > Well done on your curation@Mildred Anashie. I agree with@Peace Danielon the study design. It’s Cross sectional. Also the healthy samples used where adjacent healthy tissues from patients with cancer.

Aleru Divine (07:45:11) (in thread): > It’s a cross-sectional observational study and not case-control@Mildred Anashie. I agree with@Peace Danieland@Scholastica Urua

Mildred Anashie (07:45:53) (in thread): > Thank you@Scholastica Urua@Peace Daniel@idiaru Angela@Aleru Divine

Mildred Anashie (07:47:48) (in thread): > Thanks alot for your inputs > Study designs can be a bit confusing most times:face_with_peeking_eye:

idiaru Angela (07:50:48) (in thread): > Yeaah@Mildred AnashieThe case-control vs cross sectional observational and > The longitudinal vs prospective cohort always get me:sneezing_face:

Kelechi Madubuko (07:52:12) (in thread): > Thank you@Svetlana Ugarcina Perovicand co-mentors for all you do for us. Big ups to my fellow applicants. It was such an insightful period where I learnt a whole lot more about open source. I appreciate y’all:heart:

Mildred Anashie (07:52:55) (in thread): > Totally@idiaru Angela

Svetlana Ugarcina Perovic (07:54:06): > Reading this paperhttps://elifesciences.org/articles/33953and wanted to share with you another example (beside this onehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639) of the fact thatstrains of the same bacterial species can differ in gene content:the metabolism of the drug digoxinin vivoby the bacteriumEggerthella lenta requires a gene that is present in only certain strains ofE. lenta.and be part of the several BugSigDB study signatures of the same experiment. - Attachment: Attachment > During today’s talk by Liao Herui (PhD Student of City University of Hong Kong) about his work on strain identification analysis (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10433603/), I remembered our discussion on why some signatures have the same species in decrease and increase reported? > > One of Liao’s slides had a nice illustration and helpful comment that I would like to share with you: > Different bacterial strains may have different biological properties due to the different genes: > for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98% [https://pubmed.ncbi.nlm.nih.gov/30837975/]

Peace Daniel (07:54:58) (in thread): > That’strue@Mildred Anashie

Peace Daniel (07:58:36) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicAdded to my To-do for the day:rocket:

Scholastica Urua (08:15:19) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:pray:

idiaru Angela (08:28:19) (in thread): > This is really interesting:thinking_face:. Thank you for sharing@Svetlana Ugarcina Perovic

Joan C. Chukwuemeka (08:28:49) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic

Adenike Oladimeji-Kasumu (08:38:43) (in thread): > True. Thank you@Peace Daniel

Adenike Oladimeji-Kasumu (08:40:17) (in thread): > Thank you@Svetlana Ugarcina Perovicand every other mentor. Also thanks to my colleagues here. It has been an insightful experience.

Adenike Oladimeji-Kasumu (08:41:15) (in thread): > This is insightful and very helpful. Thank you@Svetlana Ugarcina Perovic

Aleru Divine (09:59:58) (in thread): > Thank you for sharing this resource@Svetlana Ugarcina Perovic:raised_hands:

Aleru Divine (10:01:23) (in thread): > Sometimes I leave it tillI’mdone curating:sleepy:that wayI’vereally really gone through the study and I’m convinced:sweat_smile:

Rahila-me (11:17:42) (in thread): > @Svetlana Ugarcina PerovicThank you. To our great mentors and my fellow contributors you all made it amazing

Rahila-me (12:07:26) (in thread): > Thank you for sharing

Glorious Katushabe (12:27:47) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Mildred Anashie (12:40:37) (in thread): > I do that most times@Aleru Divine:joy:

Mkpouto Shedrack (13:52:45) (in thread): > This is an insightful read, thanks for sharing@Svetlana Ugarcina Perovic

2024-05-02

Scholastica Urua (01:24:58): > Good morning everyone, hope we are all doing well… > Please I have a few questions about thiscurationand would appreciate your assistance: > 1. What condition will be best suited for this study? > 2. Do you think fig. 5 and supplementary table 2 are curatable? > Thank you in anticipation to your feedback.:hugging_face: - Attachment (BugSigDB): Microbial Similarity and Preference for Specific Sites in Healthy Oral Cavity and Esophagus - BugSigDB > Human microbial communities are highly complex ecosystems, but it remains unclear if microbial compositions have any similarity in distinct sites of the oral cavity and esophagus in particular.

Peace Daniel (02:20:05) (in thread): > Good morning@Scholastica UruaI’lltake a look at it

Aleru Divine (02:21:14) (in thread): > Good morning@Scholastica Urua,I’mdoing very well.Thank you! I hope you are too.Well done on your curation:hugging_face:andhere’smy input. > > The likely condition being investigated in this study is the microbial composition which we can liken to microbiome measurement (since that is available on BugSigDB) my reason is, the study aims to understand if there are similarities microbial compositions between different sites within the oral cavity. So I think that “microbiome measurement” makes sense.I also think figure 5 can be curated.The color-coded representation helps visually identify taxa that exhibit differential abundance across the different sites within the oral cavity.From the figure caption, you can interpret it.For example, > > “The yellow nodes indicate no statistically significant differences of a given taxon between the samples of three sites, the red nodes indicate significantly higher relative abundance in saliva than other two sites…”

idiaru Angela (02:44:52) (in thread): > Hey@Scholastica Uruawell done. > I agree with@Aleru Divineon the condition > For Fig 5, it is curatable, the text and description of the figure provide guidance in its curation. > “the red nodes indicate significantly higher relative abundance in saliva than other two sites, the green nodes indicate significantly higher relative abundance in the supragingival plagues than other two sites, and the blue nodes indicate significantly higher relative abundance in tongue dorsum than other two sites in oral cavity.” > So the experiments contained in figure 5 for instance will include > Saliva vs teeth and tongue denoted by the red nodes > Teeth vs saliva and tongue denoted by the green nodes > Tongue vs teeth and saliva denoted by the blue nodes

Peace Daniel (02:50:43) (in thread): > @Scholastica UruaFig 5 looks curatable but I’m still trying to find the taxas represented with letters (q,p, n…) in fig 5 > > It should be in the paper somewhere

Peace Daniel (02:53:41) (in thread): > I don’t think Suppl. tableS2 is curatable, look at this and take a look at fig 1@Scholastica UruaIt looks like relative abundance and not differential abundance > > “A great diversity of microbial community was observed in the oral cavity and the esophagus (Figure 1 and Supplementary Table S2)”

Peace Daniel (02:58:03) (in thread): > For the lettered taxas in fig 5, seems like you’d curate the letters in fig 3 (looks like the only figure with letters in your study) > I’m not quite sure tho@Scholastica UruaIt’s a suggestion > > > Lastly I agree with@Aleru Divine@idiaru Angelaon the condition

Joan C. Chukwuemeka (03:03:48) (in thread): > Good morning@Scholastica Urua“The focus of this present study is *******to measure and compare the composition and relative abundance of the bacterial population inhabiting: ******(1) the oral cavity and esophagus; (2) three distinct oral niches including the saliva, tongue dorsum and supragingival plaque; (3) three distinct esophagus segments including upper, middle and lower esophagus, in a population with high-risk of esophagus cancer.”Based on the above Excerpt, for condition, I thinktaxonomic microbiome measurement ***is a closer fit, as it refers to taxonomic variation which I believe is what they want measure through the comparisons done of the bacterial population. - File (PNG): image.png - File (PNG): image.png

Joan C. Chukwuemeka (03:14:48) (in thread): > Supplementary table 2 is relative abundance, so it’s not curatable

Scholastica Urua (03:15:57) (in thread): > Thank you everyone for your feedback, I really appreciate:pray:

Scholastica Urua (03:18:56) (in thread): > Yes, fig 3 is the only one with taxa assigned to the letters@Peace Daniel. Fig 5 does not have that so I was confused how to decode the alphabet if I’m curating it…

Joan C. Chukwuemeka (03:21:24) (in thread): > Unlike Cladogram in Figure 3, cladogram in Figure 5 has no key, so there’s really no clear pointer to decipher what the letterings mean. Not certain it can be curated, ’cause it won’t sound right to assume the letterings mean the same as that used for figure 3

idiaru Angela (03:22:26) (in thread): > @Scholastica Uruathe text under figure 5 states the taxa that are abundant

Peace Daniel (03:23:17) (in thread): > It’s curatablebut the letters are the issue@Scholastica Urua

Scholastica Urua (03:23:41) (in thread): > I get you@Joan C. Chukwuemeka. I’m not sure fig 3 key should be used for 5…

Scholastica Urua (03:29:39) (in thread): > Thank you for pointing that out@idiaru Angela. It’ll make more sense curating the significant taxa mentioned in text:pray:. Also I agree with your groupings but I’m stuck on the alpha diversity… > Table 1 explains the alpha diversity. In the experiment withSubgingival Plaque vs Saliva and tonguefor example where Chao is higher in SP than tongue but lower than Saliva how should that be recorded?..

Joan C. Chukwuemeka (03:29:56) (in thread): > @Scholastica UruaPerhaps you can use the the text explanation where Figure 5 was referenced as a source/guide. > However, since it was referenced with Supplementary table 2, could it be a relative abundance measure?:thinking_face: - File (PNG): image.png

Peace Daniel (03:30:06) (in thread): > I just checked some taxas in both fig 3 and 5, the key in fig 3can’tbe used@Scholastica UruaI propose to curate the taxas listed and add a note for the ones without key

Joan C. Chukwuemeka (03:33:23) (in thread): > @Peace Danielbut there’s no key on Figure 5 & the letters are not Taxa names

Peace Daniel (03:35:01) (in thread): > The significance and how to read it is in the caption and text beneath and the letters are supposed to be taxa names like in fig 3@Joan C. Chukwuemeka

idiaru Angela (03:37:28) (in thread): > @Scholastica UruaSee this excerpt for alpha diversity > “Regarding alpha diversity, Shannon Diversity and Simpson Index revealed that microbial profiles in the specimens from both the saliva and the tongue dorsum were statistically less diverse compared to those from the supragingival plaque, but no apparent differences among three sites measured by the Chao1 richness (p < 0.001, Table 1).”

idiaru Angela (03:38:54) (in thread): > So@Scholastica UruaI think the alpha diversity followed the same groupings with the differential abundance measurement

idiaru Angela (03:39:42) (in thread): > But Table 1 presentation though:face_with_peeking_eye:

Joan C. Chukwuemeka (03:40:33) (in thread): > Yea,@Peace Daniel, In a cladogram, due space constraints letters are inputted as representative of the taxas and then a key provided to show what each letter denotes, just as figure 3. > > Possibly the authors forgot to Include that of figure 5. > I’m not certain how she would curate that without key and add a note. Perhaps if you give an instance, I could get you view completely.

Scholastica Urua (03:50:43) (in thread): > @idiaru AngelaI don’t think I understand you when you saythe alpha diversity followed the same groupings with the differential abundance measurement. > For Table 1, I used the mean to determine the alpha diversity for the first experiment since this excerpt (image below) aligned with a the mean on the table… > Simpson and Shannon are decreased in Esophagus while Chao is increased - File (PNG): Screenshot_20240502-084557.png

idiaru Angela (04:00:57) (in thread): > @Scholastica UruaIn the way I interpreted the excerpt in the text I sent you, they had grouped the saliva and tongue together against the subgingival plague just as they did with the differential abundance, so I interpreted that to mean that they used the same groupings for the alpha diversity > And in this excerpt > > “Alpha diversity was estimated for each sample using the Chao1 richness (representing the community richness), Shannon’s Diversity and Simpson Index (representing the community diversity) and then plotted using Origin 7.5. Statistical difference of the alpha diversity between two groups was determined by Student’s t-tests and that among three or more groups by one-way ANOVA tests followed by Dunnet’s test for multiple comparisons.” > > We see that ANOVA was used for alpha diversity comparing 3 groups:thinking_face:. > > Also if you read the image below, it says that no statistical differences were observed, meaning the alpha diversity indices would be unchanged. - File (JPEG): Screenshot_20240502_085627_Chrome.jpg

Joan C. Chukwuemeka (04:02:09) (in thread): > From the excerpt > > “Regarding alpha diversity, Shannon Diversity and Simpson Index revealed that microbial profiles in the specimens from both the saliva and the tongue dorsum were statistically ******less diverse compared to those from the supragingival plaque*******, *******but no apparent differences among three sites measured by the Chao1 richness******* (p < 0.001, Table 1). > Groupings -** ****Saliva(Sa) vs Supragingival plaque(SP) (group 1)*****Shannon Diversity - Increased****Simpson Index - Increased****Chao1 richness - Unchanged*****Tongue dorsum (TD) Vs Supragingival plaque(SP) (group 1)*****Shannon Diversity - Increased****Simpson Index - Increased****Chao1 richness - Unchanged****(********Supragingival plaque was more diverse in Shannon and Simpson)*********Explanation: ***The study found that the microbial profiles (the types of microbes present) in both saliva and the tongue dorsum (the top surface of the tongue) were less diverse compared to those in the supragingival plaque (the bacteria on the surface of teeth above the gum line). However, when they looked at the “Chao1 richness,” which estimates the total number of different types of microbes, there were no clear differences among the three sites (saliva, tongue dorsum, and supragingival plaque).

Scholastica Urua (04:14:41) (in thread): > Thank you@idiaru Angela@Joan C. ChukwuemekaI’ll go through them again

Svetlana Ugarcina Perovic (04:26:48): > Good morning:teapot:hope you are all doing well. > > On May 7, there is aWebinar:NCCR Microbiomes Seminar SeriesWith a very important and interesting topic:The impact of antibiotics on the human gut microbiota. Speaker is Camille Goemans. > > After this talk, it should be more clear why we have the bugsigdb curation box “Antibiotics exclusion”. - Attachment (NCCR): Camille Goemans on antibiotics and the gut microbiome - NCCR > On 7 May 2024, the NCCR Microbiomes Seminar Series is thrilled to host Camille Goemans, Professor in the Global Health Institute at EPFL. Prof. Goemans heads the Laboratory of Drug-microbiota Interactions, which investigates how antibiotics interact with the human gut microbiota and lead to dysbiosis, the associated emergence of antibiotic resistance, and ultimately the design […]

idiaru Angela (04:30:09) (in thread): > Looking forward to it:blush:. Thank you for sharing!

Scholastica Urua (04:41:02) (in thread): > Thank you@Svetlana Ugarcina Perovic. Looking forward to it.

Adenike Oladimeji-Kasumu (04:43:49) (in thread): > Thank you for the invite@Svetlana Ugarcina Peroviclooking forward to attending.

Bolanle Wahab (04:46:12) (in thread): > Thank you@Svetlana Ugarcina Perovic!!!

Peace Daniel (05:04:57) (in thread): > Thank you@Svetlana Ugarcina Peroviclooking forward to it

Joan C. Chukwuemeka (05:16:34) (in thread): > Oh wow!:smiley:That’s awesome. > Good morning & Thanks for the Invite@Svetlana Ugarcina Perovic. > Calendar marked:nerd_face:7 May 2024, from 12h00 to 13h00 CEST. > (11AM to 12PM WAT.)

Aleru Divine (06:59:29) (in thread): > Looking forward to it@Svetlana Ugarcina PerovicThanks for sharing:blush:

Peace Daniel (07:13:42) (in thread): > I was occupied earlier and couldn’t give a timely response@Joan C. Chukwuemeka@Scholastica UruaI was going to interpret fig 5 but on a second thought, I agree with Joan that it shouldn’t be curated. Take a look at this excerpt and also it was tagged with suppl table s2 which is also relative abundance > > “the green nodes indicate significantly higherrelative abundancein the supragingival plagues than other two sites, and the blue nodes indicate significantly higher relative abundance in tongue dorsum than other two sites in oral cavity”

Peace Daniel (07:15:28) (in thread): > Don’t forgetto mark experiment 1 as complete too@Scholastica Urua

Scholastica Urua (07:21:09) (in thread): > Thank you, I’ll mark it.@Peace Danielare you saying there should be no additional experiments?

Peace Daniel (07:22:51) (in thread): > NahI’mtalking about fig 5@Scholastica Urua

Scholastica Urua (07:24:48) (in thread): > Okay, thanks

idiaru Angela (07:24:58) (in thread): > Going by that@Peace Danielthen fig3 should also not be curated.:thinking_face:I’m not convinced yet. I still think the text points to differential abundance because it is denoting the abundance between multiple sites

Peace Daniel (07:25:55) (in thread): > Hold on:joy:

Peace Daniel (07:26:26) (in thread): > Yh, I just checked again@idiaru AngelaI’llgo ahead to read fig 5

Peace Daniel (07:29:44) (in thread): > So@Scholastica UruaBacteroidia is increased in saliva and decreased in teeth and tongue > Flavobacteriia is increased in teeth and decreased in saliva and tongue

Scholastica Urua (07:33:34) (in thread): > Yes@Peace Danielfrom the fig. I think the taxa mentioned in text/fig should be curated but those alphabets in the figure without key shouldn’t…

Peace Daniel (07:40:52) (in thread): > Yea@Scholastica Urua

Mkpouto Shedrack (08:23:27) (in thread): > Welldone on your curation@Scholastica Uruaand to add, I think the condition should be taxonomic microbiome measurement because the study is comparing bacterial populations and high variability of microbial compositions. > > For second question, nothing to add just so excited to read the intelligent responses of all commenters. Learnt a lot.

Scholastica Urua (08:42:35) (in thread): > Thank you@Mkpouto Shedrack

Mildred Anashie (10:01:57) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:blush:

Joan C. Chukwuemeka (12:03:58): > Congrats@Scholastica Urua. Wishing you the best:four_leaf_clover:

idiaru Angela (12:06:12): > Congratulations@Scholastica Urua. I wish you a successful internship:heart::rose:

Peace Daniel (12:07:54): > Congratulations@Scholastica Urua:dancer::dancer:Wishing you the best

Aleru Divine (12:09:25): > Congratulations@Scholastica Urua:sparkles::rocket:wishing you all the best.

Scholastica Urua (12:09:31) (in thread): > Thank you@Joan C. Chukwuemeka:sparkling_heart:

Scholastica Urua (12:10:11) (in thread): > Thank you@idiaru Angela:heart:

Scholastica Urua (12:11:23) (in thread): > Thank you@Peace Daniel:sparkling_heart:

Scholastica Urua (12:11:47) (in thread): > Thank you@Aleru Divine

Adenike Oladimeji-Kasumu (12:14:59): > Congratulations@Scholastica Uruawell deserved:heart:All the best

Bolanle Wahab (12:16:12): > Congratulations@Scholastica Urua:partying_face::partying_face::heart:

Peace Daniel (12:16:53): > @Svetlana Ugarcina Peroviccan we still ask questions and curate papers?I’dlove to keep working on papers thatI’minterested in

Mildred Anashie (12:20:27): > Congratulations@Scholastica Urua:confetti_ball::heart:Wishing you all the best

Mkpouto Shedrack (12:20:35): > Huge congratulations@Scholastica Urua

Victoria (Burah) Poromon (12:21:18): > Congratulations@Scholastica Urua:relieved::relieved::relieved:Have an amazing internship!

Oluwatomisin Omojokun (12:27:10): > Congratulations:confetti_ball::confetti_ball::clinking_glasses::clinking_glasses:

Aleru Divine (12:31:18) (in thread): > Co-ask:sweat_smile:I’dalso love to keep curating and contributing to BugSigDB.

Flourish Ralph (12:35:21): > Congratulations@Scholastica Uruawishing you the best, have a great internship!:tada::sparkles:

Linda Uchenwoke (12:39:36): > Congratulations!:tada::tada::tada::tada:@Scholastica UruaWishing you all the best:sparkles:

Scholastica Urua (12:41:41) (in thread): > Thank you@Adenike Oladimeji-Kasumu:hugging_face:

Scholastica Urua (12:42:11) (in thread): > Thank you@Bolanle Wahab:hugging_face:

Scholastica Urua (12:42:51) (in thread): > Thank you@Mildred Anashie:hugging_face:

Scholastica Urua (12:43:18) (in thread): > Thank you@Mkpouto Shedrack:blush:

Scholastica Urua (12:44:01) (in thread): > Thank you@Victoria (Burah) Poromon:hugging_face:

Scholastica Urua (12:44:29) (in thread): > Thank you@Oluwatomisin Omojokun:hugging_face:

Scholastica Urua (12:45:06) (in thread): > Thank you@Flourish Ralph:pray:

Rahila-me (12:45:38): > @Scholastica Uruacongratulations:dancer:have a wonderful internship

Scholastica Urua (12:46:26) (in thread): > Thank you Linda:sparkling_heart:

Scholastica Urua (12:46:54) (in thread): > Thank you@Rahila-me:sparkling_heart:

Joan C. Chukwuemeka (13:35:44): > Good evening all<!here>I just curated thisstudyand would like our views. > The study aimed to investigate******the prebiotic effect and underlying************mechanism of stachyose on high-fat diet (HFD)-induced obesity************and related MetS in obese mice.****** > 1. Any other close fitting term for condition asides high-fat diet? > 2. Any other contrast/experiment? > Thanks. - Attachment (BugSigDB): Stachyose ameliorates obesity-related metabolic syndrome via improving intestinal barrier function and remodeling gut microbiota - BugSigDB > In this study, oral supplementation of stachyose significantly improved HFD-induced MetS symptom, including overweight, hyperlipidemia, hepatic steatosis and system-wide inflammation.

Nana (13:42:25): > @Scholastica Uruacongratulations:tada::tada:

idiaru Angela (13:45:17) (in thread): > Well done@Joan C. Chukwuemeka

Scholastica Urua (13:45:38) (in thread): > Thank you so much@Nana:hugging_face:

Blessing Ene Anyebe (13:48:46): > Really lovely to see! Congratulations@Scholastica Urua:partying_face::orange_heart::fire::sparkles::sparkles::tada::tada:

Scholastica Urua (13:51:43) (in thread): > Thank you so much@Blessing Ene Anyebe:sparkling_heart:

idiaru Angela (13:52:22) (in thread): > For the condition, I looked through the ontology website and didn’t find any other appropriate term. I think what you have picked is good enough > For the experiment, I believe it’s only one experiment present in the study. > Well-done

Joan C. Chukwuemeka (14:50:10) (in thread): > Alright. Thanks@idiaru Angela

Mildred Anashie (15:02:06) (in thread): > Well done@Joan C. Chukwuemeka:clap:

Aleru Divine (16:27:33) (in thread): > Well done@Joan C. ChukwuemekaI agree with HFD as the condition too. > > While I agree with the experiment you’ve curated, I’m considering the correlation analysis of the relationship between gut bacteria and intestinal epithelial barrier related indicators.<@UBNSEMS3S>mentioned during one of the office hours that it can be curated.

2024-05-03

Scholastica Urua (01:38:20) (in thread): > Well done on your curation@Joan C. Chukwuemeka. I agree with your condition. HFD seems to be the best fit

Svetlana Ugarcina Perovic (03:12:21) (in thread): > We got the supplementary material from authors of the paper!@Mildred AnashieAs I mentioned before, authors are usually happy to share with you info on their published study and this is a nice example of good open science communication. - File (PNG): Screenshot 2024-05-03 at 09.07.08.png

idiaru Angela (03:36:12) (in thread): > Good news!:grin:

Svetlana Ugarcina Perovic (03:41:06): > Good morning!We will keep on highlighting:THANK YOU ALLfor YOUR amazing contribution work! Of course, you can continue BugSigDB-ing:slightly_smiling_face:we would be honoured to have you here in our community. > > Also, we would appreciate if you can share your experience with us by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7Happy Friday!<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape@Svetlana Ugarcina Perovic - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu

Mildred Anashie (03:52:21) (in thread): > This is great > > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (03:59:32): > Just saw from my dear (previous work) mentee Tobi that there isBioinformHER initiativehttps://www.linkedin.com/posts/tobiolanipekun_bioinformatics-womeninstem-computationa[…]538912161792-Jinh?utm_source=share&utm_medium=member_desktopDo you know about it? > > Btw, feel free to contact Tobi if you have any question. - Attachment (linkedin.com): Tobi Olanipekun on LinkedIn: #bioinformatics #womeninstem #computationalbiology #underrepresented > I am happy to share that after 1 year and out of 130400 global applicants, I have been selected for the prestigious… > > Just kidding, Scratch that, lol…

Peace Daniel (04:00:01) (in thread): > Thank you@Svetlana Ugarcina Perovic

Peace Daniel (04:00:45) (in thread): > No, this is my first time reading about it. Thank you for sharing@Svetlana Ugarcina Perovic

Amarachi Lewachi (04:13:15): > Congratulations@Scholastica Urua. Wish you a successful internship.

Scholastica Urua (04:15:46) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Scholastica Urua (04:16:46) (in thread): > Thank you@Amarachi Lewachi:heart:

Aleru Divine (07:42:49) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (07:43:59) (in thread): > My first time too@Peace Daniel, thank you for sharing@Svetlana Ugarcina Perovic

Mildred Anashie (07:47:47) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:blush:

Svetlana Ugarcina Perovic (11:31:06): > I will repeat here a message about our survey:slightly_smiling_face:

Svetlana Ugarcina Perovic (11:31:13): > <!channel>If you were an outreachy applicant and contributed to any of the Bioconductor projects#BugSigDB#sweave2rmd#BSgenomeForge#miaverse, please help us in spreading the word about your amazing work. > > You can share your experience (anonymously) by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7Thank you! - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu

Azhar Ismagulova (11:55:34): > @Azhar Ismagulova has left the channel

Mildred Anashie (14:38:38) (in thread): > Thank you@Svetlana Ugarcina Perovic

2024-05-06

Mildred Anashie (03:35:48): > Hi everyone > Good morning > > Happy new week:blush:Please I’ll like your reviews on this before I submit it for review by the mentorshttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8515944/Additional supplemental information is attached > Link to curationhttps://bugsigdb.org/Study_1031I’llneed to confirm all the Alphadiversity’sand the sample size especially Experiment 2 > Thank you:pray: - Attachment (PubMed Central (PMC)): Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19 > Bacterial-viral interactions in saliva have been associated with morbidity and mortality for respiratory viruses such as influenza and SARS-CoV. However, such transkingdom relationships during SARS-CoV-2 infection are currently unknown. Here, we aimed … - Attachment (BugSigDB): Oral Microbiome Alterations and SARS-CoV-2 Saliva Viral Load in Patients with COVID-19 - BugSigDB > Bacterial-viral interactions in saliva have been associated with morbidity and mortality for respiratory viruses such as influenza and SARS-CoV.However, such transkingdom relationships during SARS-CoV-2 infection are currently unknown.

Svetlana Ugarcina Perovic (03:53:26) (in thread): > A kind reminder for our survey! Thanks!

Svetlana Ugarcina Perovic (03:53:59): > Happy Monday!

Peace Daniel (05:15:39) (in thread): > Well done@Mildred AnashieI’dtake a look

Scholastica Urua (05:20:04) (in thread): > Hi@Mildred Anashie, > > Good morning, and good job on the curation. I have a few observations and suggestions: > > 1. The study uses a case-control design, not a cross-sectional design. It compares microbiome diversity and taxonomic composition between COVID-19 patients and control subjects. Additionally, COVID-19 patients are further categorized by saliva viral load into three groups: negative, low viral load, and high viral load. > > 2. The alpha diversity measures identified in the study are Shannon and Chao. Both measures appear to be unchanged across all experiments. > > 3. Initially, it seemed that experiments 1 and 2 were identical because experiment 1 compared “Control vs. COVID-19” and experiment 2 compared “SARS-CoV-2 Negative vs. SARS-CoV-2 Positive.” After reading the article, I realized they are different: experiment 2 compares two groups of COVID-19 patients—those who are saliva-negative and those who are saliva-positive. Could you consider renaming the groups to “SARS-CoV-2 Saliva-Negative” and “SARS-CoV-2 Saliva-Positive”? Additionally, changing the group 1 description to “COVID-19 patients with detectable saliva viral load” could enhance clarity. > > 4. I’m yet to confirm the sample sizes for the experiments except exp. 1 which I agree with you on what you curated. > > 5. I couldn’t find the additional supplemental information you mentioned. I could only find Tables S1 and S2 in the article. > > I hope these suggestions are helpful. I’d love to hear other perspectives on the curation. > > Well done!

Peace Daniel (05:27:10) (in thread): > Hello@Mildred AnashieI agree with@Scholastica Uruaon points 1, 2, 3 and 5 > I agree that the group names should be different in experiment 2 as they look like a different experiment to me as well. I also found only the supplementals containing demographics for Covid 19 groups and SARS-Cov

Mildred Anashie (05:30:10) (in thread): - File (PDF): Supplemental.Information_Spectrum_revision_final_20210810

Mildred Anashie (05:32:10) (in thread): > Okay > > Thanks alot@Scholastica Urua@Peace Daniel

Peace Daniel (05:32:25) (in thread): > Also from your supplemental, sample sizzle for SARS Cov based on negative, low and high viral load > 15, 14, 14 respectively@Mildred Anashie

Mildred Anashie (05:33:49) (in thread): > In that case the sample size for Group 1 in experiment 2 would be 14 + 14 (Both those with high and low viral load) instead of 46 (Those who were SARS-COV 2 positive)

Mildred Anashie (05:34:02) (in thread): > This was my confusion > > Thanks alot

Scholastica Urua (05:34:11) (in thread): > Happy Monday@Svetlana Ugarcina Perovic:sunrise_over_mountains:

Mildred Anashie (05:34:37) (in thread): > Happy Monday@Svetlana Ugarcina Perovic:blush:

Scholastica Urua (05:34:59) (in thread): > Yes, I agree with that@Mildred Anashie

Peace Daniel (05:35:37) (in thread): > Table S4 looks curatable@Mildred AnashieYou curated it:+1:

Scholastica Urua (05:39:46) (in thread): > Yeah, she did. Fig 3 and Table S4 are same.

Scholastica Urua (05:41:36) (in thread): > I’m thinking if there should be an additional experiment;Low vs Highbased on the alpha diversity…:thinking_face:

Scholastica Urua (05:45:19) (in thread): > Scratch that. They’re unchanged and the signatures are already curated in the other experiments…

Mildred Anashie (05:55:29) (in thread): > Thanks again@Scholastica Urua@Peace Daniel

Svetlana Ugarcina Perovic (06:12:09): > Here is an excellent example of reviewing and responding to the review by@Scholastica Uruaand@Aleru Divinehttps://github.com/waldronlab/BugSigDBcuration/issues/367 - Attachment: #367 A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease > A gut microbiome signature for HIV and metabolic dysfunction-associated steatotic liver disease
> https://pubmed.ncbi.nlm.nih.gov/38162648/ > > I chose this particular article because its HIV-related. HIV remains a significant global health challenge, affecting millions of individuals worldwide. Working on research related to HIV can ultimately improve public knowledge of the virus.

Svetlana Ugarcina Perovic (06:13:11): > If you would like to review the curation of the paper that you added in the GitHub, feel free (just let me know:wink:)

Peace Daniel (06:19:20) (in thread): > Good job@Aleru Divine@Scholastica Urua

Mildred Anashie (06:20:17) (in thread): > Well done@Aleru Divine@Scholastica Urua

Aleru Divine (06:26:08) (in thread): > Well done on your curation@Mildred AnashieI’ma bit late to the partyaren’tI?:sleepy:any other concerns?

Aleru Divine (06:26:35) (in thread): > Thanks@Svetlana Ugarcina Perovicand Happy Monday!:hugging_face:

Aleru Divine (06:27:39) (in thread): > Thank you@Svetlana Ugarcina Perovic@Peace Danieland@Mildred Anashie. Well done on the review once again@Scholastica UruaI am currently going through your study:sweat_smile:

Mildred Anashie (06:29:50) (in thread): > Yea@Aleru Divine:blush:IthinkI’mall clear on this now but you could still give your review

Aleru Divine (06:30:29) (in thread): > Alright@Mildred Anashie:heart:

Scholastica Urua (06:48:22) (in thread): > Thank you@Aleru Divine:pray:

Rahila-me (07:15:42) (in thread): > @Svetlana Ugarcina Perovichappy monday to you too

idiaru Angela (08:14:33) (in thread): > Good job@Scholastica Uruaand@Aleru Divine:+1:

idiaru Angela (08:15:12) (in thread): > Happy Monday@Svetlana Ugarcina Perovic:blush:

Victoria (Burah) Poromon (10:53:56) (in thread): > Hello@Svetlana Ugarcina PerovicHappy Monday > > And yesI’dlike to review the curation of the paper I added on GitHub. > > I’ll also like to implement the reviews/feedbacks on my personal curations if that is possible.

Svetlana Ugarcina Perovic (11:09:43) (in thread): > yes please@Victoria (Burah) Poromon

2024-05-07

Scholastica Urua (03:51:19): > Good morning everyone. Kind reminder of the webinar today…:hugging_face:https://community-bioc.slack.com/archives/C04RATV9VCY/p1714638408423039?thread_ts=1714638408.423039&cid=C04RATV9VCY - Attachment: Attachment > Good morning :teapot: hope you are all doing well. > > On May 7, there is a Webinar: NCCR Microbiomes Seminar Series With a very important and interesting topic: The impact of antibiotics on the human gut microbiota. Speaker is Camille Goemans. > > After this talk, it should be more clear why we have the bugsigdb curation box “Antibiotics exclusion”.

Peace Daniel (04:11:43) (in thread): > Thanks for the reminder and good morning@Scholastica Urua

Svetlana Ugarcina Perovic (04:20:54): > <!channel>**** HELPI need your help. Only 18 people filled in the survey, out of many many many applicants that contributed duringDecember 2022 Outreachy round*****May 2023 Outreachy round******December 2023 Outreachy round******May 2024 Outreachy round***Could you please help me in reaching them. Thanks - Attachment: Attachment > <!channel> If you were an outreachy applicant and contributed to any of the Bioconductor projects #BugSigDB #sweave2rmd #BSgenomeForge #miaverse, please help us in spreading the word about your amazing work. > > You can share your experience (anonymously) by filling in this short survey https://forms.gle/brqH5M2uTYMKy23x7 > Thank you!

Scholastica Urua (04:28:40) (in thread): > Good morning@Peace Daniel

2024-05-08

Svetlana Ugarcina Perovic (05:55:54) (in thread): > Any highlights from this webinar? I could not make it. Thanks!

Svetlana Ugarcina Perovic (06:34:47): > Another excellent symposium (free and online) on Monday:https://www.hsph.harvard.edu/biostatistics/2024/04/2024-harvard-chan-microbiome-center-symposium-the-microbiome-and-cancer-register-now/ - Attachment (Department of Biostatistics): 2024 Harvard Chan Microbiome Center Symposium: The Microbiome and Cancer – Register Now! > Visit the post for more.

Aleru Divine (11:25:41) (in thread): > Thank you so much for sharing this@Svetlana Ugarcina Perovic. Registered and looking forward to it.:sparkles:

Mildred Anashie (17:11:00) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

UBNSEMS3S (17:45:56): > Hi everyone, > > Just a reminder that we have our team meeting at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. Looking forward to seeing you there.

2024-05-09

Scholastica Urua (02:02:23) (in thread): > Thank you<@UBNSEMS3S>

Scholastica Urua (02:02:43) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (03:39:42): > See you today at the meeting!:wave:

Aleru Divine (04:03:30) (in thread): > Thanks for the reminder<@UBNSEMS3S>. Looking forward to it!

Aleru Divine (04:03:53) (in thread): > See you there@Svetlana Ugarcina Perovic

Scholastica Urua (09:28:13): > @Peace Danielwould you mind working on the study (you shared on zoom) together? Looks confusing though:sweat_smile:…

Peace Daniel (09:39:23) (in thread): > Not at all@Scholastica UruaI’d be happy to share thoughts with you, I attached the link on BugSigdb here and I’ll be in your dm to discuss the groups and diversity I’ve taken note of.https://bugsigdb.org/Study_1079 - Attachment (BugSigDB): Signatures within the esophageal microbiome are associated with host genetics, age, and disease - BugSigDB > BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host.

Scholastica Urua (09:55:57) (in thread): > Okay, I’ll take a look at it

2024-05-10

Svetlana Ugarcina Perovic (04:35:24): > Good morning:tulip:As we discussed yesterday at the team meeting, here are some R tasks. > > We have a package for simple analysis of BugSigDB data calledBugSigSimplewhich is available here:https://github.com/waldronlab/bugSigSimple/and there are two good beginner issues for you to work on: > 1. https://github.com/waldronlab/bugSigSimple/issues/20 > 2. https://github.com/waldronlab/bugSigSimple/issues/21 > Working on these issues will give you an understanding of the package and its functions and will lay the groundwork for futuredevelopment of the BugSigDB dashboard.Happy Friday!<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Svetlana Ugarcina Perovic

Victoria (Burah) Poromon (05:02:57) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicI’ve been waiting for this update:blush:

Scholastica Urua (05:20:19) (in thread): > Happy Friday@Svetlana Ugarcina Perovic. Thank you for sharing:hugging_face:

Peace Daniel (05:59:00) (in thread): > Happy Friday, thank you@Svetlana Ugarcina Perovic

Rahila-me (06:00:48) (in thread): > @Svetlana Ugarcina PerovicThank you

Peace Daniel (06:01:40) (in thread): > Can I request to work on an issue?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:02:35) (in thread): > Yes, sure, please do communicate in the corresponding GitHub issue. Thanks!

Peace Daniel (06:02:51) (in thread): > Okay thank you

Aleru Divine (07:49:10) (in thread): > Thank you so much for sharing them:blush:@Svetlana Ugarcina Perovic

UBNSEMS3S (09:30:44): > Hi everyone the Advanced R book club is today at 11 AM EDT! Tram will be presenting Chapter 15: R6 at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

Sehyun Oh (10:59:16): > Hi! One quick question - where is the schema for BugSigDB metadata stored? In particular, the allowed values?

Victoria (Burah) Poromon (11:12:16) (in thread): > Hi@Sehyun OhCould this be whatyou’relooking for?https://bugsigdb.org/Property:Allows_value - Attachment (BugSigDB): Property:Allows value

Scholastica Urua (12:48:39) (in thread): > Hello@Peace Daniel, I went through the study and these are what I deduced: > * Although 3 sequencing types are mentioned in the abstract, only two (16S and shotgun) are used to identify taxonomic signatures group. > > * LEfSe is the statistical test used across all experiments. > > * I couldn’t identify sample sizes for all experiments but some are highlighted in Table 1. > Here are some of the experiments I could identify with their signatures;******Differences across disease subgroups using LEfSe analysis (16S data - Additional file 3.4)******Exp. 1: Normal vs GERD > Exp. 2: Normal vs GERD (within subjects classified as PPI NO) > Exp. 3: Normal vs GM > Exp. 4: Normal vs BE (fig 4b) > Exp. 5: GERD vs GM > Exp. 6: GERD vs BE > Exp. 7: GM vs BE******Differences across disease subgroups using LEfSe analysis (Shotgun - Additional file 3.5)******Exp. 8: Normal vs GERD > Exp. 9: Normal vs GERD (within subjects classified as PPI NO) > Exp. 10: Normal vs GM (fig 4c) > Exp. 11: Normal vs BE (fig 4b) > Exp. 12: GERD vs GM > Exp. 13: GERD vs BE > Exp. 14: GM vs BE******Differentially abundant taxa between GERD and subjects with a normal esophagus within each cluster (16S data - Additional file 3.6)******Exp. 15: Normal vs GERD (Cluster 1) > Exp. 16: Normal vs GERD (Cluster 2) > Exp. 17: Normal vs GERD (Cluster 3)******Differentially abundant taxa between GERD and subjects with a normal esophagus within each cluster (Shotgun - Fig 4a and Additional file 3.7)******Exp. 18: Normal vs GERD (Cluster 1) > Exp. 19: Normal vs GERD (Cluster 2) > Exp. 20: Normal vs GERD (Cluster 3)******PPI usage******Exp. 21: YES vs NO (in normal esophagus - Additional file 2: Figure S3A) > Exp. 22: YES vs NO (in GERD patients Additional file 2: Figure S3B)

Scholastica Urua (12:56:00) (in thread): > Also, I think Additional file 1.6 (16S) and 1.7 (Shotgun) which document taxonomic differences across clusters are curatable, although I’m not sure about the groups. Here’s what I’m thinking; > > 16S Data - Additional file 1.6 > Cluster 1 vs 2 and 3 > Cluster 2 vs 1 and 3 > Cluster 3 vs 1 and 2 > > Shotgun Data - Additional file 1.7 > Cluster 1 vs 2 and 3 > Cluster 2 vs 1 and 3 > Cluster 3 vs 1 and 2

Scholastica Urua (12:58:05) (in thread): > Please let me know what you think when you take a look at it…

Sehyun Oh (13:41:47) (in thread): > Thanks!

Peace Daniel (14:18:02) (in thread): > Alright@Scholastica UruaI’llgive a response tomorrow whenI’mdone comparing with what I have

2024-05-11

Peace Daniel (12:03:37) (in thread): > Hello@Scholastica UruaI’ve given this a thorough review. I agree with most of your observations, I’d like to add a few things. > 1. In fig 4 of the study, fig 4A, B and C can be curated > 2. I took note of the alpha diversity as unchanged in clusters 1&3 but decreased in cluster 2 > 3. Sample size was shown in table 1 and suppl table 5 > 4. I think this is a cross sectional study > 5. What do you think would be an appropriate condition? > 6. Which of these signatures would you like to curate? I’m more inclined to curate fig 4, alpha diversity and all signatures related to clusters, shotgun sequencing if that’s fine by you

Peace Daniel (12:16:08) (in thread): > What do you think could be the body site too

Scholastica Urua (12:29:22) (in thread): > Hello@Peace Danielcompliment of the day:hugging_face: > 1. I agree with you. Fig 4a, b and c are curatable. These signatures are also repeated in the supplementary material so I quoted both sources above; > Signatures for Exp. 18, 19 and 20 above are in Fig.4aand Additional file 3.7 > Signatures for Exp. 4 and 11 are in Fig.4band Additional file 3.4 and 3.5 respectively. > Signatures for Exp. 10 are in Fig.4cand Additional file 3.5… > > 2.:+1:3.:+1:4. I’m on the fence about the study design. I’m thinking cross sectional but it could also be case control:thinking_face:. We may have to seek more opinions on this. > > 5. The conditions will be different for most of the experiments seeing that there are different contrasting groups…GERDfor exp. 1,GMfor exp. 4…. We have to look at the conditions individually > > 6. I’m open to curating anyone you’re not working on. > > For the body site, samples where taken from the esophagus. I’ll have to check again to confirm.

Peace Daniel (12:34:34) (in thread): > Thank you@Scholastica UruaI agree with you on the body site but let me know if you find something else > For the study design this is why I said it’s cross sectional > “Subjects who had a normal esophagus by histological assessment were considered controls. These subjects may be prescribed PPIs due to some mild reflux symptoms; however, no reflux esophagitis is detected through histology.” > > Thanks for stating out the experiments repeated, there are a lot:smiling_face_with_tear:

Scholastica Urua (12:44:28) (in thread): > You’re welcome@Peace Daniel. Yes, there are a lot of experiments.:sleepy:I’ll let you know of anything else I find out.

2024-05-15

UBNSEMS3S (17:42:20): > Hi everyone, > > Just a reminder that we have our team meeting at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. Looking forward to seeing you there.

Scholastica Urua (18:10:40) (in thread): > Thank you<@UBNSEMS3S>

Victoria (Burah) Poromon (18:26:39) (in thread): > Thank you<@UBNSEMS3S>

2024-05-16

Svetlana Ugarcina Perovic (11:05:35): > Another great curation and reviewhttps://github.com/waldronlab/BugSigDBcuration/issues/391Well done@Scholastica Uruaand@Joan C. Chukwuemeka:clap: - Attachment: #391 Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses > Study Link -Altered Middle Ear Microbiome in Children With Chronic Otitis Media With Effusion and Respiratory Illnesses

Svetlana Ugarcina Perovic (11:07:22): > I am looking forward to:goat:microbiome study:wink:that you mentioned today at our team meeting!

Peace Daniel (11:47:27): > Hello everyone@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy<@UBNSEMS3S>Is there a way to search for taxas using OTU number?

Peace Daniel (11:51:28) (in thread): > Specifically, how do I find these species? > > Bacteroidetes.Bacteroidia.Bacteroidales.Porphyromonadaceae.Porphyromonas.Otu00113 > > Or > > Firmicutes.Bacilli.Bacillales.unclassified.unclassified.Otu00402

Scholastica Urua (13:42:40) (in thread): > I’ve always wondered this too. Like if there’s a database for all taxa with their various OTU numbers.

Victoria (Burah) Poromon (13:49:15) (in thread): > I’m on it!:sweat_smile:

Peace Daniel (13:52:42) (in thread): > :tired_face:I need it in this studyI’mcurating, I feel like the genus is specific enough

UBNSEMS3S (17:07:22): > Hi everyone the Advanced R book club is tomorrow at 11 AM EDT! Marcel will be presenting Chapter 15: S4 at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-05-18

Aleru Divine (06:47:10): > Good morning everyone and Happy Weekend!:clinking_glasses:I just completed the curation of a study and would appreciate your review and insights. > > Few notes that I’ll like your thoughts on: > 1. Since the study explored the difference in skin microbiome composition between groups of participants, I opted fortaxonomic microbiome measurementas the condition. > 2. The sampling site was sole of feet and since this wasn’t available on BugSigDB, I went forSkin of sole of pessincepesis Latin forfoot. > 3. Regarding the differential abundance,DESEQ2was used to test for differential abundance of bacterial genera, whilesPLS-DA was used to identify and rank the contribution of individual bacterial genera to the differences in microbiome composition between the attractiveness groups not necessarily differential abundance.(I hope this is correct) > Link:https://bugsigdb.org/Study_1081Thank you so much!:pray:Have a great weekend everyone:sparkles: - Attachment (BugSigDB): Skin microbiome alters attractiveness to Anopheles mosquitoes - BugSigDB > BACKGROUND: Some people produce specific body odours that make them more attractive than others to mosquitoes, and consequently are at higher risk of contracting vector-borne diseases.

idiaru Angela (06:59:56) (in thread): > Well done@Aleru Divine. I think the condition and body site you choose are perfect for this study.

Aleru Divine (07:10:34) (in thread): > Thank you so much@idiaru Angela:heart:

Mildred Anashie (10:59:16) (in thread): > Well done@Aleru Divine:clap:I agree with you on No 1 and 2 > AlsoIf the paper says DESeq2 was used for differential abundance thenthat’swhat should be recorded:blush:

Aleru Divine (11:02:27) (in thread): > Thank you so much@Mildred Anashie

2024-05-20

Svetlana Ugarcina Perovic (04:56:23): > Good morning :teapot:Tomorrow is another MVIF, this time focused on microbiome ethics! > Registration (free):https://events.ringcentral.com/events/microbiome-vif-n-29Full program with abstracts:https://www.microbiome-vif.org/en-US/-/future-events/mvif29-21-2223-may-2024Happy Monday! > (I will now respond to all your messages, thanks!) - File (PNG): may24_program (1).png

Svetlana Ugarcina Perovic (05:00:01) (in thread): > The answer is NO:slightly_smiling_face:Number next to the OTU is just a serial number of OTU in the study. For example: OTU00001, OTU00002, OTU00003 - OTU00113

Svetlana Ugarcina Perovic (05:03:26): > Still need you help:arrow_down:I’m trying to reach as many as possible former outreachy applicants to fill in our survey. We would like to write a paper about outreachy experience and especially about fruitful contribution periods. Could you please spread the word about it and maybe share with your outreachy colleagues. I’ve shared it through my social media channels as well as Slack Bioconductor to encourage people to do this short questionnaire. Now I am encouraging outreachy applicants to spread the word among them and take part in this survey. > > Thanks! > > * > > If you were an outreachy applicant and contributed to any of the Bioconductor projects#BugSigDB#sweave2rmd#BSgenomeForge#miaverse, please help us in spreading the word about your amazing work.You can share your experience (anonymously) by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7Thank you! - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu

Peace Daniel (07:01:04) (in thread): > Okay, this meanI’llonly curate the taxa Porphyromonas right?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (08:58:07) (in thread): > Yes@Peace Daniel

Peace Daniel (09:18:17) (in thread): > Okay, thank you so much@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (12:27:53): > Sounds like a good opportunity to learn clinical genomics.https://coursesandconferences.wellcomeconnectingscience.org/event/molecular-genomic-approaches-to-clin[…]inicalmicrobafrica24&utm_term=&utm_content= - Attachment (Wellcome Connecting Science Courses and Conferences): Molecular & Genomic Approaches to Clinical Microbiology in Africa  — 20240831 > Discover the revolutionary potential of molecular and genomic techniques in clinical microbiology for tackling infectious diseases

Aleru Divine (15:30:38) (in thread): > Thank you so much for sharing this opportunity@Svetlana Ugarcina Perovic:heart:

U1LCB8WEA (16:29:42) (in thread): > Sorry I didn’t reply earlier, but thank you for your testing! With your help, Wikiworks was able to complete the site upgrade.

2024-05-21

Svetlana Ugarcina Perovic (03:31:29) (in thread): > See you today at MVIF!

Scholastica Urua (03:51:27) (in thread): > Good morning@Svetlana Ugarcina Perovic. Looking forward to it.:hugging_face:

2024-05-23

UBNSEMS3S (00:09:51): > Hi everyone, > > Just a reminder that we have our team meeting at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. Looking forward to seeing you there.

2024-05-24

UBNSEMS3S (09:02:47): > Hi everyone the Advanced R book club is today at 11 AM EDT! I will be presenting Chapter 16: trade-offs at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-05-27

Scholastica Urua (12:14:28): > Hello@Svetlana Ugarcina Perovic<!here>I’m encountering a challenge with this study I’m curating and need your opinion please. One of the taxaMethanobrevibacterwith TXID -2172 doesn’t appear when I save the page. There’s a blank space where the signature is supposed to be.https://bugsigdb.org/Study_976 - File (JPEG): Missing taxa.JPG - File (JPEG): 2172.JPG

Svetlana Ugarcina Perovic (14:31:06) (in thread): > <@UBNSEMS3S>any clue what’s going on here?

2024-05-28

Svetlana Ugarcina Perovic (08:11:30) (in thread): > @Scholastica Uruasee this pleasehttps://bugsigdb.org/Special:RunQuery/Taxon_filter?pfRunQueryFormName=Taxon+filter&[…]%5D=&Taxon%5BBody+site%5D=&Taxon%5BCondition%5D=&pf_free_text= - Attachment (BugSigDB): Special:RunQuery/Taxon filter

Svetlana Ugarcina Perovic (08:13:13) (in thread): > OK, now I saw that you solved it.

Scholastica Urua (08:17:06) (in thread): > Thank you@Svetlana Ugarcina PerovicI didn’t do anything actually. Just noticed it has showed up. Going through the link though in case of future curations.

Svetlana Ugarcina Perovic (08:20:10) (in thread): > I just did a quick search of taxonhttps://bugsigdb.org/Main_Page - File (PNG): Screenshot 2024-05-28 at 14.19.54.png

Svetlana Ugarcina Perovic (08:20:31) (in thread): > to see how will appear in other studies…

Scholastica Urua (08:35:21) (in thread): > Okay. Done that as well. > Thank you

2024-05-29

Svetlana Ugarcina Perovic (05:16:18): > .@Scholastica Uruajust started to share her BugSigDB work & progress through blogging. Give her a follow - Attachment (scholastica_urua): My Journey with Outreachy and the Bioconductor Community > On May 2nd, 2024, I received an email that will forever impact the course of my career… :sparkles: Congratulations on being accepted for the May 2024 to August 2024 Outreachy internship round! :sparkles: I s…

Svetlana Ugarcina Perovic (07:07:35): > Hi everyone! We will be having our weekly team meeting at 9 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499.We currently have openings to present. Please feel free to signup here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTSee you tomorrow,<@UBNSEMS3S>&@Svetlana Ugarcina Perovic

UBNSEMS3S (10:32:59) (in thread): > Sorry I’ve been out. It’s a holiday week here. Is this resolved?

Svetlana Ugarcina Perovic (10:33:35) (in thread): > Yes it is<@UBNSEMS3S>

Svetlana Ugarcina Perovic (10:33:42) (in thread): > Thanks for asking:wink:

2024-05-30

Svetlana Ugarcina Perovic (03:47:14): > #MVIF program for June is out!:slightly_smiling_face:We will discussmicrobiome and women’s health. > > Registration:https://events.ringcentral.com/events/microbiome-vif-n-30Full program:https://www.microbiome-vif.org/en-US/-/future-events/mvif30-1112-13-june-2024Feel free to share it with your network! > Thank you!:tulip: - Attachment (events.ringcentral.com): Microbiome-VIF n.30 - Jun 12 | RingCentral Events > Get tickets to Microbiome-VIF n.30, taking place 06/12/2024 to 06/14/2024. RingCentral Events is your source for engaging events and experiences. - Attachment (microbiome-vif.org): MVIF.30 | 11/12 & 13 June 2024 > A special MVIF event, with talks and panel discussion

Scholastica Urua (05:33:07): > Good morning@Svetlana Ugarcina Perovic, > I’m getting this error message when trying to access bugsigdb. Although, it was working just fine before now. Don’t know if it’s just on my end… - File (JPEG): error.JPG

Svetlana Ugarcina Perovic (05:39:42) (in thread): > same here

Scholastica Urua (05:41:41) (in thread): > Oh, I’m guessing its from the backend then.

Scholastica Urua (06:26:37) (in thread): > Its working now

2024-05-31

Scholastica Urua (06:32:45) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:hugging_face:. > > Noticed BugSigDB is displaying this… - File (JPEG): Semantic.JPG

Scholastica Urua (07:06:38) (in thread): > It’s back now

Scholastica Urua (07:48:28): > Hello<!here>, > > I noticed some discrepancies while curating. The signature is not adopting the Group 1 name. I made some changes to the group names and definitions, but the signature still retains what was previously curated across all the signatures of the different experiments in thatstudy. I decided to try editing anotherstudyto see if the issue was isolated to one study, but the problem persists. > > Please see the attached image for clarity. - File (JPEG): Study 959.JPG - File (JPEG): Study 950.JPG - File (JPEG): Study _950.JPG

Svetlana Ugarcina Perovic (10:37:25) (in thread): > FYI@Scholastica Uruareported it herehttps://github.com/waldronlab/BugSigDB/issues/230 - Attachment: #230 Signatures not adopting Group 1 name > Hello, > > While curating this study, I noticed that the Signature section, specifically “Abundance in Group 1” was not adopting the Group 1 name. > > I made some changes to the group names, but the signature still retains what was previously curated across all the signatures of the different experiments. > > Study 959

Scholastica Urua (10:37:55) (in thread): > Thank you@Svetlana Ugarcina Perovic

2024-06-01

Peace Daniel (04:19:36): > Good day and wishing everyone a prosperous new month! > I can’t add new experiments to this studyhttps://bugsigdb.org/Study_1079 - Attachment (BugSigDB): Signatures within the esophageal microbiome are associated with host genetics, age, and disease - BugSigDB > BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host. - File (PNG): Screenshot (322)

Scholastica Urua (13:04:12) (in thread): > Hello@Peace Daniel, happy new month.:hugging_face:I noticed you’ve added two experiments,7and8, that are not currently displaying. I ran into similar issue a couple of days ago. > > Please report the issuehere. - Attachment: #221 Study 784 Experiments not showing but exist > https://bugsigdb.org/Study_784 shows no experiments on the page but they do exist: https://bugsigdb.org/Study_784/Experiment_1 > > I tried refreshing the page under … > Refresh but that did not resolve the issue.

U1LCB8WEA (14:45:59) (in thread): > Thank you@Peace Danielfor the report and@Scholastica Uruafor pointing Peace to the issue on GitHub!

U1LCB8WEA (14:46:55) (in thread): > And thank you for the bug report@Scholastica Urua! Very important to report issues like this.

U1LCB8WEA (14:47:43) (in thread): > Bugsigdb was updated yesterday,sorry for not letting you know in advance.

Peace Daniel (17:04:36) (in thread): > Oh, thank you@Scholastica Urua

Peace Daniel (17:13:36) (in thread): > @Scholastica Uruait seems you could see the experiments from your end yh?

Scholastica Urua (18:26:23) (in thread): > @Peace DanielYou can see the experiments when you add “****/Experiment_n**” to the study link. n being the experiment number. Eg;https://bugsigdb.org/Study_1079/Experiment_8 - Attachment (BugSigDB): Study 1079/Experiment 8 > .

Scholastica Urua (18:29:59) (in thread): > Oh, I see. Thank you Levi

2024-06-02

Peace Daniel (02:44:46) (in thread): > I see now, thanks@Scholastica Urua

Aleru Divine (09:55:36): > Hello everyone, I hope you’re enjoying your Sunday!:sunny:I’m in the process of reviewing a study and I have a question. > > The study mentioned that controls hadn’t taken antibiotics within the past 8 weeks. Can this be interpreted as antibiotic exclusion, given the absence of mention regarding the case group? > > Thank you so much!@Svetlana Ugarcina Perovic@Levi Waldron<@UBNSEMS3S>

2024-06-03

Scholastica Urua (03:50:25): > Happy new month and happy new week@Svetlana Ugarcina Perovicand everyone!:hugging_face:Please I’ll appreciate your input on this study I’m reviewing. > > Burkholderia, Caballeronia, and Paraburkholderia are three distinct genera within the family Burkholderiaceae. However, they are presented together in the LEFse result in this study;https://bugsigdb.org/Study_987. > > Do you think they should be curated as one group or separately? - Attachment (BugSigDB): Interaction between Cervical Microbiota and Host Gene Regulation in Caesarean Section Scar Diverticulum - BugSigDB > Cesarean section scar diverticulum (CSD) has become a formidable obstacle preventing women receiving CS from reproducing.However, the pathogenesis of CSD remains unexplored.In this study, we characterized the cervical microbiota, metabolome, and endometrial transcriptome of women with CSD. - File (PNG): Screenshot_20240603-083437.png

Mildred Anashie (03:59:02) (in thread): > Good morning and Happy new month@Scholastica UruaIdon’thave a definite answer to your question but I did some research and I agree with you that they are distinct genus but it also said they were previously grouped under “Burkholderia” > > Maybe the text in the study can guide you on if you should record all three (Depending on how it was reported) while you wait for the mentors responses

Scholastica Urua (04:31:18) (in thread): > Thank you@Mildred AnashieThey were also reported together in the text. This is an excerpt from where they were reported in text; > “The proportions of Proteobacteria genera, including Escherichia Shigella, Sphingomonas, Ralstonia and Burkholderia Caballeronia Paraburkholderia, showed various degrees of differences between the CSD group (Fig. 1G) and the CON group (Fig. 1I).” > > I curated them together but still not so sure if they should be curated that way.

Svetlana Ugarcina Perovic (04:47:44) (in thread): > Yes, it should be reported, with a note. That’s not surprising, since it can be challenging to recruit “non-healthy” participants without any recent antibiotic treatment.

Svetlana Ugarcina Perovic (04:49:54) (in thread): > Record them as it is and leave a note.

Svetlana Ugarcina Perovic (04:51:30) (in thread): > If you take a look in the literature, there’s: theBurkholderia-Caballeronia-Paraburkholderia(BCP) group

Svetlana Ugarcina Perovic (04:52:30) (in thread): > “The BCP group is composed of the three independent generaBurkholderia,Caballeronia, andParaburkholderia. The V3 +V4 segment of the 16 S rRNA selected in this sequencing could not separate the specific genera due to their close genetic relationship (Luo et al., 2021).”

Svetlana Ugarcina Perovic (04:53:06) (in thread): > That the reason why they are presented together.

Svetlana Ugarcina Perovic (04:53:17) (in thread): > btw, happy Monday:wink:

Scholastica Urua (04:56:17) (in thread): > Okay@Svetlana Ugarcina Perovicthank you so much

Svetlana Ugarcina Perovic (05:02:57): > What a nice curation and review by@Aleru Divineand@Joan C. Chukwuemekahttps://github.com/waldronlab/BugSigDBcuration/issues/371Happy Monday! And,:teapot:thanks Aleru and Joan for this nice read on Monday morning!

Aleru Divine (05:07:43) (in thread): > Thank you@Svetlana Ugarcina Perovicand well done@Joan C. Chukwuemeka:hugging_face:

Aleru Divine (05:08:14) (in thread): > Alright!@Svetlana Ugarcina PerovicThank you so much for your prompt response.

Scholastica Urua (05:44:52) (in thread): > Well done@Aleru Divineand@Joan C. Chukwuemeka:clap:

Aleru Divine (06:12:53) (in thread): > Thank you@Scholastica Urua:hugging_face:

Victoria (Burah) Poromon (08:31:24) (in thread): > Hello@Svetlana Ugarcina PerovicConcerning this, are we allowed to present any study on bugsigdb? Or is it strictly studies that we personally curated?

Svetlana Ugarcina Perovic (08:33:04) (in thread): > @Victoria (Burah) PoromonIt’s not strict, but it would great that you present what you just recently curated or REVIEWED ;)

Victoria (Burah) Poromon (08:33:38) (in thread): > Okay > Thank you:blush:

2024-06-04

Scholastica Urua (06:47:09): > Hello everyone! I’m reviewing thiscurationwere the significant taxa are presented both at family and genus level (Experiment 3 - Fig 5A and B). The taxa for the other experiments are only presented at the genus level. > > Please I’d like your opinion on this. Should both the family and genus be captured for this experiment or just the genus. > > Thank you in anticipation:pray: - Attachment (BugSigDB): The microbiome in urogenital schistosomiasis and induced bladder pathologies - BugSigDB > BACKGROUND: Human schistosomiasis is a highly prevalent neglected tropical disease (NTD) caused by Schistosoma species. - File (JPEG): Capture.JPG

Aleru Divine (08:50:45) (in thread): > Well done@Scholastica Urua! Here’s what I think:sweat_smile:The study identified specific types of bacteria at both the family and genus levels. I really think you should consider both levels in your curation. There’s likely a reason they included the family level in addition to the genus level, unlike in the other experiments (C and D) where only the genus was reported. The family level is a bit border and provides additional insights that might not be apparent from the genus level data alone.

Scholastica Urua (08:59:08) (in thread): > Thank you so much for your input@Aleru Divine:heavy_heart_exclamation_mark_ornament:

Svetlana Ugarcina Perovic (09:34:15) (in thread): > Agree@Aleru DivineThanks!

Scholastica Urua (09:36:45) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (09:44:38) (in thread): > Happy to help@Scholastica Urua@Svetlana Ugarcina Perovic

2024-06-05

UBNSEMS3S (18:32:26): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-06-06

Svetlana Ugarcina Perovic (02:29:08): > :clap:SHOUT OUT:clap:to@Victoria (Burah) Poromonwho took this task to update data transformation input based on<@UBNSEMS3S>’s observation and comment (see herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697145294410289?thread_ts=1697141457.022309&cid=C04RATV9VCY) - Attachment: Attachment > I will note that this is wrong or missing for many previously curated papers and a good cleanup task for an intrepid soul would be to try to update all of these. I’ve found a lot of DESeq2 papers that say they use relative abundances or CLR which do not make sense–DESeq2 uses a negative binomial model which requires counts* or else it will not converge. > > *Or variables that are whole numbers that approximate a negative binomial/poisson distribution.

Svetlana Ugarcina Perovic (02:29:46) (in thread): > My apologies, I can’t make it today.

Scholastica Urua (02:49:17) (in thread): > Thank you@Victoria (Burah) Poromon:hugging_face:

Victoria (Burah) Poromon (03:54:41) (in thread): > Thank youuu@Svetlana Ugarcina Perovic:blush:

Aleru Divine (07:24:08) (in thread): > Well done@Victoria (Burah) Poromon

UBNSEMS3S (08:57:47) (in thread): > Amazing. An intrepid soul indeed!

Peace Sandy (09:02:19) (in thread): > Awesome work@Victoria (Burah) Poromon

Mildred Anashie (09:08:57) (in thread): > Well done@Victoria (Burah) Poromon

UBNSEMS3S (15:26:29): > Hi everyone the Advanced R book club returns tomorrow at 11 AM EDT! I will be presenting Chapter 17: Big Picture (Metaprogramming) at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-06-10

Scholastica Urua (05:05:11): > Good morning everyone, happy new week!:tulip:@Svetlana Ugarcina Perovic<@UBNSEMS3S>please I need assistance with thecurationI’m working on. The experiments are: > * Exp. 1: Allergic asthma vs. Healthy control (Figure 4b) > * Exp. 2: Allergic rhinitis vs. Healthy control (Figure 4c) > Figure 4a is also curatable. Some, but not all, of the signatures in Figure 4a are present in Figures 4b and 4c. > My question is how best to curate Figure 4a. Should it be curated as three different experiments (one vs. all), or should the asthma (red bars) be curated with Figure 4b under Experiment 1, and the rhinitis (blue bars) be curated with Figure 4c under Experiment 2? > I’m not sure if I’m expressing my question clearly:sweat_smile:. - Attachment (BugSigDB): Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing - BugSigDB > PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. - File (JPEG): Capture.JPG

Svetlana Ugarcina Perovic (05:59:08) (in thread): > I would go for the asthma (red bars) be curated with Figure 4b under Experiment 1, and the rhinitis (blue bars) be curated with Figure 4c under Experiment 2

Svetlana Ugarcina Perovic (06:00:20) (in thread): > (b) and (c) highlight species level, (a) higher classification as well, but all 3 figures talk about 2 experiments that you described above.

Scholastica Urua (06:04:51) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (09:41:04): > On Thursday, there is another MVIF, this time focused onwomen’s health! > > Registration (free):https://events.ringcentral.com/events/microbiome-vif-n-30Full program with abstracts:https://www.microbiome-vif.org/en-US/-/future-events/mvif30-1112-13-june-2024Happy Monday!(I will now respond to all your messages, thanks!) - File (PNG): June24_program.png

2024-06-11

Svetlana Ugarcina Perovic (06:26:17): > :clap:read and enjoy thisexcellent curation and review processby@idiaru Angelaand@Mildred Anashie - Attachment: #374 Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma > @MyleeeA here you could do “Edit” (… on the right upper corner of this comment box) and add all the info for this study: > > Distinct alterations of gut microbiota between viral- and non-viral-related hepatocellular carcinoma – Thananya Jinato – Appl Microbiol Biotechnol.
> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771587/ > > • Your poor-in-information message below: Link: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10771587/ is deleted now.

Scholastica Urua (10:46:58) (in thread): > Well done@Mildred Anashie@idiaru Angela:raised_hands:

Mildred Anashie (11:05:52) (in thread): > Thank you@Svetlana Ugarcina Perovicand@Scholastica Urua:blush:

2024-06-12

Svetlana Ugarcina Perovic (03:08:53): > TOMORROW (Thursday),<@UBNSEMS3S>and I are at conferences and we will NOT have our team meeting, BUT we suggest you to join an MVIF special event. Microbiome and women’s health will be the main topic.See you at MVIF!

2024-06-13

Scholastica Urua (00:07:33): > Good morning everyone, > > Could I get your opinion on this curation:https://bugsigdb.org/Study_1051? Specifically, could you please check if Figure 4c is curatable? > I’m not so sure here. > > Thank you very much! - File (JPEG): Capture.JPG

Odigiri Great Alume (03:00:30): > I think it’s curable. > 1. It has a p value > 2. Talks of differential abundance > 3. It has a test for significance - File (JPEG): Screenshot_20240613-075803.jpg

Scholastica Urua (03:07:28) (in thread): > Thank you@Odigiri Great AlumeI was wondering how they’ll be grouped since it’s comparing 3 different groups…

Odigiri Great Alume (03:10:14) (in thread): > Oops I see now. Lemme read through the text

Svetlana Ugarcina Perovic (05:03:59) (in thread): > I adore how@Odigiri Great Alumepops up here out of the blue, thanks for yournever ending contribution!

Svetlana Ugarcina Perovic (05:07:57): > REMINDER: See you today at MVIF!:arrow_down:https://community-bioc.slack.com/archives/C04RATV9VCY/p1718176133793629 - Attachment: Attachment > TOMORROW (Thursday), @UBNSEMS3S and I are at conferences and we will NOT have our team meeting, BUT we suggest you to join an MVIF special event. Microbiome and women’s health will be the main topic. See you at MVIF!

Mildred Anashie (05:19:54) (in thread): > Yea I agree@Svetlana Ugarcina PerovicWell done and thank you@Odigiri Great Alume@Scholastica UruaI’mthinking the asterisks(the highlighted image) are showing where there is significance, I notice the placement changes butI’munsure how the comparisons will be - File (JPEG): 410a52a8-eae4-4ab9-8594-656d366014e9

Scholastica Urua (05:50:29) (in thread): > Yes@Mildred Anashie, the figure does show significance but I’m unsure of the groupings. And the statistical test used is Kruskal Wallis and not LEfSse so I don’t know if the one vs all rule applies here.

Svetlana Ugarcina Perovic (05:54:09) (in thread): > I am not sure either! Let’s ask for another opinon:@Esther Afuapecould you please help in here?

Peace Daniel (10:23:34) (in thread): > @Scholastica UruaThe heat map compared all three groups so I think you could use that > > “Community heatmap analysis at genus level revealed that gut microbial composition differed among the three groups”

Scholastica Urua (11:14:47) (in thread): > Hi@Peace DanielI’m not clear on your point. Can you clarify please:pray:

Peace Daniel (11:58:02) (in thread): > ZC vs QD > ZC vs ZZD > QD vs ZZD@Scholastica Urua

2024-06-14

Svetlana Ugarcina Perovic (05:41:18): > Happy Friday!I have a question for you: when was the last time when you were really stuck? How did you solve it (if solved:upside_down_face:)? - File (PNG): Screenshot 2024-06-14 at 11.40.53.png

Peace Daniel (08:44:00) (in thread): > Happy Friday@Svetlana Ugarcina PerovicI’m actually stuck right now and I’m not able to navigate through. In the meantime,I’mdoing whichever appeals more to me:white_frowning_face:

Scholastica Urua (09:36:46) (in thread): > Happy Friday@Svetlana Ugarcina PerovicGot really stuck on this curation yesterday:sweat_smile:https://community-bioc.slack.com/archives/C04RATV9VCY/p1718251653096539 - Attachment: Attachment > Good morning everyone, > > Could I get your opinion on this curation: https://bugsigdb.org/Study_1051? Specifically, could you please check if Figure 4c is curatable? > I’m not so sure here. > > Thank you very much!

Scholastica Urua (11:58:19): > <!here>Happy Friday everyone! > > I’m not sure what would be an appropriate condition for Experiment 2 of this curation;https://bugsigdb.org/Study_1071. > Kindly need you help:pray:. > Thank you! - Attachment (BugSigDB): Dysbiosis of gut microbiota and its correlation with dysregulation of cytokines in psoriasis patients - BugSigDB > Background: Psoriasis is an inflammatory skin disease associated with multiple comorbidities and substantially diminishes patients’ quality of life.The gut microbiome has become a hot topic in psoriasis as it has been shown to affect both allergy and autoimmunity diseases in recent studies.

Victoria (Burah) Poromon (13:29:25) (in thread): > I think Microbiome measurement can fit here. > > Because the study says experiment 2 was comparing the microbiota communities of Psoriasis vulgaris and Pustular psoriasis.

Victoria (Burah) Poromon (13:34:50) (in thread): > Hi@Svetlana Ugarcina PerovicI’ve been stuck on study 1083 for more than a week now…The goat experiment:sweat_smile:Still waiting for the authors response to complete it, and in the mean time, I’m everywhere on the streets of bugsigdb cleaning up wrongly curated data transformations. Very rewarding so far….

Scholastica Urua (13:44:45) (in thread): > Thank you@Victoria (Burah) Poromon, I think that will work.

Chioma Onyido (17:40:05) (in thread): > The last time I was really stuck was when I had to assemble a piece of furniture. I got a new shoe rack and decided to put it together myself. I struggled with figuring out which screws went where. > > After a while of getting frustrated, I decided to leave it for a while and rest. > Came back and re-read the instructions more carefully, and even called a friend who had experience with stuff like that. > > Alas we were able to finally put the shoe rack together. Even though it took a while.:sweat_smile:

2024-06-17

Svetlana Ugarcina Perovic (04:17:01) (in thread): > @Peace Danielwishing you a better week than previous one!

Svetlana Ugarcina Perovic (04:18:03) (in thread): > @Scholastica Urualet’s ask for another opinion and unstuck this!

Svetlana Ugarcina Perovic (04:18:30) (in thread): > <@UBNSEMS3S>could you please help here:slightly_smiling_face:thanks!

Svetlana Ugarcina Perovic (04:26:08) (in thread): > @Victoria (Burah) Poromonseehttps://github.com/waldronlab/BugSigDBcuration/issues/392:wink: - Attachment: #392 Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age > Microbiome analysis reveals gut microbiota alteration of early-weaned Yimeng black goats with the effect of milk replacer and age > > https://pubmed.ncbi.nlm.nih.gov/33789672/

Svetlana Ugarcina Perovic (04:27:44) (in thread): > @Chioma Onyidoyour shoe rack stuck sounds exactly as a bioinformatics stuck: frustration, going back to instructions/code and finally ask help and get unstuck together!

Svetlana Ugarcina Perovic (04:28:06) (in thread): > Have a nice week everyone!

Svetlana Ugarcina Perovic (10:35:18): > Blog post 2:writing_hand:by@Scholastica Uruaon an open source vocabulary term, don’t miss it - Attachment (scholastica_urua): Curating with BugSigDB > Welcome to another installment of my internship journey! These past few weeks have been transformative, and I’m thrilled to share some insights with you. One concept that has become central to my w…

Scholastica Urua (10:36:55) (in thread): > Thank you@Svetlana Ugarcina Perovic:heart_eyes:

Peace Daniel (12:42:06) (in thread): > Well done@Scholastica Urua:clap::purple_heart:My favorite line here “The power of curation lies in its ability to distill vast amounts of information into something meaningful and manageable. “ > > This clearly meanI’msmart:face_with_peeking_eye::sweat_smile:

Scholastica Urua (12:43:18) (in thread): > Thank you@Peace Daniel:star-struck:

Aleru Divine (14:04:10) (in thread): > Well done!@Scholastica Urua:hugging_face:this was a lovely read:heart:

Scholastica Urua (14:05:05) (in thread): > Thank you@Aleru Divine:blush:

2024-06-18

Svetlana Ugarcina Perovic (03:34:13) (in thread): > Yes@Peace Daniel! I like that part as well…

Svetlana Ugarcina Perovic (03:54:57): > I’m happy to introduce to you@JACOB A DE JESUS-CANDELARIOa rising senior undergraduate student from Puerto Rico. Jacob will be with us this summer as an NSURP 2024 intern.Welcome, Jacob!More about NSURP program you can find it herehttps://nsurp.org/ - Attachment (NSURP.org): NSURP.org > National Summer Undergraduate Research Project

Aleru Divine (04:51:31) (in thread): > Welcome,@JACOB A DE JESUS-CANDELARIO! Glad to have you join us:hugging_face:

Scholastica Urua (05:01:56) (in thread): > Welcome@JACOB A DE JESUS-CANDELARIO! > Nice to have you join us:sparkles:

Peace Daniel (06:09:13) (in thread): > Welcome:hugging_face:@JACOB A DE JESUS-CANDELARIO

Svetlana Ugarcina Perovic (07:58:59) (in thread): > @JACOB A DE JESUS-CANDELARIOsince curation is new to you I highly recommend to read@Scholastica Urua’s latest blog posthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1718634918281169 - Attachment: Attachment > Blog post 2 :writing_hand: by @Scholastica Urua on an open source vocabulary term, don’t miss it! > > https://scholasticaurua.wordpress.com/2024/06/17/curating-with-bugsigdb/

Peace Sandy (08:21:59) (in thread): > Welcome@JACOB A DE JESUS-CANDELARIOwelcome to the team:dancer:

Peace Sandy (08:22:35) (in thread): > Nice Blog Post@Scholastica Urua

Scholastica Urua (08:23:09) (in thread): > Thank you@Peace Sandy

Victoria (Burah) Poromon (18:25:48) (in thread): > Welcome@JACOB A DE JESUS-CANDELARIO!!

JACOB A DE JESUS-CANDELARIO (20:34:57) (in thread): > Hello everybody! I hope eveyone is well. It’s nice to meet you all. I’m so sure this will an amazing experience, I look to collaborate and interact with this community.:slightly_smiling_face:Thanks for welcoming me!

2024-06-19

Mildred Anashie (09:02:18) (in thread): > Welcome@JACOB A DE JESUS-CANDELARIO:blush:

idiaru Angela (15:55:07) (in thread): > Thank you@Scholastica Urua@Svetlana Ugarcina Perovic

2024-06-20

Aleru Divine (07:38:44): > Hello everyone! Trust you are having a great day:sparkles:@Svetlana Ugarcina PerovicI’d like to delete this signature.https://bugsigdb.org/Study_62/Experiment_1/Signature_1 - Attachment (BugSigDB): Study 62/Experiment 1/Signature 1 > Source: Supplementary Figure 2(b-e) Description: The most significant differentially abundant taxa from DESeq2 comparisons of PD patients with and without MCI according…

Scholastica Urua (08:58:12): > Hi<@UBNSEMS3S>will there be team meeting today?

UBNSEMS3S (08:58:59): > Yes sorry meant to post.

UBNSEMS3S (08:59:28): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT today (Thursday; in 1 minute).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

Scholastica Urua (09:49:39) (in thread): > This question was answered during the office hour by<@UBNSEMS3S>. Thank you

Odigiri Great Alume (09:51:17) (in thread): > No problem

Svetlana Ugarcina Perovic (12:00:21) (in thread): > Deleted.

Svetlana Ugarcina Perovic (12:01:33) (in thread): > @Scholastica Uruacould you please share here the conclusion, thanks!

Scholastica Urua (12:10:45) (in thread): > Fig. 4c is statistically significant as stated in the description. But it can’t be curated since the study did not clearly show comparison between two groups. > I included a note on the talk page as well.

Odigiri Great Alume (13:55:22) (in thread): > This works

UBNSEMS3S (17:06:43): > Hi everyone the Advanced R book club returns tomorrow at 11 AM EDT! Marcel will be presenting Chapter 18: Expressions at:https://us02web.zoom.us/j/88478658000?pwd=eTFIK0g5YnJtUk9CdzZTSGtHdHd1UT09

2024-06-24

Scholastica Urua (11:34:26): > Hello everyone! Happy new week:hugging_face:I’d like your opinion on this study I’m curating. I’m not sure what the best fit for the condition in experiments 3, 4, and 5 would be. The closest term would have been ‘Response to chemoradiotherapy’ but this is not available on BugSigDB. > Study link:https://bugsigdb.org/Study_1016Thank you in advance for your help!

2024-06-25

Esther Afuape (07:26:40) (in thread): > Hi!@Scholastica UruaYou seem to have sorted this out.. I just checked now and the conditions seem okay to me

Scholastica Urua (07:29:05) (in thread): > Thank you@Esther Afuape

2024-06-26

Svetlana Ugarcina Perovic (08:27:24): > Today your must read:drum_with_drumsticks:A new post by@Scholastica Uruahttps://scholasticaurua.wordpress.com/2024/06/26/a-beginners-guide-to-bugsigdb/ - Attachment (scholastica_urua): A Beginner’s Guide to BugSigDB > Introduction Welcome to another post of my blog! This is my fifth week working on the Bioconductor project with BugSigDB. In this post, I will share my experience and insight to help you understand…

Svetlana Ugarcina Perovic (08:28:00) (in thread): > @JACOB A DE JESUS-CANDELARIOread this carefully ;)

Scholastica Urua (08:28:16) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

JACOB A DE JESUS-CANDELARIO (10:09:43) (in thread): > I will do just that, thanks@Svetlana Ugarcina Perovic!

UBNSEMS3S (12:31:29) (in thread): > This is great! Extremely well-written.

Scholastica Urua (12:34:33) (in thread): > Thank you<@UBNSEMS3S>:blush:

Victoria (Burah) Poromon (14:21:30) (in thread): > Well done@Scholastica Urua:heart_hands:

Scholastica Urua (14:24:55) (in thread): > Thank you@Victoria (Burah) Poromon

2024-06-27

UBNSEMS3S (00:20:23): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT today (Thursday; in 8 hours).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

Aleru Divine (05:19:36) (in thread): > This is so detailed, well done!@Scholastica Urua:clap::clap:

Scholastica Urua (05:24:05) (in thread): > Thank you@Aleru Divine:blush:

Svetlana Ugarcina Perovic (09:09:38): > You are all invited to attend ->https://www.bioc2024.bioconductor.org/cc<@U1LCB8WEA>

Svetlana Ugarcina Perovic (09:59:38): > Data transformation art by<@UBNSEMS3S>Thanks, Chloe! - File (PNG): Screenshot 2024-06-27 at 15.52.48.png - File (PNG): Screenshot 2024-06-27 at 15.54.38.png

Victoria (Burah) Poromon (10:43:36) (in thread): > Thank you<@UBNSEMS3S>Very insightful meeting today

UBNSEMS3S (10:56:06) (in thread): > haha if I knew you’d be screenshotting my drawings I’d put more effort into them.

Peace Sandy (17:13:53) (in thread): > Nice Article@Scholastica Urua:heart:

UBNSEMS3S (17:51:43): > No Advanced R book club tomorrow or next week as I am out and then it’s the day after the 4th of July.

2024-06-28

Scholastica Urua (07:58:44) (in thread): > Thank you@Peace Sandy

2024-07-01

Svetlana Ugarcina Perovic (04:20:00): > Hello hello, please welcome back@Precious Orakwe:wave::muscle::upside_down_face:Precious re-joined us in ourreviewing efforts!Also sending a virtual hug to@Scholastica Urua@Victoria (Burah) Poromon@Aleru Divine@Mildred Anashie@Peace Daniel@Joan C. Chukwuemeka@idiaru Angela@Peace Danielcc<@U1LCB8WEA>

Svetlana Ugarcina Perovic (04:26:47): > `:hugging_face:

Mildred Anashie (04:28:11) (in thread): > Welcome@Precious Orakwe:blush:

Peace Daniel (04:28:14) (in thread): > Aww:face_holding_back_tears::face_holding_back_tears:Happy new month@Svetlana Ugarcina Perovic:purple_heart:

Peace Daniel (04:28:33) (in thread): > And welcome@Precious Orakwe:hugging_face:

Scholastica Urua (04:28:50) (in thread): > Welcome@Precious Orakwe:tulip:Thank you everyone:sparkling_heart:

Scholastica Urua (04:29:15) (in thread): > Happy new month@Svetlana Ugarcina Perovic:confetti_ball:

Victoria (Burah) Poromon (04:29:32) (in thread): > Thank you@Svetlana Ugarcina PerovicAnd welcome back@Precious OrakweHappy new month everyone!:yellow_heart::yellow_heart:

Svetlana Ugarcina Perovic (04:33:02): > African Microbiome Day 3.0: Showcasing microbiome research in Africa – Exploring Health, Ecosystems and Innovations (Virtual Event) > > Registration OPEN:https://h3africa.org/index.php/african-microbiome-day-30/#overviewIf you are going, put your fav emoji. - Attachment (h3africa.org): African Microbiome Day 3.0: Showcasing microbiome research in Africa – Exploring Health, Ecosystems and Innovations – H3Africa > Human Heredity & Health in Africa

idiaru Angela (05:07:30) (in thread): > Welcome back@Precious Orakweand thank you@Svetlana Ugarcina Perovic

Aleru Divine (05:10:20) (in thread): > Thank you@Svetlana Ugarcina Perovic:hugging_face:Welcome@Precious Orakwe:sparkles:Happy new month everyone:clinking_glasses::white_heart:

Svetlana Ugarcina Perovic (05:23:31) (in thread): > Oh, we forgot@JACOB A DE JESUS-CANDELARIO:slightly_smiling_face:my bad my bad, apologies - File (PNG): Screenshot 2024-07-01 at 11.22.35.png

JACOB A DE JESUS-CANDELARIO (05:44:16) (in thread): > Welcome@Precious Orakwe!:confetti_ball:Thanks@Svetlana Ugarcina Perovic!

2024-07-02

Joan C. Chukwuemeka (05:49:31) (in thread): > Thanks@Svetlana Ugarcina Perovic:hugging_face:Welcome@Precious Orakwe

UBNSEMS3S (09:30:08) (in thread): > I presented once to an H3Africa group. They’re a wonderful organization!

2024-07-03

Svetlana Ugarcina Perovic (06:42:23): > QUESTION to YOU :microphone:**** ****Is there a BugSigDB curation step that seemed easy, but took more time than you expected?

Svetlana Ugarcina Perovic (06:48:32): > Reminder: tomorrow (Thursday) we do NOT have our regular team meeting due to the July 4 holiday!

Scholastica Urua (06:53:21) (in thread): > Curating a LEfSe figure usually seems very easy. But then some LEfSe figures have over 30 signatures:sob:. > > Identifying the experiments/signatures, relatively easy but actually curating is a different ball game especially when you have to use the NCBI taxonomy site to resolve some of the taxa.

UBNSEMS3S (09:21:31) (in thread): > The thing that amazed me having almost no biology background before starting on the project was just how difficult bacterial taxa identification is! I had no idea there were multiple, competing references and they would use different names for the same taxon–not even considering that those names also evolve over time as the references get updated.

Victoria (Burah) Poromon (10:38:20) (in thread): > I’d say curating the signatures too:sweat_smile:Especially when you cannot find them on the NCBI site and you have to start looking elsewhere and trying to figure out taxa’s they are related to. > > A specific one for me was “Paraprevotellaceae” andI’msure the name is not leaving my head anytime soon:sweat_smile:

Mildred Anashie (12:51:05) (in thread): > For meI’dsay curating study designs in studies whereit’snot obviously a case-control, laboratory experiment or a Time series/longitudinal (The very first step:sweat_smile:) > Most times I just leave it blank carry on with the rest of the curation and return to that when I feel I have figured it out

2024-07-05

Svetlana Ugarcina Perovic (07:44:27): > Hey hey, just to sayHAPPY FRIDAY!And, next week, I will enjoy my off time. Keep up the good work and**** your wonderful discussions**here in Slack!

Svetlana Ugarcina Perovic (08:36:46): > :drum_with_drumsticks:**** Let me introduce ****@Joyce Qiu**** ****Joyce is an Applied Mathematics and Statistics major with a minor in Computer Science about to graduate, and will be going into a MPH program. This summer Joyce joined us in BugSigDB-ing efforts. > > Welcome, Joyce!

Svetlana Ugarcina Perovic (08:38:27) (in thread): > Joyce, if you have any question feel free to write here. The community is more than happy to discuss and clear doubts.

Victoria (Burah) Poromon (09:49:43) (in thread): > You’re welcome@Joyce Qiu

Mildred Anashie (10:38:59) (in thread): > Welcome@Joyce Qiu

Joyce Qiu (10:56:54) (in thread): > Thank you!

JACOB A DE JESUS-CANDELARIO (11:10:03) (in thread): > Welcome@Joyce Qiu!!:smile:

Scholastica Urua (13:17:30) (in thread): > Welcome@Joyce Qiu!

2024-07-08

UBNSEMS3S (17:58:11) (in thread): > Welcome!

2024-07-09

Scholastica Urua (16:24:36): > Hello everyone, > > I hope we are all doing fine. Please, I need a second pair of eyes on this curation I’m currently reviewing. All experiments are curated from Figure 4. For each group, samples were collected at baseline and after 24 weeks: > > 1. Control vs. naive (at baseline) > 2. Control vs. naive (at 24 weeks) > 3. Control vs. experienced (at baseline) > 4. Control vs. experienced (at 24 weeks) > > I’m having a challenge determining the exact number of participants that were dropped from the naive and experienced groups at 24 weeks (experiments 2 and 4). The excerpt below shows that not all patients at baseline were present at week 24: > > “Baseline values of 142 individuals were analyzed with 67 individuals in the ART naive cohort, 33 in the ART experienced cohort, and 42 HC (Table 1). Furthermore, for longitudinal (intra-cohort) and microbiome analysis, additional individuals were excluded because they either (1) were lost to follow-up at the 24-week visit (n = 14), or (2) were in the ART-naive cohort and did not have a viral load < 200 at the second timepoint (n = 15), indicating a lack of response to ART.” > > Please kindly review and let me know what you think about the sample sizes for experiments 2 and 4. Thank you so much in anticipation. > Link:https://bugsigdb.org/Study_917 - Attachment (BugSigDB): Differential effects of antiretroviral treatment on immunity and gut microbiome composition in people living with HIV in rural versus urban Zimbabwe - BugSigDB > BACKGROUND: The widespread availability of antiretroviral therapy (ART) has dramatically reduced mortality and improved life expectancy for people living with HIV (PLWH).

Scholastica Urua (16:31:11) (in thread): > I’m thinking for exp. 2, 15 should be subtracted from the initial sample size because of the last part of the excerpt; > “…(2) were in the ART-naive cohort and did not have a viral load < 200 at the second timepoint (n = 15)…” > Not exactly sure though:thinking_face:

2024-07-10

UBNSEMS3S (23:35:44): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT tomorrow (Thursday; in 9 hours).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-07-11

U1LCB8WEA (05:26:54) (in thread): > Welcome,@Joyce Qiu, another New Yorker!

UBNSEMS3S (11:52:42) (in thread): > Just a note here that we examined this in depth during the meeting and were not able to determine the sample size from the paper, the supplement, or even the raw data.

2024-07-12

Precious Orakwe (06:18:07) (in thread): > Welcome@Joyce Qiu

2024-07-15

Svetlana Ugarcina Perovic (03:40:47): > Svetlana is back.Happy Monday!I’ll answer to all your messages today:woman-surfing:

Scholastica Urua (03:44:42) (in thread): > Welcome back@Svetlana Ugarcina Perovic

2024-07-16

Precious Orakwe (05:47:06) (in thread): > Welcome back@Svetlana Ugarcina Perovic

Aleru Divine (07:15:40) (in thread): > Welcome back@Svetlana Ugarcina Perovic:sparkles:

Svetlana Ugarcina Perovic (07:25:11): > Hello, here’s a proud mentor!@Scholastica Uruawrote a progress report on what weve been doing for the last 7 weeks of her internship. > > feat. > Svetlina Vasileva (the author ofhttps://jamanetwork.com/journals/jamapsychiatry/article-abstract/2814638who shared with us the missing supplementary materail within a day and we completed the curation)@JACOB A DE JESUS-CANDELARIO<@UBNSEMS3S>@Victoria (Burah) PoromonAmy Houseman (https://x.com/amyhouseman__Amy is my former mentee; we worked onhttps://gmgc.embl.de/)@Esther Afuape@Chioma Onyidohttps://scholasticaurua.wordpress.com/2024/07/15/unveiling-progress-my-outreachy-experience-with-bugsigdb-so-far/

Scholastica Urua (07:32:52) (in thread): > Thank you@Svetlana Ugarcina Perovic:heart_eyes:

Chioma Onyido (07:37:23) (in thread): > A great read!:clap:Well done@Scholastica Urua:cherry_blossom:

Esther Afuape (07:38:53) (in thread): > Well done:sparkles:@Scholastica Urua

Aleru Divine (08:00:31) (in thread): > Nicely written@Scholastica Urua! Well done:clap::clap:

Scholastica Urua (08:19:52) (in thread): > Thank you@Chioma Onyido,@Esther Afuape,@Aleru Divine

Mildred Anashie (13:57:12) (in thread): > Well done@Scholastica Urua:clap:

Scholastica Urua (15:26:11) (in thread): > Thank you@Mildred Anashie

2024-07-17

U1LCB8WEA (15:06:23) (in thread): > Yeah, a great read!

U1LCB8WEA (15:11:12): > Anyone wishing to attend the BioC2024 conference virtually from July 24 - 26, please put in a request for a virtual scholarship athttps://www.bioc2024.bioconductor.org/registration. Be sure to mention your participation in BugSigDB in the field “How have you participated in the Bioconductor project in the past?” and let me know if you are putting in an application - I expect that any BugSigDB curator who wants to attend will be able to for free.

Chioma Onyido (15:15:06) (in thread): > I’ve been seeing and sharing related posts via LinkedIn/ X. So grateful for the opportunity to attend. I’m putting in an application now.:grin:

U1LCB8WEA (15:16:06) (in thread): > Wonderful, Chioma!

Esther Afuape (15:17:48) (in thread): > Definitely applying right away:partying_face:

Scholastica Urua (15:24:00) (in thread): > Already applying. Thank you Levi:blush:

U1LCB8WEA (15:24:21) (in thread): > Glad to hear it Afuape and Scholastica! I’ll put in a good word for everyone:wink:

Scholastica Urua (15:32:45) (in thread): > Thank you<@U1LCB8WEA>

Victoria (Burah) Poromon (19:39:40) (in thread): > I’ll be applying too:blush:

2024-07-18

Svetlana Ugarcina Perovic (03:02:00): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT today (Thursday).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT<@UBNSEMS3S> - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

Aleru Divine (03:03:36) (in thread): > :partying_face:thank you@Levi WaldronI’llapply right away!

Aleru Divine (03:04:09) (in thread): > Good morning@Svetlana Ugarcina PerovicI’mlooking forward to it.

Mildred Anashie (04:03:59) (in thread): > Thank you@Svetlana Ugarcina PerovicLooking forward to it > It’s been a few weeks since I last attended

Mildred Anashie (04:19:13) (in thread): > Thank you@Levi WaldronI already applied:blush:

U1LCB8WEA (04:31:47) (in thread): > Wonderful, Victoria, Aleru, and Mildred!

Aleru Divine (08:59:07): > Yoo hoo!:partying_face:I have been awarded a scholarship to attend the 2024 BioC Annual Conference. Many thanks to@Levi Waldronfor this incredible opportunity! > > Thank you so much BugSigDB!:star-struck::sparkles: - File (PNG): IMG_9378

Mildred Anashie (09:04:22) (in thread): > Congratulations:tada:Same here, looking forward to the event:blush:

Bolanle Wahab (09:09:17) (in thread): > Congratulations Divine:partying_face::heart:

Scholastica Urua (09:26:53): > <@UBNSEMS3S>This is the study where they “tried to match the subjects based on their age, sex, risk factor status, and ethnicity.”:sweat_smile:https://bugsigdb.org/Study_1041 - Attachment (BugSigDB): Intratumoral Microbiota Changes with Tumor Stage and Influences the Immune Signature of Oral Squamous Cell Carcinoma - BugSigDB > Characterization of the oral microbiota profile through various studies has shown an association between the microbiome and oral cancer; however, stage-specific determinants of dynamic changes in microbial communities of oral cancer remain elusive.

U1LCB8WEA (09:26:54): > Matching does appear to be a (optimal!) strategy in RCTs:https://www.aeaweb.org/articles?id=10.1257/aer.20201856 > > AbstractIn randomized controlled trials, treatment is often assigned by stratified randomization. I show that among all stratified randomization schemes that treat all units with probability one half, a certain matched-pair design achieves the maximum statistical precision for estimating the average treatment effect. In an important special case, the optimal design pairs units according to the baseline outcome. In a simulation study based on datasets from ten randomized controlled trials, this design lowers the standard error for the estimator of the average treatment effect by 10 percent on average, and by up to 34 percent, relative to the original designs.

Mildred Anashie (09:30:26): > Hi<!here>I actually just remembered I had a question:blush:It’s based on reviews, I have been doing a few reviews on already curated studies and I struggle most times with it > > I’ll like to know if there are any tips on how to be faster and more productive with reviews as the studyI’mabout to review has a lot of experiments and so many taxas curated under each signature

U1LCB8WEA (09:36:43) (in thread): > My perspective is to focus on the major points, and things that are often gotten wrong, with the objective of making sure there aren’t major errors that would make the study not do well in analyses of the database. Some examples (other examples welcome!): > * study design > * that each experiment corresponds to a comparison of two groups > * check Body site and Antibiotics Exclusion > * Statistical test corresponds to what was used to compare Group 1 to Group 0, and not for something else. > * that the Condition corresponds to what is different in Group 1 compared to Group 0, not something that is shared by both groups. > * that the direction of the signatures is correct, and at least a sampling of the taxa checks out > If all these are correct, I’d be satisfied that the rest of the study is probably correct too, and anyways the rest is less important.

Mildred Anashie (09:39:11) (in thread): > This is really helpful > I appreciate this > Thank you@Levi Waldron:blush:Looking forward to other responses

Svetlana Ugarcina Perovic (09:40:39) (in thread): > Before going through the curation, checking the paper and how many experiments you see is helpful in confirming that all the experiments are recorded.

Chioma Onyido (09:41:08) (in thread): > Hi@Mildred Anashieeven I too struggle with speed during review sometimes. > > During one of the office hours, the mentors suggested a helpful tip: we don’t necessarily have to read the entire paper before reviewing (something I used to do). For papers with many taxa or signatures, you can start by locating the sources of each experiment. > > For instance, if the source is Figure 1, examine Figure 1 to confirm it’s correctly curated by doing a quick match with the one in the paper. Then, count the number of taxa to ensure none are omitted by the curator. > > Regarding group sizes, most papers include information about group sizes and names under a table description, usually in Table 1. It’ll be helpful to look for this information there. > > Other details, such as variable regions, sequencing types and platforms, and statistical tests, are usually found in the methodology section.

Svetlana Ugarcina Perovic (09:41:30) (in thread): > And then checking the relevant details that Levi listed is my usual reviewing protocol.

Svetlana Ugarcina Perovic (09:43:14) (in thread): > @Chioma Onyidoif those details are not there, checking the supplementary material is the next step.

UBNSEMS3S (09:43:22) (in thread): > Honestly, reviews just take a bit of time and that’s ok. As you get more experience doing them, you’ll start understanding a bit more of what to look for and they will get faster. When I was reviewing a ton of curations during the application period I did the following that helped: > * Use your screen effectively. Lay out the curation and the article side by side. It’s much faster if you’re not flipping back and forth between the two. > * Review using the flow of BugSigDB and not the article. > * Ctrl+F (find) is very helpful for easily finding where they talk about the statistical test, matching, etc. > * There is some amount of triage that occurs when you’re reviewing. If the curator seems to be getting a lot of basic things wrong, that’s an indicator that I need to be applying a very high level of scrutiny. If the curator mostly seems to be right, you can focus on the fundamentals (that Levi mentioned). > * If you’re not sure about something or having difficulty assessing one particular element, don’t get bogged down. Just note that you’re not sure if it’s right in your review and maybe bring it to the next meeting.

Mildred Anashie (09:43:45) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@Chioma OnyidoThis are helpful tipsI’llbe implementing

Svetlana Ugarcina Perovic (09:46:41) (in thread): > This was a great question and now we are having a super helpful thread, thanks!

Aleru Divine (09:47:38) (in thread): > Thank you so much for raising this@Mildred Anashie.I am about to review a very lengthy study too:sweat_smile:Thanks for the tips everyone:pray::heart:

Svetlana Ugarcina Perovic (10:00:59) (in thread): > Here’s a summary of the key tips for reviewing curations: > 1. Use screen space efficiently by displaying curation and article side-by-side. > 2. Review following BugSigDB flow rather than article structure. > 3. Utilize Ctrl+F to quickly locate specific information (e.g. “matched on”). > 4. Adjust scrutiny level based on curator’s accuracy with basic curation elements. > 5. Note uncertainties for discussion in future meetings or in Slack. > 6. Focus on major points and common errors to ensure the study performs well in database analyses. > 7. Key areas to check: > > 1. Study design > 2. Experiment structure (comparison of two groups) > 3. Body site and Antibiotics Exclusion > 4. Statistical test accuracy > 5. Condition description > 6. Signature direction and taxa recorded (count them first to see if the counts match) > > 1. Confirm the number of experiments recorded matches the paper. > 2. Locate experiment sources (e.g., figures) and verify curation accuracy. > 3. Find group sizes and names in table descriptions (often Table 1 or Supplementary Material). > 4. Check methodology section for technical details (variable regions, sequencing types, platforms, statistical tests).

Mildred Anashie (10:03:02) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the summary:blush:Saving this for later and I also think it should be pinned for reference

Aleru Divine (10:04:18) (in thread): > Incredible summary@Svetlana Ugarcina Perovic:pleading_face:

Scholastica Urua (10:20:17) (in thread): > Thank you@Mildred Anashiefor raising this question. This thread is really helpful. I do check out all the taxa most times:face_holding_back_tears:.

Svetlana Ugarcina Perovic (10:21:45) (in thread): > hahah@Scholastica UruaI know that, and keep doing it ;)

Svetlana Ugarcina Perovic (10:22:21) (in thread): > that’s why I put:Signature direction and taxa recorded (******count them first to see if the counts match********)**

Scholastica Urua (10:23:13) (in thread): > Noted Svee. Thank you!

Svetlana Ugarcina Perovic (10:24:32) (in thread): > I appreciate this tip by<@UBNSEMS3S>If the curator seems to be getting a lot of basic things wrong, that’s an indicator that I need to be applying a very high level of scrutiny.It’s so true!

Peace Sandy (12:44:12) (in thread): > Congratulations@Aleru Divine

Peace Sandy (13:10:04) (in thread): > Really helpful tips:hugging_face:

Peace Sandy (16:02:59) (in thread): > Nice article@Scholastica Urua

Scholastica Urua (16:05:13) (in thread): > Thank you@Peace Sandy

2024-07-22

Aleru Divine (02:54:06): > Good morning and a Happy Monday everyone:sparkles::konata:! > > While curating a study over the weekend, I saw the term “p_Unmapped” in reference to an unmapped phylum. This is a bit unfamiliar to me. I am curious to know whether to leave it out entirely (as it is unmapped) or to curate it as seen. > > I added the image for reference. Your insights would be greatly appreciated.:gratitude-thank-you: - File (PNG): Screenshot 2024-07-21 at 16.13.20.png

Aleru Divine (05:24:53): > I’d like to delete this signature please.https://bugsigdb.org/Study_1096/Experiment_4/Signature_3Thank you so much! - Attachment (BugSigDB): Study 1096/Experiment 4/Signature 3 > Source: Supplemental data 4, 5 and 6 Description: Differential abundance results at phylum, genus and species level for Shotgun metagenomics sequencing. Abundance…

idiaru Angela (05:29:19) (in thread): > Good morning and Happy Monday@Aleru Divine. This looks like the phylum was unidentified so I would go with leaving it out of the curation. Well done

Aleru Divine (06:15:58) (in thread): > Yes it is unidentified. Thank you so much@idiaru Angela

Victoria (Burah) Poromon (07:16:20) (in thread): > Good morning@Aleru DivineI’d go with curating it. > This is because some authors update their studies, and sometimes those updates can include the names of previously unidentified microorganisms. > > (I came across an updated study recently) > Well done.

Svetlana Ugarcina Perovic (08:18:58) (in thread): > Deleted.

Svetlana Ugarcina Perovic (08:20:16) (in thread): > @Precious Orakweplease go through this thread!

Aleru Divine (12:33:23) (in thread): > Thank you:pray:

Aleru Divine (12:36:07) (in thread): > Thanks@Victoria (Burah) PoromonI’ll proceed with curating it then, incase it is updated in the future.

Mildred Anashie (16:03:10) (in thread): > This is an interesting one@Aleru DivineI seem to agree with@Victoria (Burah) PoromonSimply because, even though it was unidentifiedit’sstill part of the study so it could be helpful including it and possibly leaving a comment > > Well done:clap:

2024-07-23

Aleru Divine (11:17:44) (in thread): > Thank you@Mildred AnashieI’ll curate it:sweat_smile:Thanks everyone:heart_hands:

2024-07-24

Peace Sandy (08:29:24): > Have anyone been able to successfully stream BioC Conference ?

UBNSEMS3S (08:36:35) (in thread): > It just started and should be working. Are you still having issues?

Svetlana Ugarcina Perovic (08:43:21) (in thread): > All good here!

Svetlana Ugarcina Perovic (08:43:53) (in thread): > https://app.events.ringcentral.com/events/bioc2024/stages/06d9dddb-bbb1-4b12-a023-77f53bdaac1c

Scholastica Urua (08:50:34) (in thread): > Working fine on my end

Peace Sandy (08:52:00) (in thread): > Not at all@C. Mirzayi (please do not tag this account)I can stream successfully now > Thank you

Svetlana Ugarcina Perovic (08:52:33) (in thread): > Enjoy the conference!

Peace Sandy (08:52:41) (in thread): > Thank you@Scholastica Uruaand@Svetlana Ugarcina Perovic

Precious Orakwe (12:55:43): > Good day@Svetlana Ugarcina Perovic@Levi Waldron<@UBNSEMS3S>please I need help, I have been working on curating a paper for a while now, but I am having issues, everything I am curating, am not seeing them, I am only see experiment one, and even the signatures for the experiment, I didn’t c againhttps://bugsigdb.org/Study_1091 - Attachment (BugSigDB): Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study - BugSigDB > BACKGROUND: Gastric cancer is one of the global health concerns.A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases.

Scholastica Urua (13:19:47) (in thread): > Hi@Precious Orakwe, well done on your curation:raised_hands:. Please refer to this thread. Similar issue was reported here;https://community-bioc.slack.com/archives/C04RATV9VCY/p1717229976556539?thread_ts=1717229976.556539&cid=C04RATV9VCYHope this helps. - Attachment: Attachment > Good day and wishing everyone a prosperous new month! > I can’t add new experiments to this study > https://bugsigdb.org/Study_1079

Peace Daniel (13:25:20) (in thread): > Hey@Scholastica Uruathis brings me back to my unfinished curation:face_with_peeking_eye:Been really occupied, has this been resolved yet?

UBNSEMS3S (13:45:32) (in thread): > I refreshed the page and it seems Experiment 2 is now showing for me. See if it’s working for you and let me know.

Precious Orakwe (13:56:53) (in thread): > Alright, thanks to everyone

Scholastica Urua (14:01:44) (in thread): > I can also see experiments 1 and 2 from my end.

Scholastica Urua (14:04:01) (in thread): > > Hey@Scholastica Uruathis brings me back to my unfinished curation:face_with_peeking_eye:Been really occupied, has this been resolved yet? > Yes@Peace Daniel, the issue was resolved. Both experiments 7 and 8 are now displaying.

Peace Daniel (14:06:46) (in thread): > I can only see experiment 1, same with@Precious Orakwe

Peace Daniel (14:10:31) (in thread): > Also<@UBNSEMS3S>https://community-bioc.slack.com/archives/C04RATV9VCY/p1717229976556539?thread_ts=1717229976.556539&cid=C04RATV9VCYIn this curation although I can see experiments 7,8 it still shows this > Would this be an issue later on as this study had a lot of experiments? - Attachment: Attachment > Good day and wishing everyone a prosperous new month! > I can’t add new experiments to this study > https://bugsigdb.org/Study_1079 - File (JPEG): IMG_3368

Esther Afuape (15:10:21) (in thread): > Svetlana is presenting now if you’re on a break!:smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Precious Orakwe (15:23:03): > Hello<!here>@Svetlana Ugarcina Perovic<@UBNSEMS3S>can you explain this for me please, > > “No significant differences in alpha and beta diversities were detected among the patient groups.”

UBNSEMS3S (15:24:17): > Very nice talk Svetlana! Everyone seemed really interested.

UBNSEMS3S (15:24:58) (in thread): > There was no significant difference in alpha diversities–so we would curate any of those specific measured mentioned as unchanged. We do not curate beta diversity.

Scholastica Urua (15:25:20) (in thread): > Interesting presentation Svee:hugging_face:

Svetlana Ugarcina Perovic (15:25:31) (in thread): > and questions!

Scholastica Urua (15:26:01) (in thread): > Yes! and comment

Esther Afuape (15:26:19) (in thread): > Well done Sve!:clap:

Svetlana Ugarcina Perovic (15:26:49) (in thread): > Great questions and comments as well! - File (PNG): Screenshot 2024-07-24 at 21.25.46.png

Precious Orakwe (16:49:51) (in thread): > Ok, thanks<@UBNSEMS3S>

2024-07-25

Svetlana Ugarcina Perovic (03:44:56): > BIG shout-out to our dear NSURP intern@JACOB A DE JESUS-CANDELARIOwho joined us 6 weeks ago and curated 6 studies!! > * https://github.com/waldronlab/BugSigDBcuration/issues/396 > * https://github.com/waldronlab/BugSigDBcuration/issues/401 > * https://github.com/waldronlab/BugSigDBcuration/issues/402 > * https://github.com/waldronlab/BugSigDBcuration/issues/403 > * https://github.com/waldronlab/BugSigDBcuration/issues/421 > * https://github.com/waldronlab/BugSigDBcuration/issues/418 > Next week, Jacob will talk about his bugsigdb experience atNSURP Symposium (Scholar Final Presentations by Discipline,August 1). I will share a link when available. > > Well done, Jacob!:potted_plant:Special thanks to@Scholastica Uruafor her reviewing efforts. > > cc<@UBNSEMS3S><@U1LCB8WEA>

Scholastica Urua (03:46:52) (in thread): > Well done@JACOB A DE JESUS-CANDELARIO:clap::confetti_ball:Thank you@Svetlana Ugarcina Perovic:hugging_face:

2024-07-26

Svetlana Ugarcina Perovic (05:58:15): > ****#BioC2024Have you listened to yesterday’s keynote talk by Stephen Piccolo:Using Artificial Intelligence to Support Dataset Finding, Image Accessibility, and Bioinformatics Education? > > Now it’s available in the Replay section.Happy Friday!**

Scholastica Urua (05:59:39) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:blush:

Peace Sandy (16:49:25) (in thread): > Happy Friday@Svetlana Ugarcina Perovic

Peace Sandy (16:49:59) (in thread): > Well done@Svetlana Ugarcina Perovic

2024-07-29

Svetlana Ugarcina Perovic (04:26:07): > Happy Monday!Sharing a good interview with Alan Walkerhttps://www.the-microbiologist.com/careers/a-conversation-at-the-forefront-of-human-microbiome-research/3590.article“The key point is thatboth computational biology and wet lab work are important, and should be complementary!” - Attachment (The Microbiologist): A conversation at the forefront of human microbiome research > Yang Yue and Professor Alan Walker discuss everything from precision medicine and the omics approach, to challenges in the road ahead and the future of microbiome research.

Joyce Qiu (10:21:21): > What type of study design would a follow-up study fall under?

Svetlana Ugarcina Perovic (10:22:53) (in thread): > Could you please leave a link to your paper for curation? To get a better answer ;)

Joyce Qiu (10:23:45) (in thread): > Sure,https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8355081/ - Attachment (PubMed Central (PMC)): Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study > Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis. However, its role in the antipsychotic treatment response is unclear. Here, we present a 24-week follow-up study to identify …

Scholastica Urua (10:28:09) (in thread): > Excerpt from the study“We collected biological samples at baseline (all participants) and follow-up time points after risperidone treatment (SCH patients).”This should be a Time series / longitudinal observational study@Joyce Qiu

Joyce Qiu (10:28:39) (in thread): > Yes, that’s what I was thinking too. Thank you!

Joyce Qiu (11:02:26) (in thread): > I’m having some trouble filling out the Lab analysis and Statistical Analysis sections. Can someone help me?

Scholastica Urua (11:04:55) (in thread): > What trouble are you encountering?

Joyce Qiu (11:08:09) (in thread): > Finding the correct information like for example, is PCR the sequencing type and Ion Torrent the sequencing platform?

Joyce Qiu (11:08:51) (in thread): > Also where to find the information for the Statistical Analysis section

Scholastica Urua (11:10:20) (in thread): > I’ll check these out and let you know.

Joyce Qiu (11:11:08) (in thread): > Thank you!

Scholastica Urua (11:23:57) (in thread): > You are right about the sequencing platform being Ion Torrent. > > The sequencing type is******16S with V3-V4 regions******. You can find this information under the “Amplicon generation”section. > > The statistical test is******Wilcoxon (Mann Whitney)******which uses ‘******relative abundance******’ for data transformation. You can find this information under the”Differences in microbial biomarkers between SCH patients and HCs at baseline”section

Joyce Qiu (11:48:20) (in thread): > Thank you so much!

Scholastica Urua (11:56:32) (in thread): > Hi@Joyce Qiu, > > Upon revisiting the study, I’ve identified two separate experiments: > > 1.SCH vs. HCs at baseline:This experiment uses the Wilcoxon test for statistical analysis. > 2.SCH vs. HCs after risperidone treatment:This experiment utilizes LEfSe for statistical testing. > > The significance threshold for the tests is set at 0.05, which is the default value unless specified otherwise in the study. > > MHT correction is applied, as indicated by the study’s mention of using False Discovery Rate (FDR) to correct for multiple testing. > > For the LEfSe analysis, the study uses an effect-size threshold of 3.0, while the default threshold is typically 2.0 unless stated otherwise. So in this study, the LDA score = 3.0. > > I hope this clarifies your question regarding the Statistical Analysis section.

Joyce Qiu (12:00:34) (in thread): > Hi@Scholastica Urua, thanks for letting me know. Should I add these as separate experiments for this study?

Scholastica Urua (12:02:29) (in thread): > Yes, the study will have 2 separate experiments.

2024-07-30

Scholastica Urua (06:08:54): > Hello everyone:sun_with_face:Please could the following taxa be resolved as follows: > * [Clostridium] leptum subgroup as[Clostridium] leptum > * Lactobacillus gasseri subgroup asLactobacillus gasseri > * Limosilactobacillus reuteri subgroup asLimosilactobacillus reuteri > Study link:https://bugsigdb.org/Study_948Thank you!

Svetlana Ugarcina Perovic (09:49:18) (in thread): > I would leave it to the subgroup level. See for examplehttps://www.jstage.jst.go.jp/article/bmfh/36/4/36_17-006/_articlewhere “the genomic differences between twosubgroups…” were reported. - Attachment (J-STAGE): Revealing the genomic differences between two subgroups in Lactobacillus gasseri > Being an autochthonous species in humans, Lactobacillus gasseri is widely used as a probiotic for fermented products. We thoroughly compared the gene …

Scholastica Urua (09:51:16) (in thread): > Thank you@Svetlana Ugarcina Perovic

Victoria (Burah) Poromon (10:18:56): > Hi everyone. > I’m currently curating this study and I need other opinions on what the condition should be. > > The study is investigating the effect of Dimethyl Itaconate administration on High-fat diet-induced cognitive impairment. > > Should the condition be “Metabolite” or “Cognitive impairment”? > > Ps: Dimethy Itaconate is not on the list of allowed values, but it is a metabolite. > > Thank you so much…Link to study:https://bugsigdb.org/Study_1095 - Attachment (BugSigDB): Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice - BugSigDB > BACKGROUND: Gut homeostasis, including intestinal immunity and microbiome, is essential for cognitive function via the gut-brain axis.This axis is altered in high-fat diet (HFD)-induced cognitive impairment and is closely associated with neurodegenerative diseases.

Scholastica Urua (10:25:00) (in thread): > I’ve not gone through the study in question but I’m assuming both mice group were cognitively impaired?? > > In that case what is contrasted is Dimethyl Itaconate administration. So “Metabolite” will be a suitable condition.

Victoria (Burah) Poromon (10:29:30) (in thread): > Yes@Scholastica Uruaboth groups were induced with cognitive impairment.

2024-07-31

UBNSEMS3S (17:24:18): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTAlso would love to hear from everyone who attended BioC2024 about their impressions and experiences! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-08-01

Svetlana Ugarcina Perovic (02:55:14): > Today is the NSURP Research Symposium where@JACOB A DE JESUS-CANDELARIOwill present his work during his 8 weeks internship with us. You are welcome to join us! > > Also, today during our team meeting Jacob will present his work as a rehearsal, looking forward to hearing your feedback before giving the same talk to the NSURP community. > > Time: 2:20 pm EDT > Zoom: Zoom Link:https://arizona.zoom.us/j/83992451743Password: 2024 > All presenters will go to the Zoom link above. Presentations will occur in labeled breakout rooms. > > (Schedule is in PST) - File (PNG): Screenshot 2024-08-01 at 08.48.18.png

Svetlana Ugarcina Perovic (14:26:00): > Right now:rocket: - File (PNG): Screenshot 2024-08-01 at 20.25.28.png

Svetlana Ugarcina Perovic (14:40:00): > Great job, Jacob!cc<@UBNSEMS3S>@Scholastica Urua<@U1LCB8WEA> - File (PNG): Screenshot 2024-08-01 at 20.34.37.png

Svetlana Ugarcina Perovic (14:40:43): > Btw, Michael is a founder of NSURP program.

Scholastica Urua (14:41:56) (in thread): > Great job@JACOB A DE JESUS-CANDELARIO. > > Well done@Svetlana Ugarcina Perovic, you’re a great mentor:raised_hands::heart_eyes:

Peace Sandy (16:50:41) (in thread): > Well done@Svetlana Ugarcina Perovic:bouquet:

2024-08-02

Svetlana Ugarcina Perovic (06:39:49): > From zero to hero with PythonA 2 day, free, online workshop built uponthe Carpentrieslessons and learning materialsHappy Friday! - Attachment (denbi.de): From zero to hero with Python > The ‘German Network for Bioinformatics Infrastructure – de.NBI’ is a national, academic and non-profit infrastructure supported by the Federal Ministry of Education and Research providing bioinformatics services to users in life sciences research and biomedicine in Germany and Europe. The partners organize training events, courses and summer schools on tools, standards and compute services provided by de.NBI to assist researchers to more effectively exploit their data.

Scholastica Urua (06:44:54) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (06:46:28) (in thread): > Happy Friday@Svetlana Ugarcina PerovicAnd thank you for sharing:pray:

Joyce Qiu (12:18:45): > Hi everyone! I think I finished curating the study with PMID 36228569. Can it be reviewed to make sure everything is correct? I’m especially unsure about the signatures.

2024-08-04

Adeshile Oluwatosin (11:43:16): > Hello Everyone,I am Adeshile Oluwatosin. I have a BSC in Biochemistry, hoping to further my masters in bioinformatics.I am writing to volunteer in any ongoing projects particularly bugSIgDB projects.I joined this group to gain experience in this field bioconductor. Kindly navigate me through what to do to begin my journey.

Scholastica Urua (12:23:48) (in thread): > Hi@Joyce Qiu, I’m finding it difficult to access the pdf to this study. Can you kindly attach it here and any supplementary materials it has. > > Thank you

Joyce Qiu (14:15:24) (in thread): > Hi@Scholastica Urua, please see attached for the pdf of this study. > Thank you - File (PDF): Aljumaah-etal-1-Clin-Nutri-2022.pdf

Scholastica Urua (14:16:05) (in thread): > Thank you

2024-08-05

Scholastica Urua (03:42:03) (in thread): > Please also attach the supplementary material. Thank you

Svetlana Ugarcina Perovic (04:39:30) (in thread): > Welcome to the team, Adeshile!

Adeshile Oluwatosin (04:40:32) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (04:40:58) (in thread): > I look forward to working with the team

Svetlana Ugarcina Perovic (04:42:12) (in thread): > Please go through this material: > * BugSigDB project information, estimated time: 15 minutes (link) > * Reading materials on the human microbiome, estimated time: 2 hours (link) > * step-by-step guidance on how to document a signature in BugSigDB (link) > * View examples of completed BugSigDB curations, estimated time: 15 minutes (link) Video trainings on BugSigDB curation (link) > Please open your bugsigdb accounthttps://bugsigdb.org/Main_Page

Svetlana Ugarcina Perovic (04:43:09) (in thread): > And:slightly_smiling_face:the most important point: feel free to ask questions here, whenever you have doubts!

Adeshile Oluwatosin (04:43:48) (in thread): > Definitely, I will reach out > Let me follow the instructions > Thank you once again

Joyce Qiu (10:53:17) (in thread): > I’m sorry, I’m not sure what supplementary material you’re referring to

Scholastica Urua (10:56:42) (in thread): > The study has additional material(s) containing more information. - File (PNG): Capture.PNG

Svetlana Ugarcina Perovic (13:12:13) (in thread): > @Joyce QiuThroughout the text you can spot, beside Figures/Tables in the main text, additional Figures/Tables in the Supplementary Material. - File (PNG): Screenshot 2024-08-05 at 19.10.37.png

Svetlana Ugarcina Perovic (13:12:53) (in thread): > See: Fig 1. and Supplementary Fig. 1.

Joyce Qiu (19:44:42) (in thread): > Thank you. I will look for those

2024-08-06

Svetlana Ugarcina Perovic (06:13:20) (in thread): > NSURP Final Recordings are now available herehttps://www.youtube.com/watch?v=8TYTL4A7QS8Jacob’s talk starts at 1:16:34 - Attachment (YouTube): Research Symposium 2024 - Room 5 - Medical Microbiology

Victoria (Burah) Poromon (06:43:53): > Hello Everyone, > > I just finished curating this study and I want some reviews on it. > > Especially the condition and group 1 definition for Experiment 2. > > Link to study:https://bugsigdb.org/Study_1095Thank you so much. - Attachment (BugSigDB): Dimethyl itaconate ameliorates cognitive impairment induced by a high-fat diet via the gut-brain axis in mice - BugSigDB > BACKGROUND: Gut homeostasis, including intestinal immunity and microbiome, is essential for cognitive function via the gut-brain axis.This axis is altered in high-fat diet (HFD)-induced cognitive impairment and is closely associated with neurodegenerative diseases.

Joyce Qiu (10:22:17) (in thread): > Unfortunately, I can’t seem to be able to access the supplementary materials either

Svetlana Ugarcina Perovic (10:24:08) (in thread): > In this case we are writing to the authors. I will email them and cc you.

Joyce Qiu (11:03:49) (in thread): > Sounds good, thank you.

2024-08-07

Svetlana Ugarcina Perovic (04:32:43): > Hello everyone! Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTI can’t make it. Enjoy discussions with<@UBNSEMS3S>! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

Svetlana Ugarcina Perovic (04:33:19) (in thread): > @Victoria (Burah) Poromon@Joyce Qiubring up your questions tomorrow!

2024-08-08

Chioma Onyido (09:26:10): > Found this interesting paper on my LinkedIn TL! > > “Interestingly, DNA sequencing showed 101 bacterial strains. The bacterial population was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Bacteria that can cause food-borne decease were also found in some cases”. - Andrew Akbashev. > > It’s amazing that our microwaves can host such diverse bacteria. It makes you think about the hidden ecosystems we encounter daily. > > It also raises interesting questions about how these microbes adapt to survive in such extreme conditions, like high temperatures and radiation. Could this knowledge even lead to new discoveries in microbiology or sterilization techniques?:thinking_face: - File (JPEG): IMG_4923

UBNSEMS3S (09:31:18): - File (PNG): image.png

Aleru Divine (09:36:42) (in thread): > Thank you so much for the office hours session<@UBNSEMS3S>I have a much better andI’llsay deeper understanding of what is and whatisn’tcontrolling for a confounder.:blush:

Mildred Anashie (09:55:04) (in thread): > In microbiology we know about thermophilic microorganisms. These microorganisms, also known as thermophilic extremophiles, can survive and adapt to extreme conditions, including high temperatures and radiation. > > But thisis an interesting oneand worth reading more onbecausedespite the fact the organisms are heat-lovingthe temperature in the microwave oven seems too extreme even for thermophilesThank you for sharing@Chioma Onyidobecause I believe it will definitely lead to new discoveries

Peace Sandy (12:46:01) (in thread): > Really insightful session today@C. Mirzayi (please do not tag this account)Thank you for the detailed explanation.

Peace Daniel (18:02:30) (in thread): > Great find@Chioma OnyidoThis makes me wonder if these microbes adapted to fit the varying temp of the microwave, I’m curious > Could you share a link to this pls? Thanks

2024-08-09

Chioma Onyido (04:51:01) (in thread): > Here you go!@Peace Danielhttps://www.nature.com/articles/d41586-024-02553-9 - Attachment (Nature): Your microwave oven has its own microbiome > Survey of bacteria living inside household and laboratory appliances finds a robust ecosystem.

Evelyn Mary Attah (15:56:17): > Hello everyone, I and JoyceQ just finished curating this paper and would love a review on it. Link to study:https://bugsigdb.org/Study_1090Thank you very much. - Attachment (BugSigDB): Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome - BugSigDB > AIMS/HYPOTHESIS: It is widely thought that the intestinal microbiota plays a significant role in the pathogenesis of metabolic disorders.However, the gut microbiota composition and characteristics of schizophrenia patients with metabolic syndrome (MetS) have been largely understudied.

2024-08-10

Scholastica Urua (08:51:51) (in thread): > Please refer to the github issue for the review. Well done@Evelyn Mary Attahand@Joyce Qiu

2024-08-11

Joyce Qiu (18:07:11) (in thread): > I believe there was a mistake because I never curated this paper. I believe curated another paper for Study 1090 but that paper had been curated already. However, I can still help with this one since the signatures currently don’t match.

2024-08-12

Svetlana Ugarcina Perovic (04:34:43): > Hello hello, check this out:Your microwave oven has its own microbiome(https://www.nature.com/articles/d41586-024-02553-9) > > Paper link:https://doi.org/10.3389/fmicb.2024.1395751 - Attachment (Nature): Your microwave oven has its own microbiome > Survey of bacteria living inside household and laboratory appliances finds a robust ecosystem.

Svetlana Ugarcina Perovic (04:36:17) (in thread): > Here is the gh issuehttps://github.com/waldronlab/BugSigDBcuration/issues/423 - Attachment: #423 Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome > Profiles and diagnostic value of intestinal microbiota in schizophrenia patients with metabolic syndrome - Mengjuan Xing et al. – Frontiers in Endocrinology
> https://www.frontiersin.org/journals/endocrinology/articles/10.3389/fendo.2023.1190954/full

Svetlana Ugarcina Perovic (05:00:55) (in thread): > Ahh, only now I saw@Chioma Onyido’s posthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1723123570268359 - Attachment: Attachment > Found this interesting paper on my LinkedIn TL! > > “Interestingly, DNA sequencing showed 101 bacterial strains. The bacterial population was dominated by Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes. Bacteria that can cause food-borne decease were also found in some cases”. - Andrew Akbashev. > > It’s amazing that our microwaves can host such diverse bacteria. It makes you think about the hidden ecosystems we encounter daily. > > It also raises interesting questions about how these microbes adapt to survive in such extreme conditions, like high temperatures and radiation. Could this knowledge even lead to new discoveries in microbiology or sterilization techniques? :thinking_face:

Chioma Onyido (05:15:50) (in thread): > Yes Yes! An interesting read.:nerd_face:

Svetlana Ugarcina Perovic (05:22:57) (in thread): > We are following the same hype, you on LinkedIn, I on X…

Chioma Onyido (05:26:03) (in thread): > Great!:100:

Peace Daniel (07:53:08) (in thread): > A good read

Svetlana Ugarcina Perovic (10:49:23): > UN Sustainable Development Goal 10 “Reduce inequalities”, Goal 5 “Gender equality”, and Goal 3 “Good Health and Well-being”. > Main topics at Nature conference in September. The conference will also feature**** a mentorship programme**that will provide further opportunity for participants to connect and build relationships. > > A 2 day, free, virtual event - Attachment (natureconferences.streamgo.live): Breaking Barriers for Gender and Health Equity Through Research > Breaking Barriers for Gender and Health Equity Through Research

Scholastica Urua (10:53:05) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Joyce Qiu (11:19:39) (in thread): > I fixed the signatures so that they match the paper

Scholastica Urua (11:57:15) (in thread): > Hi@Joyce Qiuand@Evelyn Mary Attah, I’ve made a few changes to the curation and reported them under the GitHub issue. Please check it out. > Well done:clap:

Peace Daniel (11:57:39) (in thread): > Registered curious about the mentorship and thanks for sharing@Svetlana Ugarcina Perovic

Peace Daniel (12:00:05) (in thread): > @Scholastica Uruadid you get a confirmation mail after registering?(If you registered)

Scholastica Urua (12:02:25) (in thread): > Hi@Peace DanielYes, I got a confirmation mail after registration.

Peace Daniel (12:03:36) (in thread): > Oh seems my registrationdidn’tgo through then, thanks for the response

Peace Sandy (16:36:44) (in thread): > Interesting.

2024-08-13

Svetlana Ugarcina Perovic (05:37:48) (in thread): > We got the supplementary material from the authors! I will add it to the github issue. Please complete the curation.@Joyce Qiu@Scholastica Urua

Scholastica Urua (05:39:20) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:40:09) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/431

Mildred Anashie (06:21:42): > Hello everyone > > Please I need help confirming some signatures are actually visible in thisStudyI’mcurrently curating the signatures for the experiments andI can’tfind some of the signatures curated (especially Experiments 13 and 14, I have entered twice since the first onewasn’tvisible and I stillcan’tfind any) > > Thank you:pray: - Attachment (BugSigDB): Oral microbiota of patients with phenylketonuria: A nation-based cross-sectional study - BugSigDB > AIM: The oral microenvironment contributes to microbial composition and immune equilibrium.It is considered to be influenced by dietary habits.

Scholastica Urua (06:37:07) (in thread): > Hi@Mildred Anashie, the signatures you curated are on BugSigDB. They are just not displaying. Exp 13 has 4 and 14 has 3 signatures. Use; “https://bugsigdb.org/Study_1086/Experiment_13/Signature_4” to see each signature.

Scholastica Urua (06:38:18) (in thread): > Please report the issue here as well:https://github.com/waldronlab/BugSigDB/issues/221#issuecomment-2153119191

Mildred Anashie (06:38:26) (in thread): > In that case Signature 3 and 4 for Experiment 13 and signature 3 for Experiment 14 should be deleted

Mildred Anashie (06:38:38) (in thread): > Thank you@Scholastica Urua

Scholastica Urua (06:41:27) (in thread): > Experiment 14 has only 2. The previous message was a typo. Apologies

Scholastica Urua (06:44:00) (in thread): > > In that case Signature 3 and 4 for Experiment 13 and signature 3 for Experiment 14 should be deleted > Hi@Svetlana Ugarcina Perovicplease delete signatures 3 and 4 of experiment 13. Thank you.https://bugsigdb.org/Study_1086

Svetlana Ugarcina Perovic (08:40:43) (in thread): > Deleted.

Mildred Anashie (08:59:10) (in thread): > So I don’t know if this is a temporal fix or if it will work for other studies with same issues, but I noticed when I edited an experiment with invisible signatures and saved the page the signatures appeared. > > Currently all the signatures are visible

Svetlana Ugarcina Perovic (09:01:58) (in thread): > @Mildred Anashieplease report this as well in the open bug gh issue.

Scholastica Urua (09:04:26) (in thread): > @Mildred AnashieI experience that sometimes. But what I’ve noticed is that once the signature(s) displays, that particular signature doesn’t disappear again.

Mildred Anashie (09:05:41) (in thread): > Okay@Svetlana Ugarcina Perovic

Joyce Qiu (10:12:02) (in thread): > How can I find the GitHub issue?

Scholastica Urua (10:17:52) (in thread): > Here:https://github.com/waldronlab/BugSigDBcuration/issues/423

Mildred Anashie (10:34:26) (in thread): > Okay@Scholastica UruaExplains why ithasn’tdisappeared again

Joyce Qiu (10:38:54) (in thread): > Thank you

2024-08-14

UBNSEMS3S (21:39:38): > Hello everyone! We will be having our weekly team meeting at 9 AM EDT tomorrow (Thursday).https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-08-15

Svetlana Ugarcina Perovic (05:42:59): > I’m happy to introduce to you@Kavya Ayalasomayajulaour new intern.Welcome aboard, Kavya!

idiaru Angela (05:44:01) (in thread): > Welcome@Kavya Ayalasomayajula

Scholastica Urua (06:01:31) (in thread): > Welcome to the community@Kavya Ayalasomayajula

Mildred Anashie (06:08:52) (in thread): > Welcome@Kavya Ayalasomayajula

Chioma Onyido (06:40:41) (in thread): > You are welcome@Kavya Ayalasomayajula:cherry_blossom:

Svetlana Ugarcina Perovic (10:17:05) (in thread): > @Kavya Ayalasomayajulaha, I found only a few studies on epilepsy curated in BugSigDBhttps://bugsigdb.org/Special:RunQuery/Drill?Drill=Condition%2Blogic%3DAND%26Locatio[…]ndition+logic%5D=OR&Drill%5BNCBI%5D=&wpRunQuery=&pf_free_text= - Attachment (BugSigDB): Special:RunQuery/Drill

Svetlana Ugarcina Perovic (10:21:02) (in thread): > @Kavya Ayalasomayajulahere is a nice review articlehttps://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1276551/fullwhere you can see what we missed to curate ;) - Attachment (Frontiers): Frontiers | The interplay between microbiota and brain-gut axis in epilepsy treatment > The brain-gut axis plays a vital role in connecting the cognitive and emotional centers of the brain with the intricate workings of the intestines. An imbala…

Peace Sandy (10:44:30) (in thread): > Welcome@Kavya AyalasomayajulaCheers to fun times bug-sig-dbing:clinking_glasses:

Kavya Ayalasomayajula (11:32:01) (in thread): > Nice to meet everyone! Excited to be working with you all

2024-08-16

Peace Daniel (05:45:24): > Hi everyone this study still has issues displaying signatures, I added a signature to experiment 7 but it doesn’t showhttps://bugsigdb.org/Study_1079 - Attachment (BugSigDB): Signatures within the esophageal microbiome are associated with host genetics, age, and disease - BugSigDB > BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host.

Peace Daniel (05:45:53) (in thread): > @Scholastica Uruacan you still see the signaturesI can’t?

Peace Daniel (05:54:47) (in thread): > I just tried what@Mildred Anashiesaid she didhereand the signature is now displaying. - Attachment: Attachment > So I don’t know if this is a temporal fix or if it will work for other studies with same issues, but I noticed when I edited an experiment with invisible signatures and saved the page the signatures appeared. > > Currently all the signatures are visible

Scholastica Urua (06:09:01) (in thread): > Is this okay now@Peace Daniel?

Peace Daniel (06:12:50) (in thread): > Yh the signature now displays but I feel as though another issue might come up,there’sthis category stuff at the bottom of the page and itdoesn’tshow for other studies

Peace Daniel (06:16:51) (in thread): > Oh I just checked few other studies and they all have the category thing@Scholastica UruaThat could be the issue, probably a bug

Scholastica Urua (06:25:45) (in thread): > Yes@Peace Daniel, it appears in almost all curations if not all.

Peace Daniel (06:31:28) (in thread): > Okay

2024-08-20

Svetlana Ugarcina Perovic (09:07:44): > Happy to share that@Scholastica Urua’s workAfrican microbiome data in BugSigDB is accepted to be presented as a poster at African Microbiome day (Sept 16). Scholastica also submitted this work foran MVIF talk on Sept 17. > > What a fantastic end of her Outreachy internship this week! > > cc<@UBNSEMS3S><@U1LCB8WEA>

Scholastica Urua (09:10:15) (in thread): > Thank you@Svetlana Ugarcina Perovic:dancer:

idiaru Angela (09:14:17) (in thread): > Congratulations@Scholastica Urua:partying_face:

Victoria (Burah) Poromon (09:24:26) (in thread): > Well done@Scholastica Urua

Svetlana Ugarcina Perovic (09:27:04) (in thread): > NOTE: It’s not the end of Scholastica’s BugSigDB-ing!

Peace Sandy (09:55:49) (in thread): > Congratulations@Scholastica Urua:rocket:

Scholastica Urua (10:44:42) (in thread): > Thank you everyone:smiling_face_with_3_hearts:

2024-08-21

Mildred Anashie (06:52:21) (in thread): > Congratulations@Scholastica Urua:clap:

Scholastica Urua (07:22:44) (in thread): > Thank you@Mildred Anashie

U1LCB8WEA (10:59:43) (in thread): > Congratulations, Scholastica!!!

Scholastica Urua (11:09:00) (in thread): > Thank you<@U1LCB8WEA>

Svetlana Ugarcina Perovic (12:39:52): > I’m happy to introduce@Alisha Mahadeoand@Aaishah Mahadeo, CUNY SPH students (sisters!) doing their fieldwork this fall as BugSigDB curators.Alisha and Aaishah, welcome to the team!

Svetlana Ugarcina Perovic (12:43:02): > Hello everyone! Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTI can’t make it. Enjoy discussions with<@UBNSEMS3S>! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

Scholastica Urua (12:45:42) (in thread): > Welcome to the community@Alisha Mahadeoand@Aaishah Mahadeo

Alisha Mahadeo (14:45:49) (in thread): > Thank you so much! Looking forward to working with you all!

Aaishah Mahadeo (14:48:14) (in thread): > Hi everyone! Excited to be working with you all!

Peace Sandy (16:29:52) (in thread): > Welcome@Alisha Mahadeoans@Aaishah Mahadeo

UBNSEMS3S (17:02:57) (in thread): > Congratulations Scholastica! Glad to have you working with us.

UBNSEMS3S (17:15:54): > Thanks Svetlana! Looking forward to meeting with you all and welcoming some new people to the team.

2024-08-22

Aleru Divine (04:49:01) (in thread): > Congratulations@Scholastica Urua:clap::clap:

Aleru Divine (04:49:56) (in thread): > Welcome@Aaishah Mahadeoand@Alisha Mahadeo:hugging_face:

Scholastica Urua (04:52:30) (in thread): > Thank you<@UBNSEMS3S>

Scholastica Urua (04:52:41) (in thread): > Thank you@Aleru Divine

Mildred Anashie (05:20:23) (in thread): > Welcome@Aaishah Mahadeoand@Alisha Mahadeo:blush:

2024-08-23

Nana (03:24:45) (in thread): > @Scholastica Uruacongratulations

Rahila-me (03:26:43) (in thread): > @Scholastica Uruacongratulation dear for a work well-done

Scholastica Urua (07:01:45): > Hi<@UBNSEMS3S>, Could you kindly share the recording from yesterday’s office hour when you have a moment? I would greatly appreciate it. Thank you so much!

Scholastica Urua (07:57:18) (in thread): > Thank you@Nanaand@Rahila-me

UBNSEMS3S (09:47:44): > @Scholastica UruaHere it is. A quick demo on working with BugSigDB data. We ran into a couple bugs along the way though so sorry it’s a bit of a mess. - File (MPEG 4 Video): video1098058622.mp4

Scholastica Urua (10:25:48) (in thread): > Thank you!:blush:

2024-08-27

Joyce Qiu (08:31:40): > Hi everyone, can the study I curated with PMID 36228569 be reviewed?

Mildred Anashie (12:53:56) (in thread): > Hi@Joyce QiuI think you should drop a comment on the issue on GitHubby pasting a link to the study and also requesting for a review

2024-08-28

UBNSEMS3S (10:49:43): > Hello everyone! Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTSince it’s the beginning of the semester, I will make sure we’re all setup and ready to start curating. See you all tomorrow!

UBNSEMS3S (20:54:55): > Hi everyone, apologies for the last minute change of plans but I am testing positive for COVID again so I am headed to the doctor tomorrow morning and will have to miss our morning meeting. > > I think we will cancel the morning meeting and convene next Thursday instead. I apologize to our new students who I was hoping to make sure you had everything you needed to start curating. Please feel free to message me and Svetlana if you have any questions.

2024-08-29

Victoria (Burah) Poromon (03:05:20) (in thread): > So sorry to hear about this<@UBNSEMS3S>I hope you feel better soon. > Sending you positive thoughts:yellow_heart::yellow_heart:

Mildred Anashie (04:22:08) (in thread): > Hi<@UBNSEMS3S>I’mreally sorry to hear about this > Wishing you a quick and smooth recovery!:heart:

Scholastica Urua (09:03:59) (in thread): > Sorry to hear that<@UBNSEMS3S>. Wishing you a speedy recovery.:heavy_heart_exclamation_mark_ornament:

Peace Sandy (13:23:28) (in thread): > So sorry@C. Mirzayi (please do not tag this account)I hope you get better soon > Please take care

2024-09-02

Svetlana Ugarcina Perovic (08:27:34): > Happy Monday! Happy September!How are you doing? > Are you currently curating/reviewing some interesting study? > Is there any curation issue to tackle together?:cookie::teapot:

Svetlana Ugarcina Perovic (08:28:56) (in thread): > Sending good vibes to our<@UBNSEMS3S>Hope you are feeling better?

Svetlana Ugarcina Perovic (08:56:49): > Online event on October 1-2:https://x.com/svetlana_up/status/1830203216199364742 - Attachment (X (formerly Twitter)): Svetlana U. Perović (@svetlana_up) on X > RT @MucosalGroup: Please share with your networks. #africanmicrobiomes for #globalhealth Be part of this #transformative journey in microbi…

Scholastica Urua (09:48:19) (in thread): > Happy new month@Svetlana Ugarcina Perovic:hugging_face::bouquet:I’m doing very well. Thank you.

Victoria (Burah) Poromon (10:36:16) (in thread): > Happy new month@Svetlana Ugarcina Perovic:relaxed:I’m doing great, andI’mcurrently reviewing a study carried out on Chickens!

2024-09-03

Mildred Anashie (09:32:02) (in thread): > Happy Monday and Happy September@Svetlana Ugarcina PerovicI’m doing great, Thank you:blush:Currently do not have any curation or curation issues

2024-09-04

Scholastica Urua (10:07:33) (in thread): > Hi<@UBNSEMS3S>, > > I followed your steps to download the BugSigDBStat file and filtered it for African studies. However, I noticed that the last 11 columns (from “Signature page name” to “Reviewer”) are only displaying 22 observations instead of 89, with the rest showing as NA. These observations are all from papers curated on January 10th, 2021. > > Could you please let me know if there are any additional steps I might have missed? The file is attached for your reference. > > Thank you for your assistance. > > cc<@U1LCB8WEA>@Svetlana Ugarcina Perovic - File (CSV): Africa_filtered_data.csv

UBNSEMS3S (20:39:50): > Hello everyone! Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTApologies that last week didn’t happen but we will hit the ground running tomorrow for sure! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

UBNSEMS3S (20:42:21) (in thread): > Ok it sounds like something might be going wrong with the data export. Let’s take a look at it tomorrow morning as the developer told us that the export issue was resolved.

2024-09-05

Scholastica Urua (01:40:13) (in thread): > Okay, thank you.

Svetlana Ugarcina Perovic (10:07:58): > Before you begin curating a paper,it’s crucial to check if it has already been curated. To do this: > 1. Go to the main page of BugSigDB > 2. Look for the “Search BugSigDB” feature in the top right corner > 3. Enter the PMID (PubMed ID) of the paper you’re interested in > 4. This will help you determine if the paper has been curated previously > This step ensures you don’t duplicate efforts and helps maintain the database’s efficiency. - File (PNG): Screenshot 2024-03-14 at 10.25.00.png

Svetlana Ugarcina Perovic (10:58:44) (in thread): > @Kavya Ayalasomayajula@Alisha Mahadeo@Aaishah Mahadeoif you encounter any issues when opening your bugsigdb account, just let me know.

Alisha Mahadeo (11:23:45) (in thread): > I have opened my bugsigdb account already. I did not encounter any issues. Thank you so much!

Aaishah Mahadeo (11:25:14) (in thread): > Thank you! I have opened my account and did not encounter any issues.

2024-09-09

Scholastica Urua (05:15:21) (in thread): > Hi<@UBNSEMS3S>, happy new week:hugging_face:

Scholastica Urua (05:19:21) (in thread): > I’m still encountering some issues with the data export, as it’s providing incomplete information. The dataset appears to be smaller than what we obtained on Thursday. I would greatly appreciate your assistance, as the deadline for the poster submission is approaching on Wednesday, 11th September 2024. > > Thank you so much<@UBNSEMS3S>

UBNSEMS3S (12:57:42) (in thread): > Here is the full export from last week. Import into R by placing it in the project folder and running the following code snippet which will rename all the variables to match what they would be if using bugsigdbr: > > dat <- bugsigdbr::importBugSigDB(cache = FALSE, version="devel") > dat2 <- read.csv("full_dump.csv") > dat2 <- dat2[,1:50] > names(dat2) <- names(dat) > names(dat2) > > dat <- dat2 >

UBNSEMS3S (13:01:07) (in thread): > Sorry forgot the file. Place this in your project folder. - File (CSV): full_dump.csv

UBNSEMS3S (13:01:18) (in thread): > I will note that BugSigDB is in active development still and you should always save a copy of the data that you’re working with offline. The site can and will go offline at times (for maintenance, upgrades, bug fixes, etc.). It is good practice to have your own copy of the data so that you are not reliant on an external website being online/working at the last minute for an academic submission. > > That being said this is a bug and I am working with the developer to get a solution to it.

2024-09-10

Scholastica Urua (01:44:52) (in thread): > Thank you so much!

Svetlana Ugarcina Perovic (03:58:36) (in thread): > Thank you<@UBNSEMS3S>

Scholastica Urua (05:47:19): > Hi everyone! > > Attached is the poster presentation that@Svetlana Ugarcina Perovicand I created for the African Microbiome Day conference. Titled‘********African Microbiome Data in BugSigDB********’,this poster highlights our efforts in curating and analyzing African microbiome studies within BugSigDB. > > I would greatly appreciate feedbacks before uploading the final version. Thank you in advance for your time and insights! > > cc co-authors@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape<@UBNSEMS3S><@U1LCB8WEA> - File (PDF): scholastica_poster.pdf

Chioma Onyido (06:10:00) (in thread): > This looks great! Well done Scholar!:clap:

Scholastica Urua (06:27:36) (in thread): > Thank you@Chioma Onyido:blush:

Esther Afuape (06:28:39) (in thread): > Well done Scholar!:clap::clap:

Victoria (Burah) Poromon (06:45:54) (in thread): > Great work Scholar! Looks amazing:relaxed:

Peace Daniel (06:59:16) (in thread): > Hi@Scholastica UruaThis looks good, font and color. Although I feelit’sa bit cramped up making the information everywhere and not aligned for easy read. You can make this better by making good use of white space, well done:heart_hands:

Svetlana Ugarcina Perovic (09:31:22) (in thread): > I agree with@Peace Daniel

Svetlana Ugarcina Perovic (09:31:48) (in thread): > Better? > cc@Scholastica Urua - File (PDF): scholastica_poster.pdf

Scholastica Urua (09:34:13) (in thread): > Yes@Svetlana Ugarcina Perovic, this is better. Thank you.

Scholastica Urua (09:34:31) (in thread): > Thank you for your feedback@Peace Daniel

Peace Daniel (09:34:41) (in thread): > Yea, this is better@Svetlana Ugarcina Perovicwell done

Svetlana Ugarcina Perovic (09:35:06) (in thread): > glad my version being approved@Peace Daniel@Scholastica Urua

Svetlana Ugarcina Perovic (09:36:01) (in thread): > @Scholastica UruaI added your LinkedIn and X accounts.

2024-09-11

Svetlana Ugarcina Perovic (10:01:08): > Hello everyone! Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT@Scholastica Uruawill do a rehearsal for her MicroTalk athttps://www.microbiome-vif.org/en-US/-/future-events/mvif31-17-1819-september-2024Btw, see you at MVIF next week! The MVIF season 4 starts with some exciting news :shushing_face:**** **** - Attachment (microbiome-vif.org): MVIF.31 | 17 & 18/19 September 2024 > with Keynote talk by Prof. Ameet Pinto

Mildred Anashie (10:04:23) (in thread): > This is great work > > Well done@Scholastica Urua:clap:

2024-09-12

Scholastica Urua (02:51:49) (in thread): > Thank you@Mildred Anashie

2024-09-13

Svetlana Ugarcina Perovic (11:20:03): > Dear team, we have still someoutreachy may24 curation awaiting their reviewhttps://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aopen+is%3Aissue+label%3A%22needs+review%22Please take some for reviewing, when you can. > > Happy Friday and have a nice weekend! > (btw, I was cleaning our GitHub issues, still have to check added studies for the outreachy dec24 round, that’s why they do not have labels yet)

2024-09-16

Svetlana Ugarcina Perovic (04:12:41): > TODAYAfrican Microbiome Day 3.0: Showcasing microbiome research in Africa - Exploring health, ecosystems and innovationsRegister in advance for this meeting:https://uct-za.zoom.us/meeting/register/tJModemhqD4sGtyZb8fJnT2DejiDEkRks0smAfter registering, you will receive a confirmation email containing information about joining the meeting.https://h3africa.org/index.php/african-microbiome-day-30/#agenda - Attachment (h3africa.org): African Microbiome Day 3.0: Showcasing microbiome research in Africa – Exploring Health, Ecosystems and Innovations – H3Africa > Human Heredity & Health in Africa

Chioma Onyido (04:22:59) (in thread): > Thanks for the reminder Svet! > Almost forgot.:sweat_smile:

Scholastica Urua (08:02:36) (in thread): > It has started.

Svetlana Ugarcina Perovic (08:05:34) (in thread): > Posters will be shared during breaks!

Svetlana Ugarcina Perovic (08:06:36) (in thread): > @Scholastica Uruado not hesitate to promote your poster and work in the Meeting chat box.

Scholastica Urua (08:08:42) (in thread): > okay@Svetlana Ugarcina Perovic:blush:

Svetlana Ugarcina Perovic (08:09:27) (in thread): - File (PNG): Screenshot 2024-09-16 at 14.08.45.png

Peace Sandy (08:28:24) (in thread): > What time are you presenting@Scholastica Urua

Svetlana Ugarcina Perovic (08:30:04) (in thread): > “Antibiotics alters the microbiome. how did you deal with that in your study” interesting and important question for the first speaker…

Svetlana Ugarcina Perovic (08:30:22) (in thread): > @Peace SandyPosters will be shared during breaks!

Svetlana Ugarcina Perovic (08:30:33) (in thread): > between sessions

Scholastica Urua (08:30:34) (in thread): > Hi@Peace Sandy, I’ll not be presenting today but the poster will be displayed later

Svetlana Ugarcina Perovic (08:30:59) (in thread): > yes@Scholastica Uruayou are presenting a poster:slightly_smiling_face:

Peace Sandy (08:31:39) (in thread): > Wow…Okay > Rooting for you:rocket:@Scholastica Urua

Peace Sandy (08:32:02) (in thread): > Okay@Svetlana Ugarcina Perovic

Scholastica Urua (08:32:23) (in thread): > Yes@Svetlana Ugarcina Perovic, I’ll be presenting a poster.:blush:

Scholastica Urua (08:32:46) (in thread): > Thank you@Peace Sandy

Scholastica Urua (09:45:15) (in thread): > Presenting the posters now

Chioma Onyido (09:47:31) (in thread): > Is it just me but I can’t hear anything..

Peace Sandy (09:48:23) (in thread): > Same

Peace Sandy (09:48:48) (in thread): > The poster is up, but no sound@Scholastica Urua

Svetlana Ugarcina Perovic (09:48:55) (in thread): > there is no sound

Svetlana Ugarcina Perovic (09:49:05) (in thread): > they are just showing them

Scholastica Urua (09:49:05) (in thread): > It’s not just you. This particular session has no sound

Chioma Onyido (09:49:08) (in thread): > Ohh okay.

Svetlana Ugarcina Perovic (09:49:18) (in thread): > and you can contact the author in the chat

Peace Sandy (09:49:23) (in thread): > Oh, Okay

Esther Afuape (10:18:39) (in thread): > Well done:raised_hands:@Scholastica Urua

Svetlana Ugarcina Perovic (11:00:26) (in thread): > https://docs.google.com/forms/d/e/1FAIpQLSfxylD9TpW02ObX16IMl7uNODeBhWGv6QjVhsizAWHFvQFDpg/viewform?pli=1 - File (PNG): Screenshot 2024-09-16 at 17.00.04.png

2024-09-17

Svetlana Ugarcina Perovic (04:29:33): > Kind reminder for today’s Atlantic event with Keynote talk by Prof. Ameet Pinto and an amazing lineup!Local times, abstracts, and registration herehttps://cassyni.com/s/mvif-31Time and dates for the Pacific event can be found at the same link! > > Hope to see you today to start the new season!:slightly_smiling_face::tada: - File (PNG): program_sept24.png

Svetlana Ugarcina Perovic (08:47:17): > @Scholastica Urua:clap: - File (PNG): Screenshot 2024-09-17 at 14.38.45.png

Svetlana Ugarcina Perovic (08:49:14): > Q&A - File (PNG): Screenshot 2024-09-17 at 14.48.24.png

Chioma Onyido (08:58:17): > @Scholastica Urua:clap: - File (PNG): IMG_6277

Svetlana Ugarcina Perovic (08:59:42): > @Scholastica Uruacongrats for an excellent Q&A!!!!

Mildred Anashie (09:01:27) (in thread): > Well done@Scholastica Urua:clap:

Scholastica Urua (09:01:55) (in thread): > Thank you@Svetlana Ugarcina Perovic:hugging_face:some of the questions caught me off-guard:sweat_smile:

Svetlana Ugarcina Perovic (09:04:09) (in thread): > You did great and you got a lot of questions and attention. Great job!

Aleru Divine (09:06:36) (in thread): > Congratulations on your presentation@Scholastica Urua

Scholastica Urua (09:33:31) (in thread): > Thank you@Chioma Onyido:hugging_face:

Peace Sandy (09:41:13) (in thread): > Awesome presentation@Scholastica Urua

2024-09-18

Svetlana Ugarcina Perovic (06:37:34) (in thread): > Recordings available:https://www.youtube.com/watch?v=PEOi8_mO0vA&t=10507s - Attachment (YouTube): H3Africa: African Microbiome Day 3.0: Showcasing microbiome research in Africa - Full Worskhop

Svetlana Ugarcina Perovic (09:29:33): > Reminder: Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDTI can’t make it. Enjoy discussions with<@UBNSEMS3S>! - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-09-23

Svetlana Ugarcina Perovic (06:51:03): > Webinar: October 17Microbiome Data WebinarFree registrationhere!HAPPY MONDAY

Scholastica Urua (12:13:32) (in thread): > Happy Monday@Svetlana Ugarcina Perovic:sunflower:

Aleru Divine (12:37:56): > @Svetlana Ugarcina PerovicPlease I’d like to delete experiments 4 - 9 with their signatures in this study.https://bugsigdb.org/Study_1008My apologies for the mistake:pray: - Attachment (BugSigDB): External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells - BugSigDB > Gut microbiota are involved in many physiological functions such as metabolism, brain development, and neurodegenerative diseases.Many microbes in the digestive tract do not maintain a constant level of their relative abundance but show daily oscillations under normal conditions.

Levi Waldron (16:34:37): > Welcome@My Nguyen- My first contributed tobugsigdb.orga high school senior in 2020, and now has some time and wants to contribute again as a Junior in the Faculty of Arts and Sciences at Harvard studying molecular and cellular biology. Welcome back, My!

Scholastica Urua (21:40:01) (in thread): > Welcome@My Nguyen

2024-09-24

Chioma Onyido (03:31:06) (in thread): > Welcome back@My Nguyen! Cheers to more bugsigdb-ing!:tada:

Aleru Divine (04:06:22) (in thread): > Hi@My Nguyenwelcome!:clinking_glasses::sparkles:

Svetlana Ugarcina Perovic (05:01:45) (in thread): > Deleted.

Svetlana Ugarcina Perovic (05:02:52) (in thread): > Welcome back to the team@My Nguyen

Svetlana Ugarcina Perovic (05:27:18): > Hello, team! > > We have some curations from the previous Outreachy round awaiting review:https://github.com/waldronlab/BugSigDBcuration/issues?page=1&q=is%3Aopen+is%3Aissue+label%3A%22needs+review%22Please take a look and feel free to review some once you have time, thanks!

Peace Daniel (06:12:21): > Hi everyone@Svetlana Ugarcina Perovicdo we record viruses as part of the taxons?

Svetlana Ugarcina Perovic (06:14:42) (in thread): > no

Peace Daniel (06:15:17) (in thread): > Okay, thank you

Svetlana Ugarcina Perovic (06:17:46) (in thread): > We primarily record bacterial signatures and sometimes fungi.

Peace Daniel (06:22:14) (in thread): > Yes@Svetlana Ugarcina PerovicI needed to confirm I was doing the right thing. Thank you:purple_heart:

Aleru Divine (06:51:46) (in thread): > Thank you so much:pleading_face:

Mildred Anashie (06:53:41) (in thread): > Welcome@My Nguyen:tada:

Svetlana Ugarcina Perovic (09:29:20) (in thread): > As an example please see@Victoria (Burah) Poromon’s excellent reviewhttps://github.com/waldronlab/BugSigDBcuration/issues/431 - Attachment: #431 The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults > The gut microbiome, mild cognitive impairment, and probiotics: A randomized clinical trial in middle-aged and older adults – Aljumaah MR, Bhatia U, Roach J, Gunstad J, Azcarate Peril MA – Journal Clinical nutrition
> https://www.clinicalnutritionjournal.com/article/S0261-5614(22)00344-2/abstract

2024-09-25

Peace Daniel (07:01:08): > Hi again:wave:I’ve just completed this curation and I’d like any reviews, specifics on conditions and sample sizes (esp for experiments 24, 25)Study hereThank you and happy BugSigdb-ing! - Attachment (BugSigDB): Signatures within the esophageal microbiome are associated with host genetics, age, and disease - BugSigDB > BACKGROUND: The esophageal microbiome has been proposed to be involved in a range of diseases including the esophageal adenocarcinoma cascade; however, little is currently known about its function and relationship to the host.

Peace Daniel (07:02:18) (in thread): > Also, I was wondering if I should record these taxas Bacillales noname and Clostridiales Family XIII incertae sedis noname

Mildred Anashie (07:02:44) (in thread): > Well done on your curation@Peace Daniel:clap:I’lltake a look as soon as possible

Peace Daniel (07:03:11) (in thread): > Ahh thank you!@Mildred Anashie

Mildred Anashie (07:05:42) (in thread): > I think you should take a look at this thread if it helps concerning the taxas@Peace Danielhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710411707183289?thread_ts=1710405054.603599&channel=C04RATV9VCY&message_ts=1710411707.183289 - Attachment: Attachment > @Barakat Akinsiku note the spelling, Bacteroidales noname, not Bacteriodales noname. This seems equivalent to unclassified Bacteroidales (taxid 185291, no rank). @Mildred Anashie, Bacteria is not incorrect, but it provides less information about the lineage than unclassified Bacteroidales does, which at least tells us the order_._

Peace Daniel (07:08:16) (in thread): > Alright, thank you Anashie

UBNSEMS3S (22:41:59): > Hello everyone! Tomorrow (Thursday) is our weekly team meeting at 9 AM EDT.https://us02web.zoom.us/j/2737200499.Please signup to present here: https://bugsigdb.org/PresentationSignup#Thursday_10_AM_EDT - Attachment (BugSigDB): PresentationSignup > Use this page to sign-up for Microbiome Curation meeting presentations. Add your name, topic, and PMID (if applicable) to the table. For more detailed sign-up instructions…

2024-09-26

Peace Sandy (04:55:04) (in thread): > Welcome@My Nguyen

Svetlana Ugarcina Perovic (08:05:37): > New study reported: “Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity.” > > When in doubt, do a Wilcoxon test.https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03390-9 - Attachment (BioMed Central): A realistic benchmark for differential abundance testing and confounder adjustment in human microbiome studies - Genome Biology > Background In microbiome disease association studies, it is a fundamental task to test which microbes differ in their abundance between groups. Yet, consensus on suitable or optimal statistical methods for differential abundance testing is lacking, and it remains unexplored how these cope with confounding. Previous differential abundance benchmarks relying on simulated datasets did not quantitatively evaluate the similarity to real data, which undermines their recommendations. Results Our simulation framework implants calibrated signals into real taxonomic profiles, including signals mimicking confounders. Using several whole meta-genome and 16S rRNA gene amplicon datasets, we validate that our simulated data resembles real data from disease association studies much more than in previous benchmarks. With extensively parametrized simulations, we benchmark the performance of nineteen differential abundance methods and further evaluate the best ones on confounded simulations. Only classic statistical methods (linear models, the Wilcoxon test, t-test), limma, and fastANCOM properly control false discoveries at relatively high sensitivity. When additionally considering confounders, these issues are exacerbated, but we find that adjusted differential abundance testing can effectively mitigate them. In a large cardiometabolic disease dataset, we showcase that failure to account for covariates such as medication causes spurious association in real-world applications. Conclusions Tight error control is critical for microbiome association studies. The unsatisfactory performance of many differential abundance methods and the persistent danger of unchecked confounding suggest these contribute to a lack of reproducibility among such studies. We have open-sourced our simulation and benchmarking software to foster a much-needed consolidation of statistical methodology for microbiome research.

2024-09-27

Svetlana Ugarcina Perovic (06:09:47): > NEXT WEEK microbiome eventFree registration for online event. > Visithttp://vmrc4africa.orgto register. - File (JPEG): vmrc.jpeg

Aleru Divine (09:02:19): > Good day everyone, Happy Friday:smiley:Please I have a concern regarding the study I am currently reviewing. In some experiments, the host species involved were both seabirds, specifically Cory’s shearwaters (C. borealis) and northern fulmars (F. glacialis). However, BugSigDB allows for the curation of only one host species at a time. > > In this case, how should I proceed? > > Also, they are referred to as “Procellariiformes” collectively. > > Thank you so much!@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Scholastica Urua

Svetlana Ugarcina Perovic (09:58:42) (in thread): > And they reported for both seabird species bacterial signatures to curate?

Svetlana Ugarcina Perovic (09:59:19) (in thread): > Please share link to the study. Thanks.

Aleru Divine (09:59:28) (in thread): > Yes they did.

Aleru Divine (10:00:29) (in thread): > Link to study:https://bugsigdb.org/Study_1017Paper:https://www.nature.com/articles/s41559-023-02013-z#MOESM3Figure 2 shows the signatures. - Attachment (BugSigDB): Current levels of microplastic pollution impact wild seabird gut microbiomes - BugSigDB > Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways.A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored. - Attachment (Nature): Current levels of microplastic pollution impact wild seabird gut microbiomes > Nature Ecology & Evolution - Consuming microplastics is known to harm marine wildlife in several ways, but effects on the microbiome are understudied. Here the authors demonstrate that two…

UBNSEMS3S (10:06:23) (in thread): > I was going to add it but it looks like Svetlana beat me to the punch - File (PNG): image.png

UBNSEMS3S (10:06:58) (in thread): > The list is not in alphabetical order. I’m going to see if we can order this appropriately (maybe with humans, mice, and rats still at the top though just for convenience).

Svetlana Ugarcina Perovic (10:08:08) (in thread): > The host species are added when adding “paper to curate” in the GitHub issue@C. Mirzayi (please do not tag this account)

Svetlana Ugarcina Perovic (10:08:21) (in thread): > so both species are there

UBNSEMS3S (10:08:49) (in thread): > Ah gotcha

Svetlana Ugarcina Perovic (10:08:49) (in thread): > species from different genera - File (PNG): Screenshot 2024-09-27 at 16.06.39.png - File (PNG): Screenshot 2024-09-27 at 16.06.56.png

Svetlana Ugarcina Perovic (10:10:02) (in thread): > @C. Mirzayi (please do not tag this account)the issue is how to record two Host species?

UBNSEMS3S (10:10:16) (in thread): > They combined them in a single experiment?

Aleru Divine (10:10:25) (in thread): > Yes they did.

UBNSEMS3S (10:10:26) (in thread): > Jeeze that’s a tough one.

Aleru Divine (10:10:56) (in thread): > Buttheydo come from the same family:grimacing:

UBNSEMS3S (10:11:02) (in thread): > I think fundamentally the system does not allow for that. I would make a note in the experimental groups and also a note in the discussion for that study.

UBNSEMS3S (10:12:10) (in thread): > <@U1LCB8WEA>Interesting study where they combined two different host species (two types of seabirds) in a single experiment. Any thoughts on how to curate it when BugSigDB only allows a single host species?

Aleru Divine (10:14:00) (in thread): > Can I curate one of the host species and leave a note? Or curate none of the host species?

Svetlana Ugarcina Perovic (10:17:29) (in thread): > @C. Mirzayi (please do not tag this account)Or we can create a double host species C. borealis and F. glacialis?

Svetlana Ugarcina Perovic (10:19:27) (in thread): > OR “seabirds”

2024-09-28

U02CNMR4YEA (14:26:32): > Hi All! Is anyone else having difficulties with BugSigDB being super slow today? Also, I have curated the article 38111925. I entered 3 experiments but only 2 seem to be showing and I entered signatures but don’t see any. Any assistance would be greatly appreciated:grinning:. Thank you!

Peace Daniel (14:29:17) (in thread): > Hi Mary, you can try thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1723553950301449?thread_ts=1723544502.855119&channel=C04RATV9VCY&message_ts=1723553950.301449 - Attachment: Attachment > So I don’t know if this is a temporal fix or if it will work for other studies with same issues, but I noticed when I edited an experiment with invisible signatures and saved the page the signatures appeared. > > Currently all the signatures are visible

Peace Daniel (14:30:41) (in thread): > You can try saving the experiment as incomplete and then save again as complete > This works for me

U02CNMR4YEA (14:45:22) (in thread): > Thank you! I will give that a try!

U02CNMR4YEA (14:45:36) (in thread): > Have you reported the issue yet?

Peace Daniel (14:50:16) (in thread): > Yes, you can follow up herehttps://github.com/waldronlab/BugSigDB/issues/221 - Attachment: #221 Study 784 Experiments not showing but exist > https://bugsigdb.org/Study_784 shows no experiments on the page but they do exist: https://bugsigdb.org/Study_784/Experiment_1 > > I tried refreshing the page under … > Refresh but that did not resolve the issue.

U02CNMR4YEA (15:08:29) (in thread): > Thank you!! I also just reported the issue with mine.

Peace Daniel (15:10:35) (in thread): > Great, happy to help!

U02CNMR4YEA (15:11:43): > Hi Everyone! If any of you has a minute to look at the study I’ve attached, I think the only curatable piece is Figure 4b but was hoping for confirmation that even that data should be curated? TIA - File (PDF): iovs-62-12-13.pdf

Peace Daniel (15:17:23) (in thread): > I agree with you, I don’t think there’s any curatable data for differential abundance in this pdf. Could there be any supplemental data attached in the link to this study?

U02CNMR4YEA (16:45:58) (in thread): > Unfortunately not. Thank you for checking. I really appreciate it!

2024-09-29

Mildred Anashie (04:03:00) (in thread): > I am also in agreement > > Althoughthere’sa mention of supplementary information butI’min doubt it has anything to do with differential abundance

U02CNMR4YEA (17:30:14): > Happy Sunday Everyone! I wanted to let you know that I found an (embarrassing) error I made when curating 2 papers (PMIDs 37586456 and 34900990) that I just caught in looking at my capstone data. I had the conditions as “microbiome”:joy:and “biological sex”, respectively for all experiments. I’ve changed all to Dry eye syndrome which is more representative of the data. That being said, the entries had already been reviewed and are still marked as “reviewed” now that I’ve made the changes.@Svetlana Ugarcina Perovic<@UBNSEMS3S>and<@U1LCB8WEA>I’m not sure if there’s been any thought given to a re-review of any data that has been changed? In any event, I wanted to be completely transparent and invite any/all to double check my edits as I am using this data for capstone so didn’t want it to appear I am doing anything nefarious with it:blush:.

2024-09-30

Svetlana Ugarcina Perovic (04:33:34) (in thread): > https://bugsigdb.org/Study_757https://bugsigdb.org/Study_830reviewed. > > Thanks for letting us know! All good now. - Attachment (BugSigDB): Ocular microbiome changes in dry eye disease and meibomian gland dysfunction - BugSigDB > The most common and chronic ocular problem of aging is dry eye disease (DED) and the associated condition of meibomian gland dysfunction (MGD).The resident ocular surface bacteria may have a role in maintaining homeostasis and perturbation may contribute to disease development. - Attachment (BugSigDB): Metagenomic Analysis Reveals the Heterogeneity of Conjunctival Microbiota Dysbiosis in Dry Eye Disease - BugSigDB > Background: Dry eye disease (DED) is a multifactorial inflammatory disease of the ocular surface.It is hypothesized that dysbiosis of the conjunctival microbiota contributes to the development of DED.

U02CNMR4YEA (07:45:56) (in thread): > Thank you!:blush:

2024-10-01

Svetlana Ugarcina Perovic (03:34:09) (in thread): > Just started, see you there!African Microbiomes in Health and Disease Symposium Agenda Day 1: 1st October 2024Full agenda:https://vmrc4africa.org/wp-content/uploads/2024/09/AGENDA-ONLINE.pdf

Svetlana Ugarcina Perovic (04:03:40) (in thread): > Just learned about “TheLive Biotherapeutic Randomised Trial(VIBRANT) aims to find out whetherL. crispatusis better at colonising the vagina when combined with other kinds ofLactobacillius species. Across two study sites, the VIBRANT team is assessing the safety and efficacy of a vaginally inserted tablet containing multiple liveL. crispatusstrains donated by women with stable optimal vaginal microbiomes.”https://gift-africa.org.za/2024/05/09/the-gift-webinar-women-up-to-know-good-episode-3/

Svetlana Ugarcina Perovic (11:42:13): > Welcome to the Outreachy contribution period! We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions:https://github.com/waldronlab/BugSigDBcuration/issues/94If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion.We’re looking forward to working with you!<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Scholastica UruaTip: New to contributing? Watch this helpful video on getting started with open source contributions:https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Scholastica Urua (11:46:37) (in thread): > Welcome to all the Outreachy applicants:sparkles:

Esther Afuape (11:55:02) (in thread): > Welcome to BugSigDB!:sparkles:We’reglad to have you here:hugging_face:

Peace Sandy (11:58:17) (in thread): > Welcome all Outreachy Applicant

Adeshile Oluwatosin (12:15:08) (in thread): > Thank you everyone

Mildred Anashie (12:23:44) (in thread): > Thank you:blush:

Aleru Divine (12:52:59) (in thread): > Thank you:relieved::sparkles:

Svetlana Ugarcina Perovic (12:55:24): > Feel free to introduce yourselves whenever you’re ready.

Svetlana Ugarcina Perovic (12:59:42): > My name is Svetlana. I’m a microbiome scientist who enjoys computing microbiome data and preparing food. I have been working with Chloe and Levi on the BugSigDB project and am happy to support you in accomplishing BugSigDB contribution tasks. More about me:https://www.linkedin.com/in/svetlana-ugarcina-perovic/ - Attachment (it.linkedin.com): Svetlana Ugarcina Perovic - UniTrento CIBIO | LinkedIn > A microbiologist who computes the data. Interested in microbiome science and tools. Loves cooking.

**** Feel free to reach me on X (@svetlana_up) or Bluesky (@svetlanaup) or send an email to mailto:svetlana@microbiome-vif.org|svetlana@microbiome-vif.org **** · Esperienza: UniTrento CIBIO · Località: Italia · 258 collegamenti su LinkedIn. Vedi il profilo di Svetlana Ugarcina Perovic su LinkedIn, una community professionale di 1 miliardo di utenti.

Chioma Onyido (13:00:19) (in thread): > Welcome all Outreachy applicants!:tada:And to our previous contributors…I see you!:eyes:You’rewelcome!

Aleru Divine (13:01:27): > Hi everyone!:wave:My name is Divine Aleru, and I’m from Nigeria. I’m a biochemist with a strong interest in molecular toxicology, and I’m thrilled to be part of this community. > > This is my third time applying for the Outreachy internship (third time’s the charm, right?), and I’ve previously contributed to BugSigDB. I absolutely love contributing to BugSigDB and can’t wait to connect with fellow applicants. I’m super excited to work together and look forward to making meaningful contributions! > > Cheers and good luck to everyone!:sparkles::clinking_glasses:

Cate Ouma (13:04:23) (in thread): > Hi guys. My name is Cateline Ouma. I am a recent Biotechnology graduate from Nairobi, Kenya, and I’m so happy to be joining the BugSigDB project’s contribution phase as an Outreachy Intern. I am completely new to this, but I’m so excited I can’t wait to see what this wonderful project has in store for us:blob_cheer:

Eseoghene Orhorho (13:19:33): > Hello everyone! > My name is Eseoghene Orhorho. I’m excited to join the Bioconductor community as part of the Outreachy program. I have a background in Research with Computer Science and self-taught data science experience. I’m looking forward to contributing to open-source projects, learning from all of you, and collaborating to make a meaningful impact. I look forward to connecting and growing with this amazing community!

Chioma Peters (13:20:01): > Hello everyone, good evening. My name is Chioma Joy Peters. I’m thrilled to join this community as part of the outreachy program. I got certified as a product manager this year, and I’m a journalist (mass communication) by Education. This is my first time applying to the outreachy program. I don’t know what to expect or how this will go, but I’m open to learning and doing what it takes to enjoy this process, grow, and learn from all the seasoned professionals on this project and hopefully get an internship.

Aleru Divine (13:20:45) (in thread): > Hi@Eseoghene Orhorho, welcome

Eseoghene Orhorho (13:22:04) (in thread): > Thank you@Aleru Divine

Aleru Divine (13:24:15) (in thread): > Good evening@Chioma Petershow are you?

Adeshile Oluwatosin (13:26:33): > Hello everyone,My name is Adeshile Oluwatosin, and I’m from Nigeria. I’m thrilled to have been accepted into the contribution phase of Outreachy. With a background in biochemistry, I am eager to apply my skills, learn from this community, and make meaningful contributions. I look forward to collaborating and connecting with all of you!

Adeshile Oluwatosin (13:27:12) (in thread): > Hello:wave:

Adeshile Oluwatosin (13:27:19) (in thread): > Welcome:hugging_face:

Chioma Peters (13:32:08) (in thread): > i’m fine, thank you. Hi Aleru and hello Adeshile

George Opondi (13:52:34): > Hello everyone, my name is George Opondi from Kenya and I am eager to collaborate with you all on this project and hopefully learn a thing or two about Microbiome study curation

Aleru Divine (14:20:35) (in thread): > Welcome:blush:

Aleru Divine (14:21:11) (in thread): > Welcome:blush:@George Opondi

Adeshile Oluwatosin (14:30:37) (in thread): > :wave:

Eseoghene Orhorho (14:35:22) (in thread): > Thank you

Ibizugbe Merit (14:45:29): > Hello everyone, my name isIbizugbeMerit and I’m happy and eager to collaborate and contribute on this project

Jatinder Mahajan (14:52:23): > hi

Precious Orakwe (14:53:51): > Hello, fam. > Good day our mentors@Svetlana Ugarcina Perovic@Chloe Mirzayi@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace SandyMy name is Precious from Nigeria, I am an industrial chemist, and I am so glad to be accepted for the contribution phase again, this is my 4th time applying to Outreachy.:smiley:I am so happy to be in this community. I look forward to contributing, collaborating, and learning from this community

Scholastica Urua (14:55:57) (in thread): > Welcome to the community@Eseoghene Orhorho

Eseoghene Orhorho (14:56:36) (in thread): > Thank you@Scholastica Urua

Scholastica Urua (14:57:29) (in thread): > Welcome to BugSigDB@Chioma Peters:tulip:

Scholastica Urua (14:58:44) (in thread): > Welcome to BugSigDB@Adeshile Oluwatosin:tulip:

Scholastica Urua (15:00:10) (in thread): > Welcome@Precious Orakwe:tulip:

Scholastica Urua (15:01:30) (in thread): > Welcome to BugSigDB@Ibizugbe Merit:tulip:

Scholastica Urua (15:02:12) (in thread): > Welcome to BugSigDB@George Opondi:tulip:

Precious Orakwe (15:13:03) (in thread): > Thank you

Precious Orakwe (15:13:49) (in thread): > That you@Scholastica Urua

Kate Rasheed (15:21:32): > Hello everyone, I’m Kate. It’s so great to be here. Looking forward to working with you all.

Druscilla Nakanwagi (15:24:52): > Hello everyone, my name is Druscilla from Uganda and I am happy to be a part of this project

Chiamaka Johnfred (15:30:56): > Hello everyone, My name is Chiamaka from Lagos, Nigeria. I’m excited to join the Bioconductor community as part of the Outreachy program. I’m a new grad of Kinesiology and Sports science and a project manager. I am excitedly looking forward to contributing to the open-source projects, learning from the great minds here, and collaborating to make a meaningful impact. Looking forward to connecting and growing with this amazing community, thank you!

Martha Kisakye (15:39:07): > Hello everyone my name is Martha Kisakye . And am excited to be part of thr Bioconductor community . I hope to learn more from everyone and also apply my skills. Thank you and looking forward to work with you all

Paavni Goyal (15:42:23): > Hello everyone, good evening. > > I hope you’re all doing great! My name is Pavani Goyal, and I’m joining from India. I’m really excited to collaborate with all of you and contribute to the project. I’m passionate about contributing to open source and am here to improve my skills while learning new ones. I look forward to gaining knowledge from this community and working alongside you all.

Mary Agekameh (15:48:59): > Hello everyone, good evening. > > I hope you’re all doing great? > I’m happy to join this community as part of the Outreachy Program. > > My name is Mary Agekameh from Nigeria. I’m a programs associate. This is my first time applying for the program so I don’t know how it will go but I’m opened to collaborating, learning and growing. Thank you

Mildred Anashie (15:53:37) (in thread): > Hi@Eseoghene OrhorhoWelcome:hugging_face:

Mildred Anashie (15:54:21) (in thread): > Welcome@Chioma Peters:blush:

Mildred Anashie (15:54:50) (in thread): > Hello@Adeshile OluwatosinWelcome:hugging_face:

Mildred Anashie (15:55:11) (in thread): > Welcome@George Opondi:blush:

Mildred Anashie (15:55:38) (in thread): > Hi@Ibizugbe MeritWelcome

Mildred Anashie (15:56:07) (in thread): > Hi@Precious OrakweWelcome:hugging_face:

Aleru Divine (15:56:37) (in thread): > Looking forward to collaborating with you@Ibizugbe Merit

Mildred Anashie (15:56:44) (in thread): > Hi@Kate RasheedWelcome:hugging_face:

Mildred Anashie (15:57:03) (in thread): > Welcome:hugging_face:@Druscilla Nakanwagi

Aleru Divine (15:57:10) (in thread): > My third@Precious Orakwe:sparkles:Welcome again

Mildred Anashie (15:57:27) (in thread): > Hello@Chiamaka JohnfredWelcome:hugging_face:

Mildred Anashie (15:58:23) (in thread): > Welcome@Martha Kisakye:hugging_face:

Mildred Anashie (15:59:00) (in thread): > Welcome@Paavni GoyalLooking forward to collaborating with you as well:hugging_face:

Aleru Divine (15:59:28) (in thread): > First time coming across the term kinesiology (I had to look it up):face_with_hand_over_mouth:thanks@Chiamaka JohnfredLooking forward to collaborating with you too

Aleru Divine (15:59:57) (in thread): > Welcome@Martha Kisakye

Mildred Anashie (16:01:04) (in thread): > Same here@Aleru DivineHad to look it up:laughing:

Aleru Divine (16:02:09) (in thread): > Hi@Paavni Goyal, welcome! looking forward to working with you too.

Aleru Divine (16:04:01) (in thread): > Hi@Mary Agekamehwelcome!It’sgoing to be an amazing journey trust me.:hugging_face:Looking forward to collaborating with you too

Mildred Anashie (16:06:00): > Hello Everyone:wave:My name is Anashie, Mildred Andokie an outreachy applicant, and I’m from Nigeria. > > > I’m a Microbiologist with interest in Public health and I’m excited to be here again:hugging_face:I look forward to contributing to the Bioconductor community and connecting/collaborating with everyone:clinking_glasses:

Aleru Divine (16:07:36) (in thread): > Super excited to have you here again@Mildred Anashie:hugging_face:Looking forward to collaborating with you again:sparkles:

Mildred Anashie (16:09:01) (in thread): > Welcome@Mary Agekameh:tada:Open to collaborating as well:hugging_face:

Mildred Anashie (16:09:21) (in thread): > Thank you@Aleru Divine:blush:

Ibizugbe Merit (16:11:24) (in thread): > You’re welcome@Mary Agekameh:hugging_face:Open to collaborating andwe’llsure learn together > > Just go through the pinned message from@Svetlana Ugarcina Perovicto get started

PATIENCE ONAH (16:11:48): > Hello everyone, my name is Patience Onah. I’m exited to be here again. I look forward to learning and contributing to the Bioconductor projets.

Ibizugbe Merit (16:13:15) (in thread): > You’rewelcome:hugging_face:

Mildred Anashie (16:14:02) (in thread): > Hi@PATIENCE ONAHLooking forward to learning along side you as well:blush:

Mary Agekameh (16:14:32) (in thread): > Thank you!@Aleru Divine

Mary Agekameh (16:15:04) (in thread): > Thank you so much!@Ibizugbe Merit

Mary Agekameh (16:15:22) (in thread): > Thank you Mildred!

Aleru Divine (16:21:40) (in thread): > Hi@PATIENCE ONAH, welcome:blush:

Ibizugbe Merit (16:23:59) (in thread): > Thank you so much everyone

UBNSEMS3S (16:26:37): > Welcome all. My name is Chloe and I’ve been working on the BugSigDB project since 2018. I’m an epidemiologist by training. I’m here to provide support as an Outreachy mentor and I will be running the office hours on Thursday mornings (at 9 AM EDT). You can read more about me and my work here:https://cunyisph.org/team/chloe-mirzayi/

Chinwendu Joy Enyidiegwu (16:27:49): > Hello Everyone, > My name is Chinwendu Joy, an Outreachy applicant and I’m happy to join the Bioconductor Community. > and I’m eager to learn from all of you and contribute to this project. thank you

Liliana Garmendia (16:30:53): > Hello everyone, > I’m Liliana from Chile.I’m biochemist transitioning into tech. > This is my second time applying to Outreachy program and I’m looking forward to learning and contributing to Bioconductor community:slightly_smiling_face:

Adeshile Oluwatosin (16:41:38) (in thread): > Hello<@UBNSEMS3S>:wave:

Adeshile Oluwatosin (16:42:08) (in thread): > Hello@Chinwendu Joy Enyidiegwu:hugging_face:

Mildred Anashie (16:54:29) (in thread): > Hello<@UBNSEMS3S>And thank you:blush:

Mildred Anashie (16:55:13) (in thread): > Hello@Chinwendu Joy EnyidiegwuWelcome:hugging_face:

Mildred Anashie (16:55:52) (in thread): > Hello@Liliana GarmendiaWelcome, looking forward to contributing alongside you > You can go through this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Adeshile Oluwatosin (16:56:13) (in thread): > Welcome@Ibizugbe Merit

Adeshile Oluwatosin (16:56:39) (in thread): > Welcome:hugging_face:@Mildred Anashie

Mildred Anashie (16:57:42) (in thread): > Thank you@Adeshile Oluwatosin:blush:

adekemi balogun (16:59:54): > Hello everyone,

Ibizugbe Merit (17:00:10) (in thread): > Hi

adekemi balogun (17:02:43): > My name is Balogun Adekemi, an outreachy applicant. I’m excited to be part of this community and also make positive contributions, I’m looking forward to working with everyone as a team.

Eseoghene Orhorho (17:04:30) (in thread): > Welcome@adekemi balogun. I look forward to collaborating with you too.

Ibizugbe Merit (17:04:58) (in thread): > You’rewelcome@adekemi balogunI’mjust as excited as you, and I also look forward to working with you on this team:hugging_face:Go through the pinned message from@Svetlana Ugarcina Perovicto get started:ok_hand:

Eseoghene Orhorho (17:05:21) (in thread): > Welcome@Liliana Garmendia, Nice connecting with you.

Eseoghene Orhorho (17:06:45) (in thread): > Hii,@Paavni Goyal. I look forward to working with you.

Mildred Anashie (17:11:09) (in thread): > This should helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539Welcome:hugging_face:@adekemi balogun - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

adekemi balogun (17:12:46) (in thread): > Thank you

Blessdamy (17:40:35): > Hello everyone, and special greeting to all mentors,@Svetlana Ugarcina Perovic, @Chloe Mirzayi,@Peace Sandy,@Chioma Onyido,@Esther Afuape,@Scholastica Urua, > > My name is Blessing Ejogbamu, and I am glad to join the Bioconductor community to contribute to the “Microbiome Study Curation” project. I studied Plant Biology and Biotechnology with a major in Biotechnology, which fueled my passion for literature reviews, biological research, and curation. > > I’m particularly excited about how microbiome studies can inform health and environmental research, and I’m eager to contribute to the curation of these valuable datasets. I would love guidance on how I can begin contributing in a meaningful way. > > Looking forward to learning from this amazing community and making impactful contributions. > I’m excited to start this journey with everyone.

Blessdamy (17:43:04) (in thread): > Hi mentor Svetlana, it’s nice to meet you!

Blessdamy (17:45:16) (in thread): > Hi mentor Chloe, it’s nice to meet you!

Blessdamy (17:45:22) (in thread): > Noted!

Ibizugbe Merit (17:46:41) (in thread): > You’rewelcome:hugging_face:

Precious Orakwe (17:47:26) (in thread): > You are welcome@Blessdamy

Blessdamy (17:47:36) (in thread): > Thank you, Svetlana, will do well to go through the documentation.

Mildred Anashie (17:50:10) (in thread): > Hi@BlessdamyYou are welcome:hugging_face:Go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539to get started also looking forward to collaborating and learning - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Precious Orakwe (17:50:31) (in thread): > Thank you<@UBNSEMS3S>looking forward to learning under your mentorship

Precious Orakwe (17:52:07) (in thread): > Thank you, > It’s well

Chris Awoke (18:07:03): > Hello, friends! I’m Chris Awoke from Nigeria, and I’m thrilled to selected into the Outreachy contribution phase. I’m really excited to work on this project and collaborate with all of you. > > With my background in biological sciences and a strong foundation in data science, I’m eager to bring my skills to the Bioconductor project and contribute meaningfully. I’m also looking forward to learning from each of you and supporting my fellow participants along the way. > > A heartfelt thank you to our amazing mentors:@Svetlana Ugarcina Perovic, @Chloe Mirzayi,@Esther Afuape,@Scholastica Urua,@Chioma Onyido, and@Peace Sandy. I truly appreciate your guidance!

Mildred Anashie (18:07:51) (in thread): > Hello@Chris AwokeWelcome:hugging_face:

Aleru Divine (18:10:02) (in thread): > Thank you@C. Mirzayi (please do not tag this account):blush:

Aleru Divine (18:10:27) (in thread): > Hi@Chinwendu Joy Enyidiegwu, welcome

Aleru Divine (18:11:29) (in thread): > Another biochemist.:hugging_face::sparkles:Hi@Liliana Garmendia, welcome

Aleru Divine (18:11:48) (in thread): > Hi@adekemi balogun, welcome!

Aleru Divine (18:12:44) (in thread): > Hi@Blessdamy, welcome!

Aleru Divine (18:13:11) (in thread): > Hi again@Chris Awoke:sweat_smile:

Adeshile Oluwatosin (18:30:20) (in thread): > Hi@Chris Awoke:hugging_face::eyes:

Adeshile Oluwatosin (18:31:13) (in thread): > Welcome@Liliana Garmendiafellow biochemist:blush:

Adeshile Oluwatosin (18:31:30) (in thread): > Welcome@adekemi balogun

Adeshile Oluwatosin (18:32:39) (in thread): > Welcome@Martha Kisakye

Adeshile Oluwatosin (18:32:55) (in thread): > Welcome@Druscilla Nakanwagi:blush:

Adeshile Oluwatosin (18:33:46) (in thread): > Hello mentor@Svetlana Ugarcina Perovic:hugging_face:

Adeshile Oluwatosin (18:34:37) (in thread): > Welcome@Kate Rasheed

Adeshile Oluwatosin (18:35:10) (in thread): > Welcome@Paavni Goyal:hugging_face:

Adeshile Oluwatosin (18:35:45) (in thread): > Hi@Chiamaka Johnfrednice to meet you:hugging_face:

Adeshile Oluwatosin (18:36:11) (in thread): > Hello@Precious Orakwe:hugging_face:

Adeshile Oluwatosin (18:36:52) (in thread): > Welcome@Blessdamy

Adeshile Oluwatosin (18:38:49) (in thread): > Thank you everyone:hugging_face:

Amrita Das (18:47:26): > Hey everyone!:wave:I’m Amrita, from India. I am 23 years old, just finished my bachelor’s degree in electrical engineering. I am super excited about the Microbiome project! I’ve done some ML research before and love working on leveraging technology for healthcare applications. > > This would be my first time contributing to open source, but I’m a quick learner and really excited to learn more about a very intriguing field. I think it’d be such a cool experience! > > I’ve been reading through the messages here and on other channels - and would love to know where I could start helping out?:blush:Looking forward to working with you all!

Adeshile Oluwatosin (18:52:23) (in thread): > Welcome:hugging_face:@Amrita Das

Adeshile Oluwatosin (18:52:59) (in thread): > Look through this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Adeshile Oluwatosin (19:03:10) (in thread): > Hello@adekemi balogun:hugging_face:

Mildred Anashie (19:05:58) (in thread): > Hi@Amrita DasWelcome:hugging_face:

Aleru Divine (19:12:04) (in thread): > welcome@Amrita Das

Precious Orakwe (19:52:16) (in thread): > Welcome@Amrita Das

Precious Orakwe (19:55:36): > Please I have a question, > If I have contributed to BugSigDB before and I already have an account, can I still use that account or am I to create another account before proceeding to the second task.<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Scholastica Urua@Chioma Onyido@Peace Sandy

Aleru Divine (20:08:19) (in thread): > I believe you can use your old account, which would also save you time on account request approval.@Precious Orakwe

Precious Orakwe (20:23:38) (in thread): > Alright, > Thanks@Aleru Divine

Aleru Divine (20:26:35) (in thread): > Anytime!

Aleru Divine (20:33:11): > Hello everyone! > I just completed my first contribution, currently waiting to be assigned a paper for my second contribution. > > If you’re experiencing any blockers or confusion regarding your first contribution—or anything else—I’m more than happy to help! > > Remember, don’t hesitate to ask questions when you’re stuck; there are plenty of people here willing to assist. > > Happy contributing!:sparkles::blush:

Precious Orakwe (20:44:13): > Hello House > I just concluded my first contribution. > > If there is anyone experiencing any difficulties with the first task, I am here to help and answer your question in my own little understanding.

Aleru Divine (20:58:19): > Quick Tip for the First Contribution:Here’s how I approached my first contribution, which you might find helpful: > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles:If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Mildred Anashie (21:00:13) (in thread): > This should be pinned@Aleru Divinewell done > > Very well detailed and easy to follow:clap:

Aleru Divine (21:03:53) (in thread): > Thanks@Mildred Anashie

Aleru Divine (21:04:51) (in thread): > Don’t know where to start from?:point_down::point_down::point_down::point_down::point_down::point_down::point_down::point_down::point_down:Read the welcome intructions on github:https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Cate Ouma (21:06:34): > Thank you@Aleru Divine:pray:

Adeshile Oluwatosin (21:07:05) (in thread): > Wise words > Very detailed as well:+1:

Eniola Kolawole (21:38:21): > Good day everyone, > > My name is Eniola Kolawole, I am a graduate of Science Laboratory Technology and did my final project in the area of Environmental Chemistry where I dealt with public health and environmental problems as a result of improper waste management. I am glad to have this opportunity to apply my research skill, theoretical knowledge, and laboratory skill in making tangible contributions to the Microbiome Study Curation Project in the Bioconductor Community. I hope we will be able to work together to achieve a great result at the end. Nice to meet you all. > > To our mentors@Svetlana Ugarcina Perovic,@C. Mirzayi (please do not tag this account),@Peace Sandy,@Chioma Onyido,@Esther Afuapeand@Scholastica Urua. Thank you for starting this journey with us.

Adeshile Oluwatosin (21:53:48) (in thread): > Hello@Eniola Kolawolewelcome:hugging_face:Follow this to start:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Adeshile Oluwatosin (21:54:51) (in thread): > You can use this as well as a guideline on how to contribute ;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Eniola Kolawole (22:01:18) (in thread): > Thank you@Adeshile Oluwatosin

Adeshile Oluwatosin (22:19:09): > In contribution to what@Aleru Divinesaid > > In short: Take out time to pay attention in details to instructions. > I also just finished my first contribution > Anyone can reach out to me as well for assistance. > I am willing to help.

Adeshile Oluwatosin (22:21:25) (in thread): > Welcome:hugging_face:

2024-10-02

Martha Kisakye (00:18:03): > Thank you@Aleru Divineand@Adeshile OluwatosinI have also successfully managed to make my first contribution and in case of anything you can reach out to me for guidance .

Adeshile Oluwatosin (01:22:44) (in thread): > Well done@Martha Kisakye

Samuel Ogunleye (01:43:55) (in thread): > Just curious, is this article important for everyone to curate before picking up a second contribution? “Breast cancer patients…”

Aleru Divine (01:51:53) (in thread): > @Samuel Ogunleyeif I get that correctly, did you mean if we need to finish the first contribution before going to the second? > > yes the “Breast cancer patients…” article is part of the first contribution and very important to finish before the second contribution. > > It says so here on the welcome instructions on GitHub. > > Also note that the first contribution is the mini curation (no additional task). So just fill out the quiz form, submit and that’s it. - File (JPEG): IMG_1098

Samuel Ogunleye (01:52:34) (in thread): > Awesome. > Thank you very much!

Aleru Divine (01:52:38) (in thread): > Hi Eniola, welcome:hugging_face:

Aleru Divine (01:53:55) (in thread): > Well done:raised_hands:

Aleru Divine (01:54:02) (in thread): > Well done@Martha Kisakye

Eniola Kolawole (01:55:38): > Thank you@Adeshile Oluwatosinand@Aleru Divinefor the tips. I have successfully made my first contribution as well. Always available to assist anyone. Good Morning everyone.

Eniola Kolawole (01:57:16) (in thread): > Hi Aleru. Thanks for the headstart.

Adeshile Oluwatosin (01:58:42) (in thread): > :relieved:

Adeshile Oluwatosin (01:59:11) (in thread): > Well done:+1:

Aleru Divine (02:07:19) (in thread): > Well done@Eniola Kolawole

Aleru Divine (02:09:46): > Recording your first contribution:It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL:https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHEI’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone:sparkles::sunny: - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey - File (JPEG): IMG_1099 - File (JPEG): IMG_1102 - File (JPEG): IMG_1100 - File (JPEG): IMG_1101

Adeshile Oluwatosin (02:15:29) (in thread): > Thank you

Eniola Kolawole (02:26:51) (in thread): > About to ask how to go about this in the group, thank you.

Eniola Kolawole (02:30:21) (in thread): > Thank you<@UBNSEMS3S>

Scholastica Urua (02:34:42): > Hello everyone:wave:, welcome to the BugSigDB community. > > My name is Scholastica Urua, a past outreachy intern. I’ll be here to support you in completing the BugSigDB contribution tasks. > > More about me:https://www.linkedin.com/in/scholastica-urua-898659235/ - Attachment (ng.linkedin.com): Scholastica Urua - Outreachy | LinkedIn > A thorough data analyst with solid pharmacy background, knowledgeable about medicines functions and use with experience working with EHR/EMR programs to develop comprehensive reports on patient care, billing, and readmission risk factors. Also knowledgeable about statistics and conducting data analysis using tools like Excel, Google sheet, PowerPoint, Power BI and SQL, as well as a basic knowledge of Python. Personable individual willing to work hard and take on any task towards attainment of organizational goals. · Experience: Outreachy · Education: University of Uyo, Uyo · Location: Lagos State · 500+ connections on LinkedIn. View Scholastica Urua’s profile on LinkedIn, a professional community of 1 billion members.

Peace Sandy (02:35:49) (in thread): > Welcome to BugSigDB

Peace Sandy (02:36:12) (in thread): > Welcome

Peace Sandy (02:36:42) (in thread): > Welcome

Eniola Kolawole (02:37:02) (in thread): > Thank you@Scholastica Urua

Peace Sandy (02:37:30) (in thread): > Welcome to BugSigDB@Ibizugbe Merit

Peace Sandy (02:38:13) (in thread): > Welcome@Precious Orakwe

Peace Sandy (02:39:26) (in thread): > Nice tips > Well done@Aleru Divine

Adeshile Oluwatosin (02:40:00) (in thread): > Hello@Scholastica Urua:wave:

Peace Sandy (02:41:25) (in thread): > :white_check_mark:

Mildred Anashie (02:52:15) (in thread): > Hello@Scholastica UruaIt’sgood to know more about you

Aleru Divine (03:05:47) (in thread): > Thank you@Scholastica Urua:heart_hands:

Aleru Divine (03:06:11) (in thread): > Thank you@Peace Sandy:blush:

PATIENCE ONAH (03:22:02) (in thread): > Thank you all

Mary Agekameh (03:41:56) (in thread): > Thank you so much!@Aleru Divine

Peace Sandy (03:50:52): > Welcome to the community! We’re excited to have you join us. Feel free to dive in, share your ideas, and contribute to the project. Here are some FAQ to help you get started with your contributions.https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Chris Awoke (03:51:18): > Hey, friends! I just completed my first contribution and I’m looking forward to the second. If you need any help, please feel free to reach out.@Aleru Divinehas done a great job describing the process. > > Be sure to check out her post here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Aleru Divine (03:52:58) (in thread): > Thank you so much@Peace Sandy:hugging_face:

Eniola Kolawole (03:53:04) (in thread): > Thank you@Peace Sandyfor this:pray:

Svetlana Ugarcina Perovic (03:53:06): > Good morning!:sunny:Kind reminder: To avoid duplicate inquiries, please refrain from directly messaging or emailing BugSigDB mentors individually. > > We encourage you to discuss the project here in the#bugsigdbchannel. This collaborative approach is what makes open source projects so great - you’re part of a community, andwe’re all here to support each other.

Adeshile Oluwatosin (03:54:26) (in thread): > Thank you@Peace Sandy:blush:

Samuel Ogunleye (03:57:35): > Hello everyone, I’m really excited to share that I’ve just wrapped up the first contribution stage for BugSigDB! Thanks to@Aleru Divinebreakdown post. > > I would love to help anyone who might be navigating NCBI or just trying to make sense of microbiome studies. If you have questions or need someone to brainstorm ideas with, I’m here! > Here’s how I can help: > * Navigating NCBI:Need tips on searching for bacterial taxa? I’ve got your back! > * Research Insights:I’m more than happy to share what I’ve learned about microbial signatures and their health implications. > * Team Learning:Let’s connect! I think sharing knowledge and experiences will really help us all grow. > Feel free to reach out anytime.

Aleru Divine (03:58:58) (in thread): > Well done@Samuel Ogunleye:hugging_face:

Adeshile Oluwatosin (03:59:52) (in thread): > Well done:+1:

Adeshile Oluwatosin (04:01:58): > Good morning > I would like to state that I mistakenly submitted the form twice. > The initial and first submission is the accurate and correctly filled contribution. I will go ahead with the second contribution now. > Thank you:pray:Name:@Adeshile Oluwatosin@Svetlana Ugarcina Perovic<@UBNSEMS3S>

Svetlana Ugarcina Perovic (04:03:18) (in thread): > This is a question for the Outreachy organization team. Please double check with them.

Svetlana Ugarcina Perovic (04:06:54) (in thread): > Noted. No problem!

Adeshile Oluwatosin (04:07:21) (in thread): > Thank you so much:blush:

Chris Awoke (04:08:07) (in thread): > Thank you so much,@Svetlana Ugarcina Perovic! > > Absolutely, we will stick to that.

Mohamed Osman Omar (04:13:53): > Hi, I am Mohamed Osman Omar, one of the contributors of this project, happy to see all

Adeshile Oluwatosin (04:14:50) (in thread): > Welcome@Mohamed Osman Omar:wave:

Adeshile Oluwatosin (04:15:20) (in thread): > Check this;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Mildred Anashie (04:15:53): > Good Morning Everyone > > Wishing us all a great contribution period:blush:I have been able to complete my first contribution. > > Following the tipshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609by@Aleru Divinewhich is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divinehas also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account viahttps://bugsigdb.org/Special:RequestAccount(If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-stepwalk-throughof how to add a new study to BugSigDB” > I am also open to help:hugging_face: - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment (BugSigDB): Special:RequestAccount - Attachment (BugSigDB): Curation Policy > … - Attachment (YouTube): Adding a study to bugsigdb.org

Mildred Anashie (04:16:22) (in thread): > Hi@Mohamed Osman Omar

Chris Awoke (04:17:00) (in thread): > You’re welcome,@Mohamed Osman OmarBe sure to check out this post here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609

Adeshile Oluwatosin (04:17:01) (in thread): > Well stated@Mildred Anashie:hugging_face:

Arpita (04:18:56): > Hi everyone, I am Arpita and I am happy to contribute to the community.

Aleru Divine (04:19:25) (in thread): > Thanks for the insight@Mildred Anashie:raised_hands:

Kate Rasheed (04:19:25): > Great job to everyone that has recorded a contribution. We are doing really well. Special thanks to@Aleru Divineand everyone assisting in every way.

Adeshile Oluwatosin (04:20:52) (in thread): > Welcome:hugging_face:@ArpitaKindly read through past messages

Aleru Divine (04:22:52) (in thread): > Hi@Arpita, welcome. > 1. To get started please check out the welcome instructions on this link: > https://github.com/waldronlab/BugSigDBcuration/issues/942. Also, here’s a quick tip for your first contributionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p17278306995726093. To record your first contribution when you have submitted, you can go through this process:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny:

Arpita (04:24:08) (in thread): > Thank you!!!

Aleru Divine (04:24:11) (in thread): > Well done@Kate Rasheed

Peace Sandy (04:25:32) (in thread): > You are welcome@Aleru Divine@Eniola Kolawole@Adeshile Oluwatosin

Precious Orakwe (04:25:36) (in thread): > Thanks@Peace Sandy

Precious Orakwe (04:26:30) (in thread): > Thanks@Scholastica Urua

Mildred Anashie (04:41:22) (in thread): > Thank you so much:hugging_face:@Peace Sandy

Mildred Anashie (04:42:12) (in thread): > Well done@Samuel Ogunleye

Mildred Anashie (04:42:49) (in thread): > Well done on completing your first contribution:hugging_face:@Chris Awoke

Mildred Anashie (04:43:19) (in thread): > Welcome@Arpita:hugging_face:

Precious Orakwe (04:51:49) (in thread): > Good morning at@Svetlana Ugarcina Peroviccan I go ahead with my previous account or should I request another account? > I am confused by the response above.

Svetlana Ugarcina Perovic (04:54:21) (in thread): > Ah sorry, my bad, please proceed with your already existing account.

Precious Orakwe (04:56:32) (in thread): > Thanks@Svetlana Ugarcina Perovic

Joy (04:57:33): > Helloeveryone, > > My name is Joy, and I’m an Outreachy applicant for the December 2024 to March 2025 round. I’m excited to contribute to the MolEvolvR project and to collaborate with such a talented and diverse group! > > I have experience with R programming, bioinformatics, literature review, and I am eager to learn and grow alongside this community. I’m especially looking forward to contributing to the project’s development and learning more about bioinformatics tools. > > Looking forward to working with you all and learning from this experience!:blush:

idiaru Angela (04:58:04) (in thread): > Well done@Aleru Divine

Svetlana Ugarcina Perovic (04:59:39) (in thread): > @Joyplease go to the communication channel for theMolEvolvR project

Svetlana Ugarcina Perovic (05:00:49) (in thread): > @JoyPlease note this is a community for theMicrobiome Study Curation project

Svetlana Ugarcina Perovic (05:02:10) (in thread): > @Precious Orakweplease delete your above answers that are not correct for@Joy’s request, thanks!

Precious Orakwe (05:03:14) (in thread): > Okay@Svetlana Ugarcina Perovic

Precious Orakwe (05:03:52) (in thread): > Welcome @Joy

Mildred Anashie (05:04:44) (in thread): > Just to add to this > > I always visit the pinned messages on the channel, it helps to answer a lot of the questions I might want to ask > So I recommend this also:blush:

Arpita (05:17:22) (in thread): > Thank you !!

Svetlana Ugarcina Perovic (05:35:04): > A must-read for today:How to start tips by @Chioma Onyido**** ****https://www.linkedin.com/posts/chioma-onyido_opensource-bioinformatics-bioinformatics[…]845177880576-WrDv - Attachment (linkedin.com): Chioma Onyido on LinkedIn: #opensource #bioinformatics #bioinformaticsinternship… > Today marks exactly one year since I got accepted for the initial stage of the Outreachy internship program. Thank you Jesus! > > For those unfamiliar, Outreachy…

Aleru Divine (05:39:16) (in thread): > Thank you so much for sharing this post@Svetlana Ugarcina Perovic:heart_hands:And thank you@Chioma Onyidofor the tips:heart_hands:

Mildred Anashie (05:42:08) (in thread): > Thank you sharing@Svetlana Ugarcina PerovicThank you@Chioma Onyidofor this totally awesome piece:pray:

Adeshile Oluwatosin (05:54:55) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:thumbsup:

inyang john (05:55:12): > Hi there to all of you. > My name is Jay. My application is for the December 2024–March 2025 cohort at Outreachy. I’m ecstatic to be a part of the Microbiome study curation project and to collaborate with such an amazing group of people! > I’m eager to learn new skills and grow with this community. I’ve done literature reviews, bioinformatics, and R programming. I’m also a pharmacist and seem to have excellent expertise on public health research. I’m quite eager to contribute to the project’s advancement and learn more about bioinformatics tools.

Kate Rasheed (05:55:44) (in thread): > Thank you so much for this post. It’s really a must-read.

Adeshile Oluwatosin (05:58:54) (in thread): > Hello@inyang johnThisis a community for theMicrobiome Study Curation project

inyang john (06:18:56) (in thread): > i’m so sorry. it was a mistake

Aleru Divine (06:26:09) (in thread): > welcome@inyang johnTo get started please check out the welcome instructions on this link:https://github.com/waldronlab/BugSigDBcuration/issues/94Also, here’s a quick tip for your first contributionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609To record your first contribution when you have submitted, you can go through this process:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229Don’t hesitate to ask questions if and when you need help. Happy Contributing.:hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

inyang john (06:26:48) (in thread): > thank you so much

Joy (06:43:41) (in thread): > Ok. Thanks@Svetlana

Joy (06:45:54) (in thread): > Ok. Thanks@Svetlana Ugarcina Perovic

Joy (06:54:10): > Helloeveryone, > > My name is Joy, and I’m an Outreachy applicant for the December 2024 to March 2025 round. I’m excited to contribute to the Microbiome Study Curation project and to collaborate with such a talented and diverse group! > > I am eager to learn and grow alongside this community. I’m especially looking forward to contributing to the project’s development and learning more about the project. > > Looking forward to working with you all and learning from this experience!:blush:

Aleru Divine (06:55:32) (in thread): > Hi@Joywelcome:hugging_face:To get started please check out the welcome instructions on this link:**** > > ****https://github.com/waldronlab/BugSigDBcuration/issues/94Also, here’s a quick tip for your first contribution**** > > ****https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609To record your first contribution when you have submitted, you can go through this process:**** > > ****https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229Don’t hesitate to ask questions if and when you need help. Happy Contributing.:hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Adeshile Oluwatosin (06:56:24) (in thread): > Welcome:hugging_face:@JoyTo get started, join #bugSigDB channel ! > 1. Review the intial information; Look through this link:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 > > 1. Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > 1. Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > 1. Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Joy (07:08:45) (in thread): > Thank you

Agatha (07:10:40): > In the link provided by one the mentors is a link to the articleapplicants are going to review and questions that followed after > > I am confused, how do I connect it to “Recording contribution”? > Do answering and submitting these question means that I have recorded my contribution? > > Please I need a guide. I am confused

Mildred Anashie (07:11:00) (in thread): > Welcome@Joy:blush:You have everything you need to start in the messages sent above,don’thesitate to ask questions if you are not clearI’mopen to help if I can

Mildred Anashie (07:11:53) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229You can follow this link as a guide to record your contribution - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny:

Svetlana Ugarcina Perovic (07:12:11) (in thread): > Hi Agatha, which link is confusing?

Aleru Divine (07:12:41) (in thread): > You need to record it on the outreachy website after submitting.@Agatha

Chris Awoke (07:12:59) (in thread): > Hi,@AgathaIf I get your question correctly, are you struggling to get a hang of the project and how to make your first contribution?

Agatha (07:13:38) (in thread): > @Chris Williams@Chris Awoke, exactly

Adeshile Oluwatosin (07:13:54) (in thread): > Hi@AgathaJust follow this guideline stated by Mildred, via outreachy link. > > After answering all questions on the curation form. > > You need to record the contribution via outreachy link. > I hope this answers your question

Adeshile Oluwatosin (07:14:30) (in thread): > Welcome:hugging_face:To get started, join #bugSigDB channel ! > 1. Review the intial information; Look through this link:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 > > 1. Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > 1. Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > 1. Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!!

Agatha (07:14:31) (in thread): > @Aleru Divinehow do I record on the outreachy website?

Adeshile Oluwatosin (07:14:35) (in thread): > This could help tho !

Chris Awoke (07:14:54) (in thread): > If yes, start with this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539Thereafter, you can go through this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609If still need guidance after that kindly reach out please. > > Do you understand@Agatha?

Aleru Divine (07:16:20) (in thread): > Oh!!!@Agatha, if you’ve submitted the quiz form, thenextthing to do is record on Outreachy website. > > Here is the link to the process I shared earlierhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229. - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny:

Agatha (07:16:43) (in thread): > @Chris Awoke, I am already on it > > I am currently going through the article and I have seen the questions, and I am trying to answer them

Chris Awoke (07:19:05) (in thread): > Should you have any challenges completing your first contribution, kindly reach out@AgathaBest wishes.

Precious Orakwe (07:39:59): > Please I am finding it difficult to get the signatures of the paper I am working on, has the paper indicates that there are 7 studies on the paper, but I can’t how to get signatures for this studies, please help@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Scholastica Urua@Peace SandyThis is a link to my paper:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec10title - Attachment (PubMed Central (PMC)): Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations > Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results. Here we perform a meta-analysis of seven microbiome studies (1825 stool samples from 684 infants) to compare …

Precious Orakwe (07:41:14): > How do I go about the part of the study comparing Non-EBF, EBF and Non-BF

Aleru Divine (07:41:38) (in thread): > I’llhave a look at this@Precious Orakwe

Precious Orakwe (07:42:41) (in thread): > Thanks@Aleru Divine

Mildred Anashie (07:42:54) (in thread): > I’llhave a look too@Precious OrakweIt’sa meta-analysis

Aleru Divine (07:54:55) (in thread): > I get it@Precious Orakwethis study (meta-analysis study design) combines results from multiple studies to get a clearer picture of a specific topic.Which in this case is exclusive breastfeeding.I’mstill going through the paper:ok_hand:

Kate Rasheed (08:04:11): > As we go through our articles for contributions, be reminded of tomorrow’s meeting by 9am EDT. > > You can check out the timezone for your location here:https://www.timeanddate.com/worldclock/converter.html?iso=20241003T111500&p1=179&p2=3395&p3=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Mildred Anashie (08:12:15) (in thread): > Hi@Precious OrakweStill going through this paper > It’s quite interesting

Aleru Divine (08:24:05) (in thread): > This is a very comprehensive paper@Precious Orakwe:sweat_smile:

Aleru Divine (08:25:02) (in thread): > I’mstill trying to make sense of the data:disguised_face:

Aleru Divine (08:51:58) (in thread): > I do see differential relative abundances in the supplemental data. But I am very confused on how to differentiate group 0 and group 1. Now while I thought I had it for non-exclusively breastfed vs. exclusively breastfed infants(supplemental table 2), I saw exclusive breastfeeding, non-exclusive breastfeeding and non-breastfeeding groups using the same format (supplemental table 3). So I’m very confused too. > > Maybe I’m missing something:sob:

Precious Orakwe (08:53:32) (in thread): > That it why am confused as well here

Mildred Anashie (08:57:22) (in thread): > Yea@Aleru DivineI thought I was the one not looking in the right place

Mildred Anashie (09:02:08) (in thread): > @Precious OrakweThe supplementals should have given us the necessary information but it’s still confusing trying to identify the comparisons and the signatures > > I think we should wait for our mentors or better still bring it up during the office hour tomorrow > > AlthoughI’llkeep going through, Incase I figure it out before tomorrow

Aleru Divine (09:08:30) (in thread): > I agree too@Mildred Anashie, looking at it again with fresh eyes might help to see whatwe’remissing.If we are missing something:crossed_fingers:

Komuhangi Tumuhairwe (09:18:46): > Hi everyone, greetings. > My name is Komuhangi, komu is fine. I am a software engineer and an outreachy applicant. > I an expectant to connect and collaborate with you all that are part of this community. > Growing from each one of you is a bonus I look forward to.

Mildred Anashie (09:21:05) (in thread): > Hi@Komuhangi TumuhairweWelcome:hugging_face:

Mildred Anashie (09:21:14) (in thread): > Go through the pinned messages > > And thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539to get started - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Aleru Divine (09:21:36) (in thread): > Welcome@Komuhangi Tumuhairwe:blush:

Adeshile Oluwatosin (09:22:25) (in thread): > Welcome@Komuhangi Tumuhairwe:wave:

Eniola Kolawole (09:26:17) (in thread): > Welcome home:+1:

Onyinyechi (09:37:40): > Hello everyone, I’m Onyinyechi, an Outreachy applicant for the December 2024-March 2025 cohort. I’m excited to be here and I look forward to collaborating with you all!

Eniola Kolawole (09:40:23) (in thread): > You are welcome@Onyinyechi. Kindly go through this to start withhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Mildred Anashie (10:03:03) (in thread): > Welcome@Onyinyechi:hugging_face:

Adeshile Oluwatosin (10:16:23) (in thread): > Welcome:hugging_face:@OnyinyechiTo get started, join #bugSigDB channel ! > 1. Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > 2. Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > 1. Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > 1. Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

UBNSEMS3S (10:18:57) (in thread): > Supplementary Table 2 > Non-EBF is group 1 (cases) and EBF is group 0 (controls). > > Supplementary Table 3 > This is an advanced curation because they treated a 3-category categorical variable as continuous. So they have a variable with levels 1, 2, and 3 and each unit increase in that variable indicates less breastfeeding by the mother. > > You would enter group 1 as “reduced exclusivity of breastfeeding to non-breastfeeding” and group 0 as “increasingly exclusive breastfeeding.” > > Supplementary Table 4-6 > Non-EBF is group 1 (cases) and EBF is group 0 (controls). > > Supplementary Table 7 > This is two separate experiments stratified by delivery mode. You would enter these separately in different experiments.

Agatha (10:20:16) (in thread): > Thank you > > I just completed the curation form using the link provided > > Please how do I record my contribution in the outreach website

Mildred Anashie (10:26:53) (in thread): > @Aleru Divine@Precious Orakwe

Aleru Divine (10:27:07) (in thread): > Wow! Thank you so much for the detailed clarification<@UBNSEMS3S>.

Aleru Divine (10:31:12) (in thread): > One last thing regarding interpreting increased and decreased abundance using the pooled estimate.> 0 indicates an increase in abundance and < 0 indicates a decrease in abundance.Is this correct?:pray:<@UBNSEMS3S>

UBNSEMS3S (10:32:09) (in thread): > Correct. Yeah it’s a bit weird because it’s a log odds ratio. Usually we see the exponentiated ratio but in log odds: positive=increasing, negative=decreasing.

Aleru Divine (10:32:58) (in thread): > Well done@AgathaRecording your first contribution:**** > > ****It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project.So, here are the steps to record your first contribution: > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution.Here’s the link to the curation form that will serve as your Contribution URL:https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey - File (JPEG): IMG_1099 - File (JPEG): IMG_1100 - File (JPEG): IMG_1101 - File (JPEG): IMG_1102

Agatha (10:34:08) (in thread): > Thank you > > Please what am I expected to do in the description box?

Aleru Divine (10:34:21) (in thread): > Thank you so much<@UBNSEMS3S>:pray:

Mildred Anashie (10:35:04) (in thread): > Wow > > This narrows down alot of things in the study > Thank you<@UBNSEMS3S>:pray:

UBNSEMS3S (10:35:15) (in thread): > Happy to help!

Aleru Divine (10:35:43) (in thread): > That would be a brief description of the contribution.So here you reviewed an annotated article,foundspecific information and answeredquestions.Something like that.

Aleru Divine (10:37:06) (in thread): > Welcome@Onyinyechi

Agatha (10:37:22) (in thread): > Thank you

inyang john (10:40:07) (in thread): > @Onyinyechiyou’rewelcome

Onyinyechi (10:59:23) (in thread): > Thank you everyone:blush:

Precious Orakwe (11:36:38) (in thread): > Welcome@Komuhangi Tumuhairwe

Dorcas Samuel (11:37:38): > Hello everyone!I’m Dorcas Samuel and I’m an outreachy applicantI’m new to Microbiome but I’m ready to learn and contribute to this awesome project.Can someone guide me in what steps to take

Precious Orakwe (11:37:42) (in thread): > Welcome@Onyinyechi

inyang john (11:38:32) (in thread): > You’rewelcome

Mildred Anashie (11:38:33) (in thread): > Hi@Dorcas SamuelWelcome:hugging_face:

inyang john (11:38:59) (in thread): > GoodeveningEveryoneWishing us all a great contribution period:blush:I have been able to complete my first contribution.Following the tipshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609by@Aleru Divinewhich is quite straightforward and easy to follow you should be able to finish your first contribution.I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divinehas also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account viahttps://bugsigdb.org/Special:RequestAccount(If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-stepwalk-throughof how to add a new study to BugSigDB” > I am also open to help:hugging_face: - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment (BugSigDB): Special:RequestAccount - Attachment (BugSigDB): Curation Policy > … - Attachment (YouTube): Adding a study to bugsigdb.org

Adeshile Oluwatosin (11:39:09) (in thread): > Welcome:hugging_face:To get started, join #bugSigDB channel ! > 1. Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > 2. Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > 1. Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > 1. Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Precious Orakwe (11:40:25) (in thread): > Hello@Dorcas Samuelyou are welcome

Aleru Divine (11:41:34) (in thread): > Welcome@Dorcas Samuel:hugging_face:

Dorcas Samuel (11:45:11) (in thread): > Thank you everyone

Precious Orakwe (11:51:24) (in thread): > OMG thank you so much, I appreciate all your effort to help me, thanks<@UBNSEMS3S>for the easy interpretation,@Aleru Divine@Mildred Anashiethank you for your effort. > I appreciate. > > This signature thing must enter my head in Jesus’ name, whether they like it or not. > I am a chosen > Paper and signatures who are you?

Onyinyechi (11:56:41) (in thread): > Welcome@Dorcas Samuel

Paavni Goyal (13:03:53) (in thread): > Welcome@Dorcas Samuel

Paavni Goyal (13:04:33) (in thread): > Welcome@Onyinyechi

Paavni Goyal (13:05:40) (in thread): > Welcome@Komuhangi Tumuhairwe, All the Best for ahead:slightly_smiling_face:

adekemi balogun (13:42:55) (in thread): > Welcome@Onyinyechi, kindly read up on pinned messages to catch up

adekemi balogun (13:44:43) (in thread): > Welcome@Komuhangi Tumuhairwe, wishing you all the best on this new journey:heart_hands:

Janani Ravi (13:47:30) (in thread): > See you on#molevolvr@Joy. Thanks Svetlana for passing along the instructions!

BOLARINWA AISHAT (14:48:51) (in thread): > Welcome Dorcas > > Check out the pinned messages,I found them helpful.

Mary Agekameh (14:56:16) (in thread): > Please@Aleru Divinewhich URL do we put?

Aleru Divine (15:12:35) (in thread): > @Mary AgekamehHere’s the link to the curation form that will serve as your Contribution URL:https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Mary Agekameh (15:18:09) (in thread): > Thank you so much

Mary Agekameh (16:30:13) (in thread): > @Mildred AnashiePlease can you send the GitHub link I can use to request for one of the studies

Mildred Anashie (16:31:34) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22

Mildred Anashie (16:32:35) (in thread): > This should take you there@Mary Agekameh

Mary Agekameh (16:32:46) (in thread): > Thank you!

Agatha (16:40:33): > If I click on the “paper to curate” it open up a page that shows various work to be curated. > Please, if I open one of them, how do I request that it should be assigned to me?

Aleru Divine (16:43:30) (in thread): > Hi@Agatha.To claim an article for curation, just post a response to the issue (a comment) with your name.Here for example:****“Divine Aleru > > I’d like to claim this issue for curation”****Also check if someonehasn’trequested for it yet.It’sa on a first come first serve basis.

Mildred Anashie (16:43:54) (in thread): > Your name and telling the mentorsyou’lllike to claim it for curation

Mildred Anashie (16:45:20) (in thread): > You can also go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389It might help@Agatha - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Adeshile Oluwatosin (17:09:15) (in thread): > As they’ve both explained, > > Just comment under the particular issue > Tag@Svetlana Ugarcina Perovicand input a requestHello, I’d like to curate this paper for my second contribution

Dorcas Samuel (17:15:40) (in thread): > Does this mean I finished the first contribution task@Adeshile Oluwatosin@Aleru Divine - File (JPEG): IMG_1130

Adeshile Oluwatosin (17:21:12) (in thread): > Yes@Dorcas Samuelit confirms it has submitted

Dorcas Samuel (17:24:08) (in thread): > Thank you@Adeshile OluwatosinDo we record this particular contribution becausethere’sno contribution link to reference to right

Adeshile Oluwatosin (17:25:58) (in thread): > Yes, you need to record the contribution as mentors can choose to not accept any more contributions once they’ve gotten enough. This gives you the chance to be considered to be an intern. > > Very important!!! > You need to go to Outreachy Link to record this contribution > > Click on record initial contribution, input a description, save and submit > > Then you can proceed to the next contribution. > Check this on how to go about ithttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny:

Adeshile Oluwatosin (17:31:59): > NOTE; Just putting it out here again!!! > > Ensure you record your contribution. > As mentors can choose not to accept contributions anymore when they’ve gotten enough. > This gives you the chance to be considered to be an intern. > > Very important !!! > > A short description; > * Go to Outreachy link > * Click on Microbiome study curation > * Click Record a contribution > * Write a brief description on what you did > * Input the linkhttps://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHEas the contribution link (same for everyone). > * Then save - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

UBNSEMS3S (17:38:26): > Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. Please come with lots of questions.

Adeshile Oluwatosin (17:38:40) (in thread): > Noted:+1:

Adeshile Oluwatosin (17:41:38) (in thread): > Have you figured it out yet?@Dorcas SamuelI am here to assist, if you are still confused

Precious Orakwe (17:58:53) (in thread): > Okay

Dorcas Samuel (18:30:10) (in thread): > @Adeshile OluwatosinI know how to record a contribution,I’masking for the input on the recording form, that asked for the contribution link

Mildred Anashie (18:31:01) (in thread): > If it’s the first contribution link > > This is ithttps://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHEA link to the survey is what should be recorded@Dorcas Samuel - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Dorcas Samuel (18:33:48) (in thread): > Thank you@Mildred Anashie

Precious Orakwe (20:00:06): > Please, how do I add another experiment to my study, I clicked on duplicate experiment after inserting my signature for the first experiment, but it’s still not showing. What can i do here. > Please assist me<@UBNSEMS3S>@Svetlana Ugarcina Perovic@anyone > Thanks.

Mildred Anashie (20:09:25) (in thread): > If I understand you correctly, you have added your study and the first experiment and you want to add subsequent experiments?@Precious OrakweIf that’s the case you can go back to the section with the study information and click on “Add a new experiment” and do that every time you want to add a different experiment

Mildred Anashie (20:11:27) (in thread): > Here’san image on where to go to - File (PNG): IMG_1106

Kate Rasheed (21:20:08) (in thread): > That’s really correct@Mildred Anashie. Thank you for always helping out. Hope you’ve sorted it@Precious Orakwe?

2024-10-03

Precious Orakwe (00:39:05) (in thread): > Thank you@Mildred AnashieI will fix it now

Precious Orakwe (01:00:51): > Good morning house, > Good morning to our mentors, hope we all had a great night rest.

Precious Orakwe (01:03:00) (in thread): > @Mildred Anashiethis is what am seeing after I created my signature, there is no place for creating an experiment again, should I use the duplicate experiment block - File (PNG): Screenshot_20241003-055755.png

Precious Orakwe (01:05:33) (in thread): > @Mildred Anashiesorry for the stress, I found it

Adeshile Oluwatosin (01:13:28) (in thread): > Good morning@Precious Orakwe

PATIENCE ONAH (01:23:22): > Hello everyone, I have submitted my first contribution, I have also commented on an article to curate for the second contribution on the GitHub, I want to confirm if I can start working on it right away or wait until it’s assigned to me.

Mildred Anashie (01:48:29) (in thread): > You are welcome@Precious OrakweThank you@Kate Rasheed:blush:

Chris Awoke (02:02:15) (in thread): > Hello,@PATIENCE ONAHGlad to hear your progress. Kindly wait for it to be assigned to you before you start working on it. > > It doesn’t take much time, except our mentors (the maintainer) are busy at the moment. > > However, kindly go ahead and request for an account while you wait. > > You can as well go through the guide to understand better the curation process if you haven’t. > > I hope this helps.

Aleru Divine (02:03:56) (in thread): > Hi@PATIENCE ONAHwell done on completing your first contribution. > > Yes you’ll have to wait to get assigned an issue before you proceed.While you wait, you can request an account. > > Incase you don’t already have the link here it is.https://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Aleru Divine (02:04:35) (in thread): > Good morning@Precious OrakweI had a good night, I hope you did too:blush:

Aleru Divine (02:05:28) (in thread): > Thanks for the reminder

PATIENCE ONAH (02:23:52) (in thread): > Thanks to you both@Aleru Divine@Chris Awokefor your response, I already have an account.

Agatha (02:35:10) (in thread): > Ok > > Thank you > > Please how do I get to know that I have been issued a paper? > Secondly, can I pick more than one paper?

Mildred Anashie (02:35:48) (in thread): > Also, you can go through the paper to get more acquainted with what it’s about and what you will be curating from it while you wait for it to be assigned to you, because it’ll surely be assigned if you are the first and only one who commented on it > > And see this post as well@PATIENCE ONAHhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

PATIENCE ONAH (02:44:51) (in thread): > Thank you

Mary Agekameh (02:55:56) (in thread): > Please is there a time converter we can use?

Adeshile Oluwatosin (02:56:30) (in thread): > Welcome@PATIENCE ONAH:hugging_face:

Adeshile Oluwatosin (02:56:54) (in thread): > We have a meeting today, do well to join

Adeshile Oluwatosin (02:58:08) (in thread): > Yesthereis

Adeshile Oluwatosin (02:59:02) (in thread): > Hi@Agathayou will see that the issue you requested has been markedassigned to you.A mentor would respond under the comment as well.

Adeshile Oluwatosin (03:00:55) (in thread): > Yes, you can select more than one paper, but you must complete one before starting the next. Mentors will notify you when it has been marked. > And you can’t start the next till the previous one has been graded. > > It is advisable to focus on one paper to ensure it is done thoroughly and well.

Mary Agekameh (03:01:16): > Hello everyone. > > I have submitted my first contribution and I have commented on an issue to curate for the second contribution but it hasn’t been assigned to me, do I still wait or go ahead to work on it

Mildred Anashie (03:01:21) (in thread): > No@AgathaYou should work with completing one at a time > > And you would see the assigned tag accompanying the paper onceit’sassigned, I also get a mail so I think you should too

Mary Agekameh (03:02:24) (in thread): > Okay > Thank you@Adeshile OluwatosinI’ll look for it now

Aleru Divine (03:03:02) (in thread): > Hi@Mary Agekamehwell done on completing your first contribution.Yes you’ll have to wait to get assigned an issue before you proceed.While you wait, you can request an accountand while that is being approved, you can also go through the article.Incase you don’t already have the link here it is.https://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Mildred Anashie (03:03:24) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727937348960619?thread_ts=1727933002.034469&channel=C04RATV9VCY&message_ts=1727937348.960619https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389Please see this if it helps - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Aleru Divine (03:04:23) (in thread): > @Agatha, you only claim one article for curation until you have completed this curation and it has been graded.

Mary Agekameh (03:04:52) (in thread): > Thank you@Aleru Divine@Mildred AnashieI requested for it to be assigned to me since last night that’s why I asked

Aleru Divine (03:05:27) (in thread): > Oh! As soon as the mentors are availableyou’llbe assigned to it.No worries

Aleru Divine (03:05:44) (in thread): > Here’sthe converter@Mary Agekamehhttps://www.timeanddate.com/worldclock/converter.html?iso=20240508T140000&p1=5805 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Adeshile Oluwatosin (03:07:30) (in thread): > Welcome@Mary Agekameh:hugging_face:

Adeshile Oluwatosin (03:08:04) (in thread): > Do well to jointoday’smeeting

Samuel Ogunleye (03:10:05) (in thread): > 2pm WAT right?

Aleru Divine (03:10:36) (in thread): > Yesthat’sit:+1:

Adeshile Oluwatosin (03:11:19) (in thread): > Yes

Mary Agekameh (03:20:02) (in thread): > Thank you!@Aleru Divine

Samuel Ogunleye (03:23:23): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>I requested an account but I was unable to verify the account through the verification link that was provided (error message - Invalid confirmation code. The code may have expired). How can I pass that stage inorder to add a study, please? > > Username: Sproff

Svetlana Ugarcina Perovic (03:27:49) (in thread): > Account Creation Process: > 1. After requesting an account, check your spam folder for two emails: > > * A confirmation email > * A temporary password email > > 1. If the confirmation code has expired, proceed to log in using the temporary password provided. > 2. If you don’t receive the temporary password email, you may request an account again using a different email address and username.

inyang john (03:32:25) (in thread): > Remain calm. The project will be assigned

inyang john (03:35:24): > Making mistakes is an inevitable aspect of learning. Continue pushing and don’t give up. - File (JPEG): IMG_6335

Svetlana Ugarcina Perovic (03:37:15) (in thread): > I just approved your account.@Samuel Ogunleyeplease let me know does it work now?

Samuel Ogunleye (03:38:35) (in thread): > Oh, yeah. I just got an email for the first account created. You can ignore the second one. > > Thank you.

adekemi balogun (03:50:48) (in thread): > Good morning@Precious Orakweyes i did. Thank you for asking:heart_hands:

Svetlana Ugarcina Perovic (03:50:59): > Good morning:coffee::white_check_mark:GitHub issues assigned:white_check_mark:I read all your discussion.Keep up the good TEAM work!

Kate Rasheed (03:51:31) (in thread): > Thank you

Mildred Anashie (03:51:50) (in thread): > Good morning@Svetlana Ugarcina Perovic:teapot:Thank you:blush::raised_hands:

Aleru Divine (03:57:04) (in thread): > Good morning@Svetlana Ugarcina Perovicand thank you so much! > > Teamwork makes the dream work!:muscle:

Kate Rasheed (03:58:05) (in thread): > You get it@Aleru Divine

Eniola Kolawole (04:02:16) (in thread): > Noted:heart:

Adeshile Oluwatosin (04:02:47) (in thread): > Thank you@Svetlana Ugarcina PerovicGood morning:hugging_face:

Adeshile Oluwatosin (04:03:03) (in thread): > :muscle:

Svetlana Ugarcina Perovic (04:03:58) (in thread): > Reminder for today’s meeting. See you there!

Onyinyechi (04:07:15) (in thread): > Good morning@Svetlana Ugarcina Perovic:raised_hands:

PATIENCE ONAH (04:24:08) (in thread): > Thank you so much@Adeshile Oluwatosin2pm Nigeria time right?

Precious Orakwe (04:29:40) (in thread): > Good morning@Svetlana Ugarcina Perovicthank you:heart:

Precious Orakwe (04:32:54) (in thread): > :hugging_face::hugging_face::hugging_face:

Mary Agekameh (04:34:19) (in thread): > Thank you@inyang johnI’ve been assigned to the paper

Precious Orakwe (05:17:43): > Please I need some assistance with my study, I am confused on how to identify the increase and decrease of my signature. > Please help my<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Peace Sandy@Aleru Divine@Mildred AnashieThank you

Kate Rasheed (05:18:32) (in thread): > Go to the figure you want to use in your signature and check details of the signature. You would see something like a decrease/ reduction in the article that captures the figure. Hope this helps@Precious Orakwe

Aleru Divine (05:18:49) (in thread): > @Precious Orakwethis has been answered in your previous thread.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727869199267069Check the last messages - Attachment: Attachment > Please I am finding it difficult to get the signatures of the paper I am working on, has the paper indicates that there are 7 studies on the paper, but I can’t how to get signatures for this studies, please help @Svetlana Ugarcina Perovic @UBNSEMS3S @Chioma Onyido @Scholastica Urua @Peace Sandy > > This is a link to my paper: > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec10title|https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6177445/#Sec10title

Precious Orakwe (05:19:02): > Here it is - File (PNG): Screenshot_20241003-101428.png

Aleru Divine (05:19:37) (in thread): > <@UBNSEMS3S>has answered this in your last thread.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727879529641009?thread_ts=1727869199.267069&channel=C04RATV9VCY&message_ts=1727879529.641009 - Attachment: Attachment > Correct. Yeah it’s a bit weird because it’s a log odds ratio. Usually we see the exponentiated ratio but in log odds: positive=increasing, negative=decreasing.

Precious Orakwe (05:21:03) (in thread): > Yes@Aleru Divinebut I can’t find these sign >0 signifying increase and <0 signifying decrease or positive=increase and negative=decrease

Aleru Divine (05:22:15) (in thread): > Any signature that is - is decreasing

Precious Orakwe (05:23:58) (in thread): > I’m sorry, my bad > I understand now. > Thank you@Aleru DivineI will buy sweets for you soon for teaching me

Aleru Divine (05:24:20) (in thread): > You’ll be using the pool estimate to interprete the result.So the positive figures are increased and the negative figures are decreased. - File (JPEG): IMG_1119

Precious Orakwe (05:25:06) (in thread): > Yeah, I understand now

Precious Orakwe (05:25:12) (in thread): > Thank you

Mildred Anashie (05:41:47) (in thread): > Yea@Precious Orakwe@Aleru Divineasked that in the previous thread and<@UBNSEMS3S>answered alreadyI’mglad you figured it out

Rahila-me (05:55:52): > Good morning my fellow team mates, if you are stuck you can always reach out. Also is very important to read the pinned messages it will go a long way in answering some of your questions

adekemi balogun (05:59:34) (in thread): > Hello everyone, i tried the second command that is installing the bugsigdbr but i keep getting this response and its not corresponding to what i watched in the tutorial video. Can anyone be of help please - File (PNG): Screenshot (37).png

Mildred Anashie (06:02:24) (in thread): > @Svetlana Ugarcina Perovicshould be able to give a better response > > But can I ask if you are trying to download it to get started with this project?@adekemi balogun

Mildred Anashie (06:03:55) (in thread): > Thank you@Rahila-meI totally agree with you, the pinned messages should be everybody’s go to because it definitely is mine > Good morning:teapot:

adekemi balogun (06:05:11) (in thread): > yes yes i’m trying to install the packages into R or don’t i need that before i can get started on the paper i was assigned to?

Rahila-me (06:05:50) (in thread): > morning dear:+1:

Mildred Anashie (06:06:47) (in thread): > No you do not > > Please go through the project description again and the onboarding materials which you can find herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Mildred Anashie (06:07:10) (in thread): > I’mhappy to help you get started if you have other questions

Aleru Divine (06:07:16): > Hi everyone! > > As many of us wrap up our first contributions and dive into the second, I wanted to share some resources that were very helpful to me. > 1. FAQs: This document addresses many common questions, and the mentors have provided some great insights. > https://github.com/waldronlab/BugSigDBcuration/issues/96A big thank you to co-mentor@Chioma Onyidofor creating thisdocument:heart_hands:https://docs.google.com/document/d/1tPBVLw8O-SsGF-LuGVfO1W_mEw8NEKeTJfJaQrnZLUk/edit2.The curation policy:Here we have the outlines work flow process of curation, also there are detailed explanations of the study designs, explanation of the input fields and links to help too. The curation policy is very very detailed and contained almost all the information you’ll need while curating(I say almost all because some studies can require additional information sometimes).https://bugsigdb.org/Curation_Policy3.A completed study: Here is a completed and reviewed study that you can check out as you prepare to start your second contributionhttps://bugsigdb.org/Study_6004.Adding a Study Video:if you learn better visually, this video walks you through adding a study on BugSigDB.https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=6Always reach out for help on the channel as one question answered can be helpful to another person. We’re all learning:muscle:Happy BugSigDB-ing:sparkles::grin: - Attachment (BugSigDB): Curation Policy > … - Attachment (BugSigDB): Alteration of the fecal microbiota in Chinese patients with Parkinson’s disease - BugSigDB > Emerging evidences suggest that gut microbiota dysbiosis plays a role in Parkinson’s disease (PD).However, the alterations in fecal microbiome in Chinese PD patients remains unknown.This case-control study was conducted to explore fecal microbiota compositions in Chinese PD patients. - Attachment (YouTube): Adding a study to bugsigdb.org - Attachment: #96 Outreachy Frequently Asked Questions > Hi Outreachy applicants! > > We wanted to share some answers to some frequently asked questions we received during our last contribution period. > > I asked a question on Slack but haven’t received an answer yet. Are you ignoring me? > > We are not ignoring you. We do our best to answer questions as soon as possible. Please note that I am on American Eastern time and Svetlana is on Central European Time so we may not be quick to answer questions outside normal business hours in these time zones. > > Can I make more than one second contribution? > > We ask that you only claim one article for your second contribution initially. You should focus on making that curation as perfect as possible as it will be used when we assess your performance during the contribution period. We strongly encourage you aim for quality over quantity. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, here is some ways you can help out with BugSigDB: > > • Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > • Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID Please note that the majority of these cannot be solved and that’s ok. > • See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > I submitted my second contribution for grading. Why hasn’t it been graded yet? > > Grading takes us some time. We aim to have your contribution graded within a week. Thank you for patience! > > How do I record my contribution in the outreachy website? > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > How do I know if my first contribution is accepted or merged? > > Once you complete the survey we will have a record of it. Don’t worry! > > Should I always send a DM to mentors? > > Please ask questions in the bugsigdb channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > I have a question not covered here. > > Communications regarding specific tasks should be done on the Slack Bioconductor channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Adeshile Oluwatosin (06:07:57) (in thread): > You do not need that@adekemi balogunJust go ahead to download the pdf and go through the article thoroughly > To fill in each details required in adding an experiment and signature.

Mildred Anashie (06:08:25) (in thread): > Well done@Aleru Divine:raised_hands::raised_hands:You beat me to this:laughing:

Adeshile Oluwatosin (06:08:39) (in thread): > You can as well highlight pinpoints in the article to make it easy for you.

Mildred Anashie (06:09:39) (in thread): > See this also@adekemi balogunhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727861704083179 - Attachment: Attachment > A must-read for today: > > How to start tips by @Chioma Onyido https://www.linkedin.com/posts/chioma-onyido_opensource-bioinformatics-bioinformatics[…]845177880576-WrDv

Aleru Divine (06:09:46) (in thread): > @Mildred Anashietwiiiiiins

Adeshile Oluwatosin (06:10:06) (in thread): > Thank you@Aleru Divinenice write up:thumbsup:

Rahila-me (06:12:31) (in thread): > Thanks@Aleru Divine

Svetlana Ugarcina Perovic (06:13:14) (in thread): > For FAQ check out this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/96 - Attachment: #96 Outreachy Frequently Asked Questions > Hi Outreachy applicants! > > We wanted to share some answers to some frequently asked questions we received during our last contribution period. > > I asked a question on Slack but haven’t received an answer yet. Are you ignoring me? > > We are not ignoring you. We do our best to answer questions as soon as possible. Please note that I am on American Eastern time and Svetlana is on Central European Time so we may not be quick to answer questions outside normal business hours in these time zones. > > Can I make more than one second contribution? > > We ask that you only claim one article for your second contribution initially. You should focus on making that curation as perfect as possible as it will be used when we assess your performance during the contribution period. We strongly encourage you aim for quality over quantity. > > Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, here is some ways you can help out with BugSigDB: > > • Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation > • Try to figure out some of the taxa with missing NCBI ids: https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID Please note that the majority of these cannot be solved and that’s ok. > • See other possible ways to help on the help page: https://bugsigdb.org/Help:Contents > > I submitted my second contribution for grading. Why hasn’t it been graded yet? > > Grading takes us some time. We aim to have your contribution graded within a week. Thank you for patience! > > How do I record my contribution in the outreachy website? > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > How do I know if my first contribution is accepted or merged? > > Once you complete the survey we will have a record of it. Don’t worry! > > Should I always send a DM to mentors? > > Please ask questions in the bugsigdb channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > I have a question not covered here. > > Communications regarding specific tasks should be done on the Slack Bioconductor channel, to join, view https://slack.bioconductor.org/ then search for the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors.

Aniebiet Afia (06:20:34): > @Aniebiet Afia has left the channel

Eniola Kolawole (06:47:06): > Hi guys > > How long does it take to be assigned on GitHub?

Kate Rasheed (06:47:37) (in thread): > Not so long. Just be patient.

Mildred Anashie (06:47:45) (in thread): > As soon as the mentors get to itIt’llbe assigned to you, be patient

Eniola Kolawole (06:49:26) (in thread): > Thank you@Kate Rasheedand@Mildred Anashie

Svetlana Ugarcina Perovic (06:51:30) (in thread): > Please tag the mentor to be automatically notified. (Btw, I found it manuallyhttps://github.com/waldronlab/BugSigDBcuration/issues/489) - Attachment: #489 Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model > Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model - Donald D Nyangahu – Parasite Immunol. > > https://pubmed.ncbi.nlm.nih.gov/32277499/

Eniola Kolawole (06:53:00) (in thread): > Thank you mentor.

Chinwendu Joy Enyidiegwu (07:28:50): > @Svetlana Ugarcina Perovicis the meeting still holding ? am still waiting to be let in<@UBNSEMS3S>

Mildred Anashie (07:31:02) (in thread): > Hello@Chinwendu Joy EnyidiegwuThe meeting is slated for 9am EDT > > Please convert to your local time, ithasn’tstarted yet

Scholastica Urua (07:31:07) (in thread): > Hi@Chinwendu Joy Enyidiegwu, the meeting is starting by 9 AM EDT. That will be 2 PM Nigerian time.

Chinwendu Joy Enyidiegwu (07:32:39) (in thread): > Oh thank you > Very much appreciated.

USLACKBOT (07:41:02): > This message was deleted.

Mildred Anashie (07:42:43) (in thread): > Not@Scholastica Uruabut if I get you correctly > You would be curating both increase and decrease signatures from the image

Rahila-me (07:44:10) (in thread): > ok..thank you just wanted to be sure

Scholastica Urua (07:44:51) (in thread): > Hi@Rahila-me, > > Like@Mildred Anashiesaid, the image has 2 signatures > group 0: control and group 1: GDM.

Rahila-me (08:00:55): > @Scholastica Urua@Svetlana Ugarcina Perovici just added a study and i am seeing this, when i added an experiment i could not find it - File (PNG): Screenshot 2024-10-03 125939.png

Scholastica Urua (08:02:04) (in thread): > Please share a link to the study@Rahila-me

Rahila-me (08:02:31): > https://bugsigdb.org/Study_1117 - Attachment (BugSigDB): Role of the Gut Microbiota in the Increased Infant Body Mass Index Induced by Gestational Diabetes Mellitus - BugSigDB > The connection between gestational diabetes mellitus (GDM) and the offspring’s development, such as obesity, is well established.Emerging evidence indicates that the microbiota of the neonate’s meconium is associated with maternal GDM status.

Svetlana Ugarcina Perovic (08:04:12) (in thread): > It’s herehttps://bugsigdb.org/Study_1117/Experiment_1 - Attachment (BugSigDB): Study 1117/Experiment 1 > .

Scholastica Urua (08:08:20) (in thread): > I think this is a bug and it appears in most (if not all) of the curations on BugSigDB. You should be able to proceed with your curation regardless@Rahila-mewith the link@Svetlana Ugarcina Perovicprovided.

Rahila-me (08:15:54) (in thread): > ok Thank you this now the default behaviour so when i also add signatures it will be separate

Rahila-me (08:16:05) (in thread): > with the link i can see it

Svetlana Ugarcina Perovic (08:17:40) (in thread): > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format:https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Rahila-me (08:32:08) (in thread): > @Svetlana Ugarcina Perovicok thank you

PATIENCE ONAH (08:37:26): > I added the ‘DIO’ of the article am curating and selected auto mode but other information on the form data didn’t populate automatically, and I couldn’t locate the PMID in the article. I want to know if there is a case like that or I made a mistake.

Rahila-me (08:37:45): > @Scholastica Uruawhat can one make out of the match-on from this screenshot, > Also alpha diversity were just mentioned but no image to show for it or further details about it i have checked all the supplementary materials no has information about it and it was only mentioned once, should i leave it blank, also a screenshot - File (PNG): Screenshot 2024-10-03 132838.png - File (PNG): Screenshot 2024-10-03 132921.png

Mildred Anashie (08:38:54) (in thread): > Please search your topic herehttps://pubmed.ncbi.nlm.nih.gov/You’llfind the PMID - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Rahila-me (08:39:53) (in thread): > use this link:https://pubmed.ncbi.nlm.nih.gov/when it opens input the name of the article here and use the pmid and paste on you study everything will populate

Svetlana Ugarcina Perovic (08:41:19) (in thread): > @PATIENCE ONAHI have checked your paper for curation and it has PMID. Follow the steps above.

Svetlana Ugarcina Perovic (08:42:53): > TIP: When submitting a question here, it’s helpful to**** include a link to the paper**you’re curating and wish to discuss. This provides valuable context for your inquiry.

Precious Orakwe (08:44:14) (in thread): > Thank you@Svetlana Ugarcina PerovicI have been experiencing same thing since morning, I thought it was my network.

PATIENCE ONAH (08:44:15) (in thread): > Thank you so much@Rahila-me,@Mildred Anashieand@Svetlana Ugarcina Perovicfor your support

Svetlana Ugarcina Perovic (08:45:25) (in thread): > Matched onUnless they explicitly say that they matched on age and gender, then no we cannot safely conclude that. Even if they do an analysis to show that there was no stat. sig. difference in age and gender between cases and controls that is not the same thing as matching. Matching has to be something that is specifically and deliberately done prior to data analysis. > Typically. There are ways to do matching during data analysis but I think of the 100s of papers we’ve curated I’ve seen exactly 1 do so.

Mildred Anashie (08:45:42) (in thread): > @Rahila-meplease share a link to your study

Svetlana Ugarcina Perovic (08:46:02) (in thread): > @Mildred Anashieit’s already shared above

Mildred Anashie (08:46:25) (in thread): > Okay@Svetlana Ugarcina Perovic

Rahila-me (08:47:58) (in thread): > @Svetlana Ugarcina Perovicno it was never explicitly stated

Svetlana Ugarcina Perovic (08:50:36) (in thread): > @Rahila-meAs for alpha diversity, there are results on “Indexes of α-diversity” presented in your paper for curation.

Eniola Kolawole (08:51:25): > Hey guys, > > It’s almost time for the meeting. Don’t forget to join on time to hear our mentors voices for the first time:grin:. > > Looking forward to hearing your voices as well:ok_hand::blush:.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727905106829259?thread_ts=1727905106.829259&cid=C04RATV9VCY - Attachment: Attachment > Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. Please come with lots of questions! https://us02web.zoom.us/j/2737200499.

Rahila-me (08:58:39) (in thread): > ok

Mildred Anashie (08:59:10) (in thread): > There’salpha diversity@Rahila-meCheck fig2

Aleru Divine (09:01:26) (in thread): > @Rahila-mein addition. The alpha diversity is presented in figure 2b. > > What I do is also to read the figure captions/description for better understanding of the figures.Like here > “(b) Indexes of α-diversity of the meconium microbiome in the GDM and control groups.”

Mildred Anashie (09:01:29) (in thread): > Althoughit’sjust the observedthat’sthere > > Ican’tfind where they mentioned Shannon and the others

Aleru Divine (09:03:54) (in thread): > Yeah I see only the obseved features. Maybe becauseit’sthe only significant one.:thinking_face:

Precious Orakwe (09:07:12): > The meeting has started already,

Rahila-me (10:12:02) (in thread): > @Aleru Divine@Mildred Anashiethanks but take a look at this screenshot so for the observed it will be increased since it is significant as for others it was mentioned. Pls take a look - File (PNG): Screenshot 2024-10-03 151019.png

Kate Rasheed (10:12:20): > Thank you so much<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor a wonderful QA session. I really learnt a lot.<@UBNSEMS3S>Considering the different statical analysis stated in the image below, can I go ahead to input all or I should use two that were dominantly mentioned. - File (JPEG): Screenshot_20241003-150452.jpg

Aleru Divine (10:16:05) (in thread): > This screenshotdoesn’tprovided whether it is increased or decreased but I did see it somewhere.Hold on let me find it.

Rahila-me (10:17:17) (in thread): > ok

Aleru Divine (10:18:05) (in thread): > Here@Rahila-me“The observed features of the GDM group pointed to a decreasing trend in α-diversity compared with those of the control group (Fig. 2b).” - File (JPEG): IMG_1122

Rahila-me (10:19:36) (in thread): > Ok decreased then for observed

Rahila-me (10:20:06) (in thread): > shannon and simpson was mentioned but nothing was said about it, should i leave it blank

Aleru Divine (10:23:20) (in thread): > Not<@UBNSEMS3S>:sweat_smile:But we are to record only the statistical test that was used for the differential abundance testing.Can you share the study link please.It’snot very clear here.I would like to see the paper.

Kate Rasheed (10:24:29) (in thread): > https://www.nature.com/articles/s41598-024-72057-z#citeasHere is the link@Aleru Divine - Attachment (Nature): Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis > Scientific Reports - Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis

Aleru Divine (10:24:36) (in thread): > Please search supplemental materials thoroughly to be sure.But if youdon’tfind it, please leave it blank as nothing was mentioned regarding them.

Aleru Divine (10:25:04) (in thread): > Thanks@Kate Rasheed.Let me have a good look

Mildred Anashie (10:29:24) (in thread): > Yea the screenshot just mentioned the alpha diversity indexes but I didn’t see where it said it was significant talk more of it being decreased or increased. > Except for Figure 2 which pointed us to the observed features only > But I agree with Divine, they could be something in the supplementals.@Rahila-me

Mildred Anashie (10:31:39): > Hello everyone:hugging_face::wave:Today’s session was great and I took a few notes which I’ll like to share > > Tips from Todays Meeting > 1. Enjoy the curation process > 2. Take your time during curation > 3. Ask for feedback from colleagues to be sure of what you are doing > 4. Always check for supplements in your study (You can do that by typing the keyword “Supplement”). > 5. When curating the condition, the goal is for the condition to be researchable, describable and informative. In a case where what you are looking for is not a permissible value on BugSigdb you can search for something close to the disease/condition of interest under study in the paper). > 6. For groups, Give names that are descriptive (Could be how they assigned the study participants or names given based on what is being studied) > 7. You can record a new experiment every time they change sequencing type, condition, groups, Body site etc. > 8. For matched on, we match things because they are like a pair. > N/B:You can also search (Ctrl+f) for keywords like “Matching”. Same can be done for Confounders, Supplements,MHT. But for MHT search for FDR, Bonferroni, Adjusted, Benjamini-Hochberg etc. If you don’t see any of the keywords you searched for being mentioned then leave it blank. > 1. Most of the data transformations are based on statistical tests like > LEfSe-uses relative abundance > Negative Binomial- uses Raw counts etc. > > N/B: You record the statistical tests based on the one that was used for differential abundance testing. We usually have one statistical test except for Maybe ANOVA which can be done alongside Pairwise comparisons. > > This are the few notes I took, hopefully it answers some questions and also when<@UBNSEMS3S>shares the recording we can get more from it. > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape@Scholastica Uruafor an interesting session:blush:

Rahila-me (10:31:56) (in thread): > @Mildred Anashieok

Aleru Divine (10:32:12) (in thread): > I see a figures 4(C-E) shows the significant differential abundance results.
> > According to the description, > > “LefSe analysis showed predominant gut microbiota.” > > Another excerpt “Furthermore, the histograms of the distribution of linear discriminant analysis (LDA) values obtained from the LEfSe analysis (Fig. 4C–E, LDA > 3.0 as the screening criterion) alsorevealed differences in microbial abundancebetween the Control group and the AP models.” > > This confirms LEfSe is the statistical test here. > > So in general, the statistical test is the test or computational tool used for differential abundance testing.

Adeshile Oluwatosin (10:33:27) (in thread): > Thank you@Mildred Anashie

Aleru Divine (10:34:31) (in thread): > Thanks for the detailed notes@Mildred Anashie:raised_hands:Thank you for an awesome and insightful office hours session today<@UBNSEMS3S>and@Svetlana Ugarcina PerovicAll my questions were answered and I’m really glad I asked:sweat_smile:Thanks to everyone who raised a question today, I didn’t know I had some of these questions until you asked:heart_hands:you rock!:muscle:

Mildred Anashie (10:36:52) (in thread): > You are welcome@Aleru Divineand@Adeshile Oluwatosin

Aleru Divine (10:38:42) (in thread): > Is this clear enough@Kate Rasheed

Adeshile Oluwatosin (10:39:56): > <@UBNSEMS3S>Thank you for clarifying and answering my questions.I’llgo ahead to request for another paper.:hugging_face::pray:

Aleru Divine (10:40:33) (in thread): > Omg you were Tosin:heart_hands:Thank you so all your questions:sweat_smile:

Kate Rasheed (10:40:42) (in thread): > Yes it’s clear. I just wanted to be sure. Thanks for your help:slightly_smiling_face:.

Aleru Divine (10:41:11) (in thread): > Happy to!:hugging_face:

Adeshile Oluwatosin (10:41:21) (in thread): > :eyes:yesI’llunmute my mic next time:joy_cat:

Adeshile Oluwatosin (10:41:40) (in thread): > You are welcome:hugging_face:

Kate Rasheed (10:42:29) (in thread): > Thanks Mildred for a detailed note.

Chris Awoke (10:42:56): > Thank you so much,@Mildred Anashiefor the notes. > > You’ve done well:white_check_mark:

inyang john (10:46:12): > please@Svetlana Ugarcina Perovicmy Bugsigbd account has not been confirmed. and i applied since yesterday.

Aleru Divine (10:46:43) (in thread): > Have you checked your spam folder for a confirmation email?

inyang john (10:49:26) (in thread): > it is not there. i have been checking

Adeshile Oluwatosin (10:51:37) (in thread): > @Svetlana Ugarcina Perovicshould have a better response to this

Aleru Divine (10:51:44) (in thread): > Okay, I believe the mentors will get to it when they’re available

Adeshile Oluwatosin (10:53:44) (in thread): > Go through this for now;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727940469459309?thread_ts=1727940203.037609&channel=C04RATV9VCY&message_ts=1727940469.459309 - Attachment: Attachment > Account Creation Process: > 1. After requesting an account, check your spam folder for two emails: > ◦ A confirmation email > ◦ A temporary password email > 2. If the confirmation code has expired, proceed to log in using the temporary password provided. > 3. If you don’t receive the temporary password email, you may request an account again using a different email address and username.

Dorcas Samuel (11:05:12) (in thread): > Thank you@Mildred AnashieCan I text you privately?

Mildred Anashie (11:08:28) (in thread): > Yes sure > > You can also ask questions here Incase some other people have answers:blush:

Adeshile Oluwatosin (11:33:26): > To add to what@Mildred Anashiewrote > Note; There’s usually no multiple hypothesis correction in lefse:pushpin:Don’t record an alpha diversity if not statistically significant. > > Saw this list in the pinned message; > Most of the data transformations are based on statistical tests like; > * ANCOM; centered log ratio > > * Deseq2: raw counts > > * Kruskall Wallis; relative abundances > > * LeFSe: relative abundances > > * Linear models: raw counts, relative abundances, arcsine square root (rarely). > > * MaAsLin2: arcsine square root > > * Mann Whitney U: relative abundance > > * Negative binomial: raw counts > > * Poisson: raw counts > > * T-test : relative abundance

Adeshile Oluwatosin (11:39:56): > <@UBNSEMS3S>I would appreciate the meeting recording, if it can be shared here as well > Thank you:pray:

Esther Afuape (11:50:30): > Here’sone of@Chioma Onyidoold notes on study designs. > Hope this helps - Attachment: Attachment > Wheww! What an interesting discussion today! :grin: > If you weren’t able to attend the meeting today, Here’s a summary of what I gathered from the office hour today: > -“Hallmarks of Study Designs”- by @UBNSEMS3S > > 1. Randomized controlled trial (RCT): participants are randomly divided into groups. The treatment group receives the intervention while control group don’t. Here, researchers randomly assign the conditions to people. > Classical example: > 50 people receive the real vaccine, 50 receive the placebo. Other examples: diet, exercise, etc. > > 2. Laboratory experiment: done using animal models, such as rats, pigs, mice, etc. > You’re not randomizing here because they’re all in the same condition. > > 3. Meta-analysis: this is a study design where researchers combine results from different studies. Meta analysis also means Pooling of results. > > 4. Prospective cohort studies: this is a study where researchers recruit a group of people based on a common characteristic (e.g. based on residence) and follow them up over time. > > Classical example #1: all patients recruited in a study who showed signs of depression in the month of October. > Classical example #2: 100 people develop some diseases of interest (cases) and some people don’t (control) > > 5. Longitudinal observational study: time series studies. There is no intervention by the researcher in this kind of study. > Data is collected at multiple time points. > > Classical example: observing COVID participants before and after the event. > > 6. Case control: when you recruit cases ( people with a disease of interest) and controls (people without) similar on some characteristics. You would sometimes see matched on: age, bmi, sex, etc. > > Classical example: Healthy control group (control) and JIA group (case) > > 7. Cross-sectional observational: Contrasting 2 geographical areas or based on some socio-demographical characteristic (for example), usually at a single time point. > > Classical example: community studies where they took 100 people from a neighborhood and contrasted with people from another neighborhood. > > Apologies if I left anything out, the recording will be posted soon. :pray::skin-tone-5:

Eniola Kolawole (11:52:26) (in thread): > Thank you for this:pray:

Aleru Divine (11:53:43) (in thread): > Thank you for sharing this@Esther Afuapeit’llbe very handy.

Adeshile Oluwatosin (12:16:46) (in thread): > Thank you mentor:hugging_face:

Rahila-me (12:35:10): > Today’s meeting was awesome and insightful. Got answers to my questions and learnt from other’s people questions as well<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Scholastica Urua@Esther Afuape@Peace Sandy@Chioma OnyidoThanks for the wonderful tips shared

Rahila-me (12:46:20): > @Svetlana Ugarcina Perovici Cannot find the ncbi of this when searched: Burkholderia_Caballeronia_Paraburkholderia

Kate Rasheed (12:46:54) (in thread): > Are they together like this or separated?

Rahila-me (12:47:12) (in thread): > exactly like this

Kate Rasheed (12:48:54) (in thread): > You would need to input separately. I found the first one. The first one is under b-protobacteria

Aleru Divine (12:50:13) (in thread): > @Rahila-meYou can record it as seen and leave a note.@Svetlana Ugarcina Perovichas answered this question before.https://community-bioc.slack.com/archives/C04RATV9VCY/p1717404750699539?thread_ts=1717401025.174749&cid=C04RATV9VCY - Attachment: Attachment > “The BCP group is composed of the three independent genera Burkholderia, Caballeronia, and Paraburkholderia. The V3 +V4 segment of the 16 S rRNA selected in this sequencing could not separate the specific genera due to their close genetic relationship (<https://www.sciencedirect.com/science/article/pii/S0098847223003829#bib35|Luo et al., 2021>).”

Aleru Divine (12:51:16) (in thread): > They’re a group I understand.

Rahila-me (12:54:02) (in thread): > @Aleru DivineRead thank you

Aleru Divine (12:54:34) (in thread): > Anytime!

UBNSEMS3S (13:53:31): > Thank you to everyone who attended today’s meeting. Here is the recording. Apologies that I forgot to start recording until 10 minutes in (please someone remind me next week to start recording!). Looking forward to out next meeting. - File (MPEG 4 Video): video1868881068.mp4

Adeshile Oluwatosin (13:54:57) (in thread): > Thank you:hugging_face:

Chris Awoke (14:00:32) (in thread): > Thank you so much,@C. Mirzayi (please do not tag this account)! > > I enjoyed every bit of the session.

BOLARINWA AISHAT (14:09:38) (in thread): > Thank you very much

Rahila-me (14:52:18) (in thread): > Thank you for the lecture

adekemi balogun (15:26:46): > Hello@Svetlana Ugarcina Perovici need your help please during curation i noticed my experiment 1 got duplicated and i can’t see to find my signatures underneath my experiment can you please help

Aleru Divine (15:28:14) (in thread): > Thank you for the recording<@UBNSEMS3S>

Svetlana Ugarcina Perovic (15:29:00) (in thread): > I can’t do anything without a link to your curation:slightly_smiling_face:please do post it here

adekemi balogun (15:30:27): > https://bugsigdb.org/Study_1125# - Attachment (BugSigDB): Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese - BugSigDB > OBJECTIVE: This study intended to determine the associations between gut microbiota and glucose response in healthy individuals and analyze the connection between the gut microbiome and glucose-metabolism-related parameters.

adekemi balogun (15:31:13) (in thread): > This is the link to my curation@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (15:32:06) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&cid=C04RATV9VCY - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Svetlana Ugarcina Perovic (15:32:58) (in thread): > So, I see (when I manually entered the link) the Experiment 1 with 2 signatures and Experiment 2 without signatures.

adekemi balogun (15:34:51) (in thread): > Oh you can see my two signatures? i can’t see them on my end, is that a problem ? Would it be possible to remove my second experiment cause it’s a duplicate of my first experiment

Svetlana Ugarcina Perovic (15:36:28) (in thread): > When you manually enter the link:https://bugsigdb.org/Study_1125/Experiment_1/Signature_1https://bugsigdb.org/Study_1125/Experiment_1/Signature_2then you can see them. - Attachment (BugSigDB): Study 1125/Experiment 1/Signature 1 > Source: Figure 1 Description: The diagram depicts the overlapping OTUs between Chinese and Africans Abundance in Group 1: increased abundance in African citizens… - Attachment (BugSigDB): Study 1125/Experiment 1/Signature 2 > Source: Figure 1 Description: The diagram depicts the overlapping OTUs between Chinese and Africans Abundance in Group 1: decreased abundance in African citizens…

Svetlana Ugarcina Perovic (15:37:22) (in thread): > Experiment 2 deleted.

adekemi balogun (15:39:36) (in thread): > Thank you so much

Svetlana Ugarcina Perovic (15:58:23) (in thread): > @inyang john, I checked it again and there is no request in the queue, that means all requests have been approved.

Svetlana Ugarcina Perovic (15:59:46) (in thread): > Please see above the steps 1-3.

USLACKBOT (16:19:10): > This message was deleted.

Mildred Anashie (16:20:44) (in thread): > Hello@inyang johnPlease what do you mean by highlight?

Mildred Anashie (16:21:44) (in thread): > Hi@Adeshile OluwatosinI’msure it would be sent

Adeshile Oluwatosin (16:22:21) (in thread): > She has dropped it already > Thank you

Aleru Divine (16:22:21) (in thread): > @inyang johndo you mean to identify your signatures?

Mildred Anashie (16:22:42) (in thread): > Yea > > Was about too delete my response > Just saw it

inyang john (16:23:11) (in thread): > @Aleru Divineyeah

Adeshile Oluwatosin (16:23:17) (in thread): > @inyang johnI personally used pdf highlighter

Aleru Divine (16:23:42) (in thread): > Please share a link to the study/article@inyang john

Precious Orakwe (16:27:14) (in thread): > :hugging_face::hugging_face::hugging_face:

Precious Orakwe (16:31:17) (in thread): > This is good, thanks@Mildred Anashie

Chris Awoke (16:33:56): > As we work through the study curation process for BugSigDB, I understand the importance of maintaining attention to detail. One tool that has been particularly helpful for me in keeping track of online resources is the Glasp Web Highlighter. It’s a free Chrome extension that allows for easy highlighting and note-taking on web content. > > If you’d like to try it out, here’s the link:https://chromewebstore.google.com/detail/glasp-web-highlighter-pdf/blillmbchncajnhkjfdnincfndboieik - Attachment (chromewebstore.google.com): Glasp Web Highlighter: PDF & Web Highlight - Chrome Web Store > AI-powered Web Highlighter for Websites, PDF, and YouTube videos. YouTube Summary with ChatGPT, Claude, and Gemini.

Aleru Divine (16:35:11) (in thread): > @inyang johnin general,signaturesrefer tobacterial species or fungi.In BugSigDB, we curate the differential abundance of these signatures > > This is where the concepts of ‘increase’ and ‘decrease’ come into play.Increase/Decrease: refers to whether a species is found in higher numbers (increase) or lower numbers (decrease) when compared to how it usually appears or compared to a reference group.

Mildred Anashie (16:35:32) (in thread): > I’llbe sure to check it out > > Thank you@Chris Awoke

Aleru Divine (16:38:19) (in thread): > Wow! Thanks@Chris AwokeThis is going to come in very handy. > > Off to installllllllllll:woman-running::dash:

Kate Rasheed (16:52:43) (in thread): > Thank you for sharing@Chris Awoke

Adeshile Oluwatosin (17:25:44) (in thread): > Thank you@Chris Awoke:hugging_face:

inyang john (17:26:51) (in thread): > @Svetlana Ugarcina PerovicI have this issue of duplicated experiment 1 and I can’t see my signatures > Here is my link. Thank youhttps://bugsigdb.org/Study_1126 - Attachment (BugSigDB): The skin microbiome stratifies patients with cutaneous T cell lymphoma and determines event-free survival - BugSigDB > Mycosis fungoides (MF) is the most common entity of Cutaneous T cell lymphomas (CTCL) and is characterized by the presence of clonal malignant T cells in the skin.The role of the skin microbiome for MF development and progression are currently poorly understood.

inyang john (17:27:22) (in thread): > Thank you

BOLARINWA AISHAT (17:42:59) (in thread): > Thank you so much@Chris Awoke

BOLARINWA AISHAT (18:00:36): > Hello everyone. > I just completed my first contribution. > > If you seem lost, overwhelmed or don’t know where to start from > > Read this article :https://cunysph.az1.qualtrics.com/CP/File.php?F=F_09C6LErMWXUBOVUlike you’re preparing for an exam and > > Answer the questions here :https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHEAnd boom, you’ve completed your first contribution. Don’t forget to record it on your outreachy dashboard - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Ruqayyah (18:17:06) (in thread): > Thank you so much for this. I was literally lost and didn’t know where to even start from. > I’ll follow on this and wouldn’t mind any future information.

Mildred Anashie (18:34:55) (in thread): > Hi@RuqayyahThe article for the first contribution is annotated (most of the information you need for the contribution has been highlighted already) > But yea reading the article like@BOLARINWA AISHATsays would be very helpful > > Also pay attention to the instructions on the form

Adeshile Oluwatosin (18:45:40) (in thread): > @Ruqayyahyou can check this; > To get started, join #bugSigDB channel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Samuel Ogunleye (22:54:56) (in thread): > Sometimes, it doesn’t reflect in real-time, you will have to wait for some minutes.

Ibizugbe Merit (23:36:39): > Hello@Svetlana Ugarcina Perovicwhile adding a study, I just noticed the PMID number brought out a new study design different from the study I was originally assignedhttps://bugsigdb.org/Study_1127Here’sthe link to the study,just help me go through it. If youdon’tget my question.I’dreally appreciate your assistance - Attachment (BugSigDB): Spiral tibial fractures of children: a commonly accidental spiral long bone fracture - BugSigDB > Pediatric training in child abuse has consistently emphasized a strong association between nonaccidental injuries and spiral fractures of long bones.

2024-10-04

Inimfon Ebong (01:59:01): > Hello Everyone, > I am Inimfon Ebong a Pharmacist with experience in public writing, I am happy to be a part of this work. > Sorry this is coming so late i was having technical issues but thankfully it has been resolved. I have seen all the pinned messages and will go through all the tips and explanation videos as this is my first time working with open source materials.

inyang john (01:59:48) (in thread): > You’rewelcome Inimfon Ebong

inyang john (02:00:21): > Always stay positive:100: - File (JPEG): IMG_6338

Kate Rasheed (02:00:58) (in thread): > You’re welcome Inimfon. If you need any further help, don’t hesitate to reach out. We are always happy to help.

BOLARINWA AISHAT (02:20:45) (in thread): > Welcome on board

Svetlana Ugarcina Perovic (02:28:41) (in thread): > @inyang johnI see you are curating. Does that mean your account was approved and there is no problem to report?

Svetlana Ugarcina Perovic (02:29:30) (in thread): > @inyang johnplease follow instructions above.

inyang john (02:31:49) (in thread): > @Svetlana Ugarcina PerovicGood morning. I did it manually and still nothing. I don’t know if I should input the information again as it could be network issue.

Svetlana Ugarcina Perovic (02:34:01) (in thread): > https://bugsigdb.org/Study_1126/Experiment_1/Signature_1https://bugsigdb.org/Study_1126/Experiment_1/Signature_2 - Attachment (BugSigDB): Study 1126/Experiment 1/Signature 1 > Source: fig 2b Description: Differential abundance analysis of microbial species for N = 65 metagenomic samples. Abundance in Group 1: increased abundance in Mycosis… - Attachment (BugSigDB): Study 1126/Experiment 1/Signature 2 > Source: fig 2a Description: Differential abundance analysis of microbial species for N = 65 metagenomic samples. Abundance in Group 1: decreased abundance in Mycosis…

Aleru Divine (02:34:45) (in thread): > Welcome@Inimfon Ebong:hugging_face:

inyang john (02:38:22) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (02:41:07) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727966772447019Btw,@inyang johnI see you are curating. Does that mean your account was approved and there is no problem to report? - Attachment: Attachment > please @Svetlana Ugarcina Perovic my Bugsigbd account has not been confirmed. and i applied since yesterday.

Adeshile Oluwatosin (02:42:40) (in thread): > Welcome:hugging_face:

inyang john (02:43:51) (in thread): > Yeah it was@Svetlana Ugarcina PerovicThank you once again:pray:

Svetlana Ugarcina Perovic (02:44:45) (in thread): > Ok, please when we report the issue and when solved it we report that as well, thank you.

inyang john (02:47:18) (in thread): > Yes Ma@Svetlana Ugarcina Perovic:saluting_face:

Monisa Hasnain (02:48:15): > hello every one > I am monisa hasnain, with the strong background of over 10 years as a software developer/ engineer. currently, I switched my career as a data professional. I need help to start participating in “Microbiome Study Curation” . i missed the meetings . any help would be appreciated. > thanks

Aleru Divine (02:50:42) (in thread): > Hi@Monisa Hasnain, welcome:hugging_face:So all the information you needto begin contributingis here in this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94Just go through it carefully. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Aleru Divine (02:51:42) (in thread): > Also go through the channel and the pinned messages.A lot of resources have been shared.

Aleru Divine (02:52:47) (in thread): > Take your time, no rush, prioritize quality over quantity.

Aleru Divine (02:53:59) (in thread): > I already completed my first contribution and I made a list of tips that can be helpfulhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Monisa Hasnain (03:06:24) (in thread): > thanks for your reply. ill go through and get back for further help. > could you help me with mentor thing. i need to know if i have to select a mentor and stick with him?

Svetlana Ugarcina Perovic (03:17:41): > Good morning:potted_plant:Today I have a special invitation for you:join us next week at MVIF (Microbiome Virtual International Forum), a virtual, free and inclusive alternative to a traditional multi-day microbiome conference.https://www.microbiome-vif.org/en-US/-/future-events/mvif32-78-9-october-2024We’ve been organizing this event monthly since 2021, you can see recordings here:https://www.youtube.com/@MicrobiomeVIF/playlists - Attachment (microbiome-vif.org): MVIF.32 | 7/8 & 9 October 2024 > with Keynote talk by Prof. Susan Bullman

Ibizugbe Merit (03:25:05) (in thread): > You’rewelcome@Inimfon Ebong

Ibizugbe Merit (03:26:42) (in thread): > The mentors are on here too…@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Scholastica UruaYou could reach out to any of them

Aleru Divine (03:45:01) (in thread): > @Monisa Hasnainwedon’tget to select mentors,it’sgeneral, whatever issues you have or questions you just tag them on the channel.

Svetlana Ugarcina Perovic (03:46:08) (in thread): > @Ibizugbe Meritit seems that you did not enter the correct PMID of your paper.

Svetlana Ugarcina Perovic (03:47:42) (in thread): > Please do post a link to your paper when asking questions

Svetlana Ugarcina Perovic (03:47:45) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/404 - Attachment: #404 Oral and gut microbial profiling in periodontitis and Parkinson’s disease > Oral and gut microbial profiling in periodontitis and Parkinson’s disease – Ekin Yay – Journal of Oral Microbiology
> https://www.tandfonline.com/doi/full/10.1080/20002297.2024.2331264

Svetlana Ugarcina Perovic (03:48:27) (in thread): > Solution:https://pubmed.ncbi.nlm.nih.gov/?term=Oral+and+gut+microbial+profiling+in+periodontitis+and+Parkinson%E2%80%99s+disease - Attachment (PubMed): Oral and gut microbial profiling in periodontitis and Parkinson’s disease - Search Results - PubMed > Oral and gut microbial profiling in periodontitis and Parkinson’s disease - Search Results - PubMed

Inimfon Ebong (03:50:06) (in thread): > Thank you:hugging_face:I’ll reach out if I need any clarifications

Chris Awoke (03:56:36) (in thread): > Awesome:smiling_face_with_3_hearts:Thanks for sharing,@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (03:57:23) (in thread): > Welcome:hugging_face:

Adeshile Oluwatosin (03:57:43) (in thread): > I will be there:thumbsup:

Adeshile Oluwatosin (03:58:14) (in thread): > Welcome@Inimfon Ebong:hugging_face:

Mildred Anashie (04:04:52) (in thread): > Welcome@Monisa Hasnain:blush:

Kate Rasheed (04:05:55) (in thread): > Thank you for sharing. Looking forward to it.

Mildred Anashie (04:06:13) (in thread): > Thanks for the invitation@Svetlana Ugarcina PerovicGood morning:teapot:

Kate Rasheed (04:10:33) (in thread): > @Svetlana Ugarcina PerovicWhat organization should we register under? Should we choose anyone as it is a mandatory fill.

Aleru Divine (04:14:44) (in thread): > Thank you so much@Svetlana Ugarcina Perovicfor the invitation.

Ibizugbe Merit (04:15:25) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Ibizugbe Merit (04:15:53) (in thread): > :pushpin:

Oluwatomisin Omojokun (04:16:48) (in thread): > Thanks@Svetlana Ugarcina Perovic

Rahila-me (04:18:30) (in thread): > Thanks for the invite:smiling_face_with_3_hearts::smiling_face_with_3_hearts:

Adeshile Oluwatosin (04:28:54) (in thread): > @Monisa Hasnaincheck the recording;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727978011885959 - Attachment: Attachment > Thank you to everyone who attended today’s meeting. Here is the recording. Apologies that I forgot to start recording until 10 minutes in (please someone remind me next week to start recording!). Looking forward to out next meeting.

Chinwendu Joy Enyidiegwu (04:38:44) (in thread): > sure. > thank you for sharing.@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:02:57) (in thread): > @Kate Rasheedyou can put outreachy

Kate Rasheed (05:08:10) (in thread): > Alright@Svetlana Ugarcina Perovic. Thank you.

Mildred Anashie (05:16:29): > Good morning everyone:blush:Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape@Scholastica UruaPlease I have a question regarding the paper I’m currently curating > > One of the taxas in Figure 2E for one of the comparisons Hispanic Ms vs Control is S24-7 > > I checked for it on the taxonomy browser and I found family S24-7 instead, with taxonomy ID 2005473 and common name Muribaculaceae > > I’m unsure if I can substitute this for the S24-7 recorded in the paper > > Link to the articlehttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC6841666/Thank you:pray: - Attachment (PubMed Central (PMC)): Gut microbiome of treatment-naïve MS patients of different ethnicities early in disease course > Although the intestinal microbiome has been increasingly implicated in autoimmune diseases, much is unknown about its roles in Multiple Sclerosis (MS). Our aim was to compare the microbiome between treatment-naïve MS subjects early in their disease …

Mildred Anashie (05:17:41) (in thread): > An image showing the taxa I found - File (JPEG): IMG_1147

Aleru Divine (05:21:40) (in thread): > @Mildred Anashieyes you can. Actually S24-7 is now known as Muribaculaceae. > > Found it on Wikipediahttps://en.wikipedia.org/wiki/MuribaculaceaeHere’s a message from<@UBNSEMS3S>“unrelated and related:sweat_smile:”https://community-bioc.slack.com/archives/C04RATV9VCY/p1698177815616049?thread_ts=1698080347.724249&channel=C04RATV9VCY&message_ts=1698177815.616049 - Attachment: Muribaculaceae > Muribaculaceae, previously known as S24-7, is a family of bacteria within the order Bacteroidales. Muribaculaceae is a prevalent and abundant bacterial component of the gut microbiome of mammals. > In 2016, family S24-7 was studied in-depth and given the name “Homeothermaceae”, however, as no isolates were provided as type material, the name was not validated. > The first isolated member of this family was Muribaculum intestinale as part of the mouse intestinal bacterial collection (miBC) in 2016. However, validation of the family only occurred in 2019 after detailed analysis of this family, along with description of Duncaniella and Paramuribaculum, two additional genera within this family. > In a recent study on mice, members of the family Muribaculaceae were shown to be major utilisers of mucus-derived monosaccharides in the gut. - Attachment: Attachment > Please only curate the lowest taxonomic rank. That is to say in this case for the first row do not curate Bacteroidetes, bacteroidia, or bacteroidales–instead curate S24-7 which is a family better known as muribaculaceae (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2005473&lvl=3&lin=f&keep=1&srchmode=1&unlock)

Mildred Anashie (05:22:47) (in thread): > This is quite helpful > > Thank you@Aleru Divine:blush:

Aleru Divine (05:23:23) (in thread): > Anytime!

Princess Rehoboth Asuelimen (05:26:09): > Hello everyone, my name is Princess Asuelimen. I’m excited to be here. Looking forward to contributing to the Bioconductor project and learning a lot on this platform.

Mildred Anashie (05:29:19) (in thread): > Hi@Princess Rehoboth Asuelimen:hugging_face:

Aleru Divine (05:29:45) (in thread): > Hi@Princess Rehoboth Asuelimen,
> welcome:hugging_face:Looking forward to collaborating with you too:blush:Please go through this welcome message to get started with contributinghttps://github.com/waldronlab/BugSigDBcuration/issues/94

Princess Rehoboth Asuelimen (05:38:13) (in thread): > Thank you so much, and I look forward to collaborating with you as well.

Rahila-me (05:43:16) (in thread): > Hello princess welcome and happy contributions

Adeshile Oluwatosin (05:45:26) (in thread): > Welcome:hugging_face:To get started, join #bugSigDB channel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Kate Rasheed (06:40:28): > Good day everyone. > > I found this collection of links that would be really helpful to us as curators. It captures what the human Microbiome is about alongside the different types of sequencing. > > It’s one of the materials shared on the GitHub welcome page. > > Happy reading:hugging_face:https://docs.google.com/document/u/0/d/1cpY8RoOHjJ_oxkDRGwlpqL-I29IN9B5BifhZIlqTjhE/mobilebasic

inyang john (06:57:52): > I’d like to delete this experiment please.https://bugsigdb.org/Study_1126/Experiment_2 - Attachment (BugSigDB): Study 1126/Experiment 2 > .

Chris Awoke (07:12:30): > Hello,@Svetlana Ugarcina Perovic, > > I would appreciate some guidance on how to keep track of the changes I’m making in the study I’m curating. It seems the system isn’t tracking them, or I might be missing something. > > For instance, I added two signatures together, but I can’t see them reflected as I do in other people’s work. > > Here’s the link to the article:https://peerj.com/articles/14449/https://bugsigdb.org/Study_1124 - Attachment (PeerJ): Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries > Background Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). The objective of this study was to characterize the vaginal microbiomes across a more diverse intercontinental group of women (N = 151) of different ethnicities (African American, African Kenyan, Afro-Caribbean, Asian Indonesian and Caucasian German) using 16S rRNA gene sequence analysis to determine their structures and offer a comprehensive description of the non-Lactobacillus dominant CSTs and subtypes. Results In this study, the bacterial composition of the vaginal microbiomes differed significantly among the ethnic groups. Lactobacillus spp. (L. crispatus and L. iners) dominated the vaginal microbiomes in African American women (91.8%) compared to European (German, 42.4%), Asian (Indonesian, 45.0%), African (Kenyan, 34.4%) and Afro-Caribbean (26.1%) women. Expanding on CST classification, three subtypes of CST IV (CST IV-A, IV-B and IV-C) (N = 56, 37.1%) and four additional CSTs were described: CST VI Gardnerella vaginalis—dominant (N = 6, 21.8%); CST VII (Prevotella—dominant, N = 1, 0.66%); CST VIII (N = 9, 5.96%), resembling aerobic vaginitis, was differentiated by a high proportion of taxa such as Enterococcus, Streptococcus and Staphylococcus (relative abundance [RA] > 50%) and CST IX (N = 7, 4.64%) dominated by genera other than Lactobacillus, Gardnerella or Prevotella (e.g., Bifidobacterium breve and Anaerococcus vaginalis). Within the vaginal microbiomes, 32 “taxa with high pathogenic potential” (THPP) were identified. Collectively, THPP (mean RA ~5.24%) negatively correlated (rs = −0.68, p < 2.2e−16) with Lactobacillus species but not significantly with Gardnerella/Prevotella spp. combined (r = −0.13, p = 0.1). However, at the individual level, Mycoplasma hominis exhibited moderate positive correlations with Gardnerella (r = 0.46, p = 2.6e−09) and Prevotella spp. (r = 0.47, p = 1.4e−09). Conclusions These findings while supporting the idea that vaginal microbiomes vary with ethnicity, also suggest that CSTs are more wide-ranging and not exclusive to any particular ethnic group. This study offers additional insight into the structure of the vaginal microbiome and contributes to the description and subcategorization of non-Lactobacillus-dominated CSTs. - Attachment (BugSigDB): Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries - BugSigDB > BACKGROUND: Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV).

Mildred Anashie (07:14:51) (in thread): > Hi@Chris AwokeCheck this outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&channel=C04RATV9VCY&message_ts=1727957860.907319 - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Aleru Divine (07:16:19) (in thread): > Was just about to share that@Mildred Anashie

Chris Awoke (07:17:58) (in thread): > Thanks so much,@Mildred Anashieand@Aleru DivineI’ll go through it now.

Mildred Anashie (07:27:30) (in thread): > Also, I just tried using my phone to do a quick demo on how I easily do it, that seems to be like a short cut for me:joy:(Others might disagree) > I hope it’s clear enough for you > > Once I go to the contributions I’ve made, everything appears there and I just click on what I might have been searching for - File (MPEG 4 Video): copy_4A25B0A6-6CCF-4EFC-9461-AB7256C9EEC6

Chris Awoke (07:37:03) (in thread): > While this approach works:https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber], you can replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values. > > However, I was wondering if there might be a more seamless way to get everything in a single path (URL). > > What do you think,@Svetlana Ugarcina Perovic? > > If it’s a bug in the website’s codebase, is there any way I can help fix it? I believe I should be able to, depending on the language the website is built with.

Svetlana Ugarcina Perovic (08:19:45) (in thread): > Deleted.

Svetlana Ugarcina Perovic (08:21:29) (in thread): > @Chris Awokewe are aware of this bughttps://github.com/waldronlab/BugSigDB/issues/221and our colleagues have been working on it. > cc<@UBNSEMS3S> - Attachment: #221 Study 784 Experiments not showing but exist > https://bugsigdb.org/Study_784 shows no experiments on the page but they do exist: https://bugsigdb.org/Study_784/Experiment_1 > > I tried refreshing the page under … > Refresh but that did not resolve the issue.

Chris Awoke (08:28:46) (in thread): > Thank you so much,@Svetlana Ugarcina Perovic. > > I’m glad to hear that the bug is being fixed! If any assistance is needed, I’d be happy to help the team involved. > > Thanks again for the prompt response.

U02CNMR4YEA (08:50:30): > @Svetlana Ugarcina PerovicGood day! My apologies but I erroneously entered a signature twice because it was not showing in the system. Would you please be so kind as to delete the following: Study 1103, Expt 1, Signature 3? Thank you!

Svetlana Ugarcina Perovic (08:54:57) (in thread): > https://bugsigdb.org/Study_1103/Experiment_1/Signature_3deleted. - Attachment (BugSigDB): Study 1103/Experiment 1/Signature 3 > Source: Paragraph on page 1990 Description: Linear Discriminant Analysis Effect Size (top 5 relatively abundant taxa at the family and genus levels) Abundance in…

U02CNMR4YEA (09:17:14) (in thread): > Wow! You are fast:grinning:. Thank you and I hope you have a wonderful day!

U02CNMR4YEA (09:53:43) (in thread): > One more quick question, please- I have curated Expt 3 as well. When I pull the data into R, Expt 1 and 2 are showing up with the signatures but Expt 3 has “NA” as follows: - File (PNG): image.png

U02CNMR4YEA (09:53:55) (in thread): > Any thoughts?

Svetlana Ugarcina Perovic (09:55:20) (in thread): > <@UBNSEMS3S>please take a look at this issue, thanks!

Kate Rasheed (10:12:41): > Good day@Svetlana Ugarcina Perovic<@UBNSEMS3S>I am having a little issue with Signature 2. In the article I am curating, just one signature was stated for having a decreased abundance. However, when I checked the supplementary table, I discovered some others. > > In filling the taxa, I’m confused if I should stick to the signature mentioned in the article or I should list all the signatures with decreased abundance as seen in the supplementary table. > > Here is my article:https://www.nature.com/articles/s41598-024-72057-z#citeasHere is the supplementary table:https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-024-72057-z/MediaObjects/41598_2024_72057_MOESM2_ESM.xlsx - Attachment (Nature): Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis > Scientific Reports - Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis

Mildred Anashie (10:14:08) (in thread): > Hello@Kate RasheedI think you should record all the taxas mentioned > > What you can do in my opinion is check if the one mentioned in the article is mentioned in supplementary table and you then focus on the supplemental

Kate Rasheed (10:14:51) (in thread): > @Mildred AnashieMentioned in the article or supplementary table?

Aleru Divine (10:16:39) (in thread): > They can mention/talk about one signature in the paper sometimes and then list the rest in a figure or in the supplemental material. You’ll have to curate all that are significant.

Mildred Anashie (10:16:51) (in thread): > All the significant taxas mentioned for a particular comparison should be recorded@Kate Rasheed

adekemi balogun (10:22:09): > Hello@Svetlana Ugarcina Perovicplease i’m in need of your help cause i’m kind of confused/stuck, the topic of my paper doesn’t exactly have a particular condition so i’m really confused on what the condition should be - Attachment (BugSigDB): Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese - BugSigDB > OBJECTIVE: This study intended to determine the associations between gut microbiota and glucose response in healthy individuals and analyze the connection between the gut microbiome and glucose-metabolism-related parameters.

Mildred Anashie (10:31:02) (in thread): > I see you used Glucose metabolism measurement@adekemi balogunI’m thinking that should be okay because of this excerpt from the study “This study intended to determine the associations between gut microbiota and glucose response in healthy individuals and analyze the connection between the gut microbiome and glucose-metabolism-related parameters”.

Cate Ouma (11:23:43): > Hello Team, I have a question. If the study had an initial sample size and some subjects were excluded in the final analysis, what number should I use in the sample size? Here is the link to the study:https://www.nature.com/articles/s41467-024-51464-w - Attachment (Nature): Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia > Nature Communications - Here, the authors profile the gut microbiome of Ethiopian children suffering from acute and prolonged diarrhea, showing the latter group to exhibit a higher degree of…

Aleru Divine (11:24:39) (in thread): > It’llbe the final sample size@Cate Ouma

Mildred Anashie (11:24:56) (in thread): > Hi@Cate OumaIn my opinion the final sample size used for the experiment/study > > Those excluded are already not part of the study

Cate Ouma (11:25:35) (in thread): > Noted. Thank you

abdulwasiu maryam (13:57:33): > Good day everyone, I am Maryam, A microbiologist and a Software developer. i would be glad to contribute to ‘Microbiome Study Curation’

Cate Ouma (13:58:01): > Hi,@Svetlana Ugarcina Perovic, when adding my study, I have used the auto option in Citation. However, when I save the page, information about the paper isn’t populated. Should I proceed, or do I need to manually enter the info? - File (PNG): image.png

Kate Rasheed (13:58:11) (in thread): > Great to have you here. Kindly engage the pinned messages for helpful tips.

Svetlana Ugarcina Perovic (13:58:37) (in thread): > you should add the PMID

Samuel Ogunleye (13:58:38) (in thread): > Use the Pubmed link to auto generate it

Kate Rasheed (13:58:39) (in thread): > Enter the pimd. It should work

Cate Ouma (13:59:08) (in thread): > Okay. Thank you

Cate Ouma (14:01:44): > @Svetlana Ugarcina Perovic, kindly delete thishttps://bugsigdb.org/Study_1104 - Attachment (BugSigDB): - BugSigDB > .

Ibizugbe Merit (14:10:54) (in thread): > Welcome@abdulwasiu maryam

Svetlana Ugarcina Perovic (14:11:15) (in thread): > This study andsignaturedeleted.

aziz gueye (14:18:44): > Hi, I’m new to this group. Actually, I need to contribute to the project on microbiome conservation. My problem is that I don’t know how to make a contribution, and I really need your help. Thank you!

Mildred Anashie (14:20:38) (in thread): > Hi@aziz gueye:blush:Welcome to the group > I’ll share a few resources that can help you get started and if you have any questions feel free to ask

Aleru Divine (14:21:21) (in thread): > Welcome@aziz gueye:hugging_face:So all the information you need to begin contributing is here in this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94Just go through it carefully. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

abdulwasiu maryam (14:22:05) (in thread): > Thanks, I will go through the pinned message.

Adeshile Oluwatosin (14:23:19) (in thread): > Welcome:hugging_face:To get started, join #bugSigDB channel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Mildred Anashie (14:23:29) (in thread): > @Aleru Divineshared one already > > But if you need any more information you can go through this, I find it to be more comprehensivehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728035126462569?thread_ts=1728033969.827949&channel=C04RATV9VCY&message_ts=1728035126.462569 - Attachment: Attachment > Welcome :hugging_face: > > To get started, join #bugSigDB channel ! > • Review the intial information; Look through this link: https://github.com/waldronlab/BugSigDBcuration/issues/94 > • Make Your first contribution; Follow the guideline provided here: https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > • Ensure you record a first contribution via outreachy link; https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > • Follow this steps to proceed to the second contribution; https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!!

Adeshile Oluwatosin (14:26:20) (in thread): > Welcome@abdulwasiu maryam:hugging_face:

Cate Ouma (14:57:48): > Question: My paper mentions that Alpha diversity measures were based on the number of observed zOTUs and Shannon diversity metrics. Since zOTU represents the number of unique operational taxonomic units (zOTUs) observed in each sample, can I use the “richness” option in the BugSigDB page to represent it? This is the link to the paper:https://www.nature.com/articles/s41467-024-51464-w - Attachment (Nature): Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia > Nature Communications - Here, the authors profile the gut microbiome of Ethiopian children suffering from acute and prolonged diarrhea, showing the latter group to exhibit a higher degree of…

Aleru Divine (14:59:57) (in thread): > Yes you can use richness. > Observed OTUs/Features/Species represents richness.

Cate Ouma (15:00:35) (in thread): > Thank you@Aleru Divine

aziz gueye (15:02:02) (in thread): > For the review, do I need to use the annotated article by Shrode in PDF format, or can I find and use resources online?

aziz gueye (15:02:37): > For the review, do I need to use the annotated article by Shrode in PDF format, or can I find and use resources online?

Cate Ouma (15:04:39) (in thread): > You should use the annotated version, since the highlighted bits are important

Aleru Divine (15:04:42) (in thread): > @aziz gueyeYes, the annotated article. > > Everything you need for the first contribution is in there. No need for external resource. I didn’t need one.

inyang john (15:17:00) (in thread): > The annotated article is better

adekemi balogun (15:17:12) (in thread): > Hm, this could be the condition?@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)could you kindly share more light

Zara Adwan (17:11:53): > Hello everyone! > My name is Zara and I’m a biomedical and data scientist > I’m excited to contribute to this project

Ibizugbe Merit (17:14:12) (in thread): > You’re welcome@Zara AdwanGo through the pinned message by@Svetlana Ugarcina Perovicto get acquainted and get started…..It’s really exciting to be here.:face_with_hand_over_mouth:

Samuel Nnanna (17:34:28): > Hello Everyone, i’m Samuel. Looking forward to getting started

Ibizugbe Merit (17:35:18) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Kate Rasheed (17:36:00) (in thread): > You are welcome Samuel. Please loook through the pinned messages for tips on how to navigate.

Ibizugbe Merit (17:36:58) (in thread): > You’rewelcome@Samuel NnannaGo through this message from one of our mentors to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727797333337539 - Attachment: Attachment > Welcome to the Outreachy contribution period! > > We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > > We’re looking forward to working with you! > @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Samuel Nnanna (17:38:35) (in thread): > thank you@Ibizugbe Merit

Ibizugbe Merit (17:41:32) (in thread): > You’rewelcome….I’mhappy I could help.

Ibizugbe Merit (17:48:19) (in thread): > Well done guys:blush:The team work on here is really great

Mildred Anashie (17:49:04) (in thread): > Hi Zara > > Welcome:hugging_face:

Mildred Anashie (17:49:24) (in thread): > Hi Samuel > > Welcome:hugging_face:

Samuel Nnanna (18:10:39) (in thread): > I’ll familiarize myself with the Getting started Tips. Thank you for the warm welcome and assistance

Mildred Anashie (18:12:49) (in thread): > Let me try to explain@adekemi balogunHopefully I do it right:sweat_smile::crossed_fingers:In research, a conditionrefers to a specific state of health,which can include diseases, disorders, or any identifiable health issue or physiological process.A condition is what researchers are investigating to better understand, prevent, manage, or treat either through an analysis or intervention > > So, basically it is what is being studied in the paper not necessarily a disease condition.In some cases, the condition could be a broader category like metabolic disordersor specific to a subset of the population, such as asthma in children.In this paper the condition of interest does not entail a disease, but refers to the physiological process of glucose metabolism. > > I’m also attaching something from the curation policy that talks about condition. > Do let me know if this is clear to you, if not we might need to wait for our mentors because they would explain it better - File (JPEG): IMG_1161

Mildred Anashie (18:17:07) (in thread): > Okay@Samuel NnannaIfyou need any more information you can go through thisput together by@Adeshile Oluwatosinhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728035126462569?thread_ts=1728033969.827949&channel=C04RATV9VCY&message_ts=1728035126.462569 - Attachment: Attachment > Welcome :hugging_face: > > To get started, join #bugSigDB channel ! > • Review the intial information; Look through this link: https://github.com/waldronlab/BugSigDBcuration/issues/94 > • Make Your first contribution; Follow the guideline provided here: https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > • Ensure you record a first contribution via outreachy link; https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > • Follow this steps to proceed to the second contribution; https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugSigDB channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!!

Adeshile Oluwatosin (18:26:39) (in thread): > Welcome@Zara Adwan:hugging_face:

Adeshile Oluwatosin (18:27:18) (in thread): > Welcome@Samuel Nnanna:hugging_face:

aziz gueye (19:15:35): > after reading the article annotate now I must answer the questions asked inhttps://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Cate Ouma (19:23:51) (in thread): > Yes, then post the link to the form in Outreachy as your contribution

Adeshile Oluwatosin (19:23:54) (in thread): > Yes you must, ifthat’swhat you are asking

Adeshile Oluwatosin (19:24:20) (in thread): > Carefully go through it to fill it accurately

Adeshile Oluwatosin (19:33:00) (in thread): > Follow this guideline;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

aziz gueye (19:41:26): > do we know we need software to answer questions I think everything is in the document I speak French, it’s sometimes difficult to understand

aziz gueye (19:47:11) (in thread): > do we know we need software to answer questions I think everything is in the document I speak French, it’s sometimes difficult to understand

aziz gueye (19:59:27): > do we know we need software to answer questions I think everything is in the document I speak French, it’s sometimes difficult to understand

Adeshile Oluwatosin (20:08:17) (in thread): > Could you please clarify what you need directions on?

Adeshile Oluwatosin (20:10:04) (in thread): > In the intial contribution, all answers are in the article > Focus on the annotated parts to make it easier.

aziz gueye (20:19:01) (in thread): > @Adeshile Oluwatosinthank you for your help

aziz gueye (20:22:09) (in thread): > I must make my contribution I ask is there any data analysis to be done in the questions

Adeshile Oluwatosin (20:26:36) (in thread): > You are welcome

Adeshile Oluwatosin (20:32:28) (in thread): > @aziz gueyeI dropped a guideline to follow already. > All you need to do after making your contribution is recording it via outreachy link

Adeshile Oluwatosin (20:37:11) (in thread): > @aziz gueyefollow these steps, a step at a time: > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > Please pay close attention to the instructions!!! > You can ask me any further questions - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Mildred Anashie (21:03:53) (in thread): > Yea@aziz gueyefollow the steps@Adeshile Oluwatosinhas shared and you are free to ask more questions if you have > > I’m willing to help

Kate Rasheed (21:05:52) (in thread): > We don’t need software to answer questions. You can use Google translations to translate the words to French for comprehensive understanding.

aziz gueye (22:00:41): > I think that after the quizzes, I should receive a link to assign but I received nothing

Samuel Ogunleye (22:01:51) (in thread): > Not at all. > After the quiz, you will need to go through the GitHub issues to indicate an interest in a paper.

Samuel Ogunleye (22:02:49) (in thread): > View the issues herehttps://github.com/waldronlab/BugSigDBcuration/issues

aziz gueye (22:03:43) (in thread): > but how do I register my contribution?

aziz gueye (22:06:20) (in thread): > I think that after the quizzes, I should receive a link to assign but I received nothing

Samuel Ogunleye (22:06:20) (in thread): > Go to the outreachy project and click on Bioconductor project(curating of papers), then you will see where you can record a contribution.

Samuel Ogunleye (22:07:10) (in thread): > For your ease, see the direct link herehttps://www.outreachy.org/outreachy-dec-2024-internship-cohort/communities/bioconductor/#microbiome-study-curation - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

aziz gueye (22:08:21) (in thread): > I have a link to insert, what link is it?

Samuel Ogunleye (22:14:10) (in thread): > Since it pertains to the first contribution, so attach the link to the quiz.

aziz gueye (22:20:04) (in thread): > this linkhttps://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Samuel Ogunleye (22:23:32) (in thread): > Yeah

2024-10-05

Adeshile Oluwatosin (01:37:20) (in thread): > @aziz gueyethe contribution link requested is;https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Aleru Divine (01:56:08) (in thread): > Welcome@Zara Adwan:hugging_face:

Aleru Divine (01:56:29) (in thread): > Welcome@Samuel Nnanna

Inimfon Ebong (02:06:07): > I have a question > is the quiz the first contribution I’m a little confused

Adeshile Oluwatosin (02:14:11) (in thread): > @Inimfon EbongYes, the quiz is the first contribution

Adeshile Oluwatosin (02:17:40) (in thread): > Could you specify what you need directions for?

Aleru Divine (02:18:33) (in thread): > Yes that’s the first contribution.@Inimfon EbongThe article is what we’re to study to answer the questions. The annotated parts provide answers to thequestions. > > So for the first contribution, we’re not exactly curating like shown in the tutorial video, I think that’s why it’s called “Mini-curation”

Samuel Nnanna (02:45:33) (in thread): > So the first contribution isn’t what we need to record on the outreachy project application page?@Adeshile Oluwatosinand@Aleru Divine

Inimfon Ebong (02:48:35) (in thread): > ok I’ve taken the quiz but what url do i submit - File (PNG): Screenshot 2024-10-05 074718.png

Inimfon Ebong (02:49:20) (in thread): > a link to fresh quiz or the link that says ive submitted

Adeshile Oluwatosin (02:50:25) (in thread): > @Samuel Nnannayou are recording both contributions

Adeshile Oluwatosin (02:50:38) (in thread): > But you need to record the intial contribution first

Adeshile Oluwatosin (02:50:50) (in thread): > Before you can record a final contribution

Samuel Nnanna (02:51:53) (in thread): > @Adeshile Oluwatosinalright thank you

Adeshile Oluwatosin (02:52:32) (in thread): > @Inimfon Ebongare you trying to record the first contribution?

Adeshile Oluwatosin (02:55:40) (in thread): > Ifit’sthe first contribution > The contribution link to be filled is;https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Samuel Nnanna (02:55:49) (in thread): > @Adeshile OluwatosinI have also completed the first task and i want to record that, but i have a couple questions: > > what would be the date the cntribution was accepted or merge? ( would it be the day of completion of task)? > > Is there a specific description for the contribution or is it custom filled basically applicant’s preference?

Adeshile Oluwatosin (02:57:25) (in thread): > @Samuel Nnannathe merged date is the date you submitted your contribution

Adeshile Oluwatosin (02:57:59) (in thread): > The description is custom filled > You can write a brief description on how you went about taking the quiz.

Samuel Nnanna (02:58:17) (in thread): > Ok thank you@Adeshile Oluwatosin

Adeshile Oluwatosin (02:58:37) (in thread): > You are welcome@Samuel Nnanna

Princess Rehoboth Asuelimen (03:04:00) (in thread): > Thank you so much. I appreciate it.:grin:

Adeshile Oluwatosin (03:04:51) (in thread): > You are welcome@Princess Rehoboth Asuelimen:blush:

Kate Rasheed (03:16:42): > Good day@Svetlana Ugarcina Perovic<@UBNSEMS3S>. Kindly help delete Study 1109. The article is curated in Study 1110.

Adeshile Oluwatosin (03:17:30) (in thread): > @Samuel Nnanna@Inimfon EbongIf you have successfully recorded your intial contribution. > Go ahead to request to curate an issue on github. > Tag a mentor > And add a note likeI’d like to curate this articleWait for the issue to be assigned to you before you commence curating.

Adeshile Oluwatosin (03:18:00) (in thread): > Let me know if you have any further issues.

Kate Rasheed (03:23:58): > Also<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Scholastica UruaWhen the NCBI is showing orange as seen in the image below, what’s the best thing to do? Leave it like that or use the bacteria family?@Mildred Anashie - File (JPEG): 1000644417.jpg

Aleru Divine (03:24:25) (in thread): > @Kate Rasheedhave you searched the signature using the taxonomy browser?https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi

Kate Rasheed (03:24:40) (in thread): > Yes I have. It isn’t found there.

Aleru Divine (03:26:34) (in thread): > Okay another thing I do is search directly on google. > > For example, I got this:****“Clostridium” cluster IV (now Ruminococcaceae) > **** - File (JPEG): IMG_1134

Samuel Nnanna (03:26:51) (in thread): > @Adeshile Oluwatosinthank you andI’vealready done that. Waiting to be assigned an article so I can begin . > > I guess after being assigned an article, I can proceed to requesting an account on bugsigdb yes?

Adeshile Oluwatosin (03:27:51) (in thread): > I was about to say this > Thank you@Aleru Divine

Kate Rasheed (03:29:07) (in thread): > Okkk. Thank you

Adeshile Oluwatosin (03:29:40) (in thread): > You can actually proceed to request an account on bugsigdb. > If you have any issues with this, you can reach out to@Svetlana Ugarcina Perovic

Aleru Divine (03:29:49) (in thread): > Funny enough “Ruminococcaceae” is “Oscillospiraceae”:sweat_smile:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216572&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Kate Rasheed (03:31:01) (in thread): > @Aleru DivineThat’s the family that Clostridium IV belongs to. Should I use the family instead of the bacteria name?

Samuel Nnanna (03:31:49) (in thread): > Alright

Adeshile Oluwatosin (03:37:04) (in thread): > No,@Aleru Divinecorrect me if I’m wrong

Aleru Divine (03:37:19) (in thread): > I found a resource that helps with thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697193924756799 - Attachment: Attachment > Hello @Levi Waldron I need clarification on this for NCBI clean up: > This person work is mark as incomplete do I have the right to complete it: https://bugsigdb.org/Study_572/Experiment_1/Signature_1 > About this clostridia group xiv > Clostridium clusters XIVa and IV are groups of bacteria that have been known as major players in the human microbiome(Hold et al., 2002;Frank et al., 2007; Manson et al., 2008). The designation of these clusters was first proposed by Collins et al. 1994 using 16S rRNA phylogeny. > > The genus Clostridium was a dumping ground for species with certain phenotypes (e.g., anaerobic endospore-forming). Clostridium clusters XIVa and IV do not represent formal nomenclature nor do they indicate a single taxa such as genus or family. Since 1994, Many of the originally designated species belonging to Clostridium clusters XIVa and IV have been reclassified into new genera. However, there are still misclassified, thereby holding old names, Clostridium species in these clusters. > > Since the definition of these two clusters is not consistent in recent publications and somewhat ambiguous, it is highly recommended to avoid using these terms. There are still many Clostridium species that require re-classification. Perhaps, the genome-based method can resolve this problem in the near future. > What happens to things like this (clostridia) Made some research and this and many more I saw.

Kate Rasheed (03:42:03) (in thread): > Thanks. It’s clarified

Aleru Divine (03:42:16) (in thread): > Alright:+1:

Kate Rasheed (04:00:51): > How about in this case where it is found in NCBI? I noticed about seven viruses with this situation, hence, I was thinking maybe it’s because they are viruses. Should I record this way? Or remove them from entry?@Svetlana Ugarcina Perovic - File (JPEG): IMG_20241005_085722_895.jpg

Aleru Divine (04:06:18) (in thread): > @Kate Rasheedwe curate bacterial signatures and fungal signatures in BugSigDB.No Viral signatures.Please still confirm.Also, if you find a signature(bacterial and fungal that is) in NCBI you can curate it.Paste the TaxID andit’llautomatically populate the name.

Kate Rasheed (04:07:25) (in thread): > This explains it. I thought as much as I noticed the viral signatures were bringing out the review sign.

Adeshile Oluwatosin (04:07:25) (in thread): > Noted@Aleru Divine

Precious Orakwe (04:20:16) (in thread): > Thanks@Aleru Divine

Adeshile Oluwatosin (04:38:55): > I wrote out these steps for people who might not know how to go about this in curating an article. > Navigating NCBI: > > When entering taxa in BugSigDB while editing signatures, and you cannot find the desired taxa in the dropdown list, follow these steps: > 1. Go to the NCBI Taxonomy Database to find the numeric NCBI taxon identifier. > > * Search for the taxa and check the taxonomy. > * Click on the taxa to locate the taxon ID. > > 1. Return to BugSigDB (experiment/signature). > 2. Input the taxon ID in the NCBI field. > 3. Click Save. The orange highlight should disappear. > Note: Always verify the taxon ID using these steps to ensure accuracy. Do not assume!

Aleru Divine (04:40:50) (in thread): > Thank you for taking the time to do this and sharing@Adeshile Oluwatosin:pray:

Adeshile Oluwatosin (04:41:24): > In the case where you search for it on NCBI, and you can’t find it. > Check it out on Google if the name has been changed.

Adeshile Oluwatosin (04:42:09) (in thread): > Welcome:hugging_face:

Esther Afuape (04:47:55) (in thread): > Good morning:sparkles:Please, always remember to check thediscussion pagewhen you can’t find a taxon on NCBI. This is because a lot of times, such a taxa has already been noted down in the discussion page by someone who came across it in the past. > You can find the discussion page by going to “help” (next to the search bar on bugSigDB), select “NCBI clean up” (number 5 on the contents list), select “signatures with missing NCBI ID”, you’ll see Discussion page on the first line. > > Here’s a direct link to it:https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_IDPlease go through this for an idea on how to resolve taxa issues:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189 - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in… - Attachment: Attachment > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonym on NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replace Escherichia coli with Escherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the 2-hour video of @U1LCB8WEA solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose:

Adeshile Oluwatosin (04:48:42) (in thread): > Thank you for this@Esther Afuape:pray:

Esther Afuape (04:53:50) (in thread): > Well done Tosin:sparkles:Discussion page first, then google.It’llsave you the time in many cases.

Aleru Divine (04:53:59) (in thread): > Thank you so much@Esther Afuape

Kate Rasheed (04:54:45) (in thread): > Thank you so much for this.

Adeshile Oluwatosin (05:06:12) (in thread): > Okay, noted mentor

Samuel Nnanna (05:09:33): > This is such a wonderful community, and I truly appreciate how we’re all supporting each other with relevant information. A big thank you to@Aleru Divine@Adeshile Oluwatosinfor all the guidance so far. > Another helpful tip as you move forward: After successfully completing the first task and recording your contribution, while waiting to be assigned an article, take the opportunity to read through the article you’d like to curate. This proactive approach will help you familiarize yourself with the content. Additionally, rewatch the video tutorials providedhereand go through an example of a completed BugSigDB curationhere. Doing this will not only build your confidence but also enhance your ability to contribute meaningfully to the BugSigDB project. > Remember, we’re all here to learn and hopefully do more, and no one expects anyone to know it all. If you have questions—no matter how simple or “ridiculous” they may seem—don’t hesitate to ask. Closed mouths don’t get fed, and this community is here to support you. Every question is an opportunity to learn. You’ve got this! - Attachment (YouTube): BugSigDB HOWTO videos > Videos describing the functionality and purpose of BugSigDB.org - Attachment (BugSigDB): Alteration of the fecal microbiota in Chinese patients with Parkinson’s disease - BugSigDB > Emerging evidences suggest that gut microbiota dysbiosis plays a role in Parkinson’s disease (PD).However, the alterations in fecal microbiome in Chinese PD patients remains unknown.This case-control study was conducted to explore fecal microbiota compositions in Chinese PD patients.

Adeshile Oluwatosin (05:17:07) (in thread): > I’malways here to assist:blush::hugging_face:

Aleru Divine (05:18:23) (in thread): > Really useful tips there@Samuel Nnannathanks! > My favorite thing about this community is the team spirit!:muscle::heart_hands:

Adeshile Oluwatosin (05:18:25) (in thread): > Nice write up btw:+1:

Samuel Nnanna (05:19:25) (in thread): > Naaahhh, y’all are the real heroes.

Chris Awoke (05:21:03) (in thread): > Thanks,@Samuel Nnannafor the useful tips, you shared.

Samuel Nnanna (05:22:23) (in thread): > The mentors also did a great job simplifying how to get started.

Ochogwu Emmanuel (05:34:19): > Hello everyone, my name is Emmanuel, I am an outreachy applicant. I am excited to contribute to this project as it align perfectly with my goals. Please I will need a work through or guidance on how to contribute effectively to this project.

Aleru Divine (05:36:51) (in thread): > Hi@Ochogwu Emmanuelwelcome:hugging_face::blush:Please go through this welcome message to get started with contributinghttps://github.com/waldronlab/BugSigDBcuration/issues/94It is very detailed but you can ask questions on whereyou’renot clear here in the channel. - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Aleru Divine (05:39:43) (in thread): > Having completed my first contribution, I share a few tips that I thought would be helpful here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Aleru Divine (05:43:24) (in thread): > I highly recommend you go through the Prep work section in the GitHub link I send earlier.There’sa lot of resources to help you understand the project, help you get started and videos (even more interesting).

Samuel Nnanna (05:45:22) (in thread): > Welcome Emmanuel:smiley:. Trust that all the information you need to get started can be found in the link@Aleru Divineforwarded. > > If you have any confusions, don’t hesitate to ask your questions.

Mildred Anashie (05:46:49) (in thread): > Thank you for the direct link@Esther Afuape:blush:I had forgotten how to get there

Adeshile Oluwatosin (05:51:53) (in thread): > Welcome@Ochogwu Emmanuel:hugging_face:

Mildred Anashie (05:53:50) (in thread): > Welcome to the community@Ochogwu EmmanuelDo follow the links shared to get started and you can reach out if you have any questions

Mildred Anashie (05:55:54) (in thread): > Thank you@Samuel Nnannafor the useful tips > > And thank you all for the spirit of collaboration, makes it so much easier:heart_hands:

Rahila-me (05:59:30) (in thread): > Welcome to the community@Ochogwu EmmanuelAlso always checkout the pinned messages, it will go a long way

Samuel Nnanna (06:02:51) (in thread): > For sure@Mildred Anashie

Ibizugbe Merit (06:04:09) (in thread): > Welcome@Ochogwu Emmanuel:hugging_face:

Svetlana Ugarcina Perovic (06:23:22) (in thread): > https://bugsigdb.org/Study_1109deleted. - Attachment (BugSigDB): - BugSigDB > .

Precious Orakwe (06:42:04) (in thread): > Welcome@Ochogwu Emmanuel

Aleru Divine (07:48:51): > Happy Saturday everyone:sparkles:I thought to share this with everyone cos I had fun while at it:sweat_smile:I saw this signature in the study I’m curatingNeglecta timonensis now**** “Neglectibacter timonensis”******** > > *******Study: https://bugsigdb.org/Study_1105It just had me thinking:thinking_face:why did they name itNeglecta?And then I thought maybe it was initially neglected:pleading_face:by the researchers. I’d really really love to know.Well I got to know that the genus name Neglectibacter comes from the Latin word “neglectus” meaning neglected or overlooked, likely referring to the fact that it was not identified earlier just like I had sort of predicted.:sweat_smile:ALAS! I satisfied my curiosityI also found out that some bacteria are named after peculiar traits, the scientists that discovered them, the local language, and from latinized versions of words, leading to names that may sound familiar or odd when try to translate or when we think about it outside the usual scientific context.Like:Thermus aquaticus ******* > *******Yersinia pestus ******* > *******Mediterraneibacter faecis(are you thinking what I’m thinking?) maybe it was first discovered around the Mediterranean region:sweat_smile:I had fun reading about all of this and I definitely have a favorite bacterium now -Neglectibacter timonensis ***:hugging_face:and I’m on a mission to know everything I can about it:sweat_smile: - Attachment (BugSigDB): The intensive physical activity causes changes in the composition of gut and oral microbiota - BugSigDB > This study aimed to compare the gut and oral microbiota composition of professional male football players and amateurs.Environmental and behavioral factors are well known to modulate intestinal microbiota composition.

Mildred Anashie (07:50:55) (in thread): > This sounds like you sure had a lot of fun curating this paper:sweat_smile:Thanks for sharing and Happy Saturday to you@Aleru Divine:heart_hands:

Aleru Divine (07:53:25) (in thread): > Thank you@Mildred AnashieI sure did:blush:

Adeshile Oluwatosin (07:58:19) (in thread): > @Aleru DivineI had fun while reading it as well:joy_cat::blush:Thanks once again for sharing

Aleru Divine (07:59:57) (in thread): > :blush:thank you@Adeshile Oluwatosin:sweat_smile:

Dorcas Samuel (08:32:11) (in thread): > Well-done@Aleru Divineyou made it fun to read

Aleru Divine (08:36:13) (in thread): > Thank you@Dorcas Samuel:blush:

Ibizugbe Merit (08:37:11) (in thread): > Well done@Aleru DivineGreat work:partying_face:

Aleru Divine (08:41:44) (in thread): > Thank you@Ibizugbe Merit

Chinwendu Joy Enyidiegwu (09:47:14): > Hello@Svetlana Ugarcina Perovichow are you doing. i mistakenly used the duplicate experiment button.:pray:kindly help delete experiment 2 from this study . thank youhttps://bugsigdb.org/Study_1104 - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > This study examines how the paternal gut microbiome, before conception, affects offspring development and behavior, an area less explored compared to maternal influences.

Svetlana Ugarcina Perovic (10:04:50) (in thread): > https://bugsigdb.org/Study_1104/Experiment_2deleted.

Chinwendu Joy Enyidiegwu (10:15:08) (in thread): > thank you

Precious Orakwe (10:44:20) (in thread): > @Aleru Divinethe name carry vibes

aziz gueye (11:06:00): > hi, for the second contribution what aspect should I take into account to succeed in my contribution

Mildred Anashie (11:07:34) (in thread): > Hi > > Has a paper been assigned to you?

inyang john (11:07:35) (in thread): > @Aleru Divinegave us tips earlier. Let me tag you

inyang john (11:08:23) (in thread): > @aziz gueye

Princess Rehoboth Asuelimen (11:08:47) (in thread): > Hi@aziz gueyeThis is how the second contribution is going to be graded. It may be of help.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

aziz gueye (11:09:10) (in thread): > yes I am assigned

Mildred Anashie (11:09:29) (in thread): > If yes > > Then you can start by going through the curation policylinkAnd watch the onboarding videoshttps://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=4 - Attachment (BugSigDB): Curation Policy > … - Attachment (YouTube): Adding a study to bugsigdb.org

Rahila-me (11:11:38) (in thread): > @aziz gueyewhen stuck always ask questions on the channel…you fellow contributors can be of great help also.

Aleru Divine (11:16:47) (in thread): > Hi@aziz gueye, I agree with@Mildred Anashie, going through the curation policy will be very helpful. It’ll give you an idea of the workflow for curating.It also has detailed explanations of the terms.That should be a good start.

Mildred Anashie (11:18:48) (in thread): > Also go through the pinned messages as I believe most of the questions you might have will definitely have been answered there@aziz gueye

Adeshile Oluwatosin (11:45:21) (in thread): > @aziz gueyeif still confused about anything else while curating, feel free to ask

Adeshile Oluwatosin (11:47:06) (in thread): > As stated initially, you can convert the article to French to understand it better > And use an highlighter to point out the details to fill in bugsigdb.

Chris Awoke (11:48:36): > Great work, guys. I love the support and swift responses. > > Let’s keep going!

Samuel Nnanna (12:03:15): > @Chioma Onyido@Esther Afuape<@UBNSEMS3S>where confounding factors mentioned in the article are socio-demographic and nutritional determinants, can i use socioeconomic status and nutritional supplement exposure measurement as the appropriate tags?

Aleru Divine (12:15:51) (in thread): > @Samuel Nnannawhile socio-demographics and socioeconomic status may be related, they’re quite distinct. > > Socio-demographics are basic details about people, like their age, gender, education, and job. More like the characteristics of a population.Socioeconomic status is more about how much money people make, their level of education, and the type of job they have (their status). (This is specific to an individual or group) > > They mean different things all together.You can surely fill in socio-demographic.It’llbe flagged but I thinkit’sokay.I’dlike to hear what the mentors say in this situation too:hand_with_index_and_middle_fingers_crossed:

Samuel Nnanna (12:18:39) (in thread): > @Aleru Divineyes i agree they mean different things and i was confused because it was the closest tag to what was posited in the article…..well let’s see the what the mentors say

Aleru Divine (12:19:55) (in thread): > Same with determinants and supplements.Determinants are like the factors that influence or determine a persons nutrition could be their health, their lifestyle (vegan and so on).Supplements are specific products that we take or add to our diet.

Aleru Divine (12:20:13) (in thread): > Surely:sweat_smile:

Mildred Anashie (13:44:49) (in thread): > Hi@Samuel Nnannacould you share a link to the article?I’mof the opinion that this could work if it is in line with what is being discussed in the article

Samuel Nnanna (13:45:17) (in thread): > https://www.nature.com/articles/s41598-020-74678-6 - Attachment (Nature): Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study > Scientific Reports - Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study

Mildred Anashie (13:45:59) (in thread): > Thank youI’llgo through the article now

Samuel Nnanna (13:46:17) (in thread): > Ok thank you

Aleru Divine (13:58:31) (in thread): > @Mildred AnashieI think it would’ve worked if it was the other way around. I mean replacing the latter with the former.

Mildred Anashie (14:05:35) (in thread): > @Aleru Divinedo you see where they said they controlled for this factors in the article?I’mstill reading through to find it and understand the article

Aleru Divine (14:10:27) (in thread): > “Univariable logistic regression was then performed to estimate the impact of sociodemographic, nutritional, and microbiota-related variables on the outcome.” This is one line

Mildred Anashie (14:11:51) (in thread): > I see something now,pointing towards table 3

Aleru Divine (14:12:11) (in thread): > “Table2shows single logistic regressions performed to estimate the impact of the different variables on the outcome. Notably, the analysis of socio-demographic, behavioural, and nutritional determinants revealed that having parents with at least a high school certificate seems to be a protective factor for T1D onset, even if not significant after adjusted comparisons.” > > But its table 4, they made a mistake - Attachment (Nature): Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study > Scientific Reports - Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study

Aleru Divine (14:13:09) (in thread): > Check table 4

Mildred Anashie (14:19:43) (in thread): > YeaI’veseen it now > Based on what they are discussing on, I agree with@Aleru Divinethat Socio economic status might not be the most appropriate because itdoesn’tcover socio demographic determinants and I think it even is part of the determinants

Mildred Anashie (14:19:45) (in thread): > YeaI’veseen it now > Based on what they are discussing on, I agree with@Aleru Divinethat Socio economic status might not be the most appropriate because itdoesn’tcover socio demographic determinants and I think it even is part of the determinants

Aleru Divine (14:21:18) (in thread): > Thank you for having a look too@Mildred Anashie

Samuel Nnanna (14:21:59) (in thread): > Thanks to you guys

Mildred Anashie (14:35:42) (in thread): > AndI’mguessing sociodemographic determinants is not permissible on BugSigdb > > > Ican’tcheck, becauseI’venot had access to the site all day

Aleru Divine (14:36:51) (in thread): > Omg! still? I’m so sorry

Aleru Divine (14:36:56) (in thread): > Let me check

Aleru Divine (14:39:16) (in thread): > You’re right it’s not

Mildred Anashie (14:41:33) (in thread): > Thank you@Aleru DivineI’munsure what could be wrong@Samuel Nnannacurrently thinking too far:sweat_smile::joy:I’mwondering if it would be possible to list out all the socio demographics mentioned in the study

Samuel Nnanna (16:30:41): > @Esther Afuape<@UBNSEMS3S>@Svetlana Ugarcina Perovicwhat do i do when only the Phyla is mentioned > > egThe most abundant OTU wasRikenellaceaefollowed byPrevotellaceae(Prevotella copri),Barnesiellaceae,Lachnospiraceae,andRuminococcaceae(Ruminococcus bromii), which were significantly more abundant in children with diabetes.Do i IgnoreBarnesiellaceae,Lachnospiraceae and Rikenellaceae* ?*

Samuel Nnanna (16:31:37): > and if there’s no reported decrease in signature, how do i report for signature 2?

Mildred Anashie (16:34:25) (in thread): > Hi again@Samuel Nnanna:grin:I think it’s okay to have just signature 1 either increase or decrease for an experimentIf signature 2 isn’t mentioned then you shouldn’t record anything for it

Samuel Nnanna (16:35:00) (in thread): > Ok thank you@Mildred Anashie

Aleru Divine (16:42:07) (in thread): > You should curate all these taxa levels@Samuel NnannaI’malso thinking since they gave the species for Prevotellaceae, and Ruminococcaceae, only curate the species becausethey’rethe highest taxonomic rank.Soyou’llbe curatingPrevotella copri, >Barnesiellaceae, >Lachnospiraceae,>Ruminococcus bromii, and*> Rikenellaceae** *

Mildred Anashie (16:43:37) (in thread): > Yes@Aleru DivineI was of the opinion too that only species should be curated but I needed someone too confirm that

Aleru Divine (16:44:01) (in thread): > I agree:sweat_smile:

Esther Afuape (16:44:30) (in thread): > Thank you andwell done:sparkles:You’recorrect@Aleru Divine

Samuel Nnanna (16:45:00) (in thread): > Thank you

Dorcas Samuel (16:48:54) (in thread): > Hi@Aleru Divineand@Mildred AnashieIs it okay if the groups does not have sizes.I mean if their size was not mentioned

Aleru Divine (16:50:36) (in thread): > I’venever come across this before.Usually they do have sample sizes.Can you share the link to the paper sowe’llhave a look please?

Kate Rasheed (16:52:32) (in thread): > You might need to check supplementary table (if any) for bacteria with negative figures. They signify decrease.

Dorcas Samuel (16:52:33) (in thread): > @Aleru Divineherehttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01896-9 - Attachment (BioMed Central): Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis - Microbiome > Background Intake of dietary fiber is associated with a reduced risk of inflammatory bowel disease. β-Glucan (BG), a bioactive dietary fiber, has potential health-promoting effects on intestinal functions; however, the underlying mechanism remains unclear. Here, we explore the role of BG in ameliorating colitis by modulating key bacteria and metabolites, confirmed by multiple validation experiments and loss-of-function studies, and reveal a novel bacterial cross-feeding interaction. Results BG intervention ameliorates colitis and reverses Lactobacillus reduction in colitic mice, and Lactobacillus abundance was significantly negatively correlated with the severity of colitis. It was confirmed by further studies that Lactobacillus johnsonii was the most significantly enriched Lactobacillus spp. Multi-omics analysis revealed that L. johnsonii produced abundant indole-3-lactic acid (ILA) leading to the activation of aryl hydrocarbon receptor (AhR) responsible for the mitigation of colitis. Interestingly, L. johnsonii cannot utilize BG but requires a cross-feeding with Bacteroides uniformis, which degrades BG and produces nicotinamide (NAM) to promote the growth of L. johnsonii. A proof-of-concept study confirmed that BG increases L. johnsonii and B. uniformis abundance and ILA levels in healthy individuals. Conclusions These findings demonstrate the mechanism by which BG ameliorates colitis via L. johnsonii–ILA–AhR axis and reveal the important cross-feeding interaction between L. johnsonii and B. uniformis. Video Abstract Graphical Abstract

Mildred Anashie (16:53:17) (in thread): > Yea > > Please do share the link > > It could be mentioned somewhere (most timesit’sbeing mentioned in the socio demographic table or supplemental information)

Aleru Divine (16:53:17) (in thread): > Thank you! Let me check it out.

Aleru Divine (16:56:18) (in thread): > @Samuel Nnannadoes your paper have a supplemental material? > > Ididn’tcome across any.

Mildred Anashie (16:56:55) (in thread): > It’sa laboratory experiment and I thinkI’veseen a case like that before butI’llhave to keep going through to be sure this is one of those cases

Mildred Anashie (16:59:40) (in thread): > It looks like a case of two study designs:thinking_face:Let me share screenshots - File (PNG): IMG_1188 - File (PNG): IMG_1187

Dorcas Samuel (17:03:33) (in thread): > @Mildred Anashiethe animal experimentdoesn’thave a number at all

Mildred Anashie (17:05:07) (in thread): > Yes I see that@Dorcas Samuel

Aleru Divine (17:05:27) (in thread): > 6 mice per group “ Data are presented as the mean ± SEM. n = 6 mice per group.”

Aleru Divine (17:05:51) (in thread): > Sharing a screenshot

Mildred Anashie (17:07:04) (in thread): > I’ve seen what you just shared@Aleru Divine

Samuel Nnanna (17:08:30): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>please delete exp2, i mistakenly added it (https://bugsigdb.org/Study_1109) - Attachment (BugSigDB): Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case-control study - BugSigDB > Type 1 diabetes (T1D) is a common autoimmune disease that is characterized by insufficient insulin production.The onset of T1D is the result of gene-environment interactions.

Aleru Divine (17:09:14) (in thread): > Figure 2 = 6 mice per group > Figure 3 = 6 mice per group if not specifically mentioned.…The sample size is in the figure descriptions@Dorcas Samuel

Dorcas Samuel (17:09:45) (in thread): > Oh wow thank you@Aleru DivineThank you@Mildred Anashie

Aleru Divine (17:13:05) (in thread): > Anytime@Dorcas SamuelMeanwhile the screenshot is still loading even whileit’sof no use:sob:Welp!

Aleru Divine (17:16:55) (in thread): > It does@Dorcas Samuel. It’s just very hidden:sob:Found it at figure 1 description - File (JPEG): IMG_1140

Mildred Anashie (17:20:59) (in thread): > What can you make of the mention of the Human study@Aleru DivineI’m thinking what they did was culture bacteria strains from samples gotten from humans in vitro to do some sort of comparison with what was cultured from the animal experiments > > This would mean I was wrong about it being a study with two study designs as their findings were focused on the in vivo/in vitro experiments:thinking_face:

Aleru Divine (17:28:16) (in thread): > @Mildred Anashiethat’scorrect:thumbsup:

Mildred Anashie (17:36:07) (in thread): > Oh Thank you:blush:I was almost confusing myself:woman-facepalming:

Aleru Divine (17:43:18) (in thread): > Sorry, it was a bit confusing.It’sa very interesting paper with a lot of units of measurements:sob:

Ifeoma Okafor (21:10:57): > Hello everyone, > > My name is Ifeoma, and I’m thrilled to be an Outreachy applicant for the December 2024 to March 2025 period. I’m eager to contribute to both the Microbiome Study Curation project. > > I am skilled in literature review, microbiome knowledge and have some public health research knowledge. I am especially excited to contribute to the development of the project while expanding my knowledge of microbiome research. > > I’m enthusiastic to get started and learn from this experience. Looking forward to working with everyone!

Peace Sandy (22:59:52) (in thread): > Done

Ibizugbe Merit (23:05:05) (in thread): > It really is so amazing:partying_face:

Ibizugbe Merit (23:41:02) (in thread): > You’re**** welcome ****@Ifeoma Okafor**** > Go through this and refer to pinned messages on how to get started. > And ****don’t**** hold back if you have any questions.The mentors and the rest of us are always willing to help. > > *****Welcome to the Outreachy contribution period! ******* > > ****We’re thrilled to have you join us. To get started, please check out our GitHub issue for instructions:https://github.com/waldronlab/BugSigDBcuration/issues/94If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion.We’re looking forward to working with you!**** > ****<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Scholastica UruaTip: New to contributing? Watch this helpful video on getting started with open source contributions:https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Adeshile Oluwatosin (23:59:40) (in thread): > Welcome@Ifeoma Okafor

2024-10-06

Inimfon Ebong (00:21:26): > Is anyone having issues accessing the bugsid site or is it just me?

Inimfon Ebong (00:23:01) (in thread): > Welcome@Ifeoma Okaforjust go through the pinned messages and if you have any questions ask

inyang john (00:50:06) (in thread): > It’sbeen taking time to load > Just keep refreshing > I guessthey’reworking on it

Toluwalase Abigail (00:56:48): > Hello, everyone!I’m Toluwalase, and I’m excited to be an Outreachy applicant eager to contribute to theMicrobiome Study Curationproject. I can’t wait to dive in, learn from this experience, and collaborate with all of you along the way. Looking forward to a great journey together!:hugging_face:

Aleru Divine (01:01:20) (in thread): > @Mildred Anashiehad this issue yesterdayDon’tknow about now.Sorry!

Aleru Divine (01:02:52) (in thread): > Welcome@Ifeoma Okafor:hugging_face:Carefully go through the link shared by@Ibizugbe Meritto get started.I’mlooking forward to working with you too

Aleru Divine (01:05:45) (in thread): > Hi@Toluwalase Abigailwelcome:hugging_face:To get started, please check outtheGitHub issue for instructions:https://github.com/waldronlab/BugSigDBcuration/issues/94Also check pinned messages for further information.The mentors are always available to answer any questions you may have sodon’thesitate to ask andwe’reall here to learn:hugging_face:Happy contributing:sparkles: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Toluwalase Abigail (01:17:03) (in thread): > Thank You@Aleru Divine

Samuel Nnanna (01:33:46) (in thread): > Experiencing the lags currently.

Samuel Nnanna (01:34:37) (in thread): > Welcome@Ifeoma Okafor

Mildred Anashie (01:58:16) (in thread): > I am:sob:

Mildred Anashie (01:58:46) (in thread): > Hi@Toluwalase Abigailwelcome:hugging_face:

Mildred Anashie (01:59:44) (in thread): > Welcome@Ifeoma OkaforLooking forward to working with you too:blush:

Ochogwu Emmanuel (02:05:38) (in thread): > You’re welcome Abigail

Samuel Nnanna (02:10:09) (in thread): > Thank you

Samuel Nnanna (02:18:39) (in thread): > what do we do?

Princess Rehoboth Asuelimen (03:01:23) (in thread): > You’re welcome@Toluwalase Abigail:grin:

Princess Rehoboth Asuelimen (03:03:24) (in thread): > You’re welcome@Ibizugbe Merit:grin:

Adeshile Oluwatosin (03:07:23) (in thread): > Welcome:hugging_face:@Toluwalase AbigailTo get started, join #bugsigdb channel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugsigdb channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Adeshile Oluwatosin (03:08:41) (in thread): > Not really, over here

Precious Orakwe (03:53:48) (in thread): > Hello@Toluwalase Abigailwelcome to the amazing community. > Good luck with the contributions

Precious Orakwe (03:55:50) (in thread): > We are all open to help if you have any questions

Inimfon Ebong (03:58:03) (in thread): > After trying for like an hour I just closed it and went to sleep:melting_face::melting_face:

Aleru Divine (03:58:50) (in thread): > Ihaven’tchecked today

Precious Orakwe (03:58:55) (in thread): > Welcome to BugSigDB@Ifeoma OkaforGood luck with the contributions

Ibizugbe Merit (04:42:20) (in thread): > You’rewelcome@Toluwalase Abigail:hugging_face:

Monisa Hasnain (05:54:06): > any data analyst/data scientist here

Grace Ogundaini (05:56:46) (in thread): > Hi.I’ma data analyst

Princess Rehoboth Asuelimen (06:11:54): > Hello everyone. I hope your Sunday is going well. I just want to take a moment to express my gratitude for this amazing community. I’ve been in awe, thinking about how helpful everyone is. I truly appreciate everyone’s willingness to help, and I’m excited to join in and contribute however I can. Have a lovely week ahead.:grin:

Adeshile Oluwatosin (06:14:26) (in thread): > You are welcome:blush::hugging_face:Have an amazing week ahead as well

Matthew Idungafa (06:15:05) (in thread): > Enjoy your weekend@Adeshile Oluwatosin

Adeshile Oluwatosin (06:15:41) (in thread): > Thank you and you too@Matthew Idungafa:relaxed::relieved:

Mildred Anashie (06:19:07) (in thread): > You are welcome@Princess Rehoboth AsuelimenYea excited to keep contributing alongside you and everyone:hugging_face:

Aleru Divine (06:26:44) (in thread): > It’s truly amazing@Princess Rehoboth Asuelimen:heart_hands:I wish you a lovely weekaheadas well:hugging_face:

Ruqayyah (06:26:46): > Hello everyone, > Please how long does it take for the request for bugsigdb account to be granted?

Mildred Anashie (06:28:18) (in thread): > Hi@RuqayyahItdoesn’ttake so long, as soon as our mentors get to itIt’llbe approved > > When did you request?

Aleru Divine (06:28:27) (in thread): > Hi@Ruqayyahitdidn’ttake long for me.In about an hour but that was on a weekday.The mentors will grant you access as soon asthey’reavailable I believe.Or latest tomorrow sinceit’sstill the weekend.

Princess Rehoboth Asuelimen (06:29:44) (in thread): > I think it varies. Mine was done within a few hours@Ruqayyah

Rahila-me (06:38:23) (in thread): > Same thing today

inyang john (06:39:50) (in thread): > You’rewelcome.:clap:

Adeshile Oluwatosin (06:40:03) (in thread): > It depends on the mentors > When they are available, they will grant you access > You can tag@Svetlana Ugarcina Perovic

Monisa Hasnain (07:17:53) (in thread): > Hi grace

Monisa Hasnain (07:18:51) (in thread): > I wanted to know how you can see this project help full as data analyst

Monisa Hasnain (07:19:21) (in thread): > Or are there any other projects you find related to data profession

Inimfon Ebong (09:07:53) (in thread): > Hmm

Adeshile Oluwatosin (09:08:47) (in thread): > I guess our mentors would attend to it when available

PATIENCE ONAH (10:36:45) (in thread): > Mine keeps loading indefinitely since yesterday, I taught it was my network but then I can’t access other sites.

adekemi balogun (12:37:52): > Hello everyone, this is the paper i’m working on and I’d like to know if Table 2 and Figure 3A are curatable because they are in relative abundance not differentialhttps://community-bioc.slack.com/archives/D07Q50G35E0/p1727986610007599 - Attachment (BugSigDB): Gut microbiota is associated with differential metabolic characteristics: A study on a defined cohort of Africans and Chinese - BugSigDB > OBJECTIVE: This study intended to determine the associations between gut microbiota and glucose response in healthy individuals and analyze the connection between the gut microbiome and glucose-metabolism-related parameters.

Mildred Anashie (13:04:35) (in thread): > Hi@adekemi balogunI believe Figure 3 has curatable data but I’m unsure of Table 2 even thoughit’stalking about relative abundance between two groups > > I know it’s stated that we only curate differential abundance in BugSigdb but let me share one of the pinned post, could help explain a bit > > > Just go through the threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549I’llkeep going through the paper to be sure of Table 2 - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

adekemi balogun (13:57:41) (in thread): > Thank you

Rahila-me (14:24:13) (in thread): > I have gone through it Fig 3 is curatable.

Mildred Anashie (14:38:34) (in thread): > @adekemi balogunAre you clear on this now?

Aleru Divine (15:39:30) (in thread): > Well done@Mildred AnashieThis is usually always concerning@adekemi balogunI agree with this. > > Figure 3 specifically presents the results of differential abundance testing > > Table 2 provides relative abundance data but does not emphasize the differential comparisons as effectively as Figure 3. Since we focus on differential abundance, figure 3 it is. > > Thanks for the resource again@Mildred Anashie

Cate Ouma (15:39:40): > Hi guys, I have a question. One of my confounding factors in the study is an abbreviation WAM(Water/sanitation, assets, and maternal education). Can I use socioeconomic status as the appropriate tag for this?

Mildred Anashie (15:47:54) (in thread): > Thank you@Aleru DivineAnd for confirming that for as well:blush:

inyang john (15:48:29) (in thread): > Yesyoucan

Cate Ouma (15:49:01) (in thread): > This is the study:https://www.nature.com/articles/s41467-024-51464-w#:~:text=Of%20these%2C%20650%20children%20have,compared%20to%20non%2Ddiarrheal%20controls. - Attachment (Nature): Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia > Nature Communications - Here, the authors profile the gut microbiome of Ethiopian children suffering from acute and prolonged diarrhea, showing the latter group to exhibit a higher degree of…

Adeshile Oluwatosin (15:50:53) (in thread): > Yes you can, socioeconomic status is appropriate

Cate Ouma (15:53:10) (in thread): > Thank you guys:raised_hands:

inyang john (15:54:36) (in thread): > @Cate Oumayour environment can greatly affect the gut. So yes. Socioeconomic status can be used to tag WMA

Cate Ouma (15:55:36) (in thread): > And can enrollment season be tagged as date or time?

inyang john (15:58:51) (in thread): > Both

Cate Ouma (16:01:58) (in thread): > The article says that there were seasonal variations that could affect the gut microbiome

inyang john (16:02:32) (in thread): > Enrollment season can be tagged as both

Mildred Anashie (16:53:25) (in thread): > Hi@Cate OumaI get that (WAM-Water/Sanitation, Assets and Maternal education) could be indicators used to assess living conditions hence allowing for socio economic status to be used, but I’m wondering, Have you tried listing them out individually instead of generalizing?:thinking_face:It could be permissible on BugSigdb > > I’m of the opinion that putting it all under socioeconomic status might not be so appropriate > > Let me tag the mentors to this so we can get their opinions on it@Svetlana Ugarcina Perovic@Chioma Onyido@Peace Sandy@Esther Afuape@Scholastica UruaThank you:pray:

Cate Ouma (16:59:47) (in thread): > This is actually a good suggestion. I’ll wait for the mentors’ opinions on it

Aleru Divine (17:11:54) (in thread): > Yeah, this is a lot safer@Mildred AnashieNice work everyone:heart_hands:

Adeshile Oluwatosin (17:24:27) (in thread): > Actually it is safer…I hope to hear feedback as well

Cate Ouma (19:45:42): > Hi again. Does anyone have tips on how to interpret boxplots of the differentially abundant taxa. I’m finding it really hard to understand mine because they aren’t really well aligned with the axis(e.gEscherichia spp) has been reported to be enriched in this paragraph: We found that diarrhea cases had a higher relative abundance of Escherichia spp. (16.3% vs. 8.2%; q < 0.01), Campylobacter spp. (3.6% vs. 0.83%; q < 0.001), Streptococcus spp. (8.2% vs. 4.2%; q < 0.0001) and Veillonella dispar (6.3% vs. 3.2%; q < 0.0001) > However, when I look at the box plot, it seems to be abundant in controls(the yellow line). This is really confusing me

Aleru Divine (20:08:21) (in thread): > @Cate OumaI’ve been looking at this, initially I was confused too but then I looked at unit of measurement (%) sotheyquantified it by the percentage. > > It goes from 0 to 100 > > The box for controls may seem longer, but the box for cases goes a bit further. > > For example, in 4a, the box for cases(red) goes a bit further (higher in %) compared to the controls(yellow)

Aleru Divine (20:08:28) (in thread): > Sending a screenshot

Aleru Divine (20:08:36) (in thread): - File (JPEG): IMG_1153

Aleru Divine (20:09:48) (in thread): > The further it is, the higher the percentage(%) and the more abundant the taxa.

Cate Ouma (21:45:52) (in thread): > Wow..thank you:clap:. Your explanation is really easy to understand:blush:

2024-10-07

PATIENCE ONAH (01:18:06): > Hi everyone, happy New week. Help me review if I can record two experiments for this study paper.https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-02074-1 - Attachment (BioMed Central): Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals - BMC Microbiology

Adeshile Oluwatosin (02:03:10) (in thread): > Good morning@PATIENCE ONAHokay

PATIENCE ONAH (02:05:24) (in thread): > Thank you, I will be waiting for feedback

Adeshile Oluwatosin (02:17:54) (in thread): > First of I can see that you listed two body sites; feces and blood serum > Are there results for comparison using these different body sites. > If yes, you would need to create different experiments

Adeshile Oluwatosin (02:19:03) (in thread): > One for feces and one for blood serum

Svetlana Ugarcina Perovic (02:28:09) (in thread): > Agree with@Mildred Anashie

Svetlana Ugarcina Perovic (02:47:57): > Keep up the good work, communicate, discuss and do not forget about our MVIF event this week. Happy Monday - Attachment: Attachment > Good morning :potted_plant: > > Today I have a special invitation for you: > join us next week at MVIF (Microbiome Virtual International Forum), a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > https://www.microbiome-vif.org/en-US/-/future-events/mvif32-78-9-october-2024 > > We’ve been organizing this event monthly since 2021, you can see recordings here: https://www.youtube.com/@MicrobiomeVIF/playlists

Aleru Divine (02:54:54) (in thread): > Good morning@PATIENCE ONAHLooking at the article,I understand that Gut microbiota and immune activation were studied in 36 non-HIV-infected subjects (healthy controls) and 58 HIV-infected individuals, including 28 immunological responders (IR) and 30 immunological non-responders(INR) > > You’d have 3 experiments for this paper > 1. Healthy controls vs 28 immunological responders (IR) > 2. Healthy controls vs 30 immunological non-responders (INR) > 3. INR vs IR > Additional file 4: Figure S4provides the differentiallyabundantsignatures identified by LEfSe.Additional info: we’re only to record the body sites that were relevant to the experiment were curating. > > So they examined gut microbiome and tookfecalsamples(body site = feces) for the analysis. - This is relevantThey took blood samples were collected for the measurement of the immune activation markers. (This is not relevant for curation)

Aleru Divine (02:55:39) (in thread): > Thanks for the confirmation@Svetlana Ugarcina Perovic:pray:

Aleru Divine (02:56:30) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for the reminder:hugging_face:

Adeshile Oluwatosin (03:00:28) (in thread): > Thank you for that@Aleru Divine

Adeshile Oluwatosin (03:00:47) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you:relaxed:

Adeshile Oluwatosin (03:05:05) (in thread): > Noted@Svetlana Ugarcina Perovic

inyang john (03:06:02) (in thread): > @Svetlana Ugarcina PerovicYea Ma

Samuel Nnanna (03:32:29): > https://www.nature.com/articles/s41598-020-74678-6hi guys, this is the paper i’m reviewing. I’m conflicted as to whether a 2nd exp should be added (Italians vs Migrants). I would appreciate every feedback. Thank you - Attachment (Nature): Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study > Scientific Reports - Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case–control study

Monisa Hasnain (03:45:08): > i have completed the first task via form and got the message “your response have been recorded” . Is that it?

Monisa Hasnain (03:45:42): > what if i need to edit my response for the first task do i have to attempt the quize again

Aleru Divine (03:45:56) (in thread): > Yesthat’sit@Monisa Hasnain, > > Well done!

Monisa Hasnain (03:46:30) (in thread): > thanks for your response

Aleru Divine (03:47:28) (in thread): > Yes you’d have to submit a new response.

Princess Rehoboth Asuelimen (03:47:43) (in thread): > You can’t edit your response after you have submitted.

Monisa Hasnain (03:50:45) (in thread): > actually i left one question. i didnt have idea i am on last page now have to attamt again

Aleru Divine (03:52:06) (in thread): > Just do over and inform the mentors of the mistake sothey’llbe aware of your final submission.

Adeshile Oluwatosin (03:52:25) (in thread): > Yes:+1:

Adeshile Oluwatosin (03:52:59) (in thread): > Ensure that the new form you would submit is completely filled

Precious Orakwe (03:53:08) (in thread): > Mine is making me to loss my mind

Adeshile Oluwatosin (03:53:25) (in thread): > Then notify the mentors@Svetlana Ugarcina Perovic@Esther Afuape<@UBNSEMS3S>

Monisa Hasnain (03:53:43) (in thread): > sure thanks

Adeshile Oluwatosin (03:53:56) (in thread): > You are welcome

Adeshile Oluwatosin (03:54:33) (in thread): > For now, maybe just try another browser:pleading_face:

Adeshile Oluwatosin (03:54:59) (in thread): > Or try using your laptop, just suggesting

Aleru Divine (03:56:23) (in thread): > Downloading and setting a VPN also works. At least temporarily until the network issue is fixed.I assumeit’sMTN right?

Adeshile Oluwatosin (03:57:27) (in thread): > Or use wifi

Ibizugbe Merit (03:59:29) (in thread): > Noted@Svetlana Ugarcina PerovicThanks for the reminder

Kate Rasheed (04:09:47) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for the reminder.

Adeshile Oluwatosin (04:12:53) (in thread): > @PATIENCE ONAHcheck the discussion page for the taxa you mentioned in NCBI.. just notifying you

PATIENCE ONAH (04:31:28) (in thread): > Thank you so much@Aleru Divinefor taking your time to review the paper and providing guide. Please I still need some understanding, according to the paper there’s no differential signature between IR and INR, most of the difference is between HC and IR and INR together. Do I still need to curate the experiment differently?

PATIENCE ONAH (04:34:14) (in thread): > Thank you so much@Adeshile Oluwatosin, I will have to remove the blood serum since it’s not relevant based on Aleru Divine explanation

PATIENCE ONAH (04:37:13) (in thread): > Please I didn’t get what you meant here@Adeshile Oluwatosin

Mildred Anashie (04:37:54) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy Monday:blush:

Adeshile Oluwatosin (04:41:58) (in thread): > Have you checked the discussion page to be sure they have missing NCBI - File (JPEG): IMG_1387

Aleru Divine (04:45:40) (in thread): > @PATIENCE ONAHcheck figure S4eThere’sa LEfSe plot showing differential abundance for INR and IR.

PATIENCE ONAH (04:46:48) (in thread): > Which discussion group please, sorry for too much questions, am new to this curation

Rahila-me (04:51:17) (in thread): > @Monisa Hasnainyes but you have to go and record it on the outreachy website pasting the link and a little description of the task

Adeshile Oluwatosin (04:52:21) (in thread): > Bacteroidetes, Actinobacteria, Lentisphaerae, Eubacterium rectale…. Check the discussion page incase the names have been changed to figure the taxon ID.

Adeshile Oluwatosin (04:52:31) (in thread): > A minute@PATIENCE ONAH

Adeshile Oluwatosin (04:52:57) (in thread): > Check this;https://community-bioc.slack.com/archives/C04RATV9VCY/p1728118075185899?thread_ts=1728113038.904309&channel=C04RATV9VCY&message_ts=1728118075.185899 - Attachment: Attachment > Good morning :sparkles: > Please, always remember to check the discussion page when you can’t find a taxon on NCBI. This is because a lot of times, such a taxa has already been noted down in the discussion page by someone who came across it in the past. > You can find the discussion page by going to “help” (next to the search bar on bugSigDB), select “NCBI clean up” (number 5 on the contents list), select “signatures with missing NCBI ID”, you’ll see Discussion page on the first line. > > Here’s a direct link to it: https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID > > Please go through this for an idea on how to resolve taxa issues: https://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189

Adeshile Oluwatosin (04:57:00) (in thread): > @Aleru Divinekindly see to this

Aleru Divine (05:20:13) (in thread): > @Adeshile OluwatosinI went through this, and I found this excerpt > > “To analyse the origin factor, the study population was subdivided by the children’s origins (Italian and migrant, 69 and 27 children, respectively).”So I thought maybe it needed to be curated. >
> Going further I found another piece of information > > “The analysis of microbiota and bioindicator species displayed no significant differences between Italian and migrant children:the qRT-PCR measurements showed a trend of greater value for the total bacteria (both for the experimental design with and without probe), Bacteroides and M. smithii (both using 16S rDNA and nifH) in migrant children.”Alpha diversity was also not significant > > “Additionally, the α-diversity analyses in next generation sequencing (NGS) showed a difference in taxonomic units (OTUs), i.e., there were more OTUs in migrants than in Italians,but the difference was not significant,though it was close to the limit of significance (p = 0.057).” > > But thisdidn’tmatter since it can be curated as**** “unchanged”****Looking further at table 3, I saw that there were some signatures that they highlighted to be significant.(But I am quite unsure if this is to be considered as differential abundance) and also the fact that they stated earlier that “The analysis of microbiota and bioindicator species displayed no significant differences between Italian and migrant children****.” > > So ****I didn’t**** come to a conclusion yet, I was waiting for other opinions.There are 3 possible outcomes I think > 1. Curate the experiment, recording the alpha diversity metrics as unchanged(without signatures) > 2. Not curating the experiment at all(if the signatures are not confirmed) > 3. Curate the experiment and signatures**(this has to be confirmed by the mentors, as I am not very sure) > I thinkit’sone of these 3.But we will have to confirm from the mentors@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace Sandy@Levi Waldron

Svetlana Ugarcina Perovic (05:29:31) (in thread): > This study is NOT to be curated due to NO significant differences reported. (as@Aleru Divineexplained, thanks!)@Samuel Nnannayour effort is noted, please select other paper to curate.

Samuel Nnanna (05:32:55) (in thread): > @Svetlana Ugarcina PerovicI was concerned about the Italians and Migrants comparison but significant difference were found for patients with T1D against healthy controls

PATIENCE ONAH (05:33:53) (in thread): > Okay@Aleru Divine. Thank you

Svetlana Ugarcina Perovic (05:34:28) (in thread): > oh my, how I see, my bad > let me restore it and you can continue curation > my BIG apologies

Aleru Divine (05:35:34) (in thread): > Thanks for the clarification@Svetlana Ugarcina Perovic:raised_hands:

Adeshile Oluwatosin (05:35:51) (in thread): > Thank you for clarifying@Svetlana Ugarcina Perovic

Samuel Nnanna (05:36:47) (in thread): > thank you for your efforts@Aleru Divineand i’m waiting for it to be restored@Svetlana Ugarcina Perovic

Inimfon Ebong (05:36:59): > Good morning@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Esther Afuape@Scholastica Uruaplease I have submitted a request for an account on bugsigdb.

Svetlana Ugarcina Perovic (05:37:19) (in thread): > https://bugsigdb.org/Study_1109https://bugsigdb.org/Study_1109/Experiment_1are back! - Attachment (BugSigDB): Risk factors for type 1 diabetes, including environmental, behavioural and gut microbial factors: a case-control study - BugSigDB > Type 1 diabetes (T1D) is a common autoimmune disease that is characterized by insufficient insulin production.The onset of T1D is the result of gene-environment interactions. - Attachment (BugSigDB): Study 1109/Experiment 1 > .

Kate Rasheed (05:37:31) (in thread): > Check your spam folder to see if you’ve been sent the details. If you haven’t, please wait a while.

Inimfon Ebong (05:38:23) (in thread): > Thank you

Samuel Nnanna (05:38:50) (in thread): > thank you@Svetlana Ugarcina Perovic

Kate Rasheed (05:39:03) (in thread): > You’re welcome. Don’t hesitate to reach out if you need further help.

Svetlana Ugarcina Perovic (05:39:47) (in thread): > once again my apologies,I was in a hurry to respond to you ALL

Svetlana Ugarcina Perovic (05:40:21) (in thread): > and miss that important detail: that you have been discussing a particular experiment and not the whole study

Svetlana Ugarcina Perovic (05:40:28) (in thread): > Keep up the good work!!

Svetlana Ugarcina Perovic (05:41:26) (in thread): > There is no requests in the queue. That means all have been already approved.

Inimfon Ebong (05:42:31) (in thread): > Yes, I’ve seen it in my spam thank you

PATIENCE ONAH (05:43:59) (in thread): > Thank you@Adeshile Oluwatosinfor the link I didn’t know the reason for the different in color of the taxon, I will check them out.

Adeshile Oluwatosin (05:45:06) (in thread): > First check here;https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=200643&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (05:45:26) (in thread): > The orange highlight indicates a missing NCBI

Monisa Hasnain (05:50:14) (in thread): > :+1:

Aleru Divine (06:00:48) (in thread): > Well done@Adeshile Oluwatosin

Adeshile Oluwatosin (06:01:29) (in thread): > Thank you:eyes:@Aleru Divine

Adeshile Oluwatosin (06:20:47): > @Svetlana Ugarcina PerovicKindly delete the study 1114https://bugsigdb.org/Study_1114/Experiment_1I created it when I was curating the initial article. > I am currently working on a new issue. > Thank you - Attachment (BugSigDB): Study 1114/Experiment 1 > .

Svetlana Ugarcina Perovic (06:47:31) (in thread): > deleted.

Chinwendu Joy Enyidiegwu (06:47:34): > hello there:wave:@Svetlana Ugarcina Perovic<@UBNSEMS3S>how long does it it take to be able to view a created signature on the study. for experiment 1 , i have created 2 signatures, saved, even after page reloads ,i still could not view these signatures. > > please, is there something that i am doing wrong, please what do you suggest i do. > Attached below is the study link.https://bugsigdb.org/Study_1104 - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > This study examines how the paternal gut microbiome, before conception, affects offspring development and behavior, an area less explored compared to maternal influences.

Svetlana Ugarcina Perovic (06:48:20) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&cid=C04RATV9VCY - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Adeshile Oluwatosin (06:48:27) (in thread): > Thank you

Svetlana Ugarcina Perovic (06:49:44) (in thread): > https://bugsigdb.org/Study_1104/Experiment_1/Signature_1https://bugsigdb.org/Study_1104/Experiment_1/Signature_2

Chinwendu Joy Enyidiegwu (06:50:42) (in thread): > oh thank you. i appreciate this

Svetlana Ugarcina Perovic (06:51:17) (in thread): > Do I see in thebacterial signature:mouse2::mouse2::mouse2::mouse2::mouse2:?@Chinwendu Joy Enyidiegwu

Svetlana Ugarcina Perovic (06:52:19) (in thread): > We are recording:microbe::microbe::microbe::microbe::microbe::microbe:

Chinwendu Joy Enyidiegwu (06:54:40) (in thread): > i am currently editing the signatures

PATIENCE ONAH (06:55:45) (in thread): > Thanks to you both for your support

Aleru Divine (07:02:26): > Hi everyone! I hope you’re all having a great day. > > A special thanks to our mentors and co-mentors for their prompt help and support:heart_hands:As many of us are currently on our second contribution or have already completed it, here’s a few things i recommend you do to enhance accuracy before submitting for grading.Review Your Contribution:Accuracy is Key: Always prioritize quality in your curation. > * Study Design: > > * Ensure you’re correctly identifying the study type > Resources for identifying study typeDetailed threadCuration Policy > * Number of experiments: > > * Curate only experiments/comparisons with reported significant differences in microbial abundance. > > * Condition Input: > > * The condition refers to the disease, medical treatment, drug, health status variable, genetic variant, or environmental factor that is being compared in the study. > * Make sure to enter conditions that are compared between groups (Group 1 vs. Group 0). > * Avoid using overly vague ontology terms; choose one precise term that accurately reflects the condition. > * Check through theEFOfor properly reporting the conditions. > > * Data Transformation: > > * Data transformations are usually determined by the type of statistical test used. See this thread for a detailed list - See this link -https://community-bioc.slack.com/archives/C04RATV9VCY/p1699808143495129?thread_ts=1699704087.950319&cid=C04RATV9VCY > > * Statistical Test: > > * We are to record only the statistical test that was used for the differential abundance testing. > * For instance: See this excerpt “Furthermore, the histograms of the distribution of linear discriminant analysis (LDA) values obtained from the LEfSe analysis (Fig. 4C–E, LDA > 3.0 as the screening criterion) alsorevealed differences in microbial abundancebetween the Control group and the AP models.” > This confirms LEfSe is the statistical test here. > * Taxa Validation: > > * Verify unknown taxa against the NCBI taxonomy database:NCBI Taxonomy Browser. > > * Common Errors: > > * Double-check for mistakes like: > > * Incorrectly labeling the control group. > * Confusing “increased” with “decreased” abundance in group 1. > * Entering taxa that weren’t identified as significantly different, or neglecting to enter those that were. > Offer Support: > * Consider helping fellow contributors with reviewing their curation to enhance the overall quality and integrity of BugSigDB. - Attachment: Attachment > Wheww! What an interesting discussion today! :grin: > If you weren’t able to attend the meeting today, Here’s a summary of what I gathered from the office hour today: > -“Hallmarks of Study Designs”- by @UBNSEMS3S > > 1. Randomized controlled trial (RCT): participants are randomly divided into groups. The treatment group receives the intervention while control group don’t. Here, researchers randomly assign the conditions to people. > Classical example: > 50 people receive the real vaccine, 50 receive the placebo. Other examples: diet, exercise, etc. > > 2. Laboratory experiment: done using animal models, such as rats, pigs, mice, etc. > You’re not randomizing here because they’re all in the same condition. > > 3. Meta-analysis: this is a study design where researchers combine results from different studies. Meta analysis also means Pooling of results. > > 4. Prospective cohort studies: this is a study where researchers recruit a group of people based on a common characteristic (e.g. based on residence) and follow them up over time. > > Classical example #1: all patients recruited in a study who showed signs of depression in the month of October. > Classical example #2: 100 people develop some diseases of interest (cases) and some people don’t (control) > > 5. Longitudinal observational study: time series studies. There is no intervention by the researcher in this kind of study. > Data is collected at multiple time points. > > Classical example: observing COVID participants before and after the event. > > 6. Case control: when you recruit cases ( people with a disease of interest) and controls (people without) similar on some characteristics. You would sometimes see matched on: age, bmi, sex, etc. > > Classical example: Healthy control group (control) and JIA group (case) > > 7. Cross-sectional observational: Contrasting 2 geographical areas or based on some socio-demographical characteristic (for example), usually at a single time point. > > Classical example: community studies where they took 100 people from a neighborhood and contrasted with people from another neighborhood. > > Apologies if I left anything out, the recording will be posted soon. :pray::skin-tone-5: - Attachment (BugSigDB): Curation Policy > … - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions - Attachment: Attachment > Oh wow > Could you correct this list please? @Levi Waldron > > ANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Kate Rasheed (07:06:41) (in thread): > Thanks for sharing. This is apt.

Mildred Anashie (07:07:41) (in thread): > Thank you for this@Aleru DivineIt answers a lot of questions:hugging_face:And Yea special thanks to our Mentors and Co-mentors for always helping and providing prompt responses

BOLARINWA AISHAT (07:12:49) (in thread): > Thank you very much > This is helpful

Mildred Anashie (07:14:56) (in thread): > I’ve gone through this paper and I saw that experiment but ignored it since I didn’t see signatures and the alpha diversity was Not significant > > But now I see I missed the possible signatures@Aleru Divineand I agree that if the signatures are confirmed for the experiment then it has to be curated but if not there might be no need to curate since the alpha diversity is unchanged

Precious Orakwe (07:17:29) (in thread): > Oh wow, thanks@Aleru Divinethis is wonderful

Adeshile Oluwatosin (07:50:15) (in thread): > You are welcome@PATIENCE ONAH

Princess Rehoboth Asuelimen (08:06:23) (in thread): > This is helpful. Thank you

Inimfon Ebong (08:07:56): > under conditions when i put in the condition Acute Ischemic Stroke ‘term not found’ pops up what do i do

Inimfon Ebong (08:12:55): > @Svetlana Ugarcina Perovicplease do I edit the condition?

Adeshile Oluwatosin (08:16:37) (in thread): > Well detailed:hugging_face:Thank you@Aleru Divine

Adeshile Oluwatosin (08:17:19) (in thread): > Look for a similar or the closest condition to acute ischemic stroke

Mildred Anashie (08:18:17) (in thread): > Check for that condition herehttps://www.ebi.ac.uk/efo/and find the closest term to it and use on BugSigdb - Attachment (ebi.ac.uk): The Experimental Factor Ontology < EMBL-EBI > The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for projects such as the GWAS catalog. It combines parts of several biological ontologies, such as UBERON anatomy, ChEBI chemical compounds, and Cell Ontology. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for Open Targets. We also add terms for external users when requested. If you are new to ontologies, there is a short introduction on the subject available and a blog post by James Malone on what ontologies are for.

Adeshile Oluwatosin (08:18:24) (in thread): > In the last meeting we had, it was stated that it’s best to keep it simple. > > In this case, you can use the condition ‘stroke’ if you search andcan’tfind anything else

Aleru Divine (08:19:44) (in thread): > Using “Ischemic stroke”as the condition in this case will doHere’sthe EFO linkhttps://www.ebi.ac.uk/ols4/ontologies/ncit/classes/http%253A%252F%252Fpurl.obolibrary.org%252Fobo%252FNCIT_C95802 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Adeshile Oluwatosin (08:19:50) (in thread): > Yes you can > Just click on edit

Adeshile Oluwatosin (08:22:12) (in thread): > Edit the experiment

Rahila-me (08:33:47): > @Scholastica Uruaplease how do i enter these signature, should it just be species only that i will enter, - File (PNG): Screenshot 2024-10-07 131130.png

Mildred Anashie (08:43:46) (in thread): > Hi@Rahila-meThese all appear to be species to me:thinking_face:Except of course the Butyrate producing bacterium SL7/1 which doesn’t seem like a specie name to me but I’m sure you can find the ID for that > > However, If your concern is the first one relust00054, you can check this link out, it says Streptococcus thermophile which seems to be thermophilus instead, was formerly known as Streptococcus salivarius > I think that’s why the authors reported it that wayhttps://en.m.wikipedia.org/wiki/Streptococcus_thermophilus - Attachment: Streptococcus thermophilus > Streptococcus thermophilus formerly known as Streptococcus salivarius subsp. thermophilus is a gram-positive bacterium, and a fermentative facultative anaerobe, of the viridans group. It tests negative for cytochrome, oxidase, and catalase, and positive for alpha-hemolytic activity. It is non-motile and does not form endospores. S. thermophilus is fimbriated. > It is also classified as a lactic acid bacterium. S. thermophilus is found in fermented milk products and is generally used in the production of yogurt, alongside Lactobacillus delbrueckii subsp. bulgaricus. The two species are synergistic, and S. thermophilus probably provides L. d. bulgaricus with folic acid and formic acid, which it uses for purine synthesis. > S. thermophilus has an optimal growth temperature range of 35–42 °C (95–108 °F), while L. d. bulgaricus has an optimal range of 43–46 °C (109–115 °F).

Rahila-me (08:56:37) (in thread): > @Mildred Anashieyes m y concern is relust00054 if it will be included

Mildred Anashie (09:02:54) (in thread): > Okay > > I think this solved it@Rahila-me

Rahila-me (09:04:42) (in thread): > what solves it, i was asking if this should be included even thou i have my doubts relust00054@Mildred Anashie

Mildred Anashie (09:06:38) (in thread): > My earlier message explains it along side the link I shared > > But you can also see thishttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1308&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Rahila-me (09:08:30) (in thread): > ok..thanks

Chinwendu Joy Enyidiegwu (09:32:58) (in thread): > thank you for the feedback above:smiley:i am through with the signatures@Svetlana Ugarcina Perovicyou can review again for more feed back. i ’d appreciate > please help with deletinghttps://bugsigdb.org/Study_1104/Experiment_1/Signature_3https://bugsigdb.org/Study_1104/Experiment_1/Signature_4 - Attachment (BugSigDB): Study 1104/Experiment 1/Signature 3 > Source: Brain, Behavior, and Immunity, Volume 123, January 2025 Description: This study investigates how antibiotics-induced depletion of the paternal gut microbiome… - Attachment (BugSigDB): Study 1104/Experiment 1/Signature 4 > Source: Brain, Behavior, and Immunity, Volume 123, January 2025 Description: This study investigates how alterations in the paternal gut microbiome lead to intergenerational…

Cate Ouma (09:33:19): > Hi team, if a taxon is unclassified, how I’m I supposed to curate it. E.g Unclassified Streptococcus. Am I to record it as Streptococcus spp.? - File (PNG): Screenshot_20241007-162311.png

Svetlana Ugarcina Perovic (09:33:59) (in thread): > You can do edit of the signatures.

Aleru Divine (09:34:37) (in thread): > Curate as Unclassified Streptococcus.

Svetlana Ugarcina Perovic (09:34:54) (in thread): > As for the feedback, feel free to ask your colleagues. Mentors do a final review with scores and feeback for corrections.

Mildred Anashie (09:35:38) (in thread): > Curate just the way it was reported > Exceptthere’sa homotypic synonym on NCBI

Adeshile Oluwatosin (09:37:04) (in thread): > Curate it exactly as it is

Cate Ouma (09:38:58) (in thread): > Okay. Thank you. How does one know if there is a homotypic synonym on NCBI. And incase there is, should the entry be the synonym or the exact name as is on the paper

Adeshile Oluwatosin (09:40:02) (in thread): > You would see it stated there as synonym on the NCBI link

Adeshile Oluwatosin (09:40:50) (in thread): > For instance: see this

Aleru Divine (09:41:00) (in thread): > When you search a signature on NCBI,all the information on the former names, synonyms and new name is given.All you need to do is enter the TaxID and it automatically populates when you save then signature.

Adeshile Oluwatosin (09:41:09) (in thread): > It is stated vividly that the synonym of Bacteriodetes is bacteroidia - File (JPEG): IMG_1394

Chinwendu Joy Enyidiegwu (09:41:55) (in thread): > thank you again, > to be clear, for these study i want to use just signature 1 and 2, > signature 3 and 4 are duplicates which i am considering deleting .@Svetlana Ugarcina Perovicare you suggesting that i maintain all 4 signatures rather than deleting 3 ad 4.

Mildred Anashie (09:42:40) (in thread): > Check this image > > Most timesyou’dsearch for a particular taxa and find it as something else on the NCBI browser, and when you read throughyou’dfind outit’sa synonym of what you were searching for > In that case, you record the ID for the synonym - File (JPEG): 73141e78-f709-4b38-93d4-63f3d8119aa2

Precious Orakwe (09:45:41): > Good day@Svetlana Ugarcina Perovicplease can you delete Signature 3 in Experiment 2, Signature 2 in Experiment 6, Signature 3 in Experiment 5. > Thank you > > Link to my study.https://bugsigdb.org/Study_1106 - Attachment (BugSigDB): Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations - BugSigDB > Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results.

Svetlana Ugarcina Perovic (09:48:21) (in thread): > I did not do any suggestion. Please do inform me if and what you want to be deleted.

Svetlana Ugarcina Perovic (09:50:36) (in thread): > Deleted.

Precious Orakwe (09:55:30) (in thread): > Thank you@Svetlana Ugarcina Perovic

Precious Orakwe (09:56:53): > Hello Team, > Good day everyone, i would like a review for correction for my study before I can submit it for review to our mentors. > Thank you. > > Link to my study:https://bugsigdb.org/Study_1106 - Attachment (BugSigDB): Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations - BugSigDB > Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results.

Aleru Divine (10:04:26) (in thread): > Well done@Precious OrakweI’ll have a look at thisin a few minutes:pray:and let you know about any observations I have.

Chinwendu Joy Enyidiegwu (10:06:28) (in thread): > okay, please delete signature 3 and 4 from the studyhttps://bugsigdb.org/Study_1104 - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > This study examines how the paternal gut microbiome, before conception, affects offspring development and behavior, an area less explored compared to maternal influences.

Precious Orakwe (10:08:56) (in thread): > Thank you so much@Aleru Divine

Svetlana Ugarcina Perovic (10:09:17) (in thread): > deleted.

Mildred Anashie (10:27:28) (in thread): > I’ll also take a look ASAP > > Well done:clap:

Adeshile Oluwatosin (10:37:25) (in thread): > Well done@Precious Orakwe

Inimfon Ebong (11:00:05) (in thread): > Ok that’s what I’ll use then > Thank you

PATIENCE ONAH (12:07:58) (in thread): > Thank you@Aleru Divinefor sharing

Chris Awoke (12:12:53): > Hello,@Svetlana Ugarcina Perovic. I hope you’re having a great day! > > Sorry to bother you, but I made a mistake. Could you please help me delete Signature 3 in my study? Here’s the link:https://bugsigdb.org/Study_1124. - Attachment (BugSigDB): Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries - BugSigDB > BACKGROUND: Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV).

Svetlana Ugarcina Perovic (12:33:14) (in thread): > Deleted.

Cynthia Iwuoha (12:37:31): > My name is Cynthia Iwuoha, and I am an Outreachy applicant for the December 2024 to March 2025 program. I am excited to engage with such talented individuals and contribute to the Microbiome study curation. > > I am eager to make meaningful contributions and learn from the expertises present in this community. I look forward to collaborating with all of you and am grateful for any support and guidance you may provide as I embark on this journey.

Adeshile Oluwatosin (12:37:51) (in thread): > Welcome@Cynthia Iwuoha:blush:

Kate Rasheed (12:38:07) (in thread): > Welcome welcome Cynthia. We are so glad to have you.

Adeshile Oluwatosin (12:38:46) (in thread): > To get started, join #bugsigdb channel ! > * Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Follow this steps to proceed to the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the #bugsigdb channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Cynthia Iwuoha (12:40:22) (in thread): > Thank you everyone for the warm welcome.

Cynthia Iwuoha (12:41:13) (in thread): > @Adeshile OluwatosinThank you.

Ibizugbe Merit (13:11:34) (in thread): > You’rewelcome@Cynthia Iwuoha:hugging_face:

Adeshile Oluwatosin (13:15:48) (in thread): > Welcome dear@Cynthia Iwuoha

Mildred Anashie (13:43:33) (in thread): > Welcome@Cynthia Iwuoha:blush:

Chris Awoke (13:57:26) (in thread): > Thank you so much@Svetlana Ugarcina PerovicI’m grateful.

Aleru Divine (14:00:50) (in thread): > Welcome@Cynthia Iwuoha:hugging_face:

Chinwendu Joy Enyidiegwu (14:09:43): > Hello everyone. > I just completed my second contribution. > here is the link to the study as i await feedback and reviews :<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Aleru Divine@Esther Afuape@Chioma Onyidohttps://bugsigdb.org/Study_1104 - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > This study examines how the paternal gut microbiome, before conception, affects offspring development and behavior, an area less explored compared to maternal influences.

Adeshile Oluwatosin (14:28:28) (in thread): > Okay:thumbsup:well done@Chinwendu Joy Enyidiegwu

Aleru Divine (14:43:51) (in thread): > Well done@Chinwendu Joy Enyidiegwu:clap:I’m currently reviewing a couple of studies.Will let you know as soon as I get to yours:pray:

Rahila-me (15:12:09) (in thread): > Welcome@Cynthia Iwuoha

Aleru Divine (16:05:10) (in thread): > Hi@Precious OrakweI went through your study. Well done again in your curation. > > This is a very interesting study, it is huge too! > > First I’d start with the P-value. P value of <0.05 were considered significant for the experiments. > > There was MHT correction -See “All statistical tests were two sided. p-values < 0.05 were regarded as significant and false discovery rate (FDR)-adjusted p-values < 0.1 were regarded as significant after adjusting for multiple testing.” > > For experiment 2. > > I think I understand why you didn’t include the sample sizes for experiment 2, please consult the mentors regarding that. > > Also, add a group 1 definition. > > I’d like to know how you determined the alpha diversity (chao 1) I didn’t find anything. I might be missing something. > > Signature 1, you have 2 unassigned genuses from families Lachnospiraceae and Peptostreptococcaceae. > > For experiment 3. > I believe group 1 sample size is 11. They just grouped it to (vaginally born = 10, C-section born = 1) > > Your signature 1 is table 5 and signature 2 is table 7(probably a mistake), > I believe it should be only table 5 with 1 signature(increased) > > For experiment 4. > Your location is South Africa but your signatures are from table 7 > “Four studies included are Canada, Haiti, USA (California-Florida), USA (California-Massachusetts –Missouri).” I don’t think this goes. > > Table 7 shows meta-analysis results stratified by mode of delivery in four studies. > > I’m getting very confused. I see your experiments and where you got and how you grouped them, but the signatures aren’t matching. > > For experiment 5, location is USA, the signature source you curated is table 11. This is Data from Bangladesh study only. Which is supposed to be for experiment 1. > > I think experiment 6 is okay but for the sample sizes, also consult the mentors on how to go about it. > > Same thing with experiment 7 > > For signature 1 in experiment 7, you missed the unassigned Clostridiaceae in signature 1. > > > These are the observations I have. The study is not very easy to navigate, I must commend how well you’ve done:clap::skin-tone-4::clap::skin-tone-4:

Kate Rasheed (16:08:30) (in thread): > @Aleru DivineWell done for a comprehensive review and bringing out hidden details. I’m sure@Precious Orakwewould be glad this review was done. > > The study was really an intensive one with a lot of experiments. Weldone@Precious Orakwefor a huge work done.

Kate Rasheed (16:09:56) (in thread): > Weldone@Chinwendu Joy EnyidiegwuI’ve glanced through the study. I’ll look at it deeply and give a feedback soon.

Kate Rasheed (16:26:48) (in thread): > @Chinwendu Joy EnyidiegwuIt’s saying I can’t access the full text of the article until I go through an organization. Is this so from your end?

Chinwendu Joy Enyidiegwu (16:44:20) (in thread): > @Kate Rasheednot at all

Chinwendu Joy Enyidiegwu (16:45:13) (in thread): > pls try again

Mary Agekameh (17:05:25) (in thread): > Well done@Chinwendu Joy Enyidiegwu

Aleru Divine (17:07:30) (in thread): > @Chinwendu Joy Enyidiegwucan you download the pdf and share with us, since wedon’thave access.:pray:

Precious Orakwe (18:18:53) (in thread): > Well done@Chinwendu Joy Enyidiegwu

Precious Orakwe (18:29:35) (in thread): > @Aleru Divine for signature 1 where I have the 2 unassigned, how do I curate them, for signature 1 in table 5 and sig. 2 in table 7, that was a mistake, I asked @svetlana_up to help me delete it, how do I go about sig. 4 and 5

Aleru Divine (18:58:04) (in thread): > Since we know their families, I think we can curate as > > unclassified Lachnospiraceae and unclassified Peptostreptococcaceae

2024-10-08

Monisa Hasnain (01:32:13): > @Svetlana Ugarcina Perovic@Esther Afuape<@UBNSEMS3S>I just missed one question so resubmitted the form and recorded a contribution today. please consider this second form as final.

Monisa Hasnain (01:33:25): > @Svetlana Ugarcina Perovic@Esther Afuape<@UBNSEMS3S>i need help regarding timeline.

Kate Rasheed (01:45:01) (in thread): > @Chinwendu Joy EnyidiegwuI tried accessing it again with a laptop, it’s still asking for access to full article.

Mildred Anashie (01:52:55) (in thread): > Hi@Chinwendu Joy Enyidiegwuplease share the PDF you are working with > > Same here@Kate Rasheed

Aleru Divine (02:46:46): > Good morning everyone:sunny:Please I need some clarification on my study design. > > The researchersmonitored both groups over time(professionals and amateurs) and compared them based on their exposure to different levels ofphysical activity. > > Then they measured changes in the microbiota of professional football players before and after an intensive workout (within the same group). -This part suggests a Time series.The article itself says the study is aprospective cohortstudy design.@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace SandyThis is the study:https://bugsigdb.org/Study_1105

Mildred Anashie (03:22:23) (in thread): > Good morning@Aleru DivineWell done on your curation:clap:This study is a bit tricky, it’s easy to agree it is a prospective cohort study but they collected samples from the professional team two more times and that’s the part that is making it confusing and looking like a longitudinal study design > > I believe it’s a prospective cohort though, waiting to see if I am wrong:sweat_smile:I’ll like to hear our mentors opinions on this

Mildred Anashie (03:23:15) (in thread): - File (JPEG): IMG_1231

Aleru Divine (03:24:56) (in thread): > Thanks@Mildred Anashie, I do too but I need a confirmation:pleading_face:Thank you so much:heart_hands:Fingers crossed:crossed_fingers:

Kate Rasheed (03:31:24) (in thread): > It appears to be a longitudinal study design cause there were results from “before” and “after”.

Aleru Divine (03:36:44) (in thread): > @Kate Rasheedthank you so much:heart_hands:For experiments 1 and 2, they did a prospective cohort study.Then 3 and 4 is longitudinal.But the study itself says Prospective study.That’swhy I got confused:pleading_face:

Kate Rasheed (03:37:50) (in thread): > You can add the two study designs if that’s the case. It is a longitudinal prospective cohort study:smile:

Adeshile Oluwatosin (03:40:03) (in thread): > :joy_cat::joy_cat::joy_cat:@Kate Rasheed

Aleru Divine (03:40:11) (in thread): > :joy::face_with_open_eyes_and_hand_over_mouth:Since the study aimed to compare the gut and oral microbiota composition of professional male football players and amateurs primarily, I think taking the first study design would be the best approach.But Idon’tknow, hence my bringing it up for other opinions and confirmation from the mentors.

Svetlana Ugarcina Perovic (03:41:16): > :drum_with_drumsticks:**** ****@Scholastica Urua**** is a star!****Scholar won the prize for the best#MVIF31 MicroTalk!Thank you for making us proud.Your mentors and community,@Svetlana Ugarcina Perovic<@UBNSEMS3S><@U1LCB8WEA>The recording of Scholar’s talk is available here:https://cassyni.com/events/PCDrxRvshFLTn9mPnyxdLh?cb=functi - Attachment (Cassyni): African microbiome data in BugSigDB - presented by Pharm. Scholastica Urua > The complexity and diversity in microbiome research pose difficulties in consolidating and evaluating existing knowledge. BugSigDB, an op…

Kate Rasheed (03:42:23) (in thread): > Congratulations@Scholastica Urua. A scholar star indeed.

Mildred Anashie (03:43:15) (in thread): > Congratulations@Scholastica Urua:tada::confetti_ball::clap:

Princess Rehoboth Asuelimen (03:44:16) (in thread): > Wow.:astonished:Congratulations@Scholastica Urua:clap:

Aleru Divine (03:44:24) (in thread): > Amazing!:grinning_face_with_star_eyes:Congratulations@Scholastica Urua:sparkles::partying_face:

Adeshile Oluwatosin (03:50:06) (in thread): > Congratulations@Scholastica Urua:tada::tada::tada:

Svetlana Ugarcina Perovic (03:52:03) (in thread): > feel free to ask your community here for this matter

Adeshile Oluwatosin (03:52:54) (in thread): > Deadline is October 29th, is that what you are asking for?@Monisa Hasnain

Svetlana Ugarcina Perovic (03:53:15) (in thread): > Since it’s not open access paper, we provided herehttps://github.com/waldronlab/BugSigDBcuration/issues/496also the pdf! - Attachment: #496 Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice > Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Bethany A. Masson – Brain, Behavior, and Immunity > > https://www.sciencedirect.com/science/article/pii/S088915912400624X
> 1-s2.0-S088915912400624X-main.pdf

Aleru Divine (03:55:43) (in thread): > Thanks@Svetlana Ugarcina Perovic

Kate Rasheed (03:57:48) (in thread): > @Svetlana Ugarcina PerovicIt is still requesting for organization mail or name

Svetlana Ugarcina Perovic (04:00:09) (in thread): > @Kate Rasheedclick on the 2nd link “1-s2.0-S088915912400624X-main.pdf”

Aleru Divine (04:00:11) (in thread): > @Svetlana Ugarcina Perovicdoes this confirm Prospective cohort as the study design?:pray:

Kate Rasheed (04:06:23) (in thread): > Thanks@Svetlana Ugarcina PerovicI’ve gotten it.

Aleru Divine (04:14:33) (in thread): > Okay, thank you so much:blush:

Scholastica Urua (04:21:53) (in thread): > Awwwn:smiling_face_with_3_hearts:Thank you so much@Svetlana Ugarcina Perovic:dancer:, won’t have done it if you hadn’t inspired me:blush:.

Scholastica Urua (04:22:08) (in thread): > Thank you so much everyone:heavy_heart_exclamation_mark_ornament:

Adeshile Oluwatosin (04:22:35) (in thread): > Welcome mentor@Scholastica Urua:hugging_face::partying_face:

Scholastica Urua (04:26:42) (in thread): > I’m so grateful to the co-authors and mentors@Chioma Onyido@Esther Afuape@Levi Waldron<@UBNSEMS3S>and@Svetlana Ugarcina Perovic:pray::sparkling_heart:. > > Thank you!!!!:blush:

Mildred Anashie (04:30:04) (in thread): > Prospective cohort it is then:blush:

Mildred Anashie (04:33:10) (in thread): > @Kate RasheedYou should go through this thread > > I think it will help with the “recording two study designs” suggestion:upside_down_face:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710175781553689 - Attachment: Attachment > Hi everyone, hope we are all having a splendid time. > how feasible is it for a study to employ two study designs and when that is the case, are both the study designs accounted for? > @Svetlana Ugarcina Perovic @Peace Sandy @Esther Afuape @Chioma Onyido

Precious Orakwe (04:46:40) (in thread): > Congratulation Scholarpat, u r the best, you did a great job. > Kudos:hugging_face:

Precious Orakwe (04:51:05) (in thread): > Thank you

Kate Rasheed (06:16:19): > Good day everyone. It’s few hours to this forum. See you here. > > It’s 1:30pm for WAThttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728026261034569?thread_ts=1728026261.034569&cid=C04RATV9VCY - Attachment: Attachment > Good morning :potted_plant: > > Today I have a special invitation for you: > join us next week at MVIF (Microbiome Virtual International Forum), a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > https://www.microbiome-vif.org/en-US/-/future-events/mvif32-78-9-october-2024 > > We’ve been organizing this event monthly since 2021, you can see recordings here: https://www.youtube.com/@MicrobiomeVIF/playlists

Adeshile Oluwatosin (06:19:27) (in thread): > Noted@Kate Rasheed

Mildred Anashie (06:34:04) (in thread): > Thank you for the reminder@Kate Rasheed

Svetlana Ugarcina Perovic (07:55:35) (in thread): > It is tomorrowhttps://www.timeanddate.com/worldclock/converter.html?iso=20241009T123000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Adeshile Oluwatosin (07:59:20) (in thread): > Okay, thank you@Svetlana Ugarcina Perovic

Rahila-me (08:02:38) (in thread): > @Scholastica Uruacongratulation on this. Kudos:bioc::smiling_face_with_3_hearts:

Mohamed Osman Omar (09:34:10): > Hello everyone.

Adeshile Oluwatosin (09:36:30) (in thread): > Hello@Mohamed Osman Omar:hugging_face:

Mohamed Osman Omar (09:42:15): > Hello everyone. I just completed the required one or first contribution<@UBNSEMS3S>@Aleru Divine@Esther Afuape@Chioma Onyido@Adeshile Oluwatosinplease review my onehttps://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey

Adeshile Oluwatosin (09:54:31) (in thread): > Hi@Mohamed Osman OmarI don’tthink we can view your responses for the first contribution

Adeshile Oluwatosin (09:55:17) (in thread): > The link redirects to a totally unresponded page and does not show your answers.

Adeshile Oluwatosin (09:56:09) (in thread): > Regardless, hope you answered all questions

Adeshile Oluwatosin (09:56:50) (in thread): > If yes, proceed to the second contribution

Aleru Divine (09:57:12) (in thread): > Welldoneon completing the first contribution:partying_face:@Mohamed Osman OmarOnly the mentors have access to the first contribution.

adekemi balogun (10:06:32) (in thread): > Congratulations@Scholastica Urua, weldone:tada:

PATIENCE ONAH (10:09:00) (in thread): > Hi@Aleru Divine, trust you are doing good. Please I need help again, for the experiment 1 and 2, the Wilcoxon rank sum test was used to identify the differential taxon b/w HC and IR/ INR which is represented in Additional file 1 figure S1 and also the LEfSe test represented in Additional file 4 S4 also provided the differential taxon b/w HC and IR/INR with more number of taxon. I’m confused, I don’t know which to use for both statistical test and the signatures. > Also I’m not sure how to record the Group 0 and group 1 in experiment 3 since it’s comparing IR and INR. > I recorded 28 and 30 for the group 1 in experiment 1 and 2 respectively, is it correct.

Aleru Divine (10:11:34) (in thread): > Hi@PATIENCE ONAHI’mwalking home.I’ll check this as soon as I get home.:pray:

PATIENCE ONAH (10:12:26) (in thread): > No problem, thank you

Mohamed Osman Omar (10:16:53) (in thread): > yes, I have done,

Precious Orakwe (10:17:10): > Good day@Svetlana Ugarcina Perovicplease can you delete Signature 2 in experiments 3,4 and 5, in my experiment 5, I have 3 signatures, and Signature 1 and the 3rd signature are the correct ones. > I want to delete Signature 2 and use signature 3 as sig. 2. > Thank youhttps://bugsigdb.org/Study_1106 - Attachment (BugSigDB): Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations - BugSigDB > Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results.

Adeshile Oluwatosin (10:17:38) (in thread): > Record your first contribution on outreachy > https://www.outreachy.org

Adeshile Oluwatosin (10:17:42) (in thread): > Have you done this?

Adeshile Oluwatosin (10:17:52) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny:

Precious Orakwe (10:21:06): > Good day<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Peace Sandy@Scholastica Uruaplease I need a review on my study for any corrections before I can submit my study. > Thanks > > Link to my studyhttps://bugsigdb.org/Study_1106 - Attachment (BugSigDB): Meta-analysis of effects of exclusive breastfeeding on infant gut microbiota across populations - BugSigDB > Previous studies on the differences in gut microbiota between exclusively breastfed (EBF) and non-EBF infants have provided highly variable results.

Mildred Anashie (10:21:47) (in thread): > Well done on completing your first contribution:clap:@Mohamed Osman OmarRecord following the steps@Adeshile Oluwatosinhas shared and proceed to the second contribution, if youhaven’tFeel free to ask questions, I’m very sureyou’llget prompt and timely responses:blush:

Kate Rasheed (10:24:23) (in thread): > Weldone@Precious Orakwe. I would like to find out if we are supposed to submit the study and how to go about it.

Precious Orakwe (10:34:14) (in thread): > @Kate Rasheed, you can tag the mentors here with the link to your study or on GitHub and tell them that your study is ready for review, but make sure that you are done with your study because when once the tag “needs review” has been placed on your study, you can not make further corrections.

Mildred Anashie (10:38:20) (in thread): > Hello@Kate RasheedJust comment on the issue on GitHub with a link to the study informing the mentors that it is ready for review

Mildred Anashie (10:42:13) (in thread): > @Precious OrakweIf your study is ready for grading by the mentors, you should tag them to it on GitHub > If you have done that already, then I think you should be patient asIt’llbe graded.There’salso somethinghereon that - Attachment: Attachment > For FAQ check out this link https://github.com/waldronlab/BugSigDBcuration/issues/96

Precious Orakwe (10:44:06) (in thread): > @Mildred Anashiei am not submitting for grading, I submitted for review here in the group for corrections before i submit on Github for grading.

Mildred Anashie (10:48:34) (in thread): > Okay@Precious OrakweForgive me:pray:I felt you were talking about submission for grading since you tagged the mentors to your post > In my opinion, peer review is done by fellow contributors just to get other opinions before you submit to the mentors

Precious Orakwe (10:53:50) (in thread): > Okay, thanks

Svetlana Ugarcina Perovic (10:55:44) (in thread): > This message is very hard to follow. We should try to write concise and precise as much as we can, for example:Please delete the following:https://bugsigdb.org/Study_1106/Experiment_3/Signature_2https://bugsigdb.org/Study_1106/Experiment_4/Signature_2https://bugsigdb.org/Study_1106/Experiment_5/Signature_2In https://bugsigdb.org/Study_1106/Experiment_5Signature 1 and 3 should remain.

Svetlana Ugarcina Perovic (10:56:41) (in thread): > Status: deleted.

Svetlana Ugarcina Perovic (11:02:31): > UPDATE when your experiment or signature not showing upTemporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot: - File (PNG): —.png

Mildred Anashie (11:04:36) (in thread): > Thank you for this update@Svetlana Ugarcina Perovic:pray:

Precious Orakwe (11:05:03): > Thanks@Svetlana Ugarcina Perovicfor the update

Kate Rasheed (11:12:22): > Hello everyone. Looking at this article:https://www.nature.com/articles/s41598-024-72057-z#citeas, I can see one experiment done (Control group vs AP models). I would like to seek your opinion. Do you think the experiments should be sub-divided? > > Just like@Aleru Divineclaims, looking at it from a different eyes helps see better:smile:. Looking forward to your opinions. - Attachment (Nature): Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis > Scientific Reports - Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis

Peace Daniel (11:14:23) (in thread): > Nice initiative

Aleru Divine (11:17:37) (in thread): > Wow! Thank you so much@Svetlana Ugarcina Perovicand the team that came up with this solution:relieved::heart_hands:

Adeshile Oluwatosin (11:46:25) (in thread): > Thank you for this@Svetlana Ugarcina Perovic

Aleru Divine (11:51:18) (in thread): > @PATIENCE ONAHI’m so sorry for taking so much time. I was super hungry:face_with_open_eyes_and_hand_over_mouth:so assoon as I got home, I had to eat.Okay, to address your concerns,Innon case-control studies, we are to group according to disease severityLow severityof disease = group 0 > High severity of disease = group 1 > > Forthe experiment that compares IR and INR,I’dsay group according to different immune responses. > > Immunological non-responders (INR) = group 0 > Immunological responders (IR) = group 1Addressing the Statistical Analysis > > **We are to use/curate the statistical test that was used for differential abundance testing.
> > In this study, “the Wilcoxon rank sum test was used to detect taxa with significant differences inrelative abundancesamong groups.” > > While “LEfSe used the Kruskal-Wallis rank sum test to detect features withsignificant different abundancesbetween the assigned taxa.”Here’sanother excerpt to help “In order to identify the key phylotypes responsible for the difference found in distinguishing the fecal microbiota of different groups, linear discriminant analysis (LDA) effect size (LEfSe) was performed and a threshold of three on effect size was used.” > > LEfSe was used for differential abundance testing.

Aleru Divine (11:52:51) (in thread): > Hi@Kate Rasheed:sweat_smile:I’ll have a look with fresh eyes:face_with_open_eyes_and_hand_over_mouth::sweat_smile:

Kate Rasheed (11:57:46) (in thread): > Thank you Divine

Rahila-me (12:28:58) (in thread): > This works, thank you@Svetlana Ugarcina Perovic

Aleru Divine (13:24:36) (in thread): > @Kate RasheedThe study explored the species composition and characteristics of the structure of intestinal microbiota in three AP mouse models. (The Caerulein group, the Caerulein + LPS group, and the L-arginine group) > > Figure 3(a,b,c) shows alpha diversity measures for the 3 groups and the control group > > Figure 4(c, d, e) shows differential abundance results for > > Controls vs Caerulein group > Controls vs Caerulein + LPS group > Controls vs L-arginine group > > There’s a total of 3 experiments in this study.

Kate Rasheed (13:49:28) (in thread): > You are correct. Thank you.

Princess Rehoboth Asuelimen (14:09:04): > Hello everyone, please I need your help in interpreting this figure in the study I am currently curating. I don’t know if there is any differential abundance here, I would appreciate any help I can get. Thank you. - File (PNG): Screenshot 2024-10-08 132940.png

Mildred Anashie (14:11:04) (in thread): > Hi@Princess Rehoboth AsuelimenThis looks like a cladogramI’mpositive they might be LEfSe results in the full figure > Please share the full figure

Adeshile Oluwatosin (14:14:29) (in thread): > Hi@Princess Rehoboth AsuelimenI can see D, can you share the full diagram for easy interpretation > This is a cladogram

Adeshile Oluwatosin (14:15:21) (in thread): > Definitely both colours indicate something, one for increase and the other for a decrease

Princess Rehoboth Asuelimen (14:16:24) (in thread): - File (PNG): Screenshot 2024-10-08 191536.png

Princess Rehoboth Asuelimen (14:17:06) (in thread): - File (PNG): Screenshot 2024-10-08 191352.png

Mildred Anashie (14:20:20) (in thread): > At this pointI’llhave to request for link to the paper > > Please share a link to the study

Princess Rehoboth Asuelimen (14:21:09) (in thread): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01852-7#Sec2 - Attachment (BioMed Central): Diet at birth is critical for healthy growth, independent of effects on the gut microbiota - Microbiome > Background Colostrum is the first milk for a newborn. Its high content in microbiota shaping compounds and its intake at the time of gut microbiota seeding suggests colostrum may be critical in the establishment of a healthy microbiota. There is also accumulating evidence on the importance of the gut microbiota for healthy growth. Here, we aimed to investigate the contribution of colostrum, and colostrum-induced microbiota to growth promotion. Addressing this question is highly significant because (1) globally, less than half of the newborns are fully colostrum fed (2) the evidence for the importance of the microbiota for the prevention of undernutrition has only been demonstrated in juvenile or adult pre-clinical models while stunting already starts before weaning. Results To address the importance of diet at birth in growth failure, we developed a unique mouse model in which neonates are breastfed by mothers at an advanced stage of lactation who no longer provide colostrum. Feeding newborn mice with mature milk instead of colostrum resulted in significant growth retardation associated with the biological features of chronic undernutrition, such as low leptin levels, dyslipidemia, systemic inflammation, and growth hormone resistance. We next investigated the role of colostrum in microbiota shaping. At the end of the lactation period, we found a major difference in gut microbiota alpha diversity, beta diversity, and taxa distribution in control and colostrum-deprived mice. To determine the causal relationship between changes in microbiota and growth trajectories, we repeated our experiment in germ-free mice. The beneficial effect of colostrum on growth remained in the absence of microbiota. Conclusion Our data suggest that colostrum may play an important role in the prevention of growth failure. They highlight that the interplay between neonatal gut microbiome assembly and diet may not be as crucial for growth control in the developing newborn as described in young adults. This opens a paradigm shift that will foster research for colostrum’s bioactives that may exert a similar effect to microbiota-derived ligands in promoting growth and lead to new avenues of translational research for newborn-tailored prevention of stunting. Video Abstract

Mildred Anashie (14:35:08) (in thread): > Yea I believe you should curate that, although it’s not the usual LEfSe plot I’m used to interpreting but this seems straight forward because they said “Colostrum shapes infant mice microbiota. 16S rRNA gene analysis of microbiota in faeces from 20-day-old specific pathogen-free (SPF) mice reared with (black) and without colostrum (red).” So we can see which is increased in which group for the experiment and I believe the color code also applies to the alpha diversity. > > But please wait for confirmation from the mentors@Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica UruaPlease a little help here:pray:

Adeshile Oluwatosin (14:39:41) (in thread): > From my opinion > > Colostrum shapes infant mice microbiota. 16S rRNA gene analysis of microbiota in faeces from 20-day-old specific pathogen-free (SPF) mice reared with (black) and without colostrum (red). > > Black indicates an increase > And red a decrease > > But like@Mildred Anashiesaid await the opinion of the mentors, also correct me if I’m wrong Mildred.

Princess Rehoboth Asuelimen (14:40:29) (in thread): > Alright, thank you.

Adeshile Oluwatosin (14:41:16) (in thread): > It looks curatable to me though

Mildred Anashie (14:44:16) (in thread): > Black indicates an increase in the “Specific pathogen free mice reared” which should be our Group 1 and Red indicates an increase in “Without colostrum” which should be Group 0. > > However interpreted by the experiment done and by@Princess Rehoboth Asuelimenone would be increase and the other decrease > > So yea@Adeshile Oluwatosinyou are right

Svetlana Ugarcina Perovic (14:50:46) (in thread): > This curation is full of cladogramshttps://bugsigdb.org/Study_896See, as an example, how they can be interpreted. - Attachment (BugSigDB): Effects of proton pump inhibitor on the human gut microbiome profile in multi-ethnic groups in Singapore - BugSigDB > INTRODUCTION: The objectives of this study were to examine the effects of ethnicity, gender and a proton pump inhibitor (PPI), omeprazole, on the human gut microbiome.PPIs are commonly used for the treatment of acid-related disorders.

Princess Rehoboth Asuelimen (14:52:47) (in thread): > Alright, I will check it out. Thank you.

Mildred Anashie (14:56:35) (in thread): > The interpretation is right > The color code shows you which group the taxas are increased in@Princess Rehoboth AsuelimenEventually one would be decreased (Increased in Group 0) and the other increased (Increased in your Group 1) > > Thank you so much@Svetlana Ugarcina Perovic:pray:

Adeshile Oluwatosin (14:57:53) (in thread): > Thank you@Svetlana Ugarcina Perovic

Samuel Nnanna (15:32:20): > i’d like to know what’s next after the second contribution, do i pick another paper to curate?@Svetlana Ugarcina Perovic

Princess Rehoboth Asuelimen (15:35:56) (in thread): > I think you’ll have to wait until your second contribution is reviewed before picking another paper and moving on to the next one. While waiting, you can help others review their contributions.

Mildred Anashie (15:36:49) (in thread): > you can go through this, I believe that question was answered herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727950394376939?thread_ts=1727950036.699409&channel=C04RATV9VCY&message_ts=1727950394.376939 - Attachment: Attachment > For FAQ check out this link https://github.com/waldronlab/BugSigDBcuration/issues/96

BOLARINWA AISHAT (15:39:39): > Hello everyone. > > Please how do you confirm that the paperyou’recurating will have experiment 1 (signature 1 and 2) and experiment 2 (signature 1 and 2) > > Thank you.

Aleru Divine (15:41:30) (in thread): > The experiments in a study solely depends on the comparisons they made on the paper. > > The signatures depend on whether they found differential abundance results or notfor the compared groups.Can you share a link to your paper please:pray:

Rahila-me (15:42:46) (in thread): > @Samuel Nnannaonce the paper you curated has be changed to needs review you can request for another one but as you wait, you can check the help page to fix some other things

Mildred Anashie (15:42:49) (in thread): > Have you gone through the curation policy?Here’sthe linkhttps://bugsigdb.org/Curation_PolicyIf yes share a link to your paper,let’ssee if we can guide you - Attachment (BugSigDB): Curation Policy > …

Rahila-me (15:43:43) (in thread): > @Mildred Anashiewhat she said will help you better go through the policy

Samuel Nnanna (15:47:56) (in thread): > thank you so much for the clarifications

BOLARINWA AISHAT (15:56:51) (in thread): > Thank you very much > > > The study has two contrasts soI’llbe curating for two experiments:pray:

Aleru Divine (15:59:41) (in thread): > Do you mean they compared 2 groups? > > If so, thenit’llbe one experiment (group 0 vs group 1.)

BOLARINWA AISHAT (16:06:24) (in thread): > They compared two groups about eight months apart. > > Will it still be two experiments please?

Aleru Divine (16:07:59) (in thread): > Okay,that’sjust one experiment then.

PATIENCE ONAH (16:09:26) (in thread): > I’m so sorry for my late response, I got busy with homework too, thank you so much for your sacrifice@Aleru Divine. I really appreciate. I got your explanation and it’s really helpful to clear my confusion. > Please you will help me to review the study when am done:pray:. Thank you so much:tulip::tulip:

Aleru Divine (16:10:21) (in thread): > No worries:hugging_face:Let me know whenyou’redone

BOLARINWA AISHAT (16:11:19) (in thread): > There’s a result for the samples of the offspring at birth for control and case > > and another result for the samples of the offspring at 8months of life for control and case

PATIENCE ONAH (16:13:20) (in thread): > Alright, thank you

Aleru Divine (16:14:32) (in thread): > That is two experiments then. > > One for offspring at birth where you compare cases and controls > > Another for offspring at 8 months where you again compare cases and controls

BOLARINWA AISHAT (16:15:00) (in thread): > It’s clear now. > I appreciate:pray:

BOLARINWA AISHAT (17:36:28) (in thread): > Thank you very much > > Just encountered same issue and it worked.

BOLARINWA AISHAT (18:29:55): > Hello everyone > > If the initial sample size is say 120 and after DNA extraction,it was reduced to 117. > > Which sample size are we curating please? > > Thank you.

Inimfon Ebong (20:31:13): > “The 16S rRNA sequencing data were analyzed with QIIME > 1.80. The β-diversity (differences between microbial > communities) was analyzed according to the unweighted > UniFrac distance. Principal coordinates analysis (PCoA), > a dimensionality reduction method that illustrates the relationships > between samples based on a distance matrix, > was performed to highlight the differences between different > groups using the R package “ade4.” For microbial analysis, > the Adonis test was performed. The relative abundance of > dominant taxa is shown in stacked bar plots constructed > using the R package “ggplot2.” To identify differentiated > metagenomic biomarkers, a linear discriminant analysis > (LDA) coupled with effect-size measurement (LEfSe) was > performed athttp://huttenhower.sph.harvard.edu/galaxy. > Significantly different bacteria with LDA scores of ≥2.5 > were plotted on taxonomic bar plots. The relative abundance > of microorganisms and concentrations of SCFAs are shown > as box plots. The Pearson correlation coefficients were > calculated and visualized by heat map inRusing the “shiny” > package.” > > for a situation such as this what exactly will i pick as my statistical tool if soo many were used?

Inimfon Ebong (20:31:45): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Scholastica Urua@Esther Afuape

Adeshile Oluwatosin (22:35:07) (in thread): > @Samuel Nnannasimply tag a mentor on GitHub to request for your paper to be reviewed, wait to be graded and await further instructions from mentors.

Adeshile Oluwatosin (22:37:37) (in thread): > @BOLARINWA AISHATthe final sample size: 117

Adeshile Oluwatosin (22:37:58) (in thread): > You can share your article to be sure

Adeshile Oluwatosin (22:39:37) (in thread): > In my knowledge, always curate the final sample size used for analysis.

Adeshile Oluwatosin (22:42:07) (in thread): > @Inimfon EbongIn a situation where so many statistical tests were used, you should focus and pick the ‘primary one’.

Aleru Divine (23:50:27) (in thread): > Yes@BOLARINWA AISHATdefinitely the final sample size, it means some initially selected participants were excluded from the study. > > Sometimes they state the reason, sometimes theydon’t.

2024-10-09

Aleru Divine (00:04:12) (in thread): > Hi@Inimfon EbongFor the statistical test, we’re to curate only the test that was used for differential abundance testing in the case where they mention multiple. > > According topart ofthe excerpt you shared,“To identify differentiated metagenomic biomarkers, a linear discriminant analysis (LDA) coupled with effect-size measurement (LEfSe) was performed athttp://huttenhower.sph.harvard.edu/galaxy. Significantly different bacteria with LDA scores of ≥2.5 were plotted on taxonomic bar plots.” > > LEfSe was used to identify specific microbial biomarkers with significant differences in abundancein this case.

Mildred Anashie (00:37:12) (in thread): > I agree with@Aleru DivineLEfSe is the statistical test used and the LDA score would be 2.5 from what you shared@Inimfon Ebong

Inimfon Ebong (00:41:43) (in thread): > thank you

Inimfon Ebong (00:46:33): > Please I have a question I noticed that some people have been asking to have one thing or another deleted for them, was it after the final submission or something cos I’ve been using the incomplete save button

Adeshile Oluwatosin (01:35:25) (in thread): > @Inimfon EbongThey request to delete a mistake made while curating as only mentors can do that

Adeshile Oluwatosin (01:36:34) (in thread): > For instance, I mistakenly created an experiment or signature > Only mentors can help delete this…In this case, all you need to do is tag a mentor and state which experiment or signature you want to delete.

Adeshile Oluwatosin (01:37:50) (in thread): > The incomplete button should be used when all details are not filled yet. > Ensure you change it to complete when done !!!

BOLARINWA AISHAT (01:41:39) (in thread): > Alright thank you so much@Aleru Divine@Adeshile Oluwatosin

Aleru Divine (01:58:34) (in thread): > Nicely explained@Adeshile Oluwatosin

Adeshile Oluwatosin (02:03:49) (in thread): > You are welcome

Chris Awoke (02:32:40) (in thread): > Awesome:heart_eyes:Big congratulations@Scholastica Urua:tada:

Adeshile Oluwatosin (02:46:20): > Good morning everyone > > Set your alarms for this! > 1:30PM WAT starting Today:relieved:https://community-bioc.slack.com/archives/C04RATV9VCY/p1728026261034569?thread_ts=1728026261.034569&cid=C04RATV9VCY - Attachment: Attachment > Good morning :potted_plant: > > Today I have a special invitation for you: > join us next week at MVIF (Microbiome Virtual International Forum), a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > https://www.microbiome-vif.org/en-US/-/future-events/mvif32-78-9-october-2024 > > We’ve been organizing this event monthly since 2021, you can see recordings here: https://www.youtube.com/@MicrobiomeVIF/playlists

Svetlana Ugarcina Perovic (02:54:15): > Good morning:teapot:how are you today? > > We’re curious to hear about your experience with BugSigDB.**** What do you find to be the most challenging aspect of the curation process?****We’d love to hear your thoughts and learn how you’ve overcome any obstacles you’ve faced so far.See you today at MVIF!https://community-bioc.slack.com/archives/C04RATV9VCY/p1728026261034569?thread_ts=1728026261.034569&cid=C04RATV9VCY

Aleru Divine (03:18:30) (in thread): > Good morning@Svetlana Ugarcina Perovic:blush:I’m doing great, thank you! > > My experience with BugSigDB has been amazing, and I love how we’re all collaborating and supporting each other. > > The most challenging aspect of curation for me has been the attention to detail required with signatures. It’s easy to miss something, especially when there are many signatures identified. Finding ones not already in BugSigDB can take extra time, but the discussion page has been incredibly helpful. Thanks to everyone who has contributed to it so far. > > I did face a challenge with identifying the particular statistical test in the study I just finished curating, but it was clarified during office hours, and I’ve learned a lot about the right conditions for curation. > > I’m really enjoying contributing and look forward to learning even more!:hugging_face:

Aleru Divine (03:19:40) (in thread): > Oh and see you all at MVIF:sweat_smile:

Mildred Anashie (03:46:40) (in thread): > Good morning@Svetlana Ugarcina Perovic:teapot:I’m doing well, thank you:blush:First of all this community is great and an interesting place to be. It’s been an absolute pleasure contributing and online-meeting you all:hugging_face:The most amazing aspect of curation for me has to be curating signatures Unlike Divine:smile:especially ones I can easily find on NCBI > > Then the most challenging has to be interpreting figures, especially ones that are not LEfSe plots:woman-facepalming:But with asking questions and help from fellow contributors I always figure it out and I’m grateful for the support this community provides:hugging_face:See you at MVIF

Rahila-me (03:49:06) (in thread): > Good morning@Svetlana Ugarcina Perovicsure i will be there. Thank you > > This a wonderful community and i am happy to be here bugsiging:bioc:One of the most challenging aspects of the curation process in BugSigDB for me is determining whether there ismicrobial taxonomic heterogeneity (MTH)in the dataset. This involves carefully reviewing each study to assess if the microbial communities exhibit significant variation, which can sometimes be difficult due to inconsistent or unclear reporting in the original papers. Additionally, ensuring that the correctalpha diversity metrics(such as Shannon, Chao1, and Faith’s PD) are assigned to each experiment adds to the complexity. Studies often report diversity indices differently, or in some cases, don’t report all of them, requiring me to interpret the data accurately and cross-reference with the proper metrics. > To overcome these obstacles, I’ve developed a systematic approach that involves detailed scrutiny of the study methods and results sections, combined with consulting similar studies for reference when necessary. Keeping up-to-date with standard definitions and metrics used in microbial research also helps me make informed decisions when curating data, ensuring consistency and accuracy in the final database entries.

Adeshile Oluwatosin (03:53:46) (in thread): > Good morning@Svetlana Ugarcina Perovic:hugging_face:My experience has been great so far, I love how everyone is welcoming and willing to help, assist one another. It’s a great opportunity to be contributing in this community. > > The most challenging part for me in curation is identifying signatures and experiments to create in some articles, > Especially when the study is complex. > > I’ve been super careful in providing solutions. > I’m grateful for the tips shared as this has assisted as well. > Thank you, as I look forward to contributing more.

Princess Rehoboth Asuelimen (03:55:15) (in thread): > Good morning@Svetlana Ugarcina Perovic, I am doing alright. > The journey so far has been lovely, I love the fact that everyone on this platform has a sense of togetherness. > > The most challenging part so far has been interpreting the results of the experiment, you can easily get confused on what is the right interpretation. > But this challenge is also what makes this experience more interesting. Looking forward to making more contribution.

BOLARINWA AISHAT (04:31:23) (in thread): > Good morning@Svetlana Ugarcina PerovicMy experience with BugSigDB has been great. I enjoy every part of the curation process and I love the prompt responses and helpful energy from the community. > > My challenge so far is getting my updated curations to reflect on the page but it gets better with the refresh option tip that was shared earlier. > > I look forward to learning more and curating more papers

Samuel Nnanna (04:32:02) (in thread): > Good morning@Svetlana Ugarcina Perovic. I am doing okay, how about you? > > The experience has been amazing with the BugSigDB project but the most challenging part has been the being reporting/interpreting the results as accurate as possible, there are so many important details in the papers and being able to tell which is necessary for the curation has been quite challenging.

BOLARINWA AISHAT (04:41:20): > Hello everyone > > One of the signature I have in the paperI’mcurating is Rothia and there are two entries for it with distinct taxonomic id ie 32207 and 508215 > > How do I know which one to choose please? > > Thank you

USLACKBOT (04:43:42): > This message was deleted.

Princess Rehoboth Asuelimen (04:50:56) (in thread): > Hello@BOLARINWA AISHAT, Ithink you should consider the context of your paper. If your study is focused on human health (especially oral or respiratory systems), Rothia mucilaginosa (32207) is more likely to be relevant. However, if the study involves other environments (e.g., soil, non-human hosts), the other taxonomic ID could be appropriate. I stand to be corrected.

Mildred Anashie (04:52:49) (in thread): > Hi@BOLARINWA AISHATI usually do a google search to be sure if the taxa has another name and that helps my decision > > Although if what are looking for is the Rothia <high G+C Gram-positive bacteria then you should go for 32207, which I’m thinking is the one you should use:thinking_face:Other opinions might differ though

Svetlana Ugarcina Perovic (05:11:24) (in thread): > Submitted for review. (Please update your message above)

Aleru Divine (05:19:38) (in thread): > @BOLARINWA AISHATthe context of the paper would determine which of the two you should go for I agree with@Princess Rehoboth AsuelimenIf your paper reports on Rothia in the context of microbiology, micro organisms (which is very likely the case here), you should go withRothia <high G+C Gram-positive bacteria>. This refers to a genus of bacteria. > > TheRothia reference is a different context, as eudicots refer to a group of plants. This is likely referring to a plant.

Kate Rasheed (05:21:13) (in thread): > Good morning@Svetlana Ugarcina Perovic. It’s been an amazing experience, sleeping and waking with curating thoughts:smile:. > > In the course of curating, I’ve discovered how helpful microbiomes can be. Looking forward to learning more about microbiomes.

Adeshile Oluwatosin (05:23:31) (in thread): > Hi@BOLARINWA AISHATI agree with what@Princess Rehoboth AsuelimenYou can drop the title of your issue so i can specify the exact taxonomic id to be used in your case.

Mildred Anashie (05:25:03) (in thread): > Deleted already > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:41:20) (in thread): > @Mildred Anashieplease note we are not deleting our messages, work, reports etc. instead we are updating it with the latest info, status etc.

Mildred Anashie (05:42:16) (in thread): > I apologize for this:pray:This has been duly noted

Svetlana Ugarcina Perovic (05:42:53) (in thread): > If you take a look at my message above “(Pleaseupdate your message above)”, there was no delete suggestion:slightly_smiling_face:

Kate Rasheed (05:47:19): > Good morning@Svetlana Ugarcina Perovic. Kindly delete Signature 2 under experiment 1. > > Here is the link to the studyhttps://bugsigdb.org/Study_1110 - Attachment (BugSigDB): Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis - BugSigDB > Acute pancreatitis (AP) is an inflammatory disease of the pancreas.Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy.

Mildred Anashie (05:47:59) (in thread): > Update on the request earlier made seeking for peer review on the study**** I just finished curating > > ****I already submitted for review by the mentors and the “needs review tag” has been added to it on GitHub, therefore I can’t make changes to it any longer > Thank you all for your help > > Thank you again@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (05:48:41) (in thread): > Deleted.

Svetlana Ugarcina Perovic (05:49:51) (in thread): > Thanks for the update!

Kate Rasheed (05:49:57) (in thread): > Thank you so much.

BOLARINWA AISHAT (06:37:40) (in thread): > Thank you all

Svetlana Ugarcina Perovic (06:54:50) (in thread): > You have reported challenges in: > 1. Identifying experiments and signatures: > > * Easy to miss details, especially when there are many signatures > * Finding signatures not already in BugSigDB can be time-consuming > > 1. Interpreting figures and results: > > * Difficulty interpreting complex figures, especially those that are not LEfSe* plots > > 1. Identifying particular statistical testsused in studies > Despite these challenges, I am happy that you have generally reported positive experiences and have been enjoying your team work. > > Why did I ask you about challenges? As of this morning, following a week since the initiation of the curation process, over 20 curations have encountered roadblocks (Seehttps://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aopen+is%3Aissue+label%3Aassigned). If you’ve completed your curation, please reach out to your colleagues and identify areas where they’ve faced difficulties.Collaborate to find solutions together.— > > *Interesting fact about the LEfSe: > LEfSe is indeed the most common statistical analysis still in use, but there is MaAsLin, an evolution of LEfSe that can consider a wider number and variety of metadata, recommended by the LEfSe developers to be used instead of LEfSe

Aleru Divine (07:06:50): > Hi everyone, I’m currently done with my second contribution and waiting to be graded:crossed_fingers:If you are having any blockers please reach out, you can leave a comment or tag me@AleruDivineto theissue/study or just ask your questions on the channel so we can walk through it together.:muscle:I am very available to help out:hugging_face:I’m looking forward to collaborating with you all.

Matthew Idungafa (07:14:42) (in thread): > Hy , Please how can i get started?

Adeshile Oluwatosin (07:15:25) (in thread): > With the second contribution?@Matthew Idungafa

Adeshile Oluwatosin (07:15:53) (in thread): > If yes, request for an article to curate on github

Adeshile Oluwatosin (07:16:10) (in thread): > Tag a mentor, onceit’sassigned to you > You can begin curating

Adeshile Oluwatosin (07:16:46) (in thread): > https://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

Adeshile Oluwatosin (07:17:28) (in thread): > Also, request for an account on bugsigdb if you don’t have one

Adeshile Oluwatosin (07:21:10) (in thread): > Check for an article here, please do not choose an assigned article ;https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22

Precious Orakwe (07:21:24): > @Svetlana Ugarcina Perovicgood day. > My experiment 5 is sig.1 and sig. 3 instead of sig. 1 and sig. 2. > How can I change the number to 2

Aleru Divine (07:21:43) (in thread): > Thanks@Adeshile Oluwatosin

Aleru Divine (07:22:29) (in thread): > @Matthew Idungafadid you mean starting with the first or second contribution?

Aleru Divine (07:26:01) (in thread): > @Precious OrakweThis is because you requested for signature 2 in experiment 5 to be deleted previously. Now that you added another signature, it is recognized automatically as signature 3 even if it is signature 2. > > But this is not a problem to be concerned about. > > I have encountered this previously and was assured it is okay.

Kate Rasheed (07:46:14): > Good day@Svetlana Ugarcina PerovicI’ve being manually curating my experiments and signatures. I can see them reflected on my contribution but can’t see it on my study. On my study, it stops at Signature 1 of experiment 3. > > I’ve refreshed and refreshed. I’ve also reloaded on phone and laptop. Kindly confirm if you can see the curation up to signature 2 in experiment 4. > > Here is a link to my study:https://bugsigdb.org/Study_1110 - Attachment (BugSigDB): Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis - BugSigDB > Acute pancreatitis (AP) is an inflammatory disease of the pancreas.Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy.

Adeshile Oluwatosin (07:53:00) (in thread): > Check this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Adeshile Oluwatosin (07:53:24) (in thread): > Have you tried checking this way?

Aleru Divine (07:53:56) (in thread): > I checked and I see up to signature 1 in experiment 4@Kate RasheedI refreshed a few times too and it’s still the same.

Adeshile Oluwatosin (07:55:59) (in thread): > It stops at experiment 3, signature 1 here

Adeshile Oluwatosin (07:56:38) (in thread): > Detailed explanation:relieved:

Kate Rasheed (07:57:55) (in thread): > Amazing:smile:. I’m glad it has gotten to experiment 4 in@Aleru Divinelocation:sweat_smile:. I would have to wait for it to be complete before submitting.

Aleru Divine (08:01:19) (in thread): > You really don’t have to wait until it’s completely showing. > > Since the mentors are awareof this situation. Ibelieve they will check for it to confirm if you curated it.

Aleru Divine (08:07:24) (in thread): > I noticed some highlighted signatures in your curation.For example “Ignavibacteriota” in signature 1 experiment 4.Did you check for them in NCBI taxonomy browser to copy their tax IDs?

Adeshile Oluwatosin (08:08:14) (in thread): > I was about to say thatItseems like a lot of missing NCBI IDs

Kate Rasheed (08:08:27) (in thread): > I copied them from NCBI

Kate Rasheed (08:08:56) (in thread): > That was the issue I was having on this signature thing. A lot of them aren’t on BugSigDB yet and from the curation policy, we were requested to curate them even if they aren’t on BugSigDB

Aleru Divine (08:09:42) (in thread): > Did you copy the IDs?

Aleru Divine (08:10:23) (in thread): > You have to paste the ID itselfand not the namesfor it to automatically populate in your study and remove the highlights

Adeshile Oluwatosin (08:10:28) (in thread): > Checked discussion page too?

Kate Rasheed (08:11:34) (in thread): > @Adeshile OluwatosinI’ve checked the discussion page. Nothing was said concerning some of them@Esther Afuape. > > I’ll do as@Aleru Divinesaid now. Let’s see if it would work.

Adeshile Oluwatosin (08:12:23) (in thread): > Ifyou’vechecked NCBI and discussion page > And you stillcan’tfind anything on them > Check google if the names has been changed, then check NCBI again

Adeshile Oluwatosin (08:12:32) (in thread): > If nothing, leave it as it is

Aleru Divine (08:13:21) (in thread): > @Kate Rasheed:crossed_fingers:

Adeshile Oluwatosin (08:15:36): > @Esther Afuape@Svetlana Ugarcina Perovic@Scholastica Urua@Chioma Onyido<@UBNSEMS3S>In the new article I’ve curated. Figure 2 titled ‘Gut microbiota with significantly different relative abundance between the two groups at genus level in Metastats analysis’ > > It’s noted that relative abundances are not curated in bugsigdb, but from the link below.@Chioma Onyidowrote something on special cases where some can still be curated as long as the figure states a differential abundance.https://community-bioc.slack.com/archives/C04RATV9VCY/p1711398678527379?thread_ts=1711390782.792099&channel=C04RATV9VCY&message_ts=1711398678.527379In my case, I would like to confirm that Figure 2 is curatable.https://bugsigdb.org/Study_1115Link to the article;https://www.mdpi.com/2076-3425/13/8/1217 - Attachment: Attachment > Bottomline: I know it’s stated that we only curate differential abundance on bugsigdb but in some cases (like fig 3b, 4b and 5b), these relative abundance figures clearly shows the significant differences between the groups, not just the taxa each group contains (as seen in 3a, 4a and 5a). > > Mann-Whitney results (Fig 3b, 4b and 5b) are curatable) but since they overlap significantly with the Lefse results which has larger signatures, I would curate just Lefse to avoid redundancy. > I hope this helps. Great team work here honestly! :clap::skin-tone-5: - Attachment (BugSigDB): The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia - BugSigDB > BACKGROUND: Stroke-associated pneumonia (SAP) is a common stroke complication, and the changes in the gut microbiota composition may play a role.Our study aimed to evaluate the predictive ability of gut microbiota for SAP. - Attachment (MDPI): The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia > Background: Stroke-associated pneumonia (SAP) is a common stroke complication, and the changes in the gut microbiota composition may play a role. Our study aimed to evaluate the predictive ability of gut microbiota for SAP. Methods: Acute ischemic stroke patients were prospectively enrolled and divided into two groups based on the presence or absence of SAP. The composition of gut microbiota was characterized by the 16S RNA Miseq sequencing. The gut microbiota that differed significantly between groups were incorporated into the conventional risk scores, the Acute Ischemic Stroke-Associated Pneumonia Score (AIS-APS), and the Age, Atrial fibrillation, Dysphagia, Sex, Stroke Severity Score (A2DS2). The predictive performances were assessed in terms of the area under the curve (AUC), the Net Reclassification Improvement (NRI), and the Integrated Discrimination Improvement (IDI) indices. Results: A total of 135 patients were enrolled, of whom 43 had SAP (31%). The short-chain fatty acids (SCFAs)-producing bacteria, such as Bacteroides, Fusicatenibacter, and Butyricicoccus, were decreased in the SAP group. The integrated models showed better predictive ability for SAP (AUC = 0.813, NRI = 0.333, p = 0.052, IDI = 0.038, p = 0.018, for AIS-APS; AUC = 0.816, NRI = 0.575, p < 0.001, IDI = 0.043, p = 0.007, for A2DS2) in comparison to the differential genera (AUC = 0.699) and each predictive score (AUCAISAPS = 0.777; AUCA2DS2 = 0.777). Conclusions: The lower abundance of SCFAs-producing gut microbiota after acute ischemic stroke was associated with SAP and may play a role in SAP prediction.

Chioma Onyido (08:18:21) (in thread): > Please share the link to the article, let’s take a look.

Adeshile Oluwatosin (08:19:54) (in thread): > https://www.mdpi.com/2076-3425/13/8/1217@Chioma Onyido - Attachment (MDPI): The Potential of Gut Microbiota in Prediction of Stroke-Associated Pneumonia > Background: Stroke-associated pneumonia (SAP) is a common stroke complication, and the changes in the gut microbiota composition may play a role. Our study aimed to evaluate the predictive ability of gut microbiota for SAP. Methods: Acute ischemic stroke patients were prospectively enrolled and divided into two groups based on the presence or absence of SAP. The composition of gut microbiota was characterized by the 16S RNA Miseq sequencing. The gut microbiota that differed significantly between groups were incorporated into the conventional risk scores, the Acute Ischemic Stroke-Associated Pneumonia Score (AIS-APS), and the Age, Atrial fibrillation, Dysphagia, Sex, Stroke Severity Score (A2DS2). The predictive performances were assessed in terms of the area under the curve (AUC), the Net Reclassification Improvement (NRI), and the Integrated Discrimination Improvement (IDI) indices. Results: A total of 135 patients were enrolled, of whom 43 had SAP (31%). The short-chain fatty acids (SCFAs)-producing bacteria, such as Bacteroides, Fusicatenibacter, and Butyricicoccus, were decreased in the SAP group. The integrated models showed better predictive ability for SAP (AUC = 0.813, NRI = 0.333, p = 0.052, IDI = 0.038, p = 0.018, for AIS-APS; AUC = 0.816, NRI = 0.575, p < 0.001, IDI = 0.043, p = 0.007, for A2DS2) in comparison to the differential genera (AUC = 0.699) and each predictive score (AUCAISAPS = 0.777; AUCA2DS2 = 0.777). Conclusions: The lower abundance of SCFAs-producing gut microbiota after acute ischemic stroke was associated with SAP and may play a role in SAP prediction.

Scholastica Urua (08:22:04) (in thread): > @Kate RasheedYou can always try what@Svetlana Ugarcina Perovicsuggested if refreshing it doesn’t work:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&cid=C04RATV9VCYhttps://bugsigdb.org/Study_1110/Experiment_4/Signature_2 - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values. - Attachment (BugSigDB): Study 1110/Experiment 4/Signature 2 > Source: Fig. S1, Table S1 Description: Decrease of microbiomes in L-arginine group as seen in “L-arginine sheet” of the supplementary table. Abundance in Group…

Kate Rasheed (08:23:28) (in thread): > Thanks everyone. I can see all my experiments and signatures.@Aleru DivineOne of the ID’s worked let me try for others.

Aleru Divine (08:25:10) (in thread): > Yay!:grin:

Adeshile Oluwatosin (08:26:15) (in thread): > :hugging_face:

Inimfon Ebong (08:29:33): > Good afternoon everyone ,

Inimfon Ebong (08:31:33): > please is it possible to get a curated article plus the article itself > like for the article we were given for the quiz I would also like to see the final curation. it would help me understand some points better

Mildred Anashie (08:32:28) (in thread): > Yes you can@Inimfon Ebong

Adeshile Oluwatosin (08:32:33): > Join! 1:30PM WAThttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728026261034569?thread_ts=1728026261.034569&cid=C04RATV9VCY - Attachment: Attachment > Good morning :potted_plant: > > Today I have a special invitation for you: > join us next week at MVIF (Microbiome Virtual International Forum), a virtual, free and inclusive alternative to a traditional multi-day microbiome conference. > > https://www.microbiome-vif.org/en-US/-/future-events/mvif32-78-9-october-2024 > > We’ve been organizing this event monthly since 2021, you can see recordings here: https://www.youtube.com/@MicrobiomeVIF/playlists

Inimfon Ebong (08:33:06) (in thread): > thank you@Adeshile Oluwatosinill make sure to change it once I’m done

Inimfon Ebong (08:33:27) (in thread): > do you have a sample?

Adeshile Oluwatosin (08:36:13) (in thread): > Yes,there’sa link

Mildred Anashie (08:39:06) (in thread): > Try if this workshttps://bugsigdb.org/Special:RandomInCategory/Studies - Attachment (BugSigDB): The active lung microbiota landscape of COVID-19 patients through the metatranscriptome data analysis - BugSigDB > Introduction: With the outbreak of coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the interaction between the host and SARS-CoV-2 was widely studied.

Mildred Anashie (08:39:24) (in thread): > It takes you to a random study on BugSigdb

Mildred Anashie (08:41:20) (in thread): > If you look at the top of your screenyou’dsee random page > Everytime you click on it a different study that has been reviewed pops up > > Shared a screenshot to show where you can find it@Inimfon Ebong - File (JPEG): IMG_1291

Mildred Anashie (08:47:06) (in thread): > Hi everyone > > I’m also done and awaiting grading > > You can reach out to me if you are experiencing any blockers or tag me to the issue on GitHub @MyleeeA

Inimfon Ebong (08:49:24) (in thread): > wow! > OK thank you so much this is very helpful

Adeshile Oluwatosin (08:49:54) (in thread): > Has anyone been able to join the session?

Kate Rasheed (08:51:53) (in thread): > No ooo. I’ve been trying it isn’t working@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (08:52:22) (in thread): > Same here

Svetlana Ugarcina Perovic (08:52:27) (in thread): > The point is to approach a colleague from a particular GitHub issue, and to encourage them to open for support.

Svetlana Ugarcina Perovic (08:54:19) (in thread): > General offering your support usually does not reach stuck team mates.

Kate Rasheed (08:56:13) (in thread): > I’ve joined now@Adeshile Oluwatosin. Did you register?

Aleru Divine (08:57:40) (in thread): > Got it@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (08:57:50) (in thread): > Noted@Svetlana Ugarcina Perovic

Mildred Anashie (08:58:30) (in thread): > Noted@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (08:58:41) (in thread): > Yes I did

Mildred Anashie (08:58:55) (in thread): > You are welcome:hugging_face:Glad I could help

Princess Rehoboth Asuelimen (08:59:51) (in thread): > Noted@Svetlana Ugarcina Perovic

Matthew Idungafa (09:01:22) (in thread): > Noted@Svetlana Ugarcina Perovic

Kate Rasheed (09:01:47) (in thread): > Check your reminder mail and enter through the link.

Adeshile Oluwatosin (09:03:32) (in thread): > Yeah,itsays webpage unavailable

Rahila-me (09:03:44): > <!here>Good afternoon all, I am done with my second curation and doing some cleanup on the help page. If you are stuck on anything please reach out to me I will be glad to help. > I am open for collaboration. > Thank you

Adeshile Oluwatosin (09:04:04) (in thread): > I await a response:pray:Thank you

Adeshile Oluwatosin (09:17:05) (in thread): > @Svetlana Ugarcina Perovicsuggested we reach out to people instead > As general support does not reach people that needs support

Adeshile Oluwatosin (09:18:53) (in thread): > I’min now:relieved:

Chioma Onyido (09:20:19) (in thread): > Hi Tosin, I noticed that some of the taxa in the Lefse figure overlaps with those from Figure 2.

Chioma Onyido (09:21:23) (in thread): > The stat method used for figure 2 says Metastats. Is that available in the dropdown on bugsigdb?

Adeshile Oluwatosin (09:21:43) (in thread): > Yes

Adeshile Oluwatosin (09:22:26) (in thread): - File (JPEG): IMG_1462

Chioma Onyido (09:22:44) (in thread): > Great. If that figure has significant taxa not available in the Lefse figure, I think it should be curated as a separate experiment.

Adeshile Oluwatosin (09:23:23) (in thread): > Noted, it already has been created > I just wanted to confirm > Thank you so much@Chioma OnyidoYou are amazing:hugging_face::hugging_face:I really appreciate

Adeshile Oluwatosin (09:24:02) (in thread): > As for the taxa overlaps, should I not mention them in the second experiment

Chioma Onyido (09:24:07) (in thread): > You’rewelcome!

Adeshile Oluwatosin (09:24:30) (in thread): > Or just list all of them even though they overlap with Figure 3b

Chioma Onyido (09:24:52) (in thread): > Let’s do it this way. Howmanyunique taxa were reported using metastats?

Adeshile Oluwatosin (09:26:48) (in thread): > Bacteroides > Butyricimonas > Coprococcus

Adeshile Oluwatosin (09:26:58) (in thread): > Just 3, which has an increased abundance

Adeshile Oluwatosin (09:27:19) (in thread): > So the second experiment, has just one signature

Chioma Onyido (09:28:06) (in thread): > Okay please go ahead and curate. You can list all taxa too.

Adeshile Oluwatosin (09:28:31) (in thread): > All 6 taxa have been created in the second experiment

Adeshile Oluwatosin (09:31:05) (in thread): > Also I would like to clarify the MHT correction for the article

Adeshile Oluwatosin (09:31:13) (in thread): - File (JPEG): IMG_1463

Adeshile Oluwatosin (09:32:38) (in thread): > It was stated vividly that multiple testing was done > But in the curation policy, I noted that LeFSe results do not have MHT testing. > > In this case since, there are 2 experiments > I inputted MHT correction to be No for LEFSE (Experiment 1) > And Yes for Metastats(Experiment 2)

Adeshile Oluwatosin (09:32:44) (in thread): > Kindly correct me if I’m wrong

Chioma Onyido (09:34:40) (in thread): > :+1:

Mohamed Osman Omar (09:34:42) (in thread): > thanks

Adeshile Oluwatosin (09:35:14) (in thread): > Great:hugging_face:

Rahila-me (09:35:40) (in thread): > Okay how do we reach out. How do i know does that needs help and what help they need so that i can reach out. Thank you

Adeshile Oluwatosin (09:35:46) (in thread): > Welcome@Mohamed Osman Omar:hugging_face:

Chioma Onyido (09:36:02) (in thread): > See the pvalues and adj p values under with *).

Adeshile Oluwatosin (09:38:19) (in thread): > I guess GitHub

Adeshile Oluwatosin (09:38:36) (in thread): > Assigned issues but have not been submitted

Rahila-me (09:40:52) (in thread): > Okay thank you

Adeshile Oluwatosin (09:41:22) (in thread): > You are welcome:hugging_face:

Mohamed Osman Omar (10:03:23) (in thread): > I hope this link is the expected onehttps://www.outreachy.org/outreachy-dec-2024-internship-cohort/communities/bioconductor/microbiome-study-curation/contributions/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Mohamed Osman Omar (10:03:50): > I finished the required onehttps://www.outreachy.org/outreachy-dec-2024-internship-cohort/communities/bioconductor/microbiome-study-curation/contributions/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Mildred Anashie (10:05:34) (in thread): > I’vebeen having trouble accessing the event > > But I just finally joined

Rahila-me (10:07:14) (in thread): > @Mildred Anashieplease can you send me the link

Rahila-me (10:07:37) (in thread): > i am not able to join

Mildred Anashie (10:07:53) (in thread): > https://streamyard.com/watch/VQz8nJc4fKEr - Attachment (StreamYard): MVIF 32 - with Keynote talk by Prof. Susan Bullman [ATLANTIC event] > You’ve been invited to join this webinar!

Mildred Anashie (10:08:13) (in thread): > I hope I shared the right link

Mohamed Osman Omar (10:08:21) (in thread): > @Mildred Anashiehello

Rahila-me (10:09:13) (in thread): > Thank you, i have joined. yes you did

Adeshile Oluwatosin (10:17:12) (in thread): > Okay, have you started the second contribution?

Adeshile Oluwatosin (10:17:36) (in thread): > If youhaven’tFirst request to curate an issue on Github

Adeshile Oluwatosin (10:18:49) (in thread): > @Mohamed Osman Omaryes,it’scorrect to record your first contribution

Mohamed Osman Omar (10:20:07) (in thread): > Thanks@Adeshile Oluwatosin

Adeshile Oluwatosin (10:20:41) (in thread): > Go ahead to request to curate an issue on github to begin the second contribution

Mohamed Osman Omar (10:20:45) (in thread): > @Mildred AnashieThanks

Kate Rasheed (12:12:10): > Good afternoon everyone. In curating my signature, I discovered that when I used ID 1655434, it changed Candidatus Lokiarchaeota to Promethearchaeota which is not found in NCBI. Also ID 28890 changed Euryarchaeota to Methanobacteriota which is actually a synonym in NCBI. > > What can I do concerning the first case, change the ID to taxon name or leave it like that?@Svetlana Ugarcina Perovic@Scholastica Urua@Peace SandyI’ve gone through the discussion page and saw nothing related to this.

Mildred Anashie (12:15:52) (in thread): > Hi@Kate RasheedIs the taxa you are looking for “Candidatus Lokiarchaeota”?

Kate Rasheed (12:16:08) (in thread): > Yes

Aleru Divine (12:17:50) (in thread): > @Kate RasheedIt changedCandidatus LokiarchaeotatoPromethearchaeota because that is the current name at the moment. It’s the same signature. > > They change signature names all the time.
> > If you look at the image I shared, you’ll see that “Candidatus Lokiarchaeota” is the heterotypic synonym. > > There’s no need to change it. It’s correct. - File (JPEG): IMG_1181

Mildred Anashie (12:18:25) (in thread): > Okay > I see that “Promethearchaeota” is the current name for it - File (JPEG): IMG_1292

Kate Rasheed (12:18:58) (in thread): > Amazing I checked NCBI and saw no record:sweat_smile:. Thanks everyone.

Mildred Anashie (12:19:54) (in thread): > You are welcome@Aleru Divineis right > > Taxas have synonyms on NCBI because scientific names can change over time due to various reasons.

Aleru Divine (12:21:11) (in thread): > That’s right@Mildred Anashie. Maybe I should check why they do that:sweat_smile:Adventure time now:school_satchel:

Kate Rasheed (12:21:44) (in thread): > Yes Mildred. I saw it in most cases. I’m wondering why this one said no record at first.

Mildred Anashie (12:23:43) (in thread): > I actually checked@Aleru Divineand what I got was that, scientific names often change due to taxonomic revisions, historical naming variations, and adherence to nomenclatural rules. > > These synonyms are maintained to avoid confusion, helping researchers track the classification history of organisms and ensuring accurate species identification.

Aleru Divine (12:25:36) (in thread): > Thank Goodness they maintain the synonyms cos we’ll all be confused without them.:sweat_smile:

Adeshile Oluwatosin (12:52:57) (in thread): > :+1:

Adeshile Oluwatosin (12:58:10) (in thread): > Heterotypic synonyms

Princess Rehoboth Asuelimen (13:28:23): > Hi@Svetlana Ugarcina Perovic@Scholastica Urua@Peace Sandy@Chioma Onyido@Esther AfuapePlease can you help me delete signatures 3 & 4. Here’s the link:https://bugsigdb.org/Study_1141 - Attachment (BugSigDB): Diet at birth is critical for healthy growth, independent of effects on the gut microbiota - BugSigDB > BACKGROUND: Colostrum is the first milk for a newborn.Its high content in microbiota shaping compounds and its intake at the time of gut microbiota seeding suggests colostrum may be critical in the establishment of a healthy microbiota.

BOLARINWA AISHAT (14:06:27) (in thread): > I agree with you@Mildred AnashieI encountered something similar and I had to google it to be surethey’rethe same

BOLARINWA AISHAT (14:08:43) (in thread): > Yes > Please be on the look out for issues that are tagged ‘outreachy dec2024’ and ‘paper to curate’ > > Those are the ones you should choose from

BOLARINWA AISHAT (14:10:32) (in thread): > Thank you for you kind gesture@Rahila-mePeople also post their questions on this channel for support.

BOLARINWA AISHAT (14:11:32) (in thread): > Thank you > Duly noted

Svetlana Ugarcina Perovic (16:15:25) (in thread): > Deleted.

Svetlana Ugarcina Perovic (16:18:53): > Tomorrow (Thursday) isour weekly team meeting and office hours at 9 AM EDT. Questions are the keys to understanding. Bring them all up. > cc<@UBNSEMS3S>

Kate Rasheed (16:27:32) (in thread): > Thanks for the reminder

Adeshile Oluwatosin (16:47:25) (in thread): > Thank you for reminding !

Adeshile Oluwatosin (16:47:42) (in thread): > 2PM WAT everyone

Chris Awoke (18:20:41) (in thread): > Thank you,@Svetlana Ugarcina PerovicAlways an amazing time to learn.

Aleru Divine (18:57:37) (in thread): > Looking forward to it:blush:

2024-10-10

Mildred Anashie (00:04:58) (in thread): > Looking forward to it:hugging_face:

Ibizugbe Merit (01:35:39) (in thread): > Thank you so much for the reminder:hugging_face:

inyang john (02:19:34) (in thread): > Thank you Ma. Looking forward to it:dancer:

Chinwendu Joy Enyidiegwu (03:39:48) (in thread): > thank you

Princess Rehoboth Asuelimen (03:42:24) (in thread): > Looking forward to it

Princess Rehoboth Asuelimen (03:42:48) (in thread): > Thank you@Svetlana Ugarcina Perovic

Rahila-me (03:52:30) (in thread): > Thursdays are a happy day because of this meeting:dancer::dancer::dancer:

Adeshile Oluwatosin (03:52:50) (in thread): > To be very honest@Rahila-me:sunglasses:

Cynthia Iwuoha (05:30:06): > Hi Everyone, I have a challenge, after I have saved my first contribution record on microbiome study curation, the message I got stated that I’ve recorded that I made a contribution to the following projects: Bioconductor - Developing MolEvolvR for protein analysis: extending the web app, and creating a companion R package while the contribution I recorded was for microbiome study curation as shown on the attached screenshot. Please how do I sort this out because I am applying for microbiome study curation only?

Adeshile Oluwatosin (05:30:52) (in thread): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Esther Afuape

Adeshile Oluwatosin (05:31:16) (in thread): > I suggested she probablydidn’tchoose Microbiome study curation. > Kindly help out

Adeshile Oluwatosin (05:32:31) (in thread): > This is what she can see - File (PNG): IMG_1514

Aleru Divine (05:34:23) (in thread): > @Cynthia Iwuohait seems like you recorded a contribution for theMolEvolvR projectand not theMicrobiome Curation Project. Here’s the link to theMicrobiome Curation Projecthttps://www.outreachy.org/outreachy-dec-2024-internship-cohort/communities/bioconductor/#microbiome-study-curationYou should record your contribution here instead. - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Adeshile Oluwatosin (05:35:21) (in thread): > I told her to do that already, hopefully that corrects it

Adeshile Oluwatosin (05:35:26) (in thread): > We just wanted to be sure

Adeshile Oluwatosin (05:35:32) (in thread): > Thanks@Aleru Divine

Mildred Anashie (05:36:16) (in thread): > Yea I agree with@Aleru DivineTry recording using the link she shared to see if it works

Aleru Divine (05:36:33) (in thread): > Oh!@Adeshile Oluwatosin:hugging_face:This should work

Princess Rehoboth Asuelimen (05:37:28) (in thread): > Can she record a contribution for another project?Idon’tthink so, so I think she will have to settle for the MolEvolvR project, except the mentors can delete her contribution for MolEvolvR and then she goes for Microbiome project.

Cynthia Iwuoha (05:38:33) (in thread): > Thank you@Adeshile Oluwatosin,@Aleru Divine, I will go back and do the correct.

Adeshile Oluwatosin (05:39:36) (in thread): > We will just wait for the mentors opinions as well, if notshe will probably ask again in today’s meeting@Princess Rehoboth Asuelimen

Aleru Divine (05:41:07) (in thread): > We’re allowed to contribute to more than 1 projectI believe@Princess Rehoboth AsuelimenI’mtrying to find where I saw that.

Aleru Divine (05:43:02) (in thread): > Here@Princess Rehoboth Asuelimen - File (JPEG): IMG_1187

Adeshile Oluwatosin (05:43:23) (in thread): - File (JPEG): IMG_1521

Cynthia Iwuoha (06:33:59) (in thread): > @Svetlana Ugarcina Perovic,@C. Mirzayi (please do not tag this account)@Chioma Onyido,@Esther Afuapekindly delete my previous record for molevolvr, I initially made a mistake by recording for molevolvr instead of microbiome study curation. Please, I would like to record my contribution for bugsigdb instead.

Ebuka Chinwuba (08:49:10): > Hello. Greetings Everyone! My name is Ebuka Chinwuba, From Nigeria, I majored in Microbiology. I’ve been recently accepted as an applicant on outreachy. I want to work on Project Bioconductor, But it all seem confusing. I need an insight on what to do and how to start. Please. Thank You!

Adeshile Oluwatosin (08:49:23) (in thread): > Hello, you initially stated Bioconductor, if you intend on working on Microbiome project, you joined the right channel. > Follow the processes below to get started. > If you have any questions feel free to ask

Adeshile Oluwatosin (08:49:39) (in thread): > Welcome:hugging_face:@Ebuka ChinwubaTo get started ! > * Step 1: Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Step 2: Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Step 3: Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Step 4: Follow this steps to proceed the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the this channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Precious Orakwe (08:51:57) (in thread): > Welcome@Ebuka ChinwubaYou can go through the link above to get started. Good luck

Svetlana Ugarcina Perovic (08:53:08) (in thread): > @Cynthia Iwuohaplease contact the outreachy team, we are not responsible for their platform and we can not do any editing there.

Adeshile Oluwatosin (08:53:43): > Reminder to join the Team’s meetingholding today2PM WAT!!See you there !:blush:

Ebuka Chinwuba (08:55:19) (in thread): > Thank You Very Much@Adeshile Oluwatosin@Precious Orakwe.

Adeshile Oluwatosin (08:56:44) (in thread): > You are welcome:blush:

Precious Orakwe (08:56:53) (in thread): > Thanks for the reminder:+1:

Adeshile Oluwatosin (08:57:30) (in thread): > Welcome:hugging_face:

Precious Orakwe (08:57:36) (in thread): > You’re welcome

Aleru Divine (08:58:10) (in thread): > welcome@Ebuka Chinwuba:hugging_face:

Svetlana Ugarcina Perovic (09:26:21) (in thread): > @Cynthia Iwuohahttps://www.outreachy.org/contact/contact-us/There you can find “Applicant help”https://www.outreachy.org/contact/applicant-help/ - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website! - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Ebuka Chinwuba (09:28:52) (in thread): > @Aleru DivineThose are very insightful, I really Appreciate

Cynthia Iwuoha (09:29:02) (in thread): > @Svetlana Ugarcina PerovicThank you.

inyang john (10:00:47): > @Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)thank you so much for today’s meeting.:clap:

Adeshile Oluwatosin (10:02:02): > Saw this in the chat: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > Centered log ratio -> Rare. ANCOM > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

Samuel Nnanna (10:02:14): > thanks<@UBNSEMS3S>and@Svetlana Ugarcina Perovicfor the clarifications. Very helpful

Mildred Anashie (10:02:22): > What an interesting session > Thank you<@UBNSEMS3S>and@Svetlana Ugarcina PerovicAnd thank you to everyone who asked questions > > I personally learned alot from it:clap::hugging_face:

Adeshile Oluwatosin (10:06:24): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor this session:blush:

Aleru Divine (10:15:41): > Thanks for the session<@UBNSEMS3S>@Svetlana Ugarcina PerovicToo bad I had so many network interruptions:smiling_face_with_tear:Looking forward to the recording:hugging_face:

Aleru Divine (10:16:11) (in thread): > Anytime@Ebuka Chinwuba

Mildred Anashie (10:17:50) (in thread): > Sorry about thatI’msure the recording would be shared onceit’savailable

Aleru Divine (10:31:43) (in thread): > Thanks@Mildred Anashieit was so frustrating

Rahila-me (11:32:14): > Many Thanks<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor today’s session

BOLARINWA AISHAT (14:39:16) (in thread): > Hello everyone. > > I am having a hard time curating the signatures in these images. > I have divided the experiments into three > experiment 1 to compare normal and short sleepers > experiment 2 to compare normal and long sleepers > experiment 3 to compare short and long sleepers > and I have noted, from the discussion, the signatures that are in increased and decreased abundance for each of the three comparisons. > > However, there are some signatures in the image that were not mentioned in the discussion and I don’t know how or where to place them. > > Here is a link to the paper I’m curating :https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255323Thank you very much. - File (PNG): Screenshot (715).png - File (PNG): Screenshot (716).png - File (PNG): Screenshot (717).png - File (PNG): Screenshot (718).png

Aleru Divine (14:42:11) (in thread): > Checking it out@BOLARINWA AISHAT

BOLARINWA AISHAT (14:43:50): > Hello everyone. > > I am having a hard time curating the signatures in these images. > I have divided the experiments into three > experiment 1 to compare normal and short sleepers > experiment 2 to compare normal and long sleepers > experiment 3 to compare short and long sleepers > and I have noted, from the discussion, the signatures that are in increased and decreased abundance for each of the three comparisons. > > However, there are some signatures in the image that were not mentioned in the discussion and I don’t know how or where to place them. > > Here is a link to the paper I’m curating :https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255323Thank you very much. - File (PNG): Screenshot (715).png - File (PNG): Screenshot (716).png - File (PNG): Screenshot (717).png - File (PNG): Screenshot (718).png

Mildred Anashie (14:46:34) (in thread): > Hi@BOLARINWA AISHATI don’t think you should bother about Fig 2. It looks to me like correlation analysis anddoesn’tappear curatable to me@Aleru Divinewhat do you think?Although I see differential abundance in Fig 1d:thinking_face:

Aleru Divine (14:49:29) (in thread): > @BOLARINWA AISHAT, these figures aren’t curatable. > > I checked the paper and Figure 1D is curatableas it shows differential ESV abundance among short, normal and long sleepersThe asterisks represents significance. - File (JPEG): IMG_1193

Aleru Divine (14:52:00) (in thread): > Omg I just dropped a comment on this. > > You’re absolutely right@Mildred Anashiethese figures above aren’t curatable. Figure 1D on the other hand is.With the asterisks differentiating the significant from the insignificant.https://community-bioc.slack.com/archives/C04RATV9VCY/p1728585830862539 - Attachment: Attachment > Hello everyone. > > I am having a hard time curating the signatures in these images. > I have divided the experiments into three > experiment 1 to compare normal and short sleepers > experiment 2 to compare normal and long sleepers > experiment 3 to compare short and long sleepers > and I have noted, from the discussion, the signatures that are in increased and decreased abundance for each of the three comparisons. > > However, there are some signatures in the image that were not mentioned in the discussion and I don’t know how or where to place them. > > Here is a link to the paper I’m curating : https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0255323 > > Thank you very much.

Mildred Anashie (14:53:09) (in thread): > I see your comment now@Aleru Divine

Mildred Anashie (14:55:59) (in thread): > Also@BOLARINWA AISHATyou should check Fig S2 I see some comparisons there, although the alpha diversity is not significant > > Do you think those should be curated? > If not, you can focus on the three experiments with Alpha diversity in Fig 1a and Fig S1

Aleru Divine (14:57:22) (in thread): > Let me have a look too.

Adeshile Oluwatosin (15:06:41) (in thread): > Iwill take a look as well

Kate Rasheed (15:09:54) (in thread): > Yes@Mildred Anashie. I just saw the Fig S1. From the supporting information, there’s already an intro on the difference. She can focus on Fig. S1.

Aleru Divine (15:12:03) (in thread): > Idon’tthink the alpha diversity metrics in figure S2 should be curated@Mildred Anashie.The results shows no difference among the groups and therearen’tany signatures tailored specifically to the groups in each of the country.I think 1a (Shannon) and S1 (Observed OTUs) should be curated.Then figure 1D for signatures.

Mildred Anashie (15:13:09) (in thread): > I agree@Aleru DivineThis just confirmed that - File (JPEG): IMG_1333

Princess Rehoboth Asuelimen (15:44:27) (in thread): > Hi@BOLARINWA AISHATfig 1D for sure should be curated for signature. fig 2 A-F doesn’t show any differential abundance, just reveals the co-occurrence patterns among short sleepers, normal sleepers, and long sleepers.

Cate Ouma (17:18:50): > Hello team, what did you guys say about entries such as the one highlighted in orange. I did not find that taxonomy name in the NCBI database: - File (PNG): image.png - File (PNG): image.png

Adeshile Oluwatosin (17:24:15) (in thread): > Hello@Cate OumaThe orange highlight indicates a missing NCBI ID

Adeshile Oluwatosin (17:24:51) (in thread): > Check for heterotypic synonyms or the discussion page

Adeshile Oluwatosin (17:25:54) (in thread): > The image is currently loading on my side, would check for you

Cate Ouma (17:25:59) (in thread): > Okay. Thank you. What about the one listed as a contaminant?

Mildred Anashie (18:07:12) (in thread): > Yea@Cate OumaCheck the discussion page, something might have been uploaded about it > > If not you can try resolving it by researching on it, or leave itthatway > > For the contaminant, I think itisn’tan issue for BugSigdb

Cate Ouma (18:09:55) (in thread): > Thank you@Mildred Anashieand@Adeshile Oluwatosinfor helping me. I have found it on the discussion page

Aleru Divine (18:10:00) (in thread): > Hi@Cate Ouma, Idon’tthink we should worry about the one listed as a contaminat.I have no idea why butI’mguessingit’sunusual for it to be found in the sample.

Aleru Divine (18:16:07) (in thread): > I haven’t found anything onUnclassifiedClostridium XVII > > But I found Unclassified Clostridiales Family XVIIhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2060928&lvl=3&lin=f&keep=1&srchmode=1&unlock@Mildred Anashie@Adeshile Oluwatosin@Cate OumaWhat do you think? - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (18:17:08) (in thread): > Hi@Aleru DivineI’veliterally been searching everywhere

Adeshile Oluwatosin (18:17:11) (in thread): > Even on google

Adeshile Oluwatosin (18:17:19) (in thread): > And I saw that both are not the same

Adeshile Oluwatosin (18:17:45) (in thread): > Unclassified clostridium XVIII and Unclassified Clostridiales Family XVIII

Adeshile Oluwatosin (18:17:57) (in thread): > I suggest she leaves it the way it is

Aleru Divine (18:18:26) (in thread): > Yeah.It’sbetter left that way I agree

Precious Orakwe (20:01:45): > Hello everyone, how is the contribution phase progressing? The first week of the contribution is over and the second week is gradually coming to an end, and it has been wonderful collaborating with everybody here. > > Here are some recurring questions here in the channel and some answers to them. > Please feel free to add other questions and answers under this thread. I hope this helps someone! > > Q1. I couldn’t find how to record my first contribution. > A: Steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > Q2. When recording the first contribution, what is the ‘merged date’? > A: The merged date refers to the date you submitted your contribution. > > Q3. What URL are we submitting for the first contribution? > A: The link to the curation form:https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHEQ4. After I submit my first contribution, can I go back to edit it if I notice I made a mistake, or if I didn’t add something somewhere? > A: Unfortunately, you cannot edit a submitted contribution but you can make another submission from scratch. > > Q5. Are we making 2 contributions? > A: While you can make as many contributions as possible, the first contribution is compulsory. After completing the first contribution, you may proceed to the second. Although the second contribution is not mandatory, it is advisable to complete it. Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice on the GitHub issue for that curation. > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsQ6. For the second contribution, after Adding a Study in BugSigDB, does it need to be reviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study? > A: You do not need to wait for mentors to review. You can click on the ‘Add Experiment’ button to add an experiment. > > Q7. I want to know how many times I can use the record my contribution option on the Outreachy website. > A: You can use the ‘Record My Contribution’ option as many times as needed, depending on how many contributions you make. > > Q8. How to I get assigned a paper for my second curation? > A: Find an unassigned paper you’ll like to curate viahttps://github.com/waldronlab/BugSigDBcuration/issues, then ask for it to be assigned to you by commenting on it. Mentors will assign it to you if you are the first to request for it. > Good luck to all of us. - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy Intern survey > BugSigDB Outreachy Intern survey - Attachment (BugSigDB): Category:Pages with missing NCBI ID - Attachment (BugSigDB): Help:Contents > …

Cate Ouma (21:25:08): > Hello@Chioma Onyido@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Esther Afuape, and the rest of the team. I’m having an issue when trying to interpret my box plot(Figure 4C). When looking atRuminococcus gnavusin the plot, it can be seen that it is lesser in the ProPD cases(colored grey) than in Controls(colored yellow). However, the numerical data from supplementary Table 3 shows that it is increased in my Group 1(i.e the ProPD cases. Which data should I consider and curate? This is the link to my study:https://www.nature.com/articles/s41467-024-51464-w#data-availability - Attachment (Nature): Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia > Nature Communications - Here, the authors profile the gut microbiome of Ethiopian children suffering from acute and prolonged diarrhea, showing the latter group to exhibit a higher degree of… - File (PNG): image.png - File (PNG): image.png

2024-10-11

Mildred Anashie (03:13:31) (in thread): > Hi@Cate OumaSo this is quite confusing:face_with_diagonal_mouth:I’m unsure if the screenshots I’m about to share means anything, but if it does then I’ll have to go with you focusing on the results from the figure (Fig 4) instead of the supplementary data > > Because I see that the differential abundance results are in Fig 4a-d and that was done with DESeq2 which is the statistical test stated to be used for differential abundance. Whereas the results in the supplementary Table 1-4 is just the Summary statistics with exact q values gotten after Benjamini-Hochberg correction was done > > Although I’ll like to get other opinions on it - File (JPEG): IMG_1337 - File (JPEG): IMG_1336

Aleru Divine (04:01:04) (in thread): > Oh my goodness > Thanks@Mildred Anashie:hugging_face:I totally missed this. > > Although I have a contrary opinion:thinking_face:I may be wrong. > > I think that we should generally take the results from the second test if it was performed to correct or refine the initial differential abundance results(I’m thinking because of the “corrected by Benjamini-Hochberge method…). The second test adds adjustments and corrections, and additional data (exact qvalues) that makes the results more exact and I’ll say more reliable. > > TheDESeq2test provides an initial differential abundance analysis:thumbsup:, but theWilcoxon testwent further to give results withexact q-values. > > But we’ll wait for confirmation from the mentors

Precious Orakwe (04:40:46) (in thread): > In my opinion, I would say we go with@Aleru Divineopinion, because the final result was gotten after a correction was made by Benjamini-Hochberg.

Mildred Anashie (04:46:20) (in thread): > Yea@Aleru DivineThis also makes a lot of sense > > Although, I understood the Tables like just a summary of the Benjamini-Hochberg correction method which was done. I’m of the opinion that the correction was already applied to the results reported in Fig4. > “Boxplot distributions include median, min, max, 25 and 75 percentiles, and outliers (more than 1.5 IQR). ********, ******, **, and , represents q values, <0.0001, <0.001, <0.01, <0.05, respectively, while ns: not significant and q value corrected by Benjamini-Hochberg method (two-sided Wilcoxon rank sum test).” > > But the authors decided to still give a summary of the correction that was done which is now shown in Supplementary Tables 1-4:thinking_face:We’ll have to wait for the mentors opinions

Aleru Divine (04:58:08) (in thread): > Well so why would they change one signature result.:sob:Here@Mildred AnashieSupplementaryTable 3 description: > “Taxa differentially abundant by DESeq2 differential abundance testing. Subsequently differences were tested by two-sided Wilcoxon rank sum test and corrected by the Benjamini-Hochberg method resulting in the stated exact q-values. ProPD (prolonged or persistent diarrhea).” > > A combination of both test results making it more comprehensive I guess. > > I’d like to believe the supplementary tables should be curated because after the subsequent test, the result for******Ruminococcus gnavus******changed.And a note added on the discussion pageto explain why Table 3.

BOLARINWA AISHAT (05:07:24) (in thread): > Thank you all for the contribution, I’ll work on the suggestions and give feedback

Kate Rasheed (05:14:27) (in thread): > @Cate OumaI think the supplementary table should be curated as it could be giving the accurate result after the change by Benjamin Hochberg.

Mildred Anashie (05:20:18) (in thread): > Okay then > > This seems to be 3 similar opinions > > Hopefully I’m wrong@Cate OumaBut I suggest you wait a bit before you carry on with the curation > > A little help here@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Scholastica Urua@Peace Sandy:pray:

Scholastica Urua (05:51:13) (in thread): > Everyone is making excellent points here. > > For this curation, I’ll prioritize the figures (Figure 4)@Cate Ouma. Upon reviewing both the figures and tables, they appear to show the same results, with the exception ofRuminococcus gnavus(which could be a typo). Another difference is that the figure uses * or “NS” to indicate significance, while the table presents the exact q-values numerically. > > Just a side note; It’s important to curate the corrected values if MHT was performed. For this paper, both the figures and the table provide evidence of MHT correction In the figures, it is indicated by the use of q-values (highlighted in the attached image). Additionally, the figure description explicitly mentions the MHT correction. - File (JPEG): q-value.JPG

Mildred Anashie (05:55:12) (in thread): > Thank you@Scholastica UruaFor a better explanation of this:pray:

Scholastica Urua (05:58:29) (in thread): > Based on my personal observations, and something<@UBNSEMS3S>mentioned during office hours yesterday (I believe someone had a similar issue but related to alpha diversity where the figure and text were contrasting), it seems more common to make errors in writing than in images.

Mildred Anashie (06:00:01) (in thread): > Yes thats true, I remember@Adeshile Oluwatosinstudy from yesterday

Cate Ouma (06:01:47) (in thread): > Thank you@Scholastica Uruafor the explanation

Mildred Anashie (06:08:06): > Hello@Svetlana Ugarcina Perovic@Scholastica Urua@Chioma Onyido@Esther Afuape@Peace SandyI am currently assigned to collaborate on a study but I’m yet to begin as I’m waiting on a response from the message I sent to my co-collaborator who happens to be the one originally assigned to the issue (She complained on connection issues yesterday). > > While I wait, as iwouldn’twant to make any changes without her consent, could I work on completing thisstudyI found under incomplete pages? I am sure i can do both when I get a response. > > Thank you:pray: - Attachment (BugSigDB): Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study - BugSigDB > Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis.However, its role in the antipsychotic treatment response is unclear.

Aleru Divine (06:08:44) (in thread): > Thank you so much for the detailed explanation@Scholastica Urua:hugging_face:Duly noted from now on

Adeshile Oluwatosin (06:20:01) (in thread): > Thank you so much for the detailed explanation@Scholastica UruaYesit’ssimilar to the error in my study

Adeshile Oluwatosin (06:20:19): > Hello@Svetlana Ugarcina Perovic@Chioma Onyido@Esther AfuapeI would like to confirm if I can proceed with NCBI cleanup now that I’ve submitted my second contribution.

PATIENCE ONAH (07:21:59): > Hi@Svetlana Ugarcina Perovic, please I need your support, I’m having challenge adding signature to experiment 2 for the study am working on. It doesn’t show up on the study when I save. I have tried the refreshing approach that was recommended several times but it didn’t resolve it. Kindly help me check what could be the issue. > Also help me and delete signature 3 in experiment 1.https://bugsigdb.org/Study_1118 - Attachment (BugSigDB): Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals - BugSigDB > BACKGROUND: Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood.

Adeshile Oluwatosin (07:27:21) (in thread): > Hello@PATIENCE ONAHSeen this yet?https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

PATIENCE ONAH (07:28:59) (in thread): > I have done that, it didn’t resolve it. > Thank you

Adeshile Oluwatosin (07:29:53) (in thread): > Try another browser, if it persists > Maybe@Svetlana Ugarcina Perovicwould have a better solution

Rahila-me (07:42:29) (in thread): > @PATIENCE ONAHyou can dohttps://bugsigdb.org/Study_1118/Experiment_1/Signature_1

Rahila-me (07:42:40) (in thread): > Depends on the one you are looking for

Rahila-me (07:43:01) (in thread): > This will resolve it

Rahila-me (07:43:30) (in thread): > Then when you do refresh it will appear correctly on your study going forward

PATIENCE ONAH (07:48:17) (in thread): > I have tried another browser@Adeshile Oluwatosinbut no positive result

Adeshile Oluwatosin (07:49:07) (in thread): > Kindly try out what@Rahila-mesuggested

PATIENCE ONAH (07:49:10) (in thread): > I didn’t get what you mean@Rahila-me

Rahila-me (07:50:20) (in thread): > In your study on your browser add / experiment or signature the number is the one you want to see

Adeshile Oluwatosin (07:51:08) (in thread): > For ;https://bugsigdb.org/Study_1118/Experiment_2/Signature_1 - Attachment (BugSigDB): Study 1118/Experiment 2/Signature 1 > Source: Additional file 4, figure S4 d Description: Taxonomic differences of fecal microbiota between the, immunological non-responders (INR) and healthy controls…

Cynthia Iwuoha (07:52:01) (in thread): > Thank you for this tips@Svetlana Ugarcina Perovic, I am experiencing the issue presently.

Mildred Anashie (07:52:08) (in thread): > Hi@PATIENCE ONAHCan you try either of this? Let’s see if it works > > While we wait for a better solution from@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728041250257259?thread_ts=1728040350.221289&channel=C04RATV9VCY&message_ts=1728041250.257259https://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&channel=C04RATV9VCY&message_ts=1727957860.907319 - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Adeshile Oluwatosin (07:54:33) (in thread): > I can see an output - File (PNG): IMG_1536

PATIENCE ONAH (07:58:08) (in thread): > Yes, Thank you@Rahila-meand@Adeshile Oluwatosin. I have seen it but then it still doesn’t show on the study when I refresh

Mildred Anashie (07:59:12) (in thread): > Same here@PATIENCE ONAHI can see the signatures for experiment 2 using this methodhttps://bugsigdb.org/Study_1118/Experiment_2/Signature_1

Adeshile Oluwatosin (08:01:03) (in thread): > It’sa Constant issue of which they are aware of > I guess they are working on it > This is just a temporary solution for now. > Idon’tthink you have anything to worry about since the signatures are showing in that view. > > Keep retrying > It should reflect in the study@PATIENCE ONAH

PATIENCE ONAH (08:02:30) (in thread): > Alright then, thanks to you all for your support.

Adeshile Oluwatosin (08:02:51) (in thread): > You are welcome

Kate Rasheed (08:19:40) (in thread): > Yes@PATIENCE ONAH. I’m experiencing the same. In case you want to submit your study, add the link to your study alongside the link to the signature 2.

Scholastica Urua (08:45:39) (in thread): > Before proceeding with the NCBI cleanup, please go through this post by@Esther Afuape:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189Always remember to first check thediscussion pageas some taxa has previously been noted down.Very important:Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. - Attachment: Attachment > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonym on NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replace Escherichia coli with Escherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the 2-hour video of @U1LCB8WEA solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose: - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Adeshile Oluwatosin (08:48:03) (in thread): > Thank you@Scholastica UruaI will do as stated, I just find it interesting to do. > AndI definitely willalways ask before any edit is done.

Adeshile Oluwatosin (09:27:10): > Friendly reminder: Don’t forget to record your second contribution! If you have submitted a link to your study for review on github(To do this…tag a mentor and mention you are done with curation or the issue is ready for review). > > Kindly follow these steps accordingly. > > How to record your second contribution: > * Visit the Outreachy website.https://www.outreachy.org/outreachy-dec-2024-internship-cohort/communities/bioconductor/microbiome-study-curation/contributions/ > * Select the ‘Microbiome Study Curation’ project. > * Click on ‘Record a Contribution’. > * Record your contribution and click save. > Kindly note all of these; > * “Date contribution was accepted or merged” refers to the date you submitted your contribution. > > * Contribution URL is the link to your study submitted on GitHub for review. > > * Write a brief description on how you went about curation. > Ensure you click on the appropriate project.When your github issue is tagged withNeeds review, no edit is allowed.You can always ask for assistance!!! > I’m here to assist. - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Mildred Anashie (09:30:07) (in thread): > Thank you for this@Adeshile OluwatosinAlso anyone not convinced can go through this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711452991192939?thread_ts=1711451428.212249&channel=C04RATV9VCY&message_ts=1711452991.192939. - Attachment: Attachment > This message is for anyone not sure about which merge date to enter when recording contributions on Outreachy. > > Pending when your curation will be reviewed and graded by the mentors, if you’re not sure what merge date to enter when you’re filling out your contribution on Outreachy, you can enter the date when the “needs review” label was attached to your study on GitHub. > I think that’ll fly for now @Svetlana Ugarcina Perovic @Peace Sandy @Esther Afuape @UBNSEMS3S > > See thread for ref… > https://community-bioc.slack.com/archives/C04RATV9VCY/p1711448280247749?thread_ts=1711440276.544779&channel=C04RATV9VCY&message_ts=1711448280.247749

PATIENCE ONAH (09:41:00) (in thread): > Please@Adeshile Oluwatosinkindly help me and check this to see if you can see any result, I saved it but not getting any result when I search the linkhttps://bugsigdb.org/Study_1118/Experiment_2/Signature_2 - Attachment (BugSigDB): Study 1118/Experiment 2/Signature 2 > Source: Additional file 4, figure S4 d Description: Taxonomic differences of fecal microbiota between the immunological non-responders (INR) and healthy controls…

Adeshile Oluwatosin (09:41:38) (in thread): > Okay, a minute@PATIENCE ONAH

PATIENCE ONAH (09:41:53) (in thread): > I’m getting the same result as signature 1

Adeshile Oluwatosin (09:42:31) (in thread): > Yes I can see the result

Mildred Anashie (09:43:23) (in thread): > It is same result as Signature 1@PATIENCE ONAH

Adeshile Oluwatosin (09:43:32) (in thread): > Yeah, I just noticed

Adeshile Oluwatosin (09:43:50) (in thread): > Try re editing again, then click save

PATIENCE ONAH (09:44:27) (in thread): > Hmmm, I don’t know what to do again. I have saved it several times

PATIENCE ONAH (09:44:39) (in thread): > Okay

Mildred Anashie (09:46:03) (in thread): > It could be your connection problem, I think you should restart your device, try to edit it and then save….It might work@PATIENCE ONAH

Adeshile Oluwatosin (09:47:10) (in thread): > It could be network issues, try another browser, re edit and save@PATIENCE ONAH

PATIENCE ONAH (09:51:14) (in thread): > Okay, I’ll try this, thanks to you both

UBNSEMS3S (10:33:44): > Recording of yesterday’s office hours. Thank you for your patience as I’ve been having some fairly significant computer trouble recently. - File (MPEG 4 Video): Gmt20241010-130235 Recording 3840X2160.mp4

Mildred Anashie (10:35:58) (in thread): > Thank you<@UBNSEMS3S>:pray:

Precious Orakwe (10:36:39) (in thread): > Thanks for the explanation@Scholastica Urua

Adeshile Oluwatosin (10:43:54) (in thread): > Thank you<@UBNSEMS3S>

Kate Rasheed (10:56:46) (in thread): > Thank you so much.

Ibizugbe Merit (11:12:49) (in thread): > Thank you so much@C. Mirzayi (please do not tag this account)

Aleru Divine (11:32:40) (in thread): > Yay! Thank you<@UBNSEMS3S>

Kate Rasheed (12:42:18): > Good day@Svetlana Ugarcina PerovicPlease can you delete these studies:https://bugsigdb.org/Study_1121https://bugsigdb.org/Study_1107They are being curated in other studies (1124 and another). > > I would also like to work on this study:https://bugsigdb.org/Study_1084Thank you. - Attachment (BugSigDB): Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries. - BugSigDB > Background > Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV). - Attachment (BugSigDB): - BugSigDB > . - Attachment (BugSigDB): The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life - BugSigDB > Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health.

Svetlana Ugarcina Perovic (12:52:33) (in thread): > deleted.

Kate Rasheed (12:54:23) (in thread): > Thank you@Svetlana Ugarcina PerovicCan I work on the study I mentioned?

Svetlana Ugarcina Perovic (12:57:38) (in thread): > That paper has been curated and reviewed under other study page, seehttps://bugsigdb.org/Study_1085 - Attachment (BugSigDB): The role of Bifidobacterium genus in modulating the neonate microbiota: implications for antibiotic resistance acquisition in early life - BugSigDB > Resistance to antibiotics in newborns is a huge concern as their immune system is still developing, and infections and resistance acquisition in early life have short- and long-term consequences for their health.

Svetlana Ugarcina Perovic (12:58:45) (in thread): > @Kate RasheedYou can easily check this out by putting PMID into Search BugSigDB (in the right upper corner on the platform).

Kate Rasheed (13:00:19) (in thread): > Ohh. Thank you. This is much helpful.

Svetlana Ugarcina Perovic (13:22:01): > We value teamwork, open communication and collaboration, andcontributions that prioritize quality over quantity. > > When selecting papers to curate, explore a wide range of microbiome studies (not limited to one particular disease or type of microbiome) with different statistical analysis (not limited to LEfSe!).Keep up the good work and enjoy your weekend!

Kate Rasheed (13:23:09) (in thread): > Thank you so much@Svetlana Ugarcina Perovic. Enjoy your weekend too.

Mildred Anashie (13:24:05) (in thread): > Hi@Svetlana Ugarcina Perovic:pray:

Mildred Anashie (13:25:42) (in thread): > Thank you so much@Svetlana Ugarcina PerovicDuly noted, Happy weekend:blush:

Svetlana Ugarcina Perovic (13:27:08) (in thread): > @Mildred Anashiecontact@Joyce Qiuto discuss it, seehttps://github.com/waldronlab/BugSigDBcuration/issues/422

Mildred Anashie (13:28:26) (in thread): > Okay@Svetlana Ugarcina PerovicWill do that now > Thank you:pray:

Aleru Divine (13:28:26) (in thread): > Thank you@Svetlana Ugarcina PerovicHave a great weekend:hugging_face:

Samuel Nnanna (13:34:57): > Thanks@Svetlana Ugarcina Perovicand have a great weekend too.

Adeshile Oluwatosin (13:50:33) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy weekend:hugging_face:

Rahila-me (15:44:54) (in thread): > Thanks and happy weekend to you@Svetlana Ugarcina Perovic

Precious Orakwe (17:22:59) (in thread): > Thanks@Svetlana Ugarcina Perovicfor the advice

PATIENCE ONAH (17:32:49): > Kindly help me@Svetlana Ugarcina Perovic,<@UBNSEMS3S>delete these signatures: signature 3 under experiment 1, signature 2, 3, 4, 5, 7, 8, 9, and 10 under experiment 2. I had network challenge and I kept trying to save, I didn’t know it was saving.https://bugsigdb.org/Study_1118 - Attachment (BugSigDB): Altered gut microbiota correlate with different immune responses to HAART in HIV-infected individuals - BugSigDB > BACKGROUND: Although gut microbiota dysbiosis has been reported in HIV infected individuals recently, the relationship between the gut microbiota and immune activation in patients with different immune responses to highly active antiretroviral therapy (HAART) is still not well understood.

2024-10-12

Svetlana Ugarcina Perovic (02:53:39) (in thread): > deleted.

PATIENCE ONAH (05:44:05) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Joy (09:00:13) (in thread): > I just want to be clear@Adeshile Oluwatosin. The contribution URL is something like this right?:https://bugsigdb.org/Study_1084 - Attachment (BugSigDB): - BugSigDB > .

Adeshile Oluwatosin (09:00:43) (in thread): > Yes please@Joy

Joy (09:01:17) (in thread): > Thanks

Joy (09:01:54) (in thread): > And this will go into the url space in the outreach

Adeshile Oluwatosin (09:01:57) (in thread): > This is all I see though - File (PNG): IMG_1555

Adeshile Oluwatosin (09:02:09) (in thread): > Your experiments and signatures should reflect in that one link

Joy (09:02:25) (in thread): > The Outreachy url space.

Adeshile Oluwatosin (09:03:17) (in thread): > Yes you are to fill it via outreachy

Joy (09:03:20) (in thread): > Thanks

Adeshile Oluwatosin (09:04:40) (in thread): > Welcome > If youhave more than one link, i guess you can submit both > But all experiments and signatures created in mine showed in one view

Mildred Anashie (09:07:13) (in thread): > @Adeshile OluwatosinI think shehasn’tcurated the study yet because the PMIDisn’ton BugSigdb@JoyHave you curated the study?

Joy (09:11:56) (in thread): > How do I go about that@Mildred Anashieso that the PMID will be on BugSigdb?

Mildred Anashie (09:13:26) (in thread): > @JoySearch the title of the paper herehttps://pubmed.ncbi.nlm.nih.gov/. - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Adeshile Oluwatosin (09:13:42) (in thread): > To search or get PMID of your Article/issue > 1. Go tohttps://pubmed.ncbi.nlm.nih.gov/ > 2. Search for your article title/topic > 3. Click on cite > 4. Scroll down and you will see the PMID number > 5. Input this intobugsigdb@Joy

Joy (09:14:06) (in thread): > Thanks

Mildred Anashie (09:17:43) (in thread): > Once you copy the PMID and paste on the section for PMID on BugSigDB, thats all you need. > Click on Complete and the other fields will autopopulate for the study section. > > Make sure to select the right study design for your paper@Joy

Adeshile Oluwatosin (09:18:36) (in thread): > Choose “auto”

Joy (09:19:29) (in thread): > Ok. Thanks

Joy (09:20:26) (in thread): > * PMID: 39390034 > This is what I got as the PMID and its different from the DOI right?

Adeshile Oluwatosin (09:21:17) (in thread): > Yes they are different but will direct you to same article@Joy

Adeshile Oluwatosin (09:21:36) (in thread): > Which is the article you are to curate or have curated

Mildred Anashie (09:21:37) (in thread): > Yes, its Different “39390034”

Joy (09:24:40) (in thread): > https://bugsigdb.org/Study_1084 - Attachment (BugSigDB): - BugSigDB > .

Joy (09:25:19) (in thread): > The article populated now

Mildred Anashie (09:25:33) (in thread): > Yes, it looks okay now

Chris Awoke (10:06:28): > Hey friends, > > I hope you’re all doing well and having a great weekend! > > I just wanted to take a moment to express my gratitude for the incredible sense of community, communication, and collaboration we have here at BugSigDB. Thank you all for everything you do. > > A special shoutout to our amazing mentors—@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic,@Chioma Onyido,@Scholastica Urua, and others—for your continued support and guidance. > > Wishing everyone the best. Enjoy the rest of your weekend!

Adeshile Oluwatosin (10:06:40) (in thread): > It’sgood for submission now:thumbsup:@Joy

Adeshile Oluwatosin (10:08:52) (in thread): > Hello@Chris Awoke:wave:I’m also grateful for this community:hugging_face:it’s amazing how we work togetheras a team:blush:

Mildred Anashie (10:28:05) (in thread): > Hi@Chris AwokeMy weekend is going great, Thank you:blush:Right from the first day I joined this community, I’ve felt a sense of belonging and I’m grateful to be part of this community, it’s so easy to reach out and support one another. > > Wishing you the best of the weekend too:bouquet:

Joy (10:43:39) (in thread): > Thanks guys

Aleru Divine (12:51:39) (in thread): > Hi@Chris AwokeI’m doing very well thank you! I hope you are too. > > It’s truly amazing to be part of such a supportive and collaborative team. Big shoutout to our mentors as well > > Wishing you a great weekend and the very best:sparkles:

Cynthia Iwuoha (15:04:21) (in thread): > @Chris Awokeour community is blessed with sweet amazing souls, very supportive.@Adeshile Oluwatosinthank you for all the support.

Adeshile Oluwatosin (15:04:59) (in thread): > You are welcome@Cynthia IwuohaAnytime,I’mhere:hugging_face:

BOLARINWA AISHAT (19:05:10) (in thread): > :hugging_face::hugging_face:

2024-10-13

Precious Orakwe (11:30:09) (in thread): > Thanks@Chris Awokefor the warm message. The community is a wonderful place to be as a newbie or as a pro, the community is one of a kind because of the supportive fellow contributors and our wonderful mentors, they are always here to answer our questions, no matter how wonderful or confusing the questions are.

Agatha (13:50:22): > Please what is the full meaning of MHT correction?

Victoria (Burah) Poromon (14:34:35) (in thread): > Multiple Hypothesis Testing

Samuel Nnanna (14:47:33): > I’m experiencing something weird with the BugSigDB website….I’ve added signature 2 twice for the paper i’m curating, but it’s not reflecting, but if i check the recent changes sections, i see the changes there. > > what do I do ?

Mildred Anashie (14:49:41) (in thread): > Hi@Samuel Nnanna@PATIENCE ONAHwas experiencing something similar a few days ago > > Pleasedon’ttry again, it could be your connection > > You might end up with multiple similar signatures

Samuel Nnanna (14:50:47) (in thread): > Okay…thank you

Adeshile Oluwatosin (14:52:59) (in thread): > It’sprobably network > Kindly check back later

Mildred Anashie (14:53:50) (in thread): > It’s Multiple Hypothesis Testing like@Victoria (Burah) Poromonsaid > > It is done with several methods so you can check your article for Bonferroni correction, FDR, Benjamini-Hochberg, adjusted p value (q value) > > If you come across any of this then, it’s Yes for MHT but if none of this mentioned, then you can pick No for MHT

Adeshile Oluwatosin (15:14:15) (in thread): > Try another browser but don’t try adding same signature

Agatha (15:23:19): > After saving a page, I found myself here. Please what next? - File (PNG): Screenshot_20241013-201248~2.png

Adeshile Oluwatosin (15:25:46) (in thread): > @Agathakindly input the PMID number

Mildred Anashie (15:25:55) (in thread): > Hi@AgathaIt looks like youhaven’tadded your study PMID

Mildred Anashie (15:26:32) (in thread): > You can get the PMID of your Article by searching the title herehttps://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Adeshile Oluwatosin (15:26:44) (in thread): > To search or get PMID of your Article/issue > 1. Go tohttps://pubmed.ncbi.nlm.nih.gov/ > 2. Search for your article title/topic > 3. Click on cite > 4. Scroll down and you will see the PMID number > 5. Input this into bugsigdb@Agatha - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Samuel Nnanna (15:29:01) (in thread): > The first one was in the afternoon (3pm), the saved changesdidn’treflect > > Then tried again just a couple minutes ago, nothing still until I checked the recent changes section > > But accessing directly shows nothing

Mildred Anashie (15:30:28) (in thread): > I think you should give it time@Samuel Nnanna

Adeshile Oluwatosin (15:30:39) (in thread): > @Samuel Nnannafor some people, trying another browser worked out. > > In@PATIENCE ONAHcase it was just network issues

Adeshile Oluwatosin (15:30:54) (in thread): > So just be patient

Samuel Nnanna (15:31:32) (in thread): > I’llcheck in 2hrs then try a different browser > > Thanks@Mildred Anashieand@Adeshile Oluwatosin

Agatha (15:47:25) (in thread): > @Adeshile Oluwatosin@Mildred Anashie, there is no provision for me to put the PMID, that’s why I omitted it > Take a look - File (PNG): Screenshot_20241013-204627~2.png

Adeshile Oluwatosin (15:48:00) (in thread): > That box under auto ,that’swhere you put the number@Agatha

Adeshile Oluwatosin (15:49:10) (in thread): > Where I put the yellow mark - File (JPEG): IMG_1594

Mildred Anashie (15:49:15) (in thread): > Yea@AgathaLook well you’ll see PMID there > When you paste it, Make sure you click on complete, then save the page

Agatha (15:53:52) (in thread): > Thank you guys@Mildred Anashie@Adeshile Oluwatosin, I got it now > > Please what does it mean to duplicate an experiment any need for that?

Adeshile Oluwatosin (15:54:25) (in thread): > Get same details in another experiment

Adeshile Oluwatosin (15:54:44) (in thread): > So you will have two experiments but they have same signatures, taxa, statistical/lab analysis…

Mildred Anashie (15:54:44): > Hello everyone:wave:As we approach the 3rd week of our Contribution:hugging_face:I’ll like to say, it’s okay to struggle, Everyone Does. > Personally, I struggle with “Productivity guilt” (Not sure if it’s a word):blush:. Some days feel very productive, and others feel wasted. But I believe, that’s okay. > As a way of encouragement, as long as you’re making progress, you’re being productive.:raised_hands::clap:Just to add, If you are struggling with your contributions, you do not have to wait until you’re overwhelmed by a problem to seek help, as I am positive just as myself, everyone is willing to help and that’s the beauty of the BugSigdb community:blush::bouquet:Do have a productive week:clap::blush:

Adeshile Oluwatosin (15:55:31) (in thread): > Thank you@Mildred Anashie:hugging_face::hugging_face::hugging_face:

Mildred Anashie (15:56:09) (in thread): > There’s no need to duplicate your experiment@AgathaYou can instead add a new experiment if you have more experiments

Agatha (15:56:22) (in thread): > Ok thank you

Adeshile Oluwatosin (15:56:26) (in thread): > To add to this, kindly ask questions when unsureIt’sokay to ask questions > We are always here to assist and answer any possible questions based on our knowledge > Do not assume!:relieved::relieved::relieved:

Adeshile Oluwatosin (15:57:11) (in thread): > You are right@Mildred Anashie

Adeshile Oluwatosin (15:57:46) (in thread): > Just click on Add experiment@Agatha

Kate Rasheed (16:00:18) (in thread): > Thank you Mildred. Have a productive week too.

Joy (16:47:32) (in thread): > Thanks@Chris Awokefor the lovely message . The community is such a home, the mentors are always there to help out. Thanks to everyone for the help and assistance. - File (PNG): image.png

Aleru Divine (16:57:06) (in thread): > Thank you@Mildred AnashieI wish you a productive week as well:hugging_face:

2024-10-14

Samuel Nnanna (02:14:38) (in thread): > Good morning Guys, trust you slept good. Well, now it’s reflected and i have two extra signatures.

Adeshile Oluwatosin (02:15:51) (in thread): > That’s good then@Samuel Nnanna:blush:

Adeshile Oluwatosin (02:15:58) (in thread): > Good morning

Samuel Nnanna (02:16:09): > https://bugsigdb.org/Study_1143@Svetlana Ugarcina PerovicI had some issues with the signatures not reflecting. Could you please delete signatures 2 and 3. Thank you - Attachment (BugSigDB): Imbalance of Microbacterial Diversity Is Associated with Functional Prognosis of Stroke - BugSigDB > OBJECTIVES: There is mounting evidence to suggest that the pathophysiology of stroke is greatly influenced by the microbiota of the gut and its metabolites, in particular short-chain fatty acids (SCFAs).

Mildred Anashie (02:17:17) (in thread): > :blush:I suspected it would be so@Samuel NnannaGood morning

Adeshile Oluwatosin (02:18:23) (in thread): > Is it similar signatures?

Adeshile Oluwatosin (02:18:35) (in thread): > If yes, request for one to be deleted@Samuel Nnanna

Mildred Anashie (02:19:45) (in thread): > I’veseen he has done that already@Adeshile Oluwatosin

Samuel Nnanna (02:22:02) (in thread): > Thanks guys

Svetlana Ugarcina Perovic (02:51:38) (in thread): > deleted.

Adeshile Oluwatosin (02:53:32) (in thread): > Alright then:+1:

Samuel Nnanna (03:01:37) (in thread): > Thank you:pray:

Svetlana Ugarcina Perovic (03:03:08): > Good morning! A random Monday Question for you: - File (PNG): coffeeORtea.png

Svetlana Ugarcina Perovic (03:05:12): > @Toluwalase Abigailhave you solved your issue with opening bugsigdb account? Here are steps to follow:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727940469459309?thread_ts=1727940203.037609&cid=C04RATV9VCY - Attachment: Attachment > Account Creation Process: > 1. After requesting an account, check your spam folder for two emails: > ◦ A confirmation email > ◦ A temporary password email > 2. If the confirmation code has expired, proceed to log in using the temporary password provided. > 3. If you don’t receive the temporary password email, you may request an account again using a different email address and username.

Mildred Anashie (03:05:24) (in thread): > Good morning:sunny:@Svetlana Ugarcina PerovicCan it be both?:smile:I’llsay it usually depends for me > It could be Coffee or Tea:smile:But mostly coffee:coffee:

Adeshile Oluwatosin (03:05:50) (in thread): > Love coffee for busy days:joy_cat:@Svetlana Ugarcina PerovicGood morning

Adeshile Oluwatosin (03:06:05) (in thread): > I even like it sugary:joy:

Cate Ouma (03:16:34) (in thread): > I love tea:coffee:, especially lemon flavoured tea:face_with_cowboy_hat:

Aleru Divine (03:31:40) (in thread): > Good morning@Svetlana Ugarcina PerovicDefinitely coffee:coffee:but I like tea too. > > There’s just something about it that makes me feel unstoppable—my go-to for motivation.:muscle:

Princess Rehoboth Asuelimen (03:38:02) (in thread): > Good morning@Svetlana Ugarcina PerovicIt’scoffee for me.

Mildred Anashie (03:38:09): > Hi@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica UruaHappy MondayEveryone:wave:It’sour third week of Contribution, and time seems to have gone by real fast. I hope our contributions are going well.With regards to the difficulty mentioned in identifying Experiments and Signatures in this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728471290034599?thread_ts=1728456855.831269&cid=C04RATV9VCYI decided to write out based on my understanding and gathered from some responses in the channel, what they could mean and how you might be able to identify them.Experiments: What contrasts are made in the paper?(one contrast = one experiment). Number of experiments is dependent on the number of contrasts they conducted in the study. You can have multiple experiments for a study. Each experiment is defined by a distinct contrast between two groups, where differential microbial abundance or differential alpha diversity is tested.So if differential abundance results were reported but no alpha diversity was stated, it’s still okay to record the experiments but You’d leave the alpha diversity section blank (for those experiments without alpha diversity being recorded), according to thecuration policy.Also, You can record a new experiment every time they change sequencing type, condition, groups/contrasts, Body site etc.N/B: When recording your groups avoid using acronyms for group names, try to write in full.Signatures:What taxa are differentially abundant in the contrast identified to be experiments? (This defines the signatures). The taxa abundant in Group 1 (Your group identified based on the contrasts) will be recorded as the increased signatures while the taxa abundant in Group 0 will be recorded as decreased signatures for the experiment. Most times you can find this taxa by “Ctrl+F” Differential, abundance/abundant, significantly different, significant increase etc.N/B: Be careful to read through and be sure what you identified is differential abundance and not relative abundance. If you need some sort of clarity on Differential abundance and Relative abundance you can go through this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&cid=C04RATV9VCY, you can also see<@UBNSEMS3S>explanationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697468494614279?thread_ts=1697450304.857849&cid=C04RATV9VCYIf you record a signature and it appears in Orange, do not panic. You would need to search for that taxa on the NCBI taxonomy browser (Link:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi) and find the taxonomy ID and record the ID on BugSigDB, that should resolve it. The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. In most cases, you would find the synonym.*Tip: I think a good strategy in identifying taxa’s that are significantly different would be for you to use the PDF article to highlight every sentence in the Results that reports a differential abundance result, then summarize all the contrasts they resulted from, noting what tables or figures they are reported. Although Signatures can be reported in text, sometimes not just from figures or tables. > > - Attachment: Attachment > You have reported challenges in: > > 1. Identifying experiments and signatures: > ◦ Easy to miss details, especially when there are many signatures > ◦ Finding signatures not already in BugSigDB can be time-consuming > 2. Interpreting figures and results: > ◦ Difficulty interpreting complex figures, especially those that are not LEfSe plots > 3. Identifying particular statistical tests used in studies > Despite these challenges, I am happy that you have generally reported positive experiences and have been enjoying your team work. > > Why did I ask you about challenges? As of this morning, following a week since the initiation of the curation process, over 20 curations have encountered roadblocks (See https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aopen+is%3Aissue+label%3Aassigned). If you’ve completed your curation, please reach out to your colleagues and identify areas where they’ve faced difficulties. Collaborate to find solutions together.** > — > > *Interesting fact about the LEfSe: > LEfSe is indeed the most common statistical analysis still in use, but there is MaAsLin, an evolution of LEfSe that can consider a wider number and variety of metadata, recommended by the LEfSe developers to be used instead of LEfSe - Attachment (BugSigDB): Curation Policy > … - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups - Attachment: Attachment > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (03:42:26) (in thread): > The message is quite long and I apologize :pray:* > > Additionally, > ** > Signature source and Description:The source refers to the table/ figure in your selected paper presenting the differential abundance taxa, most times results are also reported in text so you can record that as your signature source if it applies to your study. The description field is where you input a short text describing the groups that were compared, often times you can get the information from the table or figure caption.Alpha Diversity:*We do not curate Beta diversity on BugSigDB. When curating Alpha diversity you curate also based on the contrasts/groups recorded for your experiments. Make sure the alpha diversity reported in the study is statistically significant before you record as increased or decreased. If it isn’t then it’d be recorded as unchanged. You can come across statements like ‘Significantly increased’ or ‘Significantly decreased’, check in here on slack if you come across something you don’t seem to understand. Stable can also mean unchanged.N/B: Not all alpha diversity indices on BugSigDB will be found in your study/article, curate only the ones that apply. Make sure to check figures alongside results texts to confirm.Always confirm and explore additional information or Supplementary information, authors report some results using supplementary information. You can easily do “Ctrl+F” and type ‘Supplementary’ or ‘Additional’ to find them.You can ask more questions if this isn’t clear:blush:

Adeshile Oluwatosin (03:57:44) (in thread): > Nice write up@Mildred Anashie:+1:

Aleru Divine (04:09:22) (in thread): > This is so detailed@Mildred Anashiethanks:hugging_face:

Adeshile Oluwatosin (04:14:06) (in thread): > For signatures, sometimes mistakes are made in the text area. > Do well to go over the results and confirm if it is an increased or decreased signature for that particular experiment. > This happened in my case.

Kate Rasheed (05:06:41) (in thread): > Thank you so much@Mildred Anashiefor this. It’s so so helpful.

Scholastica Urua (07:35:20) (in thread): > Definitely tea for me:sweat_smile:

Yoko C (07:51:47): > Hello everyone, I wanted to get some feedback on issues I found during my curation process (https://journals.asm.org/doi/10.1128/msystems.01015-24#F4) thatI am uncertain about. > Host species (domestic rabbit) not provided in the drop down, should I contact the team to have it added? > The sequencing type isn’t mentioned but, since 27F and 1492R primers were used I selected 1V and 9V as lower and higher bounds, but I am unsure if this is correct. > For statistical tests the article mentions: The data obtained were analyzed using Student’s t-test or the Mann-Whitney U test, and the results were presented as mean ± SEM. Data with 0.05 <P< 0.1 were considered to show a trend toward significance, P< 0.05 indicated significant difference, and *****P< 0.01 indicated highly significant difference. > And it also mentions: > Differential biomarkers between two groups were identified using the Mann-Whitney U test (non-parametric test) with a threshold ofP**< 0.01 and Linear Discriminant Analysis (LDA) score of 3. > Here I assumed Mann-Whitney was used for Alpha diversity (and other experiments) and LEFse for differential abundance. But I am not too sure about this as I don’t think it is explicitly mentioned, any thoughts?

Yoko C (07:52:18) (in thread): > Super helpful

Mildred Anashie (07:59:23) (in thread): > Hi@Yoko CI’ll go through the paper now > > For the Host species I’ve checked and it doesn’t seem like Domestic rabbit (Oryctolagus cuniculus domesticus) is in the drop down, that’s the scientific name I found from my research > > So I think you can inform our mentors about it

Aleru Divine (08:03:23) (in thread): > Hi@Yoko CIf the host species isn’t providedas it is in this case, yes contact the mentors for update. > > The sequencing type in your paper is 16S rRNA > “PCR amplification of the full-length 16S rRNA gene was performed using primers 27F (5′-AGRGTTYGATYMTGGCTCAG-3′) and 1492R (5′-RGYTACCTTGTTACGACTT-3′) with barcodes (25), with 10 ng of DNA as the template.”From this excerpt “Differential biomarkers between two groups were identified using the Mann-Whitney U test (non-parametric test) with a threshold of P < 0.01 and Linear Discriminant Analysis (LDA) score of 3”I’dlike to agree that LEfSe was used for differential abundance

Mildred Anashie (08:09:58) (in thread): > @Yoko CYes the statistical test is LEfSe (I can confirm that from Figure 4H) > > And I somehow agree with V1 and V9 because on further research, I found something that says that, 27F and 1492R seems to cover the full spectrum of the hypervariable regions (V1-V9)

Aleru Divine (08:11:35) (in thread): > There’san explanation from<@UBNSEMS3S>on this statistical test confusion.LEfSe gives an LDA score/threshold and the Mann-Whitney test is just what LEfSe does behind the scenes.(IfI’mexplaining that correctly) > > In my case, it was Kruskal-Wallis and LEfSe.Here’sthe recording from one of the previous office hours.Time stamp 13:00 -14:50https://community-bioc.slack.com/archives/C04RATV9VCY/p1727978011885959 - Attachment: Attachment > Thank you to everyone who attended today’s meeting. Here is the recording. Apologies that I forgot to start recording until 10 minutes in (please someone remind me next week to start recording!). Looking forward to out next meeting.

Svetlana Ugarcina Perovic (08:14:49) (in thread): > Oryctolagus cuniculus as a host species option added.

Svetlana Ugarcina Perovic (08:18:47) (in thread): > The V1-V9 regionis the full-length of the16S rRNA geneamplified using the primers 27F (5 -AGRGTTYGATYMTGGCTCAG-3 ) and 1492R (5 -RGYTACCTTGTTACGACTT-3 ).

Yoko C (08:24:03) (in thread): > Thanks so much@Mildred Anashie,@Aleru Divineand@Svetlana Ugarcina Perovic.@Aleru Divinereviewing the vid.@Svetlana Ugarcina Perovicthan the bounds I selected, v1-v9 are correct? or since it’s the full length would the bounds not apply?

Svetlana Ugarcina Perovic (08:26:31) (in thread): > You are selecting all the gene regions sequenced, in this study it is V1-V9. See an examplehttps://bugsigdb.org/Study_804/Experiment_1 - Attachment (BugSigDB): Study 804/Experiment 1 > .

Mildred Anashie (08:50:17): > Hello everyone > > I’m currently working on completing thisstudyAnd I’m having issues interpreting some of the figures and tables. > > I’ll like to confirm what the lines above Fig 4a and b is indicating based on the contrasts especially the lines above C connecting to the other time points (See image) > > If there is an experiment between all time points would that mean the taxas in Fig4 C and D should be recorded where it shows significance? > > I know that C is for Healthy controls, SO is for Baseline, S1 and S2 is for Week 6 and Week 12 follow up during treatment, and S3 is for Week 24 after treatment. > > But the Figure caption in Supplementary Figure 5 is conflicting, with the image showing S0 (Baseline) as red and S3(Week 24) as Green and the caption says “HCs(C) were shown in green”. Would I be right to follow the image? > > Finally, I’ll like to confirm Supplementary Table 3 is curatable and I would be right to interpret the significance using the mean. E.g Unidentified_Clostridiales has mean in the HC group as 0.015242 and in the SCH group as 0.008389. > I interpreted this as a decrease in the SCH group, is this correct? > > Link to article:https://pubmed.ncbi.nlm.nih.gov/34376634/Thank you so much:blush::pray: - Attachment (BugSigDB): Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study - BugSigDB > Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis.However, its role in the antipsychotic treatment response is unclear. - Attachment (PubMed): Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study - PubMed > Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis. However, its role in the antipsychotic treatment response is unclear. Here, we present a 24-week follow-up study to identify gut microbial biomarkers for SCH diagnosis a …

Mildred Anashie (08:51:57) (in thread): - File (JPEG): fc47fda0-0af2-4c69-ad8c-fa44b517a254

Aleru Divine (08:54:30) (in thread): > Hi@Mildred AnashieI’ll have a look:crossed_fingers:

Ebuka Chinwuba (08:56:13): > @Precious OrakweI had just finished my first contribution. For a while, I was stranded after I submit, because I wasn’t given URL or nothing. I was on my way to ask questions when I was your previous post. it was very helpful. Thank you so much for your clear guidance

Mildred Anashie (09:01:50) (in thread): > Well done@Ebuka ChinwubaIncase you have other questions you can go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727950394376939?thread_ts=1727950036.699409&channel=C04RATV9VCY&message_ts=1727950394.376939They might have been answered in the FAQ - Attachment: Attachment > For FAQ check out this link https://github.com/waldronlab/BugSigDBcuration/issues/96

Mildred Anashie (09:02:18) (in thread): > Thank you@Aleru Divine:pray:

Precious Orakwe (09:17:09) (in thread): > Weldon@Ebuka Chinwubaon completing your first contribution. > I am glad that I can help. > If you have any question or assistance I and everyone here will be here to help. > Kudos

Precious Orakwe (09:22:12) (in thread): > Coffee for me, tea after taking it makes me throw up. > So I go for coffee.

Aleru Divine (09:26:39) (in thread): > Hi, I’m back again > 1. For the lines above 4a and b, to my understanding, it is comparing C and the rest of the time points (but one after the other) and the result is significantdue to the asterisk. I assume they didn’t want to have different lines on top of all of them and so, they used a longer line, from that you have (C vs S0), (C vs S1), (C vs S2), (C vs S3). And then (S0 vs S2).I really hope this is clear enough:face_with_open_eyes_and_hand_over_mouth: > 2. Yes,I believeyoucancurate the significant signatures in figure 4b and C. This would likely determine the experiments. If no othersignaturesarementioned in the paper. > 3. I’d say, sinceFigure 5doesn’t show anything regarding healthy controls, it’s probably a mistake. Only curate for S0 and S3. Yes, follow the image.Also see this excerpt****“To identify the effect of risperidone treatment on whole microbiota composition in SCH patients, we used the LEfSe algorithm to compare microbial biomarkers before and after risperidone treatment (Supplementary Figure 5A, B**)” Before and after risperidone treatment would mean S0 (Baseline) before any treatment begins and S3 (Week 24) samples collected after treatment has ended, at 24 weeks. So image is correct. > 4. I think it is curatable too. I also agree with this interpretation. > Well done:clap:@Mildred Anashie

Precious Orakwe (09:28:20) (in thread): > This is great, thanks@Mildred Anashie

Tino (09:28:40): > Hello everyone! > My** ****name is Tino from Zimbabwe. My educational background is in Applied Mathematics and l’m thrilled to be an outreachy applicant. I’m interested in**** ****contributing to the Microbiome Study Curation**** ****project. I realize**** ****I’m late to the party and I would appreciate any help to get started..

Mildred Anashie (09:33:43) (in thread): > Thank you so much@Aleru Divine:blush:Ireally needed this confirmation:pray:

BOLARINWA AISHAT (09:35:24) (in thread): > Tea

Mildred Anashie (09:36:52) (in thread): > Hi@TinoWelcome:hugging_face:

Kate Rasheed (09:37:01) (in thread): > Hi Tino. You’re welcome. Kindly go through the pinned post for questions and answers.

Adeshile Oluwatosin (09:37:35) (in thread): > Welcome@Tino

Adeshile Oluwatosin (09:38:16) (in thread): > To get started,@Tino > * Step 1: Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Step 2: Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Step 3: Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Step 4: Follow this steps to proceed the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > I’m here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Mildred Anashie (09:38:26) (in thread): > You can go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728564579579639?thread_ts=1728564550.211819&channel=C04RATV9VCY&message_ts=1728564579.579639It was put together by@Adeshile Oluwatosinand I find it to be comprehensive - Attachment: Attachment > Welcome :hugging_face: @Ebuka Chinwuba > > To get started ! > • Step 1: Review the intial information; Look through this link: https://github.com/waldronlab/BugSigDBcuration/issues/94 > • Step 2: Make Your first contribution; Follow the guideline provided here: https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > • Step 3: Ensure you record a first contribution via outreachy link; https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > • Step 4: Follow this steps to proceed the second contribution; https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > If you have any questions, feel free to drop them in the this channel. > I’m also here to assist you. > > Please pay close attention to the instructions!!!

Princess Rehoboth Asuelimen (09:38:51) (in thread): > Welcome@Tino

Adeshile Oluwatosin (09:39:37) (in thread): > Well done@Ebuka ChinwubaIf you need any clarifications on your second contribution > Feel free to askI guess@Precious Orakwehas mentioned how to go about that

Aleru Divine (09:40:21) (in thread): > Welcome@Tino:hugging_face:

Samuel Nnanna (09:43:28) (in thread): > @Svetlana Ugarcina Perovicat the time you confirmed deletion,I could still see the signatures but i thought to wait it out as it might reflect later, but upon checking now, the signatures 2&3 and still in the study……please what do i do?

Princess Rehoboth Asuelimen (10:06:25) (in thread): > Hi@Mildred Anashie, so I just went through your study. The line above 4a and b is showing the comparison of the result of the alpha diversity of SCH patients against the healthy Control (C). > > 4C and D shows the abundanceof Lachnoclostridium and Romboutsia in SCH against HC(C). This should be curated for sure.

Mildred Anashie (10:14:53): > Hi again@Svetlana Ugarcina Perovic@Scholastica Urua@Chioma Onyido@Esther Afuape@Peace Sandy:blush:I think Ace is Richness and Observed species is Richness too > > Where both Ace and Observed species are mentioned separately > What do I do? - File (PNG): Alpha diversity.png

Mildred Anashie (10:16:22) (in thread): > Thank you:hugging_face:@Princess Rehoboth Asuelimen

Agatha (10:24:13) (in thread): > Thank you@Mildred Anashie,

Adeshile Oluwatosin (10:24:44) (in thread): > @Mildred AnashieI’mguessing just record both as richness

Adeshile Oluwatosin (10:26:16) (in thread): > Specify if both ace and observed are both increased, decreased or unchanged

Princess Rehoboth Asuelimen (10:26:32) (in thread): > Also I was checking through Fig 5A and B which i think is correct. 5B looks like it can be curated, because a cladogram most times can be curated. And I will most likely say it is reduced in SCH compared to HC. Idon’tknow if this makes sense?

Agatha (10:26:35) (in thread): > Please in curating signature, am I supposed to input just one taxa for each source and abundance in group 1 or should I input all that is involved?

Aleru Divine (10:27:14) (in thread): > @Agathaall thesignificantsignatures listed should be curated.

Adeshile Oluwatosin (10:27:34) (in thread): > @Agathain curating signatures, it depends on the article, input all taxa listed in that particular source(figure or table)

Agatha (10:28:13) (in thread): > Ok thank you

Mildred Anashie (10:28:55) (in thread): > Yea@AgathaYou should record all the signatures involved like Divine said

Mildred Anashie (10:32:27) (in thread): > It does make sense@Princess Rehoboth Asuelimenbut I realized that the comparison in the caption is different from the image > > The caption says SCH vs HC while the image shows SCH (S0) vs SCH (S3) which was conflicting

Mildred Anashie (10:33:33) (in thread): > But Divine shared a part of the results text that helped me figure it out > > Thank you@Princess Rehoboth Asuelimenfor your help:heart_hands:

Mildred Anashie (10:34:30) (in thread): > Okay > SoI’llhave to leave a note in the talk page, right?

Adeshile Oluwatosin (10:36:56) (in thread): > Yes you can@Mildred Anashie

Mohamed Osman Omar (10:52:46): > can anyone explain what the Second Contribution Task (Optional) to do thanks

Adeshile Oluwatosin (10:53:39) (in thread): > You are to curate an issue@Mohamed Osman Omar

Adeshile Oluwatosin (10:53:56) (in thread): > Check here;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face:

Mildred Anashie (10:56:37) (in thread): > While you go through what@Adeshile Oluwatosinshared, you can also follow this to request for an account to get started with the curation once an article has been assigned to youhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727940469459309?thread_ts=1727940203.037609&cid=C04RATV9VCY - Attachment: Attachment > Account Creation Process: > 1. After requesting an account, check your spam folder for two emails: > ◦ A confirmation email > ◦ A temporary password email > 2. If the confirmation code has expired, proceed to log in using the temporary password provided. > 3. If you don’t receive the temporary password email, you may request an account again using a different email address and username.

Mildred Anashie (10:57:14) (in thread): > Thank you@Adeshile Oluwatosin:blush:

Adeshile Oluwatosin (10:58:34) (in thread): > Welcome@Mildred Anashie

Svetlana Ugarcina Perovic (11:30:23) (in thread): > @Samuel NnannaThere is a message: “The page or file”Study 1143/Experiment 1/Signature 2” could not be deleted. It may have already been deleted by someone else.”

Svetlana Ugarcina Perovic (11:31:23) (in thread): > Let me know tomorrow, if still these two are up, thanks!

Agatha (11:54:44): > I have been trying to load and input taxa for hours and it seems difficult. Sometimes the whole thing will just disappear including source and description. > > Is there something I am not doing right?

Kate Rasheed (11:55:59) (in thread): > Can you take a screenshot and share?

Mildred Anashie (11:56:07) (in thread): > I’mnot sure I understand what you mean by disappear@AgathaBut from my endIt’sworking well

Mohamed Osman Omar (11:57:53) (in thread): > how long it may take review and i need to finish the signature@Adeshile Oluwatosin@Mildred Anashie@Chris Awoke - File (PNG): BugSigDB.png

Adeshile Oluwatosin (11:58:16) (in thread): > Input the PMID number

Adeshile Oluwatosin (11:58:22) (in thread): > @Mohamed Osman Omar

Mildred Anashie (12:00:05) (in thread): > Check how to herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728847592690849?thread_ts=1728847399.825169&channel=C04RATV9VCY&message_ts=1728847592.690849 - Attachment: Attachment > You can get the PMID of your Article by searching the title here https://pubmed.ncbi.nlm.nih.gov/

Adeshile Oluwatosin (12:00:36) (in thread): > To search or get PMID of your Article/issue@Mohamed Osman Omar > 1. Go tohttps://pubmed.ncbi.nlm.nih.gov/ > 2. Search for your article title/topic > 3. Click on cite > 4. Scroll down and you will see the PMID number - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Agatha (12:02:06) (in thread): > Ok let me show you - File (PNG): _20241014_170125.png

Mildred Anashie (12:03:31) (in thread): > Did you change incomplete to Complete and then save page?

Kate Rasheed (12:13:06) (in thread): > @AgathaChange the incomplete below to complete and save the page

Adeshile Oluwatosin (12:17:51) (in thread): > :thumbsup:

Precious Orakwe (12:29:22) (in thread): > Yes, change the incomplete to complete and save, sometimes it happens because if network. > It happened to me, but mine was because of network.:hugging_face:

Tino (12:37:30) (in thread): > Thank you so much@Mildred Anashie@Kate Rasheed@Adeshile Oluwatosin@Princess Rehoboth Asuelimen@Aleru Divine.

Adeshile Oluwatosin (12:37:45) (in thread): > You are welcome:hugging_face:

Samuel Nnanna (12:46:22) (in thread): > Alright I will. Thank you

Mohamed Osman Omar (12:56:38) (in thread): > I found PMID what is the next@Adeshile Oluwatosin@Mildred Anashie

Mildred Anashie (12:58:18) (in thread): > Right under Auto, you’ll see where to input the PMID, then click on complete and save the page@Mohamed Osman Omar

Mildred Anashie (12:59:12) (in thread): > Make sure you also select the right study design for your study before you save

Adeshile Oluwatosin (12:59:43) (in thread): - File (JPEG): IMG_1594

Mohamed Osman Omar (13:02:19) (in thread): > @Adeshile Oluwatosin@Mildred Anashie - File (PNG): PMID.png

Mohamed Osman Omar (13:02:58) (in thread): > @Adeshile Oluwatosin@Mildred AnashieIT SHOWS LIKE THAT AND ID IS THE RIGHT - File (PNG): PMID.png

Adeshile Oluwatosin (13:03:12) (in thread): > The study is already on bugsigdb@Mohamed Osman Omar

Mildred Anashie (13:03:25) (in thread): > It means your study already exists@Mohamed Osman OmarIt’swritten underneath the text in red

Mildred Anashie (13:06:03) (in thread): > Follow this link@Mohamed Osman Omarand see how to search for your PMID and retreive the link to your studyhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710411770059619 - Attachment: Attachment > TIP: to search quickly for a study e.g. you are not sure if it’s already curated or not, in the main page go to “Search BugSigDB” in the top right corner and type in a PMID of paper of your interest.

Mildred Anashie (13:10:46) (in thread): > Is this your study@Mohamed Osman OmarThis is what I see for the PMID you have in that screenshothttps://bugsigdb.org/Study_775 - Attachment (BugSigDB): Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria - BugSigDB > As geographical location can impact the gut microbiome, it is important to study region-specific microbiome signatures of various diseases.Therefore, we profiled the gut microbiome of breast cancer (BC) patients of the Midwestern region of the United States.

Mildred Anashie (13:11:06) (in thread): > Please share the link to your article

Mohamed Osman Omar (13:12:47) (in thread): > Thanks@Mildred Anashiefor the help

Mildred Anashie (13:12:59) (in thread): > I posted this in the wrong threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728925846492189?thread_ts=1728847399.825169&channel=C04RATV9VCY&message_ts=1728925846.492189 - Attachment: Attachment > Is this your study @Mohamed Osman Omar > This is what I see for the PMID you have in that screenshot > https://bugsigdb.org/Study_775

Mildred Anashie (13:14:00) (in thread): > I see now > > It actuallyisn’twrong:smile:

Ibizugbe Merit (13:14:15) (in thread): > Coffee:coffee::smiling_face_with_smiling_eyes_and_hand_covering_mouth:

Adeshile Oluwatosin (13:16:15) (in thread): > But it states reviewed, you sure it’s the correct study?@Mildred Anashie

Mildred Anashie (13:17:15) (in thread): > That’s why I asked for a link to the study, so I’ll be sure > > If it’s the PMID that’s wrong@Adeshile Oluwatosin

Adeshile Oluwatosin (13:18:40) (in thread): > @Mohamed Osman Omarthe PMID number is not correct, kindly send a link to your study so we can figure it out for you .

Adeshile Oluwatosin (13:23:35) (in thread): > @Mohamed Osman OmarPMID; PMC9834383

Adeshile Oluwatosin (13:24:06) (in thread): > This is the correct PMID number > Input it in bugsigdb > Choose auto. > It should auto populate.

Mildred Anashie (13:25:16) (in thread): > Thatdoesn’tlook likeit’sa PMID@Adeshile Oluwatosin

Adeshile Oluwatosin (13:25:44) (in thread): > Sorry;36631533

Adeshile Oluwatosin (13:27:03) (in thread): - File (PNG): IMG_1619

Adeshile Oluwatosin (13:27:27) (in thread): > Seems@Mohamed Osman Omarinputted the corrected PMID number, try another browser or refresh again

Mildred Anashie (13:28:15) (in thread): > That’s what brought out the reviewed study@Adeshile Oluwatosin

Mildred Anashie (13:29:07) (in thread): > We can only get the correct PMID if we know the title of the paper@Mohamed Osman Omar

Agatha (14:08:44) (in thread): > Thank you

Cynthia Iwuoha (14:15:49): > @Svetlana Ugarcina PerovicPlz, help and delete Experiment 1/signature 3, experiment 3 and experiment 4. Thank you.https://bugsigdb.org/Study_1151/Experiment_1?markasread=41795 - Attachment (BugSigDB): Study 1151/Experiment 1 > .

Mohamed Osman Omar (14:16:06): > I have finished my second contributionhttps://bugsigdb.org/Study_775@Adeshile Oluwatosin@Mildred Anashiethank you for the help - Attachment (BugSigDB): Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria - BugSigDB > As geographical location can impact the gut microbiome, it is important to study region-specific microbiome signatures of various diseases.Therefore, we profiled the gut microbiome of breast cancer (BC) patients of the Midwestern region of the United States.

Adeshile Oluwatosin (14:17:07) (in thread): > You are welcome@Mohamed Osman OmarRemember to record your second contribution

Adeshile Oluwatosin (14:17:29) (in thread): > Notify a mentor on GitHub that the article/issue is ready for review

Mildred Anashie (14:17:36) (in thread): > You are welcome@Mohamed Osman Omar

Adeshile Oluwatosin (14:17:36) (in thread): > Note that youcan’tedit once you do this

Adeshile Oluwatosin (14:32:05) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1728653230146399@Mohamed Osman Omar - Attachment: Attachment > Friendly reminder: Don’t forget to record your second contribution! If you have submitted a link to your study for review on github(To do this…tag a mentor and mention you are done with curation or the issue is ready for review). > > Kindly follow these steps accordingly. > > How to record your second contribution: > > • Visit the Outreachy website.https://www.outreachy.org/outreachy-dec-2024-internship-cohort/communities/bioconductor/microbiome-study-curation/contributions/ > • Select the ‘Microbiome Study Curation’ project. > • Click on ‘Record a Contribution’. > • Record your contribution and click save. > Kindly note all of these; > > • “Date contribution was accepted or merged” refers to the date you submitted your contribution. > • Contribution URL is the link to your study submitted on GitHub for review. > • Write a brief description on how you went about curation. > Ensure you click on the appropriate project. > When your github issue is tagged with Needs review, no edit is allowed. > > > You can always ask for assistance!!! > I’m here to assist.

Cindy Purity (15:00:32): > Hello, I’m Cindy and id like to be part of this project. Is it too late to start?

Mildred Anashie (15:01:10) (in thread): > Hello@Cindy PurityWelcome:hugging_face:

Aleru Divine (15:07:33) (in thread): > Hey@Cindy Purity, > > Welcome to BugSigDB:hugging_face:The project is still open to applicants. It’slate at all to contribute

Aleru Divine (15:08:22) (in thread): > To get started, go through the instructions on this link.https://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Adeshile Oluwatosin (15:13:47) (in thread): > Welcome:hugging_face:@Cindy PurityTo get started, > * Step 1: Review the intial information; Look through this link:https://github.com/waldronlab/BugSigDBcuration/issues/94 > > * Step 2: Make Your first contribution; Follow the guideline provided here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 > > * Step 3: Ensure you record a first contribution via outreachy link;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 > > * Step 4: Follow this steps to proceed the second contribution;https://community-bioc.slack.com/archives/C04RATV9VCY/p1727856953420389 > I’m also here to assist you. > > Please pay close attention to the instructions!!! - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses: - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny: - Attachment: Attachment > Good Morning Everyone > > Wishing us all a great contribution period :blush: > I have been able to complete my first contribution. > > Following the tips https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 by @Aleru Divine which is quite straightforward and easy to follow you should be able to finish your first contribution. > > I think you can follow the Steps below once you are done with your first contribution; > 1. Record the contribution on the outreachy website (@Aleru Divine has also provided tips on how to go about that just in case you are unsure on how to. > 2. You can then go to Github to request one of the studies tagged “Paper to curate” or “outreachydec24” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait go through the curation policy (https://bugsigdb.org/Curation_Policy) thoroughly and Check out already curated papers I find this to be very helpful in easily understanding what the curation policy is talking about) and also make sure to Watch the onboarding videos especially “a step-by-step walk-through of how to add a new study to BugSigDB” >
> I am also open to help :hugging_face: - Attachment: #94 Welcome Outreachy Applicants! > Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > Contributions > > Remember to record your contributions in Outreachy.

Adeshile Oluwatosin (15:16:11) (in thread): > @Cindy Purityit’snot late to start contributing, kindly follow the steps accordingly to begin

Precious Orakwe (16:08:34) (in thread): > Welcome@Cindy Purity

Svetlana Ugarcina Perovic (16:23:12) (in thread): > @Mohamed Osman Omaryou signed up for curation of this paperhttps://github.com/waldronlab/BugSigDBcuration/issues/509? - Attachment: #509 Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study > Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study – Lucheng Fang – BMC Microbiology
> https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03230-7

Mildred Anashie (16:24:56) (in thread): > I knew thatwasn’tthe paper@Adeshile Oluwatosin

Adeshile Oluwatosin (16:25:28) (in thread): > I was also wondering@Mildred Anashie

Svetlana Ugarcina Perovic (16:26:28) (in thread): > This onehttps://bugsigdb.org/Study_775was curated and reviewed by@Chioma Onyido@Peace Sandylast year. - Attachment (BugSigDB): Breast cancer patients from the Midwest region of the United States have reduced levels of short-chain fatty acid-producing gut bacteria - BugSigDB > As geographical location can impact the gut microbiome, it is important to study region-specific microbiome signatures of various diseases.Therefore, we profiled the gut microbiome of breast cancer (BC) patients of the Midwestern region of the United States.

Svetlana Ugarcina Perovic (16:26:56) (in thread): > deleted.

Adeshile Oluwatosin (16:28:17) (in thread): > Thank you for clarifying@Svetlana Ugarcina Perovic@Mohamed Osman Omartake note

Mildred Anashie (16:28:45) (in thread): > Thank you for the clarification@Svetlana Ugarcina Perovic

Cynthia Iwuoha (17:36:13) (in thread): > Thank you

2024-10-15

Kate Rasheed (01:51:41): > Good day@Svetlana Ugarcina Perovic. I submitted my paper for review last week. However, during the office hours,<@UBNSEMS3S>clarified a question I asked concerning the signatures in my supplementary table so I went back to my study and removed the signatures above the p-value threshold. > > Also, while going through some discussion yesterday, I learnt that taxa abundance in the control group should be curated as decrease in the case group; hence, I made some edit. > > I didn’t know that we are not supposed to make edit once our paper has the “needs review” tag not until@Adeshile Oluwatosinmentioned. I really apologize for this.

Samuel Nnanna (02:21:40) (in thread): > Good morning@Svetlana Ugarcina Perovic. I think the deletion has reflected. - File (PNG): Screenshot 2024-10-15 at 07.20.54.png - File (PNG): Screenshot 2024-10-15 at 07.20.47.png

Ibizugbe Merit (02:34:23) (in thread): > Welcome@Cindy Purity:hugging_face:

Svetlana Ugarcina Perovic (03:36:05) (in thread): > @Kate Rasheedthank you for letting us know! Yes indeedwhen curation is under review, additional edits are not allowed. Please in the GitHub issue comment which the additional edits were made. Thank you!

Kate Rasheed (03:42:16) (in thread): > Okay I will@Svetlana Ugarcina Perovic. Thank you

Joy (03:53:51): > Good day@Svetlana Ugarcina PerovicI also had the same issue with@Kate Rasheedwhere I did not know that we are not supposed to make edit once our paper has the “needs review” tag not until@Adeshile Oluwatosinmentioned. I really apologize for this. In my case, I edited the NCBI

Joy (03:57:47) (in thread): > Welcome on board@Tino.The community here is a wonderful one and will assist you all the way,

Svetlana Ugarcina Perovic (04:27:06) (in thread): > Please in the GitHub issue comment which the additional edits were made. Thank you!

Svetlana Ugarcina Perovic (04:29:25): > IMPORTANT: when the GitHub issue with your curation is claimed for review and got a label****“needs review” ****any edits from this point are not allowed. - File (PNG): Screenshot 2024-10-15 at 10.28.40.png - File (PNG): Screenshot 2024-10-15 at 10.28.48.png

Kate Rasheed (04:30:02) (in thread): > Well noted with thanks

Mildred Anashie (04:30:17) (in thread): > Thank you for the update@Svetlana Ugarcina Perovic:pray:

Aleru Divine (04:43:22) (in thread): > Got it! Thanks@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (05:10:37) (in thread): > Noted:+1:@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (05:13:29) (in thread): > Thank you

Rahila-me (05:57:59) (in thread): > Thank you, Noted

Precious Orakwe (07:01:55) (in thread): > Thank for the update@Svetlana Ugarcina Perovic

Cynthia Iwuoha (08:36:47) (in thread): > Thank you for the update@Svetlana Ugarcina Perovic

Princess Rehoboth Asuelimen (08:38:55) (in thread): > Noted@Svetlana Ugarcina Perovic

PATIENCE ONAH (09:05:21) (in thread): > Noted

Tino (09:27:08) (in thread): > @Joythank you, will be in touch.

Yoko C (10:16:21): > Hello everyone, looking for some more feed back on my curation. So the study preformed two different relative abundance analysis. One based on a network analysis, from which they selected a genus to preform a differential analysis at genus and species level. This analysis only provides increased species for group 1. The other, using Lefse at genus level. The Curation policy states that we can enter different taxon levels and enter more than one comparison on one signature, however, since these two analysis are different, I am not sure if I can include them in the same signature. A link to the graphhttps://journals.asm.org/doi/10.1128/msystems.01015-24#F4

Adeshile Oluwatosin (10:17:22) (in thread): > I would check@Yoko C

Mildred Anashie (10:18:08) (in thread): > Hi@Yoko CI’llgo through the study now

Kate Rasheed (10:23:41) (in thread): > I think for the Lefse analysis, where there is increase in the high, you would record it as decrease in low and vice versa.

Mildred Anashie (10:48:51) (in thread): > If I get you correctly@Yoko Cyou are saying your study did two analysis which are network analysis on relative abundance and LEfSe. > > > What I see regarding the nodes doesn’t appear to be differential abundance it appears to be “Spearman’s correlation analysis of the co-occurrence network of the gut microbiota based on genus level with |R|>0.6 and* P <0.05 as thresholds”. *The Paper also says this “Using ∣R∣ > 0.6 and P < 0.05 as thresholds, a co-occurrence network analysis of the relative abundance of genus was conducted for the two groups (Fig. 4F)”. And it is referring to the co-occurrence network analysis which doesn’t appear curatable to me > > What does seem curatable on the other hand is the LEfSe analysis and that is what is showing differential abundance between the High and the Low Group in my opinion.

Adeshile Oluwatosin (10:52:41) (in thread): > The highlight here states that “Spearman’s correlation analysis of the co-occurrence network of gut microbiota based on genus level (with ∣R∣ > 0.6 and P < 0.05 as thresholds, red for positive correlation and green for negative correlation).” Which doesn’t states a differential abundance between both groups.(High and Low feed intake groups for rabbit)

Adeshile Oluwatosin (10:52:58) (in thread): - File (PNG): IMG_1631

Rahila-me (11:15:18) (in thread): > Hello@Yoko Cfrom the paper the one for network analysis is not curatable..but the one that has signatures that you will curate is fig H for LDA effect size for the high as group 1 and low as group 0

Rahila-me (11:19:31) (in thread): > Here is what you can curate - File (JPEG): Screenshot_2024-10-15-16-16-07-39_40deb401b9ffe8e1df2f1cc5ba480b12.jpg

Agatha (12:10:30): > https://bugsigdb.org/Study_1152Please guys, help me to review this work. Let me also know if I am doing the correct thing. I will sincerely appreciate your suggestions and corrections. Thank you - Attachment (BugSigDB): - BugSigDB > .

Kate Rasheed (12:12:29) (in thread): > Alright. Here are some of my observations: > > There’s no abstract in the study information > The statistal test used is more of Lefse > I didn’t see pielou, inverse Simpson diversity recorded so you can leave them blank. > > Still looking through

Yoko C (12:20:31) (in thread): > Thanks everyone for the input. Initially I was only doing the Lefse, but then I started wondering. The analysis I am referring to, isn’t precisely the network graph. It is for Fig 4G, (G) Relative abundance ofBacteroidesat genus level and species level. The text states: Subsequent differential analysis of the selected genus revealed that only**g__Bacteroidesshowed differences between the two groups, withs_Bacteroides_rodentiumands_Bacteroides_caccaebeing the different strains at the species level within theg__Bacteroides**(Fig. 4G; Fig. S1C).

Kate Rasheed (12:21:56) (in thread): > @Yoko CWe don’t curate relative abundance, we only curate differential abundance.

Agatha (12:31:04) (in thread): > Ok… I am taking note

Mildred Anashie (12:34:01) (in thread): > Yea@Yoko CBugSigDB curation focuses on******Differential abundance ****not*****relative abundance. > > *****This is an excerpt from a post by@Esther Afuapeon Relative abundance and differential abundance > “******Relative abundance gives you an idea of the proportion of a microbe in a single sample *****while ******differential abundance compares the abundance levels between different samples or conditions”. > > *****Also this explains relative abundance and differential abundancehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1697468494614279?thread_ts=1697450304.857849&channel=C04RATV9VCY&message_ts=1697468494.614279 - Attachment: Attachment > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

Adeshile Oluwatosin (12:37:21) (in thread): > Okay:+1:will check

Adeshile Oluwatosin (12:37:40) (in thread): > Check this out as well@Yoko Chttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711398678527379?thread_ts=1711390782.792099&channel=C04RATV9VCY&message_ts=1711398678.527379 - Attachment: Attachment > Bottomline: I know it’s stated that we only curate differential abundance on bugsigdb but in some cases (like fig 3b, 4b and 5b), these relative abundance figures clearly shows the significant differences between the groups, not just the taxa each group contains (as seen in 3a, 4a and 5a). > > Mann-Whitney results (Fig 3b, 4b and 5b) are curatable) but since they overlap significantly with the Lefse results which has larger signatures, I would curate just Lefse to avoid redundancy. > I hope this helps. Great team work here honestly! :clap::skin-tone-5:

Adeshile Oluwatosin (12:38:56) (in thread): > Only one condition should be stated, it should be curated as simple as possible.

Adeshile Oluwatosin (12:39:27) (in thread): > Change antibiotics exclusion to just4 weeks

Adeshile Oluwatosin (12:39:49) (in thread): > No signatures have been created?

Agatha (12:40:37) (in thread): > Noted

Adeshile Oluwatosin (12:40:39) (in thread): > There should be just one statistical test per experimentIf there are more than one, I suggest you create them as different experiments

Adeshile Oluwatosin (12:41:10) (in thread): > Will check the article now

Mildred Anashie (12:41:30) (in thread): > Hi@AgathaWell done on your Curation:clap:I’llgo through it now and give my opinion

Agatha (12:41:43) (in thread): > @Mildred Anashie, I will be expecting your corrections. thank you

Mildred Anashie (12:42:52) (in thread): > Please share the PDF you are working with > > The article doesn’t seem to be open access > > Or a link to the GitHub issue, if the PDF is there@Agatha

Yoko C (12:43:36) (in thread): > @Kate Rasheed, oh I see, thanks! I am still confused though, relative abundance is what the differential analysis compares and the Lefse graph is also a representation of relative abundances, right? In this case, the differential analysis was carried out: Subsequent differential analysis of the selected genus revealed that only**g__Bacteroidesshowed differences between the two groups, withs_Bacteroides_rodentiumands_Bacteroides_caccaebeing the different strains at the species level within theg__Bacteroides**(Fig. 4G; Fig. S1C).

Adeshile Oluwatosin (12:43:44) (in thread): > There are two body sites? > Create both as different experiments

Agatha (12:43:49) (in thread): > Ok I will send the PDF link@Mildred Anashie

Adeshile Oluwatosin (12:43:58) (in thread): > Yeah send the PDF link

Agatha (12:44:17) (in thread): > http://dx.doi.org/10.1093/infdis/jiu409@Mildred Anashie

Yoko C (12:45:08) (in thread): > Oh,@Mildred Anashie,@Adeshile Oluwatosin@Kate Rasheedthanks! That clears things up.

Adeshile Oluwatosin (12:45:39) (in thread): > This is the title ofthe article via thislink; Intestinal Microbiota, Microbial Translocation, and Systemic Inflammation in Chronic HIV Infection

Adeshile Oluwatosin (12:46:05) (in thread): > Title of the article from your study is this; The laboratory investigation of vesicular skin rashes > > You sure it’s correct@Agatha

Adeshile Oluwatosin (12:46:54) (in thread): > You are welcome:+1:@Yoko C

Agatha (12:46:56) (in thread): > I was also confused@Adeshile Oluwatosin, I don’t know how that tittle emerged

Adeshile Oluwatosin (12:47:16) (in thread): > You sure the PMID is correct, let me check

Mildred Anashie (12:47:21) (in thread): > Something might be wrong or is it from my end > > The article you sent and where I was directed from your curation are different@Agatha - File (JPEG): IMG_1430 - File (JPEG): IMG_1433

Mildred Anashie (12:47:54) (in thread): > Which is correct?@Agatha

Adeshile Oluwatosin (12:53:02) (in thread): > @Agatha, is your pdf article the correct one? > So I can confirm if the PMID number is correct

Mildred Anashie (12:53:55) (in thread): > Hi@AgathaI see what is wrong now > I think the PMID you inputted isn’t the one for your article because the PDF you shared and your curation are the same but the article on the study page is different > > Try using this one, PMID:25057045It should give us the right article on the study page

Adeshile Oluwatosin (12:57:13) (in thread): > Incase you are wondering how she figured that; > * Search your article here:https://pubmed.ncbi.nlm.nih.gov/25057045/#:~:text=Background%3A%20Despite%20effective%20antiretroviral%20therapy,in%20microbial%20translocation%20and%20inflammation. > * Scroll to cite > * You should see the PMID > * Input25057045as she stated in bugsigdb - Attachment (PubMed): Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection - PubMed > Patients who have chronic HIV infection and are receiving suppressive ART display intestinal dysbiosis associated with increased microbial translocation and significant associations between specific taxa and markers of microbial translocation and systemic inflammation. This was an exploratory study, …

Adeshile Oluwatosin (13:10:43) (in thread): > This is curatable. It is already experiment 1@AgathaLeFSe, green represents increase, red decreased abundance - File (PNG): IMG_1634

Mildred Anashie (13:18:04) (in thread): > Hi@AgathaIn my opinion > 1. Condition should be something like “Response to ART” (I’ll figure out a more appropriate condition) because the article compares “Subjects with chronic HIV infection who were receiving suppressive ART and had undetectable HIV loads (cases), compared with HIV-uninfected controls”. And this is the only experiment I see > 2. Differential abundance in Fig 3 between the cases and controls (So your signatures would come from this figure, Red would be increased in cases and Green would be increased in controls which would be your decreased signatures) > > 3. Your statistical test is LEfSe so you would delete the others you recorded > > 4. For Alpha diversity, there are all unchanged > The indices mentioned in your study are Richness, Chao, Faith (Phylogenetic Diversity) and I see Shannon equality and Shannon diversity (Unsure if they mean separate things) > You would curate unchanged for only this ones and leave out the other ones > > 5. I do not see matched on or confounders controlled for being mentioned in the article. What you recorded for those are the inclusion criteria and the sociodemographic variables > > This are my observations, well done again you did a great job:clap:

Adeshile Oluwatosin (13:23:27) (in thread): > Just record stool samples as the body site@AgathaAlso@Mildred AnashieI actuallycan’tfind “Response to ART” in the dropdown options

Adeshile Oluwatosin (13:26:38) (in thread): > There are no confounders listed in the study.You’ll see sentences like “age, weight, bla bla were controlled for” “xyz were confounding factors”

Agatha (13:26:56) (in thread): > Hmmm….thank you guys. > > I am so grateful

Adeshile Oluwatosin (13:29:44) (in thread): > In my opinion, I stated “HIV infection” good enough as the condition. Sincethat’swhat is in the dropdown. > I could check for something else as well.

Mildred Anashie (13:30:29) (in thread): > @Adeshile OluwatosinYes there is no “Response to Art” > But I see “Response to antiviral drug” which can work in my opinion > > I think@Agathacan wait for other responses because on a second thought “Chronic HIV infection” also seems like an appropriate condition:thinking_face:One of them is right

Adeshile Oluwatosin (13:31:00) (in thread): > At the end of the day@AgathaYou have just one experiment, with 2 signatures

Agatha (13:31:44) (in thread): > Thank you all for your support. It is really encouraging. I appreciate

Adeshile Oluwatosin (13:31:50) (in thread): > @Mildred Anashieyes I guess she should wait for other opinions > > Yeah in the case of her study. > Chronic HIV Infection is more appropriate.Response to antiviral drug, hmmmThat’sone too

Agatha (13:32:25) (in thread): > I am already making the corrections

Adeshile Oluwatosin (13:32:25) (in thread): > You can ask in the next office hour if no one else contributes@Agatha

Agatha (13:32:44) (in thread): > Ok > > Thank you

Tino (13:47:55) (in thread): > Hello@Cindy Purityand welcome!

Yoko C (14:51:51) (in thread): > Hello@Agathafor body site, only feces were used to compare the microbiota. In this curationhttps://bugsigdb.org/Study_976, the condition used is response to antiviral drug, I think yours would be similar. - Attachment (BugSigDB): HIV-Positive Patients on Antiretroviral Therapy Have an Altered Mucosal Intestinal but Not Oral Microbiome - BugSigDB > This study characterized compositional and functional shifts in the intestinal and oral microbiome in HIV-positive patients on antiretroviral therapy compared to HIV-negative individuals.

Adeshile Oluwatosin (15:03:06) (in thread): > Thank you@Yoko C

Mildred Anashie (15:09:34) (in thread): > Thank you@Yoko Cfor taking out time to show an example

Aleru Divine (15:12:26) (in thread): > Well done everyone on the review.:clap:

2024-10-16

Inimfon Ebong (01:25:06): > Hi good morning, > Please help, > > Comparisons of the gut microbiota between healthy controls and acute ischemic stroke patients. (A) Principal coordinates (PC) analysis based on unweighted UniFrac distances. (B) Unweighted UniFrac distances of each subgroup of acute ischemic stroke patients compared with controls. (C) Taxonomic summary of the gut microbiota of mild, moderate, and severe stroke patients and controls at the family level. (D) Discriminative taxa at the family level in mild, moderate, and severe stroke patients and controls based on the linear discriminant analysis (LDA = 2.5) and effect‐size pipeline. Statistical significance was considered at P< .05, *****P< .01, and *****P**< .001. > > I’m to focus on D right?

Mildred Anashie (01:46:05) (in thread): > Hi@Inimfon EbongIn my opinion yes, from what you shared > > But you can share your articlelet’sconfirm

Inimfon Ebong (02:01:51) (in thread): > https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8048557/

Mildred Anashie (03:10:55) (in thread): > Yes you would focus on Figure 2d because your statistical test is LEfSe. See “To identify differentiated metagenomic biomarkers, a linear discriminant analysis (LDA) coupled with effect‐size measurement (LEfSe) was performed athttp://huttenhower.sph.harvard.edu/galaxy. Significantly different bacteria with LDA scores of ≥2.5 were plotted on taxonomic bar plots.” > > And the caption for 2d is describing a LEfSe plot, like you already shared. > > But I’m concerned if this is a one against all “Mild, Moderate and Severe Vs Controls” making it one Experiment, because from the last office hour I saw a LEfSe plot similar to this and<@UBNSEMS3S>said it could be curated as “The case vs All the controls as one” > > or Would this be curated as, > > Mild Vs Control > Moderate Vs Control > Severe Vs Control > > Since we have different cases and one control group?:thinking_face:I’ll really like to know@Svetlana Ugarcina Perovic@Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica UruaPlease help with this, thank you:pray:

Inimfon Ebong (03:15:14) (in thread): > That’s the problem I’ve been having since last week, do I curate as one or as multiple for both increased and diminished distribution

Inimfon Ebong (03:15:25) (in thread): > @C. Mirzayi (please do not tag this account)please help

Mildred Anashie (03:17:30) (in thread): > I’msure we would get clarification soon@Inimfon Ebong

Aleru Divine (03:20:50) (in thread): > Well done@Mildred Anashie@Inimfon EbongIn my opinion, this would be a 1 vsthe rest of the groups. > > And have only one signature(increased) for each experiment. > > controls vs the rest of the group > mild vs the rest of the group > moderate vs the rest of the group > severe vs the rest of the group > > This would be more comprehensive in my opinion

Aleru Divine (03:30:05) (in thread): > @Inimfon EbongThe paper doesn’t mention it being a pair-wise experiment and honestly that would’ve been more experiments. > > So it’s 1(case) vs the the rest(control) > > Thencurate the signature abundant in the case as increased. > > No decreasedsignaturesin this case.

Aleru Divine (03:30:57) (in thread): > Also check last week’s office hours recording > > Time stamp 21-23 for better explanation from<@UBNSEMS3S>https://waldronlab.slack.com/files/UBNSEMS3S/F07RAHD08LE/gmt20241010-130235_recording_3840x2160.mp4 - File (MPEG 4 Video): Gmt20241010-130235 Recording 3840X2160.mp4

Scholastica Urua (03:31:10) (in thread): > Hi@Inimfon Ebongcheck out this post. It’ll help with your curation.https://community-bioc.slack.com/archives/C04RATV9VCY/p1687872680081639?thread_ts=1687872680.081639&cid=C04RATV9VCY - Attachment: Attachment > If I am understanding the figure 1H of this paper(https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8748098/) correctly, it should be curated in three experiments: > 1. groups 0 and 1 as control vs constipation > 2. groups 0 and 1 as control vs non-constipation > 3. groups 0 and 1 as constipation vs non-constipation > is that right? > (The study has been curated at https://bugsigdb.org/Study_741)

Aleru Divine (03:36:12) (in thread): > Thanks for thelink@Scholastica Urua

Mildred Anashie (03:43:57) (in thread): > Thank you@Aleru Divineand@Scholastica UruaThis is much clearer to me now@Inimfon Ebongis it clear now?

Aleru Divine (03:50:16) (in thread): > @AgathaFocusing on “response to antiviral drug” as the best condition makes sense because the study discusses patients with chronic HIV infection who are receiving suppressive ART (antiretroviral therapy). The mention of ART and the associated intestinal dysbiosis, microbial translocation, and inflammation suggests that the study is exploring how these patients’ bodies respond to the antiviral treatment.

Inimfon Ebong (04:49:50) (in thread): > Yes oh my God thank you@Scholastica Urua@Aleru Divine@Mildred Anashiethis is exactly what I’m looking for

Adeshile Oluwatosin (05:13:37) (in thread): > Well stated:thumbsup:4 experiments; only increased for all signatures > * Controls (Group 1) VS mild AND moderate AND severe(Group 0) > * Mild (Group 1) VS Controls AND moderate AND severe(Group 0) > * Moderate (Group 1) VS Mild AND Controls AND Severe(Group 0) > * Severe (Group 1) VS controls AND Mild AND Moderate(Group 0)

Inimfon Ebong (06:00:52) (in thread): > Thank you this has been very helpful hopefully I’ll be done by the end of the week

Adeshile Oluwatosin (06:01:33) (in thread): > Ask questions if still confused@Inimfon Ebong

Cynthia Iwuoha (06:07:11): > @Svetlana Ugarcina Perovic, Please help and delete Experiment 1/signature 4 .https://bugsigdb.org/Study_1151/Experiment_1?markasread=41795 - Attachment (BugSigDB): Study 1151/Experiment 1 > .

Peace Sandy (06:17:06) (in thread): > Done

Cynthia Iwuoha (06:24:22) (in thread): > @Peace SandyThank you

Joy (06:25:14): > Good morning great curators, I trust we are all doing great, I want to know, my paper involves creating 3 experiments in the study, am I going to create two signatures for each experiment? Waiting patiently on you all. Thanks

Mildred Anashie (06:26:38) (in thread): > Good morning@JoyIf the paper also reports increased and decreased signatures for all the experiments, then yes > > But you can share a link to your paper let’s go through it

Aleru Divine (06:28:11) (in thread): > Good morning@JoyThe signatures to curate is kind of determined by the results provided in the paper > > For example, if they provide increased and decreased abundance then 2 signatures will be required.Please share the link to the paper so we can check it out as suggested by@Mildred Anashie:pray:

Joy (06:28:12) (in thread): > Sure, I’ll do just that

Joy (06:29:25) (in thread): > This is it:https://www.nature.com/articles/s41598-024-74513-2 - Attachment (Nature): Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species > Scientific Reports - Mild atopic dermatitis is characterized by increase in non-staphylococcus pathobionts and loss of specific species

Kate Rasheed (06:31:45) (in thread): > @JoyI can see increase and decrease signatures in Fig. 2 for healthy vs mild AD

Adeshile Oluwatosin (06:34:46) (in thread): > @Joyit depends on your paper. > > If all experiments have increased and decreased signatures

Joy (06:35:26) (in thread): > Ok, so does that mean I’ll create 2 signatures for each experiment?

Kate Rasheed (06:35:55) (in thread): > For mild AD vs healthy, yes there would be two signatures

Joy (06:36:28) (in thread): > Ok. Thanks

Aleru Divine (06:40:17) (in thread): > That’scorrect@JoyI see increased and decreased signatures in figure 2b and 2c > > Just to be clear, these comparisons were made for > > Healthy(0) vs MILD AD(1) for below 12 yearsHealthy(0) vs MILD AD(1) for 12 yearsand older.Increased group (signature 1) would be the abundant signatures in mild AD (red plots).And purple plots would be the decreased group for both experiments.

Adeshile Oluwatosin (06:46:30) (in thread): > Figure 3alooks curatable to meas wellTitle: differential analysis healthy and mild AD(Just for this)Differential abundance analysis for mild AD patients compared to healthy participants using Maaslin2 (Materials and Methods). > > Cell shading represent the effect sizes of differences in skin taxa relative abundance based on health condition (healthy or mild AD) and age (below and above 12 years old). > > Red and blue represent an increase and decrease in relative abundance of the indicated taxa, respectively. Asterisks indicate FDR adjusted significant p-values < 0.05.

Adeshile Oluwatosin (06:48:24) (in thread): > As stated there , for healthy and mild AD@JoyRED - increase > Blue - decrease

Adeshile Oluwatosin (06:49:16) (in thread): > But the signatures are not so clear here

Mildred Anashie (06:56:12) (in thread): > @JoyWhat I think is, > > They stratified the AD group based on healthy and severity and later into two groups based on age. I.e Mild AD and Moderate-to-severe AD and then Mild AD and Moderate-to-severe AD under 12 years and Mild AD and Moderate-to-severe AD above 12 years and conducted experiments for all. Based on the Alpha diversity, I see the below experiments even though they are all not significantUnder 12 Healthy vs MildAD > Healthy vs moderate-to-severe > MildAD vs moderate-to-severeAbove 12Healthy vs MildAD > Healthy vs moderate-to-severe > MildAD vs moderate-to-severe > > Also see this excerpt “we analyzed alpha diversity separately for these two age groups. No significant differences were observed for the Inverse Simpson index, which takes the evenness of taxa abundance in a sample into account (Fig. 1c). When alpha diversity was measured by overall richness (the number of taxa in a sample), we also observed no significant differences (Fig. 1d)”. > > But for signatures I see two significant results in Figure 2b and 2c for the contrasts@Aleru Divinehas pointed out which isHealthy(group 0)vs MildAD(group 1) for under 12 yearsHealthy (group 0) vs MildAD (group 1) forabove12 yearsSo this implies that you have two experiments, so far with significant increased and decreased signatures but no significant alpha diversities > > Guys please check supplementary Fig S4 and S5 as well, what do you think?

Joy (06:57:57) (in thread): > I truly appreciate guys

Aleru Divine (07:06:44) (in thread): > Thanks@Mildred AnashieFor S4 plots > > I believe it is not differential abundance analysis. > > The reason is, the figure focuses on the prevalence of genera rather than directly comparing their abundance between the two groups. > > Differential abundance would require statistical analysis to show the abundance of specific genera significantly differs between groups eg.between mild AD and healthy samples, which isn’t indicated in this description.

Mildred Anashie (07:11:06) (in thread): > Exactly my thoughts too@Aleru DivineBut the S5 on the other hand looks like they did some sort of stratification of the AD group in a model based on moderate-to-severe AD, Antibiotics topical, Antihistaminicun, corticosteroids, Allergy, Antibiotics oral and still did the Under 12 years group again (but looks likeit’sfor all AD group in this case) using multiple linear regression > > It shows significance and I believe the significant results should be curated

Kate Rasheed (07:14:46) (in thread): > That’s true@Mildred AnashieS5 seems curatable.@Joywhile curating this, take note of the adjusted p-value.

Aleru Divine (07:14:54) (in thread): > For S5 on the other hand:thinking_face:I see that this is a differential abundance analysis and some stratification.It is on AD participants only yes > > How do you think this should be curated? > > I mean the experiments? The contrast groups.

Kate Rasheed (07:16:36) (in thread): > @Aleru DivineThe orange color for the correlation matrix shows positive while the purple shows negative@Joy.

Mildred Anashie (07:17:29) (in thread): > I think she is asking based on contrasts@Kate RasheedLet me read the results text again@Aleru Divine

Aleru Divine (07:19:11) (in thread): > Yes, the grouping@Kate Rasheed@Mildred Anashie

Kate Rasheed (07:19:58) (in thread): > I just saw that. How about moderately to severe AD patients vs AD patients under 12yrs old?

Mildred Anashie (07:27:15) (in thread): > I see this ‘We also investigated whether the observed differences between the severity of the AD lesions and healthy controls could be biased by medication use or other host factors. The use of oral and topical antibiotics, topical corticosteroids, antihistaminic and allergies did not impact the differential abundances of the different taxa (Figure S5)’.:thinking_face:

Adeshile Oluwatosin (07:28:46) (in thread): > Here - File (PNG): IMG_1649

Kate Rasheed (07:29:28) (in thread): > @Mildred AnashieDoes this means S5 should be healthy controls vs AD?

Aleru Divine (07:32:42) (in thread): > I am confused still@Mildred Anashie:pleading_face:

Mildred Anashie (07:39:48) (in thread): > I’m not so sure@Kate RasheedI’m going through other studies to check if I can see an example > > But I’m thinking, since there investigated differences between the AD lesions and healthy controls > > It could be eg. > AD (Antibiotics oral) vs Controls > Or > AD (Antibiotics oral) Vs No antibiotics Oral:thinking_face:

Aleru Divine (07:43:45) (in thread): > Funny howI’vedone something similar butcan’tfind which paper it was:sob:This analysis was done for AD participantsI don’tthinkitis ideal to compare with controls.The second suggestion however:thinking_face:

Adeshile Oluwatosin (07:51:49) (in thread): > You guysI can’teven see S5 on here so I can check it out

Mildred Anashie (07:52:28) (in thread): > Ican’tseem to find an example too:slightly_frowning_face:@Aleru Divine@Adeshile Oluwatosincheck the supplementary information

adekemi balogun (08:37:40): > Hello everyone, is the Bugsigdb site having any issues or am i the only one experiencing this?

Kate Rasheed (08:38:27) (in thread): > I’ve experienced this too.

Mildred Anashie (08:39:02) (in thread): > I think it’s all good now from my end

adekemi balogun (08:41:34) (in thread): > Yes yes, it’s working now

Adeshile Oluwatosin (08:50:21) (in thread): > Was about to say might be network

Svetlana Ugarcina Perovic (09:34:33): > Tomorrow (Thursday) isour weekly team meeting and office hours at 9 AM EDT. Questions are the keys to understanding. Bring them all up. > cc<@UBNSEMS3S>

Adeshile Oluwatosin (09:37:06) (in thread): > :hugging_face:I will be there:relieved:

Precious Orakwe (10:08:41) (in thread): > thanks@Svetlana Ugarcina Perovic

Mildred Anashie (10:20:09) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (11:07:26) (in thread): > Looking forward to it:blush:

Precious Orakwe (11:11:13): > Compliment of the day to everyone, I am currently trying to do some NCBI cleaning, my question is, when I find the right Taxonomy name, what should I do next.@Svetlana Ugarcina Perovic@Scholastica Urua

Mildred Anashie (11:12:59) (in thread): > Compliments of the day@Precious Orakwe:blush:

Precious Orakwe (11:14:02) (in thread): > Thank you@Mildred Anashie

Yoko C (11:33:59) (in thread): > This one seems complicated. You have 3 curatable images in my opinion: Fig 3a (3 contrast), Fig S3 (3 contrasts) these two come from the data group of skin condition and age. Then you have S5, with 3 variables which just focuses on AD patients. I think you should check this tomorrow in office hours, though.

Adeshile Oluwatosin (12:57:19) (in thread): > Check if it’s not in the discussion page already > If it’s there, you need permission to do any edit at all. > > If you can’t find the new names in the discussion page > You still need permission on adding it there, also toedit. My opinion@Precious Orakwe

Adeshile Oluwatosin (12:57:59) (in thread): > I’m also doing NCBI cleanup@Scholastica Uruamentioned that youmustrequest permission before anything is changed.

Adeshile Oluwatosin (13:01:06) (in thread): > Just be taking notes of whatever changesyou’vecome across

Adeshile Oluwatosin (13:01:11) (in thread): > Check this;https://community-bioc.slack.com/archives/C04RATV9VCY/p1728650739686119?thread_ts=1728642019.941919&channel=C04RATV9VCY&message_ts=1728650739.686119 - Attachment: Attachment > Before proceeding with the NCBI cleanup, please go through this post by @Esther Afuape: https://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189 > > Always remember to first check the discussion page as some taxa has previously been noted down. > > Very important: Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything.

Mildred Anashie (13:03:35) (in thread): > @Precious OrakweOnce you find a taxa that needs clean up, > 1. Check the discussion page if it isn’t recorded as “unresolved” or something like that > 2. If it isn’t there and you are able to resolve it, copy a link to the study/signature, state the taxa and the ID > 3. Then inform our mentors here on slack about it and request permission to resolve it > 4. I think if permission is granted, you would also be given permission to update the discussion page > Generally, just go through this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728650739686119?thread_ts=1728642019.941919&channel=C04RATV9VCY&message_ts=1728650739.686119

Precious Orakwe (16:08:49) (in thread): > Mildred and Tosin, Thanks for the reply

Precious Orakwe (16:43:27): > I am working on this topic for NCBI cleaning; > (Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring/Experiment 1/Signature 1) and this is the missing NCBI (Christensenellaceae) and this is what I found on UNIPROT and NCBI Taxonomy browser > Christensenellaceae > Taxonomy ID - 990719 > Rank- family > Heterotypic Synonyms - Candidatus Borkfalkiaceae > What next can I do@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Scholastica Urua@Peace Sandy@Chioma Onyido

2024-10-17

Ebuka Chinwuba (04:07:47) (in thread): > Acknowledged@Svetlana Ugarcina Perovic

Ebuka Chinwuba (04:28:22): > Hello, Amazing Community!:star2:Hi everyone, > I hope this message finds you all doing well! I hope we all are having a productive week? Personally, contributing to this project made it a very productive week so far for me. I’m thrilled to contribute to this curation project and to be part of such a talented and passionate group. I’m looking forward to learning from each of you, collaborating, and helping to make this project a success. > If there’s anything I can assist with, feel free to reach out! > Wishing you all an amazing day ahead!

Aleru Divine (04:44:21) (in thread): > Hi@Ebuka Chinwubathank you so much! > Wishing you an amazing day as well:hugging_face:

Mildred Anashie (04:45:26) (in thread): > I agree with you@Ebuka ChinwubaVery talented and passionate group > > Wishing you an amazing day too:blush:

Mildred Anashie (04:52:58): > HelloEveryone:wave:A quick reminderLet’s not forget our weekly team meeting and Office hourtoday, looking forward to another opportunity to learn from everyones questions:blush:https://community-bioc.slack.com/archives/C04RATV9VCY/p1729085673626159 - Attachment: Attachment > Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. Questions are the keys to understanding. Bring them all up! https://us02web.zoom.us/j/2737200499. > cc @UBNSEMS3S

Svetlana Ugarcina Perovic (05:05:17) (in thread): > @Precious Orakweyou could team up with@Chinwendu Joy Enyidiegwuand do together corrections of this curationhttps://github.com/waldronlab/BugSigDBcuration/issues/496

Kate Rasheed (05:05:33) (in thread): > Thank you@Ebuka Chinwuba. Wishing you a productive week as well.

Svetlana Ugarcina Perovic (05:06:16) (in thread): > Do not forget to ask for assignment there first ;)

Chinwendu Joy Enyidiegwu (05:08:22) (in thread): > Noted with thanks:pray:@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (05:55:44) (in thread): > Nice to hear this:hugging_face:@Ebuka Chinwuba

Precious Orakwe (05:57:03) (in thread): > Okay, thanks for the privilege@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (05:57:58): > NCBI Cleanup: > * [ ] Impacts of Dietary Protein and Niacin Deficiency on Reproduction Performance, Body Growth, and Gut Microbiota of Female Hamsters (Tscherskia triton) and Their Offspring/Experiment 3/Signature 1: Unclassified YS2: Muribaculaceae,2006847(uniprot). > > * The gut microbiota is associated with psychiatric symptom severity and treatment outcome among individuals with serious mental illness/Experiment 3/Signature 2: Lachnospiraceae bacterium NK4A136: 877420,

Precious Orakwe (05:58:21) (in thread): > Let’s do a great job@Chinwendu Joy Enyidiegwu:+1:

Adeshile Oluwatosin (05:58:42) (in thread): > Based on my findings

Precious Orakwe (06:01:18) (in thread): > @Ebuka ChinwubaThanks for the warm message and well done on your contributions:+1:

Ebuka Chinwuba (07:58:50): > Hello. I noticed that on my Experimental 1 review, I have warning sign on the ’Matched andConfounders controlled for’ options. it happens, I didn’t find the answers on the list values there, I then typed in mine. Please I want to know if am at liberty to add a new value, since its giving me the option to?@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Scholastica Urua

Mildred Anashie (08:03:48) (in thread): > Hi@Ebuka ChinwubaI’m unsure if we have the liberty to do this > > But did you type the values in full (Without acronyms) or maybe try something related, in my opinion this works > > Like for e.g The study I am working on reported Smoking status and when I tried something related “smoking behavior” it was a permissible value, though yet to be reviewed, I believe it’s a suitable alternative for now > > I stand to be corrected though

Adeshile Oluwatosin (08:06:35) (in thread): > Hi@Ebuka ChinwubaMy opinion is to find a similar permissible value in the dropdown options.

Adeshile Oluwatosin (08:12:31) (in thread): > Only in the case of taxa do I know, if searched for on NCBI, discussion page and everywhere andit’snot found.That’swhen you can input the exact taxa seen.

Chris Awoke (08:21:33): > Hello,@Svetlana Ugarcina Perovic. I’m sorry to bother you, but could you please help me delete Signature 2 from Experiment 1 in this study:https://bugsigdb.org/Study_1124? > > Thank you so much. - Attachment (BugSigDB): Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries - BugSigDB > BACKGROUND: Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV).

Precious Orakwe (08:28:26) (in thread): > What was your own answer that you typed in?

Samuel Nnanna (08:44:30) (in thread): > @Ebuka Chinwubaif you’re absolutely sure the values you have are on the paper, then go aheadandinput what’s there provided there are no similar values in the drop down, it’d be flagged but when your paper is being reviewed, if it’s correct, it’ll be added. I think this was the same issue I had some time ago@Adeshile Oluwatosin(socio-demographic factors and nutritional intake)

Adeshile Oluwatosin (08:45:16): > 15 minutes more to join, 2PM WAT - Attachment: Attachment > Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. Questions are the keys to understanding. Bring them all up! https://us02web.zoom.us/j/2737200499. > cc @UBNSEMS3S

Adeshile Oluwatosin (08:47:07) (in thread): > @Samuel NnannaYes, you are correct > > Only if you are extremely sure that there’s no similar permissible value, only then should you input the exact confounder stated@Ebuka Chinwuba

Svetlana Ugarcina Perovic (09:05:02) (in thread): > deleted.

Adeshile Oluwatosin (09:05:39) (in thread): > You can Confirm in the meeting

Rahila-me (10:03:33): > The meeting has ended abi?

UBNSEMS3S (10:03:51): > Thank you everyone who attended. I will get the recording posted sooner today. It is processing right now.

Mildred Anashie (10:04:16): > Thank you for another amazing session<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido@Scholastica Urua@Esther Afuape@Peace Sandy@Levi Waldron:hugging_face:I have a question Ididn’tget to ask, when doing NCBI cleanup and you are able to resolve one from a reviewed paper, should it be left the way it is or shared to get permission to effect the change

Mildred Anashie (10:05:19) (in thread): > Thank you<@UBNSEMS3S>

Mildred Anashie (10:05:36) (in thread): > Yes it has@Rahila-me

Rahila-me (10:05:48): > Thank you our great Mentors@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldronfor today’s session. My network was terrible thou

Rahila-me (10:09:22): > Here is the clarification i would be need from the paper i am curating@Svetlana Ugarcina Perovic@Scholastica Urua<@UBNSEMS3S>here is the article:https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2020.01994/fullhttps://bugsigdb.org/Study_1162confused on the number of case patients to record if i will record 28 or 11 after the 180 day:ResultsPrevalence of Pathogens in Patients With EncephalitisFecal samples were collected from 28 encephalitis (ENC) patients (median age 46 years; 82.1% male; median GCS 6.5; median SOFA 6.5; median APACHE-II 14.5; median IOS 12.5). The clinical information of all encephalitis patients is shown inTable 1. Until 180 days follow-up, there were 11 patients were alive, whereas 17 patients were deceased. Twenty-eight healthy subjects served as the healthy controls (CON) and had fecal samples collected once. A principal coordinate analysis (PCoA) plot showed a significant difference in β-diversity [Bray-Curtis distance (Figure 1A) and unweighted UniFrac distance (Figure 1B)] between the ENC and CON groups (Adonis test,p> 0.05). The α-diversity, including Shannon, Chao1, PD-whole tree, observed species, and Simpson indexes, did not show significant differences between these two groups (Mann-WhitneyUtest,p> 0.05) (Figures 1C,DandSupplementary Table S3). > Second: Is table 2 curatable: To evaluate differences in microbial composition in the feces obtained from patients and controls, we compared the relative abundances in both groups, represented by read percentages (Table 2). The significantly enriched taxa in the patient group were the phylumProteobacteria, classBacilli, classGammaproteobacteria, orderLactobacillales, orderErysipelotrichales, orderEnterobacteriales, familyPorphyromonadaceae, familyEnterobacteriaceae, genusParabacteroides, and genusOscillospira. The significantly depleted taxa in the patient group were the classBetaproteobacteria, orderBurkholderiales, familyLachnospiraceae, genusPrevotella, genusFaecalibacterium, genusRuminococcus, and genusSutterella.

Aleru Divine (10:11:14): > Thanks for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina Perovic<@U1LCB8WEA>

UBNSEMS3S (10:11:15) (in thread): > It looks like they did a full comparison of 28 vs. 28 for at least one analysis. Did they specify anywhere in the paper that they only analyzed the living encephalitis patients? Table 2 at least says they analyzed all 28 cases vs. 28 contols.

UBNSEMS3S (10:11:24) (in thread): > Table 2 is curatable.

Precious Orakwe (10:11:48) (in thread): > Thanks@C. Mirzayi (please do not tag this account)for the wonderful session today

Mary Agekameh (10:32:44): > Hi<@UBNSEMS3S>These are the questions i have regarding the paper i’m curating with@Mildred Anashieand I need clarification on > 1. How would supplementary figure 3 and 5 be curated > 2. What can be made of Table 2, Supplementary Table 1 and Supplementary File 3. What comparisons/contrasts should be used to record those signatures? The paper doesn’t clearly state, it just says “Enriched with age” and “Depleted with age” in the tables and nothing much in the supplementary file. The remarks are also adding to the confusion. All the signatures in the file 3 appear to be significant and is overlapping with Table 2 and Supplementary Table 1 even though Supp. Table 1 isn’t mentioned in the paper. So we can’t really figure out what it’s saying based on the group names, Group 1 and Group 0. > 3. We see a lot of comparisons in Supplementary file 6 with a few significant signatures and comparisons should it be curated? And it’s unclear what the contrast are > 4. For alpha diversity we see only for the age related contrasts, and I think only 61-70 and 71-80 appears to be significant. If so, should I record as one experiment? With the younger age being group 0 and the other group 1? Also can I record Figure 1E for the signatures? > Thank you:pray:

Mary Agekameh (10:34:27): > This is the link to the paperhttps://www.nature.com/articles/s41467-024-52097-9 - Attachment (Nature): Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes > Nature Communications - Here, the authors employ shotgun-metagenomic sequencing to profile the microbiome of Singaporean octogenarians, finding key microbial shifts and metabolic changes in the…

Samuel Nnanna (10:38:46): > Thank you for the session today<@UBNSEMS3S>@Svetlana Ugarcina PerovicI’m quite confused. In figure 2b of my paper (https://onlinelibrary.wiley.com/doi/10.1155/2023/6297653), there’s “unclassified chloroplast” under the family level and here (https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID), chloroplast is to be curated as Cyanobacteriota….how do i curate for the unclassified chloroplast? > > In the same figure2b, i curated “cynobacteriia” under class as “Cyanophyceae” and chloroplast under order as “Acaryochloridales” > > Any thoughts on this? - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in… - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Ebuka Chinwuba (10:40:14): > Greeting@Svetlana Ugarcina PerovicThe Experiment 2 hasn’t been deleted, please kindly recheck.https://bugsigdb.org/Study_1165 - Attachment (BugSigDB): Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment - BugSigDB > Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype.

Svetlana Ugarcina Perovic (10:48:42) (in thread): > deleted. (sometime needs more time to be deleted)

Adeshile Oluwatosin (10:51:17) (in thread): > Noted, thank you@C. Mirzayi (please do not tag this account)

Adeshile Oluwatosin (10:51:34) (in thread): > @Mildred AnashieAsk for permission

Joy (10:51:48) (in thread): > Thank you<@UBNSEMS3S>for the wonderful session, I was late thou. Waiting on the recorded version. Thanks to all the mentors@Svetlana Ugarcina Perovic@Chioma Onyido@Scholastica Urua@Esther Afuape@Peace Sandy@Levi Waldron

Rahila-me (10:52:59) (in thread): > <@UBNSEMS3S>(Did they specify anywhere in the paper that they only analyzed the living encephalitis)NOOn Table 2 if i have to curate it then the Statistical test used will be Mann-WhitneyUtest? > > Thank you for this clarification.

Joy (10:53:36): > Hi guys, I need help with my paper, why can’t I find the signature button on my paper. Thanks :https://bugsigdb.org/Study_1163 - Attachment (BugSigDB): Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients - BugSigDB > INTRODUCTION: Increased bacterial translocation and alterations to gut microbiota composition have been described in HIV infection and contribute to immune activation and inflammation.These effects persist despite combined antiretroviral therapy (cART).

Adeshile Oluwatosin (10:54:25) (in thread): > @Joyyou need to add an experiment, to be able to add a signatureOr it might be network ifyou’vealready added one andcan’tsee it

Mildred Anashie (10:55:30) (in thread): > Hi@JoyIf you have already added a signature and you have refreshed itdidn’twork > > You can try this, it works for mehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728041250257259?thread_ts=1728040350.221289&channel=C04RATV9VCY&message_ts=1728041250.257259 - Attachment: Attachment > Also, I just tried using my phone to do a quick demo on how I easily do it, that seems to be like a short cut for me :joy: (Others might disagree) > I hope it’s clear enough for you > > Once I go to the contributions I’ve made, everything appears there and I just click on what I might have been searching for

Mildred Anashie (10:56:42) (in thread): > Or follow this stephttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&channel=C04RATV9VCY&message_ts=1727957860.907319 - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Joy (10:56:49) (in thread): > @Adeshile OluwatosinI did

Joy (10:57:33) (in thread): > Thanks@Svetlana Ugarcina PerovicI’ll refresh it again

Adeshile Oluwatosin (10:57:41) (in thread): > @Joyit’snetwork then

Joy (10:58:20) (in thread): > Thanks guys, Let me try all the suggestions

Svetlana Ugarcina Perovic (11:01:24) (in thread): > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697048504747639 - Attachment: Attachment > @U1LCB8WEA asked me to post here before making edits. > Here’s a link that helped me map Chloroplasts to Cyanobacteriota: https://en.wikipedia.org/wiki/Chloroplast

Svetlana Ugarcina Perovic (11:05:05) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1697048376093069 - Attachment: Attachment > @U1LCB8WEA @UBNSEMS3S @Svetlana Ugarcina Perovic I am working on one of the Papers with Missing NCBI id for one of it’s signatures: Study_764. > For the organism termed “Chloroplast” I am finding that the closest scientific name is unclassified Cyanobacteriota. Can I go ahead and edit?

Samuel Nnanna (11:06:28) (in thread): > Thank you@Svetlana Ugarcina Perovic. I already found this in this link (https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID), where chloroplast is to be curated as Cyanobacteriota, my confusion is whether to curate unidentified chloroplast as is?

Svetlana Ugarcina Perovic (11:07:07) (in thread): > cynobacteriia is a typo -> Cyanobacteria

Svetlana Ugarcina Perovic (11:10:38) (in thread): > family, order, class: - File (PNG): Screenshot 2024-10-17 at 17.10.13.png

Svetlana Ugarcina Perovic (11:11:52) (in thread): > I do not see any “Cyanophyceae” nor “Acaryochloridales”

Samuel Nnanna (11:16:11) (in thread): > So the taxonomy levels don’t matter? - File (PNG): image.png - File (PNG): image.png

Samuel Nnanna (11:17:48) (in thread): > The reason I asked asked Chloroplast was because, it’s to be curated as Cyanobacteriota (which is the phylum level) and in the paper they were seen as class, order and family > > I got confused….that’s why i’m asking for clarification

Svetlana Ugarcina Perovic (11:19:39) (in thread): > This paper reported family, order, class level.

Ebuka Chinwuba (11:22:08) (in thread): > @JoyIf you have done experiment. you will find it ontop of your experiment layout

Samuel Nnanna (11:22:29) (in thread): > Yes, hence the screenshots

Svetlana Ugarcina Perovic (11:24:37) (in thread): > I am not sure about this, let me confirm with@Esther Afuape

Svetlana Ugarcina Perovic (11:25:23) (in thread): > This is not a super clear NCBI ID interpretation…

Svetlana Ugarcina Perovic (11:25:53) (in thread): > (that’s why you asked for help:slightly_smiling_face:yes I know…)

Samuel Nnanna (11:26:56) (in thread): > Alright…thank you so much

Samuel Nnanna (11:29:17) (in thread): > i’ll be looking forward to your response

Svetlana Ugarcina Perovic (11:37:20) (in thread): > When this type of confusion happens, what I usually do is going to already curated andreviewed curation with similar signatures, seehttps://bugsigdb.org/Study_964 - Attachment (BugSigDB): Dysbiosis of the Saliva Microbiome in Patients With Polycystic Ovary Syndrome - BugSigDB > Significant differences in salivary microbiota communities between polycystic ovary syndrome (PCOS) patients and healthy controls have been reported, and interestingly, some salivary microbiota exhibit diurnal oscillation in healthy people.

Svetlana Ugarcina Perovic (11:37:54) (in thread): > Fig 3D:https://www.frontiersin.org/files/Articles/624504/fcimb-10-624504-HTML-r1/image_m/fcimb-10-624504-g003.jpg - Attachment: Attachment

Ebuka Chinwuba (11:38:47): > I have a follow up question regarding my curation please,@Scholastica Urua@Svetlana Ugarcina Perovic<@UBNSEMS3S>1) Given that the gut microbiota composition in Red River Hogs (RRHs) differed significantly between the two zoos, with Firmicutes dominating in Verona and Bacteroidetes in Rome, how might the specific dietary differences (e.g., animal protein in Verona vs. plant protein in Rome) contribute to these shifts in microbial phyla? > 2) What role might these dietary-induced changes in microbiota play in the overall health and physiological functions of the RRHs, considering their evolutionary background and captive conditions?https://www.mdpi.com/2076-2607/11/6/1542Thank you - Attachment (MDPI): Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment > Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype. As the name suggests, the Red River Hog is a wild member of the pig family living in Africa, in particular through the West and Central African rainforest. To date, very few studies have analysed the gut microbiota of Red River Hogs (RRHs) both housed under controlled conditions and in wild habitats. This study analysed the intestinal microbiota and the distribution of Bifidobacterium species in five Red River Hog (RRH) individuals (four adults and one juvenile), hosted in two different modern zoological gardens (Parco Natura Viva, Verona, and Bioparco, Rome) with the aim of disentangling the possible effects of captive different lifestyle and host genetics. Faecal samples were collected and studied both for bifidobacterial counts and isolation by means of culture-dependent method and for total microbiota analysis through the high-quality sequences of the V3–V4 region of bacterial 16S rRNA. Results showed a host-specific bifidobacterial species distribution. Indeed, B. boum and B. thermoacidophilum were found only in Verona RRHs, whereas B. porcinum species were isolated only in Rome RRHs. These bifidobacterial species are also typical of pigs. Bifidobacterial counts were about 106 CFU/g in faecal samples of all the individuals, with the only exception for the juvenile subject, showing 107 CFU/g. As in human beings, in RRHs a higher count of bifidobacteria was also found in the young subject compared with adults. Furthermore, the microbiota of RRHs showed qualitative differences. Indeed, Firmicutes was found to be the dominant phylum in Verona RRHs whereas Bacteroidetes was the most represented in Roma RRHs. At order level, Oscillospirales and Spirochaetales were the most represented in Verona RRHs compared with Rome RRHs, where Bacteroidales dominated over the other taxa. Finally, at the family level, RRHs from the two sites showed the presence of the same families, but with different levels of abundance. Our results highlight that the intestinal microbiota seems to reflect the lifestyle (i.e., the diet), whereas age and host genetics are the driving factors for the bifidobacterial population.

Samuel Nnanna (11:40:44) (in thread): > thank you@Svetlana Ugarcina PerovicI see where how unclassified cyanobacteriota was curated. > Thank you

Precious Orakwe (12:21:46): > @Chinwendu Joy Enyidiegwuplease can you share me the full pdf of the study that we are working on, I cant access the full text. Thanks

Svetlana Ugarcina Perovic (13:02:31) (in thread): > @Ebuka ChinwubaTo repeat: The Experiment 2 has been deleted. Sometimes the platform needs time to be updated with changes. Thank you for your patience!

Mildred Anashie (13:16:57) (in thread): > Okay@Adeshile OluwatosinI am asking to know based on already reviewed papers, butI’llmake a post about it

Adeshile Oluwatosin (13:17:28) (in thread): > Alright dear:thumbsup:it’sbest to ask regardless

UBNSEMS3S (13:18:32): > Recording of today’s office hours. Thank you for all the great questions. - File (MPEG 4 Video): Video1035906972.mp4

Mildred Anashie (13:19:08) (in thread): > Thank you<@UBNSEMS3S>

Adeshile Oluwatosin (13:31:22) (in thread): > Thank you<@UBNSEMS3S>

Adeshile Oluwatosin (13:45:33): > In this particular study,https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02747-z@Svetlana Ugarcina Perovicconfirmed that Figure 4 is curatable > In the office hour, I requested for confirmation on how to identify Group 0 and Group 1. > > My phone went off along the line, did anyone see her response to this. I would appreciate this.

Mildred Anashie (13:54:37) (in thread): > Hi@Adeshile OluwatosinI didn’t see the response but Fig 4 looks like an experiment based on birth outcomes (weight) > > So I think it could be something like “Low Infant birthweight <2500g vs High infant birthweight >2500 g” > > But I see Fig 4 showing significance and the text says this “We investigated the effects of the gut microbiota in pregnancy on pregnancy and birth outcomes. Low infant birth weight (< 2500 g) was significantly associated with high abundances of the phyla Spirochaetes, the families Spirochaeteceae, and Veillonellaceae and the genus Treponema (Fig. 4) though these associations lost significance after false discovery rate correction (q > 0.05)” concerning Fig 4.

Adeshile Oluwatosin (13:57:34) (in thread): > Hi@Mildred Anashieyes, but since they specified on pregnancy. > > I initiated they didn’t specifically mention if it was HIV infected pregnant women or not. > > So I was thinking, not sureControl-Pregnant women with normal birth outcomeCase-Pregnant women with adverse birth outcome > > Description; Pregnant women who experienced adverse birth outcomes, specifically giving birth to infants with low birth weight (<2500 g).

Adeshile Oluwatosin (13:58:13) (in thread): > This was were I also got clarification that two studies were involved; > > The aim of this study was to investigate the gut microbiota in HIV-infected and HIV-uninfected pregnant women and to compare and identify the association between gut microbial composition and adverse birth outcomes.

Adeshile Oluwatosin (13:59:34) (in thread): > Also ifthat’sthe case, a specific number was not mentioned for both case and control. > > Kindly check again@Mildred Anashie

Mildred Anashie (14:00:00) (in thread): > Do you mean the sample size?

Adeshile Oluwatosin (14:00:09) (in thread): > Yes

Adeshile Oluwatosin (14:00:32) (in thread): > In this particular experiment comparing the birth outcome

Mildred Anashie (14:01:17) (in thread): > The sample size is in the figure, see attached image - File (JPEG): IMG_1477

Adeshile Oluwatosin (14:01:38) (in thread): > What do you also think about my specifications?@Mildred Anashie

Adeshile Oluwatosin (14:02:08) (in thread): > Noted@Mildred Anashiefunny howI’vegone through this countless times

Adeshile Oluwatosin (14:02:17) (in thread): > Thanks

Mildred Anashie (14:03:20) (in thread): > I’ll have to scan through the article again > > But the text I shared earlier, seems to imply the experiment wasn’t significant after MHT correction and the Figure shows significance,I don’tknow if this is another error reported in results text > > “We investigated the effects of the gut microbiota in pregnancy on pregnancy and birth outcomes. Low infant birth weight (< 2500 g) was significantly associated with high abundances of the phyla Spirochaetes, the families Spirochaeteceae, and Veillonellaceae and the genus Treponema (Fig. 4)******though these associations lost significance after false discovery rate correction (q > 0.05******)”.

Mildred Anashie (14:03:50) (in thread): > You are welcome@Adeshile OluwatosinIt happens most times:blush:

Adeshile Oluwatosin (14:04:44) (in thread): > Exactly, why I initiallydidn’tspecify it to be curated.

Adeshile Oluwatosin (14:06:55) (in thread): > Here - File (JPEG): IMG_1667

Adeshile Oluwatosin (14:10:16) (in thread): > But@Mildred Anashiesometimes I don’t really trust the write up/ texts of these articles. > > > I can see that they made mention of richness species. > Which didn’t show at all in the result (what is visible here is just Shannon and Simpson which experienced a decrease).

Adeshile Oluwatosin (14:11:42) (in thread): > In this caseI’llrecord just what is reported in the result, happened in the previous curation as well.

Mildred Anashie (14:13:04) (in thread): > I seem to be towing towards the line of trusting the figures more too@Adeshile Oluwatosinbecause of allwe’vebeen seeing recently

Adeshile Oluwatosin (14:13:55) (in thread): > So in that case, I would consider Figure 4 curatable as confirmed by Svetlana.

Mildred Anashie (14:24:02) (in thread): > SoI’vegone through the paper and I think they did the last experiment based on the birth outcomes of all the women recruited for the study and not their disease status > > So I would still think you go with the Low birthweight outcome and High birthweight outcome as stated in the Figure@Adeshile Oluwatosin

Adeshile Oluwatosin (14:27:33) (in thread): > Yeah, I mentionedit’snot based on the disease status for the second experiment. > > And when I saw the result for low birthweight and high birthweight > It made more sense > Thanks@Mildred Anashie

Mildred Anashie (14:31:42) (in thread): > You are welcome:hugging_face:

Aleru Divine (15:07:11) (in thread): > Thanks!<@UBNSEMS3S>

Chinwendu Joy Enyidiegwu (15:44:08) (in thread): > here is the linkhttps://www.sciencedirect.com/science/article/abs/pii/S088915912400624X

Chris Awoke (16:00:17) (in thread): > Thanks you so much,@Svetlana Ugarcina Perovic

Chris Awoke (16:03:39) (in thread): > It seems to persist. I can still see it there. Meanwhile, the signatures for other experiments have yet to be populated.

Ebuka Chinwuba (16:03:45) (in thread): > @Svetlana Ugarcina PerovicOkay, I’ll just have to wait for the platform to update and I will keep refreshing. Thank you

Ebuka Chinwuba (16:45:55) (in thread): > @Samuel NnannaThank you for reaching out. With your past experience on this issue, I want to know what happens when it’s been flagged down?

Ebuka Chinwuba (16:47:05) (in thread): > @Adeshile Oluwatosin@Precious Orakwe@Mildred Anashiethank you fams for your helping out

Samuel Nnanna (17:07:18) (in thread): > When i say flagged, i don’t mean it’s wrong, I mean it’d just be noted as something that’s not in the database. So when the mentors see it, they’ll review and it’s correct, it’ll be added.@Ebuka Chinwuba

Precious Orakwe (18:39:27) (in thread): > you are welcome@Ebuka Chinwuba

Precious Orakwe (19:04:40) (in thread): > good day@Svetlana Ugarcina Perovici cant get the full pdf or full text of this paper, what can we do.

2024-10-18

vandana maddi (01:45:17) (in thread): > Thank you<@UBNSEMS3S>

Svetlana Ugarcina Perovic (02:51:59) (in thread): > Second link provided in thehttps://github.com/waldronlab/BugSigDBcuration/issues/496is a pdf to download.@Precious Orakwe - Attachment: #496 Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice > Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Bethany A. Masson – Brain, Behavior, and Immunity > > https://www.sciencedirect.com/science/article/pii/S088915912400624X
> 1-s2.0-S088915912400624X-main.pdf

Rahila-me (02:59:33) (in thread): > Thank you<@UBNSEMS3S>

Svetlana Ugarcina Perovic (03:02:39) (in thread): > Just rechecked this: all good.https://bugsigdb.org/Study_1143/Experiment_1/Signature_2deletedhttps://bugsigdb.org/Study_1143/Experiment_1/Signature_3deleted

Svetlana Ugarcina Perovic (03:03:50) (in thread): > Just rechecked this and it says this page does not exit.https://bugsigdb.org/Study_1165/Experiment_2deleted.

Svetlana Ugarcina Perovic (03:34:52): > :coffee::teapot::tulip:Good morning, > you are ALL doing great. Keep up the good work andHAPPY FRIDAY!Just wanted to share with you some microbiome/bioinformatics learning/fun resources that might be of your interest. Some time ago, I started compiling several lists (& still regularly updating them!):Microbiome eventshttps://github.com/SvetlanaUP/Microbiome-conferences-cMicrobiome podcastshttps://github.com/SvetlanaUP/Microbiome-etc-PodcastsBioinformatics learning resourceshttps://github.com/SvetlanaUP/A-microbiologist-wants-to-compute

Kate Rasheed (03:35:42) (in thread): > Thank you@Svetlana Ugarcina Perovicfor this. I’ll look them up and good morning to you too. A happy Friday as well.

Mildred Anashie (03:36:27) (in thread): > This is great:blush:Thank you@Svetlana Ugarcina Perovicand Good Morning:coffee:I’llbe sure to check them out

Princess Rehoboth Asuelimen (03:36:45) (in thread): > Thank you@Svetlana Ugarcina Perovic,I’llcheck it out.

Mildred Anashie (03:42:00) (in thread): > Hello Everyone:wave:Hi@Svetlana Ugarcina Perovic@Esther Afuape@Chioma Onyido@Scholastica Urua@Peace SandyMy second contribution is yet to be graded, Finding other ways to be helpful I decided to do some NCBI detective work , sharing this to know if I can effect the changes as I had concerns since some of the studies are reviewed already. > > > Taxonomic ID resolution > 1. https://bugsigdb.org/Study_958/Experiment_1/Signature_1,https://bugsigdb.org/Study_1021/Experiment_2/Signature_1https://bugsigdb.org/Study_1055/Experiment_1/Signature_1Erysipelatoclostridiaceae is on NCBI as****“Coprobacillaceae”****which is the homotypic synonym with ID 2810280 > 2.https://bugsigdb.org/Study_991/Experiment_1/Signature_2,https://bugsigdb.org/Study_999/Experiment_1/Signature_1,https://bugsigdb.org/Study_999/Experiment_3/Signature_2Clostridium senso stricto 1 has been resolved as Clostridium Genus with ID 1485 on the discussion page. Is it okay to effect the change?
> > 3.https://bugsigdb.org/Study_993/Experiment_2/Signature_2Meyerozyma guilliermondii is on NCBI with ID 4929 > > 4.https://bugsigdb.org/Study_1055/Experiment_1/Signature_1Williamsia and Vibrionimonas with ID’s 85043 and 1649511 > > Also I came across this studyhttps://bugsigdb.org/Study_1142, I think it isn’t yet reviewed and I’m unsure if I have permission to update it since it’s a curation from this cohort, so I’m posting it here so the original curator can crosscheck, confirm and update (If I am not allowed to).https://bugsigdb.org/Study_1142/Experiment_2/Signature_1**** and ****https://bugsigdb.org/Study_1142/Experiment_5/Signature_2Anaeroglobus micronuciformis with current name Megasphaera micronuciformis-***** *****ID 187326 > > PS: If you are doing NCBI cleanup, you can go through this link to get another site you can check asides NCBI Taxonomy browser and Uniprot.https://community-bioc.slack.com/archives/C04RATV9VCY/p1711489001147419?thread_ts=1711479513.033609&channel=C04RATV9VCY&message_ts=1711489001.147419Thank You:pray: - Attachment (BugSigDB): Study 958/Experiment 1/Signature 1 > Source: figure 3 A Description: Lefse analysis to identify the microbial species that exhibited the most significant differences between NT and EF Abundance in… - Attachment (BugSigDB): Study 1021/Experiment 2/Signature 1 > Source: Figure 2B, Supplementary Table S8 Description: Differentially abundant taxa identified by LEfSe in smoke exposed versus non-smoke exposed late infants… - Attachment (BugSigDB): Study 1055/Experiment 1/Signature 1 > Source: Additional file 1: Table 8 Description: Differential abundance taxa of AM and AM_EV pair Abundance in Group 1: increased abundance in Amniotic fluid-derived… - Attachment (BugSigDB): Study 991/Experiment 1/Signature 2 > Source: Figure 4A Description: Differential abundance calculated using Linear discriminant analysis (LDA) effect size (LEfSe) at genera level in skin microbiome… - Attachment (BugSigDB): Study 999/Experiment 1/Signature 1 > Source: Figure 2d + Figure 3 + Table S3 + Table S4 Description: Taxa Differing in Abundance Between Ferrous sulfate (FS) treated pups (PD 15) and Vehicle control…

Kate Rasheed (03:50:23): > Good morning everyone. Weldone for the contributions and discussions so far, it’s been learning-full:smile:. > > I have a question concerning a taxa. From the article I’m curating, it’s stated as “Ruminococcaceae incertae sedis”; looking this up in NCBI, what I can see is different variations and the closest to it is “unclassified Oscillospiraceae” which is a heterotypic synonym for “unclassified Ruminococcaceae”. > > I saw from the discussion page that “incertae sedis” means “of uncertain placement”; I would like to find out if I can represent “Ruminococcaceae incertae sedis” as “unclassified Oscillospiraceae” or I should curate as “Ruminococcaceae incertae sedis”. > > Also, I’ve looked up “uncultured Mollicutes RF9” in NCBI but can’t find anything related. Maybe a fresh eyes can help:smile:. > > Looking forward to our responses. Thank you so much.

Cate Ouma (03:51:07): > Good morning Team, Kindly help me review my study curation. I’m looking forward to your comments and corrections:https://bugsigdb.org/Study_1130 - Attachment (BugSigDB): Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia - BugSigDB > Diarrhea claims >500,000 lives annually among children under five years of age in low- and middle-income countries.Mortality due to acute diarrhea (<7 days’ duration) is decreasing, but prolonged (7-13 days) and persistent (≥14 days of duration) diarrhea remains a massive challenge.

Mildred Anashie (03:52:19) (in thread): > Hi@Cate OumaWell done on your curation,I’llgo through it asap

Cate Ouma (03:52:52) (in thread): > Thank you@Mildred Anashie

Aleru Divine (04:04:21) (in thread): > @Kate Rasheedfor your first question, sinceRuminococcaceaeis nowOscillospiraceae, I think this can workOscillospiraceae incertae sedis ID= 552397https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=552397 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (JPEG): IMG_1266

Kate Rasheed (04:04:25) (in thread): > Thank you so much fresh eyes.

Aleru Divine (04:05:54) (in thread): > I’mstill searching if I can find anything on the second,:hand_with_index_and_middle_fingers_crossed:if nothing, it should be curated as seen

Mildred Anashie (04:06:26) (in thread): > Hi@Kate RasheedI think you might have to record ‘uncultured Mollicutes RF9’ this way, I didn’t find anything as well

Aleru Divine (04:15:27) (in thread): > Well done@Cate Ouma:partying_face:I’llgo through the curation as well

Aleru Divine (04:21:39) (in thread): > @Kate Rasheed@Mildred AnashieI found something on theMissing NCBI ID page“Experiment_2/Signature_2 > Stratification of the Gut Microbiota Composition Landscape across the Alzheimer’s Disease Continuum in a Turkish Cohort/Experiment 2/Signature 2Mollicutes_RF39_Unclassifiedwas updated tounclassified Mollicuteswhich is the closest name to the family name recorded in the study’s supplementary table S2d” > > I believe we can use “unclassified Mollicutes” in the case too - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in… - File (JPEG): IMG_1267

Mildred Anashie (04:27:47) (in thread): > I am unsure how this resolves Mollicutes_RF39_Unclassified and also Unclassified Mollicutes RF9. I believe the number could mean different strains, wouldn’t this mean classifying them all under unclassified Mollicutes?:thinking_face:@Aleru Divine

Adeshile Oluwatosin (04:29:16) (in thread): > Well doneI’llgo through the curation:thumbsup:

Ebuka Chinwuba (04:29:28) (in thread): > I just checked the link you sent, I can confirm that it says the page doesn’t exit. Although When I open the initial link, I still see the Experiment 2.https://bugsigdb.org/Study_1165 - Attachment (BugSigDB): Faecal Microbiota Characterisation of Potamochoerus porcus Living in a Controlled Environment - BugSigDB > Intestinal bacteria establish a specific relationship with the host animal, which causes the acquisition of gut microbiota with a unique composition classified as the enterotype.

Ebuka Chinwuba (04:30:15) (in thread): > Do you advice I leave it that way@Svetlana Ugarcina Perovic

Kate Rasheed (04:30:45) (in thread): > Yes I agree@Mildred Anashie. I saw RF39 in the discussion page but it wasn’t resolved. > > In a second thought, I think it can be classified as that cause I have the same thing with Clostridium sensu stricto 6 and I had to classify under Clostridium

Mildred Anashie (04:32:16) (in thread): > This appears to be quite tricky@Aleru Divine@Kate Rasheed

Kate Rasheed (04:32:40) (in thread): > I agree@Mildred Anashie:sweat_smile:

Ebuka Chinwuba (04:32:57) (in thread): > @Samuel NnannaOkay, it makes sense now. Thanks

Aleru Divine (04:33:14) (in thread): > @Mildred AnashieThe reasonI’dsay this can be curated is because it still falls under theMollicutesclass.Maybe leaving a note on the discussion page?

Kate Rasheed (04:34:00) (in thread): > But unclassified Mollicutes is different from uncultured Mollicutes or am I missing something?@Mildred Anashie@Aleru DivineHow can I leave a note too?

Mildred Anashie (04:34:04) (in thread): > Okay then > Leaving a note should work@Kate Rasheed

Ebuka Chinwuba (04:34:53): > Hello, wonderful community! > Wishing you all a productive and inspiring day! > Let’s continue to support each other and make amazing progress today! If anyone needs assistance or just wants to brainstorm ideas, don’t hesitate to reach out. > Have a fantastic day ahead!

Kate Rasheed (04:35:51) (in thread): > Well-done@Cate OumaI saw orange in your signature but at a closer look, I saw that Clostridium XVII was discussed in the discussion page. I’m still looking through.

Adeshile Oluwatosin (04:36:30) (in thread): > It’sunclassified in this case@Kate Rasheed

Adeshile Oluwatosin (04:37:20) (in thread): > Have a nice day ahead as well@Ebuka Chinwuba

Kate Rasheed (04:39:07) (in thread): > Hi people@Mildred Anashie@Aleru DivineI just saw something I can use: uncultured Mollicutes bacterium. > > Thank you so much.

Mildred Anashie (04:40:56) (in thread): > Okay@Kate Rasheed:hugging_face:I believe that could work, still leave a note in the talk page stating how it was reported in the paper

Aleru Divine (04:41:13) (in thread): > Click on Page tooks(the 3dots) > Then click on discussion > The start a discussion(that’sthe note) - File (JPEG): IMG_1269 - File (JPEG): IMG_1268 - File (JPEG): IMG_1268 - File (JPEG): IMG_1270

Aleru Divine (04:41:27) (in thread): > Yes this works@Kate Rasheed:sweat_smile:

Samuel Nnanna (04:42:39) (in thread): > For sure@Ebuka Chinwuba

Samuel Nnanna (04:43:34) (in thread): > Yeaheverything’sfine now. Thank you

Mildred Anashie (04:44:44) (in thread): > Thank you@Ebuka ChinwubaI believe Divine and I need some help with Confounders:smile:I’lltag you to it once I type out the question

Cate Ouma (04:45:29) (in thread): > Yes, I asked about it earlier and was advised to record it as it is

Adeshile Oluwatosin (04:45:44) (in thread): > It’sokay that way@Cate Ouma

Aleru Divine (04:46:49) (in thread): > Wishing you a productive day as well@Ebuka Chinwuba:hugging_face:

Precious Orakwe (04:51:54) (in thread): > Wishing you a great day and weekend, Thank you

Precious Orakwe (04:53:10) (in thread): > Well-done@Cate Ouma

Cate Ouma (04:59:24) (in thread): > Thank you for your feedback. I had curated signatures for Exp 4 days ago, but I don’t know why they aren’t isn’t showing up even after refreshing multiple times. Does that mean that I have to record them again?

Precious Orakwe (04:59:36) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic, Good morning to you too and have a great day and weekend.

Adeshile Oluwatosin (05:00:41) (in thread): > No, don’t record again > Keep refreshing > So youdon’thave duplicates@Cate Ouma

Precious Orakwe (05:01:34) (in thread): > Oh, great. Thanks@Svetlana Ugarcina Perovicfor the update

Mildred Anashie (05:03:19) (in thread): > Do not record again@Cate OumaTry thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&channel=C04RATV9VCY&message_ts=1727957860.907319and confirm if the experiment exists or not - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Cate Ouma (05:06:55) (in thread): > :+1:Nice. Thanks

Precious Orakwe (05:07:04) (in thread): > Do not record again, use the link post above by@Mildred Anashieyou will see it all

Ebuka Chinwuba (05:17:22) (in thread): > While we’re all trying to help out a sister, we should be critical about the terminologies! > Uncultured and unclassified do not mean exactly the same thing, though they are related concepts in microbiology.@Kate Rasheed > 1. Unculturedrefers to organisms that have not been grown in a laboratory setting, whereasunclassifiedmeans that the organism’s exact taxonomic classification is not yet determined. > 2. The numberingthat comes along with it, is aunique identifierfor that particular subgroup, distinguishing it from other uncultured groups within the same family. > 3. Incertae sedis means “of uncertain placement.” Used when a bacterial genus, species, or subgroup cannot be confidently classified into an existing category within the taxonomic hierarchy@Aleru DivineRuminococcaceaeandOscillospiraceaeare not the same. While both belong to theFirmicutesphylum, they are distinct families with different taxonomic classifications and characteristics > I stand to be corrected!

Kate Rasheed (05:21:02) (in thread): > @Ebuka Chinwubaruminococcaceae might not be the same as Oscillospiraceae, but that is the current representation in NCBI taxonomy browser.

Ebuka Chinwuba (05:21:26) (in thread): > @Mildred AnashieSure, would be glad to assist

Mildred Anashie (05:24:26) (in thread): > Hi@Ebuka ChinwubaI think thislinkmight help with the Ruminococcaceae and Oscillospiraceae > > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. And this case NCBI recognizes them as synonyms in my opinion

Aleru Divine (05:26:53) (in thread): > Thank you@Ebuka ChinwubaFor point 3,I believeRuminococcaceae’s current name is Oscillospiraceae. > > Below is a link that shows Ruminococcaceae as a heterotypic synonym of Oscillospiraceae.while bacteria may change names or be regrouped, the former names are typically retained in the database under theother names tabhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216572&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - File (JPEG): IMG_1271

Ebuka Chinwuba (05:35:55) (in thread): > Alright, although i still have my reservations, am open to learning. I’ll look into every link shared. thanks@Mildred Anashie@Aleru Divine

Adeshile Oluwatosin (05:37:06) (in thread): > Thank you@Svetlana Ugarcina PerovicI will check them out:hugging_face:

Aleru Divine (05:45:08) (in thread): > @Cate Oumaa couple of observations > > There is a one-to-one comparison of age group and sex-matched Ethiopian children aged 0–59 months (ProPD vs AD) in supplementary figure 7c. > > This should be different from experiment 4 as the sample sizes are > 95 for ProPD > 95 for AD > due to it being a one-to-one comparison > > I think you have to add another experiment for this comparison. > Alpha diversity measures are also in Supplementary Figure 7a > > > For confounders, “”DESeq2 analysis was controlled for variables that were contributing to the GM variations as determined by distance-based Redundancy Analysis (db-RDA) as well as variables that were known to affect GM from other studies40includingage, enrollment site, enrollment season, sex, WAM index, current breastfeeding, diarrhea in the previous month, dysentery and children’s caretaker. > > I see hygiene as part of the confounders you listed. - Attachment (Nature): Gut microbiota patterns associated with duration of diarrhea in children under five years of age in Ethiopia > Nature Communications - Here, the authors profile the gut microbiome of Ethiopian children suffering from acute and prolonged diarrhea, showing the latter group to exhibit a higher degree of…

Aleru Divine (05:48:55) (in thread): > Okay@Ebuka Chinwuba

Precious Orakwe (05:56:01) (in thread): > @Svetlana Ugarcina PerovicI can’t download the pdf, it takes long to load, and since then it has been showing downloading pending, i have tried searching for the paper on Google scholar and even on CU scholar, but it all send me back to science direct. What else can I do. - File (PNG): Screenshot_20241018-103951.png

Aleru Divine (07:06:17) (in thread): > Good morning and thank you for the resources shared@Svetlana Ugarcina Perovic:blush:

Svetlana Ugarcina Perovic (07:08:28) (in thread): > @Precious OrakweI just sent you via email. Have you received it?

Svetlana Ugarcina Perovic (07:10:35) (in thread): > @Chris Awokehttps://bugsigdb.org/Study_1124/Experiment_1/Signature_2page does not exist. Sometimes it takes time to be updated in the study, but it’s deleted.

Svetlana Ugarcina Perovic (07:23:49): > Update: over 30 curations have encountered roadblocks (Seehttps://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aopen+is%3Aissue+label%3Aassigned). > > If you’ve completed your curation, please reach out to your colleagues and identify points where they’ve faced difficulties.Collaborate to find solutions together.

Adeshile Oluwatosin (07:47:02) (in thread): > Hello EveryoneFeel free to reach out to me if stuck. > I will reach out as well.So we can collaborate:hugging_face:

Precious Orakwe (07:50:36) (in thread): > Thanks@Svetlana Ugarcina Perovici have received it and I have downloaded it

Adeshile Oluwatosin (07:56:33) (in thread): > @Svetlana Ugarcina Perovicare we permitted to edit the issues directly when the original curator has agreed to collaborate.

Mildred Anashie (07:56:35): > Hello everyone@Aleru Divineand I have been working on completing thisstudyand we are a bit unsure of the Confounders controlled for as the paper mentioned that “Thus, confounding effects from antipsychotic treatment and disease durations were largely eliminated”. > But we believe that antipsychotic treatment can’t be controlled for as it is the treatment (risperidone) given and<@UBNSEMS3S>already said yesterday that disease duration can’t be controlled for. > > I also saw where they said “In all statistical analyses, age, gender, education, disease duration, smoking status, and BMI were used as covariates”. I believe covariates are another way of controlling for confounders. > > The question is “Does the covariates count as confounders, we already recorded that, but we want to omit the disease duration”. > > It’s confusing as to which of the statements implies that they controlled for confounders > > I’ll attach some screenshots, Thank you:pray: - Attachment (BugSigDB): Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study - BugSigDB > Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis.However, its role in the antipsychotic treatment response is unclear. - File (JPEG): IMG_1486 - File (PNG): IMG_1483 - File (PNG): IMG_1487 - File (PNG): IMG_1488

Mildred Anashie (07:58:20) (in thread): > Thank you for this question@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (07:58:39) (in thread): > @Adeshile Oluwatosinplease do not contact people who were assigned today or yesterday, there are people stuck more than a week…

Aleru Divine (07:59:30) (in thread): > Got it@Svetlana Ugarcina Perovic:hugging_face:

Svetlana Ugarcina Perovic (07:59:44) (in thread): > Also, as I wrote, IDENTIFY points where they are stuck and approach to them with solutions.

Adeshile Oluwatosin (08:00:04) (in thread): > Okay, noted@Svetlana Ugarcina PerovicI will put in consideration people stuck for a long time.

Mildred Anashie (08:00:29) (in thread): > Noted@Svetlana Ugarcina PerovicThank you for the update

Adeshile Oluwatosin (08:00:34) (in thread): > I would appreciate a response to my initial question@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (08:01:18) (in thread): > You can edit curations together, once the original curator agreed with it. (btw,:white_check_mark:means approved)

Adeshile Oluwatosin (08:01:33) (in thread): > Noted, thank you@Svetlana Ugarcina Perovic

Aleru Divine (08:01:51) (in thread): > Oh! Amazing > > Thanks@Svetlana Ugarcina Perovic

Aleru Divine (08:05:10) (in thread): > I reached out to someone on both GitHub and slack with some solutions to the questions they asked on GitHub but got no response.Both from GitHub and from slack.I’llreach out again:hand_with_index_and_middle_fingers_crossed:

Aleru Divine (08:07:47) (in thread): > :hand_with_index_and_middle_fingers_crossed:

Adeshile Oluwatosin (08:13:06) (in thread): > I will check this, hmmm

Samuel Nnanna (08:28:38) (in thread): > Noted@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (08:46:09) (in thread): > In my opinion, from the study; > > The confounders controlled for are based on the covariates listed. Which are; > Age, Gender, Education, smoking status and BMI. > > Theywere used as covariates in the statistical analysis, and since covariates are included to control for confounding effects, they count as confounders in this context. > > They likely have the potential to influence both the microbiome composition and the health outcome, which makes them important to control for. > > Exclude: > • Antipsychotic treatment (risperidone): This is not a confounder, as it is the treatment/exposure being studied. It cannot be controlled for since it is the primary variable of interest. It is the independent variable in the study. > > • Disease duration: This should not be considered as a confounder although listed as it is tightly linked with the stage of disease progression, asides that Chloe mentioned it to be excluded. > > The statements; > • The statement “confounding effects from antipsychotic treatment and disease duration were largely eliminated” likely refers to the fact that the study design or analysis attempted to minimize their confounding effects, perhaps by restricting the sample (e.g., selecting participants with similar disease durations or consistent antipsychotic treatment). > > • The other statement, “In all statistical analyses, age, gender, education, disease duration, smoking status, and BMI were used as covariates”, implies that these variables were included to adjust for their potential influence on the outcome. Since covariates can be used to control for confounding effects, this suggests they did control for some confounders.

Mildred Anashie (08:51:45) (in thread): > Thank you for the detailed reply@Adeshile OluwatosinSo you agree with what we already recorded, which is Age, BMI, Sex/gender, Education, smoking status ?

Adeshile Oluwatosin (08:52:14) (in thread): > Yes, just removedisease duration. > > I can still see that

Adeshile Oluwatosin (08:53:39) (in thread): > Matched on is sameas well. > Just 5 of them

Mildred Anashie (08:54:23) (in thread): > That would be removed > > Thank you:pray:

Mildred Anashie (08:56:14): > Hello@Svetlana Ugarcina PerovicPlease we’ll like to deleteSignature 2 for experiment 2 and 3Signature 1 in Experiment 5Signature 3 in Experiment 6 for thisstudyThe signatures were unknowingly duplicated and some entered in error > Thank you:pray: - Attachment (BugSigDB): Gut microbial biomarkers for the treatment response in first-episode, drug-naïve schizophrenia: a 24-week follow-up study - BugSigDB > Preclinical studies have shown that the gut microbiota can play a role in schizophrenia (SCH) pathogenesis via the gut-brain axis.However, its role in the antipsychotic treatment response is unclear.

Aleru Divine (08:56:31) (in thread): > Thanks@Adeshile Oluwatosin:pray:

Adeshile Oluwatosin (08:58:39) (in thread): > Welcome:hugging_face:

Adeshile Oluwatosin (09:02:36) (in thread): > Other people can weigh in

Ebuka Chinwuba (09:03:48) (in thread): > @Mildred Anashie@Adeshile OluwatosinI am of different opinion. Disease duration can sometimes influence microbiota composition and clinical outcomes

Ebuka Chinwuba (09:12:05) (in thread): > May argue that it is not a significant confounder in your specific analysis, that will be when/if it’s unrelated to both the microbiome and treatment response. However, this decision depends on the study’s context. Disease duration can sometimes influence microbiota composition and clinical outcomes. It’s essential to validate whether disease duration impacts the variables of interest; if not, omitting it might streamline the model.

Mildred Anashie (09:31:59) (in thread): > I agree with you@Ebuka ChinwubaDisease duration can influence microbiota composition but I think it is only controlled for when it influences both the exposure (or treatment) and the outcome. And I think controlling for it is usually done by stratification or using a model to adjust forits effects. > > But this studydidn’tdo any of those, this is why I agree with omitting it

Aleru Divine (09:35:04) (in thread): > I agree,@Ebuka Chinwuba. Disease duration does influence microbiota composition. I’ve curated studies that showed differential abundance in microbiota associated with disease severity. > > My point is, a longer duration can lead to increased severity, as the condition causes cumulative damage over time and impacts microbiota composition. > > The study also stated, > > “Most previous studies have reported the impact ofdisease duration and antipsychotic medicationuses on the composition of gut microbiota,our study minimized such confounding effects.” > > “Thus, confounding effects from antipsychotic treatment and disease durations were largely eliminated.” LARGELY ELIMINATED could mean the confounding effects (minus Antipsychotic treatment) were kinda controlled for. > > Maybe they did@Mildred Anashiebut didn’t mention.:sob:

Svetlana Ugarcina Perovic (09:47:12) (in thread): > deleted.

Adeshile Oluwatosin (09:50:08) (in thread): > @Aleru Divinesometimes it can be confusing. > I would just state that if they did anddidn’tmention. > Do not assume > Just follow the details in the article itself. > > Although, I could be wrong > But I believe the:white_check_mark:means that someone agrees with me as well.

Aleru Divine (10:00:52) (in thread): > @Adeshile OluwatosinBut theydidn’tmention stratification/model adjustment for the other covariates > > But they mentioned controlling for them, disease duration included.“In all statistical analyses, age, gender, education, disease duration, smoking status, and BMI were used as covariates.”

Aleru Divine (10:01:41) (in thread): > Thanks@Svetlana Ugarcina Perovic

Chris Awoke (10:02:23) (in thread): > Thank you so much,@Svetlana Ugarcina Perovic. I’ll check them out.

Ebuka Chinwuba (10:06:28) (in thread): > @Aleru DivinePlease don’t cry:face_holding_back_tears:.@Mildred AnashieIt’s important to assess whether disease duration is correlated with the outcome to determine if it should be omitted or controlled. It’s understandable why we’re confused. The article mentions that confounding effects from antipsychotic treatment and disease duration were “largely eliminated.” This implies that while these factors were initially considered as potential confounders, the study accounted for them in a way that minimized their impact on the results. > Hmmm.. In this case, omitting disease duration might be reasonable if you believe its effects were controlled for effectively or if it doesn’t significantly influence the microbiome and treatment response in your specific analysis

Mildred Anashie (10:14:47) (in thread): > Thank you@Svetlana Ugarcina Perovic

Rahila-me (10:19:53) (in thread): > Ok..Noted. the curators pain-point@Svetlana Ugarcina Perovic

Mildred Anashie (10:21:33) (in thread): > Yea@Aleru DivineMaybe they did and didn’t mention:disappointed:Thank you@Ebuka Chinwubafor your inputs, truly making us look in another direction, you could go through the article with us you might pick something we missed > > But we have gone through the paper and it didn’t really state if it correlated or not, also what I think they were focused on more is the response to treatment at the different time points > > Thank you@Adeshile Oluwatosin:blush:

Aleru Divine (10:23:16) (in thread): > Truly truly remarkable@Ebuka ChinwubaThank you so much for your inputs@Adeshile Oluwatosin@Ebuka Chinwuba

Adeshile Oluwatosin (10:30:00) (in thread): > :wink:

Chris Awoke (10:36:11): > The signatures for my study have yet to populate since yesterday. Signature 2 in Experiment 1 is still persisting with a hyperlink, even after@Svetlana Ugarcina Perovicdeleted it. > > Here’s the link to the study:https://bugsigdb.org/Study_1124. - Attachment (BugSigDB): Insights into the vaginal microbiome in a diverse group of women of African, Asian and European ancestries - BugSigDB > BACKGROUND: Intra-continentally, vaginal microbiome signatures are reported to be significantly different between Black and Caucasian women, with women of African ancestry having the less well defined heterogenous bacterial community state type (CST) deficient of Lactobacillus species (CST IV).

Svetlana Ugarcina Perovic (10:38:36) (in thread): > Today [1:10 PM]:https://community-bioc.slack.com/archives/C04RATV9VCY/p1729249835498359?thread_ts=1729167693.214319&cid=C04RATV9VCYThank you for your patience. - Attachment: Attachment > @Chris Awoke https://bugsigdb.org/Study_1124/Experiment_1/Signature_2 page does not exist. Sometimes it takes time to be updated in the study, but it’s deleted.

Svetlana Ugarcina Perovic (10:39:35) (in thread): > Move on with adding the signatures. Deletion action will be updated.

Chris Awoke (10:40:53) (in thread): > Okay, thank you so much@Svetlana Ugarcina PerovicI have added all the signatures to the respective experiments.

Mildred Anashie (10:40:57) (in thread): > Hi@Chris AwokeI see your signatures when I do thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&channel=C04RATV9VCY&message_ts=1727957860.907319And the hyperlink states that the signature has been deleted - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Chris Awoke (10:42:18) (in thread): > Yeah,@Mildred AnashieThey are there, but yet to populate on the main page. > > It seems to be taking longer.

Chris Awoke (10:45:54) (in thread): > I would need a review of the study before I request that it be graded.

Mildred Anashie (10:47:18) (in thread): > Okay@Chris AwokeI’llgo through your curation, well done on your curation:clap:

Chris Awoke (10:48:25) (in thread): > Thank you so much,@Mildred Anashie. I’ll be looking forward to your feedback.

Mildred Anashie (10:50:06) (in thread): > Hi<@UBNSEMS3S>Just bringing your attention to thisstudyfrom the office hour yesterday > > Thank you:pray: - Attachment (Nature): Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes > Nature Communications - Here, the authors employ shotgun-metagenomic sequencing to profile the microbiome of Singaporean octogenarians, finding key microbial shifts and metabolic changes in the…

Mildred Anashie (10:51:39) (in thread): > Hi@Svetlana Ugarcina PerovicJust bringing your attention to this > Thank you:pray:

Svetlana Ugarcina Perovic (10:53:43) (in thread): > @Scholastica Uruaplease take a look at@Mildred Anashiesuggestions for changes, thanks!@Mildred Anashiethank you for your patience!

Kate Rasheed (10:54:33) (in thread): > @Chris AwokeIt might not populate on your main page. You might need to add the links to all signatures that aren’t in your main page while submitting for review.

Chris Awoke (11:40:08) (in thread): > @Kate RasheedDo you mean I should include the links when informing the mentors via GitHub?

Kate Rasheed (11:40:45) (in thread): > Yes@Chris Awoke

Chris Awoke (11:41:00) (in thread): > Oh, thank you.

Ebuka Chinwuba (12:52:19) (in thread): > @Aleru Divine@Mildred Anashieit was really insightful. I was happy giving my own input.

Mildred Anashie (13:41:33) (in thread): > Hello@Chris AwokeI am going through your article and I must say, this is an interesting article and you have done a great job in your curation, Well done:clap::blush:I have a few observations, > 1. In my opinion, The study didn’t mention that they did MHT correction, so MHT should be No and not YES. > 2. I also have scanned through and I didn’t see a mention of any exclusion criteria which included Antibiotics, so I think the Antibiotic Exclusion should be left blank, if I’m missing something you can point me to it. > 3. This is an excerpt from the study“There was no definable core microbiome or singular vaginal microbiome signature identified at the species level among all women. This is perhaps a consequence of the involvement of a plethora of confounding variables (such as menstrual cycle phase and hormonal levels, age, parity, marital status, coitus, body mass index [BMI], diet, culture, etc.)”.Another one says,“In this study with a small sampling size (N = 151), the potential effects of confounders (such as age disparities, sociodemographic characteristics, menstrual status, sexual activity etc.) on microbial composition were not analysed due to unavailability of data for subsamples from the various ethnic groups”.I believe this implies that confounders were not controlled for. > 4. For the Alpha diversity indices, the article says “Distribution of species richness and evenness within the vaginal microbiomes of the ethnic groups using Shannon diversity matrix” and only Shannon seem to have been mentioned throughout the paper. I do not see a mention of Chao1 and you recorded this across all the experiments. Maybe you could point me to where it was mentioned, I believe it might help me understand the Alpha diversity plot and Table S4 in the supplemental.@Aleru DivineIs it possible to take a look at the Supplementary Table 4 (S4)? I see a table showing pairwise comparisons, what can you make of it? The article doesn’t say much about it. Thank you:pray:

Chris Awoke (13:43:25) (in thread): > Thank you so much@Mildred Anashie. I’ll look at that again.

Aleru Divine (13:44:25) (in thread): > Of course@Mildred AnashieI’llhave a look at this as soon asI’mfree. In a couple of hours:pray:I’llalso give a general peer review@Chris Awoke

Mildred Anashie (13:45:46) (in thread): > You are welcome@Chris AwokeWell done again > > And thank you@Aleru Divine

Mildred Anashie (13:52:21) (in thread): > Also, is it okay to say the condition here is ’Ethnic group”? Or it should remain as Vaginal microbiome measurement:thinking_face:

Chris Awoke (13:58:23) (in thread): > No, I don’t think so@Mildred Anashie

Adeshile Oluwatosin (14:01:32) (in thread): > @Chris Awokewell done on your curation. > I can see the statistical test for Experiment 1 to be different. > > It’s LeFSe

Chris Awoke (14:02:51) (in thread): > Please can you highlight where it is?@Adeshile Oluwatosin

Mildred Anashie (14:02:56) (in thread): > Thank you@Adeshile OluwatosinI forgot to include that and from the lefse plot too@Chris Awokealso see “To identify the bacterial taxa that accounted for meaningful variance in the microbial composition among the various ethnicities, linear discriminant analysis (LDA) effect size (LEfSe)” and this “Kruskal–Wallis sum-rank test within LEfSe identified the differentially abundant taxa and LDA quantified their effect on microbial composition variance” > > Please@Adeshile Oluwatosinalso help go through the study > Thank you:pray:

Adeshile Oluwatosin (14:03:43) (in thread): > Hi@Chris Awokeit’sin the description - File (PNG): IMG_1680

Adeshile Oluwatosin (14:04:29) (in thread): > Also take note@Chris Awokeonce you see a result in this manner,it’smostly LeFSe. Just know!

Adeshile Oluwatosin (14:05:32) (in thread): > I’m still going through the study. > > And also note, if a study has different statistical test, then they are to be created asdifferentexperiments@Chris Awoke

Mildred Anashie (14:08:41) (in thread): > I can see why you choose Kruskal-wallis but you can go through this thread@Chris Awoke, it’ll help you Understand betterhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728907895887159?thread_ts=1728906707.891419&cid=C04RATV9VCY - Attachment: Attachment > There’s an explanation from @UBNSEMS3S on this statistical test confusion. > > LEfSe gives an LDA score/threshold and the Mann-Whitney test is just what LEfSe does behind the scenes. (If I’m explaining that correctly) > > In my case, it was Kruskal-Wallis and LEfSe. > > Here’s the recording from one of the previous office hours. > > Time stamp 13:00 -14:50 > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727978011885959

Chris Awoke (14:09:45) (in thread): > Okay, let me do that now@Mildred AnashieThank you.

Chris Awoke (14:10:46) (in thread): > @Adeshile OluwatosinI’ll look into the things you pointed out. Thank you.

Adeshile Oluwatosin (14:44:33) (in thread): > Supplementary S4. > > Is showing comparison between groups using Kris-wall statistical test. > > I’m only focusing on alpha diversity and I can also see that they all have multiple hypothesis testing. > > In relation to the curation, I’ll suggest it’s left out . > Because of the comparisons listed out in the experiments already curated. I can’t find any correlation. > > Although I’m yet to confirm if they actually also used Kristal-Wallis in this study.

Mildred Anashie (14:46:44) (in thread): > Check this message@Adeshile Oluwatosinhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1729274576380759?thread_ts=1729262171.297589&channel=C04RATV9VCY&message_ts=1729274576.380759 - Attachment: Attachment > Thank you @Adeshile Oluwatosin I forgot to include that and from the lefse plot too @Chris Awoke also see “To identify the bacterial taxa that accounted for meaningful variance in the microbial composition among the various ethnicities, linear discriminant analysis (LDA) effect size (LEfSe)” and this “Kruskal–Wallis sum-rank test within LEfSe identified the differentially abundant taxa and LDA quantified their effect on microbial composition variance” > > Please @Adeshile Oluwatosin also help go through the study > Thank you :pray::skin-tone-5:

Adeshile Oluwatosin (14:52:48) (in thread): > @Mildred Anashiedefinitely I have, so in that case > I believe S4 should not be curated as the main statistical test used in this study is LeFse.Chloe explained this in the video you tagged.I await other opinions

Adeshile Oluwatosin (14:54:39) (in thread): > I can see this tho - File (PNG): IMG_1681

Adeshile Oluwatosin (14:58:41) (in thread): > Also,@Chris AwokewhydoI see chao1 mentioned as an alpha diversity. > I can only see evenness and Shannon. > > Can you please share a screenshot of where you saw chao1

Adeshile Oluwatosin (14:59:59) (in thread): > Idon’twant the messages to be a lot, but kindly see from this angle@Chris Awoke - File (PNG): IMG_1682

Chris Awoke (15:05:07) (in thread): > OMG! Thank you so much,@Adeshile Oluwatosin. I guess I missed these details.

Adeshile Oluwatosin (15:06:32) (in thread): > Welcome@Chris Awoke

Chris Awoke (15:07:45) (in thread): > So regarding the statistical test, what do you suggest finally?@Adeshile Oluwatosin

Adeshile Oluwatosin (15:08:22) (in thread): > The correctmainstatistical test is LeFSe.

Adeshile Oluwatosin (15:09:52) (in thread): > If you’ve watched the video Chloe mentioned kruskal-Wallis sum-rank test was done within LeFSe. > > Mildred already pointed out the statement. > > So your article should have 5 experiments, just make the corrections.

Chris Awoke (15:10:25) (in thread): > Alright. Thanks again

Adeshile Oluwatosin (15:11:13) (in thread): > You can notify whenyou’vecorrected, > So we can all check again.

Chinwendu Joy Enyidiegwu (15:43:40) (in thread): > https://bugsigdb.org/Study_1104@Svetlana Ugarcina Perovic@Precious Orakweare we to edit the current study or create a new study > and how do i this please:point_right:Do not forget to ask for assignment there first ;) - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > The paternal environment prior to conception has been demonstrated to influence offspring physiology and behavior, with the sperm epigenome (including noncoding RNAs) proposed as a potential facilitator of non-genetic inheritance.

Aleru Divine (16:34:52) (in thread): > Well done everyone!:clap:I’llhave a good look at the study and note any further observations.

Precious Orakwe (18:12:35) (in thread): > I think we are editing

Yoko C (19:30:31) (in thread): > Hello, I think this is a very interesting question. For example, as far as I understand, Mann Whitney does not allow for covariates or multiple stratification, so while they may have controlled for some factors on the overall research, I don’t think these were included in the specific experiment (experiment 1). So should these factors still be included?

2024-10-19

Svetlana Ugarcina Perovic (02:09:21) (in thread): > You are editing already existing curation. As for the assignment, if you collaborate with the original curator, ask in the GitHub issue to be added as an assignee.

Adeshile Oluwatosin (03:23:52): > Good morning everyone@Esther Afuape@Chioma Onyido@Svetlana Ugarcina Perovichttps://journals.asm.org/doi/10.1128/msystems.00839-24?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub%20%200pubmedI have few things I noticed which I might need clarification on in this study;https://bugsigdb.org/Study_1151 > * For Experiment 1: I want to confirm if the matched on and confounders are correctly listed. > “The fully matched algorithm was devised based on previously identified microbiota-confounding variables, which included BMI, sex, age, geographical location, frequency of alcohol consumption, and dietary intake of meat/eggs, dairy, vegetables, whole grains, and salted snacks (19). “ > > From this statement, my speculation is both matched on and confounders are same. > > - experiment 2 is to compare metagenomic and metabolomic signatures between LI patients and HCs in China: I don’t see any matched on and confounders stated for this experiment. > > Or should it be same as experiment 2. > * although, experiment 3 was mentioned, this time around for rats….I can’t find any curatable figure, I don’t believe figure 7d is curatable. kindly check on if you can see(there are supplementary documents below). If confirmed that there aren’t figures, then I believe this experiment should be deleted. - Attachment (BugSigDB): Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP) - BugSigDB > UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.Recent evidence suggests that the gut microbiome may influence lactose levels in the gut.

Aleru Divine (03:27:36) (in thread): > Good morning@Adeshile OluwatosinI’llhave a look at this.Hopefully I understand too:pray:

Adeshile Oluwatosin (03:27:57) (in thread): > Thank you:thumbsup:I’m expecting.

Kate Rasheed (03:30:25) (in thread): > You’re right@Adeshile Oluwatosin. Figure 7d is not curatable. It’s a comparison of the relative abundance among genera.

Adeshile Oluwatosin (03:32:32) (in thread): > I recently started collaborating so I noticed it was already curated.I’maware of that@Kate RasheedI’masking if you can help point out a curatable figure for experiment 3. > Before I tell the original curator to ask for it to be deleted.

Kate Rasheed (03:34:24) (in thread): > For your speculation on matched on, you’re right as well. > > See what I found “Figure S1 Demographic profile comparison between 562 patients self-reporting LIs and an equal number of 562 self-reporting non-LIs. No disparities were observed in (a) age, (b) BMI, (c) sex between LIs and their matched controls, (d) geographical location, (e) alcohol consumption, (f) meat/egg frequency, (g) vegetable frequency, (h) whole grain frequency, (i) salted snack frequency, or (k) sugary sweet consumption frequency. >”

Mildred Anashie (03:34:34) (in thread): > Good morning@Adeshile OluwatosinI’llalso take a look asap

Adeshile Oluwatosin (03:37:07) (in thread): > @Kate RasheedThis statement, “The fully matched algorithm was devised based on previously identified microbiota-confounding variables, which included…” > What I deduced here is that the same previously identified confounding variables are also the matched on controls. > > I just need other opinions, just incase

Kate Rasheed (03:38:27) (in thread): > Table S3 seems curatable. It shows the difference between LI and HC at the species level.

Adeshile Oluwatosin (03:38:49) (in thread): > Yes, I saw that but I think it’s overlapping.

Aleru Divine (03:50:34) (in thread): > For experiment 1, I think you’re correct. > > The study matched LI patients and healthy controls on key confounding factors. Yes they were matched. I think the matching process is meant to control for these confounders. > > For experiment 2 > These participants weren’t matched. They used different data for each experiment, at least that’s what I can see. > > I’ll look through it thoroughly to see if you should go on with experiment 3.

Adeshile Oluwatosin (03:53:04) (in thread): > Thank you@Aleru Divine@Kate Rasheedwhat do you think about “gut microbiome measurement” as the condition for experiment 2.

Adeshile Oluwatosin (03:53:30) (in thread): > I believe the conditions are different for both experiments

Kate Rasheed (03:57:40) (in thread): > @Adeshile OluwatosinI think the condition is gut Microbiome measurement. > > See what I found “Fig 3 Differences in the gut microbial composition between Lis and HCs in the Chinese cohort. (a) Venn diagram analysis showing the total number of core species shared and unique. (b) LEfSe analysis reveals significant taxonomic differences between LI patients and HCs.”

Adeshile Oluwatosin (03:57:46) (in thread): > Also, Figure 3b > Unclassified proteobacteria was mentioned4 times. > > This was curated once. > I want to believethat’scorrect as well.

Kate Rasheed (04:00:54) (in thread): > Yes the unclassified proteobacteria is actually 1 because on the supplementary table, they have the same figure for p-value, LDA and mean. > > For the experiment 3, I think it should be dropped, I can’t see any figure/table to show signatures. Unless it is stated in the text which I would still look through.

Adeshile Oluwatosin (04:02:49) (in thread): > Thank you@Kate Rasheedmeaning all my speculations was right.

Aleru Divine (04:02:58) (in thread): > They did find gut microbiomedifferences but that’s not a condition.Thedisease condition here is still Lactose intolerance. > > And Unclassified proteobacteria, that can be curated as 1. I don’t think you can curate it twice even if you wanted to:sweat_smile:You can only leave a note afterwards

Kate Rasheed (04:03:28) (in thread): > See: “The abundances of the microbial genera Faecalibacterium, Fusicatenibacter, and Eubacterium hallii were significantly decreased, while others, such as Escherichia, Shigella, Dielma, Sutterella, and Coprobacillus, were more abundant in the FMT-LI group than in the FMT-HC group,” > > There was a significant decrease and increase for the experiment 3

Adeshile Oluwatosin (04:04:22) (in thread): > @Aleru Divinecuration is funny and interesting to me:joy_cat:I’drather just ask questions even when I believeI’msaying/doing the right thing.

Adeshile Oluwatosin (04:05:17) (in thread): > @Kate Rasheedyou can see why I asked for help, maybeI’m notseeing correctly:joy:for experiment 3

Adeshile Oluwatosin (04:06:12) (in thread): > But the description is taken from Figure 7d,that’snot curatable.@Kate Rasheed

Aleru Divine (04:06:21) (in thread): > I completely understand@Adeshile Oluwatosin

Adeshile Oluwatosin (04:07:14) (in thread): > But let’s actually not slide away Table s3@Aleru Divine@Kate RasheedDo you think regardless it should be curated.

Kate Rasheed (04:07:16) (in thread): > @Adeshile OluwatosinYou would edit the source to read from the page in the article. Let’s say “Page 5 above Fig. 7”

Kate Rasheed (04:08:15) (in thread): > That figure 7d is just a similar finding to the signatures listed. It’s not the actual source.

Adeshile Oluwatosin (04:08:51) (in thread): > Idon’tget you tho@Kate Rasheed

Kate Rasheed (04:09:19) (in thread): > Table S3 if we go by the number, it’s for experiment 2 and I saw that it’s actually curated in Fig. 3. You can quote it as a source too.

Mildred Anashie (04:09:36) (in thread): > Hi@Adeshile OluwatosinYour experiment 3 should stay because it shows significance both in the figure and text > > If you look at Figure 7d you would notice some taxa highlighted in green or red > That’s showing you decrease and increase, it also corroborates with the text@Kate Rasheedis talking about

Kate Rasheed (04:10:16) (in thread): > @Adeshile OluwatosinRead it here. - File (JPEG): Screenshot_20241019-090941.jpg

Kate Rasheed (04:11:37) (in thread): > @Mildred AnashieSee what the description of Figure 7d says: “Fig 7 Overall structural variations in the bacterial diversity and microbial community composition of the gut microbiota between the FMT-HC and FMT-LI groups. (a) Differences in body weight, number of fecal particles, AWR, and pain threshold between the two groups. (b) The differences in α-diversity between the two groups were estimated by the Sobs, ACE, Shannon, and Chao1 indices using Student’s t-test. (c) Principal coordinate analysis based on β-diversity. The closer the distance between samples is, the more similar the species. (d) Heatmap based on the relative abundance of the genera between the two groups.”

Mildred Anashie (04:14:52) (in thread): > That’s differential abundance@Kate RasheedIt says “between groups” > Also see thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549 - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Mildred Anashie (04:15:32) (in thread): > The highlighted taxa also makes it clear to curate in my opinion@Kate Rasheed

Kate Rasheed (04:15:34) (in thread): > Amazing. I’ve learnt something new. Relative abundance between groups is also differential abundance:dancer:

Kate Rasheed (04:16:27) (in thread): > Asking questions is very very good.

Aleru Divine (04:16:36) (in thread): > It’s represented in figure 7d@Kate RasheedSee the red and green boxes so she can leave out the text.:sweat_smile:About table S3,@Adeshile Oluwatosinhow would you tell the difference? I think figure 3b is enough and kind of shows us the interpretations of the table. > > I believe they’re the same. 35 signatures each

Mildred Anashie (04:17:51) (in thread): > I’mglad you have@Kate RasheedAnd I agree with you@Adeshile Oluwatosinyou’dhave to curate just the ones stated to be significantly increased or decreased from Fig 7d

Adeshile Oluwatosin (04:18:49) (in thread): > Thank you everyone, clarified that the three experiments are good to go.@Aleru Divine@Mildred Anashie@Kate RasheedTake a look atthe missing taxa in the study

Adeshile Oluwatosin (04:20:10) (in thread): > @Mildred Anashiewhat you mean in this case, is to curate only taxa specified within the text and not the figure 7d

Mildred Anashie (04:21:14) (in thread): > The figure and text are showing you the significantly increased and decreased taxas > > Look at the ones highlighted in green and red boxes from the figure@Adeshile OluwatosinCan you see it?

Adeshile Oluwatosin (04:21:19) (in thread): > @Aleru DivineI will leave out S3, I already initially stated that it was overlapping. > Thanks

Mildred Anashie (04:26:07) (in thread): > See attached image > > I think you can use both text and figure as your signature source@Adeshile Oluwatosin - File (JPEG): IMG_1505

Aleru Divine (04:27:29) (in thread): > @Adeshile OluwatosinDid you try to resolve these highlighted signatures? > > 1522 is forclostridiuminnocuum in signature 1 of experiment 3. > > I don’t think all can be resolved because I see strange letters and numbers all together.But some are in the missing NCBI ID page:hugging_face:Some are on the taxonomy browser.

Kate Rasheed (04:28:58) (in thread): > Yes@Adeshile Oluwatosin. For the missing taxa, those ones with underscore should be replaced with space and you can use the ID instead. I noticed RF39 which is uncultured Mollicutes bacterium. You would find this under the discussion page. > > Those with .c, .f, .p is giving a specification of the taxonomy rank they fall under. You should remove the dots

Mildred Anashie (04:29:45) (in thread): > @Aleru Divinelook at this image and the results text for Fig 7d for experiment 3 - File (JPEG): IMG_1505

Kate Rasheed (04:32:03) (in thread): > @Mildred AnashieIn your opinion, Tosin can quote the source to be the text and figure right? I can see some of the signatures in the text isn’t shown in the figure.

Mildred Anashie (04:33:33) (in thread): > Yes@Kate RasheedShe’dhave to curate from both

Aleru Divine (04:34:52) (in thread): > Do you think the ones in the boxes are the only significant ones@Mildred Anashie?

Aleru Divine (04:39:34) (in thread): > Cos the entire heat map can be interpreted with the colors. But then, which is significant? Is it all? > > See “The abundances of the microbial genera Faecalibacterium, Fusicatenibacter, and Eubacterium hallii were significantly decreased, while others, such as Escherichia, Shigella, Dielma, Sutterella, and Coprobacillus, were more abundant in the FMT-LI group than in the FMT-HC group,similar to the findings from the LI metagenome data(Fig. 7d).” > > They mentioned these ones in particular because of the similarity with LI group in experiment 2.I still think all should be curated.

Mildred Anashie (04:39:40) (in thread): > I think so based on the text@Aleru Divine@Kate RasheedI believe all the taxa in text are highlighted in the figure (Escherichia-Shigella is recorded as one in the figure but separate in the text, and from allwe’veseen lately the figure should be followed)

Adeshile Oluwatosin (04:39:41) (in thread): > Thank you everyone@Kate Rasheed@Mildred Anashie@Aleru Divine

Aleru Divine (04:42:27) (in thread): > See my reply above:point_up:@Mildred Anashie@Adeshile Oluwatosin@Kate Rasheed

Mildred Anashie (04:42:28) (in thread): > Maybe@Adeshile Oluwatosinwould need more help for that one as I could be wrong@Aleru DivineHi@Scholastica Urua@Chioma Onyido@Esther Afuapeplease help with Figure 7d

Kate Rasheed (04:44:56) (in thread): > I actually think the text is the main source while the figure 7d is a backup since there are no tables or figures to prove the main findings. > > I have a question though. If there are two sources that report all signatures. Do I have to pick one or use the two sources?

Mildred Anashie (04:49:21) (in thread): > I share the same thoughts@Kate Rasheed@Aleru Divinehave you noticed some taxa share the same colors for both groups? I know a taxa can be increased in both groups, but I think generally the heat map is not an easy one to curate

Mildred Anashie (04:51:18) (in thread): > @Kate RasheedI think you have to use both, since you have to record all the taxas that were reported to be significant for a particular contrast especially if some taxa in onecan’tbe found in the other

Kate Rasheed (04:51:45) (in thread): > I mean the taxa can be found in the two sources.

Aleru Divine (04:52:01) (in thread): > The ones that share same colorscan be curated as both increased and decreased.The heat map is always complicated:sob:@Mildred Anashie

Mildred Anashie (04:54:54) (in thread): > I do record both sources@Kate Rasheedbut maybe itshouldn’tbe so

Adeshile Oluwatosin (04:55:13) (in thread): > @Aleru DivineI’venot edited signature 3 at all, > > I want to believe it should even be removed@Mildred Anashiestated thatit’sbest to curate the significant taxa

Aleru Divine (04:56:27) (in thread): > Signature 3? I’m confused.Do you mean experiment 3

Adeshile Oluwatosin (04:57:19) (in thread): > @Kate Rasheedremoving the .c, .f, .p means that; > For instance - SR1, SR1.c, SR1.c.o, Sr1.c.o.fWhen the dots are cleared, everything will fall under SR1 then, right?

Aleru Divine (04:58:56) (in thread): > Those are Class, family,phylum. I think you should leave it.

Chris Awoke (04:59:54) (in thread): > Wow! I love this:heart_eyes:Well done guys@Kate Rasheed@Mildred Anashie@Aleru Divine@Adeshile Oluwatosin

Kate Rasheed (04:59:57) (in thread): > @Adeshile OluwatosinI can’t find them on NCBI. Just like@Aleru Divinesaid, .f means SR under family and on and on

Adeshile Oluwatosin (05:00:06) (in thread): > When quoting from a text and figure. > > Then the source should be something like this;Text and Figure 7d > > I’m kind of confused on this third experiment

Mildred Anashie (05:00:19) (in thread): > If you would curate SR1 then all should be curated the way they recorded them, that way you can tell the difference in my opinion@Adeshile Oluwatosin

Kate Rasheed (05:00:30) (in thread): > Yes please@Adeshile OluwatosinSource should be from text and figure. You would have to state the page of the paper where it is found.

Mildred Anashie (05:01:28) (in thread): > Source can be Results text (if you like you can add the page number like this, page…) and Figure 7d@Adeshile OluwatosinSource: Results text, page…. and Figure 7d

Adeshile Oluwatosin (05:01:43) (in thread): > @Aleru Divine:joy_cat::joy_cat::joy_cat:heuI meant signature 1/2 in experiment 3

Aleru Divine (05:01:58) (in thread): > Or the title above the text.The title/section where you got the text from.

Adeshile Oluwatosin (05:02:40) (in thread): > Figure 7d, why:joy_cat::joy:

Adeshile Oluwatosin (05:03:17) (in thread): > Noted@Aleru DivineI’llleave it the wayit’sstated.

Aleru Divine (05:03:43) (in thread): > The FMT animal study is an experiment that should be curated.Details of alpha diversity and differential abundance are in figure 7

Adeshile Oluwatosin (05:03:46) (in thread): > @Mildred Anashienoted.

Adeshile Oluwatosin (05:05:13) (in thread): > So, we are still unclear on how 7d should be curated:pleading_face:But from all, it should be curated from both text and Figure. > Will do this, then come back here:joy_cat:@Mildred Anashie@Kate Rasheed@Aleru Divine

Aleru Divine (05:06:03) (in thread): > Okay@Adeshile Oluwatosin

Chinwendu Joy Enyidiegwu (05:22:31) (in thread): > @Precious Orakwelet me know when you are through with correcting the study signatures. > we have to swap reviews before the end of the day, > and then submit for final review.

Adeshile Oluwatosin (09:52:59) (in thread): > My people,I’mhere:joy_cat:@Aleru Divine@Mildred Anashie@Kate RasheedYou can check out the signatures in experiment 3 now

Adeshile Oluwatosin (09:56:55) (in thread): > I want to believe norank ruminococcaceae means unclassified ruminococcaceae.

Adeshile Oluwatosin (10:00:37) (in thread): > Although, i left it same/exact way

Kate Rasheed (10:10:36) (in thread): > Unclassified Oscillospiraceae is better

Adeshile Oluwatosin (10:11:35) (in thread): > Yeah, I just gave an instance

Mildred Anashie (10:11:52) (in thread): > Hi@Adeshile OluwatosinI believe that can work for it, you might have to leave a note

Adeshile Oluwatosin (10:12:02) (in thread): > But in this casethey identified norank ruminococcaceae and unclassified ruminococcaceae

Adeshile Oluwatosin (10:12:57) (in thread): > Idon’tknow ifit’sbest to leave it just the way it is.

Aleru Divine (10:13:05) (in thread): > Hey again everyone:sweat_smile:

Aleru Divine (10:13:38) (in thread): > You cancurate asunclassified Oscillospiraceae and then leave a note. Cos they kind of mean the same

Aleru Divine (10:26:16) (in thread): > @Adeshile Oluwatosinthere’s a spelling error in signature 2. > > It’s Barnesiella not Bamesiella

Adeshile Oluwatosin (10:37:51) (in thread): > I’m stillediting o@Aleru DivineThanks for notifying

Adeshile Oluwatosin (10:38:46) (in thread): > Which experiment though?@Aleru Divine

Aleru Divine (10:39:31) (in thread): > I also think Parasutterella, norank__Erysipelotrichaceaebelong to increased abundance

Aleru Divine (10:39:46) (in thread): > Experiment 3@Adeshile Oluwatosin

Adeshile Oluwatosin (10:41:05) (in thread): > This was my initiative towards curating > I believe just taxa represented as dark blue should belong to decreased abundance as that’s the only negative value where I circled - File (JPEG): IMG_1696

Aleru Divine (10:42:21) (in thread): > Yes, these two are pinkish orit’smy eyes.Four eyes.Somebody please check:sob:@Kate Rasheed@Mildred Anashie

Adeshile Oluwatosin (10:44:38) (in thread): > Even light blue is increased > Just dark blue is decreased abundance

Adeshile Oluwatosin (10:45:57) (in thread): > Except if taxa belonging to zero should not be curated.@Aleru Divine

Aleru Divine (10:46:16) (in thread): > Oh!That’strue.You got it.Belonging to zero?

Mildred Anashie (10:47:35) (in thread): > The two you mentioned above@Aleru Divine? > > If so, I think I see them as significant in both groups

Aleru Divine (10:48:45) (in thread): > That would be correct@Mildred AnashieGosh! Heatmaps are a pain sometimes:sweat_smile:

Adeshile Oluwatosin (10:56:06) (in thread): > Like!@Aleru Divine

Adeshile Oluwatosin (11:01:29) (in thread): > How do you mean tho@Mildred Anashie

Mildred Anashie (11:13:06) (in thread): > The colors are highlighted under both groups for the taxas@Adeshile Oluwatosin

Adeshile Oluwatosin (11:14:08) (in thread): > Pinkish and white still falls under increased abundance according to what was circled

Mildred Anashie (11:15:40) (in thread): > Yea which means it’s increased in both groups for the no_rank Erysipelotrichaceae

Aleru Divine (11:19:40) (in thread): > You’llcurate on both signatures@Adeshile Oluwatosinfor cases like this:face_with_open_eyes_and_hand_over_mouth::sob:

Kate Rasheed (12:29:15) (in thread): > @Adeshile Oluwatosin@Mildred AnashieAre we to curate all the taxa in the figure 7d ni. I thought it’s only the circled green that would be recorded as increased signature and the circled red would be recorded as decreased.

Yoko C (12:34:14) (in thread): > Hello everyone, just wanted to give my thoughts.@Adeshile Oluwatosin, for the heat map 7d, I don’t think you would add all taxa mentioned. This heatmap doesn’t include explicit significance information, so the colors aren’t too relevant in that way, but the text tells you which taxa are significantly different. The heatmap circles the significant increased or decreased taxa in green and red and this matches the text. Also, I don’t think you include what was matched on as confounders as well, because wouldn’t the matching already be controlling for those confounders? Another thing I noticed is that for experiment 1, China is the location, but the data comes from US, UK, Canada, so I’m not sure if China is correct. I think only experiment 2 is China. I agree with what was mentioned about the condition for experiment 2 its still LI. I think the sequencing type also varies for experiment 2. A search for norank ruminococcae on bugsidb shows another curation where they seem to have changed it to unclassified Oscillopiraceae.

Mildred Anashie (12:35:46) (in thread): > @Kate RasheedI think she choose to curate all the taxa in the figure pending when she gets a response from our mentors and their opinions

Kate Rasheed (12:36:55) (in thread): > Okay. Now I understand but I think I heard Svetlana mentioned during one of our calls that for the heatmap, the circled green is the increase while the circled red is decreased

Mildred Anashie (12:37:03) (in thread): > Thank you for your feedback on this@Yoko C:blush:

Aleru Divine (12:39:11) (in thread): > Thanks for your input@Yoko CI was thinking the same for the heatmaps.Until I found this text.“The abundances of the microbial genera Faecalibacterium, Fusicatenibacter, and Eubacterium hallii were significantly decreased, while others, such as Escherichia, Shigella, Dielma, Sutterella, and Coprobacillus, were more abundant in the FMT-LI group than in the FMT-HC group,similar to the findings from the LI metagenome data(Fig. 7d).”They mentioned these ones in particular because of the similarity with LI group in experiment 2.Idon’tknow maybethey’reall relevant

Adeshile Oluwatosin (12:39:37) (in thread): > @Yoko CI’m still unsure on if all taxa should be curated for experiment 3. Maybe the mentors would have a better answer@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Scholastica UruaFor experiment 1, although china, US and UK was mentioned. But I saw a statement werethe fecalsampleswasn’t provided from participants here. - File (JPEG): IMG_1699

Yoko C (12:42:57) (in thread): > @Aleru Divine, the findings are similar in that the significant taxa are similar. The two experiments points towards the same result.@Adeshile Oluwatosinit mentions they excluded those who resided outside the US, UK and Canada or did not provide fecal samples. In the supplementary table you can see the country is mentioned

Adeshile Oluwatosin (12:48:12) (in thread): > I’m curious as to how Heatmap will be represented > Cos why will statistical test for experiment 3 be empty as it wasn’t stated.

Yoko C (12:49:13) (in thread): > @Adeshile Oluwatosin, for experiment 2 they mention metagenomic sequencing, if I read correctly. Heatmaps are usually based on correlations, and you are right they don’t mention the specific test, reading again, maybe it is mentioned.

Aleru Divine (12:54:02) (in thread): > It’sSpearman’scorrelation for the heatmap.@Yoko C@Adeshile Oluwatosin

Adeshile Oluwatosin (12:54:03) (in thread): > Now it seems like there are so many things we are unsure of. > 1. How Heatmap should be curated. > 2. Countries > 3. Matched on and confounders for experiment 1

Kate Rasheed (12:55:17) (in thread): > Let’s all go back to read and re-read the article then we return with observations.

Adeshile Oluwatosin (12:56:11) (in thread): > This particular curation has the longest thread, crazy:joy:Thank you everyone.Let’sdo as@Kate Rasheedsays > > Noted@Aleru Divine

Aleru Divine (12:59:05) (in thread): > Phew!!:sweat_smile:I completely agree@Kate Rasheed

Adeshile Oluwatosin (12:59:35) (in thread): > Up to 5 hot heads on one curation > Since morning:joy_cat::joy:

Adeshile Oluwatosin (13:00:04) (in thread): > @Yoko CI will correct the condition for experiment 2 to Lactose intolerance. I see it now

Aleru Divine (13:08:25) (in thread): > @Yoko Cconfounding factors can be controlled in a lot of ways. > > Matching, Regression, stratification,this case was matching.We still have to curate them as confounders that were controlled for.I think:thinking_face:

Adeshile Oluwatosin (13:13:02) (in thread): > let me read the article for the umpteenth time again:sweat_smile:Thank you guys for your contribution.

Adeshile Oluwatosin (13:13:15) (in thread): > Stillawaiting more feedbacks

Yoko C (13:23:53) (in thread): > @Aleru Divine, yes I agree, many ways of controlling variables. But matching, I think, is to control before you make a statistical analysis looking to answer your research question, when you actually do the statistical analysis you may further control for other variables, but the truth is I am not sure either. However, I did look at some other curations that mentioned matched or confounders and did not see any repeating both.

Yoko C (13:27:15) (in thread): > @Adeshile Oluwatosin, I think they used a LEfSe, re-reading, this is what the statistical methods part mentions, and I think they followed the same steps they did for the second experiment (where they also have a heatmap). I also searched for “heatmap” on the bugsigdb page and saw that the heatmaps can come from LEfSes, correlations or other types of analysis.

Mildred Anashie (13:29:42) (in thread): > So I think the first experiment was conducted based on datasets and the location of the participants is USA while the other two experiments were conducted in china > > Also the group name for experiment 1 says LI vs Non-LI(I don’t know if that translates automatically to Healthy controls like the second experiment) > > The condition for the second experiment is also Lactose intolerance > > I still think all the taxa in Figure 7d shouldn’t be curated > > I agree with@Aleru Divinematching is a way of controlling for confounders but I’m unsure if we should be recording the same values for both matching and confounders (because of the way it was reported) or record for just 1. > > I think the materials/methods seem to follow a sequence, giving information for the first experiment done using data sets (Exp 1), the metagenomic analysis (Exp 2) and the Animal study (Exp 3). If that is so, we can see that LEfSe was mentioned for the first one, t-test and Kruskal-Wallis was mentioned for the second (although the figure says LEfSe) and Lefse was mentioned for the third (see the statistical method right before results) and personally I believe that heat map is somehow related to LEfSe > > Also I think the antibiotic exclusion for Exp 2 is 3 months (right under case-control) > > Based on what we are confused about this is my opinion@Adeshile Oluwatosin

Adeshile Oluwatosin (13:30:08) (in thread): > Yes, I’m clear on LeFSe as the statistical test for experiment 1 and 2@Yoko C

Adeshile Oluwatosin (13:35:59) (in thread): > Tbh instead of repeating same taxa for both increase and decrease, I think it’s best to record the significant taxa.Thank you@Mildred AnashieI guess when everyone drops their last input. > Then I’ll decide on how best it’s to curate this exact article pending the mentors input.

Mildred Anashie (13:37:44) (in thread): > For our mentors input, I think it’s because it’s weekendthat’swhy we are yet to get a reply > > Well done on this one@Adeshile Oluwatosin:clap:

Adeshile Oluwatosin (13:39:34) (in thread): > Thank you@Mildred Anashie

Yoko C (14:05:37): > @Aleru Divine@Mildred AnashieI don’t want to add confusion and doubts to the previous thread, and I think this may be a very basic question, but I am confused as to why in the curation:https://bugsigdb.org/Study_1151, for Figure 3, only 3b is curated. Why aren’t 3d-3i curated as a signature at species level? Is it because it would be redundant?, although there are differences with 3b. For figure S4, does that variation in genera not matter for the types of signatures we are looking for? Sorry and thanks. - Attachment (BugSigDB): Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP) - BugSigDB > UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.Recent evidence suggests that the gut microbiome may influence lactose levels in the gut.

Esther Afuape (14:16:14) (in thread): > Oh wow…this is a pretty long discussion. I hope this provides some clarity: > * figure 7d is not curatable > * ⁠looks to me like the matched-on and confounding factors are the same like you guys said. > * ⁠since shotgun metagenomic sequencing was done for experiment 2, you can capture it under WMS for sequencing type > * ⁠it looks like 3 different experiments were carried out in this paper. First was using the AGP dataset to access microbial composition between LI and non-LI patients, second experiment did the same thing but within patients in China, third experiment was FMT. Experiments 1 and 2 will have different locations. > * The condition options should be lactose intolerance for experiments 1 and 2 (since they’re basically the same experiments, just with different data sources), and FMT for experiment 3.. > What else did I miss? The conversation is lengthy already, it’s a bit hard to follow:face_holding_back_tears::pray: - File (JPEG): IMG_8629

Kate Rasheed (14:18:31) (in thread): > Thank you so much for this clarification@Esther Afuape. Should the source of the signatures in experiment 3 be the text?

Mildred Anashie (14:21:29) (in thread): > Thank you for this@Esther AfuapeI agree that the heat map (7d) is not curatable, however the figure seems to highlight some taxas using red and green boxes > > Does that mean anything? As it seems to corroborate with the results text > Should the text be curated and the figure also referenced as a source > > Please see attached images, I know you already said it isn’t curatable. I just need some more clarification, Thank you:pray: - File (JPEG): IMG_1525 - File (JPEG): IMG_1524

Aleru Divine (14:24:47) (in thread): > Omds:face_holding_back_tears:thank you so much@Esther Afuape

Esther Afuape (14:30:56) (in thread): > Yeah I see whatyou’resaying@Mildred Anashieif that will be curated,I’drather using result text as the signature source rather than fig 7d. Ican’tsee any statistical test in the caption of the figure though, did you catch that somewhere else in the paper?

Mildred Anashie (14:32:02) (in thread): > For Figure S4 it is a Co Abundance Network Analysis > > They identified Co Abundant Groups (CAG) and the caption for the figure says “Fig. S4 Genus-level coabundance network diagram in > the AGP showing the enrichments in two groups based on significantly differential CAGs.” So I believe those taxa should not be recorded as it appears to be a Microbial function analysis > > For the 3d-i, I’m still trying to figure that out@Yoko C

Mildred Anashie (14:36:30) (in thread): > Yes@Esther AfuapeAfter they discussed the methods for FMT there’s a Heading which says Statistical Analysis and I believe it is for the 3rd experiment.It says LEfSe - File (JPEG): IMG_1526

Aleru Divine (14:40:34) (in thread): > @Esther AfuapeYeah, they mentioned the use of Spearman’s correlation analysis in the study but not exactly for the FMT experimentthough. > > It was for the coabundance network analysis.

Kate Rasheed (14:42:25): > Hello everyone. The manual experiment/signature entry bug has been fixed. > > I just noticed that all my experiments and signatures are loaded when I click on my study link.@Chris AwokeYou don’t need to submit different links for review. Verify if your study is populated with all experiments and signatures.

Mildred Anashie (14:45:14) (in thread): > Thank you for this information@Kate RasheedIt’ssame for me, I think it has been fixed:relaxed::blush:

Aleru Divine (15:00:21) (in thread): > Oh my!@Yoko Cfigure 3d-i is not entirely redundant. For example f, g and h. > > I didn’t even look at that, I focused on the questions raised.:woman-facepalming::skin-tone-4:ugh! > > I think she should curate a different experiment and use t-test as the statistical test. With p<0.05 and curate these signatures.@Mildred Anashiewhat do you think?

Esther Afuape (15:01:21) (in thread): > @Mildred AnashieI don’t see any image for lefse as they mentioned in the statistical analysis section. The result within text seems curatable but we can’t do that without a statistical test and that’s definitely not lefse:melting_face:.@Aleru Divineyeah the mention of spearman correlation is expected since they used heat maps.. > We may have to discuss this paper during the office hour but let me tag the other mentors@Chioma Onyido@Scholastica Urua@Svetlana Ugarcina Perovic<@UBNSEMS3S>I need your opinions on the fmt experiment in this paper, fig 7d in particular. I also need second opinion on the matched-on criteria and confounders

Mildred Anashie (15:03:25) (in thread): > Thank you@Esther Afuapelooking forward to the conclusion on this:blush:It’s been a long one:smile:

Aleru Divine (15:07:33) (in thread): > Okay@Esther AfuapeThanks again for the intervention:face_holding_back_tears:

Mildred Anashie (15:08:20) (in thread): > I think it should be a different experiment@Aleru DivineIt’sa different statistical test > > I actually missed that, thank you@Yoko Cfor bringing it up

Aleru Divine (15:11:35) (in thread): > Thanks again@Yoko C

Chinwendu Joy Enyidiegwu (15:17:57): > Hello Everyone,@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Aleru Divine@Chioma OnyidoOn the final Application, i need help with this informations. > 1. Some communities or projects may want you to answer additional questions. Please check with your mentor and community coordinator to see if you need to provide any additional information after you save your final application. > 2. Please work with your mentor to provide a timeline of the work you plan to accomplish on the project and what tasks you will finish at each step. Make sure take into account any time commitments you have during the Outreachy internship round. If you are still working on your contributions and need more time, you can leave this blank and edit your application later. > Eagerly waiting for response please.:pray:

Aleru Divine (15:20:00) (in thread): > Wow! Thank goodness:star-struck:It was really concerning.:face_holding_back_tears:Thanks for the update@Kate Rasheed

Yoko C (15:20:17) (in thread): > Thank you Aleru and Mildred.

Mildred Anashie (15:25:39) (in thread): > Hi@Chinwendu Joy EnyidiegwuI think our mentors will give us more clarification when they get to this question,It’sweekend and I’d say you might have to be patient > > Thank you for bringing it up:pray:

Aleru Divine (15:26:31) (in thread): > @Chinwendu Joy Enyidiegwuthis has been answered before in the previous Outreachy contribution period. Idon’tknow ifit’llbe different for this time.I think the mentors will still provide a detailed response on this later. > > But here’s what<@UBNSEMS3S>said on this topic in the last contribution period.https://community-bioc.slack.com/archives/C04RATV9VCY/p1711392049150539?thread_ts=1711375189.437029&channel=C04RATV9VCY&message_ts=1711392049.150539 - Attachment: Attachment > There are no community-specific questions. > > As for timeline, the internship begins on Monday, May 2th and runs until Friday, August 23rd and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > • Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > • Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > • The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > • Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > • The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Adeshile Oluwatosin (17:49:01) (in thread): > Hello everyone@Yoko CThank youI also believe 3(d-I) should be curated as well. > Missed that. > > Comparison of the relative abundances at the species level according to metagenomic sequencing between the two groups. The value of P indicates the parameter variance of all groups in the plot using the unpaired t-test.

Adeshile Oluwatosin (17:49:37) (in thread): > Thank you for notifying@Kate Rasheed:wink:

Adeshile Oluwatosin (17:52:03) (in thread): > @Chinwendu Joy EnyidiegwuI believe the mentors will give us an answer to this when available

Adeshile Oluwatosin (17:53:57) (in thread): > From this statement > “In addition, we constructed a coabundance network of genera and clustered the 54 genera into 10 CAGs within the identified LI patient group of AGP. Each CAG gene contained 2–10 genera. We observed a significant increase in the expression of six CAGs, namely, CAG1, CAG2, CAG3, CAG4, CAG6, and CAG7, in the LI group compared to the HC group. Similar to our case–control study, the relative abundance of CAG4, which is a genus of Bacteroides and Parabacteroides, increased in the LI group in the AGP ( Fig. S4)”. > S4 is not curatable. Thank you@Yoko C

Adeshile Oluwatosin (18:17:21) (in thread): > Thank you so much@Esther Afuapefor contributing. > Itruly appreciate:pleading_face::hugging_face:

Chris Awoke (19:42:18) (in thread): > Thanks@Kate Rasheedfor the update.

2024-10-20

Rahila-me (07:02:32) (in thread): > @Chinwendu Joy Enyidiegwureading through the link Divine sent has answered all..but still hopefully towards the end of the contributions our mentors will still visit this .

2024-10-21

Precious Orakwe (01:59:54): > Good morning to our mentors, good morning teammate, hope we all had a great weekend. > As this week has began and the contribution phase is gradually coming to end, I wish to appreciate all of us for the collaborations, and the assistance, I appreciate all of us for the hard work and also to our wonderful mentors@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Scholastica Urua@Peace Sandy@Chioma Onyidofor their guidance and the time they put in to answer our questions. I say a very big thank you. > To my fellow contributors@Aleru Divine@Mildred Anashie@Adeshile OluwatosinI appreciate you all for all you do and all your works and other teammates, I say a very big thank you. > Let’s remember to record our contributions on time and and start preparing to submit our final application and if anyone needs help, we are all here to help out. > > Good luck to us.

Adeshile Oluwatosin (02:01:22) (in thread): > Good morning@Precious Orakwe:hugging_face:Have a nice week ahead

Adeshile Oluwatosin (02:02:12) (in thread): > Thank you mentors:blush:

Mildred Anashie (02:04:37) (in thread): > Good morning@Precious Orakwe:blush:I appreciate our mentors for their guidance > > Thank you and good luck to us:pray:

BOLARINWA AISHAT (02:14:05) (in thread): > Good morning > Thank you and Good luck:hugging_face:

Adeshile Oluwatosin (03:06:56) (in thread): > Just an update@Esther Afuape@Yoko C@Mildred Anashie@Aleru DivineI just discovered figure 3c as curatable. > > “Heatmap based on the relative abundance of the genera between the two groups.” - File (PNG): IMG_1749

Mildred Anashie (03:13:17) (in thread): > I see what you are saying@Adeshile OluwatosinThis paper seems like a case of “The more you look, the more you see”@Aleru Divine:sweat_smile:See what the text says “Compositional analysis revealed significant alterations in microbial abundance at the genus and species levels between LI patients and HCs. At the genus level, LI patients showed a reduced abundance of Veilonella, Enterococcus, and Erysipelatoclostridium, while there was a greater abundance of Escherichia and Haemophilus in LI patients than in controls (Fig. 3c). At the species level, the abundances of E. coli (P = 0.023), Bacteroides fragilis (P = 0.021), Dialister massiliensis (P = 0.046), Shigella flexneri (P = 0.020) and Streptococcus salivarius (P = 0.030) decreased in HC patients (Fig. 3d through h). The only more abundant species in the HC group was Eubacterium sp. CAG:251 (P = 0.001) (Fig. 3i)”.I’mwondering if the compositional analysis mentioned allows 3c and 3d through i to be curatable:thinking_face:

Kate Rasheed (03:17:56) (in thread): > Good morning@Precious Orakwe. Thank you for your help so far. > > Special thanks to our mentors for this amazing community.

Adeshile Oluwatosin (03:22:55) (in thread): > @Mildred AnashieIcan sayI’veread this article over 10 times:joy_cat:Apparently,<@UBNSEMS3S>reviewed this article in the last office hour. > I watched it again > And she stated vividly figure 7d, 3d-I curatable. > > In that case figure 3c should be curatable as well. > > Check timestamp 32 minshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1729185512290369 - Attachment: Attachment > Recording of today’s office hours. Thank you for all the great questions.

Mildred Anashie (03:30:06) (in thread): > I’veseen it@Adeshile OluwatosinWhat heard was “potentially an experiment” > > That would mean that 3c is also potentially curatable, because the heatmap is similar to 7d. > > Phewwwww, at this point we might just need to wait for more clarification

Adeshile Oluwatosin (03:30:56) (in thread): > @Svetlana Ugarcina Perovicwants the study to be submitted for review as soon as possible.

Adeshile Oluwatosin (03:31:27) (in thread): > I guess I would curate it. > Then take to corrections whatever is said after review

Mildred Anashie (03:35:23) (in thread): > This sounds like a good plan:+1:

Aleru Divine (03:38:13) (in thread): > The more you look:eyes:@Adeshile Oluwatosin@Mildred Anashie:face_with_open_eyes_and_hand_over_mouth:

Adeshile Oluwatosin (03:39:49) (in thread): > :joy_cat::joy_cat::joy_cat:this exact article made me understand the statement read between the lines.:joy:@Aleru Divine

Aleru Divine (03:40:31) (in thread): > Good morning and thank you so much@Precious OrakweThanks to our mentors for the continuous support:pray::saluting_face:

Svetlana Ugarcina Perovic (03:44:10): > Good morning:potted_plant:Although this week is officially Outreachy contribution end, our community’s doors stay open for your future contributions. We truly value your involvement and hope you’ll continue being part of our community. > > Oct. 29, 2024 at 4pm UTC Final OUTREACHY application deadline > Always open BugSigDB contribution > > This week goals: > * submit your final Outreachy application > * help to closeopen, assigned GitHub issues: > > * Please make a comment in the GitHub issue that you want to finalize the curation and then we will see together if the original curator is up to join you or not. > * Collaboration counts as contribution!

Mildred Anashie (03:46:05) (in thread): > Thank you so much@Svetlana Ugarcina PerovicThis has been truly amazing:blush:Good morning:potted_plant:

Aleru Divine (03:46:45) (in thread): > Good morning@Svetlana Ugarcina Perovic:sparkles:Thank you so much for the update

Svetlana Ugarcina Perovic (03:53:59): > For your final application: There are no community-specific questions.As for the timeline, the internship begins on Monday, Dec 9th and runs until Friday, March 7th and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page:https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Mildred Anashie (03:56:16) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the update:sparkles:

Aleru Divine (03:58:48) (in thread): > Thank you so much for this@Svetlana Ugarcina Perovic@Chinwendu Joy EnyidiegwuI believe your question has been answered:blush:

Samuel Nnanna (04:12:03) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (04:21:06) (in thread): > Thank you@Svetlana Ugarcina Perovic

Ebuka Chinwuba (04:24:19) (in thread): > This address a lot of things, Thanks@Svetlana Ugarcina Perovic

Kate Rasheed (04:31:55) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thank you so much for this community and helping us grow in learning.

Kate Rasheed (04:34:04) (in thread): > Thank you for this update@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (04:48:07): > One more important message for today:slightly_smiling_face:We greatly appreciate you sharing**** your BugSigDB journey and experiences on social media**. > > Your posts about our community help raise awareness and connect more people with our project. Thank you for being such a valuable advocate!

Adeshile Oluwatosin (05:09:02) (in thread): > Thank you so much@Svetlana Ugarcina PerovicGood morning:smiley:I’mhere to stay:hugging_face:

Adeshile Oluwatosin (05:09:23) (in thread): > Noted@Svetlana Ugarcina Perovic:relieved:

Adeshile Oluwatosin (05:09:56) (in thread): > :relieved:

Joy (05:10:43) (in thread): > You welcome@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (05:11:47) (in thread): > To clarify the last line ma’am@Svetlana Ugarcina PerovicShould we go ahead with editing open assigned issues directly, if the original curator has not responded. > > Also, if we are collaborating with other people > Are we to record it as a contribution as well.

Chris Awoke (05:13:29) (in thread): > Sure, I will. Thank you so much,@Svetlana Ugarcina Perovic

Ebuka Chinwuba (05:14:32): > Hi everyone, > I hope you all had a restful weekend! As we kick off another week, I’m excited to dive back into our curation project and see what amazing things we can accomplish together. > Let’s keep the momentum going and support one another as we tackle our goals! > Wishing you all a fantastic week ahead!

Princess Rehoboth Asuelimen (05:14:34) (in thread): > Good morning@Svetlana Ugarcina Perovic, this has been a wonderful experience.

Svetlana Ugarcina Perovic (05:15:21) (in thread): > Please make a comment in the GitHub issue that you want to finalize the curation and then we will see together if the original curator is up to join you or not. > > Collaboration counts as contribution, yes.

Chris Awoke (05:15:37) (in thread): > Thanks so much,@Svetlana Ugarcina Perovicfor the update. I really appreciate it.

Adeshile Oluwatosin (05:15:51) (in thread): > Hi@Ebuka Chinwubacheck for open assigned github issues > Ask to collaborate with them:pleading_face:seems like they are still a lot. > > Thank you for helping out

Adeshile Oluwatosin (05:16:34) (in thread): > Thank you for clarifying@Svetlana Ugarcina Perovic

Chris Awoke (05:19:07) (in thread): > I appreciate every one of you. Special thanks to all our mentors:heart_eyes:

Precious Orakwe (05:23:16) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for the update

Precious Orakwe (05:24:34) (in thread): > Thanks@Svetlana Ugarcina Perovic

Precious Orakwe (05:26:05) (in thread): > Thanks team

BOLARINWA AISHAT (05:31:56) (in thread): > :hugging_face:

BOLARINWA AISHAT (05:33:11) (in thread): > Thank you so much for the update@Svetlana Ugarcina Perovic

Chinwendu Joy Enyidiegwu (05:43:41) (in thread): > thank you@Svetlana Ugarcina Perovic

Mildred Anashie (06:18:37) (in thread): > Okay@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (06:19:41) (in thread): > Thank you@Ebuka ChinwubaWishing you a fantastic week ahead too

Adeshile Oluwatosin (06:30:59) (in thread): > Alright then,let’ssee how it goes

Rahila-me (06:34:29) (in thread): > @Svetlana Ugarcina Perovicgood morning, thank you for the update

Rahila-me (06:35:32) (in thread): > Thank you for this update@Svetlana Ugarcina Perovic

Rahila-me (06:42:00) (in thread): > :blush::blush::blush:Sure thing

Rahila-me (06:43:04): > Happy Monday all…to you all I love:heart::heart:my wonderful contributors

Precious Orakwe (06:49:31): > @Svetlana Ugarcina Perovic@Scholastica Urua@Aleru Divine@C. Mirzayi (please do not tag this account)please i need assistance with the paper I and@Chinwendu Joy Enyidiegwuare collaborating on, please i am finding it difficult to understand how many experiment are in this paper. Here is the link to the paper: file:///C:/Users/Administrator/Downloads/1-s2.0-S088915912400624X-main%20(3).pdf

Precious Orakwe (06:55:28): > I also want to know if these are curatable, I have search for all the taxa in table one on NCBI but I couldn’t find any, i only found Muribaculum and also searched on Google i couldn’t find anything, but when i removed the underscore and join the name and the number i found something similar to the taxa name in the table. Please guide me on what to do. Thanks - File (PNG): Screenshot_20241021-114418.png - File (PNG): Screenshot_20241021-114345.png

Kate Rasheed (06:58:38) (in thread): > @Precious OrakweThe table is curatable. Check the discussion page for Clostria UCG… I’ve seen that there before.

inyang john (07:00:01): > @Svetlana Ugarcina Perovicplease i need to delete thishttps://bugsigdb.org/Study_1178/Experiment_2 - Attachment (BugSigDB): Study 1178/Experiment 2 > .

Precious Orakwe (07:02:10) (in thread): > How about Muribaculum_39. > All the Muribaculum, I can’t find any on NCBI and also UNIPROT

Kate Rasheed (07:02:51) (in thread): > You can leave a note on it or check the discussion page as well.

Adeshile Oluwatosin (07:17:24) (in thread): > @Precious OrakweI will look through this paper

Adeshile Oluwatosin (07:17:25) (in thread): > @Precious OrakweI will look through this paper

Precious Orakwe (07:19:14) (in thread): > Thanks@Adeshile Oluwatosin

Adeshile Oluwatosin (07:23:44) (in thread): > Table 1 is curatable@Precious Orakwe

Precious Orakwe (07:25:23) (in thread): > okay, how do I go about the taxa names since I cant find the on NCBI and UNIPROT

Aleru Divine (07:25:27) (in thread): > Can you share a link to this paper please@Precious Orakwe

Precious Orakwe (07:26:28) (in thread): > file:///C:/Users/Administrator/Downloads/1-s2.0-S088915912400624X-main%20(3).pdf

Aleru Divine (07:26:43) (in thread): > If youcan’tfind them on NCBI and UNIPROT, check the missing NCBI ID discussion page.If youcan’tfind anything,I’mafraidyou’llhave to curate as seen.

Adeshile Oluwatosin (07:27:22) (in thread): > I just checked NCBI and uniprot,it’snot there. > > Discussion page as well. > Just curate it the way they are stated@Precious Orakwe

Adeshile Oluwatosin (07:27:53) (in thread): > It’snot clickable@Precious Orakwe

Precious Orakwe (07:27:59) (in thread): > I have searched the missing NCBI ID discussion page, still cant see anything of such there.

Aleru Divine (07:28:51) (in thread): > Thisisn’tgoing to work outside your computer@Precious OrakweShare the title of the paper or a link to the paper itself:pray:

Adeshile Oluwatosin (07:29:01) (in thread): > Curate it the same way it is listed@Precious Orakwe

Aleru Divine (07:30:12) (in thread): > Thank you@Ebuka ChinwubaWishing you a great week ahead:sparkles:

Precious Orakwe (07:31:17) (in thread): > try this:https://mail-attachment.googleusercontent.com/attachment/u/0/?ui=2&ik=c6816ac2da&attid=0.1&perm[…]jYbwNUhydaO5fRNWuDdxedDRtLoLdWNpWMcgz_nRcnU3DNa9vk@Aleru Divine

Adeshile Oluwatosin (07:44:11) (in thread): > Okay@Precious Orakwe

Adeshile Oluwatosin (07:45:37) (in thread): - File (JPEG): IMG_1766

Mildred Anashie (07:46:19) (in thread): > I got the same thing with Adeshile@Precious Orakwe

Mildred Anashie (07:46:48) (in thread): > Please share the title to the article or the BugSigdb curated study (if you have started the curation)

Aleru Divine (07:46:57) (in thread): > Same here@Precious Orakwe

Precious Orakwe (07:49:20) (in thread): > but the pdf is opening from my end

Precious Orakwe (07:49:33) (in thread): > this is the link to the study:https://bugsigdb.org/Study_1104 - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > The paternal environment prior to conception has been demonstrated to influence offspring physiology and behavior, with the sperm epigenome (including noncoding RNAs) proposed as a potential facilitator of non-genetic inheritance.

Aleru Divine (07:50:12) (in thread): > Got it.Thanks@Precious OrakweWill go through it now

inyang john (08:00:05) (in thread): > :blush:

inyang john (08:01:11) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (08:08:03) (in thread): > I see why you shared the PDF@Precious Orakwethe article is not open access

Mildred Anashie (08:08:23) (in thread): > Anyone has the accessible file yet?

Aleru Divine (08:08:59) (in thread): > @Precious Orakweit looks to me like there’s only 1 experiment from this paper. > The contrast groups are > > Control (0) vs antibiotic treated males ATB (1) > > Figure 1G presents significant alpha diversity measures (Shannon index) for control vs ATB (decreased for ATB). > > Table 1 presents differentially abundant signatures.(Looks like they were increased in controls only) > > Looks like only 1 experiment is in this paper.

Precious Orakwe (08:09:13) (in thread): > I swear, the paper is something else,

Aleru Divine (08:10:34) (in thread): > I’m so sorry@Mildred Anashielet me share the pdf from@Precious Orakwe - File (PDF): 1-s2.0-S088915912400624X-main (3) (1)

Precious Orakwe (08:11:15) (in thread): > Exactly, what I’m thinking based on the taxa table, but reading through the paper it looks like its more than 1

Precious Orakwe (08:11:44) (in thread): > Thanks@Aleru Divinewas about to share the pdf again, thanks for saving me

Aleru Divine (08:14:38) (in thread): > @Precious Orakwethey did other experiments but that is not relevant in BugSigDB.I also noticedfigure 4a presents another Shannon index but this is not significant. > > “We also investigated the gut microbiome of F1 mice to determine whether offspring gut > microbiome was influenced by paternal treatment. We did not observe a significant > difference in α-diversity (P=0.494, Figure 4A)**” > > I don’t think this should be curated since there wasn’t any significant difference.

Precious Orakwe (08:19:25) (in thread): > Thank you@Aleru Divine, exactly my point

Precious Orakwe (08:20:08) (in thread): > So, I can curate the table one just the way it is since I cant find them on NCBI

Aleru Divine (08:21:37) (in thread): > Yes,youcan.:thumbsup:

Mildred Anashie (08:27:01) (in thread): > @Aleru DivineI agree with you and I also see there’s a mention of supplementary information > > Do you have access to it?@Precious Orakwe

Svetlana Ugarcina Perovic (08:29:18): > Reminder: If you have any questions, feel free to post them in this channel.Please do not direct message the mentors.Thank you for your patience.

Mildred Anashie (08:37:41) (in thread): > Noted@Svetlana Ugarcina PerovicThank you

Svetlana Ugarcina Perovic (08:37:42) (in thread): > deleted.

Adeshile Oluwatosin (08:44:19) (in thread): > @Precious OrakweI believe as long as the alpha-diversity was statedandthere’s no significant difference. > > Just indicate it as unchanged. > I need access to the supplementary information to confirm

Adeshile Oluwatosin (08:52:29) (in thread): > Understood@Svetlana Ugarcina Perovic

Mildred Anashie (08:57:56) (in thread): > Hello<@UBNSEMS3S>I apologize for being persistent:pray:Just bringing your attention to this > I appreciate your help, Thank you:blush:

inyang john (09:02:18) (in thread): > Thank you:pray:

inyang john (09:02:47) (in thread): > :100:

Aleru Divine (09:09:13) (in thread): > :ok_hand:got it:blush:

Adeshile Oluwatosin (09:13:14) (in thread): > From the curation policy@Precious Orakwe - File (JPEG): IMG_1773

Aleru Divine (09:16:37) (in thread): > I believe wecan’tcurate the ones without signatures ifthey’renot significant.(Just like in this case) > > Itwould’vebeen different If they had signatures, thenwe’llcurate them as unchanged in addition to curating the signatures@Adeshile Oluwatosin@Precious Orakwe

Aleru Divine (09:19:43) (in thread): > About the supplementary material.The link leads to the main article on ScienceDirectThat’sthe supplementary material(seeit’sthe doi link):sob:I’mso confused@Adeshile Oluwatosin@Mildred Anashie

Adeshile Oluwatosin (09:21:08) (in thread): > In this case, the taxaare mentioned > Theseare the signatures now!@Aleru DivineThere was even a test done - File (JPEG): IMG_1774

Svetlana Ugarcina Perovic (09:23:24) (in thread): > IMPORTANT from Outreachy:The deadline for final applications is Oct. 29, 2024 at 4pm UTC. Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline.Applicants who submit a final application will be able to continue recording and editing their contributionsto your project until the intern announcement on Nov. 26, 2024 at 4pm UTC. Applicants who have not submitted a final application will not be able to record or edit their contributions.

Kate Rasheed (09:24:35) (in thread): > Thank you so much@Svetlana Ugarcina Perovicfor this update.

Adeshile Oluwatosin (09:25:22) (in thread): > Thank you for this@Svetlana Ugarcina Perovic

Aleru Divine (09:26:02) (in thread): > This is for experiment 1 and it has already been curated. That one has significant alpha diversity measures in figure 1G (paternal F0) > > The one that is not to be curated is figure 4A referring to the F1 mice. > > See “We also investigated the gut microbiome of F1 mice to determine whether offspring gut microbiome was influenced by paternal treatment. We did not observe a significant difference in α-diversity (P=0.494, Fig. 4A) and β-diversity (PTreatment=0.452, Fig. 4B) in the F1 mice relative to the father’s treatment.”No signatures, alpha diversity measures were not significant

Rahila-me (09:27:19) (in thread): > Noted:pray::pray:

Precious Orakwe (09:30:44) (in thread): > Noted

Adeshile Oluwatosin (09:40:52) (in thread): > Ohhh it has already been curated , got it

Mildred Anashie (09:44:10) (in thread): > I believe we might need some help getting the supplementals as the article is not open access and the supplemental was cited in the results, there might be some useful information there@Aleru Divine@Svetlana Ugarcina Perovicplease we need some assistance here:pray:

Aleru Divine (09:46:24) (in thread): > That’sright@Mildred Anashiejust to be sure.

Svetlana Ugarcina Perovic (09:54:11) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/496updated with Supplementary material. - Attachment: #496 Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice > Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Bethany A. Masson – Brain, Behavior, and Immunity > > https://www.sciencedirect.com/science/article/pii/S088915912400624X
> 1-s2.0-S088915912400624X-main.pdf > > Supplementary material: > > FigS1 FigS2 FigS3_4 FigS5 FigS6 FigS7

Adeshile Oluwatosin (09:55:11) (in thread): > Noted@Svetlana Ugarcina Perovic

Mildred Anashie (09:55:25) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Aleru Divine (09:58:53) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Precious Orakwe (10:06:57): > please@Svetlana Ugarcina Perovichelp me and delete signature 2 in this study.https://bugsigdb.org/Study_1104, thank you - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > The paternal environment prior to conception has been demonstrated to influence offspring physiology and behavior, with the sperm epigenome (including noncoding RNAs) proposed as a potential facilitator of non-genetic inheritance.

Svetlana Ugarcina Perovic (10:07:20) (in thread): > deleted.

Precious Orakwe (10:07:38) (in thread): > Thanks

Mildred Anashie (10:08:28) (in thread): > I think you are on track with the curation@Precious Orakweas the supplementals doesn’t say much either > > I see a significant alpha diversity in Supplementary figure 5a but this is what the paper says “In terms of sex differences, there was no difference in ß-diversity (Psex=0.548, Fig. 4B), but overall the F1 females had more diverse gut microbiota than the male mice (P=0.001, Figure S5A)”. And they are no signatures for it, it can be left out in my opinion

Precious Orakwe (10:09:59): > please teammates i need a peer review on this studyhttps://bugsigdb.org/Study_1104, any correction will be gladly appreciated.

Precious Orakwe (10:11:05) (in thread): > Thanks for the update@Svetlana Ugarcina Perovic. Noted

Adeshile Oluwatosin (10:12:16) (in thread): > Okay:+1:

Aleru Divine (10:16:25) (in thread): > That’scorrect@Mildred AnashieEverything checks out now.:blush:

Aleru Divine (10:16:48) (in thread): > Sure thing@Precious Orakwe

Adeshile Oluwatosin (10:17:16) (in thread): > There should beone statistical test though per experiment, let me check

Cynthia Iwuoha (10:26:28): > I recently noticed that @Rahila edited my study without my permission. > > I only gave @Tosin permission for collaboration.. I was not aware of granting access for Rahila edits.@Svetlana Ugarcina PerovicI hope there’s no issue with this?

Svetlana Ugarcina Perovic (10:27:54) (in thread): > Link to the GitHub issue please?

Svetlana Ugarcina Perovic (10:29:29) (in thread): > ok I see ithttps://bugsigdb.org/Study_1151 - Attachment (BugSigDB): Gut microbiome and serum metabolome alterations associated with lactose intolerance (LI): a case‒control study and paired-sample study based on the American Gut Project (AGP) - BugSigDB > UNLABELLED: Lactose intolerance (LI) is a prevalent condition characterized by gastrointestinal symptoms that arise following lactose consumption.Recent evidence suggests that the gut microbiome may influence lactose levels in the gut.

Cynthia Iwuoha (10:29:51): > https://bugsigdb.org/Study_1151There is the link.

Svetlana Ugarcina Perovic (10:30:15) (in thread): > please keep communication in the same thread

Cynthia Iwuoha (10:32:07) (in thread): > Yes that’s the link please.

Svetlana Ugarcina Perovic (10:32:14) (in thread): > @Rahila-me(Rahila) could you please report your edits.

Rahila-me (10:33:05) (in thread): > @Svetlana Ugarcina Perovicokay i will

Svetlana Ugarcina Perovic (10:36:37) (in thread): > @Rahila-meplease do note that a curator not assigned to the task/curation should communicate to the original curator(s) first, before making any changes. Please report here changes, so that the original curator(s) could decide to accept it or not. This is a common open-source practice.

Rahila-me (10:42:10) (in thread): > @Svetlana Ugarcina Perovic@Cynthia IwuohaPlease to@Cynthia IwuohaI am sorry i did not know that i will have to report here:please do note that a curator not assigned to the task/curation should communicate to the original curator(s) first, before making any changes.before effecting the changes since i saw it on the NCBI clean-up. > Some of the minor changes i made was where you entered something Leuconostocacea_bacterium and i have to remove the _ or where you entered it together with the g. or f. and i have to remove it genus or family:pray:

Adeshile Oluwatosin (10:43:16) (in thread): > MHT is yes@Precious Orakwe

Svetlana Ugarcina Perovic (10:44:16) (in thread): > Ok, I see, please communicate between each other:slightly_smiling_face:

Rahila-me (10:45:43) (in thread): > @Svetlana Ugarcina Perovic@Cynthia IwuohaNoted. Going forward

Cynthia Iwuoha (10:46:00): > @Rahila-meit’s fine, I just wanted to be sure it’s not going to be an issues.

Cynthia Iwuoha (10:46:45): > @Svetlana Ugarcina PerovicThank you for the clarifications.

Rahila-me (10:46:56) (in thread): > Okay Thank you:people_hugging:

Aleru Divine (10:54:23) (in thread): > Well done on the curation@Precious Orakwehere are my observations and suggestions:pray:The contrast groups names should be a bit simpler. > Here’s my suggestion: > Group 0 - Controls > Group 1 - Antibiotics treated males > > There aren’t any antibiotics exclusions in the paper. (They were actually administered antibiotics) > > There was MHT correction (the studies states that P-values adjusted by FDR < 0.05 were considered significant). > > The statistical test is PERMANOVA. > See-“Differences between groups were determined using permutational multivariate analysis of variance (PERMANOVA)”There aren’t any confounders controlled for. These factors you listed as confounders are just fixed and random factors in the study. > > There was only one significant alpha diversity result Figure 1G (Shannondecreased for ATB).This text should help clarify that:point_down:“ We used the Shannon Index for α-diversity, which is a comprehensive metric that considers both evenness and richness.” > > No need to curate richness differently

Adeshile Oluwatosin (10:55:18) (in thread): > Statistical test isPERMANOVA… since the body site is feces - File (PNG): IMG_1777

Aleru Divine (11:06:58) (in thread): > This condition should be the experimental condition being studied. I’m not sureSeasonal gut microbiome measurementis the condition in this case. I’m still trying to figure it out:thinking_face:What I understand isthey tried to study how depleting the paternal gut microbiome(they used antibiotics for the depletion) in mice affects sperm small RNAs and the offspring’s physiology and behaviorThere’s nothing likeGut Microbiome depletion:sweat_smile:that would’ve been something.@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Scholastica Urua@Esther Afuape@Chioma Onyido@Peace Sandy@Levi WaldronA little help please:pray::face_holding_back_tears:

Joy (11:14:15) (in thread): > Thank you@Svetlana Ugarcina Perovic. Duly noted

Precious Orakwe (11:14:38) (in thread): > Thanks everyone for your help, I appreciate all your effort. Thank you

Precious Orakwe (11:17:07) (in thread): > please can you help me and check out the confounders

Kate Rasheed (11:18:31) (in thread): > @Precious OrakwePlease work on your sample sizes. You might need to leave it blank. > > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1710872291722169 - Attachment: Attachment > Good evening everyone, > > @Svetlana Ugarcina Perovic @UBNSEMS3S @Esther Afuape @Peace Sandy @Chioma Onyido > > For my sample size, the paper states n = 4-5 mice. > > I went with this as they didn’t exactly specify. But I’m getting this warning message. > > ““-5” can not be assigned to a declared number type with value 4.” > > What do I do in this situation? :pray:

Precious Orakwe (11:19:41) (in thread): > @Kate Rasheedthat is how it was mentioned on the paper

Precious Orakwe (11:25:21) (in thread): > thanks for sharing, i will do the changes now

Yoko C (11:45:59) (in thread): > Hello@Precious Orakwe, just wanted to give some feedback. I think your condition is Antibiotic response or something similar, since that is what was compared. In this case, I don’t think there is any exclusion since the mice are acquired from a lab. I think your sample size might be 17 for 1 group and 21 for the other (the sample size 20-27 is for the F1 generation). The text mentions using generalized regression, Maaslin2, so I think that would be your test. For this experiment time wasn’t used, nor litter effect. And the text does mention Shannon was significantly decreased.

Yoko C (11:54:35) (in thread): > I think your signature is the other way around, increased for the control group, not the antibiotic group.

Kate Rasheed (12:09:05) (in thread): > @Yoko CYou are absolutely correct… The table says “taxa higher in the control group when compared to the antibiotic group”. That would be decreased abundance in the antibiotic group.

UBNSEMS3S (12:11:50) (in thread): > Apologies. I will look at this in a few minutes.

Mildred Anashie (12:23:47) (in thread): > Thank you so much

Adeshile Oluwatosin (13:43:04): > @Svetlana Ugarcina Perovickindly deletehttps://bugsigdb.org/Study_1132/Experiment_2/Signature_2Thank you - Attachment (BugSigDB): Study 1132/Experiment 2/Signature 2 > .

Aleru Divine (14:29:01): > Hello Everyone, trust you all are doing okay:blush:@Kate Rasheedand I are currently working on thisstudyand we are seeking clarity on a few things > 1. In this study, we actually might have a confounding factor that was minimized in other words, controlled. > “These correlations were calculated after stratification by HIV status to minimize confounding by known effects ofHIVon the cytokine and chemokine environment.” > But then, this is the disease condition. Can we say it is a confounder? > > 2. For the statistical test in this study, they utilized MaAsLin2 and according to thisthread, MaAsLin2 is usually arcsine square root for data transformation. > However, the paper itself uses relative abundance. What do we go with in this case? > > 3. For experiments 3 and 4, “Association of inflammatory and vascular injury biomarkers with the gut microbiota abundanceWe determined the association of the gut microbiota with inflammatory and vascular injury biomarkers after stratification by HIV infection status using the MaAsLin2 package in R. > > Will the study condition be the same, I mean HIV? > > Thank you so much for all your help:pray:@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy - Attachment (BugSigDB): Immune activation and inflammation in lactating women on combination antiretroviral therapy: role of gut dysfunction and gut microbiota imbalance - BugSigDB > INTRODUCTION: Combination antiretroviral therapy (cART) effectively controls HIV; however, chronic low-level viremia and gut microbiota dysbiosis remain significant drivers of gut and systemic inflammation. - Attachment: Attachment > Oh wow > Could you correct this list please? @Levi Waldron > > ANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance

Scholastica Urua (14:43:43) (in thread): > Well done,@Aleru Divineand@Kate Rasheed. To answer your questions: > 1. I wouldn’t curate as confounder unless explicitly mentioned in the study. > 2. MaAsLin2 is a linear model and can use different data transformations, including relative abundance. > 3. Yes, since that’s the case of interest in the study.

Yoko C (14:48:04) (in thread): > Hi, here is someinfoon how Maaslin works: The great part of MaAsLin2 is that you can either feed it raw count data and the default is that it will do TSS normalization for you or you can feed it normalized data and within the code put normalization = “NONE”. The same goes for transforming the data the default is a LOG transformation, however you can also turn that off if you have already transformed the feature table before you run the model.

Yoko C (14:51:42) (in thread): > I agree that because that is the condition to be tested it can’t be a confounder as well, and I think they are referring to how it affects cytokines not the abundance, in that sentence

Aleru Divine (14:52:02) (in thread): > Thank you so much@Scholastica Urua:face_holding_back_tears:Here’swhat the paper says concerning the confounding effect.“These correlations were calculated after stratification by HIV status to minimize confounding by known effects of HIV on the cytokine and chemokine environment.”

Aleru Divine (14:53:19) (in thread): > Thank you so this resource@Yoko CI’mchecking it out right away

Aleru Divine (14:55:43) (in thread): > Thanks again@Yoko C

Yoko C (14:56:49) (in thread): > Welcome! Also reading the paper to see if I can be of more assistance.

Aleru Divine (14:57:22) (in thread): > Thank you so much:hugging_face:I was going to ask:face_holding_back_tears:

Scholastica Urua (15:07:15) (in thread): > Hi@Mildred Anashie, thank you for your patience. > > Nice detective work! I agree with your findings (1-4), and they are indeed available on the NCBI taxonomy browser. Please proceed with making changes for 1-4. > > ForStudy 1142, however, please tag the original curator so they can review your suggestions and decide whether to accept or reject them. - Attachment (BugSigDB): Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy - BugSigDB > Children diagnosed with severe tonsillar hypertrophy display discernible craniofacial features distinct from those with adenoid hypertrophy, prompting illuminating considerations regarding microbiota regulation in this non-inflammatory condition.

Mildred Anashie (15:09:53) (in thread): > Okay > > Thank you@Scholastica Urua:pray:I’llupdate 1-4 and contact the original curator for the other study

Mildred Anashie (15:14:17) (in thread): > Hi:wave:Late to the party:blush:I’llgive it a look as well@Aleru Divine

Aleru Divine (15:14:45) (in thread): > Thank you so much@Mildred Anashie:hugging_face:

Yoko C (15:30:53) (in thread): > For experiments 3 and 4 your condition is levels of inflammatory biomarkers, or at least I think that is what table 3 is about. I am not sure how you would curate it though. Editing: I think i would also curate like that. But on Experiment 3, I would add genre Weisella for uninfected.

Kate Rasheed (15:47:42) (in thread): > Why would you add Weisella@Yoko C

Aleru Divine (15:48:49) (in thread): > Thank you@Yoko CWeisella has been added. It’s not showing yet > > Yes I thought about the fact that for experiment 3 and 4, they focused on the association of the gut microbiota withinflammatory and vascular injury biomarkersafter stratification. > > There’s the option of biomarkers as the condition. > > The co-mentor@Scholastica Uruasuggested otherwise and it does make sense > > Both reasons do make sense.:pleading_face:

Yoko C (15:48:53) (in thread): > Maybe@Kate Rasheed, because its on the table for the 6 weeks uninfected section with significant q

Aleru Divine (15:49:10) (in thread): > Table 3@Kate Rasheed

Kate Rasheed (15:49:26) (in thread): > @Yoko CThe q-value threshold is 0.05

Yoko C (15:50:58) (in thread): > @Kate Rasheed, I see it with a negative exponential, so that would put it under 0.05.

Aleru Divine (15:53:15) (in thread): > Yep. It’s raised to the power of minus 8 > > That is0.0000000604@Kate RasheedI added it.

Yoko C (15:55:00) (in thread): > I was also wondering about the Butryvibrio, which you put as Butryvibrio and then Butryvibrio sp, but I think on the table it’s written down twice, just as genre. I think they put it twice because it associates to different biomarkers, so maybe it just goes once? Not sure about that at all. Sorry Butyrivibrio

Aleru Divine (15:56:48) (in thread): > About that. Usually when a signature (genus) appears twice we can curate Sp. just because they can be different species. But I see your point and it doesn’t count here. I’ll make the changes:pray:Thank youso much@Yoko C

Yoko C (15:58:06) (in thread): > @Aleru Divine, I see! Those details are still super confusing to me.

Aleru Divine (15:59:22) (in thread): > I know:pleading_face:it’sokay.You were right.If it were a different scenario, the second signaturewould’vecounted.

Aleru Divine (16:01:06) (in thread): > Same for Eggerthella:sweat_smile:

Svetlana Ugarcina Perovic (16:10:51) (in thread): > deleted.

Adeshile Oluwatosin (16:11:06) (in thread): > Thank you

UBNSEMS3S (16:46:07) (in thread): > It’s very possible I made a mistake during the office hours–I am reviewing the article on the spot. If 3C and 7D are the same experiment that would be a bit strange (you generally don’t want to double present the same data) but it could very well happen.

Adeshile Oluwatosin (16:47:25) (in thread): > I await your response<@UBNSEMS3S>:pray:we’vebeen so confused

UBNSEMS3S (17:03:08) (in thread): > Yeah a lot going on here. This is easily one of the most complex curations I’ve seen. They did nearly every analysis they could think of for every possible variable. > 1. Supplementary figure 3 is 8 experiments. Each column is an experiment where they did the analysis using a different combination of data, normalization, and analysis methods. We can look at each column: > > 1. Column 1 > > 1. Data/experiment: all cohorts comparing bacterial abundance with group 1 is increasing age (group 0 would be decreasing age) > 2. Normalization: TSS which is another way of saying relative abundance data transformation > 3. Analysis: linear model > > 1. Column 2 > > 1. Data/experiment: all cohorts comparing bacterial abundance with group 1 is increasing age (group 0 would be decreasing age) > 2. Normalization: Weird one we don’t see often–it’s not really an option so I would leave data transformation blank for now > 3. Analysis: linear model > > 1. Column 3 > > 1. Data/experiment: all cohorts comparing bacterial abundance with group 1 is increasing age (group 0 would be decreasing age) > 2. Normalization: ANCOM uses centered log ratio as the data transformation > 3. Analysis: ANCOM > > 1. Column 4 > > 1. Data/experiment: SG90 + CPE datasets comparing bacterial abundance with group 1 is increasing age (group 0 would be decreasing age) > 2. Normalization: relative abundances > 3. Analysis: linear model > > 1. etc. > > 1. Table 2 is a subset of supplementary file 3. Supplementary table 3 also appears to be a subset of supplementary file 3. Curate supplementary file 3 with group 1 as increasing age and group 0 as decreasing age. Positive Beta estimates are increased with group 1 (increasing with age), negative Beta estimates are decreased with group 1 relative to group 0. Remember to only curate statistically significant taxa (FDR p-value < 0.05) > 2. Each tab in supplementary file 6 is potentially curatable. Given its extensive size, I would focus on ones with significant results and only curate the age-corrected (i.e. confounder controlled for: age) columns. Once again the group 1 is the increasing value of that variable (glucose/HDL/vitamin B12) while the group 0 is that value decreasing. > 3. Given that they were treating age as continuous in their differential abundance analysis, I would not curate grouped age alpha diversity results. These are different enough that they can’t really be lumped together.

UBNSEMS3S (17:31:56) (in thread): > 3d through i is coming from a human study. 7d is coming from an animal study.

Kate Rasheed (17:33:27): > Good day@Svetlana Ugarcina Perovic. Kindly delete experiment 2 from this study.https://bugsigdb.org/Study_1180 - Attachment (BugSigDB): Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy - BugSigDB > BACKGROUND: Person with human immunodeficiency virus type-1 (PWH) are prone to chronic inflammation due to residual viral production, even with antiretroviral therapy (ART), which increases the risk of age-related diseases.

UBNSEMS3S (17:33:30) (in thread): > 3C is also curatable as part of 3D through I.

Mildred Anashie (17:42:31) (in thread): > Yes<@UBNSEMS3S>Both experiments are not the same, thank you for the clarification > > Can I tag you to the original thread? I believe there were concerns on statistical test not mentioned for 7d and 3c and if the whole heat map should be curated using the color code or just the highlighted taxa > > > The thread is quite lengthy

UBNSEMS3S (17:43:21) (in thread): > Sure but it’s the taxa that have boxes around them. Red is increased in cases relative to controls, green is decreased in cases relative to controls.

Mildred Anashie (17:47:06) (in thread): > Thank you again<@UBNSEMS3S>

Mildred Anashie (17:57:46) (in thread): > Thank you so much<@UBNSEMS3S>I believe the concerns for Supplementary file 3, Table 2 and supplementary table 1 is clear. > > File 6 is clear too but I’ll like to confirm that the ‘Without age correction’ is to be left out and would it be okay curating just the species? They reported species, genus and phylum. > > The last point is not so clear, Does this mean that we will be leaving out the age group experiments regardless of the significance in Alpha diversity and I think I see abundance in 1E:thinking_face:Lastly, Supplementary Figure 5 is still not clear and from your response in no 1. that would be referring to Supp. Figure 3 and not 8 > > Thank you again

UBNSEMS3S (17:58:14) (in thread): > Curate species, genus, and phylum.

UBNSEMS3S (17:58:44) (in thread): > Did they do categorical age group differential abundance analysis? Sorry I didn’t see that in there. If so then the alpha diversity results should go with those relevant experiments.

UBNSEMS3S (17:59:35) (in thread): > And I meant supplementary figure 3. Edited my reply.

Mildred Anashie (18:00:39) (in thread): > This is the caption for 1E > > “Relative abundance boxplots for the Bacteroides genus, and corresponding species that was identified to be associated significantly and not significantly with age. The symbols “n.s.”, “” and “****” represent p-value > 0.05, p-value ≤ 0.05 and p-value < 0.005, respectively (GLM for taxa association with age using n = 516 independent samples; FDR-adjusted p-value using Benjamini–Hochberg test; Bacteroides: 6.4 × 10–3, B. dorei: 7.61 × 10–5)”.:thinking_face:

Adeshile Oluwatosin (18:39:42) (in thread): > Thank you<@UBNSEMS3S>yes we had a lot of back and forth onIf matched on and confounders are same in the study. > Also if the whole heat map should be curated or just significant taxa.

Aleru Divine (19:14:23) (in thread): > Thank you so much<@UBNSEMS3S>:face_holding_back_tears:

Peace Sandy (21:24:57) (in thread): > Done

Kate Rasheed (21:43:06) (in thread): > Thank you so much@Peace Sandy

Kate Rasheed (23:11:12): > Good morning everyone:sparkles:. > > I would appreciate some “fresh eyes” in this study:https://bugsigdb.org/Study_1180Thank you so much as I await feedbacks. - Attachment (BugSigDB): Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy - BugSigDB > BACKGROUND: Person with human immunodeficiency virus type-1 (PWH) are prone to chronic inflammation due to residual viral production, even with antiretroviral therapy (ART), which increases the risk of age-related diseases.

2024-10-22

Adeshile Oluwatosin (01:03:58) (in thread): > Increased abundance: is escherichia shigella not escherichia@Kate Rasheed

Adeshile Oluwatosin (01:06:59) (in thread): > Both baseline and follow up are 46 participants > > Not that each are 46 in number. Check Table 1.

Adeshile Oluwatosin (01:09:53) (in thread): > I also can’t find where they mentioned 0.05 as significant thresholdfor MaAsLin2, kindly point it out

Adeshile Oluwatosin (01:48:08): > Good morning@Svetlana Ugarcina PerovicKindly give me access to the supplementary information of this study:https://www.nature.com/articles/s41598-020-66598-2 - Attachment (Nature): Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study > Scientific Reports - Revealing links between gut microbiome and its fungal community in Type 2 Diabetes Mellitus among Emirati subjects: A pilot study

Kate Rasheed (01:48:30) (in thread): > @Adeshile OluwatosinI used Escherichia in place of Escherichia Shigella since they are both under genus. > > For the participants number, I was really confused as well but I think it’s 46 each cause they were 46participants during the Baseline study and 46 participants also under this follow-up study. > > Yes, I didn’t see too but at the discussion/conclusion point, I saw 0.05 as threshold for diversity. I could be wrong too. Maybe I leave threshold blank.

Adeshile Oluwatosin (01:50:22) (in thread): > Leave threshold blank. > > Table 1 states both are 46 in number. > Specifications on each was not noted.@Kate Rasheed

Adeshile Oluwatosin (01:52:29) (in thread): > Isn’tit better to state it that way it is for escherichia shigella

Kate Rasheed (03:20:01) (in thread): > Okay. Thank you@Adeshile Oluwatosin

Kate Rasheed (03:25:27) (in thread): > Look at this: > > “Four years after the initial gut microbiota analysis in 2018, stool and blood samples were collected and analyzed for gut microbiota in 46 PWH receiving ART treatment (follow-up study, second stool collection timepoint).” > > And this: > “Based on baseline BMI, 46 PWH were classified into two groups: a high (overweight, n = 16) and a low (normal, n = 30) group with a BMI cut-off of 25 kg/m2 for gut microbiota analysis.”@Adeshile OluwatosinThis is why I think it’s 46 for both baseline and followup.

Adeshile Oluwatosin (03:27:03) (in thread): > Maybe we should wait for other opinions@Kate Rasheed

Kate Rasheed (03:30:04) (in thread): > @Adeshile OluwatosinHow about the bacteria having u.b, should I use unclassified enterobacteriaceae or enterobacteriaceae?

Adeshile Oluwatosin (03:30:44) (in thread): > Idon’tget you@Kate Rasheedcan you be more specific

Kate Rasheed (03:32:38) (in thread): > I’ve gotten it now. Thank you sis.

Chinwendu Joy Enyidiegwu (03:33:34) (in thread): > thank you everyone for your contributions and the clarity. it is well appreciated.

Mildred Anashie (04:03:10) (in thread): > I’ll take a look at this also@Kate RasheedWell done on your curation:clap:

Aleru Divine (04:08:40) (in thread): > I’ll take a look too@Kate RasheedGood morning everyone

Mildred Anashie (04:22:26) (in thread): > Hi@Kate RasheedSee this statement“All genus-level differential abundances of bacteria were tested using the Mann–Whitney U test. The significance of all tests was set at p < 0.05 or False Discovery Rate corrected p < 0.05 (two-tailed)”. It seems to carry your statistical test, MHT and Significance threshold.

Svetlana Ugarcina Perovic (04:24:39) (in thread): > @Adeshile Oluwatosinthis is an open access paper and it’s free to download the supplementary material.

Mildred Anashie (04:25:02) (in thread): > For the sample size you are correct, It’s 46 for both group 1 and 0. It’s a Before and After study and they didn’t report loosing any participant to follow-up.

Svetlana Ugarcina Perovic (04:25:14) (in thread): > If you have problem to download it, here you go: - File (PDF): 41598_2020_66598_MOESM1_ESM.pdf - File (Excel Spreadsheet): 41598_2020_66598_MOESM2_ESM (1).xlsx

Kate Rasheed (04:25:21) (in thread): > Yes I saw that too. I was only concerned since it was Mann-whitney test that has that p-value.@Mildred Anashie

Adeshile Oluwatosin (04:26:25) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (04:27:16) (in thread): > And Mann-Whitney is the statistical test not MaAslin2@Kate Rasheed

Aleru Divine (04:27:27) (in thread): > @Kate RasheedYou’re missing Data Transformation > “The analysis did not involve the centered-log ratio or any other method for normalizing or transforming relative bacterial abundance data.” > > It can be left as relative abundance. > > There was MHT correction and P-value is <0.05 > “All genus-level differential abundances of bacteria were tested using the Mann–Whitney U test. The significance of all tests was set atp< 0.05 or False Discovery Rate correctedp< 0.05 (two-tailed).”@Mildred Anashieit said All genus-level differential abundances of bacteria were tested using the Mann–Whitney U test. What do you think? > > I agree that the sample sizes are 46 each:white_check_mark:46 for baseline, 46 for follow-up > > BMI, age, sex, antibiotic use, PPIs, statins, smoking, and alcohol consumption wereconsidered as confounding factorsin the analysis. They were considered but were not controlled for.

Aleru Divine (04:28:51) (in thread): > Yes yes!!@Mildred Anashiefor Mann-Whitney. > > The figure containing the signatures show genus. It’s only right to use Mann-Whitney.

Kate Rasheed (04:29:53) (in thread): > Ohhh. This is well noted.

Mildred Anashie (04:30:18) (in thread): > I think that is the statistical test used for differential abundance, its the only test associated with differential abundance and the study has only one experiment@Aleru Divine

Kate Rasheed (04:32:16) (in thread): > Look at this@Aleru Divine@Mildred Anashie”Comparative analysis of PWH gut microbiota at the genus level between baseline and follow-up based on MaAsLin2 analysis. ”

Aleru Divine (04:32:44) (in thread): > Curate Esherichia-Shigella as seen

Adeshile Oluwatosin (04:33:34) (in thread): > The site is down atm

Mildred Anashie (04:34:40) (in thread): > I think it’s this way on BugSigdbEscherichia/shigella

Aleru Divine (04:35:17) (in thread): > yes it is@Mildred Anashie

Adeshile Oluwatosin (04:35:48) (in thread): > @Mildred AnashieEscherichia/shigella sp

Kate Rasheed (04:38:02) (in thread): > @Aleru DivineRelative abundance wasn’t stated in the paper. Do I still use it?

Adeshile Oluwatosin (04:38:26) (in thread): > Hello@Mildred Anashie@Aleru DivineThis is the description of the source: Figure 1B > Comparative analysis of PWH gut microbiota at the genus level between baseline and follow-up based on MaAsLin2 analysis.

Aleru Divine (04:39:04) (in thread): > I saw this@Kate Rasheedbut I went to the Statistics Section of the paper and saw this > > “Statistical analysis ofmetagenomic profileswas performed using multivariate analysis with linear models (MaAsLin)2” > > and > > “All genus-level differential abundances of bacteria were tested using the Mann–Whitney U test.”

Aleru Divine (04:39:22) (in thread): > We have to take it all into consideration

Aleru Divine (04:41:11) (in thread): > Relative abundance was stated in the paper@Kate Rasheed. Here “The analysis did not involve the centered-log ratio or any other method for normalizing or transformingrelative bacterial abundance data.”

Aleru Divine (04:44:11) (in thread): > @Kate RasheedBMI, age, sex, antibiotic use, PPIs, statins, smoking, and alcohol consumption wereconsidered as confounding factorsin the analysis. They were only considered but were not controlled for. > > BugSigDB asks for “Confounders controlled for”

Kate Rasheed (04:45:42) (in thread): > @Mildred Anashie@Aleru DivineEscherichia/shigella sp. is under species. I don’t think it should be used in place of g.Escherichia Shigella

Kate Rasheed (04:46:45) (in thread): > Thank you very much for the review. Peer review = peer learning:heart:. One fun fact about this community.

Mildred Anashie (04:47:41) (in thread): > So this is what the paper says “Statistical analysis of metagenomic profiles was performed using multivariate analysis with linear models (MaAsLin)2 [60]. Default values of the parameters were employed, including a minimal prevalence of 0.1 and a maximum significance of 0.25, with normalization based on TSS”. > > And this is my opinion@Kate RasheedMaAsLin2 was used for an initial multivariate analysis with specific thresholds and normalization to identify potential associations. And I don’t see a mention of model adjustments for the experiments so I doubt this is the test. (There could be an error in the caption) > > Mann–Whitney U test was used to test the significance of differences in bacterial genera between groups, with results significant at p < 0.05, and corrected for multiple comparisons using FDR. This statement actually mentions differential abundance > > The mention of normalization based on TSS (Total Sum Scaling) implies that data transformation was done and its relative abundance in my opinion because Chloe mentioned something like that for a paper I’m currently working on and TSS turns/transforms raw counts into relative abundances.

Mildred Anashie (04:50:00) (in thread): > You have a point with the genus and species thing@Kate RasheedHave you checked the talk page? > I believeI’veseen this taxa resolved there before but I don’t know the rank though > > I’ll try to check as well

Kate Rasheed (04:50:34) (in thread): > I posted it on the talk page this morning.

Aleru Divine (04:51:25) (in thread): > Thank you@Mildred Anashiefor the detailed explanation.:sweat_smile:

Kate Rasheed (04:52:02) (in thread): > Should be remove MaAsLin2 as the statistal test then?

Aleru Divine (04:52:16) (in thread): > Yes@Kate Rasheed

Adeshile Oluwatosin (04:59:36) (in thread): > You must really shine your eyes:joy_cat:

Kate Rasheed (05:01:10) (in thread): > You get that fresh eyes thing ba@Adeshile Oluwatosin:sweat_smile:

Mildred Anashie (05:03:50) (in thread): > I totally get this@Kate Rasheed@Adeshile Oluwatosin:joy:

Aleru Divine (05:06:16) (in thread): > Omg!!:smiling_face_with_smiling_eyes_and_hand_covering_mouth::sweat_smile:https://community-bioc.slack.com/archives/C04RATV9VCY/p1728402771912289?thread_ts=1728400342.252019&channel=C04RATV9VCY&message_ts=1728402771.912289 - Attachment: Attachment > Hi @Kate Rasheed :sweat_smile: I’ll have a look with fresh eyes :face_with_open_eyes_and_hand_over_mouth: :sweat_smile:

Svetlana Ugarcina Perovic (05:08:31) (in thread): > Could you please share here in the comment link(s) to your social media posting on BugSigDB experience? Thank you!

Kate Rasheed (05:26:41) (in thread): > Noted@Svetlana Ugarcina Perovic

Kate Rasheed (05:50:26) (in thread): > https://www.linkedin.com/posts/kate-rasheed-87a02b1a3_microbiome-bugsigdb-humanmicrobiome-activity-7254428295444779008-FyS4?utm_source=share&utm_medium=member_android@Svetlana Ugarcina Perovic - Attachment (linkedin.com): Kate Rasheed on LinkedIn: #microbiome #bugsigdb #humanmicrobiome > Hello family. I did a thing this month:smiley:. This graduate of English Literature went into researching, reviewing and curating articles on #Microbiome. > > In the…

Yoko C (06:23:19) (in thread): > Hey there, I just wanted to agree with@Mildred Anashieon MaasLin2 being the test with relative abundance as the transformation. The Mann-Whitney test, I think may have been used for the genus comparisons on Figure 3 (which might be curatable??). Also point out that I think Staphylococcus unclassified is pointing to species, and it seems figure 2 is genus related. Same with Enterobacteriaceae, which is a family, I think it needs the unclassified. I also noticed on NCBI that Escherichia/Shigella sp. ’s lineage is up to unclassified Enterobacteriaceae, so I think it is considered a genus and would be correct

Adeshile Oluwatosin (06:27:14) (in thread): > @Yoko Cwhat they speculated was, even though Maaslin2 was stated, > > She should report Mann- Whitney test since it was stated in the study that this was the test done fordifferentialabundance

Yoko C (06:34:10) (in thread): > @Adeshile Oluwatosin, I did see that on the text, but Mann-Whitney only compares two things at a time and the text and the figure mention Maaslin, the figure says: Comparative analysis of PWH gut microbiota at the genus level between baseline and follow-up based on MaAsLin2 analysis. But at some point someone did mention something like two tests can be used, one on the background, or something like that, so maybe that’s the case.

Adeshile Oluwatosin (06:36:05) (in thread): > @Yoko Ci’m actually of the opinion that the test is Maaslin though since it was clearly stated in text and figure like you said. ButI can’toverlook Mann-Whitney test mentioned. > > That’s why I initially asked@Kate Rasheedto ask for other opinions

PATIENCE ONAH (07:47:02) (in thread): > Noted. Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (07:59:28) (in thread): > @Cynthia IwuohaHere!

Cynthia Iwuoha (08:25:12) (in thread): > Thank you @Tosin

Cynthia Iwuoha (08:26:22) (in thread): > Thank you for the update @Svetlana_up

Kate Rasheed (09:26:31): > @Svetlana Ugarcina PerovicPlease can you add Myostatin to the disease condition. Here is the EFO: OMIT:0026289

Kate Rasheed (09:33:07) (in thread): > I have seen it as Myostatin-related muscle hypertrophy

Adeshile Oluwatosin (09:53:20): > @Svetlana Ugarcina Perovickindly deletehttps://bugsigdb.org/Study_1174Thank you - Attachment (BugSigDB): - BugSigDB > .

Mildred Anashie (09:53:25) (in thread): > Hi@Kate RasheedDo you mean Myostatin-related muscle hypertropy is available on BugSigdb?

Kate Rasheed (09:54:02) (in thread): > Yes@Mildred Anashie

Mildred Anashie (09:56:40) (in thread): > So I think with conditions you would have to search for the closest term to the condition in the article > > Could you share the article?

Kate Rasheed (09:58:15) (in thread): > The condition is Myostatin and I later discovered in the article that it is related to muscle hypertrophy. That’s why I said I’ve seen the condition as Myostatin-related muscle hypertrophy

Mildred Anashie (09:58:45) (in thread): > Okay > > I understand you now

Aleru Divine (10:01:51) (in thread): > https://www.linkedin.com/posts/aleru-divine_bugsigdb-microbiomestudycuration-activity-7254474371606478850-XGYa?utm_source=share&utm_medium=member_ios@Svetlana Ugarcina PerovicI shared a post on LinkedIn:hugging_face: - Attachment (linkedin.com): Aleru Divine on LinkedIn: #bugsigdb #microbiomestudycuration > I am super excited to celebrate over one year of contributing to the Bioconductor project, #BugSigDB. It has been incredibly rewarding to contribute to open…

Kate Rasheed (10:27:41): > Good afternoon everyone:hugging_face:. I’ve come again. I need your opinions on figure 2e and f. I believe they are curatable cause it’s looking at differential genera and species between GEF and WTF. > > However, I want to know what you think about it should I be wrong about my thoughts. > > Here is the article:https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02687-8 - Attachment (BioMed Central): Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep - BMC Microbiology

Samuel Nnanna (10:29:47) (in thread): > https://www.linkedin.com/posts/samuel-nnanna-7479b9270_bugsigdb-activity-7254498915243188225-toZd?utm_source=share&utm_medium=member_desktop - Attachment (linkedin.com): Samuel Nnanna on LinkedIn: #bugsigdb > As a Biochemistry/Microbiology graduate and a DevOps engineer, contributing to the Bioconductor open-source project, #BugSigDB over the past three weeks has…

Aleru Divine (10:33:11) (in thread): > I believe the figures are curatable@Kate RasheedThe descriptions indicate differential abundance.
> > “(E )The significantly different genera between the GEF and WTF. > > (F) The significantly different species between the GEF and WTF. (0.01 < P ≤ 0.05 , 0.001 < P ≤ 0.01 ). > > *The horizontal lines with the asterisks indicate that all signatures are significant. I think you’re on the right path.

Kate Rasheed (10:33:36) (in thread): > Thank you@Aleru Divine

Adeshile Oluwatosin (10:40:53): > @Svetlana Ugarcina Perovickindly deletehttps://bugsigdb.org/Study_1107/experiment_1/signature_2 - Attachment (BugSigDB): Feeding-Related Gut Microbial Composition Associates With Peripheral T-Cell Activation and Mucosal Gene Expression in African Infants - BugSigDB > BACKGROUND: Exclusive breastfeeding reduces the rate of postnatal human immunodeficiency virus (HIV) transmission compared to nonexclusive breastfeeding; however, the mechanisms of this protection are unknown.

Adeshile Oluwatosin (10:40:53) (in thread): > Okay, let me check:eyes:

Adeshile Oluwatosin (10:41:58) (in thread): > Definitely curatable:+1:The significantly different genera between the GEF and WTF. F The significantly different species between the GEF and WTF. (0.01 < P ≤ 0.05 , 0.001 < P ≤ 0.01 *)

Agatha (10:44:59): > @Svetlana Ugarcina Perovic, please experiment 1 signature 2 is not reflecting after saving the page. Is it normal?

Kate Rasheed (10:46:05) (in thread): > @Aleru Divine@Adeshile OluwatosinA follow-up question. Will the signatures with **** be curated as a different experiment since it has a different p-value threshold?

Aleru Divine (10:47:53) (in thread): > @Agathathis is a general problem.:pleading_face:You can access your pages using this format provided by@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&cid=C04RATV9VCY - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Adeshile Oluwatosin (10:47:54) (in thread): > No@Kate Rasheed

Aleru Divine (10:48:33) (in thread): > Also do this, it works sometimes.https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Kate Rasheed (10:50:19) (in thread): > @AgathaIf you go to contributions, you would see the record of all you’ve done. You can click on it to ascertain it is saved.

Kate Rasheed (10:51:11) (in thread): > What does the two asterisk signify please@Adeshile Oluwatosin

Yoko C (10:51:17) (in thread): > @Kate Rasheed, that is the level of significance

Aleru Divine (10:52:08) (in thread): > 2 asterisks signify p<0.01and p<0.001@Kate Rasheed

Yoko C (10:52:43) (in thread): > *means it is below 0.05, so significant. **mean it is below 0.01, so very significant

Adeshile Oluwatosin (10:53:14) (in thread): > @Yoko C@Kate Rasheedlevel of significance: 0.05Result: > At genus level, the abundance of Flavonifractor, Subdoligranulum, Ruthenibacterium, Agathobaculum, Anaerotignum, Oribacterium and Lactobacillus were significantly increased in the MSTN-edited sheep (P < 0.05). Further analysis of functional differences was found that the carotenoid biosynthesis was significantly increased and the peroxisome, apoptosis, ferroptosis, N-glycan biosynthesis, thermogenesis, and adipocytokines pathways were decreased in the MSTN-edited sheep (P < 0.05).

Kate Rasheed (10:54:48) (in thread): > Thank you so much. I understand perfectly now.

Agatha (11:01:02) (in thread): > @Kate Rasheed, contributions?

Agatha (11:01:15) (in thread): > Where?@Kate Rasheed

Kate Rasheed (11:01:31) (in thread): > Yes please. Let me send a graphic display

Agatha (11:01:54) (in thread): > Ok. Thank you

Kate Rasheed (11:03:00) (in thread): > If you are using a laptop, locate your profile icon, click on it, you’ll see contributions.

Kate Rasheed (11:04:03) (in thread): > If you are using a phone, click on the dash at the right hand, then locate the last icon. > > PS. Ensure your phone is on desktop site view.@Agatha - File (JPEG): Screenshot_20241022-160150.jpg - File (JPEG): Screenshot_20241022-160158.jpg - File (JPEG): Screenshot_20241022-160204.jpg

Agatha (11:08:27) (in thread): > Thank you@Kate Rasheed

Kate Rasheed (11:08:53) (in thread): > Have you seen it now?@Agatha

Agatha (11:09:55): > @Svetlana Ugarcina Perovic, please delete signature 2 and 3 in experiment 1https://bugsigdb.org/Study_1152 - Attachment (BugSigDB): Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection - BugSigDB > BACKGROUND: Despite effective antiretroviral therapy (ART), patients with chronic human immunodeficiency virus (HIV) infection have increased microbial translocation and systemic inflammation.Alterations in the intestinal microbiota may play a role in microbial translocation and inflammation.

Svetlana Ugarcina Perovic (11:36:51) (in thread): > Deleted.

Svetlana Ugarcina Perovic (11:38:17) (in thread): > https://bugsigdb.org/Study_1107/Experiment_1/Signature_2deleted > > Note: use capital E and capital S when you format this link

Svetlana Ugarcina Perovic (11:40:02) (in thread): > Deleted. > also Experiment_1/Signature_1 deleted.

Adeshile Oluwatosin (11:40:04) (in thread): > Okay.Noted@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (11:40:22) (in thread): > Noted

Chris Awoke (11:45:42) (in thread): > https://www.linkedin.com/posts/chrisawoke_bugsigdb-bugsigdb-outreachycontributionphas[…]837321359364-qWoH?utm_source=share&utm_medium=member_desktop - Attachment (linkedin.com): Chris Awoke on LinkedIn: #bugsigdb #bugsigdb #outreachycontributionphase #bugsigdb… > I'm excited to reflect on my journey contributing to #BugSigDB, part of the Bioconductor ecosystem, during the Outreachy contribution phase! > > What initially…

Aleru Divine (11:53:48) (in thread): > You can also check your latest changes by clicking on recent changes

Agatha (11:56:45) (in thread): > Yes@Kate Rasheed, thank you

Mildred Anashie (12:12:19) (in thread): > @Rahila-meI believe you are Rahila and you curated thisarticlewhich I found on the pages with missing NCBI. I was able to resolve one of the taxa for the signatures mentioned above, Is it okay to effect the change? - Attachment (BugSigDB): Differences in salivary microbiome among children with tonsillar hypertrophy and/or adenoid hypertrophy - BugSigDB > Children diagnosed with severe tonsillar hypertrophy display discernible craniofacial features distinct from those with adenoid hypertrophy, prompting illuminating considerations regarding microbiota regulation in this non-inflammatory condition.

Precious Orakwe (12:21:51): > Good day@Svetlana Ugarcina PerovicI and@Chinwendu Joy Enyidiegwuare done with our corrections. > > Can I start working on missing NCBI?

Rahila-me (12:22:03) (in thread): > @Mildred AnashiePlease go ahead. Thank you

Mildred Anashie (12:23:00) (in thread): > Thank you@Rahila-meI’llget to it now

Rahila-me (12:24:17) (in thread): > @Precious OrakweYes you can but here is a message@Svetlana Ugarcina Perovicleft. You just have to adhere to it:please do note that a curator not assigned to the task/curation should communicate to the original curator(s) first, before making any changes. Please report here changes, so that the original curator(s) could decide to accept it or not. This is a common open-source practice.

Chinwendu Joy Enyidiegwu (12:40:41) (in thread): > @Svetlana Ugarcina Perovicwe are requesting for review.https://bugsigdb.org/Study_1104 - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > The paternal environment prior to conception has been demonstrated to influence offspring physiology and behavior, with the sperm epigenome (including noncoding RNAs) proposed as a potential facilitator of non-genetic inheritance.

Tino (13:01:21): > @Rahila-methank you, I added the pmid as you suggested and my study is now reflecting on the BugSigDb

Tino (13:05:53): > @Rahila-meit turns out the article id is not my pmid for my study, please help me identify this pmid my study

Rahila-me (13:09:49) (in thread): > @Tinohere:https://bugsigdb.org/Study_1170I have added it the pmid now shows in bugsigdb - Attachment (BugSigDB): Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study - BugSigDB > OBJECTIVES: Functional prognosis is potentially correlated with gut microbiota alterations following the dysregulation of the gut-microbiota-brain axis after stroke.

Rahila-me (13:11:45) (in thread): > when next you are curating a study, you go here:https://pubmed.ncbi.nlm.nih.gov/And paste the title of your article, then you copy the pmid and add after inputting your study design. > every other features will automatically be filled out for you - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 37 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Rahila-me (13:12:10) (in thread): > If any issue i am open for collboration. Thank you

Tino (13:13:31) (in thread): > @Rahila-methank you are a life saver:relaxed:

Rahila-me (13:13:44) (in thread): > urw

Mildred Anashie (13:59:57) (in thread): > https://www.linkedin.com/posts/anashie-mildred-98b0721a4_bugsigdb-mvif-activity-7254550433212338178-IJfo?utm_source=share&utm_medium=member_ios@Svetlana Ugarcina PerovicI shared a post on LinkedIn:blush: - Attachment (linkedin.com): Anashie Mildred on LinkedIn: #bugsigdb #mvif > Today, I want to share a story about the incredible impact of community, open source, and building connections. > > It’s been over a year since I joined the…

Svetlana Ugarcina Perovic (15:18:20) (in thread): > This should be communicated inhttps://github.com/waldronlab/BugSigDBcuration/issues/496 - Attachment: #496 Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice > Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Bethany A. Masson – Brain, Behavior, and Immunity > > https://www.sciencedirect.com/science/article/pii/S088915912400624X
> 1-s2.0-S088915912400624X-main.pdf > > Supplementary material: > > FigS1 FigS2 FigS3_4 FigS5 FigS6 FigS7

Svetlana Ugarcina Perovic (15:19:02) (in thread): > Noted in corresponding GitHub issue.

Svetlana Ugarcina Perovic (16:15:22) (in thread): > Unfortunately, this curation is not fully corrected: > > - condition should refer to “The experimental condition / phenotype studied” > - antibiotic exclusion here is not applied > - alpha diversity: “Antibiotic-treated male mice had significantly lower number of bacterial species in the fecal microbiome compared to control mice, indicated by the Shannon α-diversity index (P=0.0464, Fig. 1G)](https://www.sciencedirect.com/science/article/pii/S088915912400624X#f0005)G)).” > - statistical test and its details should be revised > > Please ask your colleagues for help in Slack.

Inimfon Ebong (16:21:03): > @Svetlana Ugarcina PerovicHello, > I had a health emergency where I had to be with my mom at the hospital, Just got home this evening to see that the paper has been assigned to others. Do I not work on it anymore? or is it now a collaboration? > > what should i do?

Svetlana Ugarcina Perovic (16:22:45) (in thread): > I immidiately responded to your message in the GitHub issue. Please seehttps://github.com/waldronlab/BugSigDBcuration/issues/464 - Attachment: #464 Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes > Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes - Chuhong Tan – Journal of Parenteral and Enteral Nutrition > > https://aspenjournals.onlinelibrary.wiley.com/doi/10.1002/jpen.1861

Inimfon Ebong (16:23:36) (in thread): > ok I have just seen it thanks

Svetlana Ugarcina Perovic (16:24:42) (in thread): > @Inimfon Ebongyou are the main curator with support from@Mildred Anashieand@Rahila-me.

Mildred Anashie (17:14:30) (in thread): > Hi@Inimfon EbongTrust everything is okay now, just as@Svetlana Ugarcina Perovicsaid you are the main curator > > Feel free to reach out if you experience any blockers,I’mavailable to help and I thinkit’ssame for@Rahila-meIn the main timeI’llgo through the study as well and share my opinion with you, if this is okay

Rahila-me (23:16:00) (in thread): > Hello@Inimfon EbongI hope your mum is better now. Welcome back. You are still the one and only original curator just as@Svetlana Ugarcina Perovicpointed out in git. I and@Mildred Anashieare here just to help out in case you need it. More like a support system. Good luck as you add the signatures and finalize your curation. I could do a peer review with you before you submit your final review of course only with your permission

2024-10-23

inyang john (00:27:08) (in thread): > https://www.linkedin.com/posts/pharm-inyang-john_stepping-into-my-one-month-contribution-stage-activity-7254708899033849856-Dl5V?utm_source=share&utm_medium=member_ios - Attachment (linkedin.com): inyang john on LinkedIn: Stepping into my one-month contribution stage with Outreachy felt like a… > Stepping into my one-month contribution stage with Outreachy felt like a leap into the unknown. I was entering the world of microbiome study curation, using a…

Kate Rasheed (02:57:45): > Good morning everyone:sparkles:. I have come with a new episode of fresh eyes:smile:. > > From this study:https://bugsigdb.org/Study_1182, two statistical tests were used for differential abundance and they brought out different microbes. > > According to the curation policy, if there are two statistical tests with different microbes, curate as separate experiments, hence, I did the same. > > I would like to know your thoughts on this study too@Mildred AnashiePS. I don’t know if all the signatures on this study would show from your end. - Attachment (BugSigDB): - BugSigDB > .

Svetlana Ugarcina Perovic (03:03:20) (in thread): > “a support system”! Love it!Keep up the good team work.

Samuel Nnanna (03:08:00) (in thread): > Hi@Kate Rasheed, I have a similar situation in my study. Did you curate as different experiments?

Inimfon Ebong (03:09:55) (in thread): > Good morning@Rahila-me@Mildred AnashieI don’t know if we can create a group or something to share ideas, but basically before I went MIA I had listed out all the signatures for the 4 experiments. Since I’m doing a one vs many I’m confused if my one should be allocated to group 1 or 0, I think its 1 because of the way the signature page is set up but I’m not quite sure

Mildred Anashie (03:22:31) (in thread): > Yes I believe we can do that@Inimfon EbongI’llcreate one now, it will be helpful

Mildred Anashie (03:23:54) (in thread): > Good morning@Kate RasheedI’llgo through the study now@Samuel Nnannaif it is different statistical tests then yes, that would be a different experiment

Kate Rasheed (03:24:40) (in thread): > Yes@Samuel Nnanna. I curated as different experiments.

Samuel Nnanna (03:24:42) (in thread): > Ok thanks@Mildred Anashie

Rahila-me (03:25:27) (in thread): > @Mildred Anashie@Inimfon EbongI just said hi to the group. Let’s continue the discussion from the group.

inyang john (04:00:05) (in thread): > @Inimfon EbongSo sorry. Hope everything is fine now ?

Inimfon Ebong (04:14:50) (in thread): > @inyang johnit’s getting better so we are grateful

Tino (04:16:01): > Morning everyone, > I need some clarification when adding taxon, some names given in the study are the original name (basionmy) so am I on track if I take the taxon id of the new name given on the NCBI taxon browser? > What if a name cannot be identified on both the BugSigDb and NCBI database, is it okay to omit it altogether?

Chinwendu Joy Enyidiegwu (04:17:47) (in thread): > Thank you@Svetlana Ugarcina Perovic

Tino (04:18:28) (in thread): > @Inimfon EbongI hope your mom gets well soon!

Aleru Divine (04:18:36) (in thread): > Hi@Tinoif the name can’t be found on BugSigDB and NCBI or UNIPROT, you can check if it has been resolved in this pagehttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_IDIf you still can’t find it, you’ll curate as reported in the paper.Pleasedon’tomit - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Tino (04:19:40) (in thread): > @Aleru Divinethanks!

Aleru Divine (04:28:35) (in thread): > @Kate Rasheedyou were right to curate as seperated experiments for each statistical test.Well done:+1:I’lldo a peer review of the study too.

Adeshile Oluwatosin (04:36:32) (in thread): > @Tinonot all missing NCBI in the discussion page is correct > > Please make further findings on google as well.

Tino (04:37:53) (in thread): > @Adeshile Oluwatosinnoted and thanks

Aleru Divine (04:45:06) (in thread): > Wow, Iwasn’taware of that.Thanks@Adeshile Oluwatosin

Adeshile Oluwatosin (04:48:09) (in thread): > That is why permission is neededbefore edit can be done. > I guess some peopledidn’task for permission before dropping certain details on the discussion page.@Aleru Divine

Samuel Nnanna (04:52:22): > Hello everyone, in my study, i found a signature “clostridium sensu stricto 1” and during my research i found this “Clostridium sensu stricto are grouped around the type species Clostridium butyricum and belong to the Clostridium cluster 1 within the Clostridiaceae family [59]. Clostridium sensu stricto 1 contains C. perfringens and other real Clostridium species.” > > any ideas on how i should curate this signature?

Mildred Anashie (04:55:38) (in thread): > Hi@Samuel NnannaYou can check the discussion page, Clostridium senso stricto 1 has been resolved there as Clostridium genus with ID 1485

Aleru Divine (04:56:26) (in thread): > Hi@Samuel Nnanna, Clostridium sensu strictohasbeen resolved as the true Clostridium genus. > > Check this thread.https://community-bioc.slack.com/archives/C04RATV9VCY/p1711280497983449 - Attachment: Attachment > Hi everyone @Svetlana Ugarcina Perovic @C. Mirzayi (please do not tag this account) @Chioma Onyido @Peace Sandy @Esther Afuape > I found a study with a missing NCBI ID clostridium_sensu_scrito_1. After a detective search I found numerous journals refer to the taxa as the true clostridim genus, including the journal below > https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.001792-0 > May I proceed to edit the taxa as Clostridim genus with an NCBI ID of 1485 > Link to the study: > https://bugsigdb.org/Study_518/Experiment_1/Signature_1

Samuel Nnanna (04:57:17) (in thread): > Okay, seen it. Thanks@Aleru Divineand@Mildred Anashie

Adeshile Oluwatosin (04:59:13) (in thread): > @Samuel Nnannaconfirm from Google as well:relieved:

Aleru Divine (05:02:29) (in thread): > This article from the thread I shared confirms itand this has also been confirmed by a co-mentor@Adeshile Oluwatosinhttps://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.001792-0 - Attachment (microbiologyresearch.org): Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I) > The species of Clostridium comprise a very heterogeneous assemblage of bacteria that do not form a phylogenetically coherent group. It has been proposed previously that only a subset of the species of Clostridium that form a distinct cluster in the 16S rRNA tree (cluster I) should be regarded as the true representatives of the genus Clostridium (i.e. Clostridium > sensu stricto). However, this cluster is presently defined only in phylogenetic terms, and no biochemical, molecular or phenotypic characteristic is known that is unique to species from this cluster. We report here phylogenomic and comparative analyses based on sequenced clostridial genomes in an attempt to bridge this gap and to clarify the evolutionary relationships among species of clostridia. In phylogenetic trees for species of clostridia based on concatenated sequences for 37 highly conserved proteins, the species of Clostridium cluster I formed a strongly supported clade that was separated from all other clostridia by a long branch. Several other Clostridium species that are not part of this cluster grouped reliably with other species of clostridia in a number of well-resolved clades. Our comparative genomic analyses have identified three conserved indels in three highly conserved proteins (a 4 aa insert in DNA gyrase A, a 1 aa deletion in ATP synthase beta subunit and a 1 aa insert in ribosomal protein S2) that are unique to the species of Clostridium cluster I and are not found in any other bacteria. blastp searches on various proteins in the genomes of Clostridium tetani E88 and Clostridium perfringens SM101 have also identified more than 10 proteins that are found uniquely in the cluster I species. These results provide evidence that the species of Clostridium cluster I not only are phylogenetically distinct but also share many unique molecular characteristics. These newly identified molecular markers provide useful tools to define and circumscribe the genus Clostridium > sensu stricto in more definitive terms. We have also identified a 7–9 aa conserved insert in the enzyme phosphoglycerate dehydrogenase that is uniquely found in the Clostridium thermocellum, Thermoanaerobacter pseudethanolicus, Thermoanaerobacter tengcogensis and Caldicellulosiruptor saccharolyticus homologues, and is absent from all other bacteria. These species form a well-defined clade in the phylogenetic trees and this indel provides a potential molecular marker for this clostridial cluster.

Adeshile Oluwatosin (05:02:47) (in thread): > Noted then@Aleru Divine

Mary Agekameh (05:04:19): > Hello@Svetlana Ugarcina PerovicKindly delete signature 3 & 4 under experiment 2 from this study > > Thank youhttps://bugsigdb.org/Study_1149 - Attachment (BugSigDB): Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes - BugSigDB > While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging.

Svetlana Ugarcina Perovic (05:10:28) (in thread): > deleted.

Mary Agekameh (05:11:00) (in thread): > Thank you!

Aleru Divine (05:29:59) (in thread): > A few observations from my review > > Shannon index for experiment 1 & 2 is unchanged (n.s) and Simpson is increased for GE. > > Shannon decreased for GE in experiment 3 and 4 and Simpson increased for GE > > There was MHT correction in the study— see “Data analysis and FDR correction of thep-values were performed using the R package (Version 3.3.3).”

Samuel Nnanna (05:39:07): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>In my paper i came across a signature “ruminococcaceae UCG 014” which was resolved touncultured Oscillospiraceae bacterium. > Now i encountered another signature “lachnospiraceae UCG 001” which hasn’t been resolved and after carefully going through how the latter was resolved, i think “lachnospiraceae UCG 001” could be resolved to “uncultured lachnospiraceae bacterium” with tax.ID 297314 > > right above this link (https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID#changed_Ruminococcaceae_UCG-014_to_uncultured_Oscillospiraceae_bacterium), in the “how to resolve section” was how I came up with the idea. > > I might be wrong but i’d like to hear your thoughts. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Adeshile Oluwatosin (05:43:59) (in thread): > Hi@Samuel NnannaLachnospiraceae UCG 001 and uncultured Lachnospiraceae bacterium(species)are different > > Report as it is

Adeshile Oluwatosin (05:44:38) (in thread): > Still checking

Samuel Nnanna (05:47:37) (in thread): > Yeah@Adeshile Oluwatosin. I reported as it was in the paper since it’s not been resolved yet…. but i’m thinking it could be resolved to that following how others were resolved.

Svetlana Ugarcina Perovic (05:55:08): > Just to provide context fortaxonname_UCG_number: > > These were clusters of microbiome sequence data that initially lacked precise taxonomic definitions. They have now been assigned improved taxonomic classifications and names that better reflect their microbial composition:either as specific strain names or as designated uncultured groups (UCG) with numbers if there are more potential strains. This refined taxonomic framework more accurately captures microbial diversity and enables more precise identification of microorganisms in microbiome samples. > > If you search our database with “UCG” you will see a lot of relevant UCG signatures:https://bugsigdb.org/w/index.php?title=+Special%3ASearch&search=UCG&go=Go - Attachment (BugSigDB): Special:Search

Chinwendu Joy Enyidiegwu (05:57:16): > hello everyone:wave:, i need your help.:pray:i am having issues identifying the condition and the statistical analysis for this study. > link and pdf to the study:https://bugsigdb.org/Study_1104@Aleru Divine@Adeshile Oluwatosin@Mildred Anashie@Adeniji Agbolade@Precious Orakwei would appreciate a review. - Attachment (BugSigDB): Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice - BugSigDB > The paternal environment prior to conception has been demonstrated to influence offspring physiology and behavior, with the sperm epigenome (including noncoding RNAs) proposed as a potential facilitator of non-genetic inheritance. - File (PDF): 1-s2.0-S088915912400624X-main.pdf

Adeshile Oluwatosin (05:57:47) (in thread): > Thank you for this@Svetlana Ugarcina Perovic

Aleru Divine (05:57:58) (in thread): > Alright@Chinwendu Joy EnyidiegwuI’llhave a Quick Look

Svetlana Ugarcina Perovic (05:58:52): > Speaking of strains, check out this post:https://community-bioc.slack.com/archives/C04RATV9VCY/p1714564446077739 - Attachment: Attachment > Reading this paper https://elifesciences.org/articles/33953 and wanted to share with you another example (beside this one https://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639) of the fact that strains of the same bacterial species can differ in gene content: > the metabolism of the drug digoxin in vivo by the bacterium Eggerthella lenta requires a gene that is present in only certain strains of E. lenta. > > and be part of the several BugSigDB study signatures of the same experiment.

Adeshile Oluwatosin (05:58:59) (in thread): > Check the post below@Samuel Nnanna

Mildred Anashie (05:59:00) (in thread): > Okay@Chinwendu Joy EnyidiegwuI’lltake take a look at this now

Adeshile Oluwatosin (05:59:19) (in thread): > I will have a look@Chinwendu Joy Enyidiegwu

Adeshile Oluwatosin (05:59:48) (in thread): > Thank you

Samuel Nnanna (06:04:15) (in thread): > Right@Svetlana Ugarcina Perovic. Thank you

Rahila-me (06:06:41) (in thread): > Noted

Rahila-me (06:07:39) (in thread): > Okay@Chinwendu Joy Enyidiegwuwill take a look and revert back

Cynthia Iwuoha (06:07:51) (in thread): > Thank you

Aleru Divine (06:16:45) (in thread): > Oh I’ve reviewed this before.@Chinwendu Joy Enyidiegwuand I made a suggestion earlier. > > What I understand is they tried to study howdepleting the paternal gut microbiome(they usedantibioticsfor the depletion) in mice affects sperm small RNAs and the offspring’s physiology and behavior.The experimental condition in this case isgut microbiome depletion through antibiotics. > > So, I’d suggest usingresponse to antibiotics(available on BugSigDB) as it is the closest related term.

Aleru Divine (06:19:02) (in thread): > Thanks for the clarification@Svetlana Ugarcina Perovic:raised_hands:

Chinwendu Joy Enyidiegwu (06:24:53) (in thread): > thank you@Aleru Divineplease i would appreciate a quick review on the statistical analysis too especially the test

Mildred Anashie (06:33:57) (in thread): > @Chinwendu Joy EnyidiegwuThis is what I see for where you curated your signatures from Table 1 “Taking into consideration the cohort effect, we performed regression analysis to determine differentially abundant taxa between the treatment groups. We found 15 taxa to be significantly higher in the control group compared to the antibiotic-treated male mice (Table 1).’ I also see this under statistical analysis* “For analysis of F0 single timepoints, linear mixed models *(LMMs) were used with ‘treatment’ as a fixed factor and ‘cohort’ as a random factor. For repeated measures, ‘time’ was added as a fixed factor and ‘mouse ID’ added as a random factor. For analysis of F1 and F2 single timepoints, LMMs were used with ‘paternal treatment’ and ‘sex’ as fixed factors, and ‘litter’ and ‘cohort’ as random factors.”I believe your statistical test is linear regression.:thinking_face:

Aleru Divine (06:35:10) (in thread): > As for the statistical test, I’m a bit confused because I was leaning towards PERMANOVA, but we had this discussion. > > Having a look at it again, see thatMaAsLin2, a generalized regression model adjusted by false discovery rate (FDR), was used to determine themultivariable association between the identified taxa counts and antibiotic/control treatment, adjusting for experimental factors including sex and cohort (51). P-values adjusted by FDR <0.05 were considered significant.” > > So I think that while PERMANOVA is used for the group differences, MaAsLin2 was the test for differential abundance in this case because it was specifically used to determine the multivariable association between theidentified taxa counts and antibiotic/control treatment,

Aleru Divine (06:39:38) (in thread): > @Mildred AnashieI think this further confirmsMaAsLin2. > > The excerpt you shared talks about how they performed aregression analysisto determine differentially abundant taxa between the treatment groups. > > The paper also said “MaAsLin2, ageneralized regression modeladjusted by false discovery rate (FDR), was used to determine the multivariable association between the identified taxa counts and antibiotic/control treatment” > > MaAsLin2 was used for the regression analysis. > > I believe it isMaAsLin2.@Mildred Anashie@Chinwendu Joy Enyidiegwu

Mildred Anashie (06:40:56) (in thread): > So@Aleru DivineI’m thinking you are right, it might be MaAslin2 > > I didn’t see the part that mentioned MaAslin2that’s why I was leaning towards linear regressionbut with this, I can confirm that they used it for the regression analysis

Adeshile Oluwatosin (06:42:13) (in thread): > Yeah. It’s Maaslin2 - File (PNG): IMG_1832

Mildred Anashie (06:42:57) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

Aleru Divine (06:42:59) (in thread): > Thank you@Mildred AnashieIt was the excerpt you shared that kind of confirmed it. I was still a bit shaky:sweat_smile:Thank you!@Chinwendu Joy EnyidiegwuI believe this is sorted:pray:

Mildred Anashie (06:45:24) (in thread): > Do you have the supplementals for this@Chinwendu Joy EnyidiegwuI see a mention of Richness and Evenness as unchanged but Supplementary Figure 1 was cited and I noticed youdidn’tcurate that

Mildred Anashie (06:45:51) (in thread): > Thank you also@Aleru DivineTeam work:raised_hands:

Adeshile Oluwatosin (06:46:42) (in thread): > I was about to say this@Mildred Anashie:joy_cat:

Adeshile Oluwatosin (06:47:02) (in thread): > Team work:hugging_face::relieved:

Aleru Divine (06:52:17) (in thread): > See supplementary material@Mildred Anashie

Aleru Divine (06:52:21) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/496 - Attachment: #496 Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice > Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Bethany A. Masson – Brain, Behavior, and Immunity > > https://www.sciencedirect.com/science/article/pii/S088915912400624X
> 1-s2.0-S088915912400624X-main.pdf > > Supplementary material: > > FigS1 FigS2 FigS3_4 FigS5 FigS6 FigS7

Chinwendu Joy Enyidiegwu (06:53:31) (in thread): > @Mildred Anashiehere it is. > the repo has a link to the supplementary,https://github.com/waldronlab/BugSigDBcuration/issues/496 - Attachment: #496 Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice > Depletion of the paternal gut microbiome alters sperm small RNAs and impacts offspring physiology and behavior in mice – Bethany A. Masson – Brain, Behavior, and Immunity > > https://www.sciencedirect.com/science/article/pii/S088915912400624X
> 1-s2.0-S088915912400624X-main.pdf > > Supplementary material: > > FigS1 FigS2 FigS3_4 FigS5 FigS6 FigS7

Mildred Anashie (06:53:31) (in thread): > I forgot, we’ve all reviewed this before@Aleru Divine

Mildred Anashie (06:55:32) (in thread): > Just Shannon was reported even in the Supplementals@Chinwendu Joy Enyidiegwu, So i think what you have done in the Alpha diversity section is okay

Aleru Divine (06:57:48) (in thread): > Yes we have@Mildred Anashieit was the one that was always redirecting:sweat_smile:

Chinwendu Joy Enyidiegwu (06:57:52) (in thread): > @Aleru Divine@Mildred Anashiethank you everyone for your input. very much appreciated > in the study, is there an antibiotics exclusion ?

Mildred Anashie (07:00:01) (in thread): > @Chinwendu Joy EnyidiegwuI didn’t see a mention of antibiotic exclusion. Also antibiotic is the treatment administered so I doubt it can be an exclusion criteria in this study

Rahila-me (07:00:55) (in thread): > @Chinwendu Joy EnyidiegwuI did not see…it was not mentioned please leave it blank

Aleru Divine (07:01:02) (in thread): > Me neither@Chinwendu Joy Enyidiegwuno antibiotics exclusion.

Mildred Anashie (07:09:17) (in thread): > @Kate RasheedWell done on this curation. I am in agreement with@Aleru Divineobservations, For the comparisons between GEM and WTM Shannon is decreased, Simpson is increased, Chao is unchanged and for the comparisons between GEF and WTF Shannon is unchanged, Simpson id increased and Chao is unchanged.

Chinwendu Joy Enyidiegwu (07:10:22) (in thread): > thank you all for your relentless effort:rose:

Mildred Anashie (07:10:50) (in thread): > Also MHT is yes.

Kate Rasheed (07:15:05) (in thread): > Thank you so much for the observation. For the MHT, I’m really confused. I saw that part of data analysis…; however, nothing like q-value, adjusted p-value or FDR was stated all through the paper. > > Also, from the curation policy, LEfSe doesn’t correct for MHT by default. > > What do you think?@Mildred Anashie@Aleru Divine

Aleru Divine (07:16:26) (in thread): > :thinking_face:

Yoko C (07:17:21) (in thread): > Hi, I didn’t read the full study so maybe I am wrong, but for the ANOSIM test, I don’t think it was used for differential taxa, I think it was used for beta diversity, function and metabolic activity.

Kate Rasheed (07:19:14) (in thread): > Wow. Thank you for this@Svetlana Ugarcina Perovic

Yoko C (07:21:46) (in thread): > From the graph it looks like mann-whitney or maybe t-test?

Aleru Divine (07:25:06) (in thread): > Omg! That’s absolutely correct@Yoko C@Kate Rasheed“The differences in the bacterial taxa between different groups were assessed using Analysis of similarity (ANOSIM) of Bray–Curtis distances.”ANOSIM was used for beta-diversity.

Mildred Anashie (07:26:42) (in thread): > Thank you@Yoko CI think its ‘Wilcoxon rank-sum’. Read this ’We compared the difference of the abundance of gut microbiota between the GEF and WTF, as well as the GEM and WTM. We observed theMSTNediting did not change the dominant phyla of sheep, the top 7 phyla were Firmicutes, Bacteroidota, Spirochaetes, Verrucomicrobia, Proteobacteria, Euryarchaeota and Lentisphaerae (Supplementary Fig. 2B). However, the Wilcoxon rank-sum test revealed that compared to the WTF, the abundance of……….And the rest of the paragraph is talking about Fig 2 and S2. So I believe the comparisons that were not done with lefse were done with Wilcoxon which is Mann whitney (Wilcoxon) on BugSigdb

Aleru Divine (07:27:33) (in thread): > The statistical test was Wilcoxon(Mann-Whitney) > Thank you@Yoko C

Mildred Anashie (07:28:22) (in thread): > @Kate RasheedIf you believe MHT is No then you can go with that, but I have curated an article with MHT yes and LefSe as the statistical test and It wasn’t wrong. So there are exceptions to rules I believe.

Aleru Divine (07:30:21) (in thread): > I think so too@Mildred Anashie.And it was stated that FDR correction was performed.This studydidn’tuse only LEfSe.So I think that also counts.I would curate MHT as YES too@Kate Rasheed

Tino (08:13:15) (in thread): > Hello everyone,@Svetlana Ugarcina Perovicmentioned that new studies may not show all data and that can be fixed by clicking “…” and the “Refresh”. I did this but still the last signature I added is not showing up on the overall study page but when I manually enter using the format she gave us, my signature shows up. Can I go ahead and flag my study as ready for review regardless?

Kate Rasheed (08:14:15) (in thread): > Yes@Tino. This happened to me yesterday but my signatures are all showing now.

Tino (08:15:02) (in thread): > Thanks@Kate Rasheed

Precious Orakwe (08:25:52) (in thread): > Thank you team for your selfless assistance. @Aleru, @Mildred, @Chinwendu, @Adeshile, Oluwatosin, I forgot to change that when I was making some corrections in the study. There was no antibiotic exclusion; the antibiotics were administered. Thanks for the help, guys.

Adeshile Oluwatosin (08:26:36) (in thread): > You are welcome@Precious Orakwe

Kate Rasheed (08:50:57): > Good afternoon people:hugging_face:. I would like to seek your opinion concerning a study@Ebuka Chinwubaand myself are working on. > > For experiment 2, the paper says Shannon was unchanged but the figure says different unless I’m missing out something. > > I’ll appreciate some fresh eyes here :https://bugsigdb.org/Study_1121 - Attachment (BugSigDB): Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model - BugSigDB > Both maternal microbiota and helminth infection may alter offspring immunity but the relationship between these is underexplored.We hypothesized that maternal helminth exposure prior to pregnancy has lasting consequences on offspring intestinal microbiota and consequent immunity.

Kate Rasheed (08:57:04) (in thread): > Here is the article. - File (PDF): nyangahu2020.pdf

Mildred Anashie (08:59:39): > Hello Everyone > > Hi@Svetlana Ugarcina Perovic@Scholastica Urua@Chioma Onyido@Peace Sandy@Esther AfuapePlease how is Evenness curated on BugSigdb?

Aleru Divine (09:02:21) (in thread): > Hi@Kate Rasheed, they stated, “We found no significant differences in alpha diversity between breastmilk microbiota from NbM vs NvM (Fig. 2B).” > > Even if there were differences(as seen in the figure 2b), it was not significant. This can be as a result of the p value being higher than the significance threshold, which in this case is 0.05. - Attachment (PubMed Central (PMC)): Preconception helminth infection alters offspring microbiota and immune subsets in a mouse model > Both maternal microbiota and helminth infection may alter offspring immunity but the relationship between these is underexplored. We hypothesized that maternal helminth exposure prior to pregnancy has lasting consequences on offspring intestinal …

Kate Rasheed (09:03:59) (in thread): > Thanks@Aleru Divine. I wanted someone to confirm my thought.

Mildred Anashie (09:05:04) (in thread): > Thank you@Yoko CShannon is also an estimator for evenness, I need to be sure if I’ll be correct curating it that way

Svetlana Ugarcina Perovic (09:06:02) (in thread): > What’s then Pielou?

Ebuka Chinwuba (09:06:20) (in thread): > @Aleru DivineThank you

Aleru Divine (09:06:38) (in thread): > @Mildred AnashieShannon is an estimator of species richness and species evenness: more weight on species richness > > Simpson is an estimator of species richness and species evenness: more weight on species evenness > > This is from the:information_source:button in BugSigDB

Aleru Divine (09:08:27) (in thread): > And Pielou quantifies how equal the community is numerically. > > Equalness = eveness

Mildred Anashie (09:09:35) (in thread): > Thank you@Svetlana Ugarcina Perovic. I am glad I asked before going ahead:blush:

Mildred Anashie (09:10:03) (in thread): > Thank you@Aleru Divine:hugging_face:

Aleru Divine (09:11:08) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kate Rasheed (09:12:41) (in thread): > In summary, evenness= Pielou, Shannon and Simpson:hugging_face:.

Svetlana Ugarcina Perovic (09:14:16) (in thread): > they are not the same, please explore this better

Kate Rasheed (09:15:19) (in thread): > Okay@Svetlana Ugarcina Perovic

Aleru Divine (09:17:30) (in thread): > Pielou shows community equalness in other words evenness.The other two(Shannon and Simpson) estimates both richness and eveness but Shannon adds more weight on richness and Simpson adds more weight on eveness.If the paper said Evenness(as in this case) then it is Pielou.@Kate Rasheed

Aleru Divine (09:18:33) (in thread): > They’renot exactly the same.@Kate Rasheed

Mildred Anashie (09:20:19) (in thread): > Thank again@Aleru Divinefor more information and clarification:blush:

Svetlana Ugarcina Perovic (09:27:44) (in thread): > Check outIndices of diversity and eveness: https://www.davidzeleny.net/anadat-r/doku.php/en:div-ind - File (PNG): Screenshot 2024-10-23 at 15.26.33.png

Aleru Divine (09:32:23) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (09:46:30) (in thread): > Noted@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:01:07): > Reminder: Tomorrow (Thursday) isour weekly team meeting and office hours at 9 AM EDT.https://us02web.zoom.us/j/2737200499cc<@UBNSEMS3S>

Aleru Divine (10:02:09): > Hi everyone, trust you all are having a great day. > > I’d appreciate a peer review of this study I recently completed. > > These are some of the areas I am not very certain of: > 1. The condition of choice > 2. 16S variable region- I did not find anything regarding this and there are no supplementary materials in this study. Please see if you can find anything. > 3. The statistical test. > Thank you so much for the help:hugging_face:https://bugsigdb.org/Study_1183 - Attachment (BugSigDB): Microbial gut evaluation in an angolan paediatric population with sickle cell disease - BugSigDB > Sickle cell disease (SCD) is one of the most common genetic conditions worldwide.It can contribute up to 90% of under-5 mortality in sub-Saharan Africa.

Aleru Divine (10:03:02) (in thread): > Thank you for the reminder@Svetlana Ugarcina PerovicLooking forward to it:hugging_face:

Kate Rasheed (10:03:08) (in thread): > Hi@Aleru DivineI’ll take a look with a fresh eyes:smile:

Adeshile Oluwatosin (10:04:09) (in thread): > Hi@Aleru DivineWould check:wink:

Adeshile Oluwatosin (10:04:09) (in thread): > Hi@Aleru DivineWould check:wink:

Svetlana Ugarcina Perovic (10:04:27) (in thread): > “The 16S Metagenomics app v1.1.0 within BaseSpace (Illumina) was used to perform taxonomic classification, which uses the RefSeq RDP 16Sv3database18and the RDP Naïve Bayes taxonomic classification algorithm.19”

Aleru Divine (10:04:29) (in thread): > Thank you so much@Kate Rasheed@Adeshile Oluwatosin:pleading_face:

Adeshile Oluwatosin (10:04:58) (in thread): > Noted@Svetlana Ugarcina Perovic

Aleru Divine (10:05:16) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (10:09:54) (in thread): > Now I wonder if v3 means VERSION 3 of the database. This should be rechecked.

Svetlana Ugarcina Perovic (10:12:35) (in thread): > because usually you write small v and then number for version of your tool or database

Svetlana Ugarcina Perovic (10:13:00) (in thread): > and regions of the 16S rRNA gene start with capital V

Svetlana Ugarcina Perovic (10:13:20) (in thread): > also that reference [18] should be checked

Aleru Divine (10:14:12) (in thread): > Thank you so much@Svetlana Ugarcina Perovic.I’llcheck the reference right away:pray:

Adeshile Oluwatosin (10:17:09) (in thread): > I can see:Sickle cell anemia, still checking

Yoko C (10:17:39) (in thread): > I think its the version, because it was metagenomic and the Illumina app website info

Kate Rasheed (10:17:43) (in thread): > For the condition, is there “Sickle Cell Disease-SC” option?@Aleru Divine

Svetlana Ugarcina Perovic (10:20:40) (in thread): > @Yoko Cin using correct scientific terminology, companies can be very wrong sometimes (often) for example:https://support.illumina.com/downloads/basespace-16s-metagenomics-app.html16S Metagenomics does not exist as a term! - Attachment (support.illumina.com): BaseSpace 16S Metagenomics App Documentation > This guide contains instructions for using the 16S Metagenomics BaseSpace App.

Svetlana Ugarcina Perovic (10:21:00) (in thread): > Let me share with you one of my fav threads that I made on this topic.

Svetlana Ugarcina Perovic (10:21:59) (in thread): > https://x.com/svetlana_up/status/1394613676875915268 - Attachment (X (formerly Twitter)): Svetlana U. Perović (@svetlana_up) on X > “shotgun and 16S metagenomics data” > > 16S metagenomics is a misnomer – a wrong or inaccurate use of a name or term > > TL;DR 16S rRNA gene sequencing is NOT metagenomics > > Well if you are still in doubt, you should read the thread below. > 1/5

Aleru Divine (10:22:18) (in thread): > There is no information regarding the 16S variable region from the resource that was referenced@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:26:00) (in thread): > I am pretty sure it’s a version of the database: seehttps://zenodo.org/records/3951383 - Attachment (Zenodo): DADA2 formatted 16S rRNA gene sequences for both bacteria & archaea > These two combined bacterial and archaeal 16S rRNA gene sequence databases were collated from various sources and formatted for the purpose of using the “assignTaxonomy” command within the DADA2 pipeline. RefSeq+RDP: This database contains 14676 bacterial & 660 archaea full 16S rRNA gene sequences.  It was compiled in 14/05/2018 from predominantly the NCBI RefSeq 16S rrna database (https://www.ncbi.nlm.nih.gov/refseq/targetedloci/16S_process/) and was supplemented with extra sequences from the RDP database (https://rdp.cme.msu.edu/misc/resources.jsp). Genome Taxonomy Database (GTDB): The new version of our dada2 formatted GTDB reference sequences now contains 21965 bacteria and 1126 archaea full 16S rRNA gene sequences. If you wonder why there are fewer species with 16S rRNA, that is because some metagenomics assembled genomes (MAGs) lack the 16S gene and thus cannot be extracted.  The database was downloaded from https://data.ace.uq.edu.au/public/gtdb/data/releases/release95/ on 19/07/2020. Please read the release notes and file descriptions.  The formatting to DADA2 format of the databases was done using a simple awk bash scripts. The script takes as input a fasta file as provided by the core databases creators and then it outputs a fasta file with all 7 taxonomy ranks separated by “;” as required for DADA2 compatibility. Additionally, we have concatenated the unique sequence ID be it NCBI/RDP or GTDB ID to the species entry. We see this as an important QC step to highlight the issues/confidence associated with short read taxonomy assignment at the more finer rank levels.

Yoko C (10:26:44) (in thread): > @Svetlana Ugarcina Perovic, can’t see the thread since I don’t have twitter, but I think I do understand. Sequencing 16S is looking for the specific genes, while metagenomics is looking beyond just the 16S. What I meant is that since they sequence everything, I think they are not looking for specific regions of the 16S and the library is for all 16S regions. edit: see you shared another resource so will look it up. Thanks for the clarification.

Aleru Divine (10:28:21) (in thread): > Yes I believe it is a version too and not the variable region. > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (10:28:57) (in thread): > Hi@Aleru DivineDid you see this? For the statistical test > > “Distribution of metagenomic data in SCA children and healthy siblings for the levels of: (A) phylum (B) class (C) order (D) family (E) genus (F) species.******The results were filtered using a p‐value of 0.05 with a Welch’s t‐test******, effect size of 0.01 threshold and removing unclassified reads in STAMP software. > > And this “******This analysis was performed with Welch’s t‐test and an effect size filter of 0.5”.******

Svetlana Ugarcina Perovic (10:30:29) (in thread): > The 16S rRNA gene sequence is about 1,550 bp long and they stated in the paper: “. A sequencing run of 2 × 151 bp paired-end reads was performed…” so it’s NOT full gene sequenced.@Yoko C

Aleru Divine (10:30:48) (in thread): > Yes I did.Just wanted a confirmation.Thank you so much@Mildred AnashieWhat do you think about the condition.

Svetlana Ugarcina Perovic (10:32:15) (in thread): > @Yoko C”Sequencing 16S is looking for the specific genes, while metagenomics is looking beyond just the 16S.” Let’s clear this up? What’s 16S?

Svetlana Ugarcina Perovic (10:34:44) (in thread): > anyway@Aleru DivineV region is not clearly stated in the paper, so you can’t record something that’s not in the paper

Kate Rasheed (10:34:59) (in thread): > @Aleru DivineIf there is Sickle cell disease - SC, I think that’s the condition.

Adeshile Oluwatosin (10:35:40) (in thread): > @Kate Rasheedno, I only saw sickle cell anaemia, I believethat’sthe condition

Aleru Divine (10:35:42) (in thread): > Got it@Svetlana Ugarcina Perovicthank you so much!

Adeshile Oluwatosin (10:36:13) (in thread): - File (JPEG): IMG_1837

Svetlana Ugarcina Perovic (10:38:13) (in thread): > Microbial community sequencing > includes 2 methodological approaches: > > 1. microbial community amplicon sequencing == MARKER GENE SEQUENCING > *most commonly sequenced marker gene is 16S rRNA gene > > AND > > 2. microbial community whole genome shotgun sequencing == METAGENOMICS > > So, analyzing 16S ribosomal RNA gene sequences, we are doing 16S rRNA gene amplicon sequencing. > > If we are dealing with whole genome shotgun sequencing – that’s metagenomics. > > Terminology matters. > > “shotgun and 16S metagenomics data” should be > (16S rRNA gene) amplicon sequencing data > and > (whole genome) shotgun metagenomics data > > 16S metagenomics does not exist, but, yes, many researchers and companies are still using this term. Wrongly.

Mildred Anashie (10:38:53) (in thread): > @Aleru DivineI think for the first experiment > Sickle cell anaemia works > > For the second experiment, would it be okay to choose “sickle cell disease associated with another hemoglobin anomaly”?:thinking_face:

Aleru Divine (10:42:05) (in thread): > Thank you so much@Svetlana Ugarcina Perovicfor the detailed response on clarifying this.I truly apprappreciate:pray:

Aleru Divine (10:51:49) (in thread): > For the condition, thank you everyone:pray:The reason I choseSickle cell disease and related diseaseswas because the study evaluated the gut microbiota in children with Sickle cell disease. At least that is what the study and abstract implied. But then I couldn’t find “Sickle cell disease” on its own. > > Looking at this now, I’ll change toSCA, since this is specific to experiment 1. And change experiment 2 toSickle cell disease associated with an other hemoglobin anomaly. > > Thank you so much everyone** ****:heart_hands:**** ****:tulip:**** > ****@Svetlana Ugarcina Perovic**** ****@Kate Rasheed**** ****@Adeshile Oluwatosin**** ****@Mildred Anashie**** ****@Yoko C**** ****

Adeshile Oluwatosin (11:24:33): > Hello everyone! > > I would appreciate a review on this study:https://bugsigdb.org/Study_1168https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-022-02747-z - Attachment (BugSigDB): Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting - BugSigDB > BACKGROUND: Human immunodeficiency virus (HIV) severely damages the epithelial cells of the gut lining leading to an inflamed leaky gut, translocation of microbial products, and dysbiosis resulting in systemic immune activation. - Attachment (BioMed Central): Antenatal gut microbiome profiles and effect on pregnancy outcome in HIV infected and HIV uninfected women in a resource limited setting - BMC Microbiology

Mildred Anashie (11:26:43) (in thread): > Hi@Adeshile OluwatosinI think I have gone through this study before, but I’ll take another look

Kate Rasheed (12:41:02) (in thread): > Hi@Adeshile Oluwatosin. I’ll look through.

Kate Rasheed (13:08:04) (in thread): > @Adeshile OluwatosinLooking at experiment 2, the signature is decreased not increased.

Adeshile Oluwatosin (13:12:53) (in thread): > Low infant birth weight (< 2500 g) was significantly associated with high abundances of the phyla Spirochaetes, the families Spirochaeteceae, and Veillonellaceae and the genus Treponema (Fig. 4)@Kate Rasheed

Adeshile Oluwatosin (13:14:34) (in thread): > High abundance of the taxa Spirochaetes, Spirochaeteceae, Veillonellaceae and Treponema in the third trimester of pregnancy was associated with low birth weight in infants.

Kate Rasheed (13:16:18) (in thread): > @Adeshile OluwatosinIf you keep reading you would see that “though these association lost significance….”

Kate Rasheed (13:17:59) (in thread): > The abundance was for pregnancy not between the weight of infants@Adeshile Oluwatosin

Yoko C (13:18:15) (in thread): > @Kate Rasheed@Adeshile Oluwatosin, I was wondering about that as well, that they lost significance. It remains increased, but in that case would your test have to be recorded as with no correction? not sure about that

Kate Rasheed (13:19:32) (in thread): > @Yoko C@Adeshile OluwatosinSee below the image was written “Taxonomic differences between the gut microbiota of groups stratified by baby birth weight were compared by MaAsLin2 analysis. : p value < 0.05, : p value < 0.01 = , **: p value < 0.001”

Kate Rasheed (13:22:15) (in thread): > Fig. 4 is an experiment for the baby birth weight. The earlier values was when a comparison was done for the effects of gut microbiota in pregnancy on pregnancy and birth outcomes

Adeshile Oluwatosin (13:22:29) (in thread): > @Kate RasheedFigure 4: Microbiota abundance and birth outcome. > > The birth outcome here is babybirth weight

Kate Rasheed (13:23:17) (in thread): > The effects of microbiota in pregnancy on pregnancy and birth outcomes lost significance, hence, it wasn’t recorded.

Yoko C (13:23:55) (in thread): > @Kate Rasheed, I see your point about the group, the group description would have to include mother’s with infants below 2500 g

Yoko C (13:24:29) (in thread): > Or something of the sort, but the condition is birth weight

Kate Rasheed (13:25:07) (in thread): > The experiment is just birth weight below 2500 and birth weight above 2500. > > The correct signature is recorded in Fig. 4

Adeshile Oluwatosin (13:25:47) (in thread): > @Yoko CI recorded that way because of what I can see from the result, kindly check

Adeshile Oluwatosin (13:28:41) (in thread): > @Kate Rasheedsame taxa are recorded in text and figure

Adeshile Oluwatosin (13:28:45) (in thread): > They are just 4.

Kate Rasheed (13:29:39) (in thread): > But then, I don’t know why they added the figure to the text. > > Let’s wait for other opinions. The figure actually shows decrease not increase.

Kate Rasheed (13:30:21) (in thread): > @Adeshile OluwatosinThat’s the thing. Same taxa, same figure.

Adeshile Oluwatosin (13:31:11) (in thread): > Tomorrow I’ll ask for clarification in the meeting > > Thank you so much@Kate RasheedGenuinely appreciate your input

Kate Rasheed (14:35:25) (in thread): > @Adeshile Oluwatosin@Yoko CSee another statement “Higher abundance of genus Clostridium was significantly associated with a VL < 1000 cps/ml whilst higher abundances of family Paraprevotellaceae and genus Prevotella was associated with a VL > 1000 cps/ml and only Prevotella remained significant after false discovery rate correction (q < 0.05).” > > From the figure above the text, g.clostridium was actually decreased in viral <1000

Adeshile Oluwatosin (14:37:25) (in thread): > @Kate Rasheedthe study hastwo experiments > > The above is for experiment 2 which has been curated.

Kate Rasheed (14:38:20) (in thread): > Yes I know. I’m drawing your attention to something wrong with the text and figure.

Kate Rasheed (14:42:18) (in thread): > Look at this: “High abundance of the taxa Spirochaetes, Spirochaeteceae, Veillonellaceae and Treponema in the third trimester of pregnancy was associated with low birth weight in infants.” > > From what I can interpret, this high abundance of taxa was in the pregnancy, not in the low birth weight. The association of this high abundance with low birth weight lost his significance at FDR correction.

Adeshile Oluwatosin (14:43:22) (in thread): > That’s actually how the result is reported. > > That’s why in that case I reported higher abundance of taxa with viral load VL > 1000 cps/ml to be increased.@Kate Rasheed

Adeshile Oluwatosin (14:46:25) (in thread): > Experiment 2 has only increased signature curated@Kate Rasheed

Adeshile Oluwatosin (14:46:40) (in thread): > There’sno decreased signature.

Adeshile Oluwatosin (14:47:48) (in thread): > Kindly check thecuration > And thank you once again@Kate Rasheed

Kate Rasheed (14:48:12) (in thread): > I’m sorry I’m referring to experiment 3. Please check@Adeshile Oluwatosin

Adeshile Oluwatosin (14:52:02) (in thread): > I’m not quite sure@Kate Rasheedas the exact taxa in that reference are different in the ones reported in experiment 3@Yoko C

Kate Rasheed (14:52:56) (in thread): > @Adeshile OluwatosinI’m drawing your attention to this in experiment 3. > > For experiment 2, others opinion will shed more light.https://community-bioc.slack.com/archives/C04RATV9VCY/p1729708525426639?thread_ts=1729697073.513889&cid=C04RATV9VCY - Attachment: Attachment > @Adeshile Oluwatosin @Yoko C See another statement “Higher abundance of genus Clostridium was significantly associated with a VL < 1000 cps/ml whilst higher abundances of family Paraprevotellaceae and genus Prevotella was associated with a VL > 1000 cps/ml and only Prevotella remained significant after false discovery rate correction (q < 0.05).” > > From the figure above the text, g.clostridium was actually decreased in viral <1000

Kate Rasheed (14:55:38) (in thread): > All taxa should be increased for experiment 3, going by the text and figure.

Yoko C (14:57:44) (in thread): > @Kate Rasheed, I don’t have my glasses, but the figure shows Viral load<=1000 , and then the genus Clostridium

Yoko C (14:58:03) (in thread): > or does it also show Viral load > 1000 ?

Kate Rasheed (14:59:27) (in thread): > It’s decreased in <=1000 which equates to increase in >=1000@Yoko C. Unless I’m wrong in my thoughts.

Yoko C (14:59:27) (in thread): > and then if the text says: “Higher abundance of genus Clostridium was significantly associated with a VL < 1000 cps/ml”, doesn’t that mean the abundance is higher for viral load below 1000

Yoko C (15:00:48) (in thread): > @Kate Rasheed, I think I see your confusion, VL<1000 is referring to the viral load in the HIV person, it is not related to the taxa

Kate Rasheed (15:01:33) (in thread): > The figure is actually confusing me:smile:

Kate Rasheed (15:02:43) (in thread): > Can you check out the figure and share your thoughts@Yoko C. I would really need clarification on the figure.

Yoko C (15:04:09) (in thread): > Is it because of the1/8, 1/4 and so on below the graph?

Kate Rasheed (15:04:29) (in thread): > I think I shouldn’t pay attention to the relative abundance ratio. I think I’m using LEfSe analysis for the figure and it’s confusing me that way:smile:

Kate Rasheed (15:06:51) (in thread): > @Adeshile OluwatosinSincere apologies. I think everything you’ve done is correct. I was using LEfSe analysis for it.

Adeshile Oluwatosin (15:08:14) (in thread): > There’sno need to apologize@Kate Rasheedthe eagle eyes:joy_cat::joy:The exact reason why I dropped this on the channel is still unclear. I guess meeting way:pleading_face:

Kate Rasheed (15:08:15) (in thread): > It was great having this look. I’ve really learned the difference between MaAsLin and LEfSe.

Aleru Divine (17:16:31) (in thread): > Hi@Adeshile OluwatosinI’llgo through this discussion and have a look at the paper.Had quite an eventful evening.

Adeshile Oluwatosin (17:30:17): > @Svetlana Ugarcina Perovickindly deletehttps://bugsigdb.org/Study_1107/Experiment_2/Signature_3 - Attachment (BugSigDB): Study 1107/Experiment 2/Signature 3 > Source: Text: and supplementary Figure 2 Description: EBF infants defined as infants fed breast milk only (except for prescribed medicine) from birth to the study…

Samuel Nnanna (18:59:19): > @Svetlana Ugarcina PerovicPlease delete signature 3https://bugsigdb.org/Study_1160/Experiment_17/Signature_3 - Attachment (BugSigDB): Study 1160/Experiment 17/Signature 3 > Source: Figure S6A Description: The relative abundance in Phylum levels Abundance in Group 1: decreased abundance in PC4 (Patient sample 4 treated with cocktail…

Aleru Divine (22:44:50) (in thread): > I checked this study and I don’t seem to understand the confusion from this thread.:pleading_face:Everything checks out so far.

2024-10-24

Adeshile Oluwatosin (00:31:16) (in thread): > Yeah@Aleru DivineKate had an issue with how the result looked like

Adeshile Oluwatosin (00:35:30) (in thread): > It’s just how group 0 and 1 should be named for experiment 2. > > We are also unsure on the impact of correction on the taxa. They mentioned couple times that no significantobservationswere observed after correction. Something like this

Svetlana Ugarcina Perovic (03:30:43) (in thread): > deleted.

Svetlana Ugarcina Perovic (03:30:50) (in thread): > deleted.

Adeshile Oluwatosin (03:31:32) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (03:49:34): > We have 3 identifiers in PubMed: PMID: fun fact**** - ****The PMID of1is associated with an article from 1975, but older articles are assigned later PMIDs as they are digitized and added to PubMed.PMCID: PubMed Central IdentifierDOI: often found in PubMed citations, though it does not originate with PubMed > > Check out:https://library.stevens.edu/c.php?g=442331&p=6577176#:~:text=Identifiers%20in%20PubMed%3A%20PMID%2C%20PMCID,does%20not%20originate%20with%20PubMed. - Attachment (library.stevens.edu): Research Guides: PubMed: PubMed Identifiers & How to Use Them > A guide to PubMed, an open-access database for health and biomedical research.

Svetlana Ugarcina Perovic (03:56:39): > WHAT IS THE DIFFERENCE BETWEEN A PREPRINT AND PEER REVIEW?https://cdn.firespring.com/images/2d605be5-4d47-411e-ba5d-2b714dc2068a.png - Attachment: Attachment

Mary Agekameh (03:57:20): > Good day@Svetlana Ugarcina PerovicI don’t know why but I can’t add a new experiment in the study I’m curating > > This is the link to the studyhttps://bugsigdb.org/Study_1149 - Attachment (BugSigDB): Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes - BugSigDB > While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging.

Svetlana Ugarcina Perovic (03:57:30) (in thread): > @Kate Rasheedplease share here as an example what you just showed me in the GitHub issue that we discussed. Thanks!

Svetlana Ugarcina Perovic (04:00:15) (in thread): > I see you have more than 10 experiments already added. Let me tag Chloe<@UBNSEMS3S>Maybe there is a bug in the platform. Anyway, bring this question up at the team meeting today.

Mary Agekameh (04:02:08) (in thread): > Okay > Thank you

Kate Rasheed (04:02:34) (in thread): > @Svetlana Ugarcina PerovicHere it is: - File (JPEG): Screenshot_20241024-084519.jpg

Svetlana Ugarcina Perovic (04:04:49) (in thread): > @Kate Rasheedwhat we can see in the screenshot? Please explain to the others:slightly_smiling_face:

Kate Rasheed (04:09:29) (in thread): > Good morning everyone. From the picture sent, there were two PMIDs identified in PubMed. > > Upon further explanation by@Svetlana Ugarcina Perovic, one of the PMIDs is a preprint(bioRxiv) while the other is a peer review(mSphere). > > In BugSigDB, we curate peer review not preprint; and if you look at the picture closely, the preprint article says “update in mSphere”. This means that the preprint article has been published in the peer review journal. > > PS. An article has just one PMID. > > Thank you.

Adeshile Oluwatosin (04:15:03) (in thread): > Thank you for this@Svetlana Ugarcina Perovic@Kate Rasheed

Adeshile Oluwatosin (04:15:40) (in thread): > Noted, thank you

Mildred Anashie (04:42:34) (in thread): > Thank you@Svetlana Ugarcina Perovic@Kate Rasheed

Aleru Divine (05:03:29) (in thread): > This was an insightful read@Svetlana Ugarcina Perovic:raised_hands:thank you so much for sharing.

Rahila-me (05:06:37) (in thread): > @Svetlana Ugarcina PerovicWow!!, What nice article to read.

Rahila-me (05:09:23) (in thread): > @Svetlana Ugarcina Perovic@Kate RasheedThank you for this info

Aleru Divine (05:12:43) (in thread): > Oh wow! I had no idea:sweat_smile:I’ve come across a preprint article before. I don’t even remember what I was searching for:face_with_peeking_eye:Thank you for this information@Svetlana Ugarcina Perovic@Kate Rasheed

Aleru Divine (05:14:29) (in thread): > Oh! I had a problem understanding all the feedback above.Maybe because I was exhausted:pensive:Thanks for clarifying@Adeshile Oluwatosin

Mildred Anashie (05:17:57) (in thread): > So yea@Adeshile OluwatosinI believe everything is okay > > But just like the last thread about this, I’m still unsure if that statement implies that you shouldn’t curate the experiment > > You can bring it up during the office hours

Adeshile Oluwatosin (05:32:23) (in thread): > Great@Aleru Divine@Mildred Anashie:wink:Thank you, I will@Aleru Divinesometimes you need to rest to function properly, sorry

Samuel Nnanna (05:32:36) (in thread): > :blush:thank you

Samuel Nnanna (05:59:48): > https://bugsigdb.org/Study_1160Hi guys, I’d like a fresh pair of eyes to look at this study. > > I was confused in the following areas; > 1. MHT correction for ANOVA (there were adjustments made for the p-values in the paper, but there wasn’t any explicit mention of “adjusted p-value” for ANOVA just DeSeq2. > 2. Figure S5A, i’d like to know if this is curatable, in the text, samples 3.5 and 7 were ignored but the figure suggests they were significant. I thought since there were no signatures found, the alpha-diversities should would be ignored. > 3. The overall number of experiments….i’ve found 30 experiments(I was surprised), but I think there could be more as there are so many details in the paper and i may have missed one or two > I’d be looking forward to your feedback….thank you - Attachment (BugSigDB): Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome - BugSigDB > Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death.Modulating the gut microbiome is a promising therapeutic approach for managing SIRS.

Adeshile Oluwatosin (06:02:48) (in thread): > Okay,I’ll check@Samuel Nnanna

Samuel Nnanna (06:03:35) (in thread): > Thank you@Adeshile Oluwatosin

Kate Rasheed (06:04:56) (in thread): > I’ll take a look too

Samuel Nnanna (06:05:20) (in thread): > :heart_hands:@Kate Rasheed

Mildred Anashie (06:05:58) (in thread): > Hi@Samuel NnannaI’ll take a look at this

Samuel Nnanna (06:07:56) (in thread): > @Mildred Anashiethanks

Adeshile Oluwatosin (06:11:59) (in thread): > 16 experiments:pleading_face:let me calm down and go through it

Samuel Nnanna (06:13:15) (in thread): > so far….i found 30……but yes calm down:grinning:

Adeshile Oluwatosin (06:14:20) (in thread): > Not all experiments has signatures, why?

Adeshile Oluwatosin (06:15:26) (in thread): > An experiment with no signatures should not be curated, I believe.

Kate Rasheed (06:16:11) (in thread): > What I was about saying. So far, I can see 3 experiments with signatures that should be curated.

Samuel Nnanna (06:18:12) (in thread): > I’ll take a look…maybe it’s one of those that need to be deleted@Adeshile Oluwatosin

Samuel Nnanna (06:18:26) (in thread): > which ones@Kate Rasheed

Kate Rasheed (06:21:55) (in thread): > XFBD vs model > FMT-L vs control (Statistically not significant; I don’t think it should be recorded) > Uncultured model/control vs cultured model/control > SIRS vs healthy volunteers

Kate Rasheed (06:22:01) (in thread): > Still looking through

Adeshile Oluwatosin (06:26:30) (in thread): > * FIG 5B. B) A waterfall plot of significantly altered genus between model and control showing consistent trend in both uncultured and cultured groups. Differential abundance analysis was performed to assess variations in taxonomic abundances between groups using the negative binomial test (DESeq2, adjusted P < 0.05). > > * Fig 6E. E) Differential abundance bacterial changes at genus level, linear discriminant analysis effect size (LEfSe) analyses between SIRS mice and control mice (M vs N, MD vs ND). > > * Fig 8C Abundance comparison of key genera between SIRS patients and healthy volunteers.

Samuel Nnanna (06:35:12) (in thread): > @Kate RasheedI cant see “XFMD”@Adeshile Oluwatosinis figure 6E curatable? how do i tell which increased or decreased from the figure?

Samuel Nnanna (06:35:28) (in thread): > taking a look at gig 5b

Samuel Nnanna (06:38:23) (in thread): > @Kate Rasheedyes for FMT-L vs control….it was reported as not significant in fig. S5D

Kate Rasheed (06:40:05) (in thread): > @Samuel NnannaSorry I meant XFBD

Adeshile Oluwatosin (06:42:16) (in thread): > Still checking, can someone send me figure7, let me see

Samuel Nnanna (06:44:42) (in thread): - File (JPEG): msystems.00788-24.f007.jpg

Adeshile Oluwatosin (06:45:05) (in thread): > Not curatable…no need@Samuel Nnanna

Adeshile Oluwatosin (06:46:26) (in thread): > @Samuel Nnannafor 6E. Record source from this text: At the genera level, we observed a significant increase in the abundance of Bacteroides, Escherichia Shigella, Enterobacter, and Enterococcus in the cultured cecum from model mice (Fig. 6E; Fig. S5D).

Adeshile Oluwatosin (06:48:03) (in thread): > Let me go through supplementary materials

Adeshile Oluwatosin (06:53:50) (in thread): > Fig S1-S6, there’s this note. > > NS. Not significantSodon’tcurate from here@Samuel Nnanna

Samuel Nnanna (07:00:01) (in thread): > yeah, i didn’t. Thanks

Adeshile Oluwatosin (07:05:27) (in thread): > Don’t curate Fig 3D. > > 16S rRNA gene sequencing was used to analyze the gut microbiota diversity of each sample. As shown in Fig. 3A, although not statistically significant, there is a clear tendency for ….

Adeshile Oluwatosin (07:06:21) (in thread): > So you have just 3 experiments@Samuel Nnanna

Rahila-me (07:20:22) (in thread): > @Samuel Nnanna@Adeshile OluwatosinNot all experiments has signatures, why?****[11:15 AM]*******An experiment with no signatures should not be curated, I believe.***In bugsigDB an experiment can actually be curated without signatures. just that it is very rear. Taking a look too. Will revert back

Rahila-me (07:20:51) (in thread): > Also@Samuel Nnannaduring the meeting bring it up too for more clarification

Rahila-me (07:23:58) (in thread): > I have curated a study with experiment No signatures, Every information about the experiment was in the article but no signatures in the article or supplementary so i just added the experiment but it was just one experiment@Samuel Nnannahave you also looked for the supplementary materials for the signatures?

Adeshile Oluwatosin (07:25:07) (in thread): > @Rahila-meThat’s an added knowledge:wink:ThanksI’d like to see a study with no signatures.Also, the supplementary figures is not significant

Samuel Nnanna (07:25:19) (in thread): > What 3 experiments@Adeshile Oluwatosin

Adeshile Oluwatosin (07:25:44) (in thread): > @Samuel Nnannahttps://community-bioc.slack.com/archives/C04RATV9VCY/p1729765590212999?thread_ts=1729763988.172499&channel=C04RATV9VCY&message_ts=1729765590.212999 - Attachment: Attachment > • FIG 5B. B) A waterfall plot of significantly altered genus between model and control showing consistent trend in both uncultured and cultured groups. Differential abundance analysis was performed to assess variations in taxonomic abundances between groups using the negative binomial test (DESeq2, adjusted P < 0.05). > • Fig 6E. E) Differential abundance bacterial changes at genus level, linear discriminant analysis effect size (LEfSe) analyses between SIRS mice and control mice (M vs N, MD vs ND). > • Fig 8C Abundance comparison of key genera between SIRS patients and healthy volunteers.

Samuel Nnanna (07:26:53) (in thread): > Yeah I have looked at the supplementary materials@Rahila-me

Mildred Anashie (07:42:31) (in thread): > @Adeshile Oluwatosincould you point me to where it says that S1-S6 was not significant?

Mildred Anashie (07:45:12) (in thread): > @Samuel NnannaI see alot of experiments with significance and there were based on treatment and concentrations. And there are a lot:sweat_smile:

Adeshile Oluwatosin (08:01:09) (in thread): > @Mildred Anashie - File (JPEG): IMG_1861

Mildred Anashie (08:05:04) (in thread): > Well done on your curation:raised_hands:@Samuel NnannaI’ll point out my observations, then try to list out the experiments I could confirm > 1. I couldn’t find the alpha diversity for Experiment 1 and a few other experiments. Please point me to the figures or text that shows alpha diversity:thinking_face: > 2. I see an experiment M vs MD. That didn’t show significant signatures so I think it should be deleted, also you should delete signature 3 in experiment 17. > 3. I also see you missed Bacteroidetes in Experiment 17 > 4. I don’t think ANOVA was used for differential abundance because the paper says DeSeq2 and LEfSe. ANOVA was used to confirm statistical significance and I believe differential abundance and statistical significance are different. My only concern though is that, the experiments that were relative abundance between groups didn’t explicitly state the test used so I’m unclear on what the statistical test would be for those. We need to read through again. > 5. For the experiments you have two experiments in Figure 5b and I think you might have interpreted that figure differently. I see, > i. Uncultured M/N vs Cultured MD/ND model > ii. Uncultured M/N vs Cultured MD/ND control. > There’s increased signatures reported for both, so you would record those that were enriched in the model for M/N and MD/ND as increased and decreased based on how you assigned your groups. This would be same for the control. > > 6. I think figure S6 is curatable and I see about 6 experiments there. > > 7. Your experiment 21 is all good:white_check_mark:(Healthy volunteers vs SIRS patients {Fig 8}) > > 8. In S2 I see 3 experiments which you correctly recorded > > 9. The ones I’m unsure of are Supplementary figure 4f, 5c and 5d. Although I see 4 experiments showing significance in 4f, about 6 in 5c but one seems to overlap with one in 4f. And I see a lot more in 5D which makes me wonder if all of those should be recorded > > Well done again in this, it’s a lot and appears to be a difficult paper to navigate

Samuel Nnanna (08:05:34) (in thread): > @Adeshile Oluwatosinin this figure, for proteobacteria, none is significant hence the horizontal lines on top. > For lactobacillus, control vs model is not significant,model vs XFBD-L is, control vs model is and control vs XFBD-L is as well

Adeshile Oluwatosin (08:06:05) (in thread): > Which, please specify@Samuel Nnanna

Mildred Anashie (08:06:11) (in thread): > @Adeshile Oluwatosinthatdoesn’trefer to the whole paper but applies only to that figure

Adeshile Oluwatosin (08:08:33) (in thread): > @Mildred AnashieI’ma bit lost

Samuel Nnanna (08:09:32) (in thread): > Thank you@Mildred AnashieI’lllook Through again

Samuel Nnanna (08:10:00) (in thread): > For that particular figure S1@Adeshile Oluwatosin

Mildred Anashie (08:15:01) (in thread): > So@Adeshile Oluwatosinwhat you shared is the caption for Fig S1 andit’strying to explain that figure only. The information there applies only to that figure, if you look at other figures you would see that they all have different information written out like that one

PATIENCE ONAH (08:33:21): > Hi everyone, Trust we are all doing great. > Please someone should help me to confirm if “Prospective cohort” is the right study design for this paper:https://doi.org/10.1186/s12866-021-02364-2 - Attachment (BioMed Central): Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome - BMC Microbiology > Background Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes. To date, the association between yoghurt consumption and the composition of the gut microbiota is underexplored. Here we used clinical variables, metabolomics, 16S rRNA and shotgun metagenomic sequencing data collected on over 1000 predominantly female UK twins to define the link between the gut microbiota and yoghurt-associated health benefits. Results According to food frequency questionnaires (FFQ), 73% of subjects consumed yoghurt. Consumers presented a healthier diet pattern (healthy eating index: beta = 2.17 ± 0.34; P = 2.72x10−10) and improved metabolic health characterised by reduced visceral fat (beta = −28.18 ± 11.71 g; P = 0.01). According to 16S rRNA gene analyses and whole shotgun metagenomic sequencing approach consistent taxonomic variations were observed with yoghurt consumption. More specifically, we identified higher abundance of species used as yoghurt starters Streptococcus thermophilus (beta = 0.41 ± 0.051; P = 6.14x10−12) and sometimes added Bifidobacterium animalis subsp. lactis (beta = 0.30 ± 0.052; P = 1.49x10−8) in the gut of yoghurt consumers. Replication in 1103 volunteers from the LifeLines-DEEP cohort confirmed the increase of S. thermophilus among yoghurt consumers. Using food records collected the day prior to faecal sampling we showed than an increase in these two yoghurt bacteria could be transient. Metabolomics analysis revealed that B. animalis subsp. lactis was associated with 13 faecal metabolites including a 3-hydroxyoctanoic acid, known to be involved in the regulation of gut inflammation. Conclusions Yoghurt consumption is associated with reduced visceral fat mass and changes in gut microbiome including transient increase of yoghurt-contained species (i.e. S. thermophilus and B. lactis).

Kate Rasheed (08:39:44) (in thread): > @PATIENCE ONAHIt’s a prospective cohort study. > > See this “Twins reporting “Never or less than once/month” were considered non-consumers, twins reporting frequencies of “once a week” to “2-3 per day” were considered consumers.

Adeshile Oluwatosin (08:41:34) (in thread): > @Mildred Anashieevery other supplementary figure are also not significant

Adeshile Oluwatosin (08:43:10) (in thread): - File (JPEG): IMG_1862

Samuel Nnanna (08:43:17) (in thread): > @Adeshile Oluwatosinonly the oneswith “ns” are considered not significant. The ones with lines and * on top of them are significant

PATIENCE ONAH (08:43:40) (in thread): > Thank you@Kate Rasheed

Mildred Anashie (08:43:55) (in thread): > It’s a prospective cohort@PATIENCE ONAHI was leaning towards cross sectional but then I noticed they collected samples at multiple time points prospectively from the twin pairs used in the study

Samuel Nnanna (08:44:50) (in thread): > In figure s2, a has some significant differences, bdoesn’t, cdoesn’t,d does, edoesn’tand fdoesn’t

Mildred Anashie (08:45:44) (in thread): > That caption is interpreting each figure@Adeshile OluwatosinSimply saying where you see n.s within the figure it means “Not significant”

PATIENCE ONAH (08:46:55) (in thread): > Thank you@Mildred Anashie

Kate Rasheed (08:47:06): > Reminder - Attachment: Attachment > Reminder: Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. > https://us02web.zoom.us/j/2737200499 > > cc @UBNSEMS3S

Adeshile Oluwatosin (08:47:48) (in thread): > OhhhI see, let me check@Samuel Nnanna

Adeshile Oluwatosin (08:47:53) (in thread): > Ohhh I see, let me check@Samuel Nnanna

Adeshile Oluwatosin (08:49:30) (in thread): > Thanks:blush:

Mildred Anashie (08:49:51): > Hello everyone:wave:This is a gentle reminder > It’s almost time for our office hours > > Looking forward to seeing you all:blush:https://community-bioc.slack.com/archives/C04RATV9VCY/p1729692067837799 - Attachment: Attachment > Reminder: Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. > https://us02web.zoom.us/j/2737200499 > > cc @UBNSEMS3S

Samuel Nnanna (08:50:06) (in thread): > Thanks@Mildred Anashie. i missed bacteroidetes for exp 17. Added that now

Chinwendu Joy Enyidiegwu (09:03:35) (in thread): > thank you

Rahila-me (09:23:15) (in thread): > @Inimfon Ebong@Mildred Anashiestill taking a look but you can start curating these signatures will confirm if they will be more signatures: > You will 3 experiments each with 2 signatures > Experiment 1. > 2 signatures: mild vs control: > Signature 1: mild (increase) vs signature 2 : control (decrease) > > Experiment 2. > 2 signatures: Moderate vs control: > Signature 1: moderate (increase) vs signature 2 : control (decrease) > > > Experiment 3. > 2 signatures: Severe vs control: > Signature 1: severe (increase) vs signature 2 : control (decrease) > > images from your article - File (PNG): Screenshot 2024-10-23 115141.png - File (PNG): Screenshot 2024-10-23 115151.png

Rahila-me (09:23:42) (in thread): > I never knew i did not send this after typying since yesterday

Rahila-me (09:24:13) (in thread): > Then you start alternating it@Inimfon Ebong

Inimfon Ebong (09:27:17) (in thread): > Is this for the new experiments in figure 3 or for the old in figure 2

Rahila-me (09:30:39) (in thread): > it was yesterday i sent this, i never knew it did not go through..old experiment fig 2

Adeshile Oluwatosin (09:31:17) (in thread): > @Samuel Nnannatbh I just saw it now, there are so many experiments:joy_cat::joy:in the supplementary. > > Take note of what Chloe is saying though

Samuel Nnanna (09:34:17) (in thread): > Yeah@Adeshile Oluwatosin

Samuel Nnanna (09:34:30) (in thread): > Thanks everyone > I appreciate your observations

Adeshile Oluwatosin (09:46:24): > Hello everyone, I’m collaborating with@Mildred Anashieon an issue. > > We would appreciateopinionsonhow to go about thiscuration:https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-024-03230-7 - Attachment (BioMed Central): Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study - BMC Microbiology > Objective To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA. Methods Before adeno-tonsillectomy, we collected throat swab samples from different parts of the oropharynx and nasopharynx of 30 OSA patients and 10 non-OSA patients and collected throat swab samples from the oropharynx of the above patients one month after the adeno-tonsillectomy. The 16 S rRNA V3–V4 region was sequenced to identify the microbial communities. The correlation analysis was conducted based on clinical characteristics. Results There was a significant difference of alpha diversity in different parts of the upper airway of pediatric OSA, but this difference was not found in children with non-OSA. Beta diversity was significantly different between non-OSA and pediatric OSA. At the genus level, the composition of flora in different parts is different between non-OSA and pediatric OSA. The correlation analysis revealed that the relative abundance of Neisseria was significantly correlated with obstructive apnea hypopnea index. Furthermore, the functional prediction revealed that pathways related to cell proliferation and material metabolism were significantly different between non-OSA and pediatric OSA. Besides, the adeno-tonsillectomy has minimal impact on oral microbiota composition in short term. Conclusion The changes in upper airway microbiome are highly associated with pediatric OSA. The relative abundance of some bacteria was significantly different between OSA and non-OSA. These bacteria have the potential to become new diagnostic and early warning biomarkers.

Mildred Anashie (09:54:21) (in thread): > @Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica UruaPlease a little help with Supplementary figure 5, Figure 5 and Figure 6b > > Thank you:pray:

Mildred Anashie (10:05:09): > Thank you again<@UBNSEMS3S>for the office hour:blush:

Aleru Divine (10:06:01): > Thank you for the office hours session:pray:<@UBNSEMS3S>

Adeshile Oluwatosin (10:06:18): > <@UBNSEMS3S>Thank you:hugging_face:sorry I asked too many questions:sweat_smile:

Yoko C (10:19:49) (in thread): > I remember in a meeting Chloe said there could be cases of 1 vs all, so for figure 5A could that be the case? Non OSA-a vs all 3 others. For example increasedVeillonella , decreased Fusobacteria. I didn’t read anything, just looked at the figure, but that comes to mind.

Yoko C (10:23:46): > Hey everyone, doubting about the transformation for my paper, since there are 2. Thinking I should only record the log transformation? Thepaperstates: Differential abundance was analyzed using SIAMCAT (v1.14.0)30and LefSe31from the microbiome Marker package (v1.0.2)67.**** A pseudo-count of 1e-4% was added to relative abundances of 0 for logarithmic transformation.****

Joy (10:30:42) (in thread): > Thanks@Svetlana Ugarcina Perovicfor this information

Joy (10:34:37) (in thread): > Thank you@Svetlana Ugarcina Perovic@Kate Rasheed

Joy (10:37:53): > Thank you<@UBNSEMS3S>for the office hour

UBNSEMS3S (10:38:33) (in thread): > Sounds like log transformation for me for SIAMCAT. LEfSe uses relative abundances though.

Rahila-me (10:49:00): > <@UBNSEMS3S>thank you so much for today’s office hour. Learnt one or two from the questions asked and answered

Tino (11:02:27): > Hello everyone and@Svetlana Ugarcina PerovicAfter attending today’s office hour I noticed some mistakes that I made in my curation. Is it possible to ask for my issue to beuntaggedfrom ‘needs review’ so that I can make the necessary edits.

Rahila-me (11:04:51) (in thread): > @Svetlana Ugarcina PerovicLINKS TO MY POSTS THUS FAR:Medium:https://medium.com/@chinenyeozoagudikeX:https://x.com/ChineseChikki - Attachment (Medium): ozoagudike chinenye – Medium > Read writing from ozoagudike chinenye on Medium. Every day, ozoagudike chinenye and thousands of other voices read, write, and share important stories on Medium.

Samuel Nnanna (11:18:21): > @C. Mirzayi (please do not tag this account)for the session today. My questions were answered. Pheeeeewwww:blush:

Samuel Nnanna (11:18:22): > @C. Mirzayi (please do not tag this account)for the session today. My questions were answered. Pheeeeewwww:blush:

Yoko C (11:51:34): > Hello again. I’d like opinions on whether I should curate two graphs. One is an overall differential analysis, the other compares two categories of bacteria (BlOOM vs VANISH). The overall graph repeats the BLOOM and Vanish bacteria, but the researchers are answering a specific question with the Bloom vs Vanished graph. I was not going to add the Bloom vs Vanish, but now I am doubting if I should. > Bloom vs Vanished graph 3D:https://www.nature.com/articles/s41598-023-47748-8/figures/3Overall S6 (LEfSe)https://static-content.springer.com/esm/art%3A10.1038%2Fs41598-023-47748-8/MediaObjects/41598_2023_47748_MOESM1_ESM.pdf

Kate Rasheed (12:09:33) (in thread): > I learned from the questions. Thank you for asking them.

Mildred Anashie (12:26:10) (in thread): > Hi@Yoko CI haven’t been able to see what 6S is showing but I think you should curate Figure 3D. Also it doesn’t look like the comparisons are Bloom vs Vanish, but rather BloSSum seems to have individual comparisons and Vanish has its own comparisons. Does this answer your question?

Yoko C (12:33:03) (in thread): > @Mildred Anashiethanks for looking at this. You are right the full term is Blossum. The overall graph points to the idea of Vanish vs Blossum, and is subdivided even further between primers and places. It is a curatable figure, but since they repeat the info of the other, I was doubting (and lazy) to add it. Thanks again.

Mildred Anashie (12:34:07) (in thread): > Did the overall graph reference this? > > And are the signatures overlapping?

Yoko C (12:35:10) (in thread): > @Mildred Anashie, yes the signatures overlap, this is a graph that selects a specific set of bacteria that is found within the overall set.

Mildred Anashie (12:36:58) (in thread): > I’mof the opinion that if they overlap them you might have to curate the more comprehensive figure > > Hopefully you can get other opinions on this,I’llalso keep trying to open the 6c so I can get a better understanding@Yoko C

Adeshile Oluwatosin (13:01:29) (in thread): > Welcome:joy_cat:@Kate Rasheed

Adeshile Oluwatosin (13:05:05) (in thread): > Overall 6S is not opening here.@Yoko Cif you can see 6S, can you send it?So we can see the more comprehensive one.In the case where there’s an overlap.There’s no need to record bothBut we have to be very sure

Svetlana Ugarcina Perovic (13:22:31) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1728980965144859 - Attachment: Attachment > IMPORTANT: when the GitHub issue with your curation is claimed for review and got a label “needs review” any edits from this point are not allowed.

Yoko C (13:34:20) (in thread): > @Adeshile Oluwatosinsure, here is a part of the graph

Yoko C (13:35:56) (in thread): > Figure S6: Differential abundance analysis using SIAMCAT and LefSe. … (B) > LefSe analysis showing bacterial families associated with each country in primer set 1. - File (PNG): S6b.png

BOLARINWA AISHAT (13:59:32) (in thread): > Here’s mine.https://www.linkedin.com/posts/bolarinwaaishat_main-page-activity-7255276501145636864-eCof?utm_source=share&utm_medium=member_desktop - Attachment (linkedin.com): Bolarinwa Aishat on LinkedIn: Main Page > Let me plug you in on an interesting project I'm currently working on! > The Bioconductor #BugSigDB #MicrobiomeStudyCuration project. > > BugSigDB is a…

Adeshile Oluwatosin (14:03:33) (in thread): > @Yoko CI checked and saw that all taxa reported in Figure 3D are all in Figure S6. > > So onlycurateFigure S6

Mildred Anashie (14:12:54) (in thread): > @Adeshile OluwatosinI see some comparisons in Figure 3 that are not in Figure S6.@Yoko Cthe industrial, traditional, Transitional and Adadle groups are not reported in S6, do those groups mean anything?. If yes then you should record them

Yoko C (14:14:21) (in thread): > @Mildred Anashie, yes, those are in 3 other LEfSe graphs, I didn’t include them to not put to much information. But they follow the same idea. They are also part of figure S6, this is just a part so you guys get an idea.

Adeshile Oluwatosin (14:14:55) (in thread): > @Mildred Anashielet me check

Yoko C (14:17:12) (in thread): > LefSe analysis showing bacterial families associated with each lifestyle in primer set 2.@Mildred Anashie@Adeshile Oluwatosin - File (PNG): S6D.png

Adeshile Oluwatosin (14:18:28) (in thread): > @Yoko CThis curation is bulky:weary:

Adeshile Oluwatosin (14:19:05) (in thread): > All can be curated

Adeshile Oluwatosin (14:19:23) (in thread): > Is there a link to the full article, I’m giving opinion based on just what I can see

Yoko C (14:20:29) (in thread): > Yes, they are all curatable, but I was inclined to just do the LEfSes because they include everything. Here is the link to all of ithttps://www.nature.com/articles/s41598-023-47748-8

Mildred Anashie (14:20:55) (in thread): > Okay then@Yoko CI think you should focus on S6, it appears to be a more comprehensive figure

Adeshile Oluwatosin (14:21:54) (in thread): > I just viewed it…don’tcurate 3D still@Yoko C

Yoko C (14:22:36) (in thread): > @Mildred Anashie@Adeshile Oluwatosinyay! one less graph to do. Thank you both very much!

Adeshile Oluwatosin (15:08:10) (in thread): > We are not so sure too@Yoko C

UBNSEMS3S (15:20:34) (in thread): > No such thing as too many questions. I just wanted to ensure I answered everyone’s questions. Thank you for the thoughtful questions.

UBNSEMS3S (15:22:02) (in thread): > Sometimes if the site is under particularly heavy load the Experiments may not show right away. If you click the “…” in the menu bar at the top next to the search bar and then click “Refresh” that will force the page to refresh with the database and will hopefully show the missing experiments.

Adeshile Oluwatosin (15:27:24) (in thread): > <@UBNSEMS3S>You are welcome:relaxed:I understand > I’m also just trying to be playful > Don’t take me too serious on this one:grin:Thank you for always

Mary Agekameh (15:48:32) (in thread): > The issue has been resolved > > Thank you Chloe!

UBNSEMS3S (17:23:16): > Office hours recording. Thank you all who attended. - File (MPEG 4 Video): video1548107167.mp4

Mildred Anashie (17:42:19) (in thread): > Thank you for the recording<@UBNSEMS3S>

Kate Rasheed (17:58:50) (in thread): > Thank you:hugging_face:

Mildred Anashie (18:00:43): > Hi everyone > Hello<@UBNSEMS3S>@Svetlana Ugarcina PerovicI would really appreciate your opinion on this > > I have some questions regarding a study I am currently curating > 1. I am unsure if Figure 3 and 4 e-j is curatable > Also supplementary fig 1 and 2 seems to be showing differential abundance based on sequencing, if I’m correct > > 2. I was just wondering how I would curate those figures (Based on the contrasts and the sequencing):thinking_face:This is what the paper says about it > ’All samples were normalized to the same level for avoiding possible errors stemming from the use of different sequencing depths. To preserve as many sequences as possible, we set 3,100 tags as normalization, and a total of 437,100 high-quality sequences were used for further analysis. The same analysis with a normalized level of 6,000 tags (Figure S1) and DADA2 (Figure S2) were done in our study, strengthening the reliability of our conclusions’. > > Also this is the figure caption for each > *****Figure S1. Microbial analysis with a normalization of 6,000 sequences among the LR (n=41, green), MR (n=39, blue), and HR (n=31, red) groups. (A-D) Alpha diversity among the three groups. Average relative abundance of dominant microbes among the LR, MR, and HR groups at the phylum level (E) and family level (F), with each color representing a taxon. (G) Significantly discriminative taxa between the LR and HR groups were determined using linear discriminant analysis effect size (LEfSe) analysis. (H) Beta diversity comparison among the three groups. Principal coordinates analysis (PCoA) based on Bray–Curtis distance was used to illustrate the variations between the three groups. LR, low-risk group; MR, medium-risk group; HR, high-risk group; PD, phylogenetic diversity. >
> Figure S2. Microbial analysis of DADA2 among the LR (n=51, green), MR (n=52, blue), and HR (n=36, red) groups. (A-D) Alpha diversity among the three groups. Average relative abundance of dominant microbes among the LR, MR, and HR groups at the phylum level (E) and family level (F), with each color representing a taxon. (G) Significantly discriminative taxa among the LR, MR and HR groups were determined using linear discriminant analysis effect size (LEfSe) analysis. (H) Beta diversity comparison among the three groups. Principal coordinates analysis (PCoA) based on Bray–Curtis distance was used to illustrate the variations between the three groups. LR, low-risk group; MR, medium-risk group; HR, high-risk group; PD, phylogenetic diversity. > > > 3. *****Finally are the LEfSe plots showing one against all? Would I be right to curate this way?***** > *****Link to the articlehttps://pmc.ncbi.nlm.nih.gov/articles/PMC6369648/Thank you:pray: - Attachment (PubMed Central (PMC)): Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut > Objective: Gut microbiota is a newly identified risk factor for stroke, and there are no large prospective studies linking the baseline gut microbiome to long-term risk of stroke. We present here the correlation between the gut microbiota and stroke …

Aleru Divine (18:09:58) (in thread): > I’llhave a look at this@Mildred Anashie:sweat_smile:

Mildred Anashie (18:17:32) (in thread): > Thank you@Aleru Divine:blush:

Aleru Divine (18:45:32) (in thread): > About the figures 3 and 4e-j:sweat_smile:I’ll leave it to the mentors:pray:I can’t interpret it myself. The description says the letter a denotes significance. But when compared to what? It’s not very clear. > > Supplementary figures 1 and 2 are showing differential abundance results for 2 different microbial analysis methods > > For figure S1, microbial analysis by normalization, you have only one experiment which is comparing LR and HR. I’m sure you already got that covered:thumbsup:. > > For S2, DADA2, I think you’ll do a one against all experiment because of how the result is presented on the table. So a total of 3 experiments with only (increased) signatures each. > > The supplementary material S1 and S2 both present microbial analysis, but with slightly different methods I think. Can this be indicated somewhere? Maybe a note in the discussions page.The LEfSe plotswith comparing 3 groups should be a one against all type of experiment.With only increased signatures.

Mildred Anashie (18:59:28) (in thread): > I think the note idea works > > But then, what does the DADA2 imply? > I think normalization refers to relative abundanceI’mconfused a bit with that

Aleru Divine (19:09:56) (in thread): > Makes the two of us:face_with_peeking_eye:

Aleru Divine (19:26:47) (in thread): > I found a good resource on DADA@Mildred Anashie:face_holding_back_tears:https://bioconductor.org/packages/devel/bioc/vignettes/dada2/inst/doc/dada2-intro.html#:~:text=DADA2%20implements%20a%20novel%20algorithm,infer%20the%20true%20sample%20composition. > > Just like the study said > “The same analysis with a normalized level of 6,000 tags (Figure S1) and DADA2 (Figure S2) were done in our study, strengthening the reliability of our conclusions.” > > “DADA2 detects real biological variation missed by OTU methods while outputting fewer spurious sequences.” > > So both DADA and the Normalization were kind ofafurther confirmation. I suppose.

Yoko C (19:51:48) (in thread): > What an odd study, where figure 4 is before 2. For figure 3, what I understand is that since they used kruskall wallis they are testing all three groups at once. To see where the difference lies they paired groups (pair-wise test). When they paired LR to another group they put an “a”. So it would be LR vs the group with an “a”. I think for the normalization part, they preformed the analysis twice with the tag difference. This way they were sure their results didn’t change due to the different depths they mention.

Kate Rasheed (20:16:18) (in thread): > Hmmm. This your point@Yoko C:thinking_face:

Kate Rasheed (20:22:03) (in thread): > Figures 4e-j are curatable.<@UBNSEMS3S>made mention, and did further explanation on it yesterday during the office hours. > > See the description too: “E–J) The relative abundances of opportunistic pathogens in the gut among the three groups. The significances (P-value) among three groups were determined by the Kruskal–Wallis test and subsequent pairwise comparisons were adjusted by Bonferroni correction. “a” denotes instances where p < 0.05 when a comparison was performed with the LR group. LR, low-risk group; MR, medium-risk group; HR, high-risk group. PD, phylogenetic diversity.”

Kate Rasheed (20:23:29) (in thread): > @Yoko C”a” denotes instances where p<0.05.

Kate Rasheed (20:27:11) (in thread): > From Fig. 1, the comparison looks more like HR vs LR and MR (One to many).

Kate Rasheed (20:56:44) (in thread): > @Mildred AnashieFig 3G-H seems curatable. See this: “Interestingly, our results also demonstrated an increase in the average abundance of Bifidobacterium and Lactobacillus (two known probiotics) in the HR group (Figures 3G,H).”

2024-10-25

Cate Ouma (02:21:47) (in thread): > Here is a link to my post:https://www.linkedin.com/feed/update/urn:li:share:7255463288589709314/

Svetlana Ugarcina Perovic (03:12:27) (in thread): > @Kate Rasheed:arrow_up:

Mildred Anashie (03:19:22) (in thread): > Thank you@Aleru Divinefor the resource, It still seems like I am unclear about how to curate S1 and S2

Aleru Divine (03:24:05) (in thread): > @Mildred Anashiehow so?

Mildred Anashie (03:24:40) (in thread): > @Yoko CThank you, Ididn’tnotice the letter and I think the interpretation works@Kate RasheedI think the LEfSe plots are one against all while the figures 3 and 4 looks like Pairwise comparisons and the LR seems to be the group 0 > > So do you all agree I curate them?

Kate Rasheed (03:25:08) (in thread): > Well noted@Svetlana Ugarcina Perovic:hugging_face:

Kate Rasheed (03:26:36) (in thread): > Yes@Mildred AnashieLEfSe are one against all. LR &MR should be group 0.

Mildred Anashie (03:31:30) (in thread): > @Aleru DivineThe comparisons in figure 2 and S2 seems the same but with different alpha diversity results > > In trying to understand how to curate it, I noticed the sequencing information that made me think the difference was there since S2 made mention of DADA2 > > So right nowI’munclear if those are entirely different experiments and how to curate them:thinking_face:I hopeI’mcommunicating my question right

Aleru Divine (03:35:11) (in thread): > IfI’mlooking at the correct figures, the signaturesaren’tthe same are they?

Mildred Anashie (03:36:05) (in thread): > No@Aleru DivineSame statistical test, same contrast

Aleru Divine (03:38:56) (in thread): > DADA2 and normalization were done after a first microbial analysis to sort of strengthen the reliability of the study. Confirming the signatures are not the same, I think it’s okay right to curate differently. I mean you did curate S1 as a different experiment right?@Mildred AnashieThis is what I think@Mildred AnashieI’m very open to counter opinions.I’m not 100%

Mildred Anashie (03:43:32) (in thread): > Yea@Aleru DivineS1 shows results for a different contrast, just LR nd HR

Aleru Divine (03:50:53) (in thread): > I think you should curate S2 too@Mildred Anashie

Adeshile Oluwatosin (05:15:33) (in thread): > Thank you<@UBNSEMS3S>

Rahila-me (07:00:28): > @Svetlana Ugarcina Perovicplease the sequencing platform used in my study was:NovoSeq 6000 platformI can not see it from the drop down. CC@Scholastica Urua

Svetlana Ugarcina Perovic (07:07:52) (in thread): > Illumina - File (PNG): Screenshot 2024-10-25 at 13.07.39.png

Svetlana Ugarcina Perovic (07:08:47) (in thread): > or simple search in the bugsigdb platform gives you the answerhttps://bugsigdb.org/w/index.php?title=_Special:Search&search=NovaSeq+6000+&go=Go&searchToken=f1yrlpwh9j4b1ynx928qe8p2z - Attachment (BugSigDB): Special:Search

Rahila-me (07:09:26) (in thread): > @Svetlana Ugarcina PerovicThank you so much, just learnt a new today:joy:

Rahila-me (07:10:14) (in thread): > just did and seen:IlluminaNovaSeq6000The IlluminaNovaSeq6000is a high-throughput sequencing machine developed by Illumina. Read more - Attachment (BugSigDB): Illumina NovaSeq 6000 > …

Aleru Divine (07:14:05) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@Rahila-mein addition to NovaSeq, there’s also HiSeq, MiSeq etc. different variationsofthe Illumina platform.:sweat_smile:Here’s an article on thathttps://med.stanford.edu/gssc/services/sequencing1.html#:~:text=NovaSeq%20uses%20two%2Dcolor%20chemistry,on%20Illumina’s%20website%20(PDF).

Rahila-me (07:17:57) (in thread): > @Aleru Divinei see i just read up the link you sent one thing in common of all that refers to Illumina is ending inSeq. What a nice read, Thank you

Aleru Divine (07:19:13) (in thread): > Omg! yeah:sweat_smile:@Rahila-me

Mildred Anashie (07:35:12) (in thread): > Thank you so much@Svetlana Ugarcina PerovicAlready saved for later:blush::raised_hands:

Mildred Anashie (07:37:25): > Hi@Svetlana Ugarcina PerovicI added some signatures to a study I’m curating and it appears like this. I’m not sure what this could imply - File (PNG): missing signatures.png

Kate Rasheed (07:44:35) (in thread): > @Mildred AnashieI’ve experienced this before. It could mean that you duplicated the taxa (the taxa is appearing twice). You might need to check again.

Mildred Anashie (07:47:35) (in thread): > Okay@Kate RasheedI’ll check, Thank you

BOLARINWA AISHAT (07:52:22) (in thread): > This is educative > Thank you all

Rahila-me (07:59:47): > <!here>this is what my study used as statistical test (DESeq2), for theData transformation i am seeing relative abundance rather than raw counts, > Which should i go for, need a second eyes..cos the pinned msg picksDESeq2 against**** raw counts**

Mildred Anashie (08:00:35) (in thread): > So I checked, didn’t duplicate any but I kept refreshing the page, and everything looks okay now.

Mildred Anashie (08:03:31) (in thread): > Hi@Rahila-meI’mnot sure what to do, but I believe if the paper says there used relative abundance for the data transformation then you would have to record relative abundance > > Also you could attach a link to the study

Samuel Nnanna (08:04:01) (in thread): > Please send the link to the study@Rahila-me

Samuel Nnanna (08:04:37) (in thread): > I read somewhere that using relative abundance for DeSeq2 can lead to misleading results so usually it’s Raw counts

Aleru Divine (08:04:54) (in thread): > @Rahila-meThedata transformation is dependent on the test usedandfrom what I know, the data transformation for DESeq2 is raw counts.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697145085673689?thread_ts=1697141457.022309&channel=C04RATV9VCY&message_ts=1697145085.673689 - Attachment: Attachment > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio -> Rare. ANCOM > > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

Mildred Anashie (08:05:39) (in thread): > Thank you again@Kate Rasheed

Aleru Divine (08:07:43) (in thread): > Thank you for the recording@C. Mirzayi (please do not tag this account):blush:

Rahila-me (08:09:10) (in thread): > ok…Thank you@Aleru DivineI will leave it at the raw count i picked, Thanks@Mildred Anashie@Samuel Nnannafor your input

Samuel Nnanna (08:50:00): > @Svetlana Ugarcina PerovicPlease delete Signatures 1 in the experiments; 5, 7, 8 and 9https://bugsigdb.org/Study_1160 - Attachment (BugSigDB): Targeted discovery of gut microbiome-remodeling compounds for the treatment of systemic inflammatory response syndrome - BugSigDB > Systemic inflammatory response syndrome (SIRS) is a severe inflammatory response that can lead to organ dysfunction and death.Modulating the gut microbiome is a promising therapeutic approach for managing SIRS.

Svetlana Ugarcina Perovic (09:05:56) (in thread): > deleted.

Samuel Nnanna (09:06:17) (in thread): > Thank you

Yoko C (09:30:27): > Hey everyone, I want to check if I am going in the right path. I am curating a graph which has the bacteria species name on it, the supplementary material has a table with the complete nomenclature and additionally the NCBI id, so for example the graph saysStreptococcus sp. [C equinus/infantarius/lutetiensis](which I think means they need to confirm the species?), the supp table has a matching name, and then the NCBI id is 1301. This NCBI id returns the genus, Streptococcus. In some cases if the species isn’t found they put NA, but in others they put the genus NCBI id. So my reasoning is I should put the whole name as found in the graph, i.e.Streptococcus sp. [C equinus/infantarius/lutetiensis] and not go by the NCBI id in these cases. But I just want to make sure.

Adeshile Oluwatosin (09:31:36) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (09:32:18) (in thread): > Hi@Yoko Ccan you share the graph please

Yoko C (09:36:16) (in thread): > Sure, here is only part of the graph so that it is a readable size. - File (PNG): motus vs metaphlan.png

Aleru Divine (09:38:14) (in thread): > Thanks

Mildred Anashie (09:38:18) (in thread): > Hi@Yoko CDoes the paper mention anything related to this? > > Because I was going to say they were probably reporting different species of Streptococcus till I saw the graph

Samuel Nnanna (09:39:54): > @Svetlana Ugarcina PerovicI can’t reach the original curator of the correction paper. what do I do because I have made a lot of corrections on the paper already

Yoko C (09:39:55) (in thread): > No, the paper does not go into specifics about this. I think C. is for confirmation, instead of using Cf.

Svetlana Ugarcina Perovic (09:40:50) (in thread): > please share the github issue link here, I can not tell anything without more details

Samuel Nnanna (09:41:12) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/508

Svetlana Ugarcina Perovic (09:42:10) (in thread): > By the way, why you did a lot of corrections or any work without agreement from the original curator?

Samuel Nnanna (09:43:38) (in thread): > We did speak on slack and we agreed to work on it and share ideas, but since then, i’ve been trying to reach her, no response till now

Svetlana Ugarcina Perovic (09:44:09) (in thread): > ok, I do not see that part of communication

Svetlana Ugarcina Perovic (09:44:28) (in thread): > Please do finalize the curation.

Svetlana Ugarcina Perovic (09:44:47) (in thread): > I will assign it in the github issue and let know the original curator.

Samuel Nnanna (09:45:02) (in thread): > i connected with her on slack as she wasn’t responsive on github….

Samuel Nnanna (09:45:18) (in thread): > Okay, i will

Samuel Nnanna (09:45:24) (in thread): > thank you

Aleru Divine (09:46:01) (in thread): > @Mildred Anashie@Yoko Ceither they meant > 1. Streptococcus equinis or Streptococcusinfantariusor Streptococcus lutetiensis. > Or they meant > > 2. Streptococcus equinis and Streptococcus infantarius and Streptococcus lutetiensis. > > I’d say go with the NCBI ID and leave a note. > > NCBI ID returns Streptococcus genus which is correct although not precise. They all belong to the Streptococcus genus. > > Do they mention the species differently in the paper? And maybe they just put them all together in the graph.

Yoko C (09:50:23) (in thread): > @Aleru Divinethe species are not mentioned in the paper. Going with NCBI id would reduce my workload, so that’s a nice idea. I am not sure where I would leave a note?

Aleru Divine (09:52:46) (in thread): > Youcan leave a note on the discussions page - File (JPEG): IMG_1361

Yoko C (09:52:48) (in thread): > i don’t think the species are grouped, because the same genus shows up with specific species and matching ncbi ID. I think the C and brackets mean the placement is uncertain.

Mildred Anashie (09:53:49) (in thread): > I agree@Yoko CYou can click on the three dots above to leave a noteIt’syourstudy’stalk page

Yoko C (09:53:55) (in thread): > Thanks@Aleru Divineand@Mildred Anashie

Ebuka Chinwuba (11:48:19) (in thread): > Appreciate:+1:

Ebuka Chinwuba (11:51:04) (in thread): > :pray:

2024-10-26

Kate Rasheed (03:09:48): > Good morning everyone. A happy weekend to us all. > > Please I have a question. In an article I’m working on with@Agatha, it was mentioned that “LEfSe analysis confirmed enrichment in cases of Proteobacteria and revealed enrichment of Gammaproteobacteria, Enterobacteriales, and Enterobacteriaceae, enrichment of Erysipelotrichi, Erysipelotrichales, and Erysipelotrichaceae of the phylum Firmicutes, and enrichment of the genus Barnesiella in the phylum Bacteroidetes in cases, whereas Rikenellaceae and Alistipes in the phylum Bacteroidetes were enriched in controls”. However in the figure, it’s decreased.<@UBNSEMS3S>mentioned during the office hours on Thursday that in the “discussion section” people make claims to win an argument. > > Please I would like to know your thoughts on this. I’m thinking the statement was an interpretation of the Mann-whitney test. > > Here is the link to the article:https://academic.oup.com/jid/article/211/1/19/801451?login=false

Adeshile Oluwatosin (03:18:52) (in thread): > I would check

Adeshile Oluwatosin (03:18:54) (in thread): > Good morning

Agatha (03:19:12) (in thread): > Good morning

Mildred Anashie (03:25:33) (in thread): > Hi@Kate RasheedGood morning > > I’ll look at it

Mildred Anashie (03:26:14) (in thread): > Do you mean this statement in your question was reported in the discussion?

Aleru Divine (03:31:17) (in thread): > Good morning@Kate RasheedI believe the figure and the text are both correct. > > Negative as well as positive values denotes increase in abundance compared to the other group. > > Because if it were the other way round they’d say “the positive values were enriched in cases and the negative values were enriched in controls”. > > The paper isn’t wrong. The red bars although negative are enriched in cases and the green bars are enriched in controls.

Aleru Divine (03:33:54) (in thread): > Here’s a resource. Check the description of figure 3 talking about the LDA negative and positive valueshttps://www.researchgate.net/publication/350826697_Periodontal_dysbiosis_associates_with_reduced_CSF_Ab42_in_cognitively_normal_elderly - File (PNG): IMG_1368

Mildred Anashie (03:34:10) (in thread): > I see what your question is now@Kate RasheedI’d say, focus on the figure as it shows you taxa enriched in cases and those enriched in controls > > The red bars indicate enrichment in the cases while the green bars indicate enrichment in controls

Adeshile Oluwatosin (03:37:38) (in thread): > Hi@Kate RasheedFigure 3 in this article > Shows that Alistpes and Rikenellaceae are in the decreased abundance. > Red increase in cases (increased abundance) > Green Increase in controls(decreased abundance) > > Corrected

Aleru Divine (03:40:57) (in thread): > @Adeshile Oluwatosinyou’re getting it a bitmixed up, the signatures represented by the red bars were enriched in cases(according to BugSigDB curation policy, we curate those as signature 1 which is increased abundance) and curate the ones enriched in the other group (controls) as decreased (signature 2)

Mildred Anashie (03:42:43) (in thread): > Hi@Adeshile OluwatosinI’mof the opinion that taxas reported to be enriched in the case group should be recorded as increased and those said to be enriched in the controls should be the decreased > > The authors probably choose to report the taxas this way, itdoesn’tchange what we should do based on the curation policy > > Also I think BugSigdb focuses on the cases

Aleru Divine (03:45:02) (in thread): > Yes@Mildred Anashie@Adeshile Oluwatosinsignatures enriched in cases (group 1) are always curated as increased in abundanceaccording to the curation policy - File (PNG): IMG_1369

Adeshile Oluwatosin (03:57:52) (in thread): > The increased signature in this study is the exposed group@Kate Rasheedthe cases.

Kate Rasheed (04:05:19) (in thread): > If it was enriched in cases, it should have been in the positive value. > > I’ve worked on LEfSe where the control and case group were in the positive values to show higher abundance that’s why I’m quite confused@Adeshile Oluwatosin@Aleru Divine@Mildred Anashie

Kate Rasheed (04:06:55) (in thread): > See this LEfSe - File (JPEG): Screenshot_20241026-090623.jpg

Adeshile Oluwatosin (04:11:04) (in thread): > @Kate Rasheedi guess that’sthe way they chose to report the taxa. > > Paying attention to details is the thing. > I had to check all over again. > The point of curation in bugsigdb as shown is to ensure the exposed group is in the increased signature. > Which in this study is the cases(red bar). > > Since the text says enrichment in both cases and controls > And the cases are the exposed group in this case. > You curate the case as the increased signature. > > This is my opinion though, since both text and Figure says same thing.

Aleru Divine (04:13:19) (in thread): > @Kate RasheedI get the confusion. Did you see thestudyI shared?It is kind of similar to yours although not exact.They tried to explain the LDA values(both negative and positive LDA scores shows increased abundancein any of the groupscompared to the other)Enriched in cases(1)means increased in cases compared to controls.This will be curated as increased abundance in BugSigDBEnriched in controls(0)means increased in controls compared to cases.This will be curated as decreased abundance in BugSigDB > > Both the text and paper are correct.

Kate Rasheed (04:19:25) (in thread): > I understand that enriched in cases means increased and enriched in controls means decreased@Aleru Divine. This was the same thing the initial curator curated. > > However at the point of correction, her mark for correctly identifying signature directions was reduced that’s why I’m thinking the negative values should be decreased.

Aleru Divine (04:20:32) (in thread): > Can you share the paper please

Kate Rasheed (04:20:57) (in thread): > https://academic.oup.com/jid/article/211/1/19/801451?login=false

Aleru Divine (04:22:16) (in thread): > My bad, I meant the study

Kate Rasheed (04:24:17) (in thread): > https://bugsigdb.org/Study_1152 - Attachment (BugSigDB): Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection - BugSigDB > BACKGROUND: Despite effective antiretroviral therapy (ART), patients with chronic human immunodeficiency virus (HIV) infection have increased microbial translocation and systemic inflammation.Alterations in the intestinal microbiota may play a role in microbial translocation and inflammation.

Aleru Divine (04:25:40) (in thread): > Thank you Kate

Kate Rasheed (04:26:08) (in thread): > @Aleru DivineI think this negative and positive cases are enriched because of the log transformed scorehttps://www.researchgate.net/publication/350826697_Periodontal_dysbiosis_associates_with_reduced_CSF_Ab42_in_cognitively_normal_elderly - Attachment: Attachment > Here’s a resource. Check the description of figure 3 talking about the LDA negative and positive values > https://www.researchgate.net/publication/350826697_Periodontal_dysbiosis_associates_with_reduced_CSF_Ab42_in_cognitively_normal_elderly

Kate Rasheed (04:29:34) (in thread): > @Aleru Divinethe correct decreased signature is signature 4. I don’t know why it’s not reading correctly, I’ll check why later.

Aleru Divine (04:36:24) (in thread): > @Kate RasheedWhatI’veseen is that positive and negative in LDA scores indicate the direction of change in abundance between two groups but do not necessarily mean an increase or decrease in literal terms. The signatures listed are enriched in both groups.Seeing how it is curated and seeing that it was not scored.I’mpretty confused myself.:sweat_smile:

Kate Rasheed (04:37:58) (in thread): > She was scored half which means to me she was scored for the decreased.@Aleru Divine

Aleru Divine (04:38:41) (in thread): > Did she enter all relevant experiments?

Kate Rasheed (04:40:27) (in thread): > From this your statement, positive LDA scores indicate the increased abundance right and vice versa right?https://community-bioc.slack.com/archives/C04RATV9VCY/p1729931784311509?thread_ts=1729926588.880799&cid=C04RATV9VCY - Attachment: Attachment > @Kate Rasheed What I’ve seen is that positive and negative in LDA scores indicate the direction of change in abundance between two groups but do not necessarily mean an increase or decrease in literal terms. The signatures listed are enriched in both groups. > > Seeing how it is curated and seeing that it was not scored. I’m pretty confused myself. :sweat_smile:

Aleru Divine (04:42:49) (in thread): > No, not necessarily increased or decreased.Just a direction of change.

Kate Rasheed (04:47:44) (in thread): > @Aleru DivineFor the example you gave, what if the log transformation score made the negative and positive values enriched?

Aleru Divine (04:54:46) (in thread): > From allI’vebeen seeing (I may be wrong) but I think that the log-transformed values show which taxa kind of stands out more in each group, with positive and negative just representing which group is more enriched. But this enriched groups doesn’t necessarily mean an actual increase or decrease in abundance > > We are asked to curated those enriched in cases or group 1 as increased in BugSigDB though.

Adeshile Oluwatosin (05:10:59): > Good morning once again, > > I’d appreciate a peer review on this study;https://bugsigdb.org/Study_1107https://academic.oup.com/cid/article/67/8/1237/4961341?login=falseFor experiment 3 here, can’t seem to place the sample size.

Aleru Divine (05:23:19) (in thread): > I’ll have a look at thisagain:sweat_smile:@Adeshile Oluwatosin

Adeshile Oluwatosin (05:30:12) (in thread): > Thank you:joy_cat:@Aleru Divine

Kate Rasheed (05:53:33): > Good day@Svetlana Ugarcina PerovicKindly delete Signature 2 under Experiment 1 in this study:https://bugsigdb.org/Study_1152. > > It was a mistake. - Attachment (BugSigDB): Intestinal microbiota, microbial translocation, and systemic inflammation in chronic HIV infection - BugSigDB > BACKGROUND: Despite effective antiretroviral therapy (ART), patients with chronic human immunodeficiency virus (HIV) infection have increased microbial translocation and systemic inflammation.Alterations in the intestinal microbiota may play a role in microbial translocation and inflammation.

Kate Rasheed (06:47:59) (in thread): > @Adeshile OluwatosinI can’t see sample size but there was MHT correction “adjusted p-value…”

Kate Rasheed (07:00:03) (in thread): > @Adeshile OluwatosinI don’t know if this helps as the sample size: “Here, we found 12% fewer HLA-DR+CD4+ T cells in EBF infants compared to NEBF infants.” Sample size 0 could be number of EBF infants while 1 is NEBF infants.

Svetlana Ugarcina Perovic (07:00:54) (in thread): > deleted.

Kate Rasheed (07:02:21) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (07:12:40) (in thread): > @Kate RasheedI also couldn’tsee it o

Aleru Divine (07:12:42) (in thread): > @Adeshile OluwatosinI haven’t seen any mention of sample sizes for experiment 3 either. > Everything else checks out so far expect for the MHT correction as mentioned by@Kate Rasheed“ we found that counts of Akkermansia muciniphila in stool were 6.5 log2 fold higher in infants with high CD4+HLA-DR+ T-cell frequency (adjusted P = .005). CD4+HLA-DR+ cell frequency was inversely related to counts of Pantoea agglomerans, Bifidobacterium bifidum, and S. lactarius (adjusted P = .008 for all), suggesting specific taxa may partially drive immune quiescence (Figure 4B).”

Adeshile Oluwatosin (07:17:04) (in thread): > In the case of no sample size mention, should I curate the experiments without it.

Adeshile Oluwatosin (07:35:54) (in thread): > Thank you@Kate Rasheed@Aleru DivineI’ve changed the MHT correction to yes for experiment 3 as well. It was initially added for the first two experiments. > I guessI’llleave a note saying sample sizewasn’tstated.

Adeshile Oluwatosin (07:52:48) (in thread): > Also@Kate Rasheed@Aleru DivineI could only seeage is a confounder for experiment 3.I’mnot sure ifit’sfor experiment 1 and 2 as well. > Please take a look as well

Adeshile Oluwatosin (08:09:58) (in thread): > “which persisted after controlling for age in partial Mantel tests.” > > Does this mean age is a confounder for experiment 3@Kate Rasheed@Aleru DivineAlso I’m still speculating on if thebody siteis still feces or blood serum for experiment 3.@Svetlana Ugarcina Perovic@Chioma Onyido@Scholastica Urua@Esther Afuape

Kate Rasheed (08:25:51) (in thread): > Yes for experiment 3. I saw age there as well.

Adeshile Oluwatosin (08:30:36) (in thread): > I’m thinking maybe it’s not for the main experiment but just for partial mantel tests@Kate Rasheed

Kate Rasheed (08:33:23) (in thread): > I’ll go through the article again and see if it’s for all experiments. I only noticed the confounder in experiment 3.

Adeshile Oluwatosin (08:55:11) (in thread): > I’m just confused on if “age” should be considered a confounder for experiment 3:pleading_face::sob:I don’t think it was mentioned for experiment 1 and 2@Aleru Divine@Kate Rasheed

Kate Rasheed (08:56:39) (in thread): > Let’s look at the article again with a fresh eyes:smile:

Aleru Divine (08:56:44) (in thread): > I believe they controlled for age in experiment 3@Adeshile Oluwatosin

Esther Afuape (08:58:06) (in thread): > “Controlled for” “adjusted for” are typical pointers to confounding factors.It’salso possible to have a confounder adjusted for a particular experiment and not the entire study to see what difference it makes to the results of the comparison.

Adeshile Oluwatosin (09:01:08) (in thread): > Thank you@Esther Afuape:pleading_face:I’ll leave it as a confounder then.

Aleru Divine (09:04:50) (in thread): > Thank you@Esther Afuape:sweat_smile:

Inimfon Ebong (09:48:30): > Hello everyone > I have a question, I just realised that data from 2 different figures can be incorporated into my experiment one without the need for a new experiment. Should o put them together or leave it as different experiments with different sources

Inimfon Ebong (09:50:05): > Info from my figure 3 and 4 for my control vs stroke can be put into one should I leave it as one or should I split the experiment into 2 for the 2 sources

Kate Rasheed (09:51:34) (in thread): > If they have different statistical tests, curate separately. You might need to share the article for us to see.

Aleru Divine (09:52:30) (in thread): > Did they use different statistical tests?@Inimfon EbongIf yes, you should curate another experiment. > If no, you can curate as one experiment and ensure to input all the signature sources.Also for clarification, please share the study.

Mildred Anashie (09:52:49) (in thread): > Hi@Inimfon EbongI’mnot sure I fully understand your question > But if the contrast are the same with same statistical test, then it’s possible that can be curated as one experiment > > But I think you should share a link to your study

Inimfon Ebong (09:53:01) (in thread): - File (PDF): J Parenter Enteral Nutr - 2020 - Tan - Dysbiosis of Gut Microbiota and Short‐Chain Fatty Acids in Acute Ischemic Stroke and.pdf

Mildred Anashie (09:53:32) (in thread): > Okay just seeing this > > I replied to your other postI’lltake a look

Aleru Divine (09:53:51) (in thread): > Thank you@Inimfon Ebong

Inimfon Ebong (09:53:58) (in thread): > The statistical test are the same the only difference is that the took note of the fatty acid3 producing microbes

Mildred Anashie (09:55:33) (in thread): > @Inimfon EbongIdon’tthink figure 4 is showing differential abundance > > Just figure 3 is

Inimfon Ebong (09:55:54) (in thread): > But because of the way the data is arranged I have to create separate experiments for the mild moderate and severe seperatly from what I have done before

Kate Rasheed (09:56:51) (in thread): > Yes@Mildred AnashieFigure 2D is also curatable@Inimfon Ebong

Inimfon Ebong (09:57:01) (in thread): > @Mildred Anashiefigure 4 shows increased and decreased abundance specifically for the fatty acide bacteria, its part of what we asked during the office hour

Inimfon Ebong (09:57:23) (in thread): > Sorry

Inimfon Ebong (09:57:32) (in thread): > Figure 2 and 3

Inimfon Ebong (09:57:51) (in thread): > I’ve been staring at this thing so long I’m getting my numbers mixed up

Inimfon Ebong (09:58:20) (in thread): > @Kate Rasheedyes those are my first 4 experiments

Aleru Divine (09:58:27) (in thread): > That’s true@Mildred Anashiefigure 4a and b is talking about Short chain fatty acids.Figure 4C shows a heatmap but itisn’tcuratable.

Mildred Anashie (09:58:50) (in thread): > Yes for figure 3 > > Each contrast has a line with an asterisk above it@Inimfon Ebong

Aleru Divine (09:58:50) (in thread): > Oh you mean 2 and 3:sweat_smile:

Inimfon Ebong (10:00:45) (in thread): > @Aleru Divineyes:joy:I just mixed them up

Mildred Anashie (10:04:01) (in thread): > @Inimfon Ebongwhat statistical test did they use for figure 3? > > Ican’tseem to find that information and the paper said LEfSe was used for differential abundance which we see in Figure 2:thinking_face:

Kate Rasheed (10:06:35) (in thread): > @Mildred AnashieSame thoughts.

Aleru Divine (10:08:30) (in thread): > It doesn’t say@Mildred Anashiebut those aren’t typical LEfSe plots. But look at this excerpt > > “To identify differentiated metagenomic biomarkers, a linea. discriminant analysis (LDA) coupled with effect-size measurement (LEfSe) was performed athttp://huttenhower.sph.harvard.edu/galaxy. > Significantly different bacteria with LDA scores of ≥2.5 were plotted on taxonomic bar plots.The relative abundance of microorganisms and concentrations of SCFAs are shown as box plots. > **

Kate Rasheed (10:09:49) (in thread): > See this “multivariate logistic regression models > included all variables with statistical significance (P < > .10) in the univariate model as well as those with clinical > significance.” > > I don’t think it’s Mann-whitney.

Mildred Anashie (10:12:22) (in thread): > This seems to imply LEfSe@Aleru DivineBut the difference between this and the first LEfSe plot should be the SCFA’s concentration > > Also this is more of a pairwise comparison

Aleru Divine (10:14:53) (in thread): > Yes@Mildred Anashieunlike the one against all by LEfSe.

Kate Rasheed (10:15:48) (in thread): > I would like to know about this statistal test sha… I thought it’s Mann-whitney, then I saw logistics regression. > > I’ll be waiting for conclusion let me learn:smile:.

Aleru Divine (10:18:16) (in thread): > Then there’s going to be a few more comparisons from figure 3:grimacing:butdo you this needs to be curated?@Mildred Anashie:face_holding_back_tears:

Mildred Anashie (10:20:47) (in thread): > Yes@Aleru Divine<@UBNSEMS3S>said during the last office hour, if they did between group comparisons or something like that, it could be curated > > PS: I am not quoting word for word:laughing:

Aleru Divine (10:25:34) (in thread): > :joy::joy:it’s okay@Mildred AnashieI wanted a confirmation:hugging_face:Pairwise comparisons it is then.@Inimfon EbongBut don’t curate this “firmicutes/Bacteroidetes (F/B) ratio”<@UBNSEMS3S>mentioned to not curate ratiosin the last office hours.

Aleru Divine (10:26:39) (in thread): > I thinkLEfSe isthe statistical test used. I’d say LEfSe but I’m not very certain.:pray:like not very certain. I’ll go through the paper slowly. See if I can catch something.

Princess Rehoboth Asuelimen (10:33:11): > Hello everyone, I just need clarity with the submitting the final application on or before 29th of October. My question is, how do you submit the final application?

Inimfon Ebong (10:35:47) (in thread): > @Mildred Anashieyes your right I had to go back and read the intro but it seems to implie that LEfSe was used but the plots being pairwise is the reason I can’t add the data to the initial 4 experiments. However for the first experiment where its control vs stroke I want to combine it with the data from figure 3https://bugsigdb.org/Study_1140 - Attachment (BugSigDB): Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes - BugSigDB > BACKGROUND: The intestinal microbiota and its metabolites have been reported to play an important role in stroke.Gut microbiota-originating short-chain fatty acids (SCFAs) modulate brain functions directly or indirectly through immune, endocrine, vagal, and other humoral pathways.

Mildred Anashie (10:38:08) (in thread): > Are they the same microbial taxa?@Inimfon Ebong

Adeshile Oluwatosin (10:39:09) (in thread): > Hi@Princess Rehoboth AsuelimenAfter recording all contributions > Click to record final application

Inimfon Ebong (10:39:28) (in thread): > No only 1 is similar

Kate Rasheed (10:40:15) (in thread): > A side question please. Looking at this statement “The standard errors (and P values) for each model were calculated using bootstrapping with R equal to 15 000”, does this signify a yes for multiple hypothesis correction? > > PS. I did not see any q-value, adjusted p-value or FDR@Adeshile Oluwatosin@Aleru Divine@Mildred Anashie

Adeshile Oluwatosin (10:40:21) (in thread): - File (JPEG): IMG_1937

Adeshile Oluwatosin (10:41:02) (in thread): > Refer back to this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1729497239357399 - Attachment: Attachment > For your final application: There are no community-specific questions. > As for the timeline, the internship begins on Monday, Dec 9th and runs until Friday, March 7th and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Mildred Anashie (10:41:23) (in thread): > I think it’s supposed to appear as “Apply to this project” > > You can only submit a final application to the project if you have recorded a contribution for the project@Princess Rehoboth Asuelimen

Aleru Divine (10:41:36) (in thread): > @Princess Rehoboth Asuelimenthe final application deadline isOct. 29, 2024 4pm UTC.To submit your final application you must record at least one contribution for theMicrobiome Study Curation project.Then you click on “APPLY FOR THIS PROJECT” > > This takes you to the application information page.It’spretty straightforward from here on. - File (JPEG): IMG_1419

Aleru Divine (10:42:48) (in thread): > It’sa no@Kate Rasheed

Mildred Anashie (10:43:08) (in thread): > I think you should record separately > > Remember the experiments in figure 3 are focused on the concentration of SCFA’s though based on the severity of stroke@Inimfon Ebong

Mildred Anashie (10:43:33) (in thread): > @Kate RasheedIdon’tthink that implies MHT

Inimfon Ebong (10:44:22) (in thread): > Very well > Thank you

Adeshile Oluwatosin (10:45:06) (in thread): > No@Kate RasheedLike you said, itwasn’tstated that p-value was adjusted for or a mentioned q-value

Princess Rehoboth Asuelimen (10:46:42) (in thread): > Thank you everyone, so I have made contributions on the microbiome study

Adeshile Oluwatosin (10:47:26) (in thread): > Just follow the screenshot I sent@Princess Rehoboth AsuelimenClick to create a final application and you are good to go

Princess Rehoboth Asuelimen (10:48:48) (in thread): > And anytime I click edit or create a final application, it just takes my to a page that shows my project application ( update your application) and all contributions I have made

Aleru Divine (10:49:58) (in thread): > Click on APPLY FOR THIS PROJECT@Princess Rehoboth AsuelimenIt’lltake you to the application page.

Princess Rehoboth Asuelimen (11:02:20) (in thread): > @Adeshile Oluwatosinfollowing your screenshot, it takes me to this attached screenshot. - File (PNG): NOE.png - File (PNG): NOE 2.png

Adeshile Oluwatosin (11:03:09) (in thread): > Okay,@Princess Rehoboth Asuelimengo back and click > “APPLY FOR THIS PROJECT”

Adeshile Oluwatosin (11:03:43) (in thread): > A second,I’ll screenshot

Adeshile Oluwatosin (11:04:24) (in thread): > Clickmy application

Adeshile Oluwatosin (11:05:27) (in thread): > Go to “microbiome Study curation project “ > Click“Apply for This project”beneath project application@Princess Rehoboth Asuelimen

Princess Rehoboth Asuelimen (11:14:45) (in thread): > @Adeshile Oluwatosin, mine shows “Update your Application” instead of “APPLY FOR THIS PROJECT.” That means I have actually submitted the final application, right? - File (PNG): noe 3.png

Adeshile Oluwatosin (11:17:31) (in thread): > It’s feces figured, thank you everyone

Mildred Anashie (11:17:45) (in thread): > Yes@Princess Rehoboth Asuelimen

Adeshile Oluwatosin (11:18:23) (in thread): > @Princess Rehoboth Asuelimenclick on update your application, let me seeYes, you have

Kate Rasheed (11:20:00) (in thread): > @Adeshile OluwatosinShe can only update the application if she wants to make changes to the application.

Adeshile Oluwatosin (11:20:32) (in thread): > I’maware@Kate Rasheed

Adeshile Oluwatosin (11:21:17) (in thread): > Told her to click on that, cos it seems likeshe’snot done with what she filled in right?@Princess Rehoboth AsuelimenAnyways, if you want to edit your application. > > Just click on update my application

Princess Rehoboth Asuelimen (11:25:49) (in thread): > So i think i have submitted my final application, i didn’t fill some parts though cause i have no experience in those parts. - File (PNG): 4.png - File (PNG): 5.png - File (PNG): 6.png - File (PNG): 7.png

Yoko C (11:29:43) (in thread): > Just wanted to second@Mildred Anashie, the two figures are comparing different things. I also wanted to add the paper mentions Mann Whitney, so that is probably the test for figure 3? The reason they mention LEfse, I think, is because the bacteria were selected based on the lefse results.

Mildred Anashie (11:50:45) (in thread): > @Yoko Cis there any other statement that mentions Mann Whitney for statistical test asides this? (See image) > > If not, thenI’mwondering why only Mann Whitney is being selected amongst the others > Also I believe that statementdoesn’tpoint to differential abundance - File (JPEG): IMG_1610

Kate Rasheed (11:53:50) (in thread): > @Mildred AnashieWhy can’t logistics regression work since it’s looking at the significant p-values of categorical variables and continuous variables. > > The box plot is actually showing the categorical variables talked about.

Yoko C (11:53:58) (in thread): > @Mildred Anashie, if I remember the figure correctly the little lines above the bars were in pairs. Kruskal wallis is multiple comparison, the regression was for models, so all is left is mann-whitney

Kate Rasheed (11:56:40) (in thread): > @Yoko CJust like linear regression is for linear mixed model, I think logistics regression should work sha.

Adeshile Oluwatosin (11:59:05) (in thread): > @Princess Rehoboth Asuelimenokay, you are good to go:thumbsup:

Adeshile Oluwatosin (11:59:07) (in thread): > @Princess Rehoboth Asuelimenokay, you are good to go:thumbsup:

Yoko C (12:00:41) (in thread): > @Kate Rasheedit could be, but just from the graph the only thing being compared is relative abundance between two categories. Logistic regression would usually be used for something else.

Princess Rehoboth Asuelimen (12:06:48) (in thread): > Thank you@Adeshile Oluwatosinand everyone for assisting me.

Adeshile Oluwatosin (12:08:00) (in thread): > Welcome@Princess Rehoboth Asuelimen:hugging_face:

U02CNMR4YEA (13:08:03): > Hi Everyone! For some reason, when I pull in all of the data from BugSigDB, I don’t get Study 1103. This wasn’t the case previously. Can I ask if anyone knows why that study wouldn’t show up? Thank you in advance.

Kate Rasheed (13:11:23) (in thread): > Hi<@U02CNMR4YEA>. I don’t know why it isn’t showing from your end but I can see it from my end.

Mildred Anashie (13:12:35) (in thread): > Hi<@U02CNMR4YEA>I can seehttps://bugsigdb.org/Study_1103from my end.It’sa study on “Ocular surface microbiota in patients with varying degrees of dry eye severity” with 3 experiments. Could this be the correct study? - Attachment (BugSigDB): Ocular surface microbiota in patients with varying degrees of dry eye severity - BugSigDB > AIM: To elucidate the profiles of commensal bacteria on the ocular surfaces of patients with varying severity of dry eye (DE).

Adeshile Oluwatosin (13:22:16) (in thread): > <@U02CNMR4YEA>sometimes it’s network

U02CNMR4YEA (13:26:24) (in thread): > Thank you so much for your responses! I can see it in BugSigDB. However, when I pull the data from BugSigDB into R for analysis, it isn’t coming over with all of the other studies. It has in the past so I’m curious as to why it wouldn’t now. Thank you!<@UBNSEMS3S>@Levi Waldronany ideas? Thank you!

Mildred Anashie (13:29:06) (in thread): > Okay<@U02CNMR4YEA>Definitely have no idea about that:smile:

Adeshile Oluwatosin (13:29:19) (in thread): > .

Adeshile Oluwatosin (13:32:31) (in thread): > The mentors would have more answers to that. > Sorry about that<@U02CNMR4YEA>

Yoko C (14:27:21) (in thread): > <@U02CNMR4YEA>not sure if I am following the right steps, but if do importBugSigDB(), then tail(df1$BSDB ID), it shows that study 871 is the last? So if I am following the right steps to a degree, I also don’t get study 1033

UBNSEMS3S (16:15:54) (in thread): > <@U02CNMR4YEA>This study was removed from the export due to incorrect curation.

UBNSEMS3S (16:16:46) (in thread): > Also please do not mark it as needs review. I had marked it as incomplete because it had issues.

Mildred Anashie (16:21:38) (in thread): > Hello again:blush:Back to Figure 3 and 4:joy:Can anyone tell what the comparisons are? I see where they say “The significances (P-value) among three groups were determined by the Kruskal–Wallis test and subsequent pairwise comparisons were adjusted by Bonferroni correction. “a” denotes instances where p < 0.05******when a comparison was performed with the LR group”******. > > This implies they did a Pairwise comparison to the LR group. Would it mean where there’s ‘a’ on HR that would be recorded for LR vs HR and if I see ‘a’ on MR, it would be recorded for MR vs LR?:thinking_face:If so would Figure 3E meananabundance in both MR and HR?

Kate Rasheed (16:29:42) (in thread): > To me it means where the p-value was < 0.05; in other words, there were instances p-value wasn’t <0.05 when you compare HR with LR or MR with LR@Mildred Anashie. > > Remember it was stated that p-values were adjusted for

Kate Rasheed (16:34:02) (in thread): > If “a” is on HR, it means LR vs HR where p<0.05 , same applies to MR.

Mildred Anashie (16:40:15) (in thread): > That aligns with my thoughts@Kate Rasheed

U02CNMR4YEA (16:54:31) (in thread): > Okay- thank you.

Samuel Nnanna (18:04:41): > Good evening everyone, how y’all doing? > > For recording contributions, what if the curation hasn’t been graded yet?

Chris Awoke (18:08:26): > Hello, friends!:blush:Please I need help with the signatures for the Placebo in this study I’m working on with@Mildred Anashieand@Ruqayyah. Please refer to Fig. S6. - File (PDF): S6 supplementary.pdf

Mildred Anashie (18:15:04) (in thread): > Hi@Chris AwokeWhat aspect do you need help with in figure?

Samuel Nnanna (18:37:51) (in thread): > @Chris Awokelooking at the figure, there’s only one signature for Placebo which is Actinomycces graevenitzii

Chris Awoke (18:54:07) (in thread): > Thanks,@Mildred Anashieand@Samuel Nnanna! > > I’ve gained clarity on the experiment regarding the Placebo.

Mildred Anashie (18:57:06) (in thread): > Agree with@Samuel NnannaOkay@Chris AwokeAlso you should curate only taxas that have (a) beside them as that denotes abundance, those with (p) denotes prevalence which should not be curated > > Just pointing it out, Incase you missed it:relaxed:

Yoko C (19:50:15) (in thread): > After thinking about this, I think that although it looks like mann whitney, I may be assuming too much. Since the paper doesn’t explicitly say it is mann whitney, selecting it as the test might be incorrect. Sorry for the confusion.

Chris Awoke (19:52:40) (in thread): > Alright,@Mildred AnashieThanks for the reminder. I appreciate.

Aleru Divine (21:34:26) (in thread): > @Samuel Nnannayou can leave out the merge date for now or use the date they added the “needs review tag”

Samuel Nnanna (21:37:49) (in thread): > Thanks@Aleru Divine

2024-10-27

Tino (06:47:57): > Hello everyone and@Svetlana Ugarcina PerovicI noticed that not all my signatures are loaded when I click on my study link (https://bugsigdb.org/Study_1170). Signature_2 for experiment 2 is missing. However it only appears when I enter (https://bugsigdb.org/Study_1170/Experiment_2/Signature_2). I have tried refreshing the page but still no change yet. Please help - Attachment (BugSigDB): Distinctive Gut Microbiota Alteration Is Associated with Poststroke Functional Recovery: Results from a Prospective Cohort Study - BugSigDB > OBJECTIVES: Functional prognosis is potentially correlated with gut microbiota alterations following the dysregulation of the gut-microbiota-brain axis after stroke. - Attachment (BugSigDB): Study 1170/Experiment 2/Signature 2 > Source: Figure 4f Description: Subgroup analysis of gut microbiota in stroke. Abundance in Group 1: decreased abundance in chronic patients Revision editor(s)…

Chris Awoke (06:59:38) (in thread): > Hello,@TinoYes, that’s understandable. > > Be patient—it often takes some time for the signatures to fully populate after you’ve entered them.

Mildred Anashie (07:03:47) (in thread): > Hi@TinoIt’stotally okay, just like what@Chris Awokesaid > > Youdon’thave anything to worry about, BugSigdb has a record of it already and I think with time all of it will populate

Adeshile Oluwatosin (07:31:23) (in thread): > Hello@TinoIt’s probably network > You can try another browser and it will all reflect in one view > Butifyou want to submit for review. > You can drop both links and tag a mentor.

Chris Awoke (07:40:27): > Hello,@Svetlana Ugarcina Perovic. Could you please help me delete Signature 3 in Experiment 2 and Signature 2 in Experiment 3? > > Here’s the link to the study:https://bugsigdb.org/Study_1139Thanks so much. - Attachment (BugSigDB): Effect of gut microbiome modulation on muscle function and cognition: the PROMOTe randomised controlled trial - BugSigDB > Studies suggest that inducing gut microbiota changes may alter both muscle physiology and cognitive behaviour.Gut microbiota may play a role in both anabolic resistance of older muscle, and cognition.

Adeshile Oluwatosin (08:01:10) (in thread): > “Methods > We performed a prospective, longitudinal study of infants from a high-HIV-prevalence, low-income setting in South Africa. We evaluated the role of any non–breast milk feeds, excluding prescribed medicines on stool microbial communities via 16S rRNA gene sequencing, peripheral T-cell activation via flow cytometry, and buccal mucosal gene expression via quantitative polymerase chain reaction assay”. > > Good afternoon,I’vemade my research, read and gone through the curation policy. > > This exact study has two study designs- > -Prospective cohort and > -Longitudinal observational study. > > In cases like this,I’mto choose the main study design.I’mstill confused on which is the main study design in this case.

Kate Rasheed (08:03:48) (in thread): > I’ll go for prospective cohort because it has to do with studying different groups for a period of time.@Adeshile Oluwatosin

Adeshile Oluwatosin (08:11:41) (in thread): > Hi@Kate Rasheedbut comparingrepeated observations ofsame participants over time is longitudinal observational(from birth, 6 weeks, 14 weeks)

Aleru Divine (08:13:00): > Good day everyone, Trust you all are doing okay.@Dorcas Samueland I are working on this study and would like a peer review:pray:Thank you so much! > > Link to study:https://bugsigdb.org/Study_1119 - Attachment (BugSigDB): Bacteroides uniformis degrades β-glucan to promote Lactobacillus johnsonii improving indole-3-lactic acid levels in alleviating colitis - BugSigDB > BACKGROUND: Intake of dietary fiber is associated with a reduced risk of inflammatory bowel disease.β-Glucan (BG), a bioactive dietary fiber, has potential health-promoting effects on intestinal functions; however, the underlying mechanism remains unclear.

Kate Rasheed (08:13:53) (in thread): > That’s what prospective cohort study does too. Cohort because they are looking at different groups over a period of time. > > If they were not observing different groups over a period of time, it would be longitudinal.

Adeshile Oluwatosin (08:15:54) (in thread): > I understand as I’ve made research yeahBut the infants with high/low CD4+HLA-DR+ T-cell frequencyarestill EBF infants

Esther Afuape (08:18:31) (in thread): > It is specifically a prospective longitudinal study because the research follows the participants forward in time ( from birth). Following forward in time shows the prospective part. The longitudinal part is the aspect of repeatedly measuring outcomes over time. I’d pick a longitudinal design because it provides additional details about the study, rather than simply picking prospective. If “prospective longitudinal” was on bugSigDB, it’d have been a perfect choice. Since it’s not, longitudinal is a better fit in this case.

Adeshile Oluwatosin (08:19:48) (in thread): > Thank you@Esther AfuapeI needed this clarification:pleading_face::smiling_face_with_tear:I’m grateful

Kate Rasheed (08:19:51) (in thread): > Ohhh. Well noted. Thank you so much@Esther Afuape

Kate Rasheed (08:20:36) (in thread): > @Esther AfuapeI would need your opinion in this conversation too. I would like to learn something new from this.

Esther Afuape (08:20:54) (in thread): > Well done..you’reboth right in this case:sweat_smile:

Adeshile Oluwatosin (08:21:52) (in thread): > I’vebeen so stressed on this:pleading_face::face_holding_back_tears:Thank you:pray:@Esther Afuape

Esther Afuape (08:22:17) (in thread): > You’rewelcome

Adeshile Oluwatosin (08:22:49) (in thread): > Finally Ready for review:joy:

Mildred Anashie (08:28:58) (in thread): > Hello@Esther Afuape:blush:Thank you:pray:

Mildred Anashie (08:29:43) (in thread): > Well done to you both:clap:I’lltake a look asap@Aleru Divine

Aleru Divine (08:30:19) (in thread): > Thank you@Mildred Anashie:pray:

Aleru Divine (08:30:54) (in thread): > Please also check if we missed any experiments.Thank you so much:face_holding_back_tears:

Adeshile Oluwatosin (08:51:25) (in thread): > Well done:thumbsup:I would check@Aleru Divine

Adeshile Oluwatosin (09:04:39) (in thread): > Looks good to me, well done once again

Esther Afuape (09:39:11) (in thread): > @Mildred Anashieis the one vs all approach not going to work in this case?

Adeshile Oluwatosin (09:41:34) (in thread): > We were not quite sure in this instance@Esther Afuape

Esther Afuape (09:41:54) (in thread): > I think you guys should present the paper on Thursday

Adeshile Oluwatosin (09:43:10) (in thread): > We mentioned it in the last office hour@Esther AfuapeBut it was also confusing<@UBNSEMS3S>said we should post it on hereto ask for other mentors opinions.Else, it should be put asides, if I’m correct

Mildred Anashie (09:49:44) (in thread): > @Esther AfuapeIt isn’t so clear, as to if it would work because the paper collected samples from different parts (Hence, the A-D) and shared the participants into different groups based on severity. Figure 5 for example carries information for each part from 5A-D. If it is done as one against all that would mean, none OSA-A vs none OSA-B, none OSA-C, none-OSA-D. > > Typing it out seems to work, my concern was the different parts. But it looks likeit’sa case of part A against the others > Because I see the significance is on Part A in Figure 5

Dorcas Samuel (09:53:59) (in thread): > Thank you@Adeshile OluwatosinThank you@Mildred Anashie

Samuel Nnanna (09:58:05) (in thread): > @Aleru Divineand@Dorcas SamuelI will look through. Good job so far

Kate Rasheed (10:03:05) (in thread): > I’ll look through. Well done@Aleru Divine@Dorcas Samuel

Mildred Anashie (10:09:07) (in thread): > Hi@Dorcas Samuel@Aleru DivineI think you both have done a good job with the curation. Although, I see some comparisons in Figure 3b and 4h and 4k I think, I’m not so clear on if it shows differential abundance:thinking_face:

Adeshile Oluwatosin (10:15:34) (in thread): > @Mildred Anashie3b. The abundance of L. johnsonii in the feces of mice > 4h. And 4K > > They don’t seem like differential abundance to me and are not curatable,

Aleru Divine (10:30:23) (in thread): > For 3b, they administered L. johnsonni and this enhanced its abundance. I don’t think it was exactly differential abundance@Mildred AnashieFor 4h and 4k, what I thought was that the figure doesn’t directly show differential abundance instead, like the text, it describes ILA concentration and L. johnsonii colonization efficiency between control and treated mice groups. > > Differential abundance would compare the relative abundance of L. johnsonii between two groups. > > The colonization efficiency is kind of like how well L. johnsonii has grown itself in the gut in this case. So that’s what they measured. > > That’s why we opted for not curating it.

Esther Afuape (10:47:42) (in thread): > I’mnot so sure either rn…I’lltake a longer look at it

Esther Afuape (10:48:54) (in thread): > @Chioma Onyido@Scholastica Uruaa look at this paper, please:bouquet:

Yoko C (10:59:38): > Hello everyone, I am working on thishttps://bugsigdb.org/Study_1174#Lab_analysis_6, and having some issues defining the condition since they are comparing the taxonomic profiling tool being used, Metaphlan vs mOTUs. I put down copro-seq but I am not too sure about that. I know I saw experiments comparing different methods or tools before but I can’t find them now to check how they recorded this. Any ideas?

Adeshile Oluwatosin (11:16:18) (in thread): > Hi@Yoko CLet me see:thinking_face:

Inimfon Ebong (11:21:53): > Good day everyone, > So the experiments I’m adding with signatures are not showing up, but if I check contribution history it appears. What should I do or is it a network issue?

Adeshile Oluwatosin (11:21:57) (in thread): > Your question is to confirm the condition right?@Yoko C

Adeshile Oluwatosin (11:22:25) (in thread): > Hi@Inimfon EbongYes, it could be network

Adeshile Oluwatosin (11:22:46) (in thread): > Try another browserlet’ssee > Or be patient, check back later

Mildred Anashie (11:23:02) (in thread): > There’s nothing much you can do@Inimfon EbongIt could be your connection, try to refresh the study

Yoko C (11:26:13) (in thread): > right, I want to check the condition.

Kate Rasheed (11:29:20) (in thread): > The condition is related to diet.

Aleru Divine (11:30:33) (in thread): > I’ll have a look at this too@Yoko C

BOLARINWA AISHAT (11:36:48) (in thread): > Don’t worry, rest assured thatit’ssaved > > When you want to submit on GitHubyou can type out the link directly

Yoko C (11:39:08) (in thread): > @Kate Rasheed, for this specific experiment I don’t think diet is what is being contrasted but maybe I completely wrong and we don’t go by what the experiment compares but rather by what the paper is researching?

Yoko C (11:42:37) (in thread): > I think I didn’t mention this is specifically experiment 6 and the ones that come afterwards

Kate Rasheed (11:43:07) (in thread): > Ohhh. Experiment 6. Let me look.

Mildred Anashie (11:52:48) (in thread): > Makes sense@Aleru DivineIn that case, every other thing is okay

Aleru Divine (11:53:59) (in thread): > Thank you for the review@Mildred Anashieand@Adeshile Oluwatosin:pray:

Aleru Divine (12:00:25) (in thread): > @Yoko CI’ve looked at this:sweat_smile:and what I understand is, this experiment was done to confirm composition trends from amplicon sequencing and they used 2 taxonomic profilers for validation I suppose. I tried to search fortaxonomic profilingand it wasn’t available on both EFO and BugSigDB.COPRO-seq(community profiling by sequencing)on the other hand which you’ve used, is the closesttermthat makes the most sense. I think this goes. But that’s my opinion:pray:

Kate Rasheed (15:30:00): > Good day@Svetlana Ugarcina Perovic. Kindly delete experiment 1 from this study:https://bugsigdb.org/Study_1110 - Attachment (BugSigDB): Integrating metagenomics with metabolomics for gut microbiota and metabolites profiling in acute pancreatitis - BugSigDB > Acute pancreatitis (AP) is an inflammatory disease of the pancreas.Despite of a steadily increasing in morbidity and mortality, there is still no effective therapy.

Mildred Anashie (15:41:05) (in thread): > @Mary Agekamehplease see this

Mary Agekameh (15:53:05) (in thread): > Thank you so much@Mildred Anashie

Mary Agekameh (16:13:55): > Good day everyone > > I hope you all are doing okay.@Mildred Anashieand I are working on this study and would like a peer review > > I need help with the location, sample sizes, and confounders > > This is the link to the study:https://bugsigdb.org/Study_1119Thank you! - Attachment (BugSigDB): Gut metagenomes of Asian octogenarians reveal metabolic potential expansion and distinct microbial species associated with aging phenotypes - BugSigDB > While rapid demographic changes in Asia are driving the incidence of chronic aging-related diseases, the limited availability of high-quality in vivo data hampers our ability to understand complex multi-factorial contributions, including gut microbial, to healthy aging.

Aleru Divine (16:16:30) (in thread): > @Mary Agekameh@Mildred AnashieI’llhave a look

Aleru Divine (16:18:31) (in thread): > Guys!!! 19 experiments:exploding_head:Okay okay.I’mlocked in

Mildred Anashie (16:20:21) (in thread): > Sorryit’sa lot > > We really need help with this > Thank you:blush:@Aleru Divine

Mary Agekameh (16:50:49) (in thread): > Thank you@Aleru Divine

Kate Rasheed (17:17:05): > Good day@Esther Afuape. I would like to seek your opinion on Table S1 of thisarticle. Is it curatable please? It’s similar to the one you corrected me on.

Yoko C (17:45:44) (in thread): > Hello, this looks very complicated! I think this might be relevant:**** and matching other demographic characteristics (gender, ethnicity; Methods) . ****Is Experiment 1 Figure 1E curatable? It shows those 2 taxa that are significantly associated with age, but how do you tell if the increase or decrease is significant in each group?

Yoko C (17:48:53) (in thread): > And because this is the first time I have seen an analysis of this type, Experiment 4 is also confusing, how do you tell if it is increasing or decreasing? With the B value?

Aleru Divine (18:22:47) (in thread): > I’ll be dropping any observations I make here:pray:I’ll go 10 experiments at a time since it’s almost 20. > I think there were more confounders controlled for. I’ll find something on this but apart from that, > * Experiment 1 checks out > * Experiment 2 checks out except I don’t understand why you curated the signatures from paired cohorts. Since you’re comparing SG90 and SPMP individually . Should the signatures not come from the individual cohorts? Just a thought. Maybe I’m getting it wrong. I’d like some clarity:pray: > * Same thing with experiment 3 > * Experiment 4 checks out.@Yoko Cyes the beta estimate was used to determine increased and decreased abundance. > * Experiment 5Are there no signatures? I see significant signatures from supplementary file 6 > * Experiment 6 checks out > * Experiment 7 checks out. > * What about signatures for experiment 8, 9 and 10? > 9 more to go and then a good look at the confounders:sweat_smile:

Mildred Anashie (18:32:42) (in thread): > @Yoko Cthe beta estimate shows the direction, if it is an increase or decrease, for figure 1E there’s an asterisk showing significance

Inimfon Ebong (18:33:31): > Good day everyone > This is the study I’m working on with@Rahila-meand@Mildred Anashiehttps://bugsigdb.org/Study_1140We need some peer review especially for experiments 5-8 - Attachment (BugSigDB): Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes - BugSigDB > BACKGROUND: The intestinal microbiota and its metabolites have been reported to play an important role in stroke.Gut microbiota-originating short-chain fatty acids (SCFAs) modulate brain functions directly or indirectly through immune, endocrine, vagal, and other humoral pathways.

Mildred Anashie (18:40:59) (in thread): > @Aleru Divineall the signatures are curated, some are not reflecting in the study though > > We had a lot more experiments but decided to focus on those with significant signatures and were showing differential abundance > > The confounders have been confusing:face_with_diagonal_mouth:For Experiment 2 and 3 we curated the FDR adjusted p-values only which are those with ‘X’. Each column is showing increase and decrease (red is positive/increase and blue is negative/decrease) > > We curated the paired cohort because that shows comparison between***** ‘this vs that’ > ********* > ****In my opinion,**** If we curate the individual cohorts then ****there’ll**** be no comparison ****

Aleru Divine (18:42:48) (in thread): > Got it! The confounders are indeed confusing.I’lllook at it last.

Aleru Divine (18:47:54) (in thread): > I may be wrong but I have a feelingthat there’smore to it:thinking_face:they refer to the methods but Idon’tsee anything.

Mildred Anashie (18:48:49) (in thread): > You mean the confounders right?@Aleru Divine

Aleru Divine (18:49:05) (in thread): > Yes the confounders

Tino (21:36:08) (in thread): > Noted! Thank you

2024-10-28

Joy (00:24:15) (in thread): > Yes@Inimfon Ebong,I have been experiencing the same challenge for weeks now.

Kate Rasheed (02:47:40) (in thread): > For antibiotics exclusion under experiment 5, you can leave it as “3 months”

Adeshile Oluwatosin (03:51:41) (in thread): > Good morning@Inimfon EbongI would check

Rahila-me (04:29:51): > Good morning all<!here>, hope we are all doing fine. Please this is a gentle reminder to everyone who is yet to submit their final application on Outreachy website 29th been tomorrow is the deadline 5pm Nigerian time (Lagos)

Kate Rasheed (04:30:47) (in thread): > Thank you for the reminder@Rahila-me

Rahila-me (04:31:08) (in thread): > @Kate Rasheedurw

Inimfon Ebong (04:46:09) (in thread): > @Kate Rasheedok

Inimfon Ebong (04:46:11) (in thread): > @Adeshile Oluwatosinthank you

Adeshile Oluwatosin (04:59:42) (in thread): > Thank you@Rahila-me

Svetlana Ugarcina Perovic (05:00:57): > Good morning:teapot:/:coffee:Reflecting on your last 4 weeks of work with BugSigDB: What insights have you gained fromyour individual curation efforts, and what have you learned throughcollaborating with others on the project? > > I will go first. For both, I would sayPATIENCE. Being patient with myself is essential when learning new things and developing new skills. In teamwork, patience is particularly crucial, especially in remote communication settings where understanding and collaboration may take extra time. > > Thank you EVERYONE for your patience when communicating with me! > > Special thanks to@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace Sandy<@UBNSEMS3S><@U01MW62UDQR>@Maria Doyleand<@U1LCB8WEA>

Kate Rasheed (05:13:21) (in thread): > For my individual curation effort, I’ve learnt to pay more attention to details and ask questions; engage in community discussions to learn more about curations. > > In collaborating with others, I’ve learned what to curate and what not to curate. I’ve also seen the importance of having a “fresh eyes” look at a curated work. > > Special thanks to@Aleru Divine@Adeshile Oluwatosin@Mildred Anashiefor having fresh eyes.

Svetlana Ugarcina Perovic (05:16:04): > UPDATE: > > For the current week (Oct 28-Nov 3, 2024), since Europe, Nigeria and some other parts of the world have already switched to standard time but the US is still on EDT: > On Thursday (Oct 31) we will meet at 9:00 AM EDT =2:00 PM(Europe, Nigeria, etc.)https://www.timeanddate.com/worldclock/converter.html?iso=20241031T130000&p1=179&p2=5805&p3=125cc<@UBNSEMS3S> - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Kate Rasheed (05:17:08) (in thread): > Well noted with thanks.

Princess Rehoboth Asuelimen (05:17:27) (in thread): > Noted.

Mildred Anashie (05:18:31) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the update

Svetlana Ugarcina Perovic (05:19:13) (in thread): > All good now? By the way, without sharing a link, one could not help:wink:

Rahila-me (05:21:40) (in thread): > @Adeshile Oluwatosinurw:people_hugging:

Svetlana Ugarcina Perovic (05:23:41) (in thread): > @Inimfon Ebonga very good questions. Source of your signature can be multiple! For example, two different figures (usually one in the supplementary material, but not necessarily there) and text in the for example Results section could indicate the same signature to be curated.

Svetlana Ugarcina Perovic (05:25:21) (in thread): > But, be careful, they should be the results from the same groups, condition and statistical analysis applied.

Svetlana Ugarcina Perovic (05:25:30) (in thread): > All details matters.

Mildred Anashie (05:26:21) (in thread): > Yes all good now@Svetlana Ugarcina PerovicNoted:smile:Thank you:pray:

Adeshile Oluwatosin (05:27:21) (in thread): > Good morning everyone, > > Over the past four weeks with BugSigDB, I’ve gained valuable insights about the importance of adaptability. Each curation task has presented unique challenges, and being flexible has helped me navigate them effectively. > > Collaborating with the team has underscored the value of open communication; sharing our perspectives has enriched our collective understanding. > > I also want to echo the sentiment of gratitude for your support and patience throughout this process. A special thanks to@Esther Afuape,@Scholastica Urua,@Chioma Onyido@Peace Sandy<@UBNSEMS3S><@U01MW62UDQR>@Maria Doyle@Levi Waldronfor yourhelp.

Svetlana Ugarcina Perovic (05:27:22) (in thread): > @Tinoall good here now?

Svetlana Ugarcina Perovic (05:27:35) (in thread): > deleted.

Svetlana Ugarcina Perovic (05:28:58) (in thread): > Deleted.

Adeshile Oluwatosin (05:29:48) (in thread): > Noted@Svetlana Ugarcina Perovic

Rahila-me (05:31:46) (in thread): > @Svetlana Ugarcina PerovicThank you

Svetlana Ugarcina Perovic (05:33:10) (in thread): > https://www.timeanddate.com/worldclock/converter.html?iso=20241029T160000&p1=179&p2=5805&p3=125&p4=1440 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Rahila-me (05:34:58) (in thread): > Good morning all Tea or coffee:smile:For me CONSISTENCY and Team work. > Special thanks to our great mentors for always showing up@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace Sandy<@UBNSEMS3S><@U01MW62UDQR>@Maria Doyleand<@U1LCB8WEA>

Kate Rasheed (05:50:56) (in thread): > Thank you@Svetlana Ugarcina Perovic

Ebuka Chinwuba (05:53:32) (in thread): > Acknowledged,@Svetlana Ugarcina Perovic. Thank you!

Tino (06:00:29) (in thread): > @Svetlana Ugarcina Perovicsignature 2 for Experiment 2 still hasn’t been populated on the study linkhttps://bugsigdb.org/Study_1170. My colleagues have advised patience on my part because it takes time for the signatures to fully populate. So yes, it’s all good now.

Ebuka Chinwuba (06:01:33) (in thread): > Good Morning. Reflecting on my last four weeks with BugSigDB, I’ve gained several insights. One major takeaway from my individual curation efforts has been the importance ofattention to detail. I’ve learned to be thorough. > Through collaboration, I’ve come to appreciate the value ofclear communicationandopenness to feedback. Working remotely means relying on precise messaging and documentation when resolving complex issues together.

Chris Awoke (06:13:52) (in thread): > Thank you so much:hugging_face:

Aleru Divine (06:57:03) (in thread): > Good morning@Svetlana Ugarcina PerovicCoffee all day!:coffee:️ > > For me, I’d say patience too and allowing myself the time to work thoroughly. I’ve come to realize just how important it is to double-check and fully confirm that the data I intend to curate truly represents what I think it does. Sometimes, results are presented clearly, other times they can look like what you think it is, but with a closer look, they reveal otherwise. Taking the time to understand the difference has been really rewarding. > > In collaboration, I’ve learned the importance of communication especially when it comes to explaining why I think something should be approached a certain way. Being able to express my thoughts has helped in ensuring we are on the same page. > > I’d like to appreciate the mentors again for all the support and for always coming through for all of us@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace SandyAnd to the rest of the team, especially the ones I’ve collaborated with one way or another, thank you for being so kind and patient with me.@Mildred Anashie@Dorcas Samuel@Joy@Martha Kisakye@Ebuka Chinwuba@Kate Rasheed@Adeshile Oluwatosin@Chris Awoke@Samuel Nnanna@PATIENCE ONAH@Inimfon EbongThank you all for the incredible experience:heart_hands:Looking forward to more collaboration.

Aleru Divine (06:59:01) (in thread): > Thank you for the update@Svetlana Ugarcina Perovic

Aleru Divine (07:00:30) (in thread): > Thank you for the reminder@Rahila-meTruly truly appreciate

Aleru Divine (07:01:24) (in thread): > Going to get back at this in a few minutes.:sunglasses:Has anyone seen my thinking cap?

Mildred Anashie (07:15:51) (in thread): > Good morning:sunny:@Svetlana Ugarcina PerovicDefinitely Tea:teapot:for today > For my individual curation, I’ll say attention to details and not being too quick to conclude based on what you think you have seen but being patient enough to re-read as many times as possible to be sure of the information that applies to what I am working on. > > In collaborations I have learnt patienceon a different level,and being open to learn as well as listening to others opinions on things, not everyone works with the same pace and that is okay.I’lllike to appreciate my mentors@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica Uruafor your availability and patience all through > > To the rest of the team and those I have had an opportunity to collaborate with, thank you all for being great team players. Looking forward to doing more of this:hugging_face::heart_hands:

Mildred Anashie (07:22:14) (in thread): > Already found it > > Thank you again@Aleru Divine

Aleru Divine (07:22:41) (in thread): > Please share.:pray:

Mildred Anashie (07:29:48) (in thread): > I meant your thinking cap:billed_cap::sweat_smile:

Aleru Divine (07:30:42) (in thread): > :sob::sob::sob:for a minute I thought:sob::sob:Thank you:heart_hands:

Yoko C (07:49:00) (in thread): > Good morning, in these 4 weeks, the curation process has allowed me to not be so hesitant in engaging with something just because I am not fully knowledgeable about it. This in turn, has led me to be more confident in asking questions. The welcoming attitude of the team encouraged me to participate, give feedback where I could and learn from other’s insights, questions or roadblocks. Thinking about what makes a space welcoming, I realized that one must remember that in this setting, how we word things is important, and that we can’t assume people know what we are talking about, so we have to make sure to provide details and context. I’ve also definitively gained some insight in to how important my gut micriobiome is and I will be more mindful about it (I don’t want FMTs in the future:sweat_smile:). These 4 weeks were super fun and I want to thank everyone for your kindness and patience.

Chinwendu Joy Enyidiegwu (08:20:09) (in thread): > noted thanks

PATIENCE ONAH (08:21:02) (in thread): > Good afternoon everyone > > Personally I have learned to be patient too, pay attention to details and to read the article as many times as possible to understand the study. > > In collaboration, I have learnt to ask questions and seek for help whenever I encounter problem and unable to resolve it, it has helped me from wasting time trying to resolve it alone. Communication is the key in teamwork. > > Thanks to our mentors@Svetlana Ugarcina Perovic@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace Sandy@C. Mirzayi (please do not tag this account)<@U01MW62UDQR>@Maria Doyle@Levi Waldronand to everyone that have made work easy for me.@Aleru Divine@Kate Rasheed@Adeshile Oluwatosin@Rahila-me

inyang john (08:26:25) (in thread): > Good Morning Everyone. > During my four-week Outreachy contribution stage with BugSigDB, I gained essential insights into both individual data curation and collaborative work. My role involved structuring and verifying microbiome data, teaching me the importance of accuracy and attention to detail in research. Collaboration with other contributors highlighted the value of diverse perspectives; through open communication and feedback, we improved data quality and streamlined workflows. This experience strengthened my technical skills in curation and broadened my understanding of open-source collaboration, showing me how teamwork and shared problem-solving are vital for driving innovation in research. > > Special Thanks to@Svetlana Ugarcina Perovic@Scholastica Urua@C. Mirzayi (please do not tag this account)@Esther Afuape@Peace Sandy@Maria Doylefor being amazing at mentoring and also patient with us.

Joy (09:10:55) (in thread): > Duly noted. Thanks@Svetlana Ugarcina Perovic

Samuel Nnanna (09:55:18) (in thread): > Good afternoon…. > > Neither Tea nor coffee:upside_down_face::upside_down_face:Reflecting on the past four weeks, I’d say it’s been quite a life changing experience because I’ve got the opportunity to do something entirely different from what I’ve been doing for the most part of the year. It was a bit scary; because there was so much to understand but eventually I did, thanks to the supportive community and mentors for everything especially the office hours. > > While curating, I learnt to be kind to myself and also ask for help when necessary. I also improved on my research ability. > > It was also amazing because I experienced teamwork in an entirely new industry and while I worked with@Aleru Divine@Chris Awoke@Mildred AnashieI learnt how to actively listen and ask appropriate questions.I’m so grateful to have been part of this and I look forward to the future and what we can all achieve with the knowledge from here.

Yoko C (11:17:04) (in thread): > Hi, somethings I noticed are: for Experiment 1, I think the signature might be increased for the control group and not the AIS patients? Or decreased for AIS patients. And it says “acite” instead of acute. For experiment 5, you list Spearman correlation and for 6 Pearson as statistical tests but both come from the same graph. I also think for those descriptions instead of biomes you should use microbiota or bacteria. For figure 3 experiments, I don’t understand the statistical tests chosen, however if they are from LEfSe maybe you could just add the genera to the family signatures you already have?

Svetlana Ugarcina Perovic (11:26:22): > All messages answered,*** good luck with your final application tomorrow!****Please note that after submitting your final application you can continue contributing to the project. > > *if I missed your question, please do let me know here

Kate Rasheed (11:27:10) (in thread): > Well noted with thanks.

Chris Awoke (11:36:11) (in thread): > Thank you so much.

Mildred Anashie (11:42:01) (in thread): > Thank you@Svetlana Ugarcina PerovicPleaseI’lllike to know, can an ongoing contribution still be recorded after tomorrow?

Svetlana Ugarcina Perovic (11:49:59) (in thread): > Reminder: The deadline for final applications is Oct. 29, 2024 at 4pm UTC. Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline.Applicants who submit a final application will be able to continue recording and editing their contributionsto your project until the intern announcement on Nov. 26, 2024 at 4pm UTC. Applicants who have not submitted a final application will not be able to record or edit their contributions.

Mildred Anashie (11:52:16) (in thread): > Thank you for the update:blush:

Inimfon Ebong (12:13:00) (in thread): > Thank you@Yoko CI was wondering why the statistics test was showing for experiment 6 when it should have been a replica of 5. I’ll work on them

Kate Rasheed (12:19:23) (in thread): > Thank you@Yoko Cfor these observations.

Tino (12:21:12) (in thread): > For me, the last four weeks have been both a challenge and a delight. A challenge in the sense that I joined the party a bit later so I felt left behind. This resulted in me rushing through everything in an attempt to catch up with others. At first, I was embarrassed to ask questions but I quickly learned that asking and answering questions is the heart of open source contributions. > > This experience has also been delightful because from the moment I introduced myself on this platform, I felt welcomed. I experienced kindness and understanding from both my mentors and colleagues throughout the contribution phase. Each time I got stuck there was always someone willing to help out. > > I also got to expand my knowledge base in the general background of microbiome. Matching unknown taxa names to the NCBI taxonomy involved a lot of internet searching and I felt nostalgic because it was almost as though I was playing ‘hide and seek’ with me doing the seeking. > > THANK YOU ALL, both mentors and colleagues for your kindness, patience and understanding!

Kate Rasheed (12:23:44): > Good afternoon people. Trust your day is going great:hugging_face:. > > My team (@Adeshile Oluwatosin@Aleru Divine) and I would like to seek your opinion concerning Fig. S2 in this article:https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-021-02288-x#ref-CR49There’s no statistical test mentioned for it and we are unsure if it’s curatable. What do you think of it please? - Attachment (BioMed Central): Comparison of targeted metagenomics and IS-Pro methods for analysing the lung microbiome - BMC Microbiology > Background Targeted metagenomics and IS-Pro method are two of the many methods that have been used to study the microbiome. The two methods target different regions of the 16 S rRNA gene. The aim of this study was to compare targeted metagenomics and IS-Pro methods for the ability to discern the microbial composition of the lung microbiome of COPD patients. Methods Spontaneously expectorated sputum specimens were collected from COPD patients. Bacterial DNA was extracted and used for targeted metagenomics and IS-Pro method. The analysis was performed using QIIME2 (targeted metagenomics) and IS-Pro software (IS-Pro method). Additionally, a laboratory cost per isolate and time analysis was performed for each method. Results Statistically significant differences were observed in alpha diversity when targeted metagenomics and IS-Pro methods’ data were compared using the Shannon diversity measure (p-value = 0.0006) but not with the Simpson diversity measure (p-value = 0.84). Distinct clusters with no overlap between the two technologies were observed for beta diversity. Targeted metagenomics had a lower relative abundance of phyla, such as the Proteobacteria, and higher relative abundance of phyla, such as Firmicutes when compared to the IS-Pro method. Haemophilus, Prevotella and Streptococcus were most prevalent genera across both methods. Targeted metagenomics classified 23 % (144/631) of OTUs to a species level, whereas IS-Pro method classified 86 % (55/64) of OTUs to a species level. However, unclassified OTUs accounted for a higher relative abundance when using the IS-Pro method (35 %) compared to targeted metagenomics (5 %). The two methods performed comparably in terms of cost and time; however, the IS-Pro method was more user-friendly. Conclusions It is essential to understand the value of different methods for characterisation of the microbiome. Targeted metagenomics and IS-Pro methods showed differences in ability in identifying and characterising OTUs, diversity and microbial composition of the lung microbiome. The IS-Pro method might miss relevant species and could inflate the abundance of Proteobacteria. However, the IS-Pro kit identified most of the important lung pathogens, such as Burkholderia and Pseudomonas and may work in a more diagnostics-orientated setting. Both methods were comparable in terms of cost and time; however, the IS-Pro method was easier to use.

Adeshile Oluwatosin (12:29:19) (in thread): > Thank you@Svetlana Ugarcina Perovic

Yoko C (13:54:16) (in thread): > Hello, I don’t think fig S2 or the associated table are curatable, I think they are more like when we see the stacked relative abundance graphs. I think the deseq2 graph is the one you would curate. However, I didn’t fully read the paper just the excerpt where s2 is mentioned, so maybe I missed something.

Kate Rasheed (13:55:45) (in thread): > @Yoko CLook at this: “A comparison of the relative abundance of targeted metagenomics and IS-Pro methods at genus level showed that the IS-Pro method had an increased abundance of 28 genera including Burkholderia, Fusobacterium, Lactobacillus, Pseudomonas and Peptostreptococcus and a decreased abundance of 40 genera including Actinomyces, Veillonella, Granulicatella and Leptotrichia (Table 1 and Figure S2)”

Kate Rasheed (13:57:41) (in thread): > For the figure caption: Bar plots showing the relative abundance of genera in the sputum microbiome of COPD participants as characterised by targeted metagenomics and IS-Pro methods (n=23).

Yoko C (13:57:43) (in thread): > Right but that doesn’t necessarily mean the change was significant. I think that to actually see if those differences are significant they preformed the deseq test

Kate Rasheed (14:03:58) (in thread): > Looking at this afresh, > > After they mentioned using DeSeq analysis, this was said “The IS-Pro method was able to classify more OTUs [86 % (55/64)] to a species level than targeted metagenomics, which could classify only 23 % (144/631) of the OTUs to a species level. However, the unclassified OTUs accounted for a higher relative abundance of the IS-Pro method (35 %) than targeted metagenomics (5 %) (Figure S2).”

Yoko C (14:13:42) (in thread): > I think this is like saying out of 10 animals Kate saw 8 and Yoko only saw 5. But this doesn’t tell us if you seeing 8 and me seeing 5 is significantly different, it also doesn’t tell us which animals we saw, maybe I only saw cats, so that would be increased for me, and maybe you saw 8 different types of animals an no cats so those would be increased for you. I don’t know if this explanation makes any sense, sorry. I do see your point and will try to read it more carefully later.

Adeshile Oluwatosin (18:00:14) (in thread): > Thank you@Yoko Cfor your input:pray:

Joy (18:33:19) (in thread): > Thank you@Svetlana Ugarcina Perovicfor this piece of information:hugging_face:

Cynthia Iwuoha (18:38:53) (in thread): > Thank you@Svetlana Ugarcina Perovic

2024-10-29

BOLARINWA AISHAT (03:13:42) (in thread): > Duly noted > Thank you very much

Svetlana Ugarcina Perovic (03:54:32): > Our curator@Nitya Singhalwrote this piece about her#bugsigdbexperience. Thank you, Nitya, for all your work and women empowering efforts - Attachment (linkedin.com): Nitya Singhal on LinkedIn: #outreachy #bugsigdb #bioconductor #opensource #womenintech #ai… | 20 comments > :star2: 𝐅𝐫𝐨𝐦 𝐎𝐮𝐭𝐫𝐞𝐚𝐜𝐡𝐲 𝐃𝐫𝐞𝐚𝐦𝐬 𝐭𝐨 𝐎𝐩𝐞𝐧-𝐒𝐨𝐮𝐫𝐜𝐞 𝐑𝐞𝐚𝐥𝐢𝐭𝐢𝐞𝐬! :star2: > > I’m posting this a little late, but I couldn’t miss sharing the… | 20 comments on LinkedIn

Mary Agekameh (04:15:18) (in thread): > Can we record our second contribution without the needs review tag on GitHub?@Svetlana Ugarcina Perovic@Aleru Divine@Adeshile Oluwatosin

Adeshile Oluwatosin (04:21:02) (in thread): > @Mary AgekamehGood morning,I’mguessing Yes > Since we can still continue recording after the deadline. > Just leave the date it was merged empty till the needs review tag has been added.

Aleru Divine (04:27:49) (in thread): > Thanks@Yoko Cfor the input.I’lllook at this study again.:sob::hand_with_index_and_middle_fingers_crossed:

Ebuka Chinwuba (04:28:16): > Hello everyone, > As we reach the final day of our Outreachy Application, I wanted to take a moment to thank each of you for your hard work, dedication, and collaboration throughout this project. It’s been inspiring to see everyone’s efforts come together, and I’m grateful to be part of such an amazing community. > * A quick reminder: today is the submission deadline, so if you haven’t submitted your final Application, please make sure to submit it before the deadline.Let’s give this project a strong finish! > Special Thanks to@Precious Orakwe, I just wanted to express my sincere gratitude for all the support and guidance you’ve provided me during my recording. And to@Svetlana Ugarcina Perovic, Your insights, patience, and encouragement made a huge difference – it’s been a fantastic journey working with you!

Adeshile Oluwatosin (04:30:04) (in thread): > Nice write up:clap:@Nitya Singhal:hugging_face:

Svetlana Ugarcina Perovic (04:37:38) (in thread): > yes

Mary Agekameh (04:39:07) (in thread): > Thank you so much!

Kate Rasheed (04:39:32) (in thread): > Thank you for sharing this experience@Nitya Singhal… Women empower women indeed:heart:.

Aleru Divine (04:51:53) (in thread): > For the confounders.I saw something in the paper that confirms thatit’sjust age they controlled for.The other covariatesweren’tcontrolled for.I thought I saw something that looked like matched on factors for experiment 1.Itdidn’texplicitly state that it is.SoI’mconfused.:pray:

Aleru Divine (04:55:00) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicThis was a really good read@Nitya Singhal:heart_hands::bouquet:

Rahila-me (05:02:41) (in thread): > What a piece of thoughtful written experience. Thank you for sharing@Nitya Singhal:tulip::tulip:

Chris Awoke (05:08:13) (in thread): > Awesome,@Nitya SinghalWell done:+1:Thanks for sharing@Svetlana Ugarcina Perovic

Chinwendu Joy Enyidiegwu (07:04:10) (in thread): > :+1:

Mildred Anashie (07:31:18) (in thread): > Thank you so much for all the help@Aleru Divine:pray:

Joy (08:01:14) (in thread): > A really nice piece@Nitya Singhal.Thanks for sharing@Svetlana Ugarcina Perovic:hugging_face:

vandana maddi (08:10:41): > timeline of the work you plan to accomplish on the project and what tasks you will finish at each step ? In final application what is the time line !? What should I mention

Svetlana Ugarcina Perovic (08:17:18) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1729497239357399 - Attachment: Attachment > For your final application: There are no community-specific questions. > As for the timeline, the internship begins on Monday, Dec 9th and runs until Friday, March 7th and you are expected to work 30 hours a week for 12 of 13 weeks. During that time, a BugSigDB intern can provide a variety of contributions including: > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Yoko C (11:56:26): > I wanted to check if the way I am matching this family is correct. On the graph it is shown as Family XI. In the supplementary info the only matching option has the following taxonomic info: Order Clostridia, Class Peptostreptococcales-Tissierellales, Family XI. I looked up > Peptostreptococcales-Tissierellales, Family XI and variations, and didn’t find too much. There is a similar listing in the Category discussion page and on the 2 hour video there is a section where they curate family cluster XI as Peptostreptococcaceae. > Looking at the taxa listed under this family, the supplementary information has ParvimonasandPeptoniphilus grossensis. So I looked these up in NCBI and both are listed under Peptoniphilaceae family, Tissierellales class. So I am matching this Family XI to Peptoniphilaceae, however I think I may be assuming too much and maybe should leave it as Peptostreptococcales-Tissierellales Family XI?

Kate Rasheed (11:57:27) (in thread): > Picture please

Kate Rasheed (11:59:15) (in thread): > I have a signature like this too. I recorded it as Family XI.

Yoko C (12:04:27) (in thread): > Oh, maybe I should just leave it as that as well.

Kate Rasheed (12:05:05) (in thread): > @Yoko CMine did not specify the family that’s why I left it that way.

Yoko C (12:05:12) (in thread): > This is just part of the graph, I was going to change the UCG-010 to the class it seems to be associated with as well - File (PNG): image.png

Kate Rasheed (12:06:27) (in thread): > Remember to add UCG 010 to the class and search it on the NCBI taxonomy browser.

Yoko C (12:07:24) (in thread): > Yes, same as the Family XI it is listed under a class, so I was going to use that.

Aleru Divine (12:10:06) (in thread): > Hi@Yoko CI think this is the clostridia family cluster XI.I maybe wrong.:face_with_peeking_eye:But if I amcorrect, it has been resolved asPeptostreptococcaceaeTaxonomy ID: 186804 > > by@Chioma Onyidoon thediscussions page. > > Please take a look. - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Yoko C (12:13:42) (in thread): > @Aleru Divine, I thought so too because of the NCBI matching video but the genera listed under it made me doubt this. So I am not sure if I should take the genera route, the cluster route (since they don’t call it that) or just leave it as is.

Aleru Divine (12:19:24) (in thread): > Oh!!!I see your point on the family and class they both belong to though:thinking_face:I’d suggest curating as seen then:disappointed_relieved:I mean, that is what I’d do.

Samuel Nnanna (19:48:29): > Hi guys, I hope y’all doing okay? > I’d like a peer review on this paper please:pray:https://bugsigdb.org/Study_1192 - Attachment (BugSigDB): A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients - BugSigDB > BACKGROUND: Colorectal cancer (CRC) is the fifth most diagnosed cancer in Sub-Saharan Africa.In Kenya, CRC incidence rates tripled from 1997 to 2017.In the Moi Teaching and Referral Hospital, Moi University, there has been an increase in CRC cases, notably for younger patients.

2024-10-30

Kate Rasheed (01:34:49) (in thread): > Good morning@Samuel Nnanna. I’ll have a look.

Kate Rasheed (01:58:21) (in thread): > @Samuel NnannaI’ve gone through, everything looks good. > > They quoted Figure S5 in the paper but I didn’t see any supplementary information. Can you point me to where it is?

Adeshile Oluwatosin (02:03:30) (in thread): > Good morning@Samuel Nnanna

Adeshile Oluwatosin (02:18:48) (in thread): > I can’t see your experiments/signatures from here

Kate Rasheed (03:39:14) (in thread): > @Adeshile OluwatosinYou would have to enter it manually. The study has two experiments.

Adeshile Oluwatosin (03:39:57) (in thread): > Ohhh okay, thank you@Kate Rasheed

Mildred Anashie (04:06:40) (in thread): > Hi@Samuel NnannaI’lltake a look at this > Well done on your curation:clap:

Samuel Nnanna (04:30:55) (in thread): > @Kate RasheedIcouldn’tfind the supplementary files too

Samuel Nnanna (04:31:38) (in thread): > Thanks@Mildred Anashie

Aleru Divine (04:32:26) (in thread): > Good morning@Samuel NnannaI’llhave a look at this too

Samuel Nnanna (04:32:48) (in thread): > @Adeshile OluwatosinIdon’tknow theyhaven’tpopulated yet with the link

Aleru Divine (04:37:16) (in thread): > I refreshed and it just populated.:blush:

Mildred Anashie (04:40:16) (in thread): > Same@Aleru Divine@Adeshile Oluwatosintry to refresh the study on your browser

Adeshile Oluwatosin (04:40:48) (in thread): > Okay, let me check now@Samuel Nnanna@Mildred Anashie

Aleru Divine (04:58:32) (in thread): > Almost everything checks out so far@Samuel Nnannajust 2 observations. Well done:clap:I see you replaced Ruminococcus lactaris with Uncultured Lachnoclostridium sp but there is a Ruminococcus lactaris on taxonomy browser. SIGNATURE 2 of EXPERIMENT 1https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=46228Secondly, you missed data transformation in experiment 2. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Samuel Nnanna (05:02:02) (in thread): > @Aleru Divinethanks for the observations.I’llrecheck:pray::pray:

Rahila-me (06:28:21): > @TinoI discover a signature you curated on NCBI cleanup, pls permission to clean it up@Mercy CheropI discover a signature you curated on NCBI cleanup, pls permission to clean it up

Mercy Cherop (06:53:50): > @Rahila-meHi thank you but I am collaborating with someone else to make the corrections:pray:

Rahila-me (06:54:13) (in thread): > urw, ok

Yoko C (07:14:29) (in thread): > Hello, are you sure the body site is feces?

Kate Rasheed (07:18:07) (in thread): > @Yoko Cthat’s true. The body site is colon@Samuel Nnanna

Mildred Anashie (07:18:48) (in thread): > @Yoko CYou are rightthere’sno mention of Stool in the study > > See this@Samuel Nnanna“Colonic tissues from 18 CRC patients and 18 healthy controls were collected during colonoscopy.”

Samuel Nnanna (07:20:23) (in thread): > Yeahyou’reright…@Yoko Cand@Mildred Anashie

Samuel Nnanna (07:20:30) (in thread): > Thank you

Aleru Divine (07:22:09) (in thread): > Thanks for pointing that out@Yoko C:face_with_open_eyes_and_hand_over_mouth:

Kate Rasheed (07:35:52) (in thread): > The importance of fresh eyes:hugging_face:

Mildred Anashie (07:36:00) (in thread): > Also, I agree with the observations of everyone > Your curation is on point, However I didn’t notice any alpha diversity information for the second experiment. I only see those for Healthy controls and CRC patients@Samuel Nnanna

Samuel Nnanna (07:43:53) (in thread): > @Mildred AnashieI thinkyou’reright. I thought when they mentioned “all samples” it encompassed both experiments (in the first paragraph of microbiome analysis) > > But then I see they were specific for healthy controls vs crc patients and nothing was mentioned for crc under 40 and over 40 > > Thank you:pray:

Samuel Nnanna (07:48:27) (in thread): > Also to access the supplementary data, when you click on the referenced figure S1, it loads the the supplementary data

Samuel Nnanna (07:51:26) (in thread): > @Mildred Anashieyou’recorrect about the alpha diversity.Figure S1 confirms it. They were specific for CRC patients vs Healthy controls

Aleru Divine (07:51:47) (in thread): > Thank you@Mildred Anashieand@Samuel Nnannafor sharing the supplementary material

Mildred Anashie (07:52:55) (in thread): > You are welcome@Samuel Nnanna@Aleru DivineI confirmed it from the suppplementary information

Kate Rasheed (07:56:25) (in thread): > @Samuel NnannaYou meant Table S1 right?

Samuel Nnanna (08:04:38) (in thread): > @Kate Rasheedtable S1 is providing Details of quality-score based filtering of the input sequencing reads using the QIIME2-DADA2 algorithm > > > > look at figure S1

Adeshile Oluwatosin (08:11:08) (in thread): > Source in Experiment 2 :fifure 3, kindly correct@Samuel Nnanna

Samuel Nnanna (08:12:05) (in thread): > Thank you@Adeshile Oluwatosin

Tino (08:56:56) (in thread): > @Rahila-methanks for reaching out. Please share with me what it means to have a signature on NCBI cleanup.

Aleru Divine (09:01:05): > Good afternoon@Svetlana Ugarcina PerovicPlease I’d like to delete the following from thisstudy. > 1. Signature 2 in experiment 12 (duplicate signature) > 2. Experiment 29 > Thank you so much! - Attachment (BugSigDB): The human microbiota is associated with cardiometabolic risk across the epidemiologic transition - BugSigDB > Oral and fecal microbial biomarkers have previously been associated with cardiometabolic (CM) risk, however, no comprehensive attempt has been made to explore this association in minority populations or across different geographic regions.

Svetlana Ugarcina Perovic (09:02:05) (in thread): > deleted.

Aleru Divine (09:04:14) (in thread): > Wow! Thank you so much for the swift response@Svetlana Ugarcina Perovic:pray:

Kate Rasheed (09:14:31): > Good afternoon everyone. I’ll appreciate a peer review on thisstudy - Attachment (BugSigDB): Shifts in microbial diversity, composition, and functionality in the gut and genital microbiome during a natural SIV infection in vervet monkeys - BugSigDB > BACKGROUND: The microbiota plays an important role in HIV pathogenesis in humans.

Yoko C (09:15:15) (in thread): > I think she means she found the taxon here:https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID#Changed_unknown_Actinomycetales_to_uncultured_actinomycete

Yoko C (09:17:02) (in thread): > When a taxon shows up as orange in the curation and then someone finds the matching taxon on the NCBI page, they list it there.

Rahila-me (09:31:56) (in thread): > @Tinogo to help page on bugsigdb… discussion page

Tino (09:42:15) (in thread): > Noted! Let me check it out.

Ebuka Chinwuba (10:42:25): > :+1:

Tino (10:58:02) (in thread): > @Rahila-meSince my curation is claimed for review on GitHub and it has not been reviewed as yet. Are we allowed to clean up? I thought we could only make corrections or edit once the curation has been reviewed.

Svetlana Ugarcina Perovic (11:37:17): > See you tomorrow at the team meeting - Attachment: Attachment > UPDATE: > > For the current week (Oct 28-Nov 3, 2024), since Europe, Nigeria and some other parts of the world have already switched to standard time but the US is still on EDT: > On Thursday (Oct 31) we will meet at 9:00 AM EDT = 2:00 PM (Europe, Nigeria, etc.) > > https://www.timeanddate.com/worldclock/converter.html?iso=20241031T130000&p1=179&p2=5805&p3=125 > > cc @UBNSEMS3S

Kate Rasheed (11:38:44) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (12:25:12) (in thread): > Thanks for the reminder@Svetlana Ugarcina Perovic:blush:

Mildred Anashie (12:28:46) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic:blush:

Rahila-me (12:54:50) (in thread): > Thanks for the reminder:smiling_face_with_3_hearts::smiling_face_with_3_hearts:

Rahila-me (12:57:47) (in thread): > @Tinoyour signature is in need help for missing id…from that discussion page it can be corrected but nothing else should be changed except putting the correct ncbi Id on the signature you created with missing ncbi id.

Kate Rasheed (13:28:35) (in thread): > I’ll also appreciate a peer review for this study I’m working on with@BOLARINWA AISHAThttps://bugsigdb.org/Study_1186Thank you so much as I await feedbacks from fresh eyes:hugging_face:

Tino (13:39:14) (in thread): > @Rahila-methank you for that clarification, permission granted!

Rahila-me (14:15:30) (in thread): > Ok…. thanks

Aleru Divine (14:15:59) (in thread): > Hi@Kate Rasheedcan I still do a peer review on this?I’vehad a real busy day.:pray:

Kate Rasheed (14:25:08) (in thread): > Yes yes yes@Aleru Divine. Thank you so much

Adeshile Oluwatosin (16:22:08) (in thread): > ICan’twait:pleading_face::relieved:@Svetlana Ugarcina Perovic

Yoko C (17:57:25) (in thread): > Hello, so somethings I noticed going quickly through the paper were that your sample sizes in the first three experiments are the same, from the text it seems these are different. I also think that for Experiment 3 you might have increased/decreased the other way around? I also understood that Chao1 and Shannon were unchanged for experiment 2 and 3, but maybe since there is no graph or it explicitly says it, it is better to leave it as you did? not sure. For the sample size of experiment 4 you could maybe count it from supplementary table 4? Oh, and the confounders from exp 1 I think should match exp 2. That’s as far as I got.

2024-10-31

Kate Rasheed (01:19:43) (in thread): > Thank you so much for this. > > For the confounders in experiment 1, I saw it was stated in the result (below the figure) for fecal samples alone. Let me change it now. > > The sample size for experiment 1-3 is recorded for SIV individuals. I didn’t use the size of the body site samples (if I use the size of the samples, I would have to change the group name). > > For the alpha diversity in experiment 2 and 3, it was not recorded unless I don’t understand the statement:smile:. > > For the directions in experiment 3, please can you explain why it isn’t in the right direction, I guess I’m missing something. > > I just checked table 4; it’s not splitted into acidic and alkaline to enable me count. > > Thank you so much@Yoko C. I’m looking forward to your feedback.

Aleru Divine (04:01:32) (in thread): > Hi Kate, well done on your curation. > * I agree with@Yoko Cfor the sample sizes of experiments 1-3. Since each experiment is specific to a sample site, it’s best to use sample sizes from each site. I also don’t think you have to change the group names, the body sites already tells where the samples are from. > In signature 1 of experiment 1, Ruminococcaceae UCG-001, also for prevotellaceae UCG-003 please see this explanation by@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1729677308922259 > * CAG-873 is Prevotella sp. CAG:873Taxonomy ID: 1262936 (Sig 1 in exp 3****)**** > * For experiment 4 sample size, I believe what@Yoko Cmeans is using the pH to count. (Acidic pH is a pH <7 while an alkaline pH is a pH > 7). This should work. Also add this to your group 1 definition. > * For experiment 9, I think you can get the sample sizes from supplementary table 1, where the sample sizes were stratified by developmental stage(infant, young and old juvenile and adult). > * For experiment 10, 11 and 12 sample sizes, they should not be the same too.(Fecal acute = 4, fecal-chronic =23) (Rectal-acute =11 and Chronic = 43) (Vaginal acute = 6 and chronic = 30) this is more specific as they are different experiments. > Thanks!I’llmove on tohttps://bugsigdb.org/Study_1186:sweat_smile: - Attachment: Attachment > Just to provide context for taxonname_UCG_number: > > These were clusters of microbiome sequence data that initially lacked precise taxonomic definitions. They have now been assigned improved taxonomic classifications and names that better reflect their microbial composition: either as specific strain names or as designated uncultured groups (UCG) with numbers if there are more potential strains. This refined taxonomic framework more accurately captures microbial diversity and enables more precise identification of microorganisms in microbiome samples. > > If you search our database with “UCG” you will see a lot of relevant UCG signatures: https://bugsigdb.org/w/index.php?title=+Special%3ASearch&search=UCG&go=Go - Attachment (BugSigDB): Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection - BugSigDB > Recurrent C.difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT).However, the exact mechanisms that mediate a successful FMT are not well-understood.

Adeshile Oluwatosin (04:10:58) (in thread): > Hello@Kate Rasheedwell doneon your curationCan you send the link to the article for second study?

Kate Rasheed (04:16:47) (in thread): > https://bugsigdb.org/Study_1186@Adeshile Oluwatosin

Adeshile Oluwatosin (04:18:00) (in thread): > Articleitself,not study dear@Kate RasheedIcan’tsee the full texts

Kate Rasheed (04:18:02) (in thread): > Thank you so much@Aleru Divinefor this explanation.

Kate Rasheed (04:18:41) (in thread): > https://journals.asm.org/doi/10.1128/msphere.00706-24@Adeshile Oluwatosin

Aleru Divine (04:19:15) (in thread): > Clicking on the doi link took me to the article.@Adeshile Oluwatosin

Kate Rasheed (04:20:01) (in thread): > For CAG-873, I will do it now. Thanks again. > > I just noticed that I didn’t do it for CAG-873 as I did for others.

Adeshile Oluwatosin (04:24:12) (in thread): > 5C) Repeated measures correlation between abundance of important MCBAs identified by RFA and relative abundance of microbial families that were significantly different between pre- and post-FMT. Significant repeated measure correlations (P ≤ 0.05) by linear model with Benjamini and Hochberg correction are marked with an asterisk.

Adeshile Oluwatosin (04:25:31) (in thread): > Correlating this targeted panel of bile acids with the microbiome, we also discovered a significant association with bacterial families. Isoleucine/leucine, alanine, and histidine conjugated CA decreased in abundance post-FMT and positively correlated with one or more of Rikenellaceae, Veillonellaceae, and Lactobacillaceae (P ≤ 0.05 by a linear model with Benjamini and Hochberg correction; Fig. 5C).@Kate Rasheed

Kate Rasheed (04:28:06) (in thread): > Should the bile acids be curated@Adeshile Oluwatosin:thinking_face:

Adeshile Oluwatosin (04:36:50) (in thread): > I’m still thoroughly checking > 5C and 6D > Let me check Table S1 that you curated, if there’s a correlation. > > Bile acids should not be curated@Kate RasheedBut I can see this, for the microbial taxa:Families including Enterobacteriaceae, Veillonellaceae, Megasphaeraceae, and Enterococcaceae positively correlated with at least one traditional host-associated (taurine or glycine) primary bile acid amidates that decreased post-FMT. However, there is also the potential that these amino acids are being conjugated by the microbiota. Additionally, Oscillospiraceae, Lachnospiraceae, Acutalibacteraceae, Ruminococcaceae, and Coriobacteriaceae significantly positively correlated with one or more unconjugated secondary bile acids (12-oxo LCA, DCA, LCA, EDCA, isoLCA, HDCA, and 3-oxo LCA) that increased post-FMT (P ≤ 0.05 by a linear model with Benjamini and Hochberg correction; Fig. 5C).

Kate Rasheed (04:39:11) (in thread): > @Aleru DivineFor the uncultured groups you listed, I didn’t see it mentioned in BugSigDB database, what should I do with it please?

Aleru Divine (04:41:54) (in thread): > Did you check taxonomy browser? Ruminococcaceae is Oscillospiraceae so it’ll beuncultured Oscillospiraceae.

Kate Rasheed (04:50:03) (in thread): > @Aleru DivineThis name isn’t found in NCBI:smile:

Aleru Divine (04:50:31) (in thread): > :fearful:for real?

Kate Rasheed (04:51:42) (in thread): > I actually think they should be curated that way because the BugSigDB studies with uncultured groups referenced by@Svetlana Ugarcina Perovicare left that way.

Aleru Divine (04:52:02) (in thread): > https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=707003&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (04:52:33) (in thread): > @Kate Rasheed5C and Table S1 is overlapping > Confirmation that 5C should be ignored.:thumbsup:Well done, would keep checking

Aleru Divine (04:52:58) (in thread): > Okay then, curate as reported in the paper@Kate Rasheed.:grin:

Joy (05:51:24) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:52:31): > NEWS:drum_with_drumsticks:@Chioma Onyidowill talk about her Bioconductor experience on December 12 at the rsse. africa online eventhttps://rsse.africa/community_meetups/#upcoming_eventsRead more about Chioma and her work herehttps://www.linkedin.com/posts/chioma-onyido_october-2024-meet-chioma-onyido-rsse-act[…]690936995840-ZpGG?utm_source=share&utm_medium=member_desktop - Attachment (linkedin.com): Chioma Onyido on LinkedIn: :flag-ng: October 2024: Meet Chioma Onyido | RSSE Africa > I am honored to be #featured as one of the community spotlights in #RSSE Africa: https://lnkd.in/dbz9_7gt. > > It’s a community close to my heart because they’re…

Joy (05:55:40) (in thread): > Great news indeed@Svetlana Ugarcina Perovic. Nice one@Chioma OnyidoWe will virtually be in attendance!

Aleru Divine (06:01:15) (in thread): > :partying_face::partying_face:Well done@Chioma OnyidoReminder set and absolutely looking forward to it:blush:

Mildred Anashie (06:13:27) (in thread): > Will definitely not miss this:hugging_face:Well done@Chioma Onyido:partying_face::confetti_ball:

Adeshile Oluwatosin (06:14:11) (in thread): > Yayyyy:confetti_ball:looking forward to it@Chioma Onyido

Mildred Anashie (06:15:24) (in thread): > *Strolls in after the party:grin:

Chioma Onyido (06:51:01) (in thread): > Thank you so much Svet!:hibiscus:Thank you everyone!:cherry_blossom:

Kate Rasheed (07:06:32) (in thread): > Yaaayyyy:dancer:. Congratulations@Chioma Onyido

Samuel Nnanna (07:46:37) (in thread): > Well done@Chioma Onyido

Adeshile Oluwatosin (08:52:27): > Hello Everyone > Less than 10 minutes to the meeting! > See you there:wink:https://community-bioc.slack.com/archives/C04RATV9VCY/p1730106964868869 - Attachment: Attachment > UPDATE: > > For the current week (Oct 28-Nov 3, 2024), since Europe, Nigeria and some other parts of the world have already switched to standard time but the US is still on EDT: > On Thursday (Oct 31) we will meet at 9:00 AM EDT = 2:00 PM (Europe, Nigeria, etc.) > > https://www.timeanddate.com/worldclock/converter.html?iso=20241031T130000&p1=179&p2=5805&p3=125 > > cc @UBNSEMS3S

Rahila-me (09:01:18): > Link pls

Mildred Anashie (09:01:19): > Hello Everyone > > I think you can find the link to the meeting herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1729692067837799 - Attachment: Attachment > Reminder: Tomorrow (Thursday) is our weekly team meeting and office hours at 9 AM EDT. > https://us02web.zoom.us/j/2737200499 > > cc @UBNSEMS3S

Svetlana Ugarcina Perovic (09:02:05): > https://github.com/waldronlab/BugSigDBcuration/issues/95 - Attachment: #95 Office Hours > Welcome, Outreachy applicants! > > My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Svetlana (pronouns: she/her) on the BugSigDB project and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on our GitHub repo: #94 > > Also, during the Outreachy contribution month, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participate or observe these meetings as well as ask questions. > > These meetings are scheduled for: > > Thursday Oct 3, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499)
> Thursday Oct 10, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499)
> Thursday Oct 17, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499)
> Thursday Oct 24, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499) > > **Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20241003T130000&p1=179&p2=3395
> We are happy to meet with you on a different day or time upon request. Thank you!

Joy (10:02:47): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovicand to all who attended the meeting. It was an insightful one!

Chris Awoke (10:07:44): > Thank you,@C. Mirzayi (please do not tag this account)and@Svetlana Ugarcina Perovic, for today’s office hour! > > Even though I didn’t have questions, I gained a lot from the discussion. > > Thanks again!

Yoko C (10:08:14) (in thread): > @Kate RasheedAleru was right, I meant counting based on the ph value. Regarding the alpha for experiment 2 and 3, I can’t see the paper now, but they did say something like Chao1 was decreased for fecal microbiota, this not occur for rectal or vaginal. So I understood they did a test but it was unchanged, but maybe since they don’t say exactly what happened its better not to assume. For experiment 3, and my decreased/increased comment, the section below the bar was for negative and above was for positive, I think? I can’t see the paper so it’s hard to describe why I thought maybe your directions were switched.

Kate Rasheed (10:09:18) (in thread): > Okay now I understand:smile:. Thank you@Yoko C

Aleru Divine (10:10:19): > Thank you for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina Perovicand everyone thatattended and for all the questions asked:heart_hands:

Inimfon Ebong (10:12:27): > Thank you@C. Mirzayi (please do not tag this account)and@Svetlana Ugarcina Perovicquestions answered, challenges simplified

Agatha (10:28:58) (in thread): > Please@Svetlana Ugarcina Perovic, can we have a recorded video of the session. > > I was not able to join because of network issues

Svetlana Ugarcina Perovic (10:39:50) (in thread): > <@UBNSEMS3S>will put it up asap.@Agathathank you for your patience!

UBNSEMS3S (10:42:48) (in thread): > Yes working on it. I’ll have it up shortly.

UBNSEMS3S (11:17:19): > Recording of the weekly office hours/team meeting. Thank you all who attended. - File (MPEG 4 Video): officehours10312024.mp4

Mildred Anashie (11:17:51) (in thread): > Thank you so much for this<@UBNSEMS3S>:blush:

Rahila-me (11:28:59): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor today’s meeting:handshake:

Aleru Divine (11:35:41) (in thread): > Thank you so much<@UBNSEMS3S>

Yoko C (11:41:37): > Hello everyone and<@UBNSEMS3S>, in the meeting you mentioned that some heatmaps aren’t clear enough to be curatable, which made me doubt on a heatmap I was working onhttps://www.nature.com/articles/s41598-023-47748-8/figures/3. So the way I curated the heatmap is based on the cluster P+, P- orange and blue bottom bar (because it is the most clear). Now I think maybe I shouldn’t curate it. But if it is curatable, I have another question. Since this heatmap was made through SIAMCAT, and they say one of their tools is LASSO logistic regression, is that the test used ? Thanks

Mildred Anashie (11:54:30) (in thread): > Wow@Yoko Cthis looks complicated to me > > I would really like to know how you were able to curate thisIt’sthe heatmap in C right?

Yoko C (12:00:49) (in thread): > @Mildred AnashieI did, grouping with the clusters (orange and blue bar), I just saw which side had more color. Initially I wasn’t going to because it seemed like a very subjective way of curating something, but I said to myself, it’s better to curate it and discover it isn’t curatable, than to not curate and discover it was curatable.

Mildred Anashie (12:54:33) (in thread): > Well done > > I’m unsure if it is curatable because of the wayit’spresented@Yoko CButI’mhere for the clarification

UBNSEMS3S (12:57:23) (in thread): > Sorry I should always specify that everything I say during office hours comes with a caveat: there are always exceptions to every rule. It does appear that these heatmaps are curatable–though not easily. > > This figure was not made with SIAMCAT though and it’s not LASSO regression. The caption states that the differential abundance testing was done with a Wilcoxon rank-sum test. LASSO regression/SIAMCAT was used to identify clusters but we do not curate cluster identification statistical methods. We curate differential abundance testing statistical methods.

Adeshile Oluwatosin (13:04:28) (in thread): > Thank you<@UBNSEMS3S>

Adeshile Oluwatosin (13:09:24) (in thread): > Well done@Yoko CThank you for clarifying<@UBNSEMS3S>

Mildred Anashie (13:18:56) (in thread): > Thank you<@UBNSEMS3S>for the clarification

Yoko C (13:40:43) (in thread): > <@UBNSEMS3S>, thank you for clarifying this! The paper does mention they used SIAMCAT for differential abundance analysis, so that’s why I assumed it was used for this graph. Then, seeing siamcat’s vignette, it was unclear to me if I should go with the wilcoxon association test part or the model part. As you pointed out, the graph clearly states wilcoxon, so I will use that. Thanks again, have a great halloween.

2024-11-01

Mildred Anashie (05:17:29): > Hello everyone > > Happy New month of November:tada:I do have a question concerning body sites in this paper I am curating with@Adeshile OluwatosinThe methods state that samples were gotten from four parts > A-Tongue baseB-Surface of Palantine tonsilC-Palantine tonsillar capsule after tonsillectomyD-AdenoidThe study had participants who were divided into four groups as well and various comparisons were done based on the four parts and the four groups > > We were wondering if using mouth as the body site would work for all, asit’sa more general term:thinking_face:

Mildred Anashie (05:21:20): > Hi@Svetlana Ugarcina PerovicPleaseI’lllike to delete Experiment 13 in thisStudyThank you:pray: - Attachment (BugSigDB): Higher Risk of Stroke Is Correlated With Increased Opportunistic Pathogen Load and Reduced Levels of Butyrate-Producing Bacteria in the Gut - BugSigDB > Objective: Gut microbiota is a newly identified risk factor for stroke, and there are no large prospective studies linking the baseline gut microbiome to long-term risk of stroke.We present here the correlation between the gut microbiota and stroke risk in people with no prior stroke history.

Kate Rasheed (05:25:49) (in thread): > @Mildred AnashieGood morning and a happy new month to you too. > > I would have suggested using the different body site if there are separate results for them. > > However, I searched for Base of tongue, adenoid, surface of Palatine tonsil, I didn’t see them on BugSigDB. > > If they have the same results, then you can use mouth.

Mildred Anashie (05:27:09) (in thread): > Hi@Kate RasheedThank you, the results are not the same > > Various comparisons were done with the separate parts and the groups

Mildred Anashie (05:27:41) (in thread): > We are replying to the wrong thread@Kate Rasheed:joy:

Kate Rasheed (05:30:32) (in thread): > @Mildred AnashieIf the results are different then you have to curate separately > > PS. I didn’t know we were responding to the wrong thread:smile:

Mildred Anashie (05:32:30) (in thread): > I wasn’t curating as one@Kate RasheedThe question is, if using mouth for the various experiments regardless of parts would suffice or we have to look for the closest terms to the various parts mentioned as the parts on not on BugSigdb

Aleru Divine (05:32:31) (in thread): > Happy New month to you too@Mildred Anashie:hugging_face:Thesebody sitesyou mentionedarekindalocated within and around the oropharyngeal region. I think oropharynx will be more specific compared to using mouth.

Mildred Anashie (05:34:28) (in thread): > Okay@Aleru DivineOropharynx:white_check_mark:It’s always good to ask questions,I’llconfirmit’son BugSigdb > > Thank you@Kate Rasheed@Aleru Divine:hugging_face:

Aleru Divine (05:36:29) (in thread): > Happy to help:hugging_face:

Kate Rasheed (05:44:16) (in thread): > Okay@Mildred Anashie. I get it now.

Kate Rasheed (05:46:57) (in thread): > @Aleru DivineAdenoid is located at the nasopharynx. Can she use nasopharynx for that body site instead of oropharynx?

Peace Sandy (05:50:29) (in thread): > Big Win > Congratulations@Chioma Onyido:bouquet:

Aleru Divine (05:51:14) (in thread): > @Kate RasheedHere’smy suggestion, forcomparisons including adenoids and any other parts,@Mildred Anashiecan use 2 body sites, oropharynx and nasopharynx.

Kate Rasheed (05:54:08) (in thread): > @Mildred AnashieI saw another name for the body sites and they are in BugSigDB > > Tongue base - posterior part of the tongue > Surface of the Palatine - oropharynx > Palatine tonsillar capsule - Palatine tonsil > Adenoid - nasopharynx

Aleru Divine (05:54:33) (in thread): > Or wait!@Mildred Anashiejust usePharynxThe pharynx is made up of three parts: > Nasopharynx > OropharynxHypopharynx > > Instead of 2

Kate Rasheed (05:55:20) (in thread): > Ohhh. It’s fine:smile:@Aleru DivineI thought it would be good to specify the exact body site.

Mildred Anashie (05:57:15) (in thread): > Yea@Kate RasheedI think we might go with these suggestions you made > > I’ll do a bit more research to see if Pharynx would be more appropriate like@Aleru Divinehas suggested, if not we’d use the more specific terms@Adeshile Oluwatosinwhat do you think?

Mildred Anashie (05:57:34) (in thread): > Thank you guys again:hugging_face:

Aleru Divine (05:57:50) (in thread): > The pharynx contains the plenty parts including the ones we are interested in > Palatine tonsils > Oropharynx > Nasopharynx > Even the tongue base.

Adeshile Oluwatosin (05:58:15) (in thread): > Thank you everyone@Kate Rasheed@Aleru Divine

Adeshile Oluwatosin (05:58:32) (in thread): > @Mildred Anashiestill going through the thread

Adeshile Oluwatosin (06:05:13) (in thread): > Let’s go with the suggestions@Mildred AnashieWe can go with the more specific term for each experiment > Thank you once again:hugging_face:

Adeshile Oluwatosin (06:06:10) (in thread): > Happy new month as well:relieved:

Aleru Divine (06:12:17) (in thread): > Thanks for the observation@Kate Rasheed:hugging_face:

Joy (06:20:55) (in thread): > Thank you<@UBNSEMS3S>

Svetlana Ugarcina Perovic (06:58:14) (in thread): > deleted.

Mildred Anashie (07:11:22) (in thread): > Thank you@Svetlana Ugarcina Perovic:pray:

Kate Rasheed (09:39:52): > Good day@Svetlana Ugarcina Perovic. Kindly delete experiment 2 from this study.https://bugsigdb.org/Study_1180 - Attachment (BugSigDB): Sustained gut dysbiosis and intestinal inflammation show correlation with weight gain in person with chronic HIV infection on antiretroviral therapy - BugSigDB > BACKGROUND: Person with human immunodeficiency virus type-1 (PWH) are prone to chronic inflammation due to residual viral production, even with antiretroviral therapy (ART), which increases the risk of age-related diseases.

Chioma Onyido (10:59:09) (in thread): > Thank youu!:cherry_blossom:

Svetlana Ugarcina Perovic (11:21:58) (in thread): > deleted.

Kate Rasheed (11:26:32) (in thread): > Thank you@Svetlana Ugarcina Perovic

Rahila-me (11:56:04): > Good evening@Svetlana Ugarcina PerovicI don’t know if my fellow curators also experience this.? and if i will call this a bug but as i type and enter microbiome signatures once i enters it, it appears in duplicates that after creating a signature i will look for the duplicated one’s to delete. It does not happen when it is a number that i entered. > a screenshot of my experience - File (PNG): Screenshot 2024-10-29 145925.png - File (PNG): Screenshot 2024-10-29 145858.png

Aleru Divine (12:04:47) (in thread): > Good evening@Rahila-meI noticed this happens to me when I enter a space after typing out the signature name or I copy a signature name with extra space and paste > > I’d recommend you ensure there’s no additional space when copying or after you type out the name of the bacterium. > This should help. - File (JPEG): IMG_1454 - File (JPEG): IMG_1455

Aleru Divine (12:05:57) (in thread): > Sorry for the experience:pleading_face:

Rahila-me (12:08:12) (in thread): > ok.. thanks@Aleru Divinethis solves it then.:people_hugging:

Aleru Divine (12:11:16) (in thread): > Did it work@Rahila-me:crossed_fingers::grimacing:

Rahila-me (12:11:53) (in thread): > When I am creating another signature I will let you know but I believe what you said will fix it

Aleru Divine (12:12:10) (in thread): > Okay then:hugging_face:

Mildred Anashie (14:56:57): > Hello team:wave:I have a quick question please. My concern is in B, based on the comparisons there would it be right to curate the None group as group 1 and the others as group O? This is because the taxa reported are either increasing or decreasing in the None group. > Its a one against all experiment - File (PNG): image.png

Aleru Divine (15:11:34) (in thread): > Hi@Mildred Anashie, my suggestion is to follow the curation policy. SoGroup 0 should correspond to the unexposed/control group, which in this case is theNone group, whileGroup 1 will be the combined (mild, moderate, and severe groups) which corresponds to exposed/case. > > Decrease in the None group would imply increase in the combined severity group (group 1) > > Increased in thenonegroup would imply decrease in the combined severity group.

Kate Rasheed (15:13:57) (in thread): > @Aleru DivineI think I heard Chloe mentioned during one of the office hours that for one against all, the others should be group 0 while the one contrasting should be group 1. Unless I didn’t hear well.

Mildred Anashie (15:14:37) (in thread): > From my understanding signatures are supposed to be recorded as increased and decreased based on Group 1 but in this case we do not have signatures increasing in the severity groups(mild, moderate, severe) > > But rather increasing and decreasing in the none group:thinking_face:

Aleru Divine (15:17:58) (in thread): > My suggestion isbased on what I know from the curation policy@Kate Rasheedalso because when you combine the other groups they still make the exposed group but based on severity.

Aleru Divine (15:22:50) (in thread): > Can you share this study please:pleading_face:@Mildred AnashieI think that since this is a one vs all comparison, and also from what I can see in the figure (the bar plots), increase for none means decrease for the others.Decrease for none means increase for the others.Idon’tknow if this makes sense.But I just suggested:pray::face_with_peeking_eye:

Mildred Anashie (15:25:34) (in thread): > https://bugsigdb.org/Study_1181 - Attachment (BugSigDB): Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study - BugSigDB > OBJECTIVE: To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA.

Chinwendu Joy Enyidiegwu (17:20:05) (in thread): > thumbs up… weldone:raised_hands:

2024-11-02

Aleru Divine (07:41:42): > Happy weekend everyone! Trust you are having a great Saturday. > I’d appreciate a peer review of this study I just finished curating, my major concern is whether the condition I went with is appropriate for the study. > Your feedback would mean a lot to me. > Thank you so much for taking the time to help.:pray::blush:Link:https://bugsigdb.org/Study_1197 - Attachment (BugSigDB): Community composition of cecal microbiota in commercial yellow broilers with high and low feed efficiencies - BugSigDB > The cecal microbiota plays important roles in host food digestion and nutrient absorption, which may in part affect feed efficiency (FE).

Adeshile Oluwatosin (08:01:41) (in thread): > Hi@Aleru DivineI would look over the study

Aleru Divine (08:07:49) (in thread): > Thank you so much@Adeshile Oluwatosinwaiting on your feedback:hugging_face:

Adeshile Oluwatosin (08:13:01) (in thread): > Well done on your curation@Aleru DivineIt’s accurate

Adeshile Oluwatosin (08:13:14) (in thread): > Still going over other options for the condition

Aleru Divine (08:14:02) (in thread): > Thank you so much@Adeshile OluwatosinI truly appreciate your effort:heart_hands:

Adeshile Oluwatosin (08:31:02) (in thread): > From this: “The relatively subtle differences in FE-associated cecal microbiota composition suggest a possible link between cecal microbiota and FE. Moreover, Bacteroides may potentially be used as biomarkers for FE to improve growth performance in yellow broilers.” > > I’ve tried every other thing related to the topic and it’s not permissible. > Since they mentioned growth performance here. > Growth rate measurement should be good.

Mildred Anashie (08:34:32) (in thread): > Hi@Aleru DivineI’lltake a look at this as well > Well done:clap:

Aleru Divine (08:51:23) (in thread): > I tried everythingI could think oftoo:sweat_smile:@Adeshile Oluwatosinthank you so much!:heart:

Aleru Divine (08:52:00) (in thread): > Thank you so much@Mildred Anashie:hugging_face:waiting on your feedback too

Mildred Anashie (09:06:07) (in thread): > @Aleru DivineYour curation is on point:ok_hand:Well done, Ihaven’tbeen able to come up with something else for the condition > > For now, I believe the “Growth rate measurement” would be the most suitableI’lltry to think again

Aleru Divine (09:08:46) (in thread): > Thank you so much!@Mildred AnashieI truly appreciate you both:heart_hands:like so much!:hugging_face:

Kate Rasheed (09:41:49) (in thread): > @Aleru DivineFor group 1 name, change High Feeding Efficiency (LFE) to High Feeding Efficiency (HFE) > > I also noticed you didn’t choose a value for MHT correction. Is it intentional?

Aleru Divine (10:03:18) (in thread): > Oh my! Thank you so much for pointing this out@Kate Rasheed:heart_hands:

Aleru Divine (10:04:32) (in thread): > For MHT, I didn’t even click on it at all.

Kate Rasheed (10:07:44) (in thread): > @Aleru DivineFrom the curation policy, “It should only be left blank if the study did not use traditional statistical testing to determine significance (i.e. they used a Bayesian method or an effect size threshold instead)”:smile:

Aleru Divine (10:13:13) (in thread): > Thank you@Kate Rasheed:heart:

Aleru Divine (10:53:09) (in thread): > Thank you so much again everyone.I’llbe sending this in for review:relieved:

2024-11-04

Rahila-me (03:03:34): > Good morning all, and happy Monday curation. Hope our weekend was fine

Aleru Divine (03:20:34) (in thread): > Good morning@Rahila-meI had a great weekend, I hope you did too.

Rahila-me (03:24:14) (in thread): > Yeah@Aleru Divine:people_hugging::people_hugging:

Kate Rasheed (03:25:28) (in thread): > Good morning@Rahila-me. I had a great weekend. Thank you for asking:hugging_face:. Hope you had an amazing weekend too:hugging_face:?

Adeshile Oluwatosin (03:40:48) (in thread): > Good morning@Rahila-meand everyone:hugging_face:

Rahila-me (03:48:54) (in thread): > @Kate Rasheedyes..I did good morning@Adeshile Oluwatosin

Mildred Anashie (04:13:47) (in thread): > Good morning@Rahila-me, Good morning everyone:blush:Weekend was good, I am a bit under the weather this morning though > Thanks for asking, trust you are good:thumbsup:

Rahila-me (04:19:14) (in thread): > Quick recovery baby girl sending lots of:people_hugging::people_hugging::people_hugging::people_hugging:@Mildred Anashie

Kate Rasheed (04:31:58) (in thread): > Quick recovery@Mildred Anashie. Do rest well

Aleru Divine (04:39:38) (in thread): > Wishing you a speedy recovery@Mildred Anashie:heart_hands:

Adeshile Oluwatosin (04:46:05) (in thread): > Sorry darling@Mildred Anashie

Mildred Anashie (05:25:32) (in thread): > Thank you everyone:heart_hands:

Joy (06:32:39) (in thread): > Thank you@Rahila-meThe weekend was great

Joy (06:33:47) (in thread): > @Mildred AnashieWishing you a speedy recovery!

Joy (06:36:02): > Good morning@Svetlana Ugarcina PerovicI trust you are doing great, Kindly delete experiment 2. Thankshttps://bugsigdb.org/Study_1193 - Attachment (BugSigDB): Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet - BugSigDB > High-fat (HF) diet-induced neuroinflammation and cognitive decline in humans and animals have been associated with microbiota dysbiosis via the gut-brain axis.Our previous studies revealed that excretory-secretory products (ESPs) derived from the larval Echinococcus granulosus (E.

Moritz E. Beber (06:39:45): > @Moritz E. Beber has left the channel

Rahila-me (07:11:08) (in thread): > @Joyyou are welcome

Svetlana Ugarcina Perovic (07:32:50) (in thread): > deleted.

Joy (10:16:46) (in thread): > Thanks alot

BOLARINWA AISHAT (10:29:57) (in thread): > :heart:

2024-11-05

Kate Rasheed (02:42:03): > Good morning people. It’s a beautiful day:sparkles:. > > Please I have a question; how do we curate Dominance index and Shannon equitability index in BugSigDB, when we have these alpha diversity listed: > > Shannon > Dominance > Simpson > Shannon equitability > > I curated mine as just Simpson and Shannon, is this accurate please?

Adeshile Oluwatosin (02:49:59): > Hello everyone, > > Good morning > I would appreciate a peer review on this curation > > Especially with the alpha diversityas comparisons between S2, 2 and S3 are different from what we see in the results.https://bugsigdb.org/Study_1181https://pmc.ncbi.nlm.nih.gov/articles/PMC10921815/#MOESM1Thank you - Attachment (PubMed Central (PMC)): Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study > To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA. Before …

Kate Rasheed (02:51:37) (in thread): > Good morning@Adeshile Oluwatosin. I’ll look through:hugging_face:.

Adeshile Oluwatosin (02:52:05) (in thread): > Alright, thanks@Kate Rasheed

Mildred Anashie (02:59:48) (in thread): > Good morning@Kate RasheedSo I saw this “The Shannon Equitability Index is a way to measure the evenness of species in a community. The term “evenness” simply refers to how similar the abundances of different species are in the community”. > > This implies that this is more of evenness, but I am unsure how it can be curated on BugSigdb

Kate Rasheed (03:02:11) (in thread): > Thank you@Mildred Anashie

Mildred Anashie (03:03:05) (in thread): > Thank you@Kate RasheedThe confusion though is that the contrasts appear to be one against all while the Alpha diversity is clearly showing some sort of pairwise comparison, it’s quite unclear how this could be curated > > N/B: The paper has samples collected from 4 sites and there are four groups as well. The A,B,C,D is for the different sites.@Adeshile Oluwatosinthere’salpha diversity in S9 as well > > A lot of alpha diversity comparisons:weary:

Aleru Divine (03:03:20) (in thread): > Good morning to you too@Kate Rasheed:hugging_face:Thank you@Mildred AnashieLet me check this out.Can you share the paper@Kate Rasheed

Kate Rasheed (03:04:29) (in thread): > https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-020-01759-x@Aleru Divine - Attachment (BioMed Central): The penile microbiota of Black South African men: relationship with human papillomavirus and HIV infection - BMC Microbiology > Background To date, the microbiota of the human penis has been studied mostly in connection with circumcision, HIV risk and female partner bacterial vaginosis (BV). These studies have shown that male circumcision reduces penile anaerobic bacteria, that greater abundance of penile anaerobic bacteria is correlated with increased cytokine levels and greater risk of HIV infection, and that the penile microbiota is an important harbour for BV-associated bacteria. While circumcision has been shown to significantly reduce the risk of acquiring human papillomavirus (HPV) infection, the relationship of the penile microbiota with HPV is still unknown. In this study, we examined the penile microbiota of HPV-infected men as well as the impact of HIV status. Results The penile skin microbiota of 238 men from Cape Town (South Africa) were profiled using Illumina sequencing of the V3-V4 hypervariable regions of the 16S rRNA gene. Corynebacterium and Prevotella were found to be the most abundant genera. Six distinct community state types (CSTs) were identified. CST-1, dominated by Corynebacterium, corresponded to less infections with high-risk HPV (HR-HPV) relative to CSTs 2–6. Men in CST-5 had greater relative abundances of Prevotella, Clostridiales, and Porphyromonas and a lower relative abundance of Corynebacterium. Moreover, they were significantly more likely to have HPV or HR-HPV infections than men in CST-1. Using a machine learning approach, we identified greater relative abundances of the anaerobic BV-associated bacteria (Prevotella, Peptinophilus, and Dialister) and lower relative abundance of Corynebacterium in HR-HPV-infected men compared to HR-HPV-uninfected men. No association was observed between HIV and CST, although the penile microbiota of HIV-infected men had greater relative abundances of Staphylococcus compared to HIV-uninfected men. Conclusions We found significant differences in the penile microbiota composition of men with and without HPV and HIV infections. HIV and HR-HPV infections were strongly associated with greater relative abundances of Staphylococcus and BV-associated bacterial taxa (notably Prevotella, Peptinophilus and Dialister), respectively. It is possible that these taxa could increase susceptibility to HIV and HR-HPV acquisition, in addition to creating conditions in which infections persist. Further longitudinal studies are required to establish causal relationships and to determine the extent of the effect.

Aleru Divine (03:04:43) (in thread): > Thank you Kate

Adeshile Oluwatosin (03:05:37) (in thread): > Good morning@Kate RasheedDo you mean they mentioned all four alpha diversity in the paper?

Mildred Anashie (03:07:20) (in thread): > You are welcome@Kate RasheedOn BugSigdb Pielou denotes Evenness but Idon’tknow if you should curate as that

Kate Rasheed (03:08:04) (in thread): > I saw that too in one of the article@Svetlana Ugarcina Perovicshared for diversity but I don’t know if I should curate it as Pielou.

Adeshile Oluwatosin (03:09:16) (in thread): > My opinion is to select pielou for Shannon equitability > AndSimpson for dominance .

Adeshile Oluwatosin (03:12:09) (in thread): > Made a research and found this@Kate RasheedPielou: This corresponds to Pielou’s Evenness Index, which is another measure of species evenness based on the Shannon-Wiener Index, correct for Shannon equitability. > > Dominance measures how much a single species dominates an ecological sample. The Simpson’s Dominance Index (D) is commonly used to measure this.

Aleru Divine (03:13:05) (in thread): > I checked out Dominance index andit’spointing towards inverse Simpson.First “The dominance index refers to the abundance of the most abundant species. Various dominance indices are available (see the function help for a list of options).” > The table now presented Simpson as one on the list.@Adeshile Oluwatosin@Kate Rasheedwe already have Simpson in the paper, the dominance should be curated as inverse Simpson. > > Also see “The value of Simpson’s D ranges from 0 to 1, with 0 representing infinite diversity and 1 representing no diversity, so the larger the value of D, the lower the diversity. For this reason, Simpson’s index is often as its complement (1-D). Simpson’s Dominance Index is the inverse of the Simpson’s Index (1/D).”Link - Attachment (Biology LibreTexts): 22.2: Diversity Indices

Adeshile Oluwatosin (03:13:23) (in thread): > To be honest, a lot@Mildred Anashie:tired_face:I hope to hear from everyone,let’ssee

Kate Rasheed (03:14:27) (in thread): > Thank you@Aleru Divine@Adeshile Oluwatosin@Mildred Anashie

Aleru Divine (03:14:55) (in thread): > Simpson’s dominance indexI believe isInverse Simpson @Adeshile Oluwatosin@Kate RasheedThere’s already aSimpson index in the figure, that is before the dominance index.

Aleru Divine (03:18:49) (in thread): > I also agree with Pielou forShannon’sequitability.Shannon’s equitabilityis AKAevenness index(Pielou).

Aleru Divine (03:20:01) (in thread): > Well done on your curation@Adeshile Oluwatosin@Mildred Anashie:clap:I’ll have a look at the study.

Mildred Anashie (03:20:02) (in thread): > Nice resource@Aleru Divine

Aleru Divine (03:36:08) (in thread): > @Adeshile Oluwatosinregarding your concern “Especially with the alpha diversity as comparisons between S2, 2 and S3 are different from what we see in the results.” > > The alpha diversity results are actually supposed to be and are different for all. > 1. For Figure 2: The microbial alpha diversity comparison among four parts in**** OSA group.**** > 2. For Figure S2: The microbial alpha diversity comparison among four parts inno OSA group. > 3. For Figure S3: The microbial alpha diversity comparison among four parts in no OSA group. > These are all different comparisons

Adeshile Oluwatosin (03:37:12) (in thread): > They are different for all, yes I saw that > > You can check out how it was curated to understand where the confusion is coming from.

Aleru Divine (03:37:42) (in thread): > Okay, I’ll look at that.

Mildred Anashie (03:38:08) (in thread): > @Aleru Divinewe saw the description but the contrasts in the alpha diversity seems to be different from those showing the results

Adeshile Oluwatosin (03:38:29) (in thread): > Especially experiment 3,5 and 6

Adeshile Oluwatosin (03:39:21) (in thread): > The comparisons just seems to be different from what we can see in the results@Aleru Divine

Kate Rasheed (04:00:55) (in thread): > For experiment 1 whose body site should be tongue base, I saw that you recorded increased for richness. > > See what I saw “there was no difference in alpha diversity of microbiota in the tongue base of each group (P>0.05)”.@Mildred Anashie@Adeshile Oluwatosin

Adeshile Oluwatosin (04:01:40) (in thread): > Okay, let me check@Kate Rasheed

Kate Rasheed (04:06:10) (in thread): > @Mildred AnashieAre you sure it won’t be great to separate the body sites instead of categorizing as Pharynx since the four parts listed are separate.@Adeshile Oluwatosin

Aleru Divine (04:07:31) (in thread): > I’m looking at experiment 3 and the alpha diversity comparisons are not a one-to-all comparison. but you curated as a one-to-all comparison. This makes the alpha diversity curated not very accurate. > > Let’s take Shannon in figure 2 for example. The horizontal square bracket goes from A-B. Not A - (B-D). > > I don’t know how to go about this. I know during office hours, Chloe said figure 5B was a one-to-all comparison. > > Should the alpha diversity measures be ignored? (I don’t know):thinking_face:or can they curated as different experiments? > > I have a similar problem @figure 4(a and f)https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01756-6A solution to this will definitely be a solution to mine:face_holding_back_tears:A little help here please:pleading_face::pray:@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Levi Waldron@Esther Afuape@Scholastica Urua@Chioma Onyido@Peace Sandy

Mildred Anashie (04:10:05) (in thread): > @Kate RasheedI noticed S9 was pointing towards Tongue base only but it’s still showing the Pairwise comparisons > > S3 is pointing towards the four groups in the four parts > > S2 is pointing towards the four parts but No OSA > > Fig 2 is pointing towards 4 parts but OSA@Kate Rasheedmaybe we can do that for the few experiments that were separated based on body parts > > But majority of the experiments didn’t really specify, you’d see that there did all different parts together as one experiment

Adeshile Oluwatosin (04:10:18) (in thread): > Yeah, we’ve spoken about it previously@Kate Rasheedfor comparisons amongst the four different parts > We decided to use a generalized termpharynxasthebody site > > I would look into the curations again for the more specific ones

Mildred Anashie (04:11:50) (in thread): > @Aleru DivineExperiment 3 is a one against all > > Its comparing the Mild group in all the parts (A, B, C, D)

Adeshile Oluwatosin (04:13:16) (in thread): > Experiment 1,3, 5 and 6 are all one against all analysis@Aleru Divine

Adeshile Oluwatosin (04:17:54) (in thread): > Even specifications on the sample size for example > > Non A, B, C and D wasn’t mentioned > > They just said none is 10.

Aleru Divine (04:18:15) (in thread): > Yes I see it@Mildred Anashie@Adeshile Oluwatosinand I completely understand but the alpha diversityyou’vecuratedisn’tsupposed to be a one-to-all comparison.Orisn’tit from figure 2? > > For instance, figure 2 Shannon diversity, Mild OSA group A was compared toMild OSA group Anot the rest of the group.A was increased when compared to B but not the others.That’swhat I meant by the alpha diversities not being one-to-all compared.

Mildred Anashie (04:19:37) (in thread): > Okay okay > > I get your point@Aleru DivineThat iswhywe thought to share:pensive:

Aleru Divine (04:20:53) (in thread): > :pleading_face:I have the same problem too and I shared the paper above.That’s why I tagged the mentors to help clarify it for us.Here’smy paper againhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01756-6 - Attachment (BioMed Central): Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3 - Microbiome > Background Remodeling eubiosis of the gut microenvironment may contribute to preventing the occurrence and development of depression. Mounting experimental evidence has shown that complement C3 signaling is associated with the pathogenesis of depression, and disruption of the gut microbiota may be an underlying cause of complement system activation. However, the mechanism by which complement C3 participates in gut-brain crosstalk in the pathogenesis of depression remains unknown. Results In the present study, we found that chronic unpredictable mild stress (CUMS)-induced mice exhibited obvious depression-like behavior as well as cognitive impairment, which was associated with significant gut dysbiosis, especially enrichment of Proteobacteria and elevation of microbiota-derived lipopolysaccharides (LPS). In addition, peripheral and central complement C3 activation and central C3/CR3-mediated aberrant synaptic pruning in microglia have also been observed. Transplantation of gut microbiota from CUMS-induced depression model mice into specific pathogen-free and germ-free mice induced depression-like behavior and concomitant cognitive impairment in the recipient mice, accompanied by increased activation of the complement C3/CR3 pathway in the prefrontal cortex and abnormalities in microglia-mediated synaptic pruning. Conversely, antidepressants and fecal microbiota transplantation from antidepressant-treated donors improved depression-like behaviors and restored gut microbiome disturbances in depressed mice. Concurrently, inhibition of the complement C3/CR3 pathway, amelioration of abnormal microglia-mediated synaptic pruning, and increased expression of the synapsin and postsynaptic density protein 95 were observed. Collectively, our results revealed that gut dysbiosis induces the development of depression-like behaviors through abnormal synapse pruning in microglia-mediated by complement C3, and the inhibition of abnormal synaptic pruning is the key to targeting microbes to treat depression. Conclusions Our findings provide novel insights into the involvement of complement C3/CR3 signaling and aberrant synaptic pruning of chemotactic microglia in gut-brain crosstalk in the pathogenesis of depression. Video Abstract

Adeshile Oluwatosin (04:21:16) (in thread): > Now you see where the confusion is@Aleru DivineInitially weweren’tsure if it should be curated as one-to-all comparison. > Also, curating it as that and ignoring the alpha diversity > Or how the alpha diversity should be curated.

Aleru Divine (04:22:07) (in thread): > I guesswe’reasking the same questions:sweat_smile:

Adeshile Oluwatosin (04:49:52) (in thread): > Thank you everyone@Kate Rasheed@Mildred Anashie@Aleru DivineMost of the issues I bring here are sometimes not resolvable:joy::sweat_smile:it’swell

Kate Rasheed (05:00:09) (in thread): > @Adeshile Oluwatosin@Mildred AnashiePlease where did you get the decreased alpha diversity of the one-against-all experiments? > > See what I saw “Among non-OSA group and various severity of OSA groups, alpha diversity had no statistically significant difference in same parts of upper airway”. > > I believe this alpha diversity is talking about the one-against-all experiments, although the Figure S3 source quoted is still doing a pairwise comparisons.

Joy (05:55:23) (in thread): > Great conversation guys, I learnt a lot from this thread. Thanks@Adeshile Oluwatosin@Aleru Divine@Kate Rasheed@Mildred Anashie

Adeshile Oluwatosin (05:56:11) (in thread): > You are welcome:thumbsup:@Joy

Yoko C (06:30:30) (in thread): > Hi, Simpson and inverse Simpson are different, Shannon and Pielou are different too.

Aleru Divine (07:11:11) (in thread): > That’s correct@Yoko C. > In the paper, there were different alpha diversity measures > 1. Simpson > 2. Dominance > 3. Shannon > 4. Shannon Equitability > Kate’s concern was how to go about curating the second and the fourth measures. > > Shannon Equitability is also known as the eveness which is Pielou in BugSigDB > > Simpson’s is different from Simpson’s dominance. > Dominance is the opposite of diversity which is the same as Inverse Simpson also available on BugSigDB. > > We’re not really saying they’re the same. I hope this makes sense:grimacing::pray:

Aleru Divine (07:56:38): > Good afternoon@Svetlana Ugarcina Perovicmy apologies for the inconvenience.I’dlike to delete the following experiments and signatures in this studyhttps://bugsigdb.org/Study_1047 > 1. Experiments 8,9 and 10 > 2. Signature 2 in experiments 1, 2, 3 and 4. > Thank you so much! - Attachment (BugSigDB): Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3 - BugSigDB > BACKGROUND: Remodeling eubiosis of the gut microenvironment may contribute to preventing the occurrence and development of depression.

Svetlana Ugarcina Perovic (08:02:30) (in thread): > deleted.

Aleru Divine (08:03:40) (in thread): > Thank you so much:pray:

Yoko C (08:40:33) (in thread): > For your first experiment, I think you should record all as unchanged or not fill it in, since the paper says: this difference was not found in children with non-OSA. the difference they mention is alpha diversity.

Adeshile Oluwatosin (08:43:30) (in thread): > @Kate RasheedI’llgo over it again to give an explanation on how I went about the alpha diversity. Thank you for your observations@Yoko CThank you

Yoko C (08:50:54) (in thread): > Experiment 3’s description, “whose Sterile throat swab was used to wipe the mucosa of the patient’s tongue base (oropharynx site)” is a bit confusing. Maybe you can say something like sample obtained from tongue base.

Adeshile Oluwatosin (09:18:04): > Hello everyone > > I would appreciate a Peer review on this curation > Thankshttps://bugsigdb.org/Study_1204https://www.sciencedirect.com/science/article/pii/S0032579120307288#appsec1

Adeshile Oluwatosin (09:18:25) (in thread): > @Yoko C

Adeshile Oluwatosin (09:18:36) (in thread): > Tongue base is not permissible

Adeshile Oluwatosin (09:18:49) (in thread): > This particular curation stressed me > And is still confusing

Kate Rasheed (09:20:16) (in thread): > @Adeshile Oluwatosinanother name for tongue base is posterior part of the tongue.

Kate Rasheed (09:20:53) (in thread): > Weldone on your curation@Adeshile Oluwatosin. I’ll look through:hugging_face:.

Adeshile Oluwatosin (09:21:57) (in thread): > Ohh you meant the description, thank you > Let me see to that@Yoko C@Kate Rasheednoted, thanks

Yoko C (09:29:03) (in thread): > @Adeshile Oluwatosin, is oropharynx the tongue base? I think it might not be. I think it’s more like the throat area associated to the mouth, not specifically the tongue base.

Yoko C (10:05:55): > Hello everyone, if I have a suggestion for a curation, can I just add it to the issues section on BugSIgDBcuration ? or does it have to be pre-approved?

Svetlana Ugarcina Perovic (10:06:57) (in thread): > Please open a new GitHub issue and tag me. Thanks!

Kate Rasheed (10:30:01) (in thread): > @Adeshile OluwatosinFor experiment 1, please re-check your Group 1 name and its definition.

Adeshile Oluwatosin (11:48:32) (in thread): > Thank you

BOLARINWA AISHAT (13:04:50) (in thread): > Well done

BOLARINWA AISHAT (13:06:28): > Hello everyone. > Trust we’re enjoying the curation process. > > I would appreciate a peer review of this curation > Thank you very much.https://bugsigdb.org/Study_1184https://www.nature.com/articles/s41598-022-12970-3 - Attachment (BugSigDB): The lung microbiome in HIV-positive patients with active pulmonary tuberculosis - BugSigDB > Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection.Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients. - Attachment (Nature): The lung microbiome in HIV-positive patients with active pulmonary tuberculosis > Scientific Reports - The lung microbiome in HIV-positive patients with active pulmonary tuberculosis

Yoko C (13:32:01) (in thread): > Hello, I see that for all your experiments you have curated Figure 2, however this figure doesn’t seem to be curatable because it doesn’t specify which Phylums are significantly different.

Yoko C (13:32:37) (in thread): > Supplementary file 3 and 4 seem to have the graphs that you can curate.

BOLARINWA AISHAT (13:33:41) (in thread): > I’lllook into that > Thank you very much

Mildred Anashie (13:44:06) (in thread): > I agree with@Yoko CYou should curate supplementary file 3 and 4 > And curate the alpha diversity from figure 6, I noticed you missed Observed(which is Richness)@BOLARINWA AISHAT

BOLARINWA AISHAT (13:45:10) (in thread): > Thank you@Mildred Anashie

Aleru Divine (13:50:32) (in thread): > Well done@Adeshile OluwatosinThis is very similar to my previous curation. > I did a peer review and it all checks out to me.:clap:

Adeshile Oluwatosin (13:52:29) (in thread): > Thanks@Aleru Divine

Aleru Divine (13:52:45) (in thread): > Hi@BOLARINWA AISHATwell done on your curation:clap:. I’ll give it a peer review and get back to you if I have any observation/suggestions.

BOLARINWA AISHAT (13:53:18) (in thread): > Thank you

Adeshile Oluwatosin (14:01:25) (in thread): > I saw growth condition as apermissible value > That seems more like it to growth rate measurement@Aleru Divine

Aleru Divine (14:02:18) (in thread): > Just growth? At the timeI didn’tsee “growth”I’vesubmitted my study for review:pleading_face:

Adeshile Oluwatosin (14:04:21) (in thread): > That’swhy I took my time to go over the curation and asked for review > > We probably overlooked it then:pleading_face:

Aleru Divine (14:05:33) (in thread): > I checked specifically for growth at the time and itwasn’tthere.I think it was added recently.

Adeshile Oluwatosin (14:10:23) (in thread): > Growth condition* not growth

Aleru Divine (14:11:42) (in thread): > Oh! Okay.:thumbsup:

Adeshile Oluwatosin (14:12:01) (in thread): > Youdidn’tsee that

Aleru Divine (14:13:15) (in thread): > Ican’tsay for sure if I did.Like I was certainI didn’tsee growth

Kate Rasheed (14:14:03) (in thread): > Well done on your curation@BOLARINWA AISHAT. I’ll look through too.

Adeshile Oluwatosin (14:17:41) (in thread): > We probably all missed it then:pleading_face:

Adeshile Oluwatosin (14:18:25) (in thread): > I personally checked for all permissible value for condition in your curation > Anddidn’tsee it > Almost missed it now

Adeshile Oluwatosin (14:21:03) (in thread): > Hi dear, well done@BOLARINWA AISHAT

Kate Rasheed (14:26:13) (in thread): > @BOLARINWA AISHATFor the significant threshold, it is recorded that logfold change greater than 2 is accounted as significant. > > Your significant is supposed to be 2. > > In the article, I see that the exclusion criteria is 6weeks but in the supplementary table 1, I see they wrote 4weeks.

Mildred Anashie (14:27:30) (in thread): > Hi@Kate RasheedDo you mean LDA score? > > Significant thresholdshouldn’tbe 2:thinking_face:

Kate Rasheed (14:27:56) (in thread): > @Mildred Anashiethey didn’t use LDA. > > See “Over-representation of ≥ log twofold change was considered significant.”

Adeshile Oluwatosin (14:31:34) (in thread): > Body site for experiment 1 should be just sputum > Pulmonary tuberculosis for condition is okay. > > Also, as said before Figure 2 is not curatable@BOLARINWA AISHAT

Kate Rasheed (14:31:47) (in thread): > Also, the statistal test used is DeSeq2.@BOLARINWA AISHAT

Kate Rasheed (14:32:24) (in thread): > @Adeshile OluwatosinI saw that they joined samples from Sputum and BALF for experiment 1. But the specimens were actually separated for the differential abundance

Adeshile Oluwatosin (14:32:42) (in thread): > Figure 2 is not even curatable

BOLARINWA AISHAT (14:34:20) (in thread): > I’mnoting all the corrections > Thank you all

Adeshile Oluwatosin (14:35:49) (in thread): > Also take note@BOLARINWA AISHATfor the already stated experiments to curate > > Condition and body site should be one each > > If the body site is different,curate a seperate experiment

BOLARINWA AISHAT (14:36:17) (in thread): > Noted@Adeshile Oluwatosin

Mildred Anashie (14:42:14) (in thread): > @Kate Rasheedthe significant threshold indicates the p-value set by the researchers to determine significance > > And a p-value of 2 in my opinion would be a mistake, as p-values are probability measures and I think they should fall within 0-1 > > Although it is commonly set at 0.05 or below (Most times researchers set even stricter thresholds like 0.01, 0.001 or even 0.0001 with certain considerations though). > > So I’m trying to say 2 isn’t the threshold > > Most times if it isn’t mentioned I believe it’s advisable to use 0.05, but it was mentioned in this paper and I believe that can be considered for the differential abundance testing. See image - File (JPEG): IMG_1915

Aleru Divine (14:42:31) (in thread): > For experiment 1, > 1. The body site should be sputum only > 2. Your group 0 should be renamed (HIV positive control cohort) this is a bit more detailed. > 3. The condition should bePulmonary tuberculosisonly, as this particular experiment has nothing to do with pneumonia. > For experiment 2. > 1. I believe the body site is sputum only also > 2. Condition can bepneumoniahere > 3. Also your group 0 should be renamed (HIV positive control cohort) this is a bit more detailed. > For experiment 3, Body site is lungs. Pulmonary tuberculosis is okay as condition we can’t have 2 conditions and since the paper is focusing on the lung Microbiome, pulmonary tuberculosis would be the best option to go with > > SEElink- “Bronchoalveolar lavage (BAL) is a procedure that is sometimes done during a bronchoscopy. It’s done to collect a sample from your lungs” > > I did not see any mention ofsmoking status and tuberculosisas confounders controlled for in this paper. > > Yes I agree with@Mildred Anashieon the additional alpha diversity > > I also agree with curating from the additional material provided as figure 2 does not appear very interpretable. This also provides you with the body sites for the comparisons. - Attachment (medlineplus.gov): Bronchoscopy and Bronchoalveolar Lavage (BAL): MedlinePlus Medical Test > A bronchoscopy procedure uses a bronchoscope (thin, lighted tube) to look for or treat lung problems. A bronchoalveolar lavage is used to collect a sample.

BOLARINWA AISHAT (14:45:24) (in thread): > Thank you all for the reviewI’llwork on effecting the changes:pray:

Kate Rasheed (14:52:14) (in thread): > I see it now@Mildred Anashie. Thank you so much.

Aleru Divine (14:55:26) (in thread): > I also saw that antibiotics exclusion@Kate RasheedIn this case, I don’t know which to go with.ButIf I had tomake a suggestion,I’ll pick 6 weeks and leave a note on the discussions page to account for the mention of the 4weeks “No antibiotics used in the 4 weeks prior to presentation”

Cate Ouma (18:08:16): > Hi Everyone, I need your view on this paper@Mercy Cheropand I are curating. We are having difficulties curating the experiments, because we have 2 sites the samples were taken from(oral/cheek and stool). Both had differentially abundant taxa for the different geographic locations/populations. How should I curate this, especially in terms of the groups(Group 0 and 1) I am comparing?

Aleru Divine (18:09:45) (in thread): > Good evening@Cate Oumacould you share this study please so I can have a look.Thanks!

Cate Ouma (18:10:16) (in thread): > https://www.nature.com/articles/s41598-022-21779-z#MOESM1 - Attachment (Nature): Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes > Scientific Reports - Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes

Aleru Divine (18:11:12) (in thread): > Thank you@Cate Ouma

Aleru Divine (18:19:45) (in thread): > Looking at the paper, you’ll have curate different experiments for the different sample sites (cheek and stool) > > Figure 1A (alpha diversity for stools) > Figure 2(differential abundance for stool samples) > > > Figure 3A(alpha diversity for cheek) > Figure 4(differential abundance for cheek) > > If you are doing a pairwise comparison for each of the sample sites, you will curate each sample site as a different experiments even if when they are comparing the same geographic locations.

Cate Ouma (18:38:11) (in thread): > If you look at the supplementary material, you will notice that Table 6-7 compares differential abundance of the 2 different sample sites. Tables 8-15 also does this, but now focuses on the different populations. I’m not sure on how I will define my Group 0 and 1 based on this

Aleru Divine (18:47:23) (in thread): > I’m looking at the supplementary material@Cate Ouma > 1. Table S6 and S7 show differentially abundant taxa for stool samples and oral samples respectively. > 2. Stool samples— Table S8(Thailand), S9(Barbados), S10(Chile), S11(South Africa) > 3. Oral Samples— Table S12(Thailand), S13(Barbados), S14(Chile), S15(South Africa) > For numbers 2 and 3 above, I think you’ll do a one-to all experiment. > > For example, let’s say experiment 1 > group 0 will be (Barbados + Chile + South Africa) group 1 will be Thailand > > So you will curate the signatures from table S8 (Thailand) as increased or decreased. Positive log2foldchange is increased and negative is decreased. > > Repeat this until you’ve compared all the countries and then repeat for the other sample site(oral) (should be 4 experiments for each sample site) making a total of 8. > > For my point number 1, (Table S6 and S7 show differentially abundant taxa for stool samples and oral samples respectively)These will be curated as seperate experiments. > I’m not sure how these will be groupedas 0 and 1. There’sreallyno comparison. They just gave results for decreased and increased taxa for each of the sample sites.

Cate Ouma (18:49:56) (in thread): > Noted. Thank you so much for your timely help@Aleru Divine

Samuel Nnanna (19:06:16) (in thread): > You’re correct@Aleru Divine. The experiment would be a one country to other countries from table s8-15 since both samples were mentioned and have differential abundance results for each country. So@Cate Oumayou’ll compare one country to the 3 others like@Aleru Divineexplained, till they’re all accounted for. > > For table S6; I found this in the paper(Table S6) are in lower abundance in the stool representing only 10.4% of the total gut microbiota. Using Pearson’s Correlation calculated between the first five Principal Components (PCs), we examined the influential factors of lifestyle behaviors on the composition of microbial communities originating from stool among the entire study population of Barbadian, Chilean, Pretorian and Thai individuals.) > And this indicates the results is for all populations, so it wasn’t a comparison. It’s a sticky bit > > Likewise for Table S7 > > Maybe draw the mentors’ attention to it. They could provide more clarity

Cate Ouma (19:09:30) (in thread): > Thank you@Samuel Nnannafor pointing this out

Aleru Divine (19:32:20) (in thread): > But what would happen to the alpha diversity measures reported in figure 1 and 3. And the comparisons done in figure 2 and 4? > > There were significant results.For stool samples alpha diversity > The mean Shannon indices reveal that the microbiota diversity is only significant between Thailand-Chile with FDR < 0.05. In case of Chao1 diversity index Thailand-Chile, Thailand-South Africa, Chile-South Africa, Barbados-South Africa have different richness with FDR < 0.05 (Fig. 1A).For oral samples > ****The mean Chao1 indices reveal that the microbiota diversity is significant between Thailand–Barbados, Thailand–Chile, Thailand–South Africa and Chile–South Africa with FDR < 0.05. Whereas only significant difference was observed between Thailand and Chile using Shannon diversity index with FDR < 0.05 (Fig. 3A).They are certainly not a one-to-all comparison and were significant.I have a similar issue that I plan to bring up during the office hours tomorrow@Cate Ouma:pleading_face:

Yoko C (21:37:01) (in thread): > Hi, I think you wouldn’t curate Fig 2 or Fig 4, because although they are significant genera, there is no information on where the difference is between the groups. I do think you would curate S6-s15 just as increased or decreased for each table. For the countries in the supplementary tables, I don’t think you can compare each country to another country. If you could do that, than you could use the alpha values, otherwise I think you would not fill them in. I do agree with the others that it would be best to check in office hours.

2024-11-06

Adeshile Oluwatosin (01:45:40): > Good morning@Svetlana Ugarcina Perovic@Esther Afuape@Scholastica Urua@Peace SandyI’m done curating this article > However, I would like your opinion on this curation > Especially these taxa: > > Mucispirium and mucispirium schaedieri > Although I curated it exactly like this > I can’t find any research on this > Even google has no response to those > > But I’m thinking there’s a mistake in the result > And they probably meant mucisipirillum and mucisipirillum schaedleri instead.https://bugsigdb.org/Study_1206https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-020-00886-x - Attachment (BugSigDB): Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis - BugSigDB > BACKGROUND: The increasing incidence of cancer and intestinal mucositis induced by chemotherapeutics are causing worldwide concern.Many approaches such as fecal microbiota transplantation (FMT) have been used to minimize mucositis. - Attachment (BioMed Central): Microbiota from alginate oligosaccharide-dosed mice successfully mitigated small intestinal mucositis - Microbiome > Background The increasing incidence of cancer and intestinal mucositis induced by chemotherapeutics are causing worldwide concern. Many approaches such as fecal microbiota transplantation (FMT) have been used to minimize mucositis. However, it is still unknown whether FMT from a donor with beneficial gut microbiota results in more effective intestinal function in the recipient. Recently, we found that alginate oligosaccharides (AOS) benefit murine gut microbiota through increasing “beneficial” microbes to rescue busulfan induced mucositis. Results In the current investigation, FMT from AOS-dosed mice improved small intestine function over FMT from control mice through the recovery of gene expression and an increase in the levels of cell junction proteins. FMT from AOS-dosed mice showed superior benefits over FMT from control mice on recipient gut microbiotas through an increase in “beneficial” microbes such as Leuconostocaceae and recovery in blood metabolome. Furthermore, the correlation of gut microbiota and blood metabolites suggested that the “beneficial” microbe Lactobacillales helped with the recovery of blood metabolites, while the “harmful” microbe Mycoplasmatales did not. Conclusion The data confirm our hypothesis that FMT from a donor with superior microbes leads to a more profound recovery of small intestinal function. We propose that gut microbiota from naturally produced AOS-treated donor may be used to prevent small intestinal mucositis induced by chemotherapeutics or other factors in recipients. Video Abstract

Rahila-me (03:15:56): > @Samuel NnannaGood morning, have you started working onAlterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery #518 we are to work as a team

Samuel Nnanna (03:24:04) (in thread): > Good Morning@Rahila-me. I have read through the paper and I had some concerns which I needed clarity on before adding the study.

Samuel Nnanna (03:24:28) (in thread): > Also thanks for reaching out and I look forward to collaborating with you

Rahila-me (03:27:17) (in thread): > @Cate Oumagoing through the paper will revert back to you

Mildred Anashie (03:34:36) (in thread): > Hi@Adeshile OluwatosinWell done on your curation. > I think you might be right with the mistake in the taxa, but our mentors will give clarification on how to go ahead. > > However, I noticed you didn’t curate Alpha diversity for the experiments. See S1 and S3 > > Well done again:clap:

Rahila-me (03:36:49) (in thread): > @Samuel Nnannathat’s fine:ok_hand::ok_hand:

Adeshile Oluwatosin (03:37:55) (in thread): > @Mildred AnashieThank you > I already corrected the taxa sinceIdidn’t find any meaningful information on what was in the result. > > Ohhh let me check the alpha diversity.

Aleru Divine (03:39:16) (in thread): > @Adeshile Oluwatosinwell done on your curation.

Aleru Divine (03:40:52) (in thread): > I believe you’re right. It was a typographical error. > Mucispirillum and Mucispirillum schaedleri are correct.

Mildred Anashie (03:46:19) (in thread): > You are welcome@Adeshile Oluwatosin

Rahila-me (04:13:57) (in thread): > @Cate Oumayou will have to curate 3 different experiments for each body sites (oral, stool and cheek) from the supplementary material abi@Aleru Divineare they using oral and cheek interchangeably? > Second observation in relation to what@Aleru Divinealready pointed you to:Differentially abundant taxa were identified by comparisons between each location versus all the others using DESeq2which simply means you are doing many to one relationship for each body sites > Example: > For example, let’s say experiment 1 > group 0 will be (Barbados + Chile + South Africa) group 1 will be Thailand just as she said above. This pairwise it comes with lots of experiments Alpha diversity supports this proof. > for more clarity also bring this up Thursday during office hours.

Svetlana Ugarcina Perovic (04:22:43): > Good morning, just gave an online presentation to my labmates onhow to give a good online presentation. > > I would like to share my slides with you:https://github.com/SvetlanaUP/presentations/blob/main/How_to_give_a_good_online_presentation_11_2024.pdfWhat do you think about online conferencing? Do you enjoy it or you have experienced too many challenges?

Mildred Anashie (04:23:54) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:raised_hands:I’llbe sure to take:pencil:

Adeshile Oluwatosin (04:25:06) (in thread): > Thank you@Svetlana Ugarcina PerovicI appreciate

Samuel Nnanna (04:25:15) (in thread): > @Rahila-meI do think the words oral and cheek were used interchangeably. In the sample collection, they mentioned that they collected oral and stool samples. > > I looked up cheek samples and i found this; > “About Your Buccal (Cheek) Sample > Your healthcare provider needs your DNA sample for your genetic test (a test to look at your genes). You will collect your DNA sample by using an oral swab to rub the inside of your cheek” > > maybe this helps provide clarity

Adeshile Oluwatosin (04:29:39) (in thread): > I don’t trust the results but this is what I can see:Experiment 1: chao- unchanged, Shannon-decreased.Experiment 2: chao and Shannon increased

Adeshile Oluwatosin (04:29:48) (in thread): > @Mildred Anashie

Kate Rasheed (04:33:05) (in thread): > Thank you for sharing. Let me plug in. > > For me, online conferencing is a great privilege to network. > > I love the fact that I get to meet different people and learn from presentations.

Adeshile Oluwatosin (04:38:36) (in thread): > I enjoy online conferencing a lot, less stressful and seems better organizedfor me, also people can join from anywhere in the world.Network delay sometimes can be a challenge with this.

Rahila-me (04:39:45) (in thread): > @BOLARINWA AISHATwell-done on your curation, > you can make you group 0 more descriptive: HIV-positive with no respiratory disease (control cohort), > I will go with 6 weeks for antibiotic exclusion since that’s what’s is in the main paper. > From my own observation Figure 2 is not curatable as also observed. As for theSignificance threshold 0.05 is always the default value. > Thank you

Kate Rasheed (04:39:58) (in thread): > @Svetlana Ugarcina Perovic. It would be great to have the recording of this. I would really love to learn about ways to improve online presenting especially dealing with mic/video connections and connecting with the audience.

BOLARINWA AISHAT (04:40:07) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicMany people are guilty of saying “Can you see my screen?” > I’ve learnt a better way to communicate that. > “Let me know if you can not see my slides”:hugging_face:I like online conferencing because there is a lesser chance of absence or lateness since anyone can join anywhere.

Rahila-me (04:41:23) (in thread): > @Svetlana Ugarcina PerovicThank you for this,:ok_hand::ok_hand:already taking a look on it

Adeshile Oluwatosin (04:47:04) (in thread): > There’sno text or write up to back it up

Mildred Anashie (04:50:56) (in thread): > Personally, online conferences are great and absolutely organized but I feel like it’s easier to interact and meet like minded people in-person and have great conversations. > > Ihaven’tfaced any challenges with online conferences@Svetlana Ugarcina Perovic

Mildred Anashie (04:52:18) (in thread): > YeaI’vegone through the paper and I think it might be unchanged all through, as I do not see where significance is indicated@Adeshile Oluwatosin

Adeshile Oluwatosin (05:03:06) (in thread): > Exactly, I see no significance too > Thanks:pleading_face:

Aleru Divine (05:20:39) (in thread): > Thank you so much for sharing@Svetlana Ugarcina PerovicI’ll check out the slides:pray:I enjoy online conferencing because it is very convenient, it is also easier to reach to and connect with people from different locations without even moving an inch. Oneof the challenges I’ve encountered however is unstable network service,that can be really frustrating.In-person conferences on the other hand, doesn’t rely on any network (you are the network):sweat_smile:It also allows for more spontaneity in terms of discussions and connecting with peoplebeyondjust listeningorjust speaking.

Aleru Divine (05:44:10) (in thread): > Really really insightful presentation@Svetlana Ugarcina Perovicthanks again for sharing.:blush:

Rahila-me (06:06:36) (in thread): > @Svetlana Ugarcina Peroviceverything on the slide resonates with me, but this one in particular got to me:Please watch this short demonstration of bad online talk and comment below bad moments that you observed,I have seen a presentation where there was some many colors dancing on the slides. color riots > Once again thank you for this, i have learnt also what to watch out for when next i am doing a presentation:pray:

Joy (06:25:08) (in thread): > Thank you@Svetlana Ugarcina Perovicvery thoughtful of you to have shared this.

Toluwalase Abigail (06:57:25): > Good morning everyone > > I would like a peer review on this study I’m curating with@Adeshile Oluwatosinhttps://bugsigdb.org/Study_1156https://www.nature.com/articles/s41598-021-95409-5Particularly on Alpha diversity curation, the condition stated, taxa with missing NCBI ID. - Attachment (BugSigDB): Association between clinical and environmental factors and the gut microbiota profiles in young South African children - BugSigDB > Differences in the microbiota in populations over age and geographical locations complicate cross-study comparisons, and it is therefore essential to describe the baseline or control microbiota in each population. - Attachment (Nature): Association between clinical and environmental factors and the gut microbiota profiles in young South African children > Scientific Reports - Association between clinical and environmental factors and the gut microbiota profiles in young South African children

Toluwalase Abigail (06:57:57) (in thread): > Thank you.

Kate Rasheed (06:58:22) (in thread): > Weldone on your curation@Adeshile Oluwatosin@Toluwalase Abigailon your curation. > > I’ll look through.

Kate Rasheed (06:59:50) (in thread): > @Toluwalase AbigailI just saw Oscillospiraceae. If you enter the NCBI ID, it would remove the orange error.

Aleru Divine (07:01:27): > Good day everyone, trust you’re having a great day:blush:I’ll appreciate a peer review on this study I’m curating. > > Thank you so much!:pray:https://bugsigdb.org/Study_1047 - Attachment (BugSigDB): Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3 - BugSigDB > BACKGROUND: Remodeling eubiosis of the gut microenvironment may contribute to preventing the occurrence and development of depression.

Toluwalase Abigail (07:02:14) (in thread): > Thank you@Kate Rasheed, I will do that.

Aleru Divine (07:06:06) (in thread): > Well done on your curation:clap::clap:@Toluwalase Abigail@Adeshile OluwatosinI believe the NK4A136 is the same as the resolved taxaLachnospiraceae bacterium NK4A136with TaxID:877420

Kate Rasheed (07:06:26) (in thread): > For the alpha diversity, I believe it is just Shannon and Faith. > > Look at this: “The evenness and richness (alpha diversity) within groups (based on the factors defined under the demographic, clinical and environmental data section) was calculated using the Shannon (H) and Faith’s Phylogenetic Diversity (PD) diversity metrics”

Adeshile Oluwatosin (07:07:28) (in thread): > @Kate RasheedI’ve not even corrected that aspect > > But evenness is pielou andrichness was mentioned too

Adeshile Oluwatosin (07:08:02) (in thread): > I saw that@Aleru DivineDidn’twant to assume > Just wanted to be sure > Will change that now

Adeshile Oluwatosin (07:08:29) (in thread): > @Kate Rasheedit’s oscillospiraceaeUCG:002

Adeshile Oluwatosin (07:08:36) (in thread): > That’snot permissible

Adeshile Oluwatosin (07:08:49) (in thread): > Thank you guys

Adeshile Oluwatosin (07:09:02) (in thread): > OkayI’lllook through it

Kate Rasheed (07:09:49) (in thread): > @Adeshile OluwatosinIt’s just Shannon and Faith that is recorded as the alpha diversity metrics although they are calculating the evenness and richness which is normal.

Toluwalase Abigail (07:10:41) (in thread): > Thank you@Aleru Divine..For the confirmation.

Adeshile Oluwatosin (07:11:07) (in thread): > But@Aleru DivineIt was stated NK4A136 group though

Adeshile Oluwatosin (07:12:23) (in thread): > Experiment 3/signature 1. > I know Svetlana explained something on those taxa. > > UCG:002 and UCG:005

Adeshile Oluwatosin (07:13:08) (in thread): > I understand@Kate Rasheedas there was no result for evenness and richness

Adeshile Oluwatosin (07:14:45) (in thread): > Also, the interpretation isn’t clear for Shannon and faith > > Also checkTable S2

Kate Rasheed (07:16:26) (in thread): > For the group names, you can add the age bracket to it, instead of just leaving it as Group A, Group C

Aleru Divine (07:17:29) (in thread): > The alpha diversity measures are just for Shannon and Faith PD indexes.The richness and evenness were determined by calculating Shannon’s H and Faith’s PD indexes.Thanks for pointing that out@Kate Rasheed

Kate Rasheed (07:22:39) (in thread): > @Toluwalase AbigailI see you mentioned antibiotics exclusion at 12months. > > What I see is tuberculosis treatment (TB) at 12months. I don’t think that’s the same as antibiotics.

Svetlana Ugarcina Perovic (07:23:27): > INVITATION: We would be happy if you can join us next week for another amazing MVIFALSO, a proud mentor here:wave:@Victoria (Burah) Poromon, a#bugsigdbcurator, will open #MVIF 33 next week and moderate discussion with the microtalks speakers. > > Victoria, can’t wait to listen to you!:bouquet: - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Kate Rasheed (07:24:08) (in thread): > Thank you for the update@Svetlana Ugarcina Perovic

Mildred Anashie (07:25:26) (in thread): > Hello@Toluwalase Abigail@Adeshile OluwatosinWell done on your curation > I’ll take a look also

Mildred Anashie (07:25:49) (in thread): > Well done@Aleru DivineI’lltake a look at this too

Aleru Divine (07:26:13) (in thread): > @Adeshile OluwatosinThe group doesn’t matter because individual bacterial cells are almost always found in clusters or as part of a larger microbial community hence —group > > See -https://www.mdpi.com/2075-1729/13/6/1280Lachnospiraceae bacterium NK4A136 is referred to as a group here. - Attachment (MDPI): Association of Gut Lachnospiraceae and Chronic Spontaneous Urticaria > (1) Background: Chronic spontaneous urticaria (CSU) has been linked to the dysbiosis of the gut microbiota. Furthermore, various studies have highlighted the anti-inflammatory properties of short-chain fatty acids (SCFAs), whose production is primarily regulated by the gut microbiota. However, only a few studies have investigated the role of major SCFA producers, such as Lachnospiraceae, in skin inflammatory diseases. (2) Goal: This study aimed to compare the abundance of Lachnospiraceae between CSU patients and healthy controls (HCs). (3) Material and methods: In this case–control study, 16S rRNA sequencing was performed to compare the composition of the gut microbiome between 22 CSU patients and 23 HCs. (4) Results: Beta-diversity revealed significant clustering (p < 0.05) between the CSU patients and HCs. Alpha diversity in the CSU group was significantly decreased according to the Evenness index (p < 0.05). The linear discriminant analysis effect size (LEfSe) identified the significant depletion of the Lachnospiraceae family in CSU patients. (5) Conclusion: Our study revealed the dysbiosis of the gut microbiota in CSU patients, including decreased levels of Lachnospiraceae members, responsible for SCFA production, suggesting that SCFAs may contribute to immune dysfunction in the pathogenesis of CSU. We speculate that the modulation of SCFAs could serve as a prospective additional option in CSU treatment.

Aleru Divine (07:27:18) (in thread): > Thank you so much@Adeshile Oluwatosin@Mildred Anashie:hugging_face:looking forward to your feedbacks

Mildred Anashie (07:28:39) (in thread): > I’llsure be in attendance > Thank you@Svetlana Ugarcina Perovicfor sharing:hugging_face:Can’twait to listen also@Victoria (Burah) Poromon:blush:

Aleru Divine (07:28:42) (in thread): > Thank you for the invite@Svetlana Ugarcina Peroviclooking forward to it@Victoria (Burah) Poromon:hugging_face:

Toluwalase Abigail (07:29:03) (in thread): > @Kate RasheedSo it will be explicitly mentioned that it was tuberculosis treatment since the study emphasize on the non-exposed group not being exposed to antibiotics treatment ?

Adeshile Oluwatosin (07:29:45) (in thread): > Noted@Aleru DivineThat’swhy I specifically mentioned missing taxa ID there > I didn’t just want to assume

Adeshile Oluwatosin (07:30:19) (in thread): > @Kate Rasheedmentor confirmed that to be correct . > That’s why it wasn’t changed

Adeshile Oluwatosin (07:30:30) (in thread): > I’llgo through the paper to check for a context

Adeshile Oluwatosin (07:34:37) (in thread): > Thank you > I would definitely be there@Svetlana Ugarcina Perovic:tada:Looking forward to it@Victoria (Burah) Poromon

Adeshile Oluwatosin (07:37:09) (in thread): > Well done@Aleru DivineYou’vedone well especially with the taxa. > Idon’twant to rush through > Let me check properly and give my feedback

Kate Rasheed (07:37:35) (in thread): > @Toluwalase Abigail@Adeshile OluwatosinThere was no antibiotics exclusion in this paper. > > I also see Benjamin-Hochberg correction for multiple hypothesis testing “where appropriate” . I don’t know how this would be recorded though:smile:.

Adeshile Oluwatosin (07:38:08) (in thread): > The correction is for alpha diversity@Kate Rasheed

Adeshile Oluwatosin (07:38:25) (in thread): > Have you checked the supplementary information > A second

Svetlana Ugarcina Perovic (07:40:13): > MVIF is always open for new team members– there are many ways to contribute to MVIF as a community-driven effort! > > We are always looking for feedbacks and suggestions (e.g. topics or speakers to invite, changes in format, time, etc) and for new members willing to contribute in a more continuous way, dadicating more time and effort as members of the organizing and program committees. > > Feel free to share your feedbacks / suggestions here, and if you are thinking to join the team, you can send an introduction/motivational letter* to this email addresssecretariat@microbiome-vif.org*you can send us a few lines about you and then a few lines about why you would like to join the MVIF committee (personal / scientific growth, willingness to increase the MVIF outreach in your local network, whatever really moves you to join us:slightly_smiling_face:). It doesn’t need to be an official motivational letter, a few lines are ok!

Kate Rasheed (07:40:19) (in thread): > Looking forward to listening to@Victoria (Burah) Poromon:smile::dancer:

Adeshile Oluwatosin (07:43:45) (in thread): > Thank you@Svetlana Ugarcina PerovicI’malways eager to dedicate, volunteer and work in communities like this. > I definitely would send a mail.

Kate Rasheed (07:44:49) (in thread): > @Aleru Divine@Mildred AnashieWell-done on this curation. A whole lot of taxa. > > For experiment 7, is there a reason why there’s no condition? I see the groups contrasted are healthy controls samples.

Aleru Divine (07:45:33) (in thread): > Oh my days!!!:face_with_open_eyes_and_hand_over_mouth:Apologies everyone > > I meant this studyhttps://bugsigdb.org/Study_1047 - Attachment (BugSigDB): Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3 - BugSigDB > BACKGROUND: Remodeling eubiosis of the gut microenvironment may contribute to preventing the occurrence and development of depression.

Aleru Divine (07:47:39) (in thread): > Thank you so much for the opportunity@Svetlana Ugarcina Perovic:pray:

Rahila-me (07:48:33) (in thread): > Weldon for the curation@Aleru Divine..okay

Aleru Divine (07:48:39) (in thread): > My apologies@Mildred Anashie:pray::face_with_peeking_eye:

Rahila-me (07:49:38) (in thread): > Thanks for the opportunity@Svetlana Ugarcina Perovic

Mildred Anashie (07:50:20) (in thread): > Totally fine@Aleru DivineI didn’t even notice it was the study we are still working on:sweat_smile:When I saw it, I knew it was a mistake

Aleru Divine (07:50:56) (in thread): > Thank you:blush:

Mildred Anashie (07:51:20) (in thread): > Thank you for the opportunity@Svetlana Ugarcina Perovic:pray:

Rahila-me (07:51:59) (in thread): > Thank you@Svetlana Ugarcina Perovicalso@Victoria (Burah) Poromoncan’t wait to hear you Bugsiging making us proud

Rahila-me (07:55:13) (in thread): > Weldone to you both@Toluwalase Abigail@Adeshile Oluwatosinthis has to be left this way it has not been resolved NK4A136

Adeshile Oluwatosin (08:01:04) (in thread): > @Rahila-me:pleading_face:

Adeshile Oluwatosin (08:02:36) (in thread): > First of, mark your study as complete@Aleru Divine:eyes:

Aleru Divine (08:03:26) (in thread): > It’snot complete yet. I have a question for office hours tomorrow@Adeshile Oluwatosinwhen I get clarification, I can now mark as complete.

Aleru Divine (08:05:01) (in thread): > @Rahila-meyou’reone of the people that stated this particular taxa has been resolved in the discussions page.:sweat_smile:https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Adeshile Oluwatosin (08:06:20) (in thread): > Google says it’s lachnospiraceaebacteriumNK4A136

Adeshile Oluwatosin (08:06:31) (in thread): - File (JPEG): IMG_2130

Adeshile Oluwatosin (08:10:52) (in thread): > Trust me I saw that antibiotics exclusion or is it my eyes > Can someone else check:joy:@Aleru Divine

Adeshile Oluwatosin (08:11:55) (in thread): > Also,what’swith UCG:002 and UCG:005@Kate Rasheed@Aleru Divine

Aleru Divine (08:12:31) (in thread): > My advice would be to curate as seen in the paper@Adeshile Oluwatosin

Kate Rasheed (08:15:15) (in thread): > Yes yes yes. Curate as seen for uncultured groups.

Adeshile Oluwatosin (08:15:39) (in thread): > Experiment 1/signature 1 > > Only UCG:002 was mentioned > > But I saw this in the text“When comparing the age groups A and C, only three features (an uncultured genus-level group (UCG) from the Oscillospiraceae (UCG-002), “Hence, the curation oscillospiraceae UCG:002

Adeshile Oluwatosin (08:19:30) (in thread): > That should be kept as that right? > Instead of UCG:002

Aleru Divine (08:21:57) (in thread): > Yes@Adeshile Oluwatosin:+1:

Rahila-me (09:23:06) (in thread): > @Aleru Divinethe one I resolved has the full name but with just the number no..and it was just the number she sent..here is the screenshot - File (JPEG): Screenshot_2024-11-06-15-21-17-66_40deb401b9ffe8e1df2f1cc5ba480b12.jpg

Rahila-me (09:24:11) (in thread): > And in one of my curations that has just the number I left it that way because even in gene bank it was not found

Rahila-me (09:26:11) (in thread): > I didn’t resolve just a number NK4A136…. > I resolved a full name in Gen bank this number was not found so in my curation I left that way

Samuel Nnanna (09:38:27) (in thread): > Thank you,@Svetlana Ugarcina Perovic, for sharing. They’ll definitely come in handy. > > Personally, I prefer in-person conferences and meetings over virtual ones. While online conferences certainly have their benefits, I find they can feel a bit overwhelming. Beyond the subtle distractions from one’s surroundings, the online format often requires splitting attention between watching the speaker, listening closely, and simultaneously reading the slides. > In a physical setting, I find it easier to direct my focus and process information effectively at each moment during the session. Online conferences, in comparison, make this more challenging. > > I’m curious,@Svetlana Ugarcina Perovicdo you think incorporating moments of humor during online presentations helps keep the audience engaged, or does it risk coming across as unprofessional and reducing engagement?

Samuel Nnanna (09:39:46) (in thread): > Good Job@Aleru Divine. I’ll go through this and send my observations

Aleru Divine (09:40:44) (in thread): > @Rahila-meThis number is the same as the one for the resolved taxa.But even in the paper, it is referred to as “Lachnospiraceae NK4A136 group” I believe they just shortened in the figure. - File (JPEG): IMG_1510

Samuel Nnanna (09:41:21) (in thread): > Thank you@Svetlana Ugarcina PerovicAlways a thing or two to learn. I’ll be there.

Rahila-me (09:43:51) (in thread): > Ok..unless that. in one paper I curated in the same figure they used the full name and also used just the number so I resolved the full name and kept the one that has just the number. We learn everyday

Aleru Divine (09:49:34) (in thread): > Please can you share this paper,I’dlike to have a look:pray:thanks

Aleru Divine (09:50:04) (in thread): > Thank you@Samuel Nnannalooking forward to your feedback:blush:

Rahila-me (09:53:14) (in thread): > When I am on my system I will send you it to you

Yoko C (10:00:51) (in thread): > Hello, regarding the antibiotics doubt, I think there is an exclusion. “Exclusion criteria included …receiving isoniazid or any fluoroquinolone treatment for ≥ 14 days at screening, receiving TB treatment in the previous 12 months.” isoniazid and fluoroquinolone are antibiotics and TB treatment is antibiotic based.

Svetlana Ugarcina Perovic (10:08:50) (in thread): > @Samuel Nnannain my opinion, making jokes is very risky online because you can not control/adjust it without seeing profile of your audience and their reaction. I would avoid it.

Samuel Nnanna (10:12:15) (in thread): > @Svetlana Ugarcina PerovicThanks…. I would also avoid making jokes cos what if they don’t get it or laugh:new_moon_with_face:. Best to stay on business

Svetlana Ugarcina Perovic (10:24:07) (in thread): > or on science:wink:

Samuel Nnanna (10:25:09) (in thread): > Smooth:grin::grin:.

Samuel Nnanna (10:41:27) (in thread): > @Aleru Divinei noticed the condition you used is response to antidepressants. > While reading I understood the paper was studying Depression induced through CUMS then experiments were now conducted to see the reaction to antidepressants. > > Still going through. just thought to point that out

Kate Rasheed (11:25:05) (in thread): > Thank you so much for this opportunity@Svetlana Ugarcina Perovic

BOLARINWA AISHAT (11:56:19) (in thread): > Thank you@Svetlana Ugarcina Perovic

BOLARINWA AISHAT (11:57:03) (in thread): > Thank you for sharing,I’llbe there

Cynthia Iwuoha (14:06:22) (in thread): > @Svetlana Ugarcina PerovicThank you for the opportunity.

Aleru Divine (17:03:40) (in thread): > Thank you for your feedback@Samuel NnannaIn the study, theyused XYS and FLX (antidepressants), to explore the role of gut microbiota in the treatment of depression caused by the induced CUMS. That’s why I used response to antidepressantsfor experiments 1-4instead of depression itself.

Kate Rasheed (23:16:57) (in thread): > Well-done on this curation. I see that you didn’t curate Figure 4G-I which is actually a pairwise comparison.@Aleru DivinePairwise comparison of control and cums group in Figure 4G-I can be added to experiment 5. > > See this: ” At the genus level (Fig. 4G–I; Fig. S4e), the abundance of Bacteroides and Klebsiella was significantly increased in the CUMS group”

2024-11-07

Joy (00:27:39) (in thread): > Thank you@Svetlana Ugarcina PerovicThis is definitely something I would love to be part of.

Joy (00:35:00): > Good morning everyone, I would like a peer review on this paper I am curating. I patiently await your feedbacks. Thanks.https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.710513/fullhttps://bugsigdb.org/Study_1193 - Attachment (Frontiers): Frontiers | Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet > High-fat (HF) diet-induced neuroinflammation and cognitive decline in humans and animals have been associated with microbiota dysbiosis via the gut-brain axi… - Attachment (BugSigDB): Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet - BugSigDB > High-fat (HF) diet-induced neuroinflammation and cognitive decline in humans and animals have been associated with microbiota dysbiosis via the gut-brain axis.Our previous studies revealed that excretory-secretory products (ESPs) derived from the larval Echinococcus granulosus (E.

Aleru Divine (02:06:35) (in thread): > Well done on your curation@Joy:clap:I’ll have a look:blush:

Mildred Anashie (02:22:05) (in thread): > Well done on your curation@JoyI’llalso take a look

Rahila-me (02:24:18) (in thread): > @JoyGood morning, I will look at it. Well done on your curation

Aleru Divine (02:27:30) (in thread): > @JoyI believe there should be 2 experiments in this study > > In figure 5 I see alpha diversity measures (5b and 5C) and LEfSe differential abundance results (5i and 5j) for > 1. LF vs HF > 2. HFE vs HF > For group definitions, you should just focus on describing group 1. > Please look at thisstudyand see how group 1 was defined. > > Condition should be 1, I believe it should be high fat diet. > > Sample sizes are 6 per group. Check figure 5 description. > > OnlyV4 regionof the 16S was amplified. > > Only one statistical test should be curated per experiment and for this studyLEfSewas used to test for differential abundance. Data transformation is relative abundance.MHT correction is NO for LEfSe.LDA score is3from figure 5 description. “LDA score > 3.0 was considered significant.” > > I don’t see any confounders controlled for in this study. > > Your signatures sources are figure > 1. 5i for LF vs HF and > 2. 5j for HFE vs HF - Attachment (BugSigDB): Oral and gut microbial profiling in periodontitis and Parkinson’s disease - BugSigDB > OBJECTIVES: We tested the hypothesis that Parkinson’s disease (PA) alters the periodontitis-associated oral microbiome.METHOD: Patients with periodontitis with Parkinson’s disease (PA+P) and without PA (P) and systemically and periodontally healthy individuals (HC) were enrolled.

Aleru Divine (02:29:28) (in thread): > @Joycheck out this thread for the log transformations for different statistical tests.https://community-bioc.slack.com/archives/C04RATV9VCY/p1699808143495129?thread_ts=1699704087.950319&channel=C04RATV9VCY&message_ts=1699808143.495129 - Attachment: Attachment > Oh wow > Could you correct this list please? @Levi Waldron > > ANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance

Mildred Anashie (02:40:46) (in thread): > I see what you are saying@Kate Rasheed@Aleru DivineIs S5 not curatable?:thinking_face:

Kate Rasheed (02:45:30) (in thread): > Weldone on this review@Aleru Divine. Weldone on your curation@Joy. > > Let me have a look too.

Mildred Anashie (02:53:26) (in thread): > Hi@JoyWell done again > > I agree with@Aleru DivineCurate the signatures in Figure 5i and j which will give you 2 experiments. LEfSe is the statistical test (We usually curate the statistical test used for differential abundance). > > > Alpha diversity is in Fig 5 as well > > For the antibiotic exclusion, just the duration is okay. E.g 3 days, 2 weeks, 3 months etc. > > But for your study, please leave it blank as I do not see any exclusion mentioned for antibiotics (In your paper, the mice were given water containing different antibiotics).@Aleru Divineshould 5d-h be curated?:thinking_face:It seems to show comparisons with significance at the phylum level

Kate Rasheed (02:55:01) (in thread): > @Joy. The alpha diversity (Shannon and Simpson) for the HF groups was significantly decreased. > > The body site should be Feces. > > LDA is 3

Kate Rasheed (03:06:25) (in thread): > @Aleru DivineFor the statistical test, two statistal tests were mentioned but we can see one shown in the figures. > > See this: “The linear discriminant analysis (LDA) effect size (LEfSe) was used to detect the features of gut microbiota with significant difference abundances between designated taxa with the Kruskal−Wallis ranksum test.”

Aleru Divine (03:08:24) (in thread): > Thank you@Kate Rasheedand@Mildred Anashiefor the feedback.I’llcurate figure 4G-I, there I was wondering what to do with the alpha diversity measures:sweat_smile:@Mildred Anashiepearson’s correlation was used for S5 and it is indeed curatable.Ididn’tsee the comparisons made.Ididn’teven think there was any.Thanks for the feedback everyone:heart_hands:I truly truly appreciate.

Kate Rasheed (03:09:27) (in thread): > @Aleru DivineI also did not see the confounders. Maybe@Joycan point us to where it is.

Aleru Divine (03:11:02) (in thread): > @Kate RasheedI stated that “only one statistical test should be curated per experiment” > > I still believe it is LEfSe. LEfSe is done with other tests.See thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728907895887159?thread_ts=1728906707.891419&cid=C04RATV9VCY - Attachment: Attachment > There’s an explanation from @UBNSEMS3S on this statistical test confusion. > > LEfSe gives an LDA score/threshold and the Mann-Whitney test is just what LEfSe does behind the scenes. (If I’m explaining that correctly) > > In my case, it was Kruskal-Wallis and LEfSe. > > Here’s the recording from one of the previous office hours. > > Time stamp 13:00 -14:50 > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727978011885959

Mildred Anashie (03:11:20) (in thread): > Hi@Kate RasheedI think that statement is implying this:thinking_face:https://community-bioc.slack.com/archives/C04RATV9VCY/p1728907895887159?thread_ts=1728906707.891419&channel=C04RATV9VCY&message_ts=1728907895.887159 - Attachment: Attachment > There’s an explanation from @UBNSEMS3S on this statistical test confusion. > > LEfSe gives an LDA score/threshold and the Mann-Whitney test is just what LEfSe does behind the scenes. (If I’m explaining that correctly) > > In my case, it was Kruskal-Wallis and LEfSe. > > Here’s the recording from one of the previous office hours. > > Time stamp 13:00 -14:50 > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727978011885959

Aleru Divine (03:13:11) (in thread): > Yes@Mildred Anashiethat’sit.

Aleru Divine (03:18:08) (in thread): > @Mildred Anashiethe signatures in figure 5d-h are represented in the LEfSe results. > > Except for firmicutes (d) for HFE vs HF which isn’t in the LEfSe results (5J) for HFE vs HF.:eyes:

Mildred Anashie (03:20:06) (in thread): > Alright then > > Although are they the same statistical tests?I’mnot sureShe’llhave to focus on 5i and j if they are though@Aleru Divine

Aleru Divine (03:29:39): > Good morning everyone!:sunny:I was wondering if we’ll have office hours today?@Svetlana Ugarcina Perovic<@UBNSEMS3S>

Kate Rasheed (03:31:50) (in thread): > @Mildred Anashie@Aleru DivineDoesn’t that mean that the Figure 5D-H asides 5F could be Kruskal-Wallis test:thinking_face:

Kate Rasheed (03:32:32) (in thread): > Same thoughts I had this morning since I didn’t see a reminder yesterday but I think there would be:smile:. > > It should be the same link.

Aleru Divine (03:42:39) (in thread): > LEfSe was used to detect the features with Kruskal-Wallis (together) not differently.Look at one of my previouspapersI think that was ANOVA but again, LEfSe detected these signatures and even some more signatures.Except for firmicutes 5d. - Attachment (Nature): The intensive physical activity causes changes in the composition of gut and oral microbiota > Scientific Reports - The intensive physical activity causes changes in the composition of gut and oral microbiota

Aleru Divine (03:43:12) (in thread): > I hope so:crossed_fingers::pleading_face:

Svetlana Ugarcina Perovic (03:49:38) (in thread): > See you today atour weekly team meeting and office hours at 9 AM EDT (>>3:00 PM<<**** ****in Europe, Nigeria, etc.).https://us02web.zoom.us/j/2737200499cc<@UBNSEMS3S>

Aleru Divine (03:51:20) (in thread): > Thank you for the update@Svetlana Ugarcina PerovicI’mlooking forward to it:blush:

Adeshile Oluwatosin (04:14:59) (in thread): > Thank you@Svetlana Ugarcina Perovic:heart:

Kate Rasheed (04:18:07) (in thread): > Thank you for the update@Svetlana Ugarcina Perovic.

Kate Rasheed (04:18:50) (in thread): > Thanks for the clarity@Aleru Divine

Mildred Anashie (04:20:12) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

Chinwendu Joy Enyidiegwu (05:07:40) (in thread): > yeah, looking forward forward to joining the team

Kate Rasheed (08:03:38) (in thread): > Has anyone been able to join the meeting? From my end it’s saying meeting is yet to start. > > I just realized it’s 3pm:smile:

Adeshile Oluwatosin (08:04:16) (in thread): > @Kate RasheedShe said 3PM. I also tried to join as well and saw that

Rahila-me (08:11:04): > No meeting…i have been waiting in the room

Adeshile Oluwatosin (08:11:58) (in thread): > Hello@Rahila-meIt’sby 3PM Nigeria time

Adeshile Oluwatosin (08:11:58) (in thread): > Hello@Rahila-meIt’sby 3PM Nigeria time

Mildred Anashie (08:12:15) (in thread): > It’s3pm@Rahila-me

Rahila-me (08:12:27) (in thread): > Ok..thank you… thinking 2pm as usual

Svetlana Ugarcina Perovic (08:12:53) (in thread): > 9 AM EDT as usual

Svetlana Ugarcina Perovic (08:13:30) (in thread): > only last week was an hour difference due to time savings differences > now we are back at 3 PM

UBNSEMS3S (08:58:21): > Sorry I am going to have to cancel the meeting. I am not feeling well.

Kate Rasheed (08:59:25) (in thread): > So sorry to hear. Please do well to take care of yourself and I wish you speedy recovery<@UBNSEMS3S>

Cate Ouma (08:59:59) (in thread): > Get well soon<@UBNSEMS3S>

Adeshile Oluwatosin (09:01:04) (in thread): > So sorry<@UBNSEMS3S>I hope you get better soon:mending_heart:

Yoko C (09:01:04) (in thread): > Feel better soon!

Samuel Nnanna (09:03:00) (in thread): > Yikes…..get well soon<@UBNSEMS3S>

Aaishah Mahadeo (09:03:17) (in thread): > Feel better soon!

Aleru Divine (09:03:22) (in thread): > Sorry to hear that<@UBNSEMS3S>Hope you feel better soon!:love_letter:

Chinwendu Joy Enyidiegwu (09:03:49) (in thread): > Get well soon<@UBNSEMS3S>

Alisha Mahadeo (09:04:19) (in thread): > I hope you feel better soon

Mildred Anashie (09:05:08) (in thread): > Hope you feel better:mending_heart:<@UBNSEMS3S>

Svetlana Ugarcina Perovic (09:06:40): > Feel free to write here below as commentsYOUR QUESTIONS prepared for the meeting. And we will answer them asap.

Agatha (09:06:54) (in thread): > Get well soon@C. Mirzayi (please do not tag this account)

Mildred Anashie (09:10:23) (in thread): > Thank you@Svetlana Ugarcina Perovic:pray:https://www.nature.com/articles/s41598-022-12970-3I’ll like some clarification on the alpha diversity in this paper for the experiments I’m working on. The paper points to Fig 4 and Table 2 but I’m unsure how to interpret Table 2 and if I should curate the table. > > Thank you:pray: - Attachment (Nature): The lung microbiome in HIV-positive patients with active pulmonary tuberculosis > Scientific Reports - The lung microbiome in HIV-positive patients with active pulmonary tuberculosis

Adeshile Oluwatosin (09:11:48) (in thread): > Thank you@Svetlana Ugarcina PerovicPlease I would like clarifications in these studies: > 1. https://bugsigdb.org/Study_1181 > https://pmc.ncbi.nlm.nih.gov/articles/PMC10921815/#MOESM1 > * Alpha diversities issues as the contrasts is different from what we can see in the results. The experiments were curated as one against all analysis. So we are confused on if it should be ignored or how to go about it, > * Also confusion of the body sites as there are different experiments and comparisons. > 2.:https://www.nature.com/articles/s41598-020-69111-x#MOESM2https://bugsigdb.org/Study_1194 > * How can Figure S2 be curated as some figures (colours) are not so visible. > * I chose human papillovirus as the condition but I can also see the mention of bacterial vaginosis in the study. > 3. :https://bugsigdb.org/Study_1156https://www.nature.com/articles/s41598-021-95409-5 > * Alpha diversity issue, Kindly check Figure S2. > * Also antibiotics exclusion was written out, but I believe from this statement “Exclusion criteria included …receiving isoniazid or any fluoroquinolone treatment for ≥ 14 days at screening, receiving TB treatment in the previous 12 months.” isoniazid and fluoroquinolone are the antibiotics. kindly confirm. > * There was a confusion on if NK4A136 group means Lachnospiraceae NK4A136 group as it was mentioned in the paper as NK4A136 group only. > 4. :https://www.sciencedirect.com/science/article/pii/S0888754319305774https://bugsigdb.org/Study_1207Confirmation of the condition, group 0 and 1 in the study. - Attachment (BugSigDB): Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study - BugSigDB > OBJECTIVE: To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA. - Attachment (PubMed Central (PMC)): Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study > To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA. Before … - Attachment (Nature): Changes in the vaginal microbiota across a gradient of urbanization > Scientific Reports - Changes in the vaginal microbiota across a gradient of urbanization - Attachment (BugSigDB): Changes in the vaginal microbiota across a gradient of urbanization - BugSigDB > The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations.Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity. - Attachment (BugSigDB): Association between clinical and environmental factors and the gut microbiota profiles in young South African children - BugSigDB > Differences in the microbiota in populations over age and geographical locations complicate cross-study comparisons, and it is therefore essential to describe the baseline or control microbiota in each population.

Kate Rasheed (09:12:07) (in thread): > Good day@Svetlana Ugarcina Perovic, please I have questions from an article I’m working on: > > 1. The sequencing platform used is BooterShot and this is not on BugSigDB. I tried researching another name for Boostershot and I saw that it can be referred to as Illumina MiSeq, I would like to find out if this is accurate. > 2. Two statistical tests with different results were used: ANCOM and ALDE. ALDE isn’t on BugSigDB and I discovered it’s not a popular statistal test used for Microbiome analysis. What do I do in this regards. > > Here is the article:https://www.nature.com/articles/s43856-024-00630-8Thank you so much. - Attachment (Nature): Oral and gut microbiome profiles in people with early idiopathic Parkinson’s disease > Communications Medicine - Stagaman et al. investigate the associations between early idiopathic Parkinson’s disease (PD) and the diversity and composition of both saliva and stool microbiomes…

Aleru Divine (09:15:41) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@BOLARINWA AISHATand I are correcting this study > 1. we would like to know if we are to curate a different experiment for each confounder adjusted for. > 2. What significance threshold should we use for these experiments since FDR was carried out at 5% and 10% > Source: Supplementary material -Date sheet 1 (sheet S3 - S12) > > 3. What is the data transformation for Pearson’s Correlation? > > Thank you so muchStudy Link - Attachment (Frontiers): Frontiers | Comparative Studies of the Gut Microbiota in the Offspring of Mothers With and Without Gestational Diabetes > Background: Offspring of mothers with gestational diabetes mellitus (GDM) have increased risk of developing metabolic disorders as they grow up. Microbial co…

Svetlana Ugarcina Perovic (09:27:09) (in thread): > @Mildred AnashieFigure shows only the Inverse Simpson results and Table shows the other indices that should be curated. There, you are curating results with “****” significance.

Aleru Divine (09:29:45): > Good afternoon@Svetlana Ugarcina PerovicPlease I’d like to delete experiment 3 from this study > The alpha diversity measures were not significant and no statistically significant features were found when the groups in experiment 3 were compared. > > Thank you!:pray:https://bugsigdb.org/Study_1127 - Attachment (BugSigDB): Oral and gut microbial profiling in periodontitis and Parkinson’s disease - BugSigDB > OBJECTIVES: We tested the hypothesis that Parkinson’s disease (PA) alters the periodontitis-associated oral microbiome.METHOD: Patients with periodontitis with Parkinson’s disease (PA+P) and without PA (P) and systemically and periodontally healthy individuals (HC) were enrolled.

Joy (09:31:59) (in thread): > Wishing you speedy recovery<@UBNSEMS3S>

Svetlana Ugarcina Perovic (09:32:34) (in thread): > deleted.

Aleru Divine (09:33:02) (in thread): > Thank you so much:blush:

Mildred Anashie (09:34:16) (in thread): > Okay@Svetlana Ugarcina PerovicI’m not sure how to tell increase and decrease > Thank you:pray:

Svetlana Ugarcina Perovic (09:34:34) (in thread): > @Mildred Anashiefrom the values in the table

Mildred Anashie (09:35:32) (in thread): > Okay,I’lltake a look again > Thank you:pray:

Svetlana Ugarcina Perovic (09:35:43) (in thread): > e.g. HIV vs. Pneumonia ->
> 279.5 (213.0–342.5) vs. 130.0 (74.0–240.0) > > meaning decreased alpha diversity of Pneumonia group compared to HIV group > OR > increased alpha diversity of HIV group compared to Pneumonia group

Mildred Anashie (09:37:43) (in thread): > I see it now > > Thank you again:blush:

Joy (09:38:09) (in thread): > Thank you guys, you all are wonderful curators. I truly appreciate the peer review.:heart:

BOLARINWA AISHAT (09:38:11) (in thread): > I wish you quick recovery > Take care:heart:

Svetlana Ugarcina Perovic (09:40:17) (in thread): > @Adeshile Oluwatosin1. > * If alpha diversities issues as the contrasts are different from what we can see in the Signature results. then we do not curate alpha diversities because they are not talking about the same experiments.. > * Name body sites and make notes.

Aleru Divine (09:40:19) (in thread): > You are amazing@Joy:heart_hands:

Svetlana Ugarcina Perovic (09:43:15) (in thread): > 2. Figure S2: The microbial alpha diversity comparison among four parts in no OSA group. A: Tongue base; B: Surface of palatine tonsil; C: Palatine tonsillar capsule after tonsillectomy; D: Adenoid (ns: no significance, *P<0.05, **P<0.01). - File (PNG): Screenshot 2024-11-07 at 15.41.52.png

Svetlana Ugarcina Perovic (09:43:35) (in thread): > I do not see the problem of colors. Please specify.

Adeshile Oluwatosin (09:44:21) (in thread): > @Svetlana Ugarcina PerovicBody sites : pharynx: general term for comparison amongst none, moderate, mild and severeposterior part of the tongue, Oropharynx and naso pharynx: comparison amongst none A, B, C and D for instance

Svetlana Ugarcina Perovic (09:46:54) (in thread): > Chao: C vs D > ACE: A vs C > ACE: C vs D

Adeshile Oluwatosin (09:46:59) (in thread): > @Svetlana Ugarcina PerovicFor number 2, I mean this

Svetlana Ugarcina Perovic (09:47:08) (in thread): > condition: urbanization

Adeshile Oluwatosin (09:47:16) (in thread): - File (JPEG): IMG_2144

Adeshile Oluwatosin (09:51:22) (in thread): > @Svetlana Ugarcina PerovicAlso, experiment 7 and 8 in the first study. > > I curated non OSA c as the group 1 and the combination of mild, moderate and severe C as Group 0 > > I’m confused on if that’s right > As mild, moderate and severe according to the curation policyI believehave higher severity.

Adeshile Oluwatosin (09:52:58) (in thread): > For study 2 listed : urbanization is not permissible as a condition@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:00:53) (in thread): > right now, I am searching for EFO related to urbanization…

Svetlana Ugarcina Perovic (10:02:21) (in thread): > I would sayhttps://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0010724 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Svetlana Ugarcina Perovic (10:02:40) (in thread): > lifestyle measurement

Svetlana Ugarcina Perovic (10:02:48) (in thread): > as nearest term

Svetlana Ugarcina Perovic (10:04:16) (in thread): > As for Fig S2, follow text/description in the paper when colors not visible and make a note.

Adeshile Oluwatosin (10:04:35) (in thread): > Okay, thank you

Adeshile Oluwatosin (10:05:24) (in thread): > The problemof the colours in study 2 is in the recent image I dropped@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:06:00) (in thread): > yes, I saw it

Svetlana Ugarcina Perovic (10:08:33) (in thread): > 3. > * Alpha diversity issue, Kindly check Figure S2.That’s I believe answered, from my screenshot, right? > * Also antibiotics exclusion was written out, but I believe from this statement “Exclusion criteria included …receiving isoniazid or any fluoroquinolone treatment for ≥ 14 days at screening, receiving TB treatment in the previous 12 months.” isoniazid and fluoroquinolone are the antibiotics. kindly confirm.YES, but make a note. > * There was a confusion on if NK4A136 group meansLachnospiraceae NK4A136group as it was mentioned in the paper as NK4A136 group only.It is Lachnospiraceae NK4A136.

Adeshile Oluwatosin (10:12:26) (in thread): > 3. I mean this Table S2, sorry - File (PNG): IMG_2145

Adeshile Oluwatosin (10:14:44) (in thread): > @Svetlana Ugarcina PerovicAlso in the case of the first study, FIGURE S2 > You mentioned ACE A vs C, C vs D > In the case where one is increase and one is decrease. > Which should be curated. > > Also from the initial question I asked, I believe the combination of mild, moderate and severe is the accurate Group 1.

Adeshile Oluwatosin (10:15:43) (in thread): > Also, body sites for study 1hasn’tbeen attended to:pray:@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (10:24:29) (in thread): > I’mso sorry,I’mtaking you back@Svetlana Ugarcina PerovicFor study 2: this was mentioned “ A gynecologist sampled vaginal introitus and cervicovaginal (endo/ectocervix/posterior fornix) sites”. > > The accurate body sites seems confusingfor comparison between amerinians and Mestizos as 2 samples were mentioned.Vaginal Introitus: vaginalPHCervicovaginal : fecal sample

Svetlana Ugarcina Perovic (10:25:53) (in thread): > @Adeshile Oluwatosinthis communication is very confusing, please summarize everything concisely in a new slack post per each study. thank you!

Adeshile Oluwatosin (10:26:28) (in thread): > @Svetlana Ugarcina PerovicDo you mean out of this thread ma’am

Svetlana Ugarcina Perovic (10:27:39) (in thread): > yes please

Adeshile Oluwatosin (10:29:14) (in thread): > Okay, I will do that now > Thank you

Adeshile Oluwatosin (10:30:50): > Hello@Svetlana Ugarcina PerovicIn this studyhttps://www.nature.com/articles/s41598-020-69111-x#MOESM2https://bugsigdb.org/Study_1194 > * This was mentioned “ A gynecologist sampled vaginal introitus and cervicovaginal (endo/ectocervix/posterior fornix) sites”. > The accurate body sites seems confusing for comparison between Amerindians and Mestizos as 2 samples were mentioned. > > Vaginal Introitus: vaginal PH as seen in Figure 1 > Cervicovaginal : fecal sample > * This was mentioned: ACE A vs C, C vs D, for Alpha diversity. > In the case where one is increase and one is decrease. > Which should be curated. - Attachment (Nature): Changes in the vaginal microbiota across a gradient of urbanization > Scientific Reports - Changes in the vaginal microbiota across a gradient of urbanization - Attachment (BugSigDB): Changes in the vaginal microbiota across a gradient of urbanization - BugSigDB > The vaginal microbiota of healthy women typically has low diversity, which increases after perturbations.Among these, lifestyle associated with certain sexual and antimicrobial practices may be associated with higher diversity.

Adeshile Oluwatosin (10:33:14): > Hello@Svetlana Ugarcina Perovichttps://pmc.ncbi.nlm.nih.gov/articles/PMC10921815/#MOESM1https://bugsigdb.org/Study_1194I would like to really understand how to go about curation of the body sites in the experiments. > > These are few body sites, we came up with. > > Body sites : pharynx: general term for comparison amongst none, moderate, mild and severe > > posterior part of the tongue, Oropharynx and naso pharynx: comparison amongst none A, B, C and D for instance - Attachment (PubMed Central (PMC)): Changes in the nasopharyngeal and oropharyngeal microbiota in pediatric obstructive sleep apnea before and after surgery: a prospective study > To explore the changes and potential mechanisms of microbiome in different parts of the upper airway in the development of pediatric OSA and observe the impact of surgical intervention on oral microbiome for pediatric OSA. Before …

Adeshile Oluwatosin (10:46:21): > Hello@Svetlana Ugarcina Perovichttps://www.nature.com/articles/s41598-021-95409-5https://bugsigdb.org/Study_1156I’m a bit confused on how to curate the alpha diversity for Shannon and Faith in all experiments in this study as well. > Please check Table S2. > > This was stated “An increase in richness and evenness was observed during the first 3 years of life, as shown by Shannon’s H index (Fig. 3A) and Faith’s PD (Supplementary Table S2).” > > Group C is >2-5 age and in Table S2, > It was seperated. - Attachment (Nature): Association between clinical and environmental factors and the gut microbiota profiles in young South African children > Scientific Reports - Association between clinical and environmental factors and the gut microbiota profiles in young South African children - Attachment (BugSigDB): Association between clinical and environmental factors and the gut microbiota profiles in young South African children - BugSigDB > Differences in the microbiota in populations over age and geographical locations complicate cross-study comparisons, and it is therefore essential to describe the baseline or control microbiota in each population.

Adeshile Oluwatosin (10:52:26): > Lastly@Svetlana Ugarcina PerovicThank you:pray:https://www.sciencedirect.com/science/article/pii/S0888754319305774https://bugsigdb.org/Study_1207Confirmation of the condition, Group 0 and 1 in this study - Attachment (BugSigDB): Whole metagenome sequencing of cecum microbiomes in Ethiopian indigenous chickens from two different altitudes reveals antibiotic resistance genes - BugSigDB > We analyzed the whole genomes of cecum microbiomes of Ethiopian indigenous chickens from two distinct geographical zones: Afar (AF) district (Dulecha, 730 m above sea level) and Amhara (AM) district (Menz Gera Midir, 3300 m).

Rahila-me (10:53:24) (in thread): > <@UBNSEMS3S>Get well soon. Take care

Svetlana Ugarcina Perovic (11:06:03) (in thread): > @Kate RasheedI’ve spent some time searching for BoosterShot specification and could not find it. Make a note in your curation with this commercial name of sequencing service. > > As for ALDEX, in the paper we find: “thealdex.glmfunction” and in the method specification (https://www.bioconductor.org/packages/release/bioc/html/ALDEx2.html) we find: “a generalized linear model (viaaldex.glm)” -> linear model - Attachment (Bioconductor): ALDEx2 > A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch’s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.

Kate Rasheed (11:10:41) (in thread): > Thank you so much for this@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (11:18:02) (in thread): > @Aleru Divine@BOLARINWA AISHAT > 1. we would like to know if we are to curate a different experiment for each confounder adjusted for.YES > 2. What significance threshold should we use for these experiments since FDR was carried out at 5% and 10%0.05 > Source: Supplementary material - Date sheet 1 (sheet S3 - S12) > > 3. What is the data transformation for Pearson’s Correlation?Leave it unspecified.I am not sure about this one. We will ask<@UBNSEMS3S>as soon as she feels good.

Aleru Divine (11:19:27) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (11:20:49) (in thread): > If you search in bugsigdb for Pearson’s Correlation recorded, you will see it’s unspecified@Aleru DivineI read it now about Pearson, but could not clearly understand its Data Transformation.

Svetlana Ugarcina Perovic (11:21:28) (in thread): > Probably you did the same, just sharing with you all how I am solving my doubts…

Aleru Divine (11:23:27) (in thread): > Okay@Svetlana Ugarcina PerovicI’llleave the data transformationblank for now.Until it is resolved.Again, thank you so much for all the answers.:blush:

Svetlana Ugarcina Perovic (11:28:00) (in thread): > You are curating Table S6, right? And there are two body sites: Cervicovaginal site and Introitus

Svetlana Ugarcina Perovic (11:30:46) (in thread): > For alpha diversity, which figure you have been curating?

Svetlana Ugarcina Perovic (11:34:03) (in thread): > They are all different parts of mouth sites. So body site is mouth and then for each experiment specify parts which are compared.

Adeshile Oluwatosin (11:39:04) (in thread): > Yes, I’m to curate Table S6 as well. > I haven’t curated it > > ButI can see Figure 2c and d

Adeshile Oluwatosin (11:43:39) (in thread): > Thank you@Svetlana Ugarcina PerovicI really appreciate

Svetlana Ugarcina Perovic (11:45:15) (in thread): > condition:Restricted to specific locationgroup 0::chicken:from one location > group 1::chicken:from other location

Adeshile Oluwatosin (11:47:23) (in thread): > The two regions states are lowland and highland region

Svetlana Ugarcina Perovic (11:47:50) (in thread): > @Adeshile Oluwatosincorrection, different parts of throat, right?

Svetlana Ugarcina Perovic (11:48:11) (in thread): > Anyway the same logic applies.

Adeshile Oluwatosin (11:49:29) (in thread): > AM and AF

Adeshile Oluwatosin (11:49:41) (in thread): > From Fig S1 and S2. > > It seems like either can be group 0 and 1 > Or better still the lowland region (AF)

Svetlana Ugarcina Perovic (11:50:10) (in thread): > “It seems like either can be group 0 and 1” YES

Adeshile Oluwatosin (11:51:38) (in thread): > Yes please > > Differnt part of the throat > 4 parts were mentioned in the article

Svetlana Ugarcina Perovic (11:53:36) (in thread): > Figure 2c and d do not show significant differences.

Svetlana Ugarcina Perovic (11:54:01) (in thread): > So body site is throat and then for each experiment specify parts which are compared.

Svetlana Ugarcina Perovic (11:54:27) (in thread): > and in text you can read no significance in alpha diversity…

Adeshile Oluwatosin (11:58:02) (in thread): > Noted, thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (11:58:12) (in thread): > Noted

Svetlana Ugarcina Perovic (11:58:39) (in thread): > You should record onlysignificant increase or decrease.

Svetlana Ugarcina Perovic (12:04:59) (in thread): > This is something that<@UBNSEMS3S>discussed at the last meeting, right?

Svetlana Ugarcina Perovic (12:06:08) (in thread): > Please play again recordings from the last meeting.

Svetlana Ugarcina Perovic (12:07:05) (in thread): > I have to go off now. Please do let me know if after rewatching is still unclear.

Adeshile Oluwatosin (12:08:19) (in thread): > No,<@UBNSEMS3S>hasn’tgone through this article yet@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (12:08:41) (in thread): > It was assigned 2 days ago

Adeshile Oluwatosin (12:10:34) (in thread): > That was an oversight , thank you > > I will go over it again > I also can’t find any other figure or Table on alpha diversity for Table S6 curation.

Rahila-me (14:32:46): > @Svetlana Ugarcina PerovicGood evening, Please help me delete from this study:https://bugsigdb.org/Study_1169Signature 3 in experiment 9 > Also delete Experiment 11 and 12 and their respective signatures. > Thank you

Svetlana Ugarcina Perovic (14:51:03) (in thread): > deleted.

Rahila-me (14:59:12) (in thread): > @Svetlana Ugarcina PerovicThank you

Svetlana Ugarcina Perovic (15:02:11) (in thread): > @Adeshile Oluwatosinok, then curate only the signatures. Our primary goal is to record the signatures, and it can happen that alpha diversity for their corresponding experiments is not provided.

Adeshile Oluwatosin (15:04:01) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (15:05:21) (in thread): > any opinion on the body sites issue mentioned

Svetlana Ugarcina Perovic (15:05:27) (in thread): > @Adeshile OluwatosinHere, I need another pair of eyes to confirm my observation. Let’s randomly pick someone, 1, 2, 3…

Svetlana Ugarcina Perovic (15:05:51) (in thread): > @Chris Awokehelp in here.

Adeshile Oluwatosin (15:06:04) (in thread): > This as well@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (15:06:58) (in thread): > @Adeshile OluwatosinHere, again I need another pair of eyes to confirm my observation:slightly_smiling_face:Let’s randomly pick someone, 1, 2, 3…

Svetlana Ugarcina Perovic (15:07:29) (in thread): > @Yoko Cplease help in here.

Svetlana Ugarcina Perovic (15:08:02) (in thread): > I am looking at this study again.

Yoko C (15:08:58) (in thread): > Hello! Sure, I will go over all questions with@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (15:09:32) (in thread): > I am reading it again, but I am too tired.

Svetlana Ugarcina Perovic (15:09:47) (in thread): > I will be here until we finalized it.

Adeshile Oluwatosin (15:10:26) (in thread): > Thank you@Yoko CI await a responseI’mso sorry@Svetlana Ugarcina Perovicmy questions were quite a lot today

Svetlana Ugarcina Perovic (15:10:44) (in thread): > no worries at all@Adeshile Oluwatosin

Adeshile Oluwatosin (15:14:48) (in thread): > @Chris Awoke:eyes:@Svetlana Ugarcina PerovicThank you

Svetlana Ugarcina Perovic (15:15:17) (in thread): > FigS2: cervicovaginal (a) and introital samples (b). > They are both vaginal samples, different parts. Even in paper they said “both vaginal sites”…

Svetlana Ugarcina Perovic (15:15:27) (in thread): > What’s here confusing?

Adeshile Oluwatosin (15:17:29) (in thread): > Exactly, what I saw as wellThat’swhy I curated the body sites as vagina > But I felt like there could be something more , maybe myeyes isn’tseeing

Svetlana Ugarcina Perovic (15:18:23) (in thread): > Ok, I am observing Fig1 right now… - File (PNG): Screenshot 2024-11-07 at 21.17.42.png

Svetlana Ugarcina Perovic (15:18:57) (in thread): > We are here interested ONLY what’s sent for sequencing, right?

Svetlana Ugarcina Perovic (15:20:32) (in thread): > In the Methods: “DNA was extractedfrom swabs(two vaginal sites) and feces”

Adeshile Oluwatosin (15:22:52) (in thread): > Yes, but in comparison between Amerindians and Mestizos > Icouldn’tplace ifit’svagina or feces

Svetlana Ugarcina Perovic (15:23:58) (in thread): > Fig2e?

Svetlana Ugarcina Perovic (15:24:47) (in thread): > That’s under sectionCervicovaginal and introital microbiota -> vaginal samples

Svetlana Ugarcina Perovic (15:24:58) (in thread): > Is now all clear here?

Adeshile Oluwatosin (15:26:08) (in thread): > Yes

Svetlana Ugarcina Perovic (15:27:50) (in thread): > In the caption of Fig 1: “and fecal samples for parasite detection were also collected for ancillary studies.DNA was extracted from swabs,” > I think they did not actually do any fecal samples sequencing or at least they did not provide in this paper. Maybe they did it in this study/project, but finally did not include it in the paper.

Adeshile Oluwatosin (15:28:57) (in thread): > Then it specifies that feceswasn’tused in all experiments

Adeshile Oluwatosin (15:29:42) (in thread): > Exactly, thank you > Needed clarification on that@Svetlana Ugarcina PerovicI appreciate

Svetlana Ugarcina Perovic (15:29:57) (in thread): > oh my, what a paper!

Adeshile Oluwatosin (15:31:00) (in thread): > :joy_cat::joy:I’veread these papers over 10 times, and dropped for peer review > But sometimes I get more confused:smiling_face_with_tear:

Svetlana Ugarcina Perovic (15:31:02) (in thread): > Probably this was quite complex project with several different samples and then they selected which samples to analyze and report for the paper.

Svetlana Ugarcina Perovic (15:31:46) (in thread): > By the way, the title isVAGINAL MICROBIOME :smile:

Adeshile Oluwatosin (15:31:50) (in thread): > Although,I won’tlie > > Table S6 comparison is a bit…:face_holding_back_tears::face_holding_back_tears:@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (15:32:54) (in thread): > Little details o@Svetlana Ugarcina PerovicThank you so much > I kept wondering why feceswasn’tused

Svetlana Ugarcina Perovic (15:39:40) (in thread): > You are not curating Table S6. > To curate is Table S7: and only taxa with**** p-values <0.05 has are shown with * ****skipping ns (not significant differences)

Svetlana Ugarcina Perovic (15:39:50) (in thread): > Ok?

Yoko C (15:39:58) (in thread): > This is what I can figure out: they tested children 0-5 years old.For the differential abundance experiments the children were grouped: group A (0–1), group B (> 1 to 2) and group C (> 2 to 5). > > There are pairwise comparisons for the alpha indexes of each year band. > For example: 0 to 1vs>1 to 2, or 0 to 1vs>2 to 3. > The comparisons for the experiments are: A vs B, A vs C, B vs C. > For A vs B, 0 to 1vs>1 to 2, Shannon’s H increase can be seen on Figure 3 a and you can also see the significance in table S2. Although there is no graph for Faith, the text mentions: “An increase in richness and evenness was observed during the first 3 years of life”, so I interpret this as Faith’s to have increased. Table S2 also shows it is significant. > > The issue is A vs C and B vs C, because the ages in C have been grouped, and there is no measure for the alpha index of children 2-5 year old. So there is no exact comparison for these. The only way I think you could compare is if you assumed that because there is no significant change for 2 to 3 vs 3 to 4, or 3 to 4 vs 4-5, or 2 to 3 vs 4 to5, you can assume that the comparison of A (0 to 1) vs 2 to 3 (or 3 to 4, 4 to 5) is equivalent to A vs C. But I don’t know if that would be correct.

Adeshile Oluwatosin (15:40:33) (in thread): > Sorry S7, the one with p values

Yoko C (15:41:27) (in thread): > I would say that for A vs C, and C vs B, you would not fill in Shannon or Faith.

Svetlana Ugarcina Perovic (15:43:18) (in thread): > No assuming:slightly_smiling_face:@Yoko Cjust reporting what you read!

Svetlana Ugarcina Perovic (15:43:47) (in thread): > :drum_with_drumsticks:@Yoko Cthe saver! Thanks!

Svetlana Ugarcina Perovic (15:44:10) (in thread): > @Adeshile Oluwatosinare we also clear here?

Adeshile Oluwatosin (15:48:31) (in thread): > Tbh Chloe mentioned how to curate this, but it was kind of rushed > So I didn’t really get the comparisons > > For instance: 1. dialistermicraerophilus2. Brevibacterium linens

Adeshile Oluwatosin (15:50:07) (in thread): > Thank you for taking your time to explain@Yoko CI totally get it@Svetlana Ugarcina Perovic

Kate Rasheed (15:51:15) (in thread): > Thank you@Yoko Cfor this broad explanation.

Svetlana Ugarcina Perovic (15:55:39) (in thread): > ok, so I was right that Chloe covered some of your questionshttps://community-bioc.slack.com/archives/C04RATV9VCY/p1730387839493909after 54 mins there it is - Attachment: Attachment > Recording of the weekly office hours/team meeting. Thank you all who attended.

Svetlana Ugarcina Perovic (15:59:52) (in thread): > Dialister micraerophilus: significant difference in Amerindian urbanization groups (increase in high) > Brevibacterium linens: significant difference in Ethnicity (increase in Amerindian compared to Mestizos group)

Adeshile Oluwatosin (16:00:09) (in thread): > Yes, just on this particular study > Hahaha > > Thank you<@UBNSEMS3S>I’ve watched it couple of times though > Would go over it again

Adeshile Oluwatosin (16:01:53) (in thread): > Idon’tlike guessing,that’swhy I keep emphasizing > > You’ve been more than helpful today > I appreciate:smiling_face_with_tear:Finally! Let me focus on curation now > If I have any further questions, hopefully I get a response

Svetlana Ugarcina Perovic (16:03:36) (in thread): > Dialister micraerophilus: significant difference in Amerindian urbanization groups (increase in high Amerindian urbanization group) > Brevibacterium linens: significant difference in Ethnicity (increase in Amerindian compared to Mestizos group)

Adeshile Oluwatosin (16:17:26) (in thread): > Thank you once again@Svetlana Ugarcina Perovic

Inimfon Ebong (17:04:15): > Good evening everyone > please what’s the difference between differential abundance and relative abundance and in terms of choosing the analysis used which of them should be taken into consideration

Svetlana Ugarcina Perovic (17:05:33) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549 - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Svetlana Ugarcina Perovic (17:09:39) (in thread): > We are recording the signatures of differential abundance based on curation of differential abundance analysis.

Svetlana Ugarcina Perovic (17:12:45) (in thread): > Relative abundanceis how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1).Differential abundanceis when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations).The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

Inimfon Ebong (17:21:14) (in thread): > OK, thank you@Svetlana Ugarcina Perovicthis makes a lot more sense to me

Aleru Divine (17:29:37) (in thread): > Thanks for the explanation@Svetlana Ugarcina Perovic:blush:

Samuel Nnanna (17:34:11) (in thread): > Hello@Svetlana Ugarcina Perovic, apologies for sending this so late. I didn’t see the message. > > This is the link to the paper@Rahila-meand I are working on “https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01925-7”. > > We have some concerns and we’d appreciate your input. > There are more than one study designs in the paper, how do we curate that? > > There is also some missing data for the figure s2 > > For the differential abundance, they referenced figure s7 (an excel sheet) but I don’t understand what’s being compared in the data provided. - Attachment (BioMed Central): Alterations of the gut microbiome in HIV infection highlight human anelloviruses as potential predictors of immune recovery - Microbiome

Adeshile Oluwatosin (18:00:47) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Mildred Anashie (18:32:10) (in thread): > Thank you for the detailed explanation@Svetlana Ugarcina Perovic

Inimfon Ebong (23:57:05): > Eighty-two HIV-infected Ugandan subjects were recruited as part > of the Uganda AIDS Rural Treatment Outcomes (UARTO) study at > the Immune Suppression Syndrome Clinic at Mbarara Regional > Referral Hospital, comprising 40 HIV-infected subjects on ART > treatment (HIV-treated) and 42 HIV-infected, ART-naive (HIV-untreated) > subjects. An additional 40 HIV-negative subjects were recruited > from the HIV testing clinic after a negative HIV test result > (Figure 1A and Table 1). The median time on ART for treated subjects > was 6.7 years (interquartile range [IQR] 6.1–7.1) and 87.5% > (n = 35) of ART-treated participants had undetectable viral loads > (<20 copies/mL). Twenty-five participants (20.5%) had CD4 > T cell counts < 200 (CD4 < 200) at the time of stool collection > > > HIV infects > and depletes CD4 T cells, leading to the development of > acquired immunodeficiency syndrome (AIDS), defined by the > presence of less than 200 CD4 T cells/mL circulating in the blood > (denoted herein as CD4 > 200 or < 200)

Inimfon Ebong (23:59:26): > Good morning everyone > Given these 2 points I dropped above is it OK for me to say that the sample size for cd4> 200 is 57 > > That’s 82 positive patients - 25 patients with cd4<200

2024-11-08

Inimfon Ebong (00:41:52): > https://bugsigdb.org/Study_1210please@Svetlana Ugarcina Peroviccan you delete experiment 2 it’s a mistake - Attachment (BugSigDB): Altered Virome and Bacterial Microbiome in Human Immunodeficiency Virus-Associated Acquired Immunodeficiency Syndrome - BugSigDB > Human immunodeficiency virus (HIV) infection is associated with increased intestinal translocation of microbial products and enteropathy as well as alterations in gut bacterial communities.

Mildred Anashie (00:58:36) (in thread): > Hi@Inimfon EbongFrom what you shared, I see 25 to be the sample size. I’m not sure what exactly your contrast is but it says CD4 <200 had 25 participants. > > “Twenty-five participants (20.5%) had CD4 > T cell counts < 200 (CD4 < 200) at the time of stool collection”

Aleru Divine (03:08:21) (in thread): > Good morning@Inimfon EbongI like to believe so, since they mentioned 25 patientsout of the 82had cd4<200, it would mean the rest (57) had cd4> 200. > > Can you share the paper so we can have a better lookplease? Thanks!

Mildred Anashie (03:10:54) (in thread): > Thank you for your reply@Aleru DivineIt made me to read the question again

Mildred Anashie (03:11:13) (in thread): > Please share your paper@Inimfon Ebong

Aleru Divine (03:13:37) (in thread): > That’sokay@Mildred AnashieA look at the paper would help clarify, although all signs point to the sample size for the cd4 > 200 being 57.

Svetlana Ugarcina Perovic (05:14:47) (in thread): > deleted.

Chinwendu Joy Enyidiegwu (05:40:52) (in thread): > thank you for the presentation@Svetlana Ugarcina PerovicI enjoy online conferencing; it’s always a good experience, aside from the occasional distractions like birds chirping or neighborhood sounds.

Svetlana Ugarcina Perovic (06:50:37) (in thread): > @Samuel Nnanna > * more than one study designs -> report all. How? We’ve had these two-in-one studies before. It should just be one study with multiple experiments. Make a note and be sure to record the one that is the source of your recorded signatures. See for examplehttps://bugsigdb.org/Study_997 > * some missing data for the figure s2 -> this figure shows correlation between different factors not bacterial abundance differential analysis results between groups. Also you can spot in the Methods: “No collinearity was observed between the selected variables (pairwise Spearman correlation coefficients < 0.7) (Supplementary Figure S2).” > * For the differential abundance, they referenced figure s7 (an excel sheet) -> I do not see comparison between groups. Also in the text I do not see significant differences reported. > What they reported is significant differences in viruses, but we do not record them yet. > > Conclusion: this study is not bugsigdb curatable.

Adeshile Oluwatosin (06:52:34) (in thread): > @Svetlana Ugarcina PerovicGood afternoon, I have a question > I would like to know what cases should experiments be curated even when there are no signatures.

Samuel Nnanna (06:52:51) (in thread): > @Svetlana Ugarcina Perovicthank you so much for the clarification.

Svetlana Ugarcina Perovic (06:55:46) (in thread): > @Adeshile Oluwatosinwe do not curate experiments with no signatures.

Adeshile Oluwatosin (06:56:41) (in thread): > Noted and clarified@Svetlana Ugarcina PerovicAs someone made a comment on this last month > And my research says otherwise > > Thank you

Rahila-me (08:06:52) (in thread): > @Svetlana Ugarcina Perovicthanks for the clarification on the paper assigned to@Samuel Nnannaand i

Inimfon Ebong (11:17:17) (in thread): > Thank you

Adeshile Oluwatosin (13:26:59) (in thread): > @Svetlana Ugarcina PerovicI figured we omitted this figure I initially statedI would appreciate a response - File (JPEG): IMG_2163

2024-11-09

Peace Daniel (06:42:02): > Hi everyone, > > Can someone help confirm the statistical test used for differential abundance in Fig 4C, 4D and Suppl 10E > Study herehere - Attachment (BioMed Central): Distinct intestinal microbial signatures linked to accelerated systemic and intestinal biological aging - Microbiome > Background People living with HIV (PLWH), even when viral replication is controlled through antiretroviral therapy (ART), experience persistent inflammation. This inflammation is partly attributed to intestinal microbial dysbiosis and translocation, which may lead to non-AIDS-related aging-associated comorbidities. The extent to which living with HIV — influenced by the infection itself, ART usage, sexual orientation, or other associated factors — affects the biological age of the intestines is unclear. Furthermore, the role of microbial dysbiosis and translocation in the biological aging of PLWH remains to be elucidated. To investigate these uncertainties, we used a systems biology approach, analyzing colon and ileal biopsies, blood samples, and stool specimens from PLWH on ART and people living without HIV (PLWoH) as controls. Results PLWH exhibit accelerated biological aging in the colon, ileum, and blood, as measured by various epigenetic aging clocks, compared to PLWoH. Investigating the relationship between microbial translocation and biological aging, PLWH had decreased levels of tight junction proteins in the intestines, along with increased microbial translocation. This intestinal permeability correlated with faster biological aging and increased inflammation. When investigating the relationship between microbial dysbiosis and biological aging, the intestines of PLWH had higher abundance of specific pro-inflammatory bacteria, such as Catenibacterium and Prevotella. These bacteria correlated with accelerated biological aging. Conversely, the intestines of PLWH had lower abundance of bacteria known for producing the anti-inflammatory short-chain fatty acids, such as Subdoligranulum and Erysipelotrichaceae, and these bacteria were associated with slower biological aging. Correlation networks revealed significant links between specific microbial genera in the colon and ileum (but not in feces), increased aging, a rise in pro-inflammatory microbe-related metabolites (e.g., those in the tryptophan metabolism pathway), and a decrease in anti-inflammatory metabolites like hippuric acid. Conclusions We identified specific microbial compositions and microbiota-related metabolic pathways that are intertwined with intestinal and systemic biological aging. This microbial signature of biological aging is likely reflecting various factors including the HIV infection itself, ART usage, sexual orientation, and other aspects associated with living with HIV. A deeper understanding of the mechanisms underlying these connections could offer potential strategies to mitigate accelerated aging and its associated health complications. Video Abstract

Kate Rasheed (06:46:23) (in thread): > Hi@Peace DanielI’ll look through.

Kate Rasheed (06:48:40) (in thread): > @Peace Danielit’s linear model for 4C and D. > > Look at this: “Linear models estimated abundance changes, and adjustments for multiple tests used the Benjamini–Hochberg method. Significance markers: FDR < 0.05 (purple), FDR < 0.1 (cyan), and P < 0.05 (green)”. > > I can’t open supplementary figure 10E. You can share picture if possible.

Aleru Divine (06:53:40) (in thread): > Good morning@Peace DanielI’velooked through and according to the description provided by@Kate Rasheedabove for figure 4C and 4D it is Linear models (linear regressionavailable on BugSigDB) because linear model is often synonymous with a linear regression model.I believeit’salso what was used for supplementary file 10E since the figures are alike.

Peace Daniel (06:53:43) (in thread): > Thanks thanks,it’s thesame. I needed a confirmation@Kate Rasheed

2024-11-10

Inimfon Ebong (12:38:42): > Good day everyone please I need a second opinion on this table. Can Tab 3 be curated? if so how. This is the study there is no statistical analysis for sCD14 other than one line on log-log transformation mentioned in the supplementary material@Svetlana Ugarcina Perovic - File (Excel Spreadsheet): mmc2.xlsx - File (PDF): mmc3.pdf

Aleru Divine (13:10:19) (in thread): > Good evening@Inimfon EbongI’m not very sure if that should be curated, since we curate only differential abundance results. Tab 3 is showing correlation between bacteria and sCD14 levels. It’s not showing differential abundance between groups unlike Tab 1 and Tab 2. > > Also to confirm it is not differential abundance,hereDifferential abundance would refer to comparing bacterial abundance across different groups or conditions (like infected vs. uninfected) to identify taxa that are more or less in one group over the other group.Figure 5, Tab 1 and Tab 2 show results for Differentially abundant bacterial taxaBut if it is confirmed to be curatable, you would have to look at the direction of the correlation (r value) > > Positive r-value means increased and negative means decreased correlation/abundance. - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Aleru Divine (13:21:05) (in thread): > They performed correlation analysis to identify bacterial OTUs associated with circulating sCD14 levels. > > See excerpt “Spearman’s rank correlationswere used to examine bivariate associations between study variables.” > > The statistical test here is Spearman’s correlation.AlthoughI’mnot still very sure if it is to be curated:pray:I’msureyou’llget a confirmation from one of the mentors tomorrow

Kate Rasheed (14:43:04) (in thread): > Thanks for your input@Aleru Divine. Let’s wait for confirmations.

Mildred Anashie (17:19:33) (in thread): > Hi@Inimfon EbongI’malso not sure if it should be curated but I think itshouldn’t, the text talking about that figuredoesn’tpoint to differential abundance in my opinion

Adeshile Oluwatosin (23:45:49) (in thread): > Hello@Inimfon EbongI went through the paper > > Tab 3 should not be curated. > It states Bacterial OTUs associated with sCD14. There’s no differential abundance here in my opinionTable S5, Related to Figure 5: Differentially abundant bacterial taxa in subjects with low CD4 T cell counts and bacterial OTUs significantly associated with sCD14. > > Tab 1: Differentially abundant bacterial taxa in subjects with CD4 <200 compared to HIV-negative subjects. > > Tab 2: Differentially abundant bacterial taxa in subjects with CD4 <200 compared to subjects with CD4 > 200. > > Also from here, “Differentially Abundant Bacterial Taxa in Subjects with Low CD4 T Cell Counts > > Given the decrease in bacterial phylogenetic diversity in HIV-positive subjects with CD4 < 200, we next identified specific bacterial operational taxonomic units (OTUs) differentially abundant by CD4 T cell group (Table S5, tabs 1 and 2) using variance stabilization techniques based on mixture models of microbiome data (McMurdie and Holmes, 2014). These discriminant OTUs were then plotted by bacterial family association (Figure 5).

Adeshile Oluwatosin (23:48:08) (in thread): > You can see that in Tables S5, tabs 1 and 2 and Figure 5 differential abundance were vividly mentioned.

2024-11-11

Tino (03:41:49) (in thread): > @Inimfon EbongI think Tab 3 should not be curated because it is not making any reference to the differential abundance, it only mentions the bacterial OTUs associated with sCD14 levels.

Inimfon Ebong (04:03:26) (in thread): > Thank you everyone for your input I think@Kate Rasheedand I will leave it and wait for the feedback after review

Svetlana Ugarcina Perovic (05:06:18): > See you tomorrow at MVIF - Attachment: Attachment > INVITATION: We would be happy if you can join us next week for another amazing MVIF! > https://microbiome-vif.org/en-US > > ALSO, a proud mentor here :wave: > > @Victoria (Burah) Poromon, a <#C04RATV9VCY|> curator, will open #MVIF 33 next week and moderate discussion with the microtalks speakers. > > Victoria, can’t wait to listen to you! :bouquet:

Svetlana Ugarcina Perovic (05:06:40): > Happy Monday and wishing you a good week!

Mildred Anashie (05:07:37) (in thread): > Happy Monday to you@Svetlana Ugarcina Perovic:blush:Wishing you the best of the week

Adeshile Oluwatosin (05:12:04) (in thread): > Happy Monday@Svetlana Ugarcina Perovic:relaxed::hugging_face:

Aleru Divine (05:12:24) (in thread): > Happy Monday to you too@Svetlana Ugarcina PerovicHave a great week:sparkles:

Aleru Divine (05:13:06) (in thread): > Woohoo:grinning_face_with_star_eyes:Looking forward to it!

Adeshile Oluwatosin (05:14:12) (in thread): > Noted:relieved:

Kate Rasheed (05:20:20) (in thread): > Thank you@Svetlana Ugarcina Perovic. Happy Monday to you too and wishing you a good week.

Ebuka Chinwuba (05:20:48) (in thread): > Thanks! Excited for what the week has in store@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:32:29): > @Adeshile Oluwatosinquestion: How can Figure S2 be curated as some figures (colours) are not so visible? > > paper:https://www.nature.com/articles/s41598-020-69111-xcuration:https://bugsigdb.org/Study_1194Answer: colors/bars are ordered in the same way in the graph and in the legend, that’s how you will define for which group is the result. As of invisible bars, you can check the numbers of their relative abundance in the Table S6. Do not forget to put a note about this curation strategy next to these signatures.

Adeshile Oluwatosin (05:33:42) (in thread): > Thank you once again@Svetlana Ugarcina PerovicI truly appreciate > I will do this

Inimfon Ebong (05:34:34) (in thread): > Happy Monday to you too@Svetlana Ugarcina Perovic

Joy (06:02:37) (in thread): > This is wonderful. I can’t wait. Thanks@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (06:05:03): > Hello@Svetlana Ugarcina PerovicCan you kindly help delete these signatures in this study.https://bugsigdb.org/Study_1209Experiment 2: signature 2-8. - Attachment (BugSigDB): Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets - BugSigDB > BACKGROUND: The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear.

Joy (06:07:02) (in thread): > Thank you@Svetlana Ugarcina Perovic.Happy Monday to you. Wishing you a lovely week ahead!:hugging_face:

Svetlana Ugarcina Perovic (07:33:10) (in thread): > deleted.

Adeshile Oluwatosin (07:47:10) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (09:15:42): > Hello@Svetlana Ugarcina PerovicCan you kindly help delete signature 2, Exp 7 in this study. > Thank youhttps://bugsigdb.org/Study_1140 - Attachment (BugSigDB): Dysbiosis of Gut Microbiota and Short-Chain Fatty Acids in Acute Ischemic Stroke and the Subsequent Risk for Poor Functional Outcomes - BugSigDB > BACKGROUND: The intestinal microbiota and its metabolites have been reported to play an important role in stroke.Gut microbiota-originating short-chain fatty acids (SCFAs) modulate brain functions directly or indirectly through immune, endocrine, vagal, and other humoral pathways.

Rahila-me (10:11:52) (in thread): > Happy Monday to you too@Svetlana Ugarcina Perovic

Yoko C (10:23:39): > Hello everyone, I need some help curating this figurehttps://www.nature.com/articles/s41467-020-17541-6/figures/5. This figure was made using sparse discriminant analysis which is a type of LDA. This isn’t on the statistical tests section, so I’m not sure if I should choose the most similar, which is LEfSe or leave it blank. > I also doubt if for the signatures, I should use the ASV labels as used on the graph or the taxa name in the source material? For example: > * On the graph you have ASV 1403, Christensenellaceae > * on the source material it is ASV_1403_Christensenellaceae_R-7_group, > * The genus on the source material is Christensenellaceae_R-7_group. > I think ASV numbers aren’t part of the NCBI naming convention, but if I don’t include it I would reduce the number of taxa on the signature, because some just differ on the ASV number. For example: ASV_1403_Christensenellaceae_R-7_group and ASV_1404_Christensenellaceae_R-7_group. > Hope this isn’t too confusing, looking forward to your feedback.

Kate Rasheed (10:25:59) (in thread): > :smile:Welldone@Yoko C. I’ll look through.

Kate Rasheed (10:33:02) (in thread): > I believe you should use the taxa names. The figure looks like LEfSe cladogram so I believe it’s statistical test is LEfSe. > > I also tried checking the numbers on NCBI but it’s giving a different name. So for ASVs with taxa name, please use the name while the others can be recorded as the ASV numbers. > > PS. I don’t think we are to leave out signatures if they are not virus.

Yoko C (10:35:43) (in thread): > @Kate Rasheed, do you mean use ASV 1403 Christensenellaceae R-7_group or use Christensenellaceae R-7 group?

Yoko C (10:36:44) (in thread): > The one with the number right? And this isn’t a LEfSe cladogram, so I think it’s best to just leave it blank.

Yoko C (10:37:36) (in thread): > I think I will use Christensenellaceae R-7 group ASV 1403

Kate Rasheed (10:40:20) (in thread): > @Yoko CI used ASV 1403 and 1403

Aleru Divine (10:49:15) (in thread): > Hi@Yoko CI think for the statistical test it’s best to leave it, they used a tree-based Linear Discriminant Analysis, not LEfSe. > I think this can be added by the mentors or something. It also mentions LDA cut offs so for this statistical test, we’ll be indicating LDA. > > For the signatures, mysuggestionwill be to curate the families and indicate the number of ASVs in the discussions page.

Yoko C (10:52:05) (in thread): > Thank you both!

Kate Rasheed (11:12:16) (in thread): > @Yoko C@Aleru DivineLEfSe stands for:Linear discriminant Analysis Effect SizeThis statistical test should be LEfSe because the phylogenetic tree uses LDA effect size. > > My thoughts though:smile:

Yoko C (11:15:45) (in thread): > Hello again! I forgot to ask, in thissame study, they sampled people with two different designs. One was in 2009, where they sampled people once. The other was in 2012-2013, where they sampled people from another set of villages at several points in time. For the graph I am curating, they mixed all these together. They don’t mention if they kept all the samples from different points in time per person, or if they just kept one, but since they mixed everything, I think I should curate it as cross-sectional? not sure

Kate Rasheed (11:21:15) (in thread): > @Yoko CFor the study design. I would say prospective cohort study though since they looked at different people at different times.

Yoko C (11:23:55) (in thread): > @Kate RasheedI also doubted on using Lefse because it is close, but its not the same. From what I understand it is a type of LDA that focuses on using the effect size to determine how to divide the taxa or characteristic that is being looked at. But this tree uses a different type of LDA, so I think it’s best to leave it blank.

Yoko C (11:24:55) (in thread): > Thanks again Kate, will check out prospective.

Aleru Divine (11:33:53) (in thread): > I agree with@Kate Rasheedon using prospective cohort as the study design. > > I still stand on it not being LEfSe@Kate RasheedThe key point of LEfSe is the LDA score (effect size), which quantifies the strength of the relationship between a feature and the class separation. > > Now for tree based analysis, the concept of effect size is not used in the same manner. The trees highlight the importance of features, there isn’t a direct effect size measure as in LEfSe. > > Also if you notice in this study, there’s no mention of effect size. Hence why I don’t think it’s LEfSe.

Kate Rasheed (11:42:32) (in thread): > @Aleru DivineI saw something like effect size in the study unless I didn’t see it well that’s why I pointed at LEfSe.

Adeshile Oluwatosin (11:42:51) (in thread): > Hello@Yoko Cwell done on your curation. > > I agree with what has been said so far > * The statistical test should be left blank > * Curate the taxa with the names and drop a note on the different ASV values. > * Prospective cohort as study design. > Well done once again

Aleru Divine (11:44:41) (in thread): > I didn’tsee anything pointing to that in the study@Kate Rasheedcan you check again:pleading_face:

Aleru Divine (11:48:11): > Good evening@Svetlana Ugarcina PerovicI’d like to delete signature 2 in experiment 1 of this studyhttps://bugsigdb.org/Study_1212Thank you so much! - Attachment (BugSigDB): Oral, Vaginal, and Stool Microbial Signatures in Patients With Endometriosis as Potential Diagnostic Non-Invasive Biomarkers: A Prospective Cohort Study - BugSigDB > OBJECTIVE: To identify a microbial signature for endometriosis for use as a diagnostic non-invasive biomarker.DESIGN: Prospective cohort pilot study.SETTING: Nepean Hospital and UNSW Microbiome Research Centre, Australia.

Kate Rasheed (11:52:49) (in thread): > Yes I will. Thanks@Aleru Divine

Svetlana Ugarcina Perovic (13:42:42) (in thread): > deleted.

Svetlana Ugarcina Perovic (13:43:47) (in thread): > deleted.

Aleru Divine (13:51:16) (in thread): > Thank you so much

Mildred Anashie (13:55:36) (in thread): > Thank you:pray:

2024-11-12

Kate Rasheed (05:16:53): > Good morning people. Trust our day is going great:hugging_face:. > > I’ll appreciate a peer review on thisstudy. There was mention of increased bacterial diversity but the bacterial diversity wasn’t specified(Shannon, Chao1, etc). Is it okay to leave it blank? > > Thank you so much. - Attachment (BugSigDB): Differences in the microbial profiles of early stage endometrial cancers between Black and White women - BugSigDB > OBJECTIVE: Black women suffer a higher mortality from endometrial cancer (EC) than White women.Potential biological causes for this disparity include a higher prevalence of obesity and more lethal histologic/molecular subtypes.

Mildred Anashie (05:26:25) (in thread): > Hi@Kate RasheedWell done on your curation > > I’ll give this a look

Mildred Anashie (05:27:04) (in thread): > When you say ‘bacterial diversity’ are you referring to Alpha diversity?

Kate Rasheed (05:29:24) (in thread): > Thank you@Mildred Anashie. The bacterial diversity wasn’t referred to as alpha diversity.

Mildred Anashie (05:33:05) (in thread): > Okay,I’llgo through the study to get a better understanding

Adeshile Oluwatosin (06:37:34) (in thread): > Hello@Kate RasheedI’ll look through it

Adeshile Oluwatosin (06:40:36) (in thread): > Do you mean no result was found > But it was mentioned in the text@Kate Rasheed

Kate Rasheed (06:42:05) (in thread): > Thank you@Adeshile Oluwatosin. I meant there was no specific mention of Shannon, Chao1 or any of the alpha diversity measures

Adeshile Oluwatosin (06:43:17) (in thread): > Can you send the exact text so I can be sure

Adeshile Oluwatosin (06:43:58) (in thread): > We characterized the EC microbiota (N=95) and benign endometrium microbiota (N=16) . > > Experiment 1, sample size should be 95 not 96for EC microbiota

Kate Rasheed (06:45:56) (in thread): > @Adeshile OluwatosinI saw it but the differential abundance is showing 96. Check the figure 1.

Adeshile Oluwatosin (06:46:40) (in thread): > If they didn’t specify it, you can’t know what to record > So definitely blank > > But I’d like to see the exact text > Still going through the paper.

Adeshile Oluwatosin (06:47:05) (in thread): > Great work@Kate Rasheedthat text is probably an error

Kate Rasheed (06:47:29) (in thread): > @Adeshile OluwatosinIt’s actually 96. It was stated that there was 1 from another race. Let me look for the excerpt. > > I just saw the one from another race is for the Benign. I will go with 95. In the sequencing details, it was stated that 95 ECs. > > Thank you once again.

Aleru Divine (06:53:43) (in thread): > Well done on your curation@Kate RasheedI’ll take a look too.

Aleru Divine (07:18:45) (in thread): > @Kate Rasheedin figure 5a, the microbial diversity is estimated with Shannon.I think that answers the diversity question.

Kate Rasheed (07:22:25) (in thread): > Thank you so much for pointing it out@Aleru Divine.

Aleru Divine (07:26:26) (in thread): > The study checks out so far, well done@Kate Rasheed

Svetlana Ugarcina Perovic (07:26:57): > See you in an hour at MVIF - Attachment (Cassyni): MVIF 33 - with Keynote talk by Prof. Seth Bordenstein - seminars · Cassyni > Microbiome Virtual International Forum (MVIF) is a recurring bite-sized alternative to multi-day microbiome conferences: Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference. > > Forum n. 33 is an Atlantic-first event, with live talks starting 12th November 2024, 8:30 am New York time (see what time it is where you are here and add to your calendar here). Professor Seth Bordenstein will be the keynote speaker for this event. > > For Pacific time zones, recorded talks with live hosting and discussion will start on 14th November at 9:30 am Tokyo time (see what time and date it is where you are here and add to your calendar here). > > MVIF is a non-profit association registered in Italy > If you’d like to support MVIF, you can donate to our crowdfunding campaign . > > Thanks to our co-organizing non-commercial partners the Seerave Foundation and CUNY Graduate School of Public Health & Health Policy and our Gold Sponsor Roche for their support. > > Matanu!

Mildred Anashie (07:29:07) (in thread): > Hi@Kate RasheedI believe you should go with the sample size used for the analysis and I thinkit’sthe one on the Figure

Aleru Divine (07:29:45) (in thread): > Thanks for the reminder@Svetlana Ugarcina PerovicLooking forward to it!:blush:

Mildred Anashie (07:29:46) (in thread): > Also I agree with Divine, 5a is pointing towards alpha diversity

Adeshile Oluwatosin (07:29:48) (in thread): > Thanks for the reminder

Kate Rasheed (07:30:24) (in thread): > @Mildred AnashieYou mean 96?

Kate Rasheed (07:30:52) (in thread): > Thanks for the reminder:hugging_face:

Mildred Anashie (07:32:39) (in thread): > Yes@Kate RasheedIt could be the final sample size and it’s best to record the final sample size > > The text could be wrong but I doubt the figure is

Mildred Anashie (07:34:42) (in thread): > Thank you@Svetlana Ugarcina PerovicSee you:blush:

Aleru Divine (07:34:58) (in thread): > One of them is a typo:sweat_smile:and a typo twice is highly unlikely.Unlike the one time “96”don’tyou think? > > 95 is from the results@Mildred Anashie

Kate Rasheed (07:39:05) (in thread): > Hmmmm:thinking_face:. I guess 96 is a typo. 95 appears to be consistent.

Aleru Divine (07:39:36) (in thread): > Yes I think so too.

Mildred Anashie (07:40:40) (in thread): > 96 could be an error then@Aleru Divine@Kate Rasheed

Aleru Divine (07:41:54) (in thread): > It should be:grimacing:

Kate Rasheed (07:42:30) (in thread): > Thanks my fresh eyes@Adeshile Oluwatosin@Mildred Anashie@Aleru Divine:heart:

Adeshile Oluwatosin (07:42:44) (in thread): > Welcome:joy_cat:

Joy (07:43:30) (in thread): > Thanks@Svetlana Ugarcina PerovicSee you there too

Kate Rasheed (07:53:33): > I would also like some clarity on this article:https://www.nature.com/articles/s41598-022-21779-z#MOESM1I’m thinking of lifestyle measurement as the condition but I’m not certain. > > Also, aside experiment 1 and 2 which would involve negative controls and all countries, for the remaining experiments, it’s stated in the supplementary table that it’s a one-to-all analysis but I’m not sure how to go about the alpha diversity, because the text result is giving a pairwise comparison. - Attachment (Nature): Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes > Scientific Reports - Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes

Joy (07:55:49): > Hi@Svetlana Ugarcina PerovicKindly delete signatures 3 & 4. Thankshttps://bugsigdb.org/Study_1193 - Attachment (BugSigDB): Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet - BugSigDB > High-fat (HF) diet-induced neuroinflammation and cognitive decline in humans and animals have been associated with microbiota dysbiosis via the gut-brain axis.Our previous studies revealed that excretory-secretory products (ESPs) derived from the larval Echinococcus granulosus (E.

Aleru Divine (07:56:55) (in thread): > Hi@Kate Rasheedregarding the alpha diversity concern,@Svetlana Ugarcina Perovichas answered it. The alpha diversity should not be curated.Check out this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1730990417235779?thread_ts=1730988400.486679&channel=C04RATV9VCY&message_ts=1730990417.235779 - Attachment: Attachment > @Adeshile Oluwatosin > 1. > • If alpha diversities issues as the contrasts are different from what we can see in the Signature results. then we do not curate alpha diversities because they are not talking about the same experiments.. > • Name body sites and make notes.

Svetlana Ugarcina Perovic (07:58:08) (in thread): > As for condition, check out this one:https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0010724 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Svetlana Ugarcina Perovic (08:00:32) (in thread): > deleted.

Kate Rasheed (08:01:15) (in thread): > Thank you so much@Aleru Divine@Svetlana Ugarcina Perovic.

Svetlana Ugarcina Perovic (08:01:22) (in thread): > OR check this option as well:https://bugsigdb.org/Health_study_participation - Attachment (BugSigDB): Health study participation > Aliases…

Svetlana Ugarcina Perovic (08:03:40) (in thread): > OR population:https://bugsigdb.org/Population@Kate Rasheed - Attachment (BugSigDB): Population > …

Aleru Divine (08:04:43) (in thread): > Wow! Thank you so much@Svetlana Ugarcina Perovic

Kate Rasheed (08:05:29) (in thread): > Thank you@Svetlana Ugarcina Perovic. I was looking at population as well but discovered the study talks about the influence of the participants lifestyle and dietary habits on the microbiota. Hence, I thought lifestyle measurement would be a good choice.

Aleru Divine (08:05:49): > Good afternoon everyone, I hope you are having a great day.@Toluwalase Abigailand I would appreciate a peer review of this study. We’re particularly concerned about the confounders controlled for in each experiment. > If you have time, we’d be grateful for any feedback. > Thank you so much - Attachment (BugSigDB): Alteration of the gut fecal microbiome in children living with HIV on antiretroviral therapy in Yaounde, Cameroon - BugSigDB > Multiple factors, such as immune disruption, prophylactic co-trimoxazole, and antiretroviral therapy, may influence the structure and function of the gut microbiome of children infected with HIV from birth.

Kate Rasheed (08:06:31) (in thread): > I’ll take a look. Welldone@Aleru Divine@Toluwalase Abigail

Mildred Anashie (08:07:07) (in thread): > Well done@Toluwalase Abigail@Aleru DivineI’llalso take a look

Aleru Divine (08:07:24) (in thread): > Thank you so much@Kate Rasheed@Mildred Anashie:hugging_face:

Kate Rasheed (08:12:30) (in thread): > @Aleru Divine. I think experiment 1 is controlling for HIV status alone. > > See this: “To resolve which bacterial strains were driving these changes, we identified ASVs that were differentially abundant by HIV status.” > > Experiment 2 would be controlling for ART alone. > See this: “We observed differential ASV distribution according to ART regimen with ASVs classified in the Blautia, Prevotella, Oscillospira and Faecalibacterium genera more abundant in the NNRTI cohort compared to PI/r cohort (Fig. 6A).”

Joy (08:12:47) (in thread): > @Svetlana Ugarcina PerovicI truly appreciate.

Adeshile Oluwatosin (08:17:22) (in thread): > I’lltake a look@Aleru Divine

Aleru Divine (08:19:18) (in thread): > See this excerpt from the discussion for experiment 1 > > “When controlling forHIV treatment status, we identified differences in microbial composition among Cameroonian ethnic groups. It is unknown how these compositional differences are driven by genetic background, diet, and environmental exposures.” > > For experiment 2, > > “Using linear models, we were unable to detect a relationship between alpha-diversity and ART duration. Increasing model complexity by controlling for age, CD4 count, and viral burden did not improve predictive power. (Figure S2).”

Aleru Divine (08:19:45) (in thread): > Thank you so much@Adeshile Oluwatosin

Mildred Anashie (08:20:24) (in thread): > I was going to ask if Experiment 2wasn’tdone using linear models@Aleru Divine

Aleru Divine (08:22:36) (in thread): > For differential abundance, thestatistical test was also Wilcoxon@Mildred Anashie

Aleru Divine (08:23:34) (in thread): > So what do you think about the confounders now@Kate RasheedPlease check too@Mildred Anashie@Adeshile Oluwatosin

Kate Rasheed (08:24:19) (in thread): > @Aleru DivineI didn’t see any differential abundance result to show for the confounders in Fig. S2. Maybe it’s the same as Fig. 6A.

Mildred Anashie (08:26:57) (in thread): > I’m not sure what’s going on with the ethnic groups but I see this and I’m thinking it applies to the Experiment one because it was repeated in a few places that HIV status was controlled for. ’When controlling for HIV status, ADONIS testing of weighted and unweighted UniFrac distances revealed compositional differences by ethnicity (p < 0.05), excluding Bamenda, Eton, and Haoussa ethnic groups as there were no HIV negative representatives belonging to these ethnic groups, indicating that there are population-level differences in microbiome structure.’@Aleru Divine

Aleru Divine (08:33:13) (in thread): > @Mildred Anashieyes HIV status was controlled forI don’tquite understand what you mean but this excerpt is referring to beta diversity.

Mildred Anashie (08:34:07) (in thread): > For Experiment 2 I don’t think there were any confounders controlled for@Aleru Divineand the statistical test should remain as Wilcoxon in my opinion. Because the linear model results aren’t curatable and doesn’t seem to show significance

Svetlana Ugarcina Perovic (08:36:23): > Our@Victoria (Burah) Poromonjust opened the MVIF 33!! - File (PNG): Screenshot 2024-11-12 at 14.31.35.png

Mildred Anashie (08:36:46) (in thread): > Yea@Aleru DivineI used that to indicate that they mentioned controlling for HIV status in more than one place based on the ethnic groups. I believe you shared an excerpt on that already

Kate Rasheed (08:37:37) (in thread): > :dancer:Go Victoria:smile:

Adeshile Oluwatosin (08:47:36) (in thread): > There’s no confounder for experiment 2. > > I saw this for experiment 1 : > “This test is a permutational multivariate analysis that assesses the group-wise, phylogenetic clustering of microbiomes. When controlling for HIV status, ADONIS testing of weighted and unweighted UniFrac distances revealed compositional differences by ethnicity (p < 0.05), excluding Bamenda, Eton, and Haoussa ethnic groups as there were no HIV negative representatives belonging to these ethnic groups, indicating that there are population-level differences in microbiome structure.” > > So I believe HIV status is the confounderfor experiment 1.Ohhthey’veresponded. > > You are good to go then@Aleru DivineWell done

Aleru Divine (09:11:27) (in thread): > Well done@Victoria (Burah) Poromon:clap:

Aleru Divine (10:07:21) (in thread): > What about this “When controlling for HIV treatment status, we identified differences in microbial composition among Cameroonian ethnic groups.”@Mildred Anashie@Adeshile OluwatosinThis is for experiment 2 no? > > Also I see it now@Mildred AnashieI understand this statement “Using linear models, we were unable to detect a relationship between alpha-diversity and ART duration. Increasing model complexity by controlling for age, CD4 count, and viral burden did not improve predictive power.” > > When they controlled for these, it was to detect a relationship between alpha-diversity and ART duration. And experiment 2 is relationship with ART regimen only. > > I do thinkHIV treatment statuswas controlled for in experiment 2. But I don’t know if it’s correct to include it in experiment 1.

Samuel Nnanna (10:47:11) (in thread): > @Victoria (Burah) PoromonGood Job.:raised_hands:

Cynthia Iwuoha (10:47:53) (in thread): > Nice one @Victoria

Adeshile Oluwatosin (11:02:16) (in thread): > @Aleru DivineApologies for the late response. > > I believe that in experiment 1, definitely HIV status is a confounder for experiment 1. > > I don’t believe it should be added for experiment 2. > > From the article. > > Is there a reason why you are doubting?

Adeshile Oluwatosin (11:06:07): > Hello everyone > > I’d appreciate a peer review on this study:https://bugsigdb.org/Study_1209https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01734-4#MOESM1 - Attachment (BugSigDB): Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets - BugSigDB > BACKGROUND: The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. - Attachment (BioMed Central): Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets - Microbiome > Background The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and untargeted metabolomics. Results Porcine epidemic diarrhea virus (PEDV) infection leads to significant changes in the gut microbiota of piglets. Notably, Landrace pigs lose their resistance quickly after being infected with PEDV, but transplanting the fecal microbiota of Min pigs to Landrace pigs alleviated the infection status. Macrogenomic and animal protection models identified Lactobacillus reuteri and Lactobacillus amylovorus in the gut microbiota as playing an anti-infective role. Moreover, metabolomic screening of the secondary bile acids’ deoxycholic acid (DCA) and lithocholic acid (LCA) correlated significantly with Lactobacillus reuteri and Lactobacillus amylovorus, but only LCA exerted a protective function in the animal model. In addition, LCA supplementation altered the distribution of intestinal T-cell populations and resulted in significantly enriched CD8+ CTLs, and in vivo and in vitro experiments showed that LCA increased SLA-I expression in porcine intestinal epithelial cells via FXR receptors, thereby recruiting CD8+ CTLs to exert antiviral effects. Conclusions Overall, our findings indicate that the diversity of gut microbiota influences the development of the disease, and manipulating Lactobacillus reuteri and Lactobacillus amylovorus, as well as LCA, represents a promising strategy to improve PEDV infection in piglets. Video Abstract

Kate Rasheed (11:06:24): > Good evening everyone. I have come again:smile:. > > I would appreciate a peer review on this study we(@Mercy Cherop@Cate Ouma) are working on.https://bugsigdb.org/Study_1172 - Attachment (BugSigDB): Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes - BugSigDB > Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals.As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome.

Adeshile Oluwatosin (11:07:59) (in thread): > Well done@Kate RasheedI would look through > 10 experiments, will take my time

Yoko C (11:09:56) (in thread): > Hello, a little late to this, but I think 5a might not be for the study whole study, I think its for the people from the TCGA database?

Kate Rasheed (11:16:20) (in thread): > Thank you so much@Adeshile Oluwatosin

Kate Rasheed (11:18:20) (in thread): > You’re welcome@Yoko C. That’s true it’s not for the study but I saw that the microbial diversity was used for this study.

Adeshile Oluwatosin (11:24:01) (in thread): > Check out the condition (as PEDV isn’t permissible) andtaxa with missing ID.Thanks

Aleru Divine (11:57:17) (in thread): > But wouldn’t the treatment status mean the ART regimens (NNRTI andPI/r).This is what is being contrasted in experiment 2.

Yoko C (11:58:21) (in thread): > Hello, although confounders still confound me a bit, I don’t think you have confounders for any of your experiments. I think the confounders were used to test alpha and beta diversity differences.

Aleru Divine (11:58:22) (in thread): > I’ll have a look at this@Adeshile OluwatosinWell done on the curation

Aleru Divine (11:59:13) (in thread): > Well done on the curation@Kate RasheedI’llhave a look too

Yoko C (11:59:29) (in thread): > In experiment 2 you just have HIV+ children who are using nnrti or pi/r.

Aleru Divine (12:10:51) (in thread): > Omg! I see your point@Yoko CAll clear for experiment 1. > > But then for experiment 2, I think they controlled for the treatment status. > > “When controlling for HIV treatment status, we identified differences in microbial composition among Cameroonian ethnic groups.”I think thissuggests that they took into account the type of ART regimen ( NNRTI and PI/r) that participants were receiving.

Yoko C (12:21:50) (in thread): > That’s what I understand too, experiment 2 compares microbiomes between kids on different treatments. But I don’t think it’s a confounder in the differential analysis, because the differential analysis doesn’t include ethnicities or other variables, as far as i understand.

Adeshile Oluwatosin (12:23:19) (in thread): > I see your pointfor experiment 1, well done@Aleru Divine@Yoko C

Mildred Anashie (12:23:30) (in thread): > Makes sense@Yoko C@Aleru DivineI stilldon’tthink Experiment 2 has any confounders controlled for

Aleru Divine (12:25:12) (in thread): > Yes yes@Mildred AnashieI’mleaving out the confounders.Thanks for the input everyone.I truly truly appreciate:heart_hands:

Adeshile Oluwatosin (12:28:32) (in thread): > Hi dear, you can record escherichia-shigella as escherichia/shigella sp (experiment 1/signature 1).@Kate Rasheed

Yoko C (12:36:32) (in thread): > Hello, I think your condition is good. Something that confuses me though is that if I understood correctly they also tested for piglet race (Min vs Landrace) so in this case would race be a confounder? Maybe I didn’t read the paper carefully enough so I am not sure if that is even a thing.

Yoko C (12:37:22) (in thread): > for unidentified Actinobacteria you can use unclassified Actinomycetota, I believe

Yoko C (12:38:32) (in thread): > Oscillospirales I think is Eubacteriales.

Adeshile Oluwatosin (12:51:18) (in thread): > First of for Figure 4D there was mention of a taxa > Eubacterium eubacterium Hallii > I curated it as eubacterium hallii since that’s the species. > > For others, I curated it as other (unidentified) > > I saw unclassified actinomycetota but I believe unidentified and unclassified means different things.

Adeshile Oluwatosin (12:53:38) (in thread): > For Oscillospirales there was mention of clostridiales which is also eubacterialesin same figure.I also checked the discussion page and saw that it was noted to be clostridiales not Oscillospirales.

Adeshile Oluwatosin (12:54:54) (in thread): > They didn’t mention race as a confounder soI don’tthink so.

Yoko C (12:57:39) (in thread): > If you check NCBI Clostridiales is a synonym for Eubacteriales, and Oscillospirales takes you to Eubacteriales.

Adeshile Oluwatosin (12:59:56) (in thread): > Yes both takes me to eubacteriales on NCBI > I was contemplating curating both as eubacteriales and writing a note about it.I would just do this

Adeshile Oluwatosin (13:00:59) (in thread): > Btw experiment 5 has 2 signatures o, just incase lol

Mildred Anashie (13:09:48) (in thread): > Hi@Adeshile Oluwatosinwell doneI’lltake a look at this too

Aleru Divine (13:11:04) (in thread): > Is there a way to define these abbreviations? Maybe in the signature source description.It’sa lot of abbreviations.@Adeshile Oluwatosin

Adeshile Oluwatosin (13:12:09) (in thread): > @Aleru DivineI looked into doing that but itwasn’tdefined in the study > Asides PEDV, and for the experiments i highlighted the full definition

Adeshile Oluwatosin (13:12:52) (in thread): > I couldn’t come to terms on if M-CON means min pigs as control. The definition given was min pigs challenged with PBS

Aleru Divine (13:14:06) (in thread): > You should add what you can find then.I mean PEDV.

Adeshile Oluwatosin (13:17:04) (in thread): > Yes, I highlighted the full description of PEDV in experiment 2/group 1.Do you thinkitshouldbe described as well in the group names? > E.g M-PEDV as M-PEDV (Porcine epidemic diarrhea virus)

Adeshile Oluwatosin (13:18:34) (in thread): > I still wrote it as that in the description > It would cause redundancy, don’t you think?

Aleru Divine (13:19:05) (in thread): > The first time it is mentioned, you should write it in full then subsequently abbreviate.

Aleru Divine (13:25:37) (in thread): > @Kate Rasheedfor the antibiotics exclusion, I think a better phrase would be “current antibiotic use” or better still, report it in full for clarity.“Participants currently taking antibiotics were excluded from the study”

Adeshile Oluwatosin (13:25:54) (in thread): > It’swritten in full in experiment 1 now > I might as well re edit it for all experiments. > > M-CON and L-CONcan’tbe written in full > AsI’mnot sure if it means min-control and Landrace-control

Adeshile Oluwatosin (13:27:37) (in thread): > Did you by any chance come across that@Aleru Divinet

Aleru Divine (13:28:53) (in thread): > Itwasn’twritten in full as at the time I made the suggestion@Adeshile Oluwatosinhence the suggestion.

Adeshile Oluwatosin (13:30:18) (in thread): > Yh,I’vere edited that part. > Did you see that in the study for M-CON meaning Min-control. > AsI’m sureI didn’tsee it

Yoko C (13:50:38) (in thread): > Hello, I got stuck on experiment 1 because I’m not sure if the negative controls are tested for increased or decreased bacteria. I think they are used to test for contaminants, from what I googled. I’m also not sure about the condition, since it specifies a quantification and although they do measure things like BMI, the comparison overall is by the country. But maybe lifestyle measurement extends to that as well.

Mildred Anashie (14:08:56) (in thread): > Hi@Adeshile OluwatosinWell done on your curation. I also didn’t come across the definition for M-CON and L-CON, so I think you should leave it that way. > > However, I believe Figure 4B should be curated as well.It’sthe same comparison as 4D but different statistical test. > > 4B is Metastats while 4D is LEfSe

Adeshile Oluwatosin (14:09:36) (in thread): > Figure 4B I saw that > > The taxa are already in 4D

Adeshile Oluwatosin (14:09:41) (in thread): > It’sa repetition

Adeshile Oluwatosin (14:10:11) (in thread): > Thank you@Mildred Anashie

Mildred Anashie (14:12:08) (in thread): > See this “We analyzed the different species among the virus-infected and control groups in the same period through metagenomics. After the genes were assembled and screened, we found that the Min pigs infected with PEDV had a significantly increased number of gut microbe genes (Fig. 4A). We then calculated the relative abundances of the bacteria after species annotation. The abundances of Lactobacillus reuteri, Lactobacillus amylovorus, Prevotella sp. CAG:604, Phasolarctobacterium succinatutens, and Faecalibacterium prausnitzii all increased following virus infection, whereas the abundances of Bacteroides plebeius, Prevotella copri, Prevotella sp. CAG:520, Bacteroides plebeius CAG:211, and Phascolarctobacterium succinatutens were depleted (Fig. 4C). In addition, cluster statistics (Fig. S4A), ******Metastat (Fig. ****4******B), and LEfSe (Fig. ****4******D) ******were used to analyze the differences in species.’** - Attachment (BioMed Central): Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets - Microbiome > Background The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and untargeted metabolomics. Results Porcine epidemic diarrhea virus (PEDV) infection leads to significant changes in the gut microbiota of piglets. Notably, Landrace pigs lose their resistance quickly after being infected with PEDV, but transplanting the fecal microbiota of Min pigs to Landrace pigs alleviated the infection status. Macrogenomic and animal protection models identified Lactobacillus reuteri and Lactobacillus amylovorus in the gut microbiota as playing an anti-infective role. Moreover, metabolomic screening of the secondary bile acids’ deoxycholic acid (DCA) and lithocholic acid (LCA) correlated significantly with Lactobacillus reuteri and Lactobacillus amylovorus, but only LCA exerted a protective function in the animal model. In addition, LCA supplementation altered the distribution of intestinal T-cell populations and resulted in significantly enriched CD8+ CTLs, and in vivo and in vitro experiments showed that LCA increased SLA-I expression in porcine intestinal epithelial cells via FXR receptors, thereby recruiting CD8+ CTLs to exert antiviral effects. Conclusions Overall, our findings indicate that the diversity of gut microbiota influences the development of the disease, and manipulating Lactobacillus reuteri and Lactobacillus amylovorus, as well as LCA, represents a promising strategy to improve PEDV infection in piglets. Video Abstract

Aleru Divine (14:20:44) (in thread): > @Mildred Anashiefigure 4D contains all the signatures in 4B and more.That’swhy the LEfSe (4D) is curated.Sincetheywere both used for differential abundance testing, 4B will be repeating signatures already in 4D.

Mildred Anashie (14:25:53) (in thread): > Okay@Aleru Divine@Adeshile OluwatosinMeaning we would ignore that regardless of the different statistical tests?

Aleru Divine (14:27:11) (in thread): > Yesthat’scorrect.Maybe just include it on the discussions page for reference.Butthere’sno need curating another experiment.

Aleru Divine (14:29:46) (in thread): > Yes@Kate Rasheedthis experiments 1 and 2 you’ve curated comparing negative controls and all the locations. I’m not very certain either. > > In the paper, comparisons are between the four countries, not between the countries and negative controls.

Kate Rasheed (14:34:13) (in thread): > That’s my main doubt actually@Yoko C@Aleru Divine. > > For experiment 1 and 2, it wasn’t specified that there was a comparison between negative controls and all countries. > > I was wondering what group 0 will be and then I saw that in the sequencing details, there was 206 samples (for all countries participants) plus 11 negative controls. That’s why I used it for experiment 1 and 2. > > Do you think I should take out the negative controls and leave group 0 blank? > > The results in Table S6 and S7 is for all countries together so I reasoned they did a comparison with negative controls(hence the additional samples).

Aleru Divine (14:34:50) (in thread): > M-CON isn’t Min-control@Adeshile Oluwatosinyou should leave that as you have defined it. (Min pigs challenged with PBS)

Aleru Divine (14:42:06) (in thread): > Unless stated, which in this case isn’t. I don’t think we should assume what was compared.@Kate RasheedI really don’t know how to go about this, but first remove the negative controls:sweat_smile:Also the controlsweren’tfor differential abundance testing if I understood the paper correctly.

Kate Rasheed (14:43:32) (in thread): > What is the negative controls doing in the study now:smile:@Aleru Divine

Adeshile Oluwatosin (14:44:23) (in thread): > No another experiment is not needed, lol > > Yesit’sleft as that > Thanks > I guess it’s ready for review now

Kate Rasheed (14:45:16) (in thread): > @Adeshile OluwatosinThe Escherichia Shigella used in the study is genera. This one you stated is species. Should I curate that way:thinking_face:

Adeshile Oluwatosin (14:46:15) (in thread): > @Kate RasheedI’vehad similar studies where I curated the taxa as Escherichia/shigella spThat’swhat is permissible > > Andwe’vehad this discussion previously on this exact taxa

Aleru Divine (14:47:27) (in thread): > The controls were used in this study to monitor/identify contamination.That’swhat I understand.

Aleru Divine (14:47:52) (in thread): > This is the first timeI’mseeing this.But they’redefinitely not for the differential abundance test.

Kate Rasheed (14:50:41) (in thread): > It’s true they were not used for the differential abundance test. Let me remove it first. I’ll understand it later.

Aleru Divine (14:51:12) (in thread): > :sweat_smile:okay

Yoko C (14:54:54) (in thread): > But once you remove the controls, what where the countries in table s6 tested against? This is a weird paper because they mention significantly different taxa in different graphs and table but its very unclear what the contrast is.

Kate Rasheed (14:57:30) (in thread): > Exactly@Yoko Cthat’s why I used the negative controls cause it could be they were used as comparison.

Kate Rasheed (15:00:35) (in thread): > The paper actually withheld some information. It’s only in this excerpt that negative controls value was mentioned. > > “Sequence reads from the 206 samples obtained plus 11 negative controls were processed using an in-house 16S rRNA gene data analysis pipeline.”

Aleru Divine (15:03:00) (in thread): > It is indeed confusing@Yoko C@Kate RasheedS6 shows the differentially abundant genera in stool samples. I’m guessing all countries because when they referenced S6and S7in the paper, they said between countries.Figure 3 and figure 4 shows all countries too.Not one mention of controls:sob:Idon’t know I don’t know:sob:

Kate Rasheed (15:04:53) (in thread): > The alpha diversity in the paper is showing pairwise comparison, whereas there is no differential abundance for pairwise comparison. > > I guess I should leave the negative controls that way.

Yoko C (15:07:36) (in thread): > I think it’s like an ANOVA test where it shows you which variables are significant but it doesn’t tell you what group it’s significant for. To find out where the differential abundance difference is, they would have to do a second test. I would go as far as saying that table s6 might not be curatable. But I think I need to re-read to really understand.

Kate Rasheed (15:09:43) (in thread): > Table S6 and S7 are curatable ooo:smile:

Adeshile Oluwatosin (15:25:33) (in thread): > Thank you@Mildred Anashie@Aleru Divine

Yoko C (15:31:48) (in thread): > For the sample number of group 1, I think this should be taken into account ” This left 197 samples …”

Kate Rasheed (15:38:11) (in thread): > In the supplementary table and further analysis, 206 samples were still used@Yoko C

Joy (15:53:08) (in thread): > @Victoria (Burah) Poromondid a great job!

Yoko C (16:34:46) (in thread): > After reading, I think the condition for exp 1 might be related to the geolocation signal significance, meaning they are looking for bacteria that are important when trying to find a location (the forensic part). This article was hard to understand so maybe that’s not it at all:sweat_smile:

2024-11-13

Tino (06:23:07): > Hello@Svetlana Ugarcina PerovicFor this studyhttps://bugsigdb.org/Study_1216The sequencing was done on the Ion S5TM XL platform which is currently not found on the BugSigDb database. I don’t know if you can add it or I just leave it blank. > > Also the study stated ‘disease’ as one of the confounders controlled for, which is also currently not found on the BugSigDb database. So do I exclude it since they didn’t specify which disease? - Attachment (BugSigDB): Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing - BugSigDB > Understanding the violence behaviors in schizophrenia patients has always been the focus of forensic psychiatry.Although many studies show gut microbiota could regulate behavior, to our knowledge, no studies have profiled the gut microbiota structure in schizophrenia patients with violence.

Aleru Divine (06:24:46) (in thread): > @TinoI believe that is ion torrentIt’savailable on the BugSigDB database

Aleru Divine (06:25:18) (in thread): > https://tools.thermofisher.com/content/sfs/brochures/Ion-S5-S5XL-Brochure.pdf

Tino (06:25:57) (in thread): > Thank you@Aleru Divine

Aleru Divine (06:27:53) (in thread): > As for the confounder, whenit’snot found in BugSigDB, you can just curate it as presented in the paper.Or find the closest related term.

Aleru Divine (06:29:31) (in thread): > It may be flagged, butI thinkthat’s okay.

Kate Rasheed (07:07:46) (in thread): > well done@Tinoon your curation. Thank you@Aleru Divinefor the response:hugging_face:

Mildred Anashie (07:30:47) (in thread): > Well done on your curation@TinoI agree with@Aleru Divine, that should be Ion torrent

Rahila-me (07:59:53) (in thread): > Weldon@Tinoon your curation at@Aleru Divine:ok_hand:

Svetlana Ugarcina Perovic (09:21:03): > SURVEYTHANK YOU ALLfor YOUR amazing contribution, keep up the good work! > > We would appreciate if you can share your experience with us by filling in this short surveyhttps://forms.gle/brqH5M2uTYMKy23x7and help us improve experience for future contributors. > > Thank you,<@U1LCB8WEA><@UBNSEMS3S>@Chioma Onyido@Peace Sandy@Esther Afuape@Svetlana Ugarcina PerovicP.S. if you already filled in this survey in some previous rounds, please provide your feedback again, maybe something changed. - Attachment (Google Docs): Outreachy-Bioconductor survey > Dear Outreachy-Bioconductor contributor, > Thank you for participating in the Outreachy-Bioconductor program. In order to improve the experience for future contributors as well as to spread the word about your amazing contribution to the Bioconductor projects in the form of a conference talk and publication, we would appreciate you taking just a few minutes to complete an online survey about your experience. > > All survey responses are collected anonymously. If you have any questions, please contact us. > > Many thanks in advance and best wishes, > Bioconductor team > Email address: mailto:jennifer.wokaty@sph.cuny.edu|jennifer.wokaty@sph.cuny.edu

BOLARINWA AISHAT (09:33:52) (in thread): > Hello@Svetlana Ugarcina PerovicI noticed that there is not option for December 2024 contribution stage in the survey. - File (PNG): IMG_6475

Svetlana Ugarcina Perovic (09:35:38) (in thread): > Added.

BOLARINWA AISHAT (09:36:57) (in thread): > Thank you very much

Adeshile Oluwatosin (09:45:23) (in thread): > Hello@Svetlana Ugarcina PerovicOkay, no problem

Aleru Divine (09:53:30) (in thread): > Will do@Svetlana Ugarcina PerovicThank you so much for your support:heart_hands:

Kate Rasheed (10:18:38): > Good afternoon everyone. Please I would need your opinion on this article I’m working on. I’m unsure of the number of curatable experiments. > > Here is the link:https://www.nature.com/articles/s41467-024-53934-7 - Attachment (Nature): Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders > Nature Communications - Here, Manghi et al. identify potential salivary microbial biomarkers for autism through a large-scale metagenomic analysis of 2,000 families, revealing shifts in…

Mildred Anashie (10:25:48) (in thread): > Done@Svetlana Ugarcina PerovicThank you:blush:

Mildred Anashie (10:26:23) (in thread): > Hi@Kate RasheedI’lltake a look at it

Mildred Anashie (10:28:13): > Hi everyone@BOLARINWA AISHATand I just finished curating thisstudyand would appreciate peer review. > > One of the things we are concerned about is the study design, are we right by going with Case-control? > > Thank you:pray: - Attachment (BugSigDB): The lung microbiome in HIV-positive patients with active pulmonary tuberculosis - BugSigDB > Tuberculosis poses one of the greatest infectious disease threats of our time, especially when associated with human immunodeficiency virus (HIV) infection.Very little data is available on the lung microbiome in pulmonary tuberculosis (PTB) in HIV-positive patients.

Kate Rasheed (10:34:10) (in thread): > Well-done@Mildred Anashie@BOLARINWA AISHATI’ll take a look.

Aleru Divine (10:38:01) (in thread): > Good afternoon@Kate RasheedI’llhave a look at this too.

Aleru Divine (10:38:51) (in thread): > Well done on the contribution@Mildred Anashie@BOLARINWA AISHATI’llgive it a peer review.

Kate Rasheed (10:44:29) (in thread): > @Mildred AnashieI’ll say it’s a cross-sectional study. > > From the curation policy, one pointer to a study being case-control is the presence of “matched on…”. > > I don’t see the case cohorts being matched with the control cohorts. > > I’ll settle for cross-sectional.

Kate Rasheed (10:49:51) (in thread): > Thank you@Mildred Anashie@Aleru Divine

Mildred Anashie (11:28:24) (in thread): > @Kate RasheedThis paper is a lot:face_with_diagonal_mouth:ButI’mpicking some things,I’llshare them soon

Aleru Divine (11:30:01) (in thread): > Yes it is@Mildred Anashie:sweat_smile:

Kate Rasheed (11:41:46) (in thread): > @Mildred AnashieI’ve been staring at the paper since yesterday. I’ve been able to curate two experiments from it though:smile:

Adeshile Oluwatosin (12:03:22) (in thread): > Well done@Mildred Anashie@BOLARINWA AISHATI would check

Aleru Divine (12:45:47) (in thread): > @Kate Rasheed:sweat_smile:there are a lot of figures showing associations with microbial load and associations with some other variables. I don’t know if those should be curated since they are not showing differential abundance results. > > Here’s my observations: > 1. Figure 2C and 3C for differential abundance results for ASDs and NTs are identical. (Full cohort) > 2. Figure S4a shows differentially abundant genera in theSPARK-WGS cohortbetween ASDs and NTs. > > * Figure 2e show results for association of species with microbial load. > * The rest of the plots in 3C shows associations between the oral microbiome and IQ, picky factor etc. I’m not sure how to curate those but we have colors differentiating those associated with high IQs and from those associated with low IQs. IQ and IQ adjusted for picky factor are showing the same differences. > * Figure S7b is the same as figure 2c and 3C. In addition to the first plot, the others show associations between species and SCQ, DCDQ, and RBS-R) > I’m looking at 3-9 experiments so far > > As for the supplementary data, they show results for all the species, both significant and insignificant signatures found for all the comparisons made in the paper, and they’re a lot:sweat_smile:This is all I’ve been able to see from the paper. I might have missedsomething. Looking out for other opinions too.

Aleru Divine (12:52:12) (in thread): > This is a cross-sectional observational study@Mildred Anashienot case-control.

Adeshile Oluwatosin (12:54:30) (in thread): > It’sa cross-sectional study

Aleru Divine (13:02:45) (in thread): > Everything checks out so far for me@Mildred Anashie@BOLARINWA AISHATwell done!

BOLARINWA AISHAT (13:03:35) (in thread): > Thank you all

Kate Rasheed (13:22:20) (in thread): > Thank you so much@Aleru Divine. I curated Supplementary Data 3 in place of Fig.2C and 3C is a subset of ASV vs NTs so I curated separately.

Kate Rasheed (13:44:13) (in thread): > @Aleru DivineFigure S4a is the same as experiment 1. It’s giving the result of genus as seen in supplementary data 5.

Aleru Divine (13:46:14) (in thread): > Okay:thumbsup:@Kate Rasheednicely done

Mildred Anashie (15:44:03): > Hi everyone@Joyand I just finished curating thisstudyand would appreciate peer review. > > > Thank you:pray: - Attachment (BugSigDB): Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet - BugSigDB > High-fat (HF) diet-induced neuroinflammation and cognitive decline in humans and animals have been associated with microbiota dysbiosis via the gut-brain axis.Our previous studies revealed that excretory-secretory products (ESPs) derived from the larval Echinococcus granulosus (E.

Kate Rasheed (15:47:47) (in thread): > Well-done people. I’ll look through.

BOLARINWA AISHAT (20:45:47): > Hello everyone.@Aleru Divineand I just finished curatingthis studyand we’ll appreciate peer reviews.https://bugsigdb.org/Study_1114Thank you very much.

Aleru Divine (21:09:53) (in thread): > Well done on the curation@Mildred Anashie@Joy:clap:Please check the alpha diversity for experiment 2? It’s increased for HFE compared to HF. I mean Shannon is pretty clear. > > For the condition, I think it should beCognitive impairmentwithout the measurement. I was also thinking response to diet since the high-fat (HF) diet induced cognitive impairment. But I think cognitive impairment works for this study.

Adeshile Oluwatosin (22:57:17) (in thread): > Well done@Mildred Anashieeverything else checks out for me > Asides what aleru has mentioned

Adeshile Oluwatosin (22:57:45) (in thread): > Hello@BOLARINWA AISHATIt’sa lot of experiments, I will look through

Adeshile Oluwatosin (22:58:32) (in thread): > Cognitive impairment is permissible so use that instead

Kate Rasheed (23:38:20) (in thread): > Good morning@Mildred Anashie. You can check Ruminoclostridium in experiment 1, signature 1. > > I guess Ruminoclostridium is a typo, the right one is Ruminiclostridium. I’ve been seeing Ruminiclostridium in the signatures I’ve encountered.

Kate Rasheed (23:42:05) (in thread): > Welldone@Aleru Divine@BOLARINWA AISHAT.

2024-11-14

Adeshile Oluwatosin (00:14:02) (in thread): > Yeah I saw that > > But I wasn’t sure if it was a typo, checked google and saw that there’s nothing like Ruminoclostridium now > But for Ruminiclostridium:1508657

Kate Rasheed (00:43:06) (in thread): > @Adeshile OluwatosinThe ID is for Ruminiclostridium right?

Adeshile Oluwatosin (01:01:37) (in thread): > Yes Ruminiclostridium@Kate Rasheed

BOLARINWA AISHAT (01:05:13) (in thread): > Thank you so much:pray:

Mildred Anashie (01:26:32) (in thread): > I’ve come across Ruminoclostriduim a couple of times when curating, that’s why I left it that way > > I’ve always left it that way:thinking_face:

Mildred Anashie (01:28:53) (in thread): > Okay@Aleru DivineThank you so much

Mildred Anashie (01:29:09) (in thread): > Thank you@Kate Rasheed@Adeshile Oluwatosin:pray:

Mildred Anashie (01:43:37) (in thread): > Guys I just checked andit’sactually a typo on my part > > Thank you all again:blush:Fresh set of eyes:heart_hands:

Mildred Anashie (01:46:03) (in thread): > Well done@Aleru Divine@BOLARINWA AISHATI’ll take a look

Adeshile Oluwatosin (02:31:02) (in thread): > :joy::wink:

Aleru Divine (02:40:39) (in thread): > Thank you@Adeshile Oluwatosin@Kate Rasheed@Mildred Anashie

Svetlana Ugarcina Perovic (02:41:01): > Good morning! > > See you today atour weekly team meeting and office hours at 9 AM EDT (>>3:00 PM<<**** ****in Europe, Nigeria, etc.).https://us02web.zoom.us/j/2737200499cc<@UBNSEMS3S>

Mildred Anashie (02:43:05) (in thread): > Thank you:blush:

Adeshile Oluwatosin (02:52:18) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kate Rasheed (02:56:43) (in thread): > Thank you for the reminder:hugging_face:.

BOLARINWA AISHAT (03:28:19) (in thread): > Thank you for the reminder

Mildred Anashie (04:37:17) (in thread): > Hi@Kate Rasheedthis is a good paper to present today because….. > * So I identified Fig 2c (ASD and NTs) and 2E (ASD and high/low microbial load) the color codes in the figure shows the groups/contrasts. > > * Supplementary figures 4a used linear model and adjusted for a few covariates and I think the data is curatable > * S7 and 3c(the ASD vs neurot.) are showing the same thing. For the others I thinkyou’dcurate as SPARK-WGS associated with low and High IQ etc. Also, the caption says “Colors for the significant (q<0.2) associations are reported. Grey refers to q>0.2”. I believe you wouldn’t curate those in grey as they are not significant. This applies for the rest in 3c and S7 > * The supplemental tables are the most confusing:face_with_diagonal_mouth: > This is all I can pick so far from the paper

Kate Rasheed (04:59:35) (in thread): > Thank you so much@Mildred Anashie. I’ve curated these ones you mentioned. > > The supplementary table is quite confusing but it’s related to the curatable figures and it has more taxa. > > Thanks once again@Aleru Divine@Mildred Anashie.

Cynthia Iwuoha (05:27:27) (in thread): > Thank you for the reminder.

Rahila-me (06:00:32) (in thread): > Thank you

Mildred Anashie (07:50:52) (in thread): > Hi@Aleru DivineCan you guide me through your interpretation of the supplementary tables?

Chinwendu Joy Enyidiegwu (08:01:54) (in thread): > thank you

Aleru Divine (09:02:03) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic

Aleru Divine (09:26:06) (in thread): > It’s in the descriptionfor each of the tables. For each variable controlled for, red bars represent increased abundance inchildren born to mothers withGDMand blue bars represent decreased abundance.

Svetlana Ugarcina Perovic (10:04:23): > Today’s<@UBNSEMS3S>’s data analysis art! - File (PNG): Screenshot 2024-11-14 at 15.15.02.png

Aleru Divine (10:05:59) (in thread): > Thank you@Svetlana Ugarcina Perovicand thank you for the office hours session<@UBNSEMS3S>:pray:

Adeshile Oluwatosin (10:12:25) (in thread): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina PerovicThe weekly meetings is always my highlight:hugging_face::pray:

Kate Rasheed (10:36:01) (in thread): > Thank you for sharing.

Kate Rasheed (10:37:04): > Good afternoon@Svetlana Ugarcina Perovic. Kindly delete experiment 1 and 2 from this study:https://bugsigdb.org/Study_1172Thank you. - Attachment (BugSigDB): Sampling from four geographically divergent young female populations demonstrates forensic geolocation potential in microbiomes - BugSigDB > Studies of human microbiomes using new sequencing techniques have increasingly demonstrated that their ecologies are partly determined by the lifestyle and habits of individuals.As such, significant forensic information could be obtained from high throughput sequencing of the human microbiome.

UBNSEMS3S (12:18:06) (in thread): > You know I love to do a good impromptu lecture in MS Paint.

Adeshile Oluwatosin (12:18:32) (in thread): > We love to see it:hugging_face:

BOLARINWA AISHAT (12:29:05): > Good afternoon@Svetlana Ugarcina PerovicKindly delete ; > Experiment 23 Signature 2 and > Experiment 22 Signature 2https://bugsigdb.org/Study_1114Thank you very much.

Svetlana Ugarcina Perovic (13:55:49) (in thread): > Deleted.

Svetlana Ugarcina Perovic (13:55:59) (in thread): > Deleted.

Kate Rasheed (14:02:57) (in thread): > Thank you

BOLARINWA AISHAT (14:07:02) (in thread): > Thank you

BOLARINWA AISHAT (14:47:19) (in thread): > Done

Yoko C (14:49:12) (in thread): > Hello, I started reading this paper and was wondering if maybe it’s a longitudinal study or prospective cohort since it follows the same group of people for a period of time?

BOLARINWA AISHAT (15:01:12) (in thread): > Thank you@Yoko Cfor taking out time to go through our curation, we really appreciate it. > > One of the mentors actually confirmed thatit’sa cross-sectional observational study. > I understand your point, I feelitwon’treally qualify as longitudinal or time series since there were only two time instances where samples were collected; one week and nine months. > > However I am open to more suggestions as regards this.@Mildred Anashie@Adeshile Oluwatosin@Kate RasheedThank you:pray:

Adeshile Oluwatosin (15:02:52) (in thread): > Could you specify what you need clarification on dear@BOLARINWA AISHAT:face_holding_back_tears:

BOLARINWA AISHAT (15:03:55) (in thread): > Why it could be a longitudinal study instead

Yoko C (15:19:39) (in thread): > I’m also not sure if the antibiotics exclusion for experiment 1 is correct, since these are 1 week old newborns and the 2 months was for the mothers.

Tino (23:20:55) (in thread): > Thank you

2024-11-15

Adeshile Oluwatosin (01:54:14): > Good morning@Svetlana Ugarcina PerovicKindly delete: signature 1 in experiment 4. Thank youhttps://bugsigdb.org/Study_1220 - Attachment (BugSigDB): Hormonal contraception alters vaginal microbiota and cytokines in South African adolescents in a randomized trial - BugSigDB > Young women in sub-Saharan Africa are disproportionally affected by HIV infection and unintended pregnancies.However, hormonal contraceptive (HC) use may influence HIV risk through changes in genital tract microbiota and inflammatory cytokines.

Joy (02:05:23) (in thread): > Done@Svetlana Ugarcina Perovic.Thank you:hugging_face:

Adeshile Oluwatosin (02:12:44): > Good morning everyone > How was your night > I would appreciate a peer review on this study:https://bugsigdb.org/Study_1220

Mildred Anashie (02:15:25) (in thread): > Good Morning@Adeshile OluwatosinWell done on your curation,I’lltake a look at this

Adeshile Oluwatosin (02:15:36) (in thread): > Thank you

Adeshile Oluwatosin (02:19:22): > Also, in this study:https://bugsigdb.org/Study_1209 > * If unclassified clostridium hiranonsis is to be curated > And clostridium hiranonsis is peptacetobacter hiranonsis > > Should unclassified clostridium hiranonsis be curated as “unclassified peptacetobacter hiranonsis” or left exactly the way it is. > Either will still have a missing NCBI taxa Id. > * The significance for 4B curation states 0.0001 but I think it’s same as other test which is 0.05. > Also kindly give a general review on experiment 5 and 6 curation. - Attachment (BugSigDB): Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets - BugSigDB > BACKGROUND: The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear.

Kate Rasheed (02:53:25) (in thread): > @Adeshile Oluwatosinleave unclassified clostridium hiranonsis that way.

Adeshile Oluwatosin (02:55:39) (in thread): > Thanks,that’swhat I didI’m justcurious@Kate Rasheed

Kate Rasheed (02:57:23) (in thread): > For 4B, the 0.0001 is just describing the p-value. That shouldn’t be the threshold. > > I’ll look through experiment 5 and 6.

Aleru Divine (03:01:22) (in thread): > Good morning@Adeshile OluwatosinI’ll have a look too. Well done:clap:

Aleru Divine (03:09:06) (in thread): > Hi@Adeshile OluwatosinI’d say to curate as unclassified Peptacetobacter hiranonis since this is the current name. Clostridium hiranonis is theoldname according to the taxonomy browser. > > For example we now curate Unclassified Ruminococcaceae as unclassified Oscillospiraceae since this is the current name. > > The significance threshold is still 0.05:ballot_box_with_check:

Adeshile Oluwatosin (03:10:14) (in thread): > Alright, great > Thank you

Aleru Divine (03:12:38) (in thread): > Good morning@Yoko C, I completely understand your point,the reason for including this is that recruitment was based on the mothers. So, if a mother was excluded due to antibiotic use within a certain timeframe, her child was also excluded.

Aleru Divine (03:19:22) (in thread): > This is a study correction@Yoko C, the antibiotic exclusionand the study designwas suggested for correctionsby the reviewer.

Mildred Anashie (03:23:37) (in thread): > Hi@Adeshile OluwatosinThe threshold should be 0.05 > Well done:clap:

Adeshile Oluwatosin (03:25:46) (in thread): > Thanks everyone:heart:

Agatha (04:14:32): > Good morning everyone, please we will appreciate a peer review of this study curated by I and@Aleru Divinehttps://bugsigdb.org/Study_1198/Experiment_1 - Attachment (BugSigDB): Study 1198/Experiment 1 > .

Mildred Anashie (04:42:06) (in thread): > Well done@Adeshile OluwatosinIn my opinion everything checks out > > This taxa “lactobacillus johnsonii gasseri taiwanensis” appears to be different species of Lactobacillus from the research I did. > > ButI’munsure how it should be recorded

Mildred Anashie (04:43:27) (in thread): > Okay@AgathaWell done@Agathaand@Aleru Divine:+1:

Adeshile Oluwatosin (04:44:07) (in thread): > Same here,that’swhy I curated it that way > Thank you@Mildred Anashie

Adeshile Oluwatosin (04:50:04) (in thread): > Exactly Johnosnii, Gasseri And taiwanensis are different species but it was mentioned as one species in the result

Adeshile Oluwatosin (04:52:09) (in thread): > Well done@Agatha@Aleru DivineI’llgo through it

Kate Rasheed (04:55:37) (in thread): > @Aleru DivineI get your point about using the new name but I think since the new name isn’t on NCBI too she should go for how it’s written. > > It’s just like Firmicutes that is now Bacillota. We still have Firmicutes Bacterium.

Svetlana Ugarcina Perovic (04:56:09) (in thread): > Deleted.

Adeshile Oluwatosin (04:57:55) (in thread): > Data transformationfor Deseq2is raw countsMost of the time

Aleru Divine (05:00:08) (in thread): > @Kate RasheedIdon’treally understand.

Aleru Divine (05:01:04) (in thread): > Yesit’sraw counts.Thanks@Adeshile Oluwatosindon’t know how we missed that.

Adeshile Oluwatosin (05:01:52) (in thread): > Well done, asides that you are good to go

Adeshile Oluwatosin (05:02:07) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:03:23): > Good morning, resharing with you a good microbiome science read:Common/emerging myths and misconceptions in the human microbiome field, and explains why they are likely incorrect:https://www.nature.com/articles/s41564-023-01426-7.epdf“…correlating gut microbiome changes > with systemic markers or data is fraught with challenges. This often > fails to account for confounders such as age, body mass index (BMI), > sex and medication, factors such as microbial community interactions > or for changes that occur as a result of immunological, metabolic > or other functional changes in the host rather than being directly > causal (Fig. 2). Attempts to define ‘tipping points’ at which changes in > microbiome composition definitively influence disease progression > have so far largely failed to generate a clear consensusdue to a lack of consistency between different studies. It is, therefore, a leap that is > not yet evidence based to conclude that a characteristic pathobiome > has a role in ‘most’ diseases.” > > Happy Friday! - Attachment (nature.com): Human microbiome myths and misconceptions > Nature Microbiology - Walker and Hoyles highlight selected myths and misconceptions in the human microbiota literature. - File (PNG): Screenshot 2024-11-15 at 10.57.31.png

Aleru Divine (05:04:12) (in thread): > Thank you for the review@Adeshile Oluwatosin

Adeshile Oluwatosin (05:04:40) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (05:05:08) (in thread): > You are Welcome

Adeshile Oluwatosin (05:12:02) (in thread): > I would curate seperately

BOLARINWA AISHAT (05:13:43) (in thread): > Thank you

Aleru Divine (05:24:14) (in thread): > Thanks for sharing again@Svetlana Ugarcina Perovic:hugging_face:

Kate Rasheed (05:24:39) (in thread): > Thanks for sharing. I’ll go through

Kate Rasheed (05:25:20): > Good day@Svetlana Ugarcina Perovic. Kindly delete experiment 8 from this study.https://bugsigdb.org/Study_1218 - Attachment (BugSigDB): Large-scale metagenomic analysis of oral microbiomes reveals markers for autism spectrum disorders - BugSigDB > The link between the oral microbiome and neurodevelopmental disorders remains a compelling hypothesis, still requiring confirmation in large-scale datasets.

Adeshile Oluwatosin (05:27:16) (in thread): > @Kate RasheedThank you > I would curate as the new taxonomical name since it has changed. > I want to believe everything else checks out in the study right?@Aleru Divine@Mildred Anashie@Kate Rasheed

Kate Rasheed (05:28:38) (in thread): > I’m talking about using unclassified clostridium hiranonsis instead of unclassified peptoacetobacter hiranonsis.@Aleru Divine

Kate Rasheed (05:30:29) (in thread): > @Adeshile OluwatosinClostridium sensu stricto 1 is Clostridium. > > Chloe mentioned yesterday that unidentified can be referred to as unclassified. So you can change your unclassified actinobacter

Aleru Divine (05:31:15) (in thread): > Idon’tknow ifit’sjust me but this article is closed access.Orit’smy browser although I also tried with my phone.But since this has been shared before I just used this link andI’msharing just in case.https://community-bioc.slack.com/archives/C04RATV9VCY/p1712737342711339?thread_ts=1712735363.114669&cid=C04RATV9VCY - Attachment: Attachment > Here you go https://t.co/9dZUxlg8Nk

Aleru Divine (05:33:00) (in thread): > But Clostridium hiranonsis is the old name.Just like Ruminococcaceae is the old name.Hence my suggestion to curate unclassified(new name)

Kate Rasheed (05:33:14) (in thread): > Experiment 4 signature 2, use NCBI ID to correct Veillonellales and selenomonadales.@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (05:33:34) (in thread): > Deleted.

Kate Rasheed (05:34:56) (in thread): > Thank you.

Mildred Anashie (05:35:20) (in thread): > Yes@Adeshile Oluwatosinsome of the missing NCBI can be resolved using the taxonomy browser > > Check them out,@Kate Rasheedmentioned them already

Svetlana Ugarcina Perovic (05:35:35) (in thread): > I shared the open access link:thinking_face:

Kate Rasheed (05:35:55) (in thread): > It’s closed for me too:smile:

Adeshile Oluwatosin (05:36:01) (in thread): > You are suggesting I curate them seperately even when mentioned together

Adeshile Oluwatosin (05:37:23) (in thread): > @Mildred Anashie@Kate Rasheed

Svetlana Ugarcina Perovic (05:37:30) (in thread): > Let me try to download it for you

Aleru Divine (05:37:49) (in thread): > It was closed for me too:pleading_face:

Aleru Divine (05:38:55) (in thread): > Thank you@Svetlana Ugarcina PerovicYou’veshared the pdf before herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1712737342711339?thread_ts=1712735363.114669&cid=C04RATV9VCY - Attachment: Attachment > Here you go https://t.co/9dZUxlg8Nk

Mildred Anashie (05:39:36) (in thread): > No@Adeshile OluwatosinI’msuggesting you check NCBI to resolve some of them, like Clostridium senso stricto 1 and others

Kate Rasheed (05:39:55) (in thread): > I think it’s a typo from their end.@Adeshile Oluwatosin. You can curate separately and add a note.

Svetlana Ugarcina Perovic (05:40:43) (in thread): > Yes, and I shared the very same link for free epdf here again in the main post.

Svetlana Ugarcina Perovic (05:41:40) (in thread): > Yes that’s the link copy-paste above. And it’s not visible to you?

Svetlana Ugarcina Perovic (05:42:03) (in thread): > Strange…

Adeshile Oluwatosin (05:42:18) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina PerovicCould you please clarify unclassified actinobacteriais same as unidentified ActinobacteriaAs my research says otherwise, I could be wrong

Aleru Divine (05:42:38) (in thread): > The one in this post is closed access frompage 2It’sbeen blurred out. - File (PNG): IMG_1586

Svetlana Ugarcina Perovic (05:43:18) (in thread): > what is the difference between these two links?

Adeshile Oluwatosin (05:43:21) (in thread): > @Mildred Anashiethere’s no taxa ID for clostridium senso stricto 1

Svetlana Ugarcina Perovic (05:43:29) (in thread): > I copy paste it.

Kate Rasheed (05:43:48) (in thread): > @Adeshile Oluwatosinit has been corrected as Clostridium. > > You can check NCBI clean up page

Svetlana Ugarcina Perovic (05:43:48) (in thread): > How is possible one is open access to you and the other not?

Mildred Anashie (05:43:56) (in thread): > It’s been resolved on the Discussion page as Clostridium genus@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (05:44:15) (in thread): > Could you please copy paste here: the one that works for you. Thanks!

Aleru Divine (05:45:15) (in thread): > Check this thread@Adeshile Oluwatosinhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1711280497983449 - Attachment: Attachment > Hi everyone @Svetlana Ugarcina Perovic @C. Mirzayi (please do not tag this account) @Chioma Onyido @Peace Sandy @Esther Afuape > I found a study with a missing NCBI ID clostridium_sensu_scrito_1. After a detective search I found numerous journals refer to the taxa as the true clostridim genus, including the journal below > https://www.microbiologyresearch.org/content/journal/ijsem/10.1099/ijs.0.001792-0 > May I proceed to edit the taxa as Clostridim genus with an NCBI ID of 1485 > Link to the study: > https://bugsigdb.org/Study_518/Experiment_1/Signature_1

Aleru Divine (05:45:34) (in thread): > Alright

Aleru Divine (05:46:00) (in thread): > This is the linkhttps://www.nature.com/articles/s41564-023-01426-7.epdf?sharing_token=zQcEAK8DkvIZ39Q6snyXitRgN0jAjWel9jnR3ZoTv0MtUJKrqQX_wY1o8_YeHDleC3olDY1QGElUiiMuyrOCy-09py6AfYe5fhbnf7mawZf6dBpsRf9Mbti7HkP2JyQ-1lsMDs2aXl754ynqTyA-2rlHeQC5jTEtfEGnZPI8EiU%3D - Attachment (nature.com): Human microbiome myths and misconceptions > Nature Microbiology - Walker and Hoyles highlight selected myths and misconceptions in the human microbiota literature.

Svetlana Ugarcina Perovic (05:47:19) (in thread): > ok so maybe the catch is in “sharing_token”…

Adeshile Oluwatosin (05:49:13) (in thread): > Thanks for pointing that out guys.

Aleru Divine (05:49:59) (in thread): > Oh! Yeahit looks like it.

Samuel Nnanna (06:46:48) (in thread): > Thanksfor sharing@Svetlana Ugarcina Perovicand@Aleru Divine

Rahila-me (07:14:36) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Precious Orakwe (11:06:57): > hello, good evening to all of us here, trust we are all doing great? please i would appreciate a peer review on my study:https://bugsigdb.org/Study_1224Thank you - Attachment (BugSigDB): Insights into the gut microbiome of vitiligo patients from India - BugSigDB > BACKGROUND: Vitiligo is an autoimmune disease characterized by loss of pigmentation in the skin.It affects 0.4 to 2% of the global population, but the factors that trigger autoimmunity remain elusive.

Yoko C (11:07:18) (in thread): > thank you for clarifying that@Aleru Divine, glad that was cleared by the reviewer !

Kate Rasheed (11:22:49) (in thread): > Well-done on your curation@Precious Orakwe. I’ll look through.

Kate Rasheed (11:28:31) (in thread): > @Precious OrakweCaecibacter, Peptidiphaga, Reyranella has NCBI ID. You can use it to correct the error. > > Nanosynbacter is now called Candidatus Nanosynbacter

Aleru Divine (11:30:10) (in thread): > Well done on your curation@Precious OrakweI’ll have a look too.

Precious Orakwe (11:33:31) (in thread): > i saw that@Kate Rasheedjust wanted to be sure

Kate Rasheed (11:33:51) (in thread): > There was antibiotics exclusion too

Kate Rasheed (11:34:05) (in thread): > Individuals taking antibiotics were excluded@Precious Orakwe

Precious Orakwe (11:35:23) (in thread): > there was no specific date or duration for that, that’s why i didn’t curate it

Kate Rasheed (11:35:33) (in thread): > There’s another experiment based on health status in the supplementary table. > > I’m not sure it’s an experiment. I think it’s additional species you can add to the previous experiment. TableS7, Fig. S5.

Precious Orakwe (11:36:23) (in thread): > @Kate RasheedIndividuals receiving antibiotic or steroid treatment were excluded from this study

Kate Rasheed (11:39:23) (in thread): > You can state it that way: “Individuals receiving antibiotics were excluded from the study.”

Aleru Divine (11:39:37) (in thread): > I’dsuggest you simplify the group 0 name toHealthy Control @Precious Orakwe**** > ****Regarding antibiotics exclusion, you should just report that “individuals on antibiotics were excluded”Also I’d suggest you curate the genus only, for example Romboutsia_B and Clostridioides_A should be curated as Romboutsia and Clostridioides.It’s still correct since they’re all under the same genus and makes the curation clean.

Samuel Nnanna (11:43:35) (in thread): > @Precious Orakwethere are more signatures in sheet two of supplementary material 8 > > Add those as well

Samuel Nnanna (11:48:18) (in thread): > Signature 1 should be 2 and 2 should be 1. The signatures are reversed.@Precious Orakwe

Yoko C (11:52:52) (in thread): > I do agree with the others that you should add the antibiotics exclusion, the species on the supplementary material and put Prevotella as increased not decreased for Vitiligo. And that there are several genera you can find NCBI matches for.

Aleru Divine (13:08:25): > Good evening@Svetlana Ugarcina Perovic<@UBNSEMS3S>please can you help with the recording from yesterday’s office hours?:pleading_face:Thank you so much!

Mildred Anashie (13:47:14) (in thread): > Yea@Precious Orakwethere are a few things you left out and it has already been pointed out > > Well done guys:clap:

UBNSEMS3S (14:46:32) (in thread): > I’ll have it ready in an hour.

Aleru Divine (14:54:14) (in thread): > Alright, thank you so much:blush:

UBNSEMS3S (15:09:38): > Office hours recording. Thanks to everyone who attended and your always great questions! - File (MPEG 4 Video): bugsigdb20241114.mp4

Kavya Ayalasomayajula (15:15:11): > Hi all, question about p-value vs FDR. I am provided with both values in my studyfor each measured taxa. Should I use the p value or FDR to determine if each is significant?https://www.wjgnet.com/1007-9327/full/v23/i33/6164.htmI am using the supplementary table 5 (supplementary materials found in a pdf on the left hand side of website) > > Thank you very much! - Attachment (wjgnet.com): Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy > Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy

Kate Rasheed (15:15:53) (in thread): > Hello@Kavya Ayalasomayajula. You would use the FDR. Also curate values below the 0.05 threshold.

Kavya Ayalasomayajula (15:21:14) (in thread): > Okay, thank you!

Mildred Anashie (15:31:31) (in thread): > That’scorrect@Kavya AyalasomayajulaCurate using FDR (that’sthe adjusted P value)

Mildred Anashie (15:31:49) (in thread): > Thank you<@UBNSEMS3S>

Kavya Ayalasomayajula (15:57:00): > Hi all, another question about this studyhttps://www.wjgnet.com/1007-9327/full/v23/i33/6164.htmSupplementary table 5 found on the left hand side under supplementary materials. > How would I compare whether there is an increase or decrease in abundances between groups? Initially I was comparing means for taxa that had a statistically significant FDR value. However, some values are statistically significant but have the mean listed as 0 for compared groups (perhaps because the values were so small to begin with). Let me know if my question makes sense. The table is a bit confusing and formatted oddly. - Attachment (wjgnet.com): Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy > Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy

Mildred Anashie (16:01:05) (in thread): > Hi@Kavya AyalasomayajulaYour question does make sense butI’munsure ifI’llbe correct to say you curate as decrease or leave them outI’lllike to know what can be done in this case, well done on this curation:clap:

Mildred Anashie (16:20:23): > Hello everyone, > I just completed this curation and would appreciate a peer review > Thank you:blush:https://bugsigdb.org/Study_1222 - Attachment (BugSigDB): Tumor microbial diversity and compositional differences among women in Botswana with high-grade cervical dysplasia and cervical cancer - BugSigDB > INTRODUCTION: We characterized the cervical 16S rDNA microbiome of patients in Botswana with high-grade cervical dysplasia and locally advanced cervical cancer.METHODS: This prospective study included 31 patients: 21 with dysplasia and 10 with cancer.

Kate Rasheed (16:48:06) (in thread): > @Kavya AyalasomayajulaFrom what I can see, you would check the mean value of health vs p1. If the value of a taxon is higher in health, that would be decreased abundance. > > E.g. Cronobacter is increased in P1. > Bacteroides is decreased in P1 > Erysipelaclostridium is increased in P1. > Faecalibacterium is decreased in P1

Kate Rasheed (16:48:40) (in thread): > Weldone on this curation@Mildred Anashie. I’ll look through.

Yoko C (16:54:39) (in thread): > I think you were comparing it correctly, I think you shouldn’t worry about the mean being 0.

Kavya Ayalasomayajula (16:55:29) (in thread): > @Kate Rasheedthank you for the input. I noticed for Parvimonas both the health and P1 mean values are 0. The FDR is still significant but I am unsure how to tell whether it is an increase or decrease with both means as 0. I appreciate your response!

Kate Rasheed (16:57:52) (in thread): > @Mildred AnashieI saw in an article that:Betaproteobacteriales were reassigned to the class Betaproteobacteria. > **I guess that’s why when I tried searching for betaproteobacteriales, I got the result for betaproteobacteria. > > Here is the article:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2020.00154/full - Attachment (Frontiers): Frontiers | Ecological Differentiation in Two Major Freshwater Bacterial Taxa Along Environmental Gradients > Polynucleobacter (Burkholderiaceae, Betaproteobacteria) and Limnohabitans (Comamonadaceae, Betaproteobacteria) are abundant freshwater bacteria comprising la…

Kate Rasheed (21:50:52) (in thread): > I think the ones with 0 mean, you can use thestandard deviation(SD).I just looked through the table again and saw that most times, when there is 0 mean for the contrasting groups, the standard deviation has a higher value.@Kavya AyalasomayajulaHowever, there are some taxa like Solobacterium, oceanobacillus whose SD still remain 0, you can leave them out since they aren’t showing increase or decrease.

2024-11-16

Adeshile Oluwatosin (00:40:47) (in thread): > Thank you<@UBNSEMS3S>

Adeshile Oluwatosin (00:40:48) (in thread): > Thank you<@UBNSEMS3S>

Aleru Divine (01:15:28) (in thread): > Thank you so much<@UBNSEMS3S>

Aleru Divine (01:17:19) (in thread): > Well done on your curation@Mildred AnashieI’lltake a look

Adeshile Oluwatosin (01:24:09) (in thread): > Well done@Mildred Anashieseems good:white_check_mark:For the taxa betaproteobacteria(class)is not a synonym for betaproteobacteriales(order).

Adeshile Oluwatosin (01:29:57) (in thread): > Hello guys, i had a look on the study again > > Forexperiment 6 with metastats as the statistical testI’m surethe sample size remains the same. But they listed out 8 per group but I believethat’sfor the genes not bacteria. > > Kindly have a look

Adeshile Oluwatosin (01:30:42) (in thread): > @Mildred Anashie@Aleru Divine@Kate Rasheed

Adeshile Oluwatosin (01:30:48) (in thread): > Good morning

Aleru Divine (01:41:01) (in thread): > I’ll have a look right away@Adeshile Oluwatosin

Aleru Divine (01:51:54) (in thread): > For this experiment, it’s 8 per group@Adeshile Oluwatosin

Aleru Divine (02:00:18) (in thread): > @Mildred Anashiethe LDA score for experiment 2 is 2.0 > Check figure 1 description.

Adeshile Oluwatosin (03:18:04) (in thread): > Okay, thanks

Mildred Anashie (04:25:05) (in thread): > @Kate RasheedI saw it butI wasn’tsure if I should curate as Betaproteobacteriathat’swhy I left it that way because the taxa belong to a different taxonomic rank

Mildred Anashie (04:25:45) (in thread): > Thank you@Aleru Divine@Kate Rasheed@Adeshile Oluwatosin:heart_hands:l will edit the LDA

Kate Rasheed (05:03:36) (in thread): > @Adeshile OluwatosinBased on what Chloe mentioned during office hours on Thursday, I think instead of doing only a LEfSe-one against all analysis, you should also do a pairwise comparison alone since the alpha diversity is showing pairwise comparison. > > Just as we have in experiment 6 and 7.

Kate Rasheed (05:07:11) (in thread): > @Adeshile OluwatosinSee what the caption says: > > “LEfSe counted species with LDA scores greater than 4between groupsand screened for statistically significant differences in biomarkers.” > > What do you think@Aleru Divine@Mildred Anashie?

Mildred Anashie (05:12:51) (in thread): > Hi@Kate RasheedI’mnot surethat’sin this paper:thinking_face:Or am I wrong?

Kate Rasheed (05:14:56) (in thread): > Okkkk. I was thinking because it’s stated that the LEfSe analysis wasbetween groupsthen, it should be a pairwise comparison like the alpha diversity@Aleru Divine

Mildred Anashie (05:22:15) (in thread): > I think the comparison is between two groups andit’sPairwise > > These are the groups M-CON and M-PEDV piglets@Kate Rasheed

Kate Rasheed (05:28:17) (in thread): > There’s L-CON and L-PEDV too. See Fig. 2G. > > I get what Chloe talked about in the last meeting now. The one-against-all experiments is okay but I think she should also add pairwise comparison to the LEfSe analysis.@Mildred Anashie

Mildred Anashie (05:35:02) (in thread): > Okay you are talking about a different figure

Aleru Divine (05:42:13) (in thread): > Figure 2g is actually a one-to-all figure.@Kate Rasheedwhere’s the pairwise comparison coming from? Cos the alpha diversity can be left out in this case. If we do a pairwise comparison, there’s going to be a lot of repeated signatures. The between groups keyword doesn’t really matterbecause M-CON vs the rest of the group is still “between groups” they were all compared to all the others.

Kate Rasheed (05:43:57) (in thread): > Okay. I understand now. It’s fine. Thanks for clarifying@Aleru Divine.

Aleru Divine (05:44:37) (in thread): > Alright@Kate Rasheed

Adeshile Oluwatosin (06:46:34) (in thread): > Thanks guysI’mlate to the discussion, lol

Yoko C (10:50:00) (in thread): > Oh, I see what you mean now. I don’t know if you can use the standard deviation, since sd is both over and under the mean. But as Kate said, maybe leave out the one’s where both means are zero.

Yoko C (11:28:10) (in thread): > Hello, I think Kate might have a point, andherethey give a an update for the database in 2019:Betaproteobacteriales(formerly known asBetaproteobacteria) is nowBurkholderiales, an order ofGammaproteobacteria. So maybe the order is now Burholderiales.

Mildred Anashie (11:59:24) (in thread): > Thank you@Yoko C@Kate RasheedI’ll leave a review note on the signature

Tino (12:01:11) (in thread): > Thank you

Kate Rasheed (14:00:54): > Good evening people. Happy weekend to us all.@PATIENCE ONAHand I would appreciate a peer review on this study:https://bugsigdb.org/Study_1187The major point of doubt is in the confounder “******family structure******”. It was stated that family structure was a******random effect not fixed effect******. Would it be okay to add it as a confounder like in experiment 1 - 5? For the other experiments, it wasn’t added as a confounder. > > Thank you so much. - Attachment (BugSigDB): Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome - BugSigDB > BACKGROUND: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes.

Kavya Ayalasomayajula (14:53:15): > Hi all, apologies if this has been answered before. I added some new signatures to an experiment and they do not show up on the original study page. They show up in my history and contributions but not on the overall page. Is there a reason for this/way around it? Thank you for your time.

Mildred Anashie (14:55:23) (in thread): > Hi@Kavya Ayalasomayajulatry refreshing > > See how tohere - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Mildred Anashie (14:56:01) (in thread): > Hi@Kate RasheedI’ll check this out > Well done:clap:

Aleru Divine (14:56:02) (in thread): > Hi@Kavya Ayalasomayajula.This is a general issue.I usually mark my study as incomplete/complete a few times and it all comes up.I refresh the page too (thisdoesn’twork all the time)

Kavya Ayalasomayajula (14:59:40) (in thread): > Thank you both

Kate Rasheed (15:49:27) (in thread): > @Kavya AyalasomayajulaI make edits on the experiment by either adding a full-stop to group 1 definition or removing a full stop. > > Sometimes I omit filling the group sample size at the initial entry and come back to add the sample size after entering my signatures. > > This works a lot.

Kate Rasheed (15:49:45) (in thread): > Thank you@Mildred Anashie

Chinwendu Joy Enyidiegwu (15:52:21): > hello everyone , pls i need peer review for this study.:pray:i curated 3 experiments for this study: One for microbiome analysis, molecular marker correlation, for the longitudinal networkhttps://bugsigdb.org/Study_1219https://www.nature.com/articles/srep04985#Sec2there are 2 signatures, dont know if its visible yet. pls use these navigation:https://bugsigdb.org/Study_1219/Experiment_2/Signature_1https://bugsigdb.org/Study_1219/Experiment_1/Signature_1thanks. i would appreciate your feedback. - Attachment (BugSigDB): Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer - BugSigDB > The role of bacterial colonization in the gut has been implicated in the progression of colitis-associated colorectal cancer (CAC); however, the dynamic shifts within the gut microbiota during colorectal carcinogenesis remain poorly understood. - Attachment (Nature): Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer > Scientific Reports - Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer - Attachment (BugSigDB): Study 1219/Experiment 2/Signature 1 > Source: Figure 1B, 1C Description: Increased levels of inflammation- and cancer-associated markers: p65, p53, COX-2, PPARγ, CCR2, β-catenin Abundance in Group 1… - Attachment (BugSigDB): Study 1219/Experiment 1/Signature 1 > Source: Figure 4B, Table S2 Description: Enrichment of Streptococcus luteciae, Lactobacillus hamster, Bacteroides uniformis, Bacteroides ovatus in Group 1 Abundance…

Kate Rasheed (15:54:54) (in thread): > @Chinwendu Joy EnyidiegwuWelldone on your curation. > > From what I can see experiment 2 is not curatable. It’s not showing differential abundance of taxa. It’s rather showing markers. > > I’ll look through the main article to see what should be curated. > > Well-done.

Kate Rasheed (16:01:47) (in thread): > I just looked through the paper. We have more than three experiments to curate and the signatures are in: > > Table S4: Control vs AOM/DSS treatment cycle 1, AOM/DSS treatment cycle 2, AOM/DSS treatment cycle 3, AOM/DSS treatment cycle 4. > Table S3: Mice with inflammation vs Mice with cancer > Table S2(Related to Fig.4b, you can curate from the table instead) Control mice vs Mice with AOM/DSS. > > For your experiment 1, the statistical test isFisher Exact testalone. Add more taxa to your experiment 1 signatures. > > Table S4 useslinear regression

Yoko C (18:42:12) (in thread): > Hello in figure 1 and 2 they state family structure was used as a random effect, so I think experiments 3-5 and 6-13 would be mixed effects regression. About using it as a confounder, I’m really not sure, but because they mention family structure as being corrected for, I think you can put it as a confounder. I also think experiments 8 and 9 might have an extra taxa? I could be wrong about that since there are many comparisons.

Kate Rasheed (19:35:40) (in thread): > Thank you@Yoko C. I’ll look at experiment 8 and 9 again. For experiment 3-13, it was stated under the caption that linear regression was used for the analysis or does that translate to mixed effects regression?:thinking_face:

Kate Rasheed (19:54:54) (in thread): > Thanks for pointing it out@Yoko C. I’ve seen it. I’ll request for signature 1 in experiment 9 to be deleted. It was actually a mistake:smile:.

Kate Rasheed (20:12:16) (in thread): > @Yoko CI’m clear now with the confounders. From the supplementary table information, experiment 1 and 2 actually used family structure as the confounder. > > For the other experiments, family structure was omitted from the confounders. > > I agree that the statistical test for other experiments should be mixed-effects cause it was stated that “******P values were obtained from linear regression including family structure as random effect and age, BMI, HEI and sex as fixed effects******.”

Kavya Ayalasomayajula (21:12:02): > Thanks everyone for help with my past few questions. I have finished curating my article and welcome feedback/review. I used data for both pairwise and one against the rest analysis in my experiments.https://bugsigdb.org/Study_1145Thanks! - Attachment (BugSigDB): Ketogenic diet poses a significant effect on imbalanced gut microbiota in infants with refractory epilepsy - BugSigDB > AIM: To investigate whether patients with refractory epilepsy and healthy infants differ in gut microbiota (GM), and how ketogenic diet (KD) alters GM.METHODS: A total of 14 epileptic and 30 healthy infants were recruited and seizure frequencies were recorded.

2024-11-17

Adeshile Oluwatosin (01:00:11) (in thread): > Hi@Chinwendu Joy EnyidiegwuYou’ve donewellI’llgo through the paper

Adeshile Oluwatosin (01:08:19) (in thread): > We curate only differential abundance of taxa or relative abundance between two groups and in your curations either follow this. > > Table S2: Differential OTUs between control (Group 0) and DSS treated groups(Group 1). Curatable as we can see P values. > > Table S3: Differential OTUs between mice with inflammation (Group 0) vs Mice with cancer (Group 1). There are P values and taxa here. > > Table S4: Differential OTUs after treatment of different AOM/DSS styles. There are 4 experiments here. Could be one against all analysis. AOM/DSS cycle 1-4. > > No comparison in Table S6/S7.

Adeshile Oluwatosin (01:17:39) (in thread): > So in short@Chinwendu Joy EnyidiegwuExperiment 2/signature 1 should not be curated. > > Table S2 and Fig 4B are interrelated. > So if it’s overlapping we curate one with more taxa.

Adeshile Oluwatosin (01:21:08) (in thread): > Well done on your curation,I’lllook through it

Adeshile Oluwatosin (01:57:58) (in thread): > The sample size for epileptic patients were 14. They didn’t explicitly mention it’s 14 for P1 and P2.

Adeshile Oluwatosin (01:59:14) (in thread): > I alsocouldn’taccess the supplementary information maybe there are other details@Kavya Ayalasomayajula

Cynthia Iwuoha (02:29:04) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Joy (02:31:03) (in thread): > This is really helpful. Thanks, everyone!:pray:

Kavya Ayalasomayajula (03:01:36) (in thread): > @Adeshile OluwatosinTry this link from the original study website and navigate to the left hand side, there should be a tab for supplementary materials that will lead to a pdfhttps://www.wjgnet.com/1007-9327/full/v23/i33/6164.htmI assumed P1 and P2 were the same group of 14 followed over time, but if not explicitly stated I am unsure of what else to put for sample size, thoughts? > > Thank you very much!

Adeshile Oluwatosin (03:25:24) (in thread): > Okay, I would go through it

Adeshile Oluwatosin (04:39:28) (in thread): > I’mnot quite sure if it should be left clear or if it should be recorded as 14.

Adeshile Oluwatosin (04:39:53) (in thread): > Also matched on is just for case control studies

Adeshile Oluwatosin (04:40:03) (in thread): > @Kavya Ayalasomayajula

Adeshile Oluwatosin (04:41:50) (in thread): > I also can’t find where antibioticsexposurewas mentioned as a confounder

Adeshile Oluwatosin (04:46:39) (in thread): > I just checked supplementary Table2, there are no p values for alpha diversity so it seems insignificant. Don’t curate it.@Kavya Ayalasomayajula

Adeshile Oluwatosin (04:53:39) (in thread): > You didn’t curate experiment between P1 and P2 from supplementary Table 5.It’s curatable, you should curate it.You are right not to curate STable4. > > Well done once again@Kavya Ayalasomayajula

Chinwendu Joy Enyidiegwu (14:22:50) (in thread): > Thank you@Adeshile Oluwatosin@Kate Rasheed

Kavya Ayalasomayajula (14:28:11) (in thread): > @Adeshile Oluwatosinthanks for this awesome feedback. I suppose I included antibiotic exposure as a confounder because it was mentioned in the exclusion criteria for groups. NowI’mwondering if I should just take it out. I did not curate between P1 and P2 because it didn’t appear that there were any significant FDR values. Thanks again

Adeshile Oluwatosin (14:31:02) (in thread): > P values were mentioned regardless for P1 vs P2 soit’sstill significant in my opinion@Kavya Ayalasomayajula

Adeshile Oluwatosin (14:31:26) (in thread): > Take out antibiotic exposure,I don’tsee it as a confounder

vandana maddi (14:52:46): > hello everyone , pls i need peer review for this study.:pray:Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin womenhttps://www.nature.com/articles/s41598-018-35230-9https://bugsigdb.org/Study_1191thanks. i would appreciate your feedback. - Attachment (Nature): Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women > Scientific Reports - Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women - Attachment (BugSigDB): Decreased microbial co-occurrence network stability and SCFA receptor level correlates with obesity in African-origin women - BugSigDB > .

Kate Rasheed (15:23:35) (in thread): > Welldone on your curation@vandana maddi. I’ll look through.

Kate Rasheed (15:29:48) (in thread): > @vandana maddiI see that you didn’t record alpha diversity for experiment 1. Chao1, Shannon and Inverse Simpson should be recorded as unchanged. > > Look at this excerpt: “However, no significant difference in alpha and beta diversity existed between lean and obese women independent of the country (Figs S2, S3, Tables S6, S7).” > > For the data transformation, it should be centered log ratio since they made use of log-fold change. > > I also see that you didn’t curate Fig. 5c which is an experiment done after the fecal transplant on mice.

Yoko C (16:07:17) (in thread): > Hello, I agree with Oluwatosin that antibiotics aren’t a confounder. I think for experiments 1 and 2 you could fill in Shannon diversity, since the difference isn’t significant you would mark it as unchanged. I also went through experiment 1’s signatures, and some taxa I’m not sure should be included, for example Blautia, Bacteroides, Hungatella. I didn’t check the other signatures, but those are some things I noticed.

Aleru Divine (16:52:56) (in thread): > Thank you so much for this observation@Kate RasheedWe needed confirmation on whether figure 5 should be curated. Thanks! > > Log-fold change does not mean the data transformation was CLR, unless it is stated in the study that an additional data transformation was added. In this case it isn’t.

Yoko C (17:42:01) (in thread): > Hello, some observations that I have are that for the source of experiment 1 maybe you should add a text reference since the graph doesn’t show all that information. I also seeBacteroides unifromis, B. caccae and Faecalibacterium prausnitziias increased? From the text I think they might have used wilcoxon, but I am definitively not sure about this since they don’t really specify anything, or do they? I agree with centered log not being the transformation used. In the text they specify that they only corrected for age when comparing location and obesity differences. I also checked table S4 and I think it is curatable. Throughout the study they mention other supplementary tables that seem potentially curatable as well but I didn’t check those. This was another one of the confusing ones.

Kavya Ayalasomayajula (17:57:00) (in thread): > Thank you@Yoko Cwhy do you feel those specific taxa should not be included? Thanks again

Yoko C (18:32:36) (in thread): > Hi and welcome! I see the FDR is 0.09 (blautia and bacteroides) and 0.06 (hungarella) which are above 0.05

Yoko C (18:33:51) (in thread): > I could be wrong about this, because I copied the table into a google sheet and maybe it wasn’t properly copied.

Mildred Anashie (18:48:48) (in thread): > Hello@vandana maddi@Aleru DivineWell done on your curation. I’m of the opinion that 5c is not curatable because it seems to be showing Co-occurrence network analysis done using ESVs (Exact Sequence Variants) and on murine samples (animal model) and human samples. > > Although I am open to other opinions and if it is established that the figure is curatable then the data transformation for those experiments would be “raw counts” as the paper says they employed DADA2 sequencing and DADA2 uses Raw counts.@Yoko CThis is actually confusing, also the supplementary tables being cited in the paper appear to be XML files and I’ve not been able to convert to readable format. I wonder if@Aleru Divineand@vandana maddihave the files

Yoko C (19:00:11) (in thread): > @Mildred Anashieyou can open it as a regular excel sheet, I use libreoffice Calc and opened it from there with no issues, excel probably opens it too.

Mildred Anashie (19:05:22) (in thread): > Exceldidn’tfrom my end > > I’ll possibly try again in a few hours@Yoko C

Yoko C (19:21:05) (in thread): > that’s supp table 4 - File (Excel Spreadsheet): SREP-18-15117-s05.xlsx

Aleru Divine (21:36:04) (in thread): > Thank you all so much for the review.@Yoko CBacteroides uniformiswas significantly more abundant in lean women, irrespective of country. The figure does say it was decreased for Lean Ghanaians. I think the text was on a more general note.Bacteroides caccaeand strains ofFaecalibacterium prausnitziiwere more abundant in US stool. This is curated rightly I believe as it falls under the decreased signatures for Lean Ghanaians. > > This is a one-vs-all comparison. > > I think Wilcoxon was used to calculate network featureshere. Not determine differential abundance. > > For the confounders controlled for,:face_with_open_eyes_and_hand_over_mouth:Idon’tknow how Iskip-read it because it’s quite obvious. Thank you so much for pointing it out. > > Thank you for pointing out the data transformation@Mildred AnashieThank you for sharing this table@Yoko Cwhen I viewed it, it did not make any sense at all. Yes they’re XML files@Mildred Anashie:cry:I get raw data when I open them.About 5C I was on the fence on this one, but I think it shows differential abundance results from murine samples.

Aleru Divine (21:39:22) (in thread): > On second thoughts@Kate RasheedI don’t think I should record alpha diversity for experiment 1, since this is a one-vs-all experiment.I thinkthat’swhy I left it.

Aleru Divine (22:10:25) (in thread): > Thanks again for this sheet@Yoko Cthere are some comparisons made and they are to be curated(althoughIdon’t understand the 7th comparison in the table).As for the murine samples. I’m confused because they say there were no significant differences in bacterial phyla between the 4 murine samples > > “Interestingly,there were no significant differences in the abundance of bacterial phyla between the 4 murine cohorts (p > 0.01; Table S14, Fig. 5a).” > > Then figure 5C, which I kind of believed was curatable goes > “Phylogenetic tree of sequences identified using DADA2 significant in human (open dots) and mice (closed dots) for the comparison of interest (GO, UO, UL versus GL).” > > I’m confused. The first instance I’m sure means no significant signatures. > > Please help@Yoko C@Mildred Anashie@Kate RasheedI’m so sorry:pray:

Yoko C (22:25:34) (in thread): > @Aleru Divine, you are right! I didn’t look properly at the 3f graph, sorry about that. For the 5C section, I think what they mean is that for mice, there were no differences at the phylum rank, but there are differences between human phyla and mice phyla. To better understand, it seems that table s16 has more information. And I don’t think DADA2 is a differential abundance test, I think it’s what is used to identify the ESVs.

Yoko C (22:28:55) (in thread): - File (Excel Spreadsheet): SREP-18-15117-s17.xlsx

Aleru Divine (22:32:03) (in thread): > The differential abundance test used was generalized linearmodels that’sright@Yoko Cshedidn’texactly mean differential abundance test.Data transformation for linear models are often raw counts too and considering DADA was used to identify sequences, raw counts would be the data transformation.This is how I understand this.I could be wrong.

Aleru Divine (22:35:49) (in thread): > Thank you for this table@Yoko C:face_holding_back_tears::pray::pray:One final question. > Do you have an idea what this comparison is? > “(USA1 + USA0 + Ghana1)/3 - Ghana0”I’dlike to confirm if it means > (USA1 + USA0 + Ghana1) vsGhana0:grimacing:

Aleru Divine (22:36:52) (in thread): > So figure 5C is curatable then?@Yoko C

Yoko C (22:40:22) (in thread): > “(USA1 + USA0 + Ghana1)/3 - Ghana0”, I think is (USA1 + USA0 + Ghana1) vs Ghana0. About 5C, I’m not too sure, I think it would have the same info as the table s16.

Aleru Divine (22:42:11) (in thread): > Okay.Got it! > Thank you so much!

Yoko C (22:43:56) (in thread): > Welcome! if you need any other tables converted let me know.

Aleru Divine (22:50:02) (in thread): > Can you help with S11 and S15 please.:pray:Thank you so much!

Yoko C (23:00:25) (in thread): - File (Excel Spreadsheet): SREP-18-15117-s12.xlsx

Yoko C (23:00:50) (in thread): - File (Excel Spreadsheet): SREP-18-15117-s16.xlsx

Aleru Divine (23:06:43) (in thread): > Thank you so much,@Yoko CI really appreciatethis:hugging_face::heart_hands:

2024-11-18

Kavya Ayalasomayajula (00:10:22) (in thread): > Good eye! I will take them out

Kavya Ayalasomayajula (00:24:44) (in thread): > @Yoko Cnoticed that I did the same thing for experiment two so I edited this

Mildred Anashie (02:11:15) (in thread): > Well done for this@Yoko C:clap:@Aleru DivineI’mstill of the opinion 5c be left out, if the supplemental has more information you might want to focus on those instead

Aleru Divine (04:05:46) (in thread): > Yesthat’swhat I’ll do@Mildred AnashieThank you so much!

Kate Rasheed (04:49:10): > Good morning@Svetlana Ugarcina Perovic. Happy new week. > > Kindly delete Signature 1 in experiment 9 of this study, it was a mistake.https://bugsigdb.org/Study_1187Thank you. - Attachment (BugSigDB): Yoghurt consumption is associated with changes in the composition of the human gut microbiome and metabolome - BugSigDB > BACKGROUND: Yoghurt contains live bacteria that could contribute via modulation of the gut microbiota to its reported beneficial effects such as reduced body weight gain and lower incidence of type 2 diabetes.

Svetlana Ugarcina Perovic (04:50:42) (in thread): > Deleted.

Svetlana Ugarcina Perovic (04:58:28): > <!channel>please feel in our survey and help us to improve outreachy contribution experience. Thank you - Attachment: Attachment > SURVEY > > THANK YOU ALL for YOUR amazing contribution, keep up the good work! > > We would appreciate if you can share your experience with us by filling in this short survey https://forms.gle/brqH5M2uTYMKy23x7 > and help us improve experience for future contributors. > > Thank you, > @U1LCB8WEA @UBNSEMS3S @Chioma Onyido @Peace Sandy @Esther Afuape @Svetlana Ugarcina Perovic > > P.S. if you already filled in this survey in some previous rounds, please provide your feedback again, maybe something changed.

Kate Rasheed (04:59:32) (in thread): > Thank you.

Adeshile Oluwatosin (05:00:28) (in thread): > Done ma’am@Svetlana Ugarcina Perovic:hugging_face:

Chinwendu Joy Enyidiegwu (05:12:12): > hello@Svetlana Ugarcina Perovickindly deletehttps://bugsigdb.org/Study_1219/Experiment_2/Signature_1thank you - Attachment (BugSigDB): Study 1219/Experiment 2/Signature 1 > Source: Figure 1B, 1C Description: Increased levels of inflammation- and cancer-associated markers: p65, p53, COX-2, PPARγ, CCR2, β-catenin Abundance in Group 1…

Svetlana Ugarcina Perovic (05:13:14) (in thread): > deleted.

Rahila-me (05:30:21) (in thread): > Done already..last week

Chinwendu Joy Enyidiegwu (06:01:59): > hello everyone, hope we had a great weekend. > pleasei need peer review for this study.:pray:https://bugsigdb.org/Study_1219https://www.nature.com/articles/srep04985#Sec2experiment 3 has 3 signatures, here is the link to the last signature, if you are unable to view it yet:https://bugsigdb.org/Study_1219/Experiment_1/Signature_1 - Attachment (BugSigDB): Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer - BugSigDB > The role of bacterial colonization in the gut has been implicated in the progression of colitis-associated colorectal cancer (CAC); however, the dynamic shifts within the gut microbiota during colorectal carcinogenesis remain poorly understood. - Attachment (Nature): Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer > Scientific Reports - Dynamic microbe and molecule networks in a mouse model of colitis-associated colorectal cancer - Attachment (BugSigDB): Study 1219/Experiment 1/Signature 1 > Source: Table S2, related to Fig. 4B Description: Differential OTUs between control and AOM/DSS-treated mice Abundance in Group 1: increased abundance in AOM/DSS…

Aleru Divine (06:04:44) (in thread): > Hi@Chinwendu Joy EnyidiegwuWell done on your curation.I’llhave a look at it

Aleru Divine (06:08:51) (in thread): > Hi everyone, sorry to be here again. > About table S16, I don’t think this is differential abundance results instead it is coabundance > “Table S16. Human-murine co-abundance: Ghana0: Ghana lean, Ghana1: Ghana obese, USA0=USA lean, and USA1=USA obese” > > I agree with you on this now@Mildred AnashieI think this just looked at similarity between human and murine samples. Like the overlap. > > I don’tthink we shouldgo ahead with the curation of S16? > > S4 and S15 on the other hand I believe show differential abundance results for human and murine samples respectively. > > Thank you for checking this again:pray:

Adeshile Oluwatosin (06:26:21) (in thread): > Well done@Chinwendu Joy EnyidiegwuI will look through

Adeshile Oluwatosin (06:40:59) (in thread): > Condition: colorectal cancer is permissible. > You also didn’t curate decreased abundances. > The increased abundances curated across all experiments don’t seem to be complete as well. > You curated Experiment 3to have2 signatures,both with increased abundances, kindly see to it > Also elaborate your descriptions too. > Table S2, FDR is 0.05.@Chinwendu Joy Enyidiegwu

Mildred Anashie (07:10:03) (in thread): > Hi@Chinwendu Joy EnyidiegwuWell doneI’lltake a look at this

Aleru Divine (07:12:47) (in thread): > @Chinwendu Joy Enyidiegwufor the condition, useColorectal cancer. The other ones aren’t necessary. > > There are some other significant signatures you didn’t included in your curation from Table S2, S3 and S4. > > All alpha diversity measure for experiment 2 are unchanged because there aren’t any significant results from Figure S4. Only significant results I see are between control and inflammation. > > Also check alpha diversity for experiment 1. > > In addition to this, for experiment 3, I believe each cycle should have a different experiment as there are increased and decreased signatures for each cycle vs control looking at the log fold change direction. A total of 4 experiments will be curated from table S4. > > Control vs AOM/DSS cycle 1 > Control vs AOM/DSS cycle 2 > Control vs AOM/DSS cycle 3 > Control vs AOM/DSS cycle 4 > > So there’s a total of 6 experiments in this study.

Aleru Divine (07:22:47) (in thread): > Thumbs up = agree?@Mildred Anashie:face_holding_back_tears:

Mildred Anashie (10:16:51) (in thread): > With S16 not to be curated?@Aleru Divine

Aleru Divine (10:21:59) (in thread): > Yeah:grimacing:I’masking

Mildred Anashie (10:32:55) (in thread): > Yes Thumbs up =agree:blush:

Adeshile Oluwatosin (11:30:37): > Hello everyone > > I and@Aleru Divineare working on this curation. > Kindly help look into Figure S6. i personally don’t think it should be curated. > > I would also appreciate a general reviewhttps://bugsigdb.org/Study_1221https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01820-1 - Attachment (BugSigDB): Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments - BugSigDB > BACKGROUND: Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. - Attachment (BioMed Central): Overcoming donor variability and risks associated with fecal microbiota transplants through bacteriophage-mediated treatments - Microbiome > Background Fecal microbiota transplantation (FMT) and fecal virome transplantation (FVT, sterile filtrated donor feces) have been effective in treating recurrent Clostridioides difficile infections, possibly through bacteriophage-mediated modulation of the gut microbiome. However, challenges like donor variability, costly screening, coupled with concerns over pathogen transfer (incl. eukaryotic viruses) with FMT or FVT hinder their wider clinical application in treating less acute diseases. Methods To overcome these challenges, we developed methods to broaden FVT’s clinical application while maintaining efficacy and increasing safety. Specifically, we employed the following approaches: (1) chemostat-fermentation to reproduce the bacteriophage FVT donor component and remove eukaryotic viruses (FVT-ChP), (2) solvent-detergent treatment to inactivate enveloped viruses (FVT-SDT), and (3) pyronin-Y treatment to inhibit RNA virus replication (FVT-PyT). We assessed the efficacy of these processed FVTs in a C. difficile infection mouse model and compared them with untreated FVT (FVT-UnT), FMT, and saline. Results FVT-SDT, FVT-UnT, and FVT-ChP reduced the incidence of mice reaching the humane endpoint (0/8, 2/7, and 3/8, respectively) compared to FMT, FVT-PyT, and saline (5/8, 7/8, and 5/7, respectively) and significantly reduced the load of colonizing C. difficile cells and associated toxin A/B levels. There was a potential elimination of C. difficile colonization, with seven out of eight mice treated with FVT-SDT testing negative with qPCR. In contrast, all other treatments exhibited the continued presence of C. difficile. Moreover, the results were supported by changes in the gut microbiome profiles, cecal cytokine levels, and histopathological findings. Assessment of viral engraftment following FMT/FVT treatment and host-phage correlations analysis suggested that transfer of phages likely were an important contributing factor associated with treatment efficacy. Conclusions This proof-of-concept study shows that specific modifications of FVT hold promise in addressing challenges related to donor variability and infection risks. Two strategies lead to treatments significantly limiting C. difficile colonization in mice, with solvent/detergent treatment and chemostat propagation of donor phages emerging as promising approaches. Video Abstract

Aleru Divine (11:55:47) (in thread): > Although baseline and before CDI were not significant according to this excerpt“To do so, we verified that there were no initial differences (p > 0.3) in the bacterial and viral gut microbiome profiles at both baseline (before antibiotics) and before C. difficile infection (after antibiotic treatment) between the mice that were later either euthanized or survived the C. difficile infection (Fig. 5 & Fig. S6).”We’d like to confirm if the figures should be curated becausethere’san additional comparison survived vs euthanized-(terminated)

Yoko C (12:05:28) (in thread): > Hello, I can’t see s6 because my internet is too slow, but from the description I don’t think it’s curatable. I don’t think fig. 5 is curatable either, as there isn’t any significance information that I can see. The text also talks about trends in changes rather than significant changes.

Adeshile Oluwatosin (12:15:37) (in thread): > Thank you@Yoko C

Aleru Divine (12:21:50) (in thread): > Thank you for having a look@Yoko CLet me add that S6 is made of 3 comparisons at the following time points. > * Baseline (before antibiotic treatment), > * Before C. difficile infection (after antibiotic treatment), and > * Termination of mice that either survived until termination or were euthanized regardless of the treatment. > In the paper there were no initial differences (p > 0.3) in the bacterial and viral gut microbiome profiles atboth baseline (before antibiotics) and before C. difficile infection**** ****not at**** termination(****the third time point****)****

Yoko C (12:25:02) (in thread): > What about figure 2, for viruses, would that be curatable?

Aleru Divine (12:27:29) (in thread): > No, figure 2 doesn’t refer todifferentially abundantviral signatures

Yoko C (12:30:10) (in thread): > @Aleru Divine, I thought it did because it has the phage names and the relative abundance. But it really isn’t clear if it is differential abundance to me.

Aleru Divine (12:37:45) (in thread): > Do you mean figure 2? I don’tthose are curatable. > My concern is S6:pleading_face:Could you go through this section of the paper please.:pray:Sub-title: Fecal virome treated with solvent/detergent supports recovery of the bacterial community in a dysbiotic gut microbiome > > This is where refered to S6 (the heatmaps)

Yoko C (12:43:28) (in thread): > Because of this “The latter posed the inherent comparability challenge by the time difference between the euthanized mice and the mice that survived the infection…” and this “however, the mice that survived the infection tended to be more similar to baseline, compared with the time beforeC. difficileinfection and the euthanized mice.” I don’t think those figures have significant information.

Yoko C (12:44:44) (in thread): > If S6 is similar to figure 5 than the graphs don’t seem to have information on what changes were significant.

Yoko C (12:47:40) (in thread): > phages are viruses

Aleru Divine (12:48:36) (in thread): > Figure S5 and S6 are not similar > > Even figure 5 and S6 aren’texactlysimilar either. > S6 is a lot more specific > > Here; - File (JPEG): IMG_1648

Yoko C (12:50:40) (in thread): > But do they have anything that points to significant changes? I don’t see that (but I do need glasses). In any case, I would say not curatable.

Aleru Divine (12:55:05) (in thread): > @Yoko CThe paper says baseline and beforeCDI had no differences because of a higher p-value.Wouldn’tthat mean the termination(after CDI) time point is significant? Since theydidn’tadd it to the sentence.“Although baseline and before CDI were not significant according to this excerpt“To do so, we verified that there were no initial differences (p > 0.3) in the bacterial and viral gut microbiome profiles at both baseline (before antibiotics) and before C. difficile infection (after antibiotic treatment) between the mice that were later either euthanized or survived the C. difficile infection (Fig. 5 & Fig. S6).”

Aleru Divine (12:55:50) (in thread): > This is what I was considering.

Yoko C (13:00:07) (in thread): > I understand that for the experiment to work, they wanted the difference between baseline and before infection to not be significant. After infection there could be different outcomes depending on the treatment. I think they couldn’t really do like a valid statistical test between the three points because the mice didn’t survive. that’s what I understand, but as always I could be wrong. Hopefully somebody else can also check and give us a more clear opinion.

Aleru Divine (13:10:47) (in thread): > Thank you@Yoko CI was thinking,aren’ttheyspearman’scorrelation heatmaps? > The study does mention.Idon’twant to go through with the curation unsure or leave it out unsure. IDK!

Adeshile Oluwatosin (13:12:09) (in thread): > I still stand on it not to be curated@Aleru Divine

Aleru Divine (13:16:02) (in thread): > @Adeshile OluwatosinI thought I had a fair reason for it to be curatedbutI’mstill on the fence. Can you explain again why it shouldn’tbe curatedplease. Maybe it’d help look at this differently. And also help anyone giving a peer review.

Mildred Anashie (13:33:06) (in thread): > Hi guys > > Late to the party, butI’llgive this a this a look

Aleru Divine (13:56:01) (in thread): > Thank you@Mildred Anashie

Kate Rasheed (14:46:08) (in thread): > A learn-full thread. Welldone people. > > Phages are viruses:thinking_face:.

Aleru Divine (14:52:36) (in thread): > In the case of figure 2. I don’t thinkthey’recuratable@Kate Rasheed

Mildred Anashie (14:57:18) (in thread): > Yup@Kate RasheedBacteriophages (Phages) are viruses

Mildred Anashie (15:38:00) (in thread): > Hi guys….I would like to know why S6 isn’t curatable:thinking_face:…..There seems to be clear contrasts in S6C and S6f (unsure of this F because its reporting viral). My only concern is the paper, doesn’t say much about the figure and Its not clear what the statistical test is, it looks like correlation like Divine pointed out

Aleru Divine (15:44:40) (in thread): > Chloe confirmed we can curate viral taxa in the last office hours session@Mildred Anashie

Yoko C (16:10:30) (in thread): > From what I see s6 reports percentages of abundance not correlations. The paper mentioned spearman for a correlation between virus and bacterial loads.

Aleru Divine (16:50:59) (in thread): > True@Yoko Cbut looking at the figures,there’sa similarity.I thinkwe’llleave curating this for now until we get an answer from the mentors.Thank you so much@Yoko C@Mildred Anashiefor the feedback.

Yoko C (21:15:14): > Hello, I’d appreciate a peer review forhttps://bugsigdb.org/Study_1226. > It’s a pretty straightforward study, I think. > Things I’m doubting on are: the body site, I recorded the site where the gut content was taken from, but I’m doubting if “material entity in digestive tract” is a better choice. The reason I chose the body site is because they mentioned those specific parts are important for salmon. > Group names and group descriptions? I feel like they could be improved? Maybe not, not sure. And another thing is confounders, they aren’t mentioned directly but the studies are stratified by development stage and body site, so not sure if I should record those as confounders. > Thanks!

Aleru Divine (21:22:09) (in thread): > Well done@Yoko C:clap:I’llhave a look at this right away.

Aleru Divine (22:17:09) (in thread): > For experiment 1 and 2, > I think hindgut is okay as the body site.Tissue samples were collected from the hindgut from what I understand.The group names can be > Group 0: Control Diet (CTR) > Group 1: Experimental Diet (MC2) (change for experiment 2) > > The description looks okay to me.For the signature in experiment 1,I’mquite confused, using the colors to interpret this heatmap, I see significant results for only MC2 (green) and MN3(purple).idon’tthinkthis figure compares them with only controls.I think this is a one-to-all comparison.Either way, the signatures will be repeated.So:sleepy:Also, you are missing the source, description and abundance direction of signature 1 in experiment 2. > > Stratification factors might be confounders, but we only curate them if they were controlled or adjusted for in the study.I’vehad one of such studies before and it was stated that they adjusted for the factors.

Yoko C (22:28:03) (in thread): > Oh, thanks for pointing out the missing info.

Aleru Divine (22:29:28) (in thread): > For experiment 3, you can follow the group namesI’vesuggested above, > > Youdidn’tcurate other genus?:sweat_smile:in signature 1.For signature 2, I believe you curated Gallicola, Tepidimicrobium, and lactobacillus by accident because they are only abundant in the pyloric caeca and this experiment is for hindgut.Check signatures 1 and 2 in experiment 4 for the same mixup

Adeshile Oluwatosin (22:30:56) (in thread): > Well done@Yoko C

Yoko C (22:35:59) (in thread): > @Aleru Divine, you are right, I switched those two.

Yoko C (22:47:46) (in thread): > Not sure about if it’s a 1 to all comparison or 1 treatment vs control, but I chose 1 treatment vs control because it’s a pairwise comparison and you can only compare 2 things at a time.

Adeshile Oluwatosin (23:50:36) (in thread): > Fig 1: Hindgut samples as body site. Beta diversity was assessed using Bray–Curtis dissimilarity for 16S rRNA gene data obtained from the hindgut samples (n = 156 samples). “ > > “The experimental groups are labeled as CTR (Control), MC1 (Diet 1), MC2 (Diet 2), and MN3 (Diet 3), indicating the different diets administered to fish.” “smolts (T2) “. “and two different types of α-mannans (MC1 and MC2). “ > > Group 0: CTR T2 (0.2% control diet for smolts) > Group 1: MC2 T2(0.2% α-mannansdiet2 for smolts) > > Seems like a pairwise comparison but for MC2 T2 and MN3 T2. > That’s only where I can see significance. > > > There are no confounders. Couldn’t find a statement were they stated they controlled for …

Adeshile Oluwatosin (23:50:37) (in thread): > @Yoko C

2024-11-19

Adeshile Oluwatosin (00:12:26) (in thread): > Fig 2F. The experimental groups are labeled as CTR (Control) and 4%MN3 diet (4% β-mannan diet). > > Group 0: CTR (control) > Group 1: 4%MN3 diet (4% β-mannan diet). > > For 2F there are samples taken from Hindgut (orange) > Samples taken from pyloric caeca (blue) > > So that’s 2 separate experiments with different body sites. > Experiment 3/signature 1: curate other genus just as stated. > > > Experiment 4/signature 1: BCP group, other genus, comamonadaceae > > Signature 2: pseudomonas, limosillactobacillus, peptostreptococcus, lactobacillaceae, enterococcus, streptococcus, ligilactobacillus.

Kate Rasheed (01:08:11) (in thread): > Welldone on this curation@Yoko C. > > I’ll take a look:hugging_face:

Mildred Anashie (01:56:47) (in thread): > Well done@Yoko CWell done everyone > I’ll take a look

Chinwendu Joy Enyidiegwu (04:20:58) (in thread): > @Adeshile Oluwatosinthanks, experiment 3 has 3 signatures

Adeshile Oluwatosin (04:48:30) (in thread): > Experiment 3 should have only 2 signaturesBut 4 experiments.One for increased abundance and one for decreased abundance > > Not 2 with increased abundance, I saw that signature 1 was deleted that’s why I mentioned it as 2@Chinwendu Joy Enyidiegwu

Adeshile Oluwatosin (04:49:01) (in thread): > Good morning

Chinwendu Joy Enyidiegwu (05:13:34) (in thread): > @Aleru Divinei had to combine each DSS cycles in experiment 3, so i need to separate each cycles to capture the microbial changes..will look into it, thanks > > what about the statistical test, i am using fishers but i am not sure if its same for the DSS cycles in table 4?

Aleru Divine (05:40:55) (in thread): > I’lllook at the statistical test again just to be sure but I think you are right.

Chinwendu Joy Enyidiegwu (05:59:42): > @Svetlana Ugarcina Perovicplease help with deleting the signature:pray:https://bugsigdb.org/Study_1219/Experiment_3/Signature_2 - Attachment (BugSigDB): Study 1219/Experiment 3/Signature 2 > Source: Table S4 Description: Differential OTUs after 2 AOM/DSS cycles Abundance in Group 1: increased abundance in Mice treated with AOM/DSS cycles 1, 2, 3, or…

Svetlana Ugarcina Perovic (06:01:32) (in thread): > Deleted.

Mildred Anashie (07:01:26) (in thread): > Well done on this@Yoko C….I believe the body site, Group names and Group description are okay. But I noticed you have some missing taxa in the last two experiments, also Exp 4, signature 1 you should remove Ligilactobacillus it isn’t significant.

Svetlana Ugarcina Perovic (07:09:50): > Free online courseIn this 1-h course, you will learn whatmetadatais, someelementsof metadata, commonusesof metadata in bioinformatics, in order to understandwhymetadata are essential.https://www.sib.swiss/training/course/2024_MDIBI - Attachment (sib.swiss): Metadata in Bioinformatics > Have you heard the word metadata but have no idea what it refers to, what type of content is found in metadata, how it is being used and why to use it

Adeshile Oluwatosin (07:17:00) (in thread): > Thank you so much for this > I truly appreciate@Svetlana Ugarcina Perovic

Chinwendu Joy Enyidiegwu (07:45:02) (in thread): > thank you.

Aleru Divine (07:47:36) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:pray:

Aleru Divine (07:56:07) (in thread): > Yes the statistical test is correct.@Chinwendu Joy Enyidiegwu

Rahila-me (07:58:22) (in thread): > @Svetlana Ugarcina PerovicThank you for this information

Chinwendu Joy Enyidiegwu (07:58:28) (in thread): > @Mildred Anashiedefinitely expecting your feedback@Adeshile Oluwatosinyou can check again:pray:@Aleru Divinepls do recheck.. > i defeinitely appreciate your feedbacks

Aleru Divine (08:06:47) (in thread): > Okay, will do

Rahila-me (08:16:45): > Good afternoon all, i have a question from this paper, the RESULT:https://journals.asm.org/doi/full/10.1128/msystems.01237-24Supplemental Figures:https://journals.asm.org/action/downloadSupplement?doi=10.1128%2Fmsystems.01237-24&file=msystems.01237-24-s0001.pdfPaired gut and oral microbiome data from the same individual were obtained from 40 BC, 12 DCIS, and 24 healthy participants (Fig. S1B). > How will the signature be curated and groups be grouped here, Thank you. Information needed can be found in the result and Supplemental. > Can the body sites be both gut and oral

Adeshile Oluwatosin (08:19:01) (in thread): > Okay, I’ll check

Adeshile Oluwatosin (08:19:23) (in thread): > Hello. Well done@Rahila-meI will go through it

Aleru Divine (08:19:50) (in thread): > Sure thing@Rahila-me

Rahila-me (08:20:18) (in thread): > @Adeshile Oluwatosin@Aleru DivineThank you

Adeshile Oluwatosin (08:20:43) (in thread): > First of, I believe if there are two body sites with different results > We curate as different experiments > Going through it

Adeshile Oluwatosin (08:29:52) (in thread): > Sample size: Eighty-three percentage (n = 154) of the sample kits were returned (73 BC, 32 DCIS, and 49 healthy). > > Fig 2A-F curatable. LEFse score 3 > > Curate Fig2A-C with body site asfecesFig 2D-F body site:saliva2A. Group 0: Healthy. (2 signatures) > Group 1: BC > > 2B. Group 0: Healthy. (2 signatures) > Group 1: DCIS > > 2C. Group 0: BC. (2 signatures) > group 1: DCIS >
> 2D. Group 0: Healthy. (1 increased abundance signature, no decrease) > Group 1: BC > > 2E & F. Group 0: Healthy. (1 increased abundance with 8 signatures, no decrease) > Group 1: DCIS

Adeshile Oluwatosin (08:31:03) (in thread): > Everything is in here “Taxonomic biomarkers identified by LEfSe. LDA bar graphs plotted from LEfSe analyses of gut (A–C) and oral (D–F) microbiota. The color of the bars represents the cohort. The logarithmic LDA score threshold was 3.0 for discriminative features. (A and D) BC vs healthy; (B and E) DCIS vs healthy; (C and F) BC vs DCIS.” and in the text.

Aleru Divine (08:31:57) (in thread): > @Rahila-mefor this study there were comparisons made between groups but for each body sites.Figure 2 shows LEfSe analyses of gut (A–C) and oral (D–F) microbiota so that is a total of 6 experiments.A-C will be the feces as body site > D-F is saliva as body site.There’salso an additional differential abundance test done using DESeq2 in figure 3 also for the different body sites.A-Cisfeces as body siteD-F is saliva as body site.In addition to this, figure 6 has alpha diversity for fecal and oral samples but comparing high and low breast density.It also has differential abundance results but only for fecal samples (6C) > > In thesupplementary material,there are differential abundance results for comparing the gut and oral samples.In this case,you’llcurate both body sites.Hope this helps.

Adeshile Oluwatosin (08:37:43) (in thread): > Deseq2, MHT yes, Fig 3A-C body site:fecesFig 3D-F body site:salivaUse the write up to curate these signatures. > I don’t want these texts to be bulky. > Fig 3A. Group 0: Healthy. Group 1: BC > Between BC and DCIS. DCIS is group 1. > > > Fig 6C. LeFSe, score 3. > Group 0: low breast density > Group 1: High breast density

Adeshile Oluwatosin (08:39:53) (in thread): > Also curate Fig S5.@Rahila-me

Aleru Divine (08:46:23) (in thread): > @Chinwendu Joy Enyidiegwucan you replace Lactobacillus hamsteri with 96565. Found it on the taxonomy browser. This is for signature 1 in experiment 1. I didn’t find Streptococcus luteciae:face_holding_back_tears:Also S24-7 is now Muribaculaceae this is for signature 2 in experiment 2. > > Clostridium innocuum is 1522 signature 2 in experiment 3 > > Flexithrix dorotheae is 70993 signature 2 in experiment 5 > > I’ll look at the study properly in bit please:pray:

Mildred Anashie (09:12:49) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Rahila-me (09:53:04) (in thread): > @Aleru Divineand@Adeshile Oluwatosinthank you thus far…but can you both check for paired gut and oral in the results and supplemental material on the gut and oral signature where they mentioned phylum, family and genus level..that’s the one that I am concerned about and confused on what group should be curated and signatures

Rahila-me (09:53:31) (in thread): > Waiting for your kind reply

Mildred Anashie (10:30:54) (in thread): > I see two statements pointing to statistical test and I think it is edgeR.* > > ‘The ‘edgeR’ package was employed to evaluate the differences in OTU abundance between control mice and all AOM/DSS-treated mice as well as the OTU abundance differences between mice treated with different AOM/DSS cycles’. > *and > > ’For comparison of control and all AOM/DSS treated mice, an exact test was employed; for comparison of control group and groups treated with different AOM/DSS cycles, the generalised linear model likelihood ratio test59 was performed’. > > @Aleru Divine **@Adeshile Oluwatosinwhat do you think?

BOLARINWA AISHAT (10:31:01) (in thread): > Thank you for sharing@Svetlana Ugarcina PerovicThis will be helpful

Kate Rasheed (11:02:44) (in thread): > @Rahila-me. If you’re talking about Figure S5 which is between gut and oral. You curate all signatures there. Group 0 would be gut samples and group 1 would be oral samples. > > You would curate S5A-C > > The alpha diversity for this experiment is in Figure S4. > > For the body site, you would use both feces and saliva.

Rahila-me (11:08:41) (in thread): > Okay…so I won’t compare those 3 groups when checking for gut and oral

Kate Rasheed (11:08:56) (in thread): > Thank you so much for sharing.

Kate Rasheed (11:09:44) (in thread): > Not at all@Rahila-me. Just saliva samples and fecal samples

Rahila-me (11:12:16) (in thread): > Body site will be both feces and saliva….then I will enter phylum, family and genus in creating the signature

Kate Rasheed (11:14:30) (in thread): > Exactly@Rahila-me. Welldone:hugging_face:

Vince Carey (12:33:39): > @Vince Carey has left the channel

Rahila-me (13:18:57) (in thread): > Okay thank you@Kate Rasheed@Aleru Divine@Adeshile Oluwatosinonce again.

Adeshile Oluwatosin (14:16:22) (in thread): > Hello@Rahila-meI just checked, kindly curate only Fig s5C alone. > > That’sthe bacterial taxa lowest in the rank.

Adeshile Oluwatosin (14:19:15) (in thread): > You are not to curate Fig S5A and B

Rahila-me (14:26:37) (in thread): > ok@Adeshile Oluwatosinthe genus level only? Thank you for this clarification

Adeshile Oluwatosin (14:26:53) (in thread): > Yes only genus level

Kate Rasheed (14:28:43) (in thread): > @Adeshile OluwatosinI believe she should curate all the figures. > > I went to the curation policy and confirmed this: > > “If two different figures/tables differ only in which taxonomic level they provide (e.g. one figure for species, one supplemental table for genera, but these resulted from the same contrast), these can be combined into a single signature.”

Adeshile Oluwatosin (14:31:58) (in thread): > Hi@Kate RasheedIn my second contribution that was scored, I worked on an article exactly like this > > And I curated just the genus level. > I was scored perfectly. > > My believe is as long as they mentioned for genus, species, phylum and family. > > Bacterial taxas of the lowest rank should be curated. > I went through Fig S5 and saw that the taxa mentioned were similar across A-C but different ranks. > > I don’t know if I explained well

Kate Rasheed (14:33:14) (in thread): > Issorite:hugging_face:.

Adeshile Oluwatosin (14:34:18) (in thread): > Bacteroidetes. (S5A), Bacteroidaceae(S5B), Bacteroides (S5C). > > > There’s no need for repetition. > > Just curate S5C( Bacteroides).

Kate Rasheed (14:38:03) (in thread): > I’ve worked on articles where this different levels of taxa was reported and according to the curation policy, > > “Curate all taxa irrespective of the taxonomy rank” > > If I remember yours, it was a table that have different taxa in each row, in that case, you pick the last one but I don’t think it applies to figures. > > It’s fine though. We’ll understand by and by:smile:@Adeshile Oluwatosin

Adeshile Oluwatosin (14:43:03) (in thread): > No o@Kate RasheedMy second contribution, i don’t think I even posted it up for peer review. > You should only curate the one lowest in the taxonomy rank. And i worked on Figures and not Tables. > > I’m very sure of what I’m saying lol@Kate Rasheed

Rahila-me (14:44:48) (in thread): > ok

Adeshile Oluwatosin (14:46:22) (in thread): > Curate all taxa irrespective of taxonomical rank, I believe whenit’snot same taxa mentioned across all ranks. > > In this particular study like I highlighted before taxa “Bacteroidetes was mentioned for genus and the rest”. > > > If it was phylum, family, genus, species mentioned in just a particular table or figure. You curate > > In this case: it was stated for three different figures. And the taxonomical rank was same per figure. > Maybe this might explain it better.@Kate Rasheed

Rahila-me (14:46:38) (in thread): > @Adeshile Oluwatosinand@Kate RasheedThis gut and oral venn diagram was used showing each groups, since i am curating gut vs oral what becomes the group size can the group size be left blank

Kate Rasheed (14:47:31) (in thread): > If there’s no specific sample size for each site, you can leave blank@Rahila-me

Rahila-me (14:50:14) (in thread): > Thank you ok

Adeshile Oluwatosin (14:51:09) (in thread): > My intial description might not explain well. > > But since the comparison is same.Just the description of Figure S5, i know I should curate just C

Rahila-me (14:52:56) (in thread): > Ok@Adeshile Oluwatosin

Adeshile Oluwatosin (14:54:57) (in thread): > For the sample size, you can leave blank if it was not mentioned but have you checked well. What figure is it please@Rahila-meSo I check briefly

Rahila-me (15:19:01) (in thread): > Ok@Adeshile Oluwatosin…for gut and oral.. sample size was not mentioned in the article

Adeshile Oluwatosin (15:38:34) (in thread): > Leave it blank@Rahila-me

Joy (16:23:41) (in thread): > Thanks for sharing@Svetlana Ugarcina Perovic

Kate Rasheed (16:25:04): > Good evening everyone. Please I need your thoughts on how to curate the column “Effect size(Dutch)” in the table below. > > Some rows have something like “0:-0.57, 0:3:5”; I’m thinking of leaving the ones with 0:-0.57 since it is not showing increase or decrease. > > What do you think please? Thank you so much. - File (Excel Spreadsheet): mmc9.xlsx

Yoko C (18:53:54) (in thread): > I think it could be something like a type-o. If you exclude those, it seems you would exclude all the Dutch Pet and Smokers data. Could you take what comes after the “:” as the valid data?

Yoko C (18:56:20): > Hello, I know that during the Outreachy period we couldn’t change anything if it had been submitted for review, is this still the case? Or can I correct NCBI matches, descriptions, ect from a study submitted for review, which has been labeled “needs review” but has not been claimed to be reviewed?

Tino (22:00:04): > @Yoko Chttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728980965144859 - Attachment: Attachment > IMPORTANT: when the GitHub issue with your curation is claimed for review and got a label “needs review” any edits from this point are not allowed.

Kate Rasheed (23:46:50) (in thread): > Alright@Yoko C. Thank you so much

Kate Rasheed (23:59:49): > Good morning people. Trust we are doing well? > > Please I have another question concerning this table. I’m curating based on sub-phenotype. For household essentials, most of the increased signatures are reported in decreased abundance. > > Do you think I should curate it that way? > > Thank you for your input. > > Here is the link:https://us.docworkspace.com/d/sIF3Y_LE4-4P2uQY - File (Excel Spreadsheet): Household essentials.xlsx

2024-11-20

Kate Rasheed (00:06:12) (in thread): > I just saw that it was comparison of the countries dataset to check for common associations not differential abundance. It shouldn’t be curated.

Aleru Divine (00:56:47) (in thread): > Good morning@Kate RasheedIcan’topen the file,:pleading_face:But I have a question, are they reporting species or from genuses upwards?

Kate Rasheed (01:06:12) (in thread): > They are reporting all but I’m using the species alone. > > Let me paste the link so you can access it.

Aleru Divine (01:07:03) (in thread): > @Kate RasheedIf the taxa reported is at the genus level, it could imply the presence of different species. Also, if it’s at the family level, it could mean there are different genera and species included. So, these should still be curated regardless of the abundance direction > > For species-level taxa on the other hand, I’m not entirely sure if the same logic applies.

Kate Rasheed (01:08:10) (in thread): > https://us.docworkspace.com/d/sIDbY_LE4i_n1uQYHere is the link@Aleru DivineLet me know if you can access it. Thank you so much.

Aleru Divine (01:08:26) (in thread): > Thank you so much!

Aleru Divine (01:11:04) (in thread): > It works! I should have downloaded and opened the file not view on Slack:woman-facepalming:I’m so sorry. I’m looking at it now.

Aleru Divine (01:13:53) (in thread): > This table has no headings/title for each column@Kate Rasheedhow do you tell what increased and what decreased?

Mildred Anashie (01:22:26) (in thread): > I was going to ask@Aleru DivineHowever@Kate Rasheedif there are organisms in both increase and decrease I believe you curate them that way > > This should helphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710517652414799?thread_ts=1710516856.042729&channel=C04RATV9VCY&message_ts=1710517652.414799 - Attachment: Attachment > Ohh got it! > > “Different bacterial strains may have different biological properties due to the different genes: > for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98%” > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639

Aleru Divine (01:23:24) (in thread): > Oh! Thank you@Mildred Anashie

Kate Rasheed (01:23:29) (in thread): > Apologies please. Check through the link. Thank you@Aleru Divine@Mildred Anashie

Aleru Divine (01:33:36) (in thread): > Can you take a screenshot of the titles for me?It’sall I need.My computer is asking to install WPS,I’vedone that but it stillwon’topen.It says Ihaven’tinstalled it.:sob:

Kate Rasheed (01:35:36) (in thread): > Sorry@Aleru Divine - File (JPEG): Screenshot_20241120-073503.jpg

Aleru Divine (01:36:01) (in thread): > Thank you@Kate Rasheed

Mildred Anashie (01:40:18) (in thread): > Okay, I see it now@Kate RasheedThank you > > So I think you are working with the P-adjusted column > > HoweverI’mcurious on how you are curating the three phenotype columns:thinking_face:Is it a one against the others?

Aleru Divine (01:43:23) (in thread): > @Mildred Anashiesocioeconomic and economic factors are consistent across the columns. So the focus is probably thefirst phenotype.Unless I don’t understand you.

Kate Rasheed (01:43:56) (in thread): > Not at all. I’m curating the sub-phenotype “Household essentials”. These sub-phenotype has about eight other phenotypes.

Kate Rasheed (01:44:56) (in thread): > Let me share the link to the article. Focus is on Supplement table 1.

Kate Rasheed (01:45:44) (in thread): > https://www.cell.com/cell-reports/fulltext/S2211-1247(24)00771-X#mmc2

Kate Rasheed (01:48:33) (in thread): > @Aleru DivineNo electronics and others are subcategories for Household essentials. > > For this experiment, we are curating based on individuals of wealthy households and those of less wealthy households. > > The sheet contains those of wealthy households. Some of them have no electronics but are still moderately wealthy. > > Although it is reported that the individuals from the study are all poor but you know “poor” has levels. > > I don’t know if you understand. You can look through the article for more explanation

Aleru Divine (01:49:10) (in thread): > I wanted to clarify my question.@Kate RasheedThanks:pray:

Aleru Divine (01:50:15) (in thread): > Yes I got it.Thanks:blush:

Aleru Divine (02:06:11) (in thread): > @Kate Rasheedlooking at the species names on table again, I noticed that after the species (s) they mention (t) I assume that refers to type/strain. We still need to account for the strain since they provided data on that.
> So curate all taxa even if they appear in both abundance directions. > > Interesting study by the way@Kate RasheedI don’t think I’ve ever read a paper that also focused on strain-level information to explore the influence of “the factors in question” on the microbiome. It’s always been genus/species. Or maybe I just didn’t realize until now:sweat_smile:

Aleru Divine (02:06:38) (in thread): > Hi@Mildred AnashieI missed this somehow:sob:

Aleru Divine (02:12:56) (in thread): > @Mildred Anashiehere’s why I agreed with the Fisher’s test. > > “Next, usingan exact test, 70 97% OTUs were found to be significantly different between the control group and the AOM/DSS-treated group (Fig. 4b and Table S2, FDR < 0.05).” > > Figure 4b refers to differential abundance results. > > But you do have a pointand I did see it, I went with the exact test because it was specific.But Idon’t know.We’ll ask tomorrow?Could be similar to that LEfSe case (LEfSe using Kruskal-Wallis behind the scenes)

Adeshile Oluwatosin (02:13:57) (in thread): > Good morning@Mildred AnashieI would check it as well.

Kate Rasheed (02:34:03) (in thread): > I’ve been curating the species, but for repeated species, I curate the “t”. Thank you for explaining what “t” stands for:smile:@Aleru DivineThe study is really an interesting one. > > Thanks@Mildred Anashie. I’ll curate the decreased too.

Rahila-me (03:39:44) (in thread): > Ok@Adeshile Oluwatosinthank you

Aleru Divine (07:10:44) (in thread): > @Rahila-mehere > “Overall, we analyzed137 gut samples(66 from women with BC, 29 from women with DCIS, and 42 from healthy women) and93 oral samples(47 from women with BC, 15 from women with DCIS, and 31 from healthy women) (Fig. S1A)”

Svetlana Ugarcina Perovic (09:07:02): > See you tomorrow atour weekly team meeting and office hours at 9 AM EDT (>>3:00 PM<<**** ****in Europe, Nigeria, etc.).https://us02web.zoom.us/j/2737200499cc<@UBNSEMS3S>

Kate Rasheed (09:11:11) (in thread): > Thank you for the reminder.

Kate Rasheed (09:32:24): > Good afternoon@Svetlana Ugarcina PerovicKindly delete Signature 1 of experiment 1, and experiment 2 from this study:https://bugsigdb.org/Study_1205Thank you so much. - Attachment (BugSigDB): Structural changes in the oral microbiome of the adolescent patients with moderate or severe dental fluorosis - BugSigDB > Dental fluorosis is a very prevalent endemic disease.Although oral microbiome has been reported to correlate with different oral diseases, there appears to be an absence of research recognizing any relationship between the severity of dental fluorosis and the oral microbiome.

Svetlana Ugarcina Perovic (09:34:19) (in thread): > Deleted.

Kate Rasheed (09:34:32) (in thread): > Thank you

Mildred Anashie (09:53:16) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (10:00:52) (in thread): > Thank you@Svetlana Ugarcina Perovic

Rahila-me (10:22:08) (in thread): > @Svetlana Ugarcina PerovicThank you for the reminder

Yoko C (11:18:51) (in thread): > Hello, like Mildred, I’m wondering how you would compare this. If you only select Household wealth index, the text says you have 5 levels of wealth but the table doesn’t show those. So you curate as either wealth index (poor or rich) has an effect on this strain or it doesn’t effect this strain? Also in regressions, do we curate effect size?

Kate Rasheed (13:03:18) (in thread): > @Yoko CCan you check this article:https://www.cell.com/cell-reports/fulltext/S2211-1247(24)00771-X#mmc2You would understand the comparison. The household wealth is a phenotype under the sub-phenotype “economic factor”. > > I didn’t curate based on phenotype but sub-phenotype.

Kate Rasheed (14:29:20) (in thread): > I see you have read the article, I thought you were making reference to Mildred’s statement earlier. > > Based on economic factors, the comparison is between the “wealthier household and less wealthy household” although everyone is actually poor. > > Based on what I understood from the text, the wealthier household has household essentials amongst other things(TV, concrete roof, ceramic floor). The household essentials was weighed using household wealth index. > > I wasn’t doing a comparison on the household essentials but on economic factors sub-phenotype > > Do you understand now:smile:@Yoko C

Yoko C (14:35:48) (in thread): > I read a bit, but I don’t know if you can group the different factors of the economic factor sub category (travel, wealth index, ceramic, household size, ect) with each other and make an overall signature. I now understand why you have repeating strains. I think here each factor within economic factor sub category was tested separately. This is why they say this: In total 78,597 separate regressions were performed (639 species times 123 phenotypes), in the description of table S1. Figure 2A I think also represents those associations. And here I don’t know if effect size necessarily means more or less abundant. Since tomorrow there are office hours (and I think this is always my final conclusion, sorry ) it would be a good question.

Yoko C (14:36:44) (in thread): > I also think that keeping the strain is important since they also mention that in the paper.

Aleru Divine (16:31:30) (in thread): > Thank you for the reminder@Svetlana Ugarcina PerovicLooking forward to it:hugging_face:

Joy (17:10:38) (in thread): > Thank you@Svetlana Ugarcina Perovic!

Kavya Ayalasomayajula (18:53:18): > Hi all, I am curating a study in which Ruminococcaceae is listed as a family and Clostridiales is listed as orderand they are displayed on a lefse table .Iam having trouble as as I seem to be only able to find a number of species within these different categories, but not necessarily the broader taxa they are listed as. It seems the specific genus/species under these are not specified in the article. Any suggestions welcomehttps://www.sciencedirect.com/science/article/abs/pii/S0920121118301578?via%3Dihub(I could not find a link to the full article and had to log into my cuny account to access)

Yoko C (21:13:12) (in thread): > Hi, Ruminococcaceae is a heterotypic synonym for Oscillospiraceae. NCBI taxonomyhttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216572&lvl=3&lin=f&keep=1&srchmode=1&unlockMaybe that helps?

Adeshile Oluwatosin (23:41:50) (in thread): > Hi@Kavya AyalasomayajulaRuminococcaceae is now oscillospiraceae > Taxa Id: 216572https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216572&lvl=3&lin=f&keep=1&srchmode=1&unlockClostridiales is now Eubacteriales > Taxa ID: 186802https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=186802&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

2024-11-21

Adeshile Oluwatosin (01:03:24): > Good morning everyone > Trust you had a great night.https://peerj.com/articles/13095/In this study, the curatable Figure 4, Table S1 are same. > However in Figure 4, I believe they represented the significant taxa, but in the text, I mean description states otherwise. > > E.g “The ASV was not unique to the sample replicates, but prevalent in five other samples but in much lower abundance. Among the families with >1% mean relative abundance, only three families within the phylum Firmicutes, Christensenellaceae, Ruminococcaceae and Lachnospiraceae, was significantly different in relative abundances between treatments and was underrepresented within freeze-dried samples.” > > In Figure 4, Ruminococcaceae and Lachnospiraceaespiraceae wasn’t shown as significant. - Attachment (PeerJ): Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples > Background The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies. However, studies conducting sample collection at remote sites without a reliable cold-chain would benefit from a sample preservation method that allows transport and storage at ambient temperature. Methods In this study we compare alpha diversity and 16S microbiome composition of 20 fecal sample replicates from Damaraland mole-rats (Fukomys damarensis) preserved in a minus 80 °C freezer and transported on dry ice to freeze-dried samples that were stored and transported in ambient temperature until DNA extraction. Results We found strong correlations between relative abundances of Amplicon Sequence Variants (ASVs) between preservation treatments of the sample, no differences in alpha diversity measures between the two preservation treatments and minor effects of the preservation treatment on beta diversity measures. Our results show that freeze-drying samples can be a useful method for cost-effective transportation and storage of microbiome samples that yields quantitatively almost indistinguishable results in 16S microbiome analyses as those stored in minus 80 °C.

Aleru Divine (01:32:04) (in thread): > Good morning@Adeshile OluwatosinI see Firmicutes Ruminococcaceae and Firmicutes Lachnospiraceae in figure 4. > > I don’t really understand how you mean they’re not shown as significant.

Adeshile Oluwatosin (02:27:15) (in thread): > Yes its there > > My interpretation is the dot in front of the taxa represents taxa with significance and those without@Aleru DivineWhat do you think?

Aleru Divine (02:36:37) (in thread): > Oh! No it’s not@Adeshile OluwatosinTable S1 shows the p and adjusted p-values. > Those dots aren’t asterisks* > > They use asterisks to show significance but not in this case andtheyusually indicate in the description.These dots are pretty common in plots like this. - File (JPEG): IMG_1658

Adeshile Oluwatosin (02:47:12) (in thread): > I was wondering. Then it clarifies that all taxa are significant in this case or just the taxamentioned in the text.

Aleru Divine (02:52:47) (in thread): > The text references table S1.I think only the ones mentioned are significant.Also looking at the P and adjusted p values.Only those 3 are.The text confirms it.

Kate Rasheed (03:17:39): > Good morning everyone. Trust we are doing well. > > I’ll appreciate a peer review on this study:https://bugsigdb.org/Study_1232Thank you so much - Attachment (BugSigDB): Bacteriome analysis of Aggregatibacter actinomycetemcomitans-JP2 genotype-associated Grade C periodontitis in Moroccan adolescents - BugSigDB > BACKGROUND: Grade C (previously aggressive) periodontitis (GCP) in adolescents is prevalent in certain parts of Africa where it is associated with JP2 genotype, a highly virulent strain of Aggregatibacter actinomycetemcomitans.

Svetlana Ugarcina Perovic (03:27:07) (in thread): > See you today at the team meeting! > > And after the meeting there is a webinar that you could join if interested inhow to write an engaging title and abstract for your research articleTime: 21 November 2024, 17:00 (CET)https://us06web.zoom.us/webinar/register/WN_N1C1eQ8USR2frCGzizn_mQ#/registration

Adeshile Oluwatosin (03:27:50) (in thread): > Noted. Thanks for clarifying

Adeshile Oluwatosin (03:28:03) (in thread): > Okay,I’lllook through

Adeshile Oluwatosin (03:28:10) (in thread): > Good morning and well done

Chinwendu Joy Enyidiegwu (03:30:01) (in thread): > i think i will stick to edgeR ,as the study explicitly references it as the analysis tool. thanks@Mildred Anashie@Aleru Divine

Mildred Anashie (03:30:57) (in thread): > You are welcome@Chinwendu Joy EnyidiegwuYou could still bring it up during the office hours today

Kate Rasheed (03:32:49) (in thread): > Thank you for this@Svetlana Ugarcina Perovic

Joy (03:33:24) (in thread): > Sure@Svetlana Ugarcina Perovic. The webinar would be a thing to attend!

Aleru Divine (03:33:35) (in thread): > Alright@Chinwendu Joy EnyidiegwuI agree too@Mildred Anashieit’sin a few hours.

Aleru Divine (03:34:51) (in thread): > Well done@Kate Rasheed:clap:

Kate Rasheed (03:44:59) (in thread): > Thank you people:hugging_face:

Rahila-me (03:48:21) (in thread): > @Svetlana Ugarcina Perovicthank you

Chinwendu Joy Enyidiegwu (03:51:03) (in thread): > will do.:+1:

Tino (04:03:06): > Hello everyone! > > I need clarity on which contribution URL to submit. Do we use the github onehttps://github.com/waldronlab/BugSigDBcuration/issues/…. or the bugsigdb onehttps://bugsigdb.org/Study….

Kate Rasheed (04:03:42) (in thread): > Good morning@Tino. You would use the BugSigDB study link.

Tino (04:04:38) (in thread): > Thanks@Kate Rasheed

Joy (04:39:36) (in thread): > That’s right@Kate Rasheedit’s the BugSigDB study link.

Joy (04:48:26): > Greetings great curators. I trust we are all doing well. I’ll appreciate a peer review of this study. Thanks.https://bugsigdb.org/Study_1230 - Attachment (BugSigDB): Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients - BugSigDB > Immune checkpoint inhibitors (ICIs) improve outcomes in advanced melanoma, but many patients are refractory or experience relapse.The gut microbiota modulates antitumor responses.However, inconsistent baseline predictors point to heterogeneity in responses and inadequacy of cross-sectional data.

Kate Rasheed (04:50:00) (in thread): > Welldone@JoyI’ll look through

Kate Rasheed (04:51:36) (in thread): > @JoyFor the antibiotics exclusion, leave it as “1 month”

Kate Rasheed (04:56:15) (in thread): > The condition can be******response to therapy******since the study is looking at the “response of melanoma patients to immune checkpoint inhibitors (ICI) therapy”. > > For the data transformation, it should be centered log-ratio. See this ” CR and nCR can be distinguished at 7–13 months on therapy by the log-ratio of pooled abundance of stable species ” > > The body site should be Feces. > > It was stated that Shotgun metagenomics and 16S were used. These would be separate experiments.

Kate Rasheed (05:22:13) (in thread): > Also, for the Shotgun metagenomics, MaAsLin was used as the statistal test while for 16S, Mann-whitney was used@JoyI see differential abundance in Fig. S2D using MaAsLin2 statistical test but I don’t know how you would curate it since the adjusted p-value wasn’t stated.

Joy (05:54:26) (in thread): > Thanks@Kate Rasheed

Adeshile Oluwatosin (06:07:24) (in thread): > I just checked back, do you mean this experiment has only decreased abundnace@Aleru Divine

Adeshile Oluwatosin (06:08:35) (in thread): > Since the significance threshold is 0.001

Adeshile Oluwatosin (06:08:47) (in thread): > And only those 3 taxa falls within

Aleru Divine (06:09:58) (in thread): > @Adeshile OluwatosinIt’s a comparison between fried and frozen chicken. Which has higher abundance. > That would be frozen for Lachnospiraceae

Adeshile Oluwatosin (06:10:29) (in thread): > I’mconfused

Adeshile Oluwatosin (06:11:08) (in thread): > The three phylum mentioned are definitely decreased for freeze drying which is group 1.

Adeshile Oluwatosin (06:12:14) (in thread): > First of, if I’m abiding by the law of the significance threshold, every other taxa infigure 4can’t be curated.

Adeshile Oluwatosin (06:12:24) (in thread): > @Aleru Divine

Adeshile Oluwatosin (06:13:38) (in thread): > Even the p adjusted values for Ruminococcaceae andlachnospiraceae are above 0.001

Aleru Divine (06:34:01) (in thread): > From the text, all 3 should be curated. From table S1, it’ll be just Christensenellaceae.But I think you should take from text.Because it still references table S1.

Adeshile Oluwatosin (06:42:16) (in thread): > Okay, thanks@Aleru DivineI’lljust ask in the office hour holding today.

Aleru Divine (06:43:05) (in thread): > Alright.That’sbetter

Mildred Anashie (08:07:30) (in thread): > Hi@JoyWell done on your curation > I’ll take a look at this soon

Joy (08:30:22) (in thread): > Thank you@Mildred Anashie

Yoko C (08:53:08) (in thread): > Hello, these are some things I can comment on: I think the only curatable graph I see is S2D which is for the shotgun method. Some inconsistencies I see are that for body site you recorded: alimentary part … , this should just be feces. The condition, I also don’t think is related to the cell line but rather to the therapy. For your signatures, the source should be the graph or table name where you found the information, for example Figure S2 D, and the description should be a description of the graph.

Joy (08:55:03) (in thread): > Thank you@Yoko C

Aleru Divine (10:01:28): > Thank you for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina Perovic:blush:

Adeshile Oluwatosin (10:23:36): > Thank you my able mentors<@UBNSEMS3S>@Svetlana Ugarcina Perovic:hugging_face:

Adeshile Oluwatosin (10:31:14): > Hi ma’am@Svetlana Ugarcina PerovicJust a Friendly reminder on thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727856118343829 - Attachment: Attachment > Good morning > I would like to state that I mistakenly submitted the form twice. > The initial and first submission is the accurate and correctly filled contribution. I will go ahead with the second contribution now. > Thank you :pray: > Name: @Adeshile Oluwatosin > @Svetlana Ugarcina Perovic @UBNSEMS3S

Svetlana Ugarcina Perovic (10:32:40) (in thread): > Noted back then.

Adeshile Oluwatosin (10:33:17) (in thread): > Thank you

Rahila-me (10:44:46): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>Thank you for the office hour today and for all the questions answered. Waiting for the recording

Joy (10:49:26): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor the office hours today.Waiting on the recording as I lost my connection.

Mildred Anashie (11:42:01): > Hello Everyone:wave:I’ll appreciate a peer review on this study:https://bugsigdb.org/Study_1228Thank you:pray:and Thank you so much<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor today’s session.:hugging_face: - Attachment (BugSigDB): Characterization of the Tissue and Strain-Specific Microbiota of Anopheles funestus Giles (Diptera: Culicidae) - BugSigDB > The mosquito microbiota is a critical determinant of mosquito life history.It is therefore a target for novel vector control strategies like paratransgenesis.However, the microbiota in Anopheles funestus, a major African malaria vector, is poorly characterized.

Kate Rasheed (11:43:20) (in thread): > Welldone on this curation@Mildred Anashie. I’ll look through.

Mildred Anashie (11:45:36) (in thread): > Well done@Kate RasheedI’ll look through

Kate Rasheed (12:17:38) (in thread): > Thank you@Mildred Anashiebut I’ve submitted already:smile:.

Mildred Anashie (13:18:33) (in thread): > Okay > > No problem > Well done:clap:

Kate Rasheed (14:56:32) (in thread): > @Mildred AnashieUnder the alpha diversity session, it was stated that Shannon and Chao1 was increased for the salivary gland. > > Since Salivary gland is your group 1, isn’t it supposed to be increased? > > Also, is there a reason why antibiotics exclusion is N/A?

Mildred Anashie (15:02:18) (in thread): > N/A > Not Applicable

Kate Rasheed (15:02:59) (in thread): > How about leaving the antibiotic exclusion blank?

Mildred Anashie (15:03:15) (in thread): > Thank you for the alpha diversity > > I actually changed the groups for the first experiment and forgot to edit the alpha diversity

Joy (15:21:58) (in thread): > Good work@Mildred Anashie

2024-11-22

Kate Rasheed (06:00:22): > Good morning people. Happy weekend:hugging_face:. > > Please I have questions concerning this article I’m working on. > 1. The study design appears to be a randomized control trial but I’m not sure of it. > 2. For the drugs administered, it was stated that “3 vials per condition” was given for each drug. Does it translate to 3 being the sample size for each drug? > 3. I can’t seem to figure out the location of the subjects. > Here is the article:https://www.nature.com/articles/s41564-024-01853-0#Fig7Thank you so much people:hugging_face: - Attachment (Nature): The Parkinson’s disease drug entacapone disrupts gut microbiome homoeostasis via iron sequestration > Nature Microbiology - Entacapone, a Parkinson’s disease medication, sequesters iron resulting in a selective inhibition of gut microbial activity.

Aleru Divine (06:48:29) (in thread): > Hi@Kate Rasheedyes I believe it’s a Randomized Controlled Trial study type too. > > Yes, n = 3 means 3 is sample size for each drug. The “3 vials per condition” means that three independent vials were incubated for each drug. At least that’s how I understand it. There’s really no mention of sample size anywhere else.For the location of subjects:thinking_face:I see from the reporting summary that “Study participants were researchers of University of Vienna (Austria) and University of Southampton (UK).Recruited by email” > > So AUSTRIA and UK

Mildred Anashie (07:05:37) (in thread): > Well done@Kate RasheedSo I saw where they said samples were gotten from 9 healthy individuals and they also said analysis was performed in triplicates > > I might buy into 3 being the sample size > > PS:Haven’tproperly read the article

Svetlana Ugarcina Perovic (08:08:03): > Nowadays, there are a lot of microbiology/science podcasts (https://github.com/SvetlanaUP/Microbiome-etc-Podcasts), but theMicrobial mattersis really a good one. Especially this episode with Pat Schloss:https://www.youtube.com/watch?v=W9b1aQ99yGw&list=PLGhmZX2NKiNkf9HG3mL4HSBKoJjmZZajU&index=3:radio:Happy Friday! - Attachment (YouTube): Matters Microbial #64: Making Sense of the Microbiome

Kate Rasheed (08:27:37) (in thread): > Thank you for sharing

Kate Rasheed (08:29:07) (in thread): > @Aleru DivineThank you so much. I’ve been using Austria but wasn’t sure if I should add those from Southampton(UK). > > Thank you@Mildred Anashie. They later mentioned the drugs were administered to six healthy individuals. I’ll go with the 3.

Mildred Anashie (09:52:19) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing > > This is new information for me

Rahila-me (11:20:05) (in thread): > @Svetlana Ugarcina Perovicthank you for sharing

Adeshile Oluwatosin (11:57:57) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Aleru Divine (12:33:19) (in thread): > Thank you so much for sharing@Svetlana Ugarcina Perovic:blush:

Adeshile Oluwatosin (13:07:08): > Hello@Svetlana Ugarcina PerovicKindly delete Experiment 1/signature 1 in this study.https://bugsigdb.org/Study_1234 - Attachment (BugSigDB): Freeze-drying can replace cold-chains for transport and storage of fecal microbiome samples - BugSigDB > BACKGROUND: The transport and storage of samples in temperatures of minus 80 °C is commonly considered as the gold standard for microbiome studies.

Joy (15:33:09) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovicthis is highly informative!:pray:

Svetlana Ugarcina Perovic (15:34:39) (in thread): > deleted.

Kate Rasheed (16:05:47): > Good evening people. Please I need your opinion on this article I’m working on. > > Figure S8d-k doesn’t seem curatable to me; I would like to know your thoughts on it. > > Here is the link:https://gut.bmj.com/content/73/5/751#DC1Thank you so much. - Attachment (Gut): Faecal microbial transfer and complex carbohydrates mediate protection against COPD

BOLARINWA AISHAT (16:38:08) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Aleru Divine (16:58:18) (in thread): > Hi@Kate RasheedFrom the description of the figure and reading the texts that references the table, it might be implying differential abundance but the absence of any information on the significance makes me question if it’s curatable.

Kate Rasheed (17:13:18) (in thread): > Exactly@Aleru Divine. It’s similar to what we have in Fig. 1B and D.

Yoko C (19:50:31) (in thread): > Hello, I think that because it is a graph about the components it is not curatable.

Kate Rasheed (21:31:46) (in thread): > Thank you so much@Aleru Divine@Yoko C

Adeshile Oluwatosin (23:12:41) (in thread): > Hello, Good morning@Kate RasheedThe supplementary articles are not directing me to the figure stated. I want to look through it

2024-11-23

Kate Rasheed (01:28:02) (in thread): > @Adeshile OluwatosinGood morning to you. Check the first supplementary article. > > Thank you so much.

Mildred Anashie (02:59:38) (in thread): > Good morning@Kate RasheedI think that is purely relative abundance, I agree itisn’tcuratable

Adeshile Oluwatosin (03:03:21) (in thread): > @Kate RasheedI just saw it. > It’s not curatable in my opinion based on the descriptionparticularly d-f

Kate Rasheed (03:04:24) (in thread): > Thank you so much my people@Mildred Anashie@Adeshile Oluwatosin

Kate Rasheed (04:36:02): > Happy Saturday:sparkles:. > > I have come again people:blush:. I’ll really appreciate a peer review on this study:https://bugsigdb.org/Study_1237Thank you so much - Attachment (BugSigDB): Faecal microbial transfer and complex carbohydrates mediate protection against COPD - BugSigDB > OBJECTIVE: Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke.The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies.

Aleru Divine (05:33:32) (in thread): > Happy Saturday@Kate RasheedWell done on your curation,I’llgive it a review

Kate Rasheed (05:58:22) (in thread): > Thank you so much@Aleru Divine

Aleru Divine (06:05:45) (in thread): > This is a laboratory experimentand RCT study@Kate RasheedThe use of mice models. I didn’t pay attention to this before:sweat_smile:but I think RCT works since they used human subjects too.

Kate Rasheed (06:08:10) (in thread): > I used laboratory experiment at first but upon further reading, I saw that it is a RCT study too:smile:

Mildred Anashie (06:14:52) (in thread): > Well done on your curation@Kate RasheedI’llgive this a review soon, hopefully before you submit:smile:

Aleru Divine (06:26:22) (in thread): > The mice were age-matched@Kate Rasheedfor the FMT experiments.For the 16s rRNA sequencing(experiment 4), the regions are V5 - V8 I believe. The details are in the supplementary material.

Adeshile Oluwatosin (06:29:39) (in thread): > Hello@Kate RasheedI’lllook through

Adeshile Oluwatosin (06:29:54) (in thread): > Well done

Adeshile Oluwatosin (06:33:21) (in thread): > Akkermansia muciniphila- Taxa ID: 239935 > > Experiment 1/signature 2 > Experiment 2/signature 2Experiment 3/signature 2

Aleru Divine (06:38:41) (in thread): > @Kate Rasheedfor the signatures that appear this way “Alistipes sp002428825” you can curate the “genus name” or “genus sp” and leave out sp002428825 because it gives a lot of unresolved taxa. I believe the genus is enough in this case.

Kate Rasheed (06:45:26) (in thread): > I saw the mice was age-matched but I wasn’t sure if that was for control mice or experiment mice. > > For the signatures with extra sp…, I thought I should report that way since it appeared that way, besides, some of the species number varies per genus name.@Aleru Divine@Adeshile OluwatosinThere is Akkermansia municiphila_A and Akkermansia municiphila that’s why I recorded the first one that way.

Kate Rasheed (06:48:09) (in thread): > Thank you for pointing out the 16S rNa region@Aleru Divine. I know I saw it somewhere but I didn’t see it again:smile:

Aleru Divine (06:54:04) (in thread): > I understand@Kate RasheedThe point is to resolve as many taxa as we can and I thoughtthat’sone way to do it.

Kate Rasheed (06:55:46) (in thread): > Okay, I will do it for Alistipes and some others since their species number is constant. How about other repeated genus with different species number, should I record one as “genus name” and the other as “genus sp”?@Aleru Divine

Adeshile Oluwatosin (07:01:44) (in thread): > @Kate Rasheedrecord both as Alkermansia municiphila > > Right a note on it specifying the different species

Adeshile Oluwatosin (07:02:23) (in thread): > Give an instance for the question you just asked

Aleru Divine (07:02:48) (in thread): > Yes you can curate that way.

Aleru Divine (07:11:56) (in thread): > About the age-matching. I don’t know@Kate RasheedSee this “Experimental controls were used as donors for the FMT to ensure the use of age-matched donors” > > I think age-matching was done between donor and recipient mice. Both the air-exposed and cigarette smoke-exposed groups were used as donors, and each donor was matched in age to its recipient.I could be interpreting this wrongly.:pray:

Rahila-me (08:20:07) (in thread): > @Kate Rasheedhappy Saturday too,.. Welldon on your curation. I will go through it.

Mildred Anashie (10:17:01) (in thread): > Hi@Kate RasheedWell done again > I think there’s an Experiment in Supplementary Figure 7e (see image) > > But I’m unsure how you’d record the reoccurring Muribaculaceae - File (PNG): IMG_2586

Kate Rasheed (10:31:00) (in thread): > Wow:star-struck:. My fresh eyes. Thank you so much. > > Do you think I should record it alongside the numbers:thinking_face:@Mildred Anashie@Aleru Divine

Mildred Anashie (10:32:00) (in thread): > I’mthinking you can > > Or leave a review note on the taxa@Kate Rasheed

Kate Rasheed (10:33:11) (in thread): > Alright@Mildred Anashie. Thank you plenty.

Mildred Anashie (10:39:04) (in thread): > Just Incase, this is what I mean by leaving a review note on the taxa@Kate Rasheed - File (MPEG 4 Video): video-output-DB3A6242-9A7A-4B70-9C51-7CC970AB86DB

Kate Rasheed (10:40:30) (in thread): > Amazing. I’m glad you figured out that I might not understand what you meant:smile:. Thank you so much for the illustration@Mildred Anashie

2024-11-25

Adeshile Oluwatosin (04:01:04): > Hello everyone > > I hopeeveryonehad a great weekend.<@UBNSEMS3S>Just a friendly reminder on the previous office hour recording. I truly appreciate in advance > Thank you

Svetlana Ugarcina Perovic (05:59:54): > You are invited to join the next**** MVIF in December! ****Registration here:cassyni.com/s/mvif-34 - File (PNG): program_dec24.png

Adeshile Oluwatosin (06:05:24) (in thread): > Noted ma’am@Svetlana Ugarcina Perovic

BOLARINWA AISHAT (06:11:09) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Joy (06:19:38) (in thread): > Thank you@Svetlana Ugarcina Perovic, this is duly noted:pray:

Kate Rasheed (06:29:07) (in thread): > Thanks for sharing. It’s well noted.

Aleru Divine (06:47:54) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

UBNSEMS3S (10:09:17) (in thread): > Sorry had some computer issues last week and couldn’t encode it. Doing that now.

Adeshile Oluwatosin (10:09:51) (in thread): > Okay, thank you

Rahila-me (11:06:38) (in thread): > Noted@Svetlana Ugarcina Perovic.

Kavya Ayalasomayajula (19:15:15): > Hi all, would appreciate feedback on this curationhttps://bugsigdb.org/Study_1233I also had some troubles in experiment2 signature 1 curating figure 3. I had troubles finding colostridium XIVa so I classified as unclassified but unsure if there is a new name for it. Figure 3 also lists Ruminococcus2. I am unsure if the “2” was a typo because I couldn’t find this in the taxonomy identifier - Attachment (BugSigDB): Altered gut microbiome composition in children with refractory epilepsy after ketogenic diet - BugSigDB > OBJECTIVE: The aim of this study was to investigate the characteristics and composition of intestinal microbiota in children with refractory epilepsy after ketogenic diet (KD) therapy and to explore the bacterial biomarkers related to clinical efficacy.

Aleru Divine (19:24:36) (in thread): > Well done:clap:@Kavya AyalasomayajulaI’llgive this a review:blush:

Aleru Divine (19:51:18) (in thread): > @Kavya Ayalasomayajulayou should curate as Clostridium XIVa since this hasn’t been resolved yet. > > Ruminococcus2 can be curated as Ruminococcus.Sometimesthey might break genuses into subcategories e.g Ruminococcus 1 or Ruminococcus 2 to reflect differences detected in the genetic data usually a species in the genus(I think)but maybe they’re not sure which species but they’re very sure it’s in the Ruminococcus genus.Soyou’dcurate as Ruminococcus.I think you should shorten group 1 description in experiment 1 to only describe group 1.This would do “Group treated for 6 months with ketogenic diet therapy.” > > For antibiotics exclusion, curate the timeline “two weeks” in this case.This is what I am able to see so far, could you share a pdf to this study please.:pray:the current link is closed access andI can’tfigure out how to get the PDF.

Kavya Ayalasomayajula (20:51:26) (in thread): > @Aleru Divinethank you for this feedbackTry this link. I have had a lot of issues finding this paper in full text. Ifit’sstill not working, I had to log into my CUNY library account to access the full text version. > > There is no option in bugsigdb for clostridium XIVa, should I still type it in as is? > Thank you!

Adeshile Oluwatosin (22:21:10) (in thread): > Hello@Kavya Ayalasomayajulawell done

Adeshile Oluwatosin (22:32:38) (in thread): > You can curateClostridiumxivA as Lachnospiraceae. > Taxa ID: 186803 > > From google: The Lachnospiraceae family is a phylogenetically and morphologically heterogeneous taxon belonging to the clostridial cluster XIVa of the phylum Firmicutes

Adeshile Oluwatosin (22:43:00) (in thread): > For Ruminococcus 2: You can curate as“1263” but write a note on it specifying that it is actually Ruminococcus 2.

2024-11-26

Kate Rasheed (02:50:16) (in thread): > Amazing@Adeshile Oluwatosin. I didn’t know Clostridium XIVa has been resolved. Let me correct the ones in my study.

Adeshile Oluwatosin (02:51:42) (in thread): > Welcome@Kate Rasheedbut leave clostridium XIVb as it is

Kate Rasheed (02:59:31) (in thread): > @Adeshile OluwatosinSee what I saw: > “Clostridium XIVa is now referred to as Faecalibacterium, Blautia, Coprococcus, Roseburia, and Ruminococcus” > > Here is the paper:https://pmc.ncbi.nlm.nih.gov/articles/PMC6070193/I think we should leave it that way. - Attachment (PubMed Central (PMC)): Rapid gastrointestinal loss of Clostridial Clusters IV and XIVa in the ICU associates with an expansion of gut pathogens > Commensal gastrointestinal bacteria resist the expansion of pathogens and are lost during critical illness, facilitating pathogen colonization and infection. We performed a prospective, ICU-based study to determine risk factors for loss of gut …

Aleru Divine (02:59:38) (in thread): > @Kate Rasheed@Adeshile Oluwatosinthis hasn’t been resolvedon the discussions page yet.I only see Clostridium cluster XIVa are also known as Clostridium coccoides and should still be curated asClostridium XIVanot Lachnospiraceae.Could you point me to this@Adeshile Oluwatosin

Kate Rasheed (03:00:16) (in thread): > I agree@Aleru Divine. Different papers with different interpretations:smile:

Aleru Divine (03:00:23) (in thread): > Yes I agree@Kate Rasheedit should be curated as reported in the paper.

Kate Rasheed (03:01:45): > Good morning people. Please what is the data transformation for Spearman correlation statistical test?

Adeshile Oluwatosin (03:01:50) (in thread): > I saw that@Aleru DivineI worked on a curation that has been scored and in that curation. I curated clostridium XIVb as lachnospiraceae and i was told to correct it as only clostridium XIVa is to be curated as lachnospiraceae. > Also mentor esther,who wrote that in the discussion pagesaid this on GitHub.Google says same thing

Adeshile Oluwatosin (03:01:59) (in thread): > @Kate Rasheed

Aleru Divine (03:02:11) (in thread): > @Kavya Ayalasomayajulathe link still points me to a closed access paper.@Kate Rasheedare you able to access this paper?

Kate Rasheed (03:07:21) (in thread): > Wooow. Thanks for clarifying@Adeshile Oluwatosin. It’s just different papers suggestions that is bringing confusion. > > I guess the discussion page needs to be updated.

Mildred Anashie (03:08:02) (in thread): > @Adeshile Oluwatosinthe discussion page says Clostridium XIVa should be curated as it is:thinking_face:@Kavya Ayalasomayajulawell done on your curation I’ll give this a look

Aleru Divine (03:08:23) (in thread): > That is kind of surprising@Adeshile Oluwatosinconsidering it is not on the discussions page. Could you share the link that confirms this as Lachnospiraceae please?
> > Google says it’s also known as Clostridium coccoides and this is what@Esther Afuaperesolved it as in the discussions page and also stated to curated as Clostridium XIVa since this is not on NCBI yet. - File (JPEG): IMG_1688

Kate Rasheed (03:10:00) (in thread): > @Aleru DivineI can’t access the paper too.

Adeshile Oluwatosin (03:12:20) (in thread): > Check this:https://pmc.ncbi.nlm.nih.gov/articles/PMC7232163/#:~:text=The%20Lachnospiraceae%20family%20is%20a,Figure%201)%20%5B13%5D. - Attachment (PubMed Central (PMC)): The Controversial Role of Human Gut Lachnospiraceae > The complex polymicrobial composition of human gut microbiota plays a key role in health and disease. Lachnospiraceae belong to the core of gut microbiota, colonizing the intestinal lumen from birth and increasing, in terms of species richness and …

Adeshile Oluwatosin (03:12:48) (in thread): > “The Lachnospiraceae family is a phylogenetically and morphologically heterogeneous taxon belonging to the clostridial cluster XIVa of the phylum Firmicutes “@Mildred Anashie@Aleru Divine

Aleru Divine (03:18:03) (in thread): > @Kate Rasheedthis paper has been reviewed and it has the data transformation for spearman’s correlationhttps://bugsigdb.org/Study_849 - Attachment (BugSigDB): Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes - BugSigDB > INTRODUCTION: South Asian refugees experience a high risk of obesity and diabetes yet are often underrepresented in studies on chronic diseases and their risk factors.

Mildred Anashie (03:25:19) (in thread): > Thank you for this@Aleru Divine:blush:….@Kate Rasheedcould you share your article too, just incase the data transformation for spearman can differ depending on what the researchers did

Aleru Divine (03:25:50) (in thread): > @Mildred Anashie@Adeshile Oluwatosin@Kate Rasheedcorrect me if I’m wrong but I don’t think this means Clostridium XIVa should be curated as Lachnospiraceae. > > What I think this means is that the Lachnospiraceae family is part of (belongs to) the Clostridial cluster XIVa, but it doesn’t mean that Clostridium cluster XIVaisLachnospiraceae. Instead, Lachnospiraceae is one of the families that fall under this cluster. I still don’t think it’s Lachnospiraceae.

Aleru Divine (03:27:18) (in thread): > @Kavya Ayalasomayajulais it possible to download and share the pdf here?:pleading_face:

Aleru Divine (03:28:21) (in thread): > Brilliant!@Mildred Anashie:hugging_face:I agree@Kate Rasheed

Kate Rasheed (03:28:51) (in thread): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-022-01364-2@Mildred Anashie@Aleru Divine. The data transformation wasn’t stated:smile: - Attachment (BioMed Central): Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis - Microbiome > Background The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE). Prior studies have demonstrated that the multiple sclerosis gut microbiota can contribute to disease, hence making it a potential therapeutic target. In addition, antibiotic treatment has been shown to ameliorate disease in the EAE mouse model of multiple sclerosis. Yet, to this date, the mechanisms mediating these antibiotic effects are not understood. Furthermore, there is no consensus on the gut-derived bacterial strains that drive neuroinflammation in multiple sclerosis. Results Here, we characterized the gut microbiome of untreated and vancomycin-treated EAE mice over time to identify bacteria with neuroimmunomodulatory potential. We observed alterations in the gut microbiota composition following EAE induction. We found that vancomycin treatment ameliorates EAE, and that this protective effect is mediated via the microbiota. Notably, we observed increased abundance of bacteria known to be strong inducers of regulatory T cells, including members of Clostridium clusters XIVa and XVIII in vancomycin-treated mice during the presymptomatic phase of EAE, as well as at disease peak. We identified 50 bacterial taxa that correlate with EAE severity. Interestingly, several of these taxa exist in the human gut, and some of them have been implicated in multiple sclerosis including Anaerotruncus colihominis, a butyrate producer, which had a positive correlation with disease severity. We found that Anaerotruncus colihominis ameliorates EAE, and this is associated with induction of RORγt+ regulatory T cells in the mesenteric lymph nodes. Conclusions We identified vancomycin as a potent modulator of the gut-brain axis by promoting the proliferation of bacterial species that induce regulatory T cells. In addition, our findings reveal 50 gut commensals as regulator of the gut-brain axis that can be used to further characterize pathogenic and beneficial host-microbiota interactions in multiple sclerosis patients. Our findings suggest that elevated Anaerotruncus colihominis in multiple sclerosis patients may represent a protective mechanism associated with recovery from the disease. Video Abstract

Mildred Anashie (03:29:14) (in thread): > Yea@Aleru DivineI believe the statement doesn’t imply that the taxa should no be curated that way

Kate Rasheed (03:32:51) (in thread): > @Mildred Anashie@Adeshile Oluwatosin@Aleru DivinePlease check the pairwise comparison. It was stated that LEfSe was used for compositional difference although the pairwise comparison doesn’t look like LEfSe. > > Is it okay to still use LEfSe as the statistical test for Fig.4 although we have the supplementary figure showing LEfSe.

Kate Rasheed (03:34:10) (in thread): > Thanks for the explanation@Aleru Divine. What do you think@Adeshile Oluwatosin. > > I guess pending when it is resolved on the discussion page, we should curate it that way.

Aleru Divine (03:34:23) (in thread): > I think it’s relative abundance@Mildred Anashie:thinking_face:

Aleru Divine (03:34:37) (in thread): > I’ll check that@Kate Rasheed

Mildred Anashie (03:37:11) (in thread): > I have been trying to find this article…Somehow I couldn’t find the issue on GitHub, but I found this (seems to not carry complete information)https://sci-hub.se/10.1016/j.eplepsyres.2018.06.015

Aleru Divine (03:37:29) (in thread): > Figure 4 isn’t LEfSe@Kate Rasheed

Adeshile Oluwatosin (03:40:06) (in thread): > Alright dear > I would check > Well done@Kate Rasheed

Aleru Divine (03:41:26) (in thread): > I’mtrying to open this link,it’staking so long.

Mildred Anashie (03:43:03) (in thread): > It’s open from my end@Aleru Divine…. You can also search the title of the article on SCI HUB

Aleru Divine (03:47:12) (in thread): > Thank you@Mildred Anashieit’sopen:partying_face:

Kate Rasheed (03:52:59) (in thread): > What would it be:thinking_face:@Aleru Divine

Kate Rasheed (03:58:39) (in thread): > @Kavya AyalasomayajulaWell-done on your curation. > > Experiment 1 condition should beKetogenic diet.Experiment 2 condition can beresponse to ketogenic diet since they diagnosed patients after the KD therapy to see the effects.

Aleru Divine (03:59:16) (in thread): > I checked statistical analysis and Ithinkit’sMann-Whitney@Kate Rasheedthe reason is,I’vehad something similar:sweat_smile:I could be wrong/rightI’mnot 100.Let’swait for other opinions and feedback.

Mildred Anashie (04:01:19) (in thread): > I believe its relative abundance too@Aleru Divine@Kate Rasheed

Kate Rasheed (04:03:12) (in thread): > I saw Mann-whitney but the figure caption says different:smile:. > > Let me curate it as Mann-whitney

Adeshile Oluwatosin (04:08:20) (in thread): > @Kate RasheedFigure 4 is not LeFSeRelative abundance it is > As for the statistical analysis, still checking

Aleru Divine (04:08:42) (in thread): > The caption doesn’t say what statistical test was used.@Kate Rasheed:thinking_face:why I thinkit’sMann-Whitney is, “the Mann-Whitney test was used for comparisons between two groups.”

Mildred Anashie (04:23:44): > Hi team, > I am working on this study and I’ll appreciate feedback on how I can curate the following, Is figure 4 curatable? Should I curate the ANCOM BC results in supplementary Table 6 and 7? > > Link to article:http://dx.doi.org/10.1186/s42523-024-00355-y - Attachment (BioMed Central): Changes in social environment impact primate gut microbiota composition - Animal Microbiome > Background The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet. Results We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families — Lactobacillaceae and Clostridiaceae — demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet. Conclusions Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.

Kate Rasheed (04:24:42) (in thread): > Welldone@Mildred Anashie. I’ll look through

Mildred Anashie (04:25:26) (in thread): > @Aleru Divinethe paper cites Fig. 4 alongside S4 and S4 says Lefse, I think that’s what she is referring to

Kate Rasheed (04:26:48) (in thread): > Yes@Aleru DivineI saw that. The caption says compositional differences… and under statistical analysis, the paper says compositional differences was measured with LEfSe that’s why I’m quite confused.

Kate Rasheed (04:27:28) (in thread): > Thanks for the data transformation for Spearman. I used relative abundance and needed to be sure.@Aleru Divine@Adeshile Oluwatosin@Mildred Anashie:star-struck:.

Aleru Divine (04:27:45): > Good morning everyone, > I’dappreciateapeerreview of this study.I’m concerned about the condition and the confounding factors controlled for. It seems that the confounders were not controlled for in the differential abundance test. Can you help confirm this please:pray:Thank you so much - Attachment (BugSigDB): Intestinal permeability before and after albendazole treatment in low and high socioeconomic status schoolchildren in Makassar, Indonesia - BugSigDB > Intestinal helminths are highly prevalent in low-SES children and could contribute to poor health outcomes either directly or via alteration of the gut microbiome and gut barrier function.

Kate Rasheed (04:28:58) (in thread): > Welldone@Aleru Divine. I’ll look through.

Aleru Divine (04:30:11) (in thread): > @Mildred Anashie@Kate RasheedI’m refering to figure 4 for Mann-Whitney.

Aleru Divine (04:31:12) (in thread): > Thank you@Kate Rasheed

Adeshile Oluwatosin (04:31:37) (in thread): > Well done@Mildred AnashieI would go through it

Adeshile Oluwatosin (04:31:59) (in thread): > Well done@Aleru DivineI’llgo through it

Aleru Divine (04:33:22) (in thread): > Thank you@Adeshile Oluwatosin

Mildred Anashie (04:58:16) (in thread): > Hi@Aleru DivineWell done > > I believe treatment works, since the study is focused on the effect of reducing helminth infections through albendazole treatment.Is there response to treatment though? It might work here, if not treatment is fine > Still looking though for the confounders

Kate Rasheed (04:59:41) (in thread): > How about treatment outcome measurement@Aleru Divine@Mildred Anashie

Kate Rasheed (05:00:14) (in thread): > Yes I know@Aleru Divine. Check the caption.

Aleru Divine (05:01:55) (in thread): > Hi@Mildred Anashiewell done.I think table S6 and S7 can be curated.

Aleru Divine (05:02:52) (in thread): > There’sno response to treatment@Mildred AnashieI didn’tsee that when I checked.Thank you Mildred

Kate Rasheed (05:07:38) (in thread): > @Mildred AnashieFigure 4 is curatable. The comparisons with significance should be curated.

Kate Rasheed (05:11:18) (in thread): > For S6 and S7, the LFC shows increase/decrease for time point 2 and 3

Adeshile Oluwatosin (05:11:44) (in thread): > I believe treatment outcome measurement can work > > Because of thetopic itself@Aleru Divine

Aleru Divine (05:12:03) (in thread): > Yes but these aren’t LEfSe plots@Kate Rasheed:sweat_smile:

Adeshile Oluwatosin (05:13:07) (in thread): > @Kate RasheedYou should know by now that the interpretations sometimes can be confusing,that’swhy we sometimes need clear eyes:joy:

Mildred Anashie (05:13:20) (in thread): > Please read what the paper says about ANCOM BC analysis, it talks about completeness…….that’sthe basis for asking@Kate Rasheed@Aleru Divine

Kate Rasheed (05:14:25) (in thread): > Exactly@Aleru Divine@Adeshile Oluwatosin. I’ll curate separately as Mann-whitney. Thank you people.

Aleru Divine (05:15:47) (in thread): > Thank you@Kate RasheedYes@Adeshile OluwatosinI think this works better.

Aleru Divine (05:20:13) (in thread): > Thanks everyone > Please check the confounders too:pleading_face:

Mildred Anashie (05:21:06) (in thread): > Also, please help with how I can interpret increase and decrease for the LEfSe plot, Would it be right to look at increase and decrease from the side with 1e-01 or 1e-04?. The caption says this, paperdoesn’tstate what it implies andI’malso not sure (Single black data points represent individuals outside that range). > > See image - File (JPEG): IMG_2634

Svetlana Ugarcina Perovic (05:28:38) (in thread): > Here is the pdf if you still need it for this great discussion. - File (PDF): zhang2018.pdf

Adeshile Oluwatosin (05:29:34) (in thread): > Okay, thank you@Svetlana Ugarcina Perovic

Kate Rasheed (05:30:43) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (05:34:33) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kate Rasheed (05:35:24) (in thread): > @Mildred AnashieI think what the completeness means is that ANCOM BC was used for further analysis of the data gotten.

Mildred Anashie (05:39:22) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (05:39:48) (in thread): > See this:thinking_face: - File (JPEG): IMG_2635

Kate Rasheed (05:47:04) (in thread): > @Mildred AnashieI could be wrong but we can look at increase/decrease from the angle of box direction. > > If it’s moving to the right that would be increased while if it’s moving to the left, it would be decreased.

Mildred Anashie (05:49:01) (in thread): > @Aleru Divinethumbs up means….?:thinking_face:

Aleru Divine (05:49:45) (in thread): > I think you should curate the ANCOMBC tables@Mildred AnashieAs for the lefse figures, left to right is decreased to increased

Aleru Divine (05:50:56) (in thread): > Thumbs up was for Kate. I am having a really bad network at the moment. Forgive me:sob:

Kate Rasheed (06:15:29) (in thread): > @Kavya AyalasomayajulaI can’t find LDA score threshold in the shared PDF because I noticed it varied for the two experiments. > > I guess it might be in the main article. Can you share a screenshot of the LDA score above 3 and 2?

Kate Rasheed (07:50:55) (in thread): > @Aleru DivineI didn’t know Ruminococcaceae UCG-002 has been resolved:smile:. Thanks for the update. > > I agree to no confounders controlled for in the differential abundance:blush:

Aleru Divine (08:10:37) (in thread): > Thank you@Kate RasheedIhaven’tupdated this study.I’vebeen out for network for about 2 hours:smiling_face_with_tear:

Aleru Divine (09:37:01) (in thread): > @Kavya AyalasomayajulaMHT correction is usually NO for LEfSe. > > I agree with@Kate RasheedResponse to ketogenic diet is a more suitable condition for both experiment actually.Since LDAisn’tspecified, the default LDA score would be 2.0 for both experiments.

Mildred Anashie (09:41:04) (in thread): > The paperdoesn’tstate that MHT was done actually@Kavya AyalasomayajulaSo I agree with@Aleru Divineon this and LDA score should be 2.0!

Kate Rasheed (11:29:55): > Good afternoon@Svetlana Ugarcina Perovic. Kindly delete > Signature 1 in experiment 26 > Signature 2 in experiment 34https://bugsigdb.org/Study_1239Thank you - Attachment (BugSigDB): Mining the microbiota to identify gut commensals modulating neuroinflammation in a mouse model of multiple sclerosis - BugSigDB > BACKGROUND: The gut microbiome plays an important role in autoimmunity including multiple sclerosis and its mouse model called experimental autoimmune encephalomyelitis (EAE).

Svetlana Ugarcina Perovic (11:58:27) (in thread): > Deleted.

Kavya Ayalasomayajula (13:23:27) (in thread): > @Adeshile OluwatosinHow/where would I write a note to specify it is Ruminococcus 2?

Kavya Ayalasomayajula (13:23:38) (in thread): > Also thank you everyone for this wonderful feedback

Mildred Anashie (13:30:00) (in thread): > I hope this is clear enough > > Click the three dots above menu page, then you will see discussion.That’syour studies discussion page, you can leave a note there - File (JPEG): 218c432e-ad7c-4e36-b4f3-9ae393422425

Kavya Ayalasomayajula (13:44:59) (in thread): > @Mildred AnashieThanks!

Kate Rasheed (15:00:00) (in thread): > Thank you

Adeshile Oluwatosin (15:33:13) (in thread): > I hope you are clear enough@Kavya AyalasomayajulaAlso curate clostridium XIVa as it is > I did a deeper research > Well done

Adeshile Oluwatosin (17:19:29): > @Kate RasheedYou can have a look at thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1698177815616049?thread_ts=1698080347.724249&channel=C04RATV9VCY&message_ts=1698177815.616049 - Attachment: Attachment > Please only curate the lowest taxonomic rank. That is to say in this case for the first row do not curate Bacteroidetes, bacteroidia, or bacteroidales–instead curate S24-7 which is a family better known as muribaculaceae (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2005473&lvl=3&lin=f&keep=1&srchmode=1&unlock)

Adeshile Oluwatosin (17:32:36) (in thread): > Apologies I just checked@Mildred AnashieFigure 4 is curatable

Kate Rasheed (18:20:35) (in thread): > @Adeshile OluwatosinThis applies to tables and figures where we have different taxonomy ranks in a row. Chloe has explained to me why this should be done. I don’t think it applies to figures with different results.

Aleru Divine (19:23:55) (in thread): > Thank you@Mildred Anashie:blush:

2024-11-27

Adeshile Oluwatosin (00:38:15) (in thread): > Hello@Kate RasheedI believe it also applies to figures with different results. Where one is of a higher taxonomical rank and one is of a lower taxonomical rank of same contrasts and test.

Adeshile Oluwatosin (00:56:51): > Hello everyone > > Good morning >
> In this particular study, I’m aware Table S3 (as same taxa were reported but in different instances) and S8 (it was mentioned that only 37 genera are significant) seems tobe curatable.I need a bit of clarification on how this should be done. I want to ensure same thoughts are shared before the curation on those tables commences. > > Also both ALDEx2 and Johnckheere-Terpstra test were mentioned and curated as Kruskal-Wallis. Although<@UBNSEMS3S>mentioned ALDEx2 to be curated as Kruskal-Wallis and t-test. > > But this was stated “ The Kruskal–Wallis module was used to identify microbes differentially abundant across all lifestyles, whereas the standard t test module was used for assessing microbes differentially abundant across two conditions.”https://link.springer.com/article/10.1186/s40168-024-01941-7 - Attachment (SpringerLink): Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized - Microbiome > Background Lifestyle plays an important role in shaping the gut microbiome. However, its contributions to the oral microbiome remain less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date. Furthermore, while the oral microbiome seems to differ between foraging and industrialized populations, we lack insight into whether transitions to and away from agrarian lifestyles shape the oral microbiota. Given the growing interest in so-called “vanishing microbiomes” potentially being a risk factor for increased disease prevalence in industrialized populations, it is important that we distinguish lifestyle from geography in the study of microbiomes across populations. Results Here, we investigate salivary microbiomes of 63 Nepali individuals representing a spectrum of lifestyles: foraging, subsistence farming (individuals that transitioned from foraging to farming within the last 50 years), agriculturalists (individuals that have transitioned to farming for at least 300 years), and industrialists (expatriates that immigrated to the USA within the last 20 years). We characterize the role of lifestyle in microbial diversity, identify microbes that differ between lifestyles, and pinpoint specific lifestyle factors that may be contributing to differences in the microbiomes across populations. Contrary to prevailing views, when geography is controlled for, oral microbiome alpha diversity does not differ significantly across lifestyles. Microbiome composition, however, follows the gradient of lifestyles from foraging through agrarianism to industrialism, supporting the notion that lifestyle indeed plays a role in the oral microbiome. Relative abundances of several individual taxa, including Streptobacillus and an unclassified Porphyromonadaceae genus, also mirror lifestyle. Finally, we identify specific lifestyle factors associated with microbiome composition across the gradient of lifestyles, including smoking and grain sources. Conclusion Our findings demonstrate that by studying populations within Nepal, we can isolate an important role of lifestyle in determining oral microbiome composition. In doing so, we highlight the potential contributions of several lifestyle factors, underlining the importance of carefully examining the oral microbiome across lifestyles to improve our understanding of global microbiomes. Video Abstract

Adeshile Oluwatosin (01:02:14) (in thread): > Except there are changes,I’maware of curations done this way. Kindly clarify@Svetlana Ugarcina Perovic<@UBNSEMS3S>What I mean is if there is significant difference between two groups at phyla level e.g Fig 1 > > And significant difference between same groups at Genus level Fig 2 > > Just Fig 2 should be curated

Kate Rasheed (01:20:47) (in thread): > Good morning@Adeshile Oluwatosin. I’ll take a look at this.

Kate Rasheed (01:21:24): > Good morning@Svetlana Ugarcina Perovic. Kindly delete experiment 5 from this study:https://bugsigdb.org/Study_1185Thank you. - Attachment (BugSigDB): Visceral adiposity in postmenopausal women is associated with a pro-inflammatory gut microbiome and immunogenic metabolic endotoxemia - BugSigDB > BACKGROUND: Obesity, and in particular abdominal obesity, is associated with an increased risk of developing a variety of chronic diseases.Obesity, aging, and menopause are each associated with differential shifts in the gut microbiome.

Mildred Anashie (01:27:18) (in thread): > Hi@Adeshile OluwatosinLet me take a look

Kate Rasheed (01:34:34) (in thread): > @Adeshile OluwatosinTable S3 is a one against the rest analysis without confounders controlled for > > Table S8 on the other hand was done with confounders controlled for. > > They are two different results that should be curated separately. One without confounders and the other with confounders. > > Since it’s a one-against-the rest analysis, Kruskal-Wallis test would be the statistical test.

Adeshile Oluwatosin (01:38:49) (in thread): > In Table S3 age and sex were mentioned as covariates. > Also, the whole study has two confounders : geography and technical variability.@Kate Rasheed

Adeshile Oluwatosin (01:42:39) (in thread): > I’m aware Kruskal-Wallis is the testandit’sa one against all analysis. Kindly have a look on what I intend to be clarified on.

Adeshile Oluwatosin (01:43:13) (in thread): > Table S3, the taxa is same across all four tabs > My question is curating same taxa would cause a lot of repetition. Since the major aim is to identify significant taxa across the lifestyles. Which tab is most accurate to curate. > And how can the tab be interpretedI’m thinking Tab 4

Adeshile Oluwatosin (01:43:43) (in thread): > Table S8, it was mentioned that 37 genera were significant.How do I identify these taxa

Adeshile Oluwatosin (01:46:49) (in thread): > When I went through Table S8, I found more than 37 genera to be significant considering 0.05 as the significance threshold

Adeshile Oluwatosin (01:47:22) (in thread): > And both Tables has confounders

Yoko C (02:00:37) (in thread): > Hello, for Table S3, the text says it’s a glm analysis, I don’t think you would curate it since there are no increases or decreases.

Adeshile Oluwatosin (02:03:30) (in thread): > Thank you for your response@Yoko CGlm analysis, the table has obvious adjusted p values and linear progression as the test as they stated it to be a glm analysis. Thats my thoughts towards the curation

Yoko C (02:09:48) (in thread): > I think you would only curate Fig 5

Adeshile Oluwatosin (02:16:22) (in thread): > @Yoko CAsin the supplementary tables should be ignored. I doubt that

Adeshile Oluwatosin (02:16:27) (in thread): > Kindly clarify

Yoko C (02:17:46) (in thread): > Except for table s5 (I think) no other tables show increased or decreased abundances. This table is associated to figure 5C

Yoko C (02:18:16) (in thread): > Maybe figure s11 and s16?

Adeshile Oluwatosin (02:19:39) (in thread): > Yes, there was no specification on increased or decreased abundance that’s why I was unsure on how to go about the curation, > > However Table S2, S4, S5, S3 and S8 > > Significant differences were mentioned in the paper itself

Yoko C (02:22:09) (in thread): > Yes, these tests show which taxa were significantly different, but they don’t specify which groups the difference is for. I think this is because they test all the groups against each other. The text might have more information though, I would have to read it more carefully to see if they mention if those taxa were increased or decreased for different groups.

Yoko C (02:25:01) (in thread): > For example for s4, they say “Results of genera tested for following the lifestyle gradient” this I think means those taxa are significant to the gradient but not necessarily different between groups.

Adeshile Oluwatosin (02:32:58) (in thread): > @Yoko CI can’t see a differential abundance in Figure S16

Adeshile Oluwatosin (02:33:33) (in thread): > For Figure S11, I think it was already referenced in one of the figures or tablesthat’swhy it was initially ignored

Yoko C (02:38:21) (in thread): > i think I see what you mean about s11. S16 shows the difference of Fusobacterium relative abundance between two populations, so I thought that was differential abundance

Kate Rasheed (03:05:40) (in thread): > @Adeshile OluwatosinIf the tables aren’t showing taxa that is increasing or decreasing then we shouldn’t curate it. > > I’ve looked through S2, S3 and S8 and I don’t think they should be curated.

Kate Rasheed (03:07:22) (in thread): > Fig. 4 is curatable as described in the text. There was decreased and increased abundance in industrialization

Adeshile Oluwatosin (03:09:49) (in thread): > Figure 4, 5C and Table S5 has initially been curated.Thank you@Yoko C@Kate Rasheed

Kate Rasheed (03:12:27) (in thread): > I’m wondering how you curated S5:smile:

Adeshile Oluwatosin (03:12:41) (in thread): > Are you also of same opinion of s11 curation. > I doubt S16.If not, in that case this study would have just two experiments

Adeshile Oluwatosin (03:13:22) (in thread): > It was just referenced as a source together with Fig 5C with just one taxa: brachymonas

Aleru Divine (03:16:05) (in thread): > Hi everyone!I’ma little late to the party but I’ll take a look too:sweat_smile:

Yoko C (03:17:37) (in thread): > Is figure 4 curatable? It says: significant across lifestyles, then that they did another test excluding American industrial. So not sure how to interpret that.

Kate Rasheed (03:18:52) (in thread): > No wonder:smile:. S11 has two experiments. > > Smokers vs Nonsmokers > Sinsu consumers vs Non-sinsu consumers@Adeshile OluwatosinS16B is also curatable as pointed out by@Yoko C

Kate Rasheed (03:19:50) (in thread): > @Yoko CFigure 4 is curatable. There was decreased and increased abundance in American industrialization compared to other lifestyles.

Adeshile Oluwatosin (03:23:50) (in thread): > @Yoko Cdefinitely,figure 4 is curatable

Adeshile Oluwatosin (03:24:00) (in thread): > I appreciate@Aleru Divine

Aleru Divine (03:57:17) (in thread): > Table S2, all tabs in table S3, table S4, table S8 are not curatable, I agree.There is no way of knowing the increased and decreased taxa.Figure 4 is curatable, only Streptobacillus and unclassifed Porphyromonadaceae are significantly different across all groups (*).The statistical test used was Kruskal-Wallis.I’mcurious to know how you curated table S5@Adeshile Oluwatosinyou mentioned that it among the onesyou’vecurated already.Figures S11A and S11b are curatable.Idon’tthink they’re referenced anywhere else.They’reboth stand alone experiments.Also, I think the statistical test used here is the t test.“the standard t test module was used for assessing microbes differentially abundant across two conditions.” > > Figure S16b is also curatable I agree.Great thread everyone@Kate Rasheed@Yoko C@Adeshile Oluwatosin

Adeshile Oluwatosin (03:58:33) (in thread): > Hello@Aleru DivineThank you for taking your time to go through the study. > > It basicallywasn’tcurated but just referenced as a source alongside 5C, in that case I probably should remove it to avoid confusion,

Adeshile Oluwatosin (03:58:48) (in thread): > I’lllook through S11 and S16. > > You guys are amazing

Adeshile Oluwatosin (03:59:02) (in thread): > Give me some minutes to come back with the exact study for review:joy::joy_cat:

Adeshile Oluwatosin (03:59:08) (in thread): > Thank you once again my people

Yoko C (04:00:40) (in thread): > For figure 4, the test used I think is similar to Kruskal-Wallis, but even Kruskal-Wallis doesn’t give you the difference between two groups, that’s why I doubted it was curatable.

Aleru Divine (04:03:00) (in thread): > @Adeshile OluwatosinI believe we should only reference the figures or tables we directly curated from, rather than those we didn’t.

Adeshile Oluwatosin (04:07:42) (in thread): > Thank you@Aleru DivineI’maware of that. > > But I added it previously because of the comparisons are same and the taxa was stated in the Table. > > Thanks everyone for the clarification once againI’llcome back with the link to the study for review later on

Adeshile Oluwatosin (04:08:20) (in thread): > @Yoko Cyou brought this up initially, I appreciate and I see your point > Thank you for always

Aleru Divine (04:26:55) (in thread): > Hi@Adeshile OluwatosinI agree with@Kate Rasheedandhere’s why.I think if we are dealing with different tables or figures, all taxonomic levels should be curated. But, if they are on the same table(one row), as in the example you shared, only the lowest taxonomic rank should be curated.

Kate Rasheed (04:29:05) (in thread): > I agree@Aleru Divine. Same thing for figures where taxa are arranged in a row. > > Thank you for your input.

Aleru Divine (04:30:03) (in thread): > Yes, figures too!:sweat_smile:thanks@Kate Rasheed

Svetlana Ugarcina Perovic (04:39:45) (in thread): > GREAT discussion ALL!

Adeshile Oluwatosin (04:40:37) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (04:43:22) (in thread): > Let me confirm:slightly_smiling_face:Here we are talking about two cases: > 1. different taxonomical levels presented as a categorisation for a particular taxon as a signature > 2. differential analysis of different taxonomical levels > In the case 1, we are not curating all the levels listed.

Kate Rasheed (04:44:21) (in thread): > Thank you so much for the confirmation@Svetlana Ugarcina Perovic. This is really helpful.

Svetlana Ugarcina Perovic (04:45:09) (in thread): > Chloe’s example and comment was on the case 1: - File (PNG): Screenshot 2024-11-27 at 10.44.26.png

Kate Rasheed (04:45:28) (in thread): > Yes@Svetlana Ugarcina Perovic. Thank you so much.

Adeshile Oluwatosin (04:45:55) (in thread): > Thank you@Svetlana Ugarcina Perovicso in the intial Illustration I gave > You are suggesting both figures should be curated as they are different figures.

Adeshile Oluwatosin (04:46:33) (in thread): > But same taxa in different taxonomical rank

Adeshile Oluwatosin (04:47:17) (in thread): > I only usedChloe’scase as a reference. > > The main clarification is on if both figures in cases like that should be curated.

Aleru Divine (04:48:29) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (04:50:14) (in thread): > Deleted.

Svetlana Ugarcina Perovic (04:51:00): > Before TODAY’s (Update: TOMORROW) official Outreachy announcement, we would like to CONGRATULATE ALL OF YOU on your outstanding achievement during the Outreachy contribution period! Hope you improved your open source/open science skills and learned new ones, and hope you got even more motivated to continue working in the open source community. > > On Thursday (tomorrow) we will not have our weekly team meeting. Instead you can schedule a 1-1 meeting with me herehttps://calendar.app.google/FtjNsqaCimaxx31P8and discuss your open source/open science plans. I am happy to hear your ideas and support your career growth. > > Once again,thank you ALL for your GREAT work!Your mentors<@U1LCB8WEA><@UBNSEMS3S><@U01MW62UDQR>@Chioma Onyido@Peace Sandy@Esther Afuape@Scholastica Urua@Svetlana Ugarcina Perovic

Kate Rasheed (04:54:08) (in thread): > Thank you so much@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Peace Sandy@Chioma Onyido@Scholastica Urua@Esther Afuapefor this community and being available to guide us through this open science contributions. > > It was really an invaluable experience.

Adeshile Oluwatosin (04:55:08) (in thread): > Thank you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Esther Afuape@Scholastica Urua@Peace Sandy@Chioma Onyidofor your great knowledge. > It was an incredible experience for me. > I’m truly honored to be a part of the community as learning is continuous.

Mildred Anashie (04:57:44) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:I have definitely improved and learnt new skills on this journey, andI’mgrateful for the learning experience > > Thank you<@UBNSEMS3S>@Chioma Onyido@Esther Afuape@Peace Sandy@Scholastica Urua:pray:

Svetlana Ugarcina Perovic (05:16:34) (in thread): > My apologies to@Adeshile Oluwatosinfor this confusion, we sorted it out herehttps://github.com/waldronlab/BugSigDBcuration/issues/472

Joy (05:18:54) (in thread): > Thank you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Esther Afuape@Scholastica Urua@Peace Sandy@Chioma Onyidoit has been an incredible journey. I have learned a lot and improved my skills in this curation journey:pray:

Aleru Divine (05:19:10) (in thread): > Thank you so much@Svetlana Ugarcina Perovic<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Scholastica UruaI’m grateful for the guidance, support, and the incredible learning experience. I had a great time, I feel I have grown so much, improved my skills, and I am even more motivated than ever to continue contributing to the open-source community, thanks to this amazing community. > A big thank you to everyone for the peer reviews, insights, and feedback. It’s an honor to keep growing and learning alongside all of you:heart_hands:

Mildred Anashie (05:25:00): > Hi Everyone, > > Anyone has an ideaon how Fisher’s alpha diversity is curated?Thank you:pray:

Adeshile Oluwatosin (05:29:50) (in thread): > Thank you for clarifying@Svetlana Ugarcina PerovicAs I was so sure then,that’swhy I kept insisting. > > Noted now

Yoko C (05:33:29) (in thread): > Thank you all! This has been such a great treat. Having the chance to contribute while learning and growing.

Ebuka Chinwuba (06:02:27) (in thread): > @Svetlana Ugarcina PerovicIt was indeed a golden experience for me. I appreciate the opportunity. Also a resounding thanks to the mentors for guidance during this journey. Good luck to All!

Adeshile Oluwatosin (06:13:37) (in thread): > No idea > > I saw this in a curationI’mworking on as well

Cynthia Iwuoha (06:13:38) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@Esther Afuape@C. Mirzayi (please do not tag this account)@Chioma Onyido@Peace Sandy@Scholastica Urua@Iwaldron, for your incredible support during the contribution period. Your guidance and mentorship have greatly enriched my experience here. Thank you for being such amazing mentors.

BOLARINWA AISHAT (06:13:54) (in thread): > Thank you very much mentors@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Scholastica Urua@Chioma Onyido@Esther Afuape@Peace Sandy<@U01MW62UDQR>@Levi WaldronThank you very much fellow curators@Aleru Divine@Mildred Anashie@Kate Rasheed@Adeshile OluwatosinetcI’mgrateful for the experience

Svetlana Ugarcina Perovic (06:24:02) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710398571165679 - Attachment: Attachment > How do I record Fisher alpha diversity? @Svetlana Ugarcina Perovic @UBNSEMS3S

Adeshile Oluwatosin (06:26:41) (in thread): > Thank you for your response > If it measures evenness, should it be curated as pielou then?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:27:08) (in thread): > It corresponds tospecies richness

Svetlana Ugarcina Perovic (06:27:39) (in thread): > It corresponds tospecies richness

Adeshile Oluwatosin (06:28:50) (in thread): > Alright, notified

Aleru Divine (06:30:03) (in thread): > Oh my days!:exploding_head:thank you@Svetlana Ugarcina Perovic

Aleru Divine (06:31:08) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:face_with_peeking_eye:

Svetlana Ugarcina Perovic (06:40:29) (in thread): > “inverse Simpson is asymptotically equal torarefied species richnessin sample of two individuals, and Fisher’s α is very similar toinverse Simpson.” > I would stick to Richness.

Aleru Divine (06:46:50) (in thread): > Thank you for the explanation@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:47:26): > FREE course:https://www.biocodexmicrobiotainstitute.com/en/pro/xpeer-course-microbiota-intimate-woman-health-through-lifespan - Attachment (Biocodex Microbiota Institute): Xpeer course: Microbiota in intimate woman health through the lifespan > Gynecologists, midwives, and pharmacists, get free training on “Microbiota in intimate woman health through the lifespan” from Professor Alessandra Graziottin in this CME course.

Adeshile Oluwatosin (06:48:05) (in thread): > This is great:relieved:Thank you

Mildred Anashie (06:56:06) (in thread): > Thank you so much@Svetlana Ugarcina PerovicI had a gut feeling it was Richness and curated as Richness. Needed this explanation, as I could have been wrong > > Thank you again:pray:

Rahila-me (07:14:46) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@Esther Afuape@Chloe Mirzayi@Chioma Onyido@Peace Sandy@Scholastica Urua@Iwaldron, > I am greatful for the experience > Thank you for being such an amazing mentors.

Rahila-me (07:16:59) (in thread): > @Svetlana Ugarcina PerovicThank you for this

Cynthia Iwuoha (08:01:41) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kate Rasheed (08:06:27) (in thread): > Thank you for this@Svetlana Ugarcina Perovic.

Kate Rasheed (08:06:48) (in thread): > Thank you for sharing.

UBNSEMS3S (09:44:27) (in thread): > Thank you all so much for your contributions. Every time we participate in Outreachy, I am always blown away by the hard work, intelligence, and dedication of all our applicants. You did not make the selection process easy for us!

BOLARINWA AISHAT (09:46:44) (in thread): > Thank you for sharing

Aleru Divine (09:59:11) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (14:14:10): > Hello everyone > > I’m back like I mentioned > Kindly reviewhttps://bugsigdb.org/Study_1240 - Attachment (BugSigDB): Nepali oral microbiomes reflect a gradient of lifestyles from traditional to industrialized - BugSigDB > BACKGROUND: Lifestyle plays an important role in shaping the gut microbiome.However, its contributions to the oral microbiome remain less clear, due to the confounding effects of geography and methodology in investigations of populations studied to date.

Mildred Anashie (14:17:48) (in thread): > Hi@Adeshile OluwatosinWell done > > In figure 5c I believe you have more than one experiment, unless I am getting it wrong > > Anyway let me take a look at the study again

Adeshile Oluwatosin (14:18:53) (in thread): > Hi@Mildred AnashieThank you for your reviewI’mcertain only brachmonas should be curated, Chloe has clarified that in the previous office hour

Mildred Anashie (14:21:39) (in thread): > Okay > > Are you referring to figure 5b? BecauseI’mwondering why only grain was selected, if 5c is curatable:thinking_face:

Adeshile Oluwatosin (14:22:58) (in thread): > I’mreferring to Figure 5c, only that was curated as it is the only taxa with p adjusted value

Mildred Anashie (14:30:13) (in thread): > 5c? > I see a lot of taxa showing significance:thinking_face:with asterisk (*) indicating significance

Adeshile Oluwatosin (14:31:51) (in thread): > Look closely, only brachymonas has two asterisks

Adeshile Oluwatosin (14:32:03) (in thread): > Indicating an adjusted p value

Adeshile Oluwatosin (14:32:31) (in thread): > Chloe mentioned the curation should be as simple as possiblewhen I asked in her explanation

Mildred Anashie (14:33:33) (in thread): > That makes alot of sense > > I see it now:clap:

Aleru Divine (17:35:17) (in thread): > Hi@Adeshile Oluwatosinwell done:clap:I’ll give this a review:blush:

Aleru Divine (19:59:41) (in thread): > Hi@Adeshile OluwatosinI went through the study and I have a few concerns > > For Experiment 1, only Streptobacillus and unclassified Porphyromonadaceae were significantly different and should be curated. In addition to this, I’d like to understand why you curated the alpha diversities as unchanged, given the significant differences reported in Figure 2. > “We observe no significant difference in Shannon diversity across the lifestyle groups (p > 0.05, Kruskal–Wallis; Fig. 2), but there is a significant difference in Faith’s phylogenetic diversity between the lifestyles (p = 0.028; Kruskal–Wallis, Fig. 2).” > > For Experiment 2, the figure you curated actually identified the specific lifestyle factors within Nepal that are associated with differences in microbiome composition. But your contrast groups are Expats and Nepalis, Is there a reason you curated it this way? From my understanding of figure 5B and 5C, this particular experiment should compareBarley/MaizeandRice/Wheat groups, withunclassified PorphyromonadaceaeandBrachymonasincreased inBarley/Maize. This would mean no sample sizes or alpha diversity measures too.Regarding all the taxa marked with (*) in figure5C, while they are significant, it’s not clear how they should be curated as the study lists the lifestyles but not the specific contrast groups the waythey’vedone in figure 5B. For this reason,I’dagree with not curating them.

Kavya Ayalasomayajula (20:21:06): > Hi all,https://bugsigdb.org/Study_1244. Accepting any feedback for this study. Thank you! - Attachment (BugSigDB): Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets - BugSigDB > OBJECTIVE: The aim of this study was to investigate the composition of the intestinal microbiota and its association with fecal short chain fatty acids (SCFAs) in children with drug refractory epilepsy (DRE) before and after treatment with a ketogenic diet (KD). - File (PDF): Gut flora and metabolism are altered in epilepsy and partially restored after ketogenic diets.pdf

Aleru Divine (21:01:13) (in thread): > Well done@Kavya AyalasomayajulaI believe there are a total of 2 experiments in this study as you had the first time I looked at this study. I am curious to know why you added 2 more experiments.I’d also like to add that your initial curation of this study was excellent. The only exceptions were the taxa you wanted further clarification on, the LDA and MHT correction, as we reviewed earlier in this thread.https://community-bioc.slack.com/archives/C04RATV9VCY/p1732580115917589 - Attachment: Attachment > Hi all, would appreciate feedback on this curation > https://bugsigdb.org/Study_1233 > > I also had some troubles in experiment 2 signature 1 curating figure 3. I had troubles finding colostridium XIVa so I classified as unclassified but unsure if there is a new name for it. Figure 3 also lists Ruminococcus2. I am unsure if the “2” was a typo because I couldn’t find this in the taxonomy identifier

Adeshile Oluwatosin (21:21:57) (in thread): > Hello@Aleru DivineI’lladdress your concerns now

Yoko C (21:24:59) (in thread): > Hello, going through the paper, these are some of my observations for experiment 1, I think the paper specifies the siblings were matched on age and gender. For the statistical test, you only want the one that shows the results, in this case, only LEfSe. Everything else is good, maybe the description for the source can be a little better, for example you can include it is a Lefse graph and you can specify its a comparison on the differential abundance. Oh, and the transformation isn’t specified so you would use the default relative abundance. For experiment 2, figure 4 doesn’t show significant differences between KD1 and KD2, only KD1 vs HC and KD2 vs HC. The figure does specify Wilcoxon was used and the p value as well. I see you used ketogenic diet in experiment 1 and response to ketogenic diet for experiment 2, I think response to KD is good for all your experiments.

Adeshile Oluwatosin (21:31:33) (in thread): > Well done@Kavya Ayalasomayajula

Adeshile Oluwatosin (21:38:04) (in thread): > Experiment 1: when you go through the study, you would understand that the test was performed with Johnckheere-Terpstra test and ALDeX2 test was also performed. > Of all taxa found significant with johnckheere test, only streptobacillus and unclassified porphyromonadaceae were also significant based on ALDEx2. My curation is accurate.“Taxa marked with * are also significantly differentially abundant across lifestyles based on ALDEx2.”I’m reporting the curation referencing johnckheere-terpstra as the test, it’s not permissible hence the use of kruskal Wallis, which will be noted up there.

Adeshile Oluwatosin (21:42:59) (in thread): > For alpha-diversity: if you look through Supplementary Figure 4, all diversities were mentioned there. > > So all should beleft blankas there’s no direct comparison according to the group names mentioned in the experiment. (Combination of Foragers, recently settled, agriculturalists, expats vs American industrial). > > The significant comparison in Faith is between only two groups (foragers vs American industrial), (recently settled vs American industrial) etc

Adeshile Oluwatosin (21:43:10) (in thread): > I’m clear on just brachymonas to be curated.

Adeshile Oluwatosin (21:53:40) (in thread): > Check out the confounders instead, those were mentioned to be used throughout the study.

Yoko C (22:03:29) (in thread): > Finally for figure 5 I see two sets of comparisons, KD1 vs HC and Good vs HC. Make sure to check the text for the figure to find the test and other details.

Kavya Ayalasomayajula (22:30:25) (in thread): > @Aleru Divinethanks for the feedback but I wonder if there was a mix up! This curation is from a different paper than the post I made from a few days ago. Similar topic. In this particular paper authors compared KD treatment group to healthy controls and did a within group comparison of the KD responders and non responders. That is why I chose to curate four experiments. Let me know if that makes sense thank you

Adeshile Oluwatosin (23:02:50) (in thread): > @Aleru Divine

Kate Rasheed (23:41:12) (in thread): > Hello@Kavya Ayalasomayajula. Weldone on your curation. I see this is a different study. > > The condition for experiment 1 should be:Response to Ketogenic dietas stated by@Yoko CGroup 1 should be fully described as Pre-Ketogenic Diet Drug resistant epilepsy group(pre-KD DRE group) > > The healthy siblings were matched onage and sex.

2024-11-28

Kate Rasheed (00:17:18) (in thread): > Also, three statistical tests were used for experiment 1. LEfSe, Metastat and Mann-whitney. These would be curated separately.

Kate Rasheed (00:23:02) (in thread): > Just as@Yoko Cpointed, there was no significant result for KD1 and KD2. You might need to change the experiment to Healthy control vs Pre-KD using Mann-whitney > > For the responders experiment, I believe the statistical test is Metastats.

Kate Rasheed (00:27:19) (in thread): > This should be different experiments as well@Kavya Ayalasomayajula”******And we further investigated the difference between gene mutation and the change of microbiome. The linear discriminant analysis (LDA) effect size (LEfSe) method was used to estimate the effect of each differentially-abundant taxon and discriminate the most biological one. The results showed that genus Tannerella, sulfurospirillum were more abundant in patients with positive gene mutation before KD treatment, and Parabacteroides significantly increased after KD treatment in patients with gene mutation. For patients without gene mutation, we found the abundance of Dactylosporangium was more abundant prior to the KD therapy and Hungatella significantly increased after KD.******” > > The source description would be “Within-text result”

Kate Rasheed (00:39:00) (in thread): > In total we have these experiments > > HC vs KD1(Pre-KD) - LEfSe > HC vs KD1(Pre-KD) - Mann-whitney > HC vs KD1(Pre-KD) - Metastat > HC vs KD2(Post-KD) - Mann-whitney > Adequate responders vs HC - Metastat > Positive gene mutation before treatment vs after treatment - LEfSe > Patients without gene mutation before treatment vs after treatment - LEfSe.

Kate Rasheed (00:49:31) (in thread): > As stated in the paper, the study design is aprospective cohort study

Aleru Divine (00:50:38) (in thread): > Oh my days! I used the one provided by@Svetlana Ugarcina Perovicearlier thinking it was the same paper.:sob:My apologies@Kavya Ayalasomayajulathe mix up is from my end

Aleru Divine (00:52:35) (in thread): > I’lllook at this particular paper

Aleru Divine (01:11:39) (in thread): > Hi@Adeshile Oluwatosinthanks for the update. For the first concern, I still think it’s still the the two signatures because remember the statistical analysis in the paper is was done using ALDEx2. > “Differential abundance analysis was conducted with microbiome count data agglomerated to the genus level using the ALDEx2 v.1.29.2.1.” > > “Because overall microbiome composition differed based on lifestyle, we next determined which specific taxa differed across the lifestyles. To do this, we conducted differential abundance analysis using ALDEx2, which accounts for compositionality in its application [41]. We observe that 2 of the 111 oral genera (1.8%) were significantly differentially abundant after accounting for multiple tests, namely Streptobacillus and an unclassified Porphyromonadaceae genus (padj = 0.011 and 0.021, respectively; Kruskal–Wallis)”. > > This actually points to Kruskal-Wallis. > > I still don’t understand the alpha diversity curation:pleading_face:if there is no direct comparison, then shouldn’t it be left blank? > > And what I understood from what<@UBNSEMS3S>meant during the office hours was that if it was too much for you to curate, you could just curate the (****). But in this case since it’s only this “grain” you should curate, I think you should add the second bacteria, because it was also significant.

Chris Awoke (01:15:19) (in thread): > Thank you so much for all the support,@Svetlana Ugarcina Perovic,<@UBNSEMS3S>,@Scholastica Urua, and all the other mentors. > > To my colleagues, I deeply appreciate your peer reviews and prompt feedback. > > I absolutely love everything about this community and look forward to contributing to this project!

Mildred Anashie (01:24:07) (in thread): > Hi@Kavya AyalasomayajulaI agree with Kate on the experiments. I’ve included the sources. > > HC vs KD1 (Pre KD)- Lefse in Fig 2 > HC vs KD1 (Also Pre KD)- Mann whitney in Fig 4 > HC vs KD2 (Post KD)- Mann whitney in Fig 4 > HC vs KD1(Pre KD) - Metastat in Fig 5 > HC vs Good/Adequate responders – Metastat in Fig 5 > Positive gene mutation before treatment vs after treatment – LefSe (Results text, towards the end of 3.3) > Patients without gene mutation before treatment vs after treatment – LefSe (Results text, towards the end of 3.3) > > Data transformation is Relative abundance not raw count > > Where Significant threshold isn’t mentioned, the default is 0.05 > > The participants were age and gender matched > > For the first experiment Chao1 and Shannon was increased it’s stated in the results text (3.2) > > The alpha diversity in Figure 3 seems to apply to the contrasts in Fig 4

Aleru Divine (01:38:03) (in thread): > @Kavya AyalasomayajulaHaving gone through this paper, I agree with the feedbacks from@Yoko C@Kate Rasheed@Mildred AnashieIn addition, you would curate age and gender as matched on factors for all comparisons to healthy controls that is for the following comparisons:HC vs KD1HC vs KD1HC vs KD2HC vs KD1HC vs Goodresponders@Kate RasheedI believe the study design is correctly curated astime series / longitudinal observational.

Kate Rasheed (01:57:54) (in thread): > See this@Aleru Divine”******Second, a prospective study was performed in the 12 children with DRE who underwent the above analysis before and after 6 months of KD treatment. The fecal samples from the KD treatment candidates before KD treatment were labeled as KD1, and after 6 months of KD treatment, the samples were labeled as KD2******.” > > This was why I said prospective study but it’s fine if it’s a time series/longitudinal study.

Adeshile Oluwatosin (02:11:26) (in thread): > @Kate RasheedA particular reference from the study might not particularly mean it’s the study design itself, > > I believe it’s alongitudinal study

Adeshile Oluwatosin (02:42:00) (in thread): > Thanks once again@Aleru Divine, yeah when there’s no exact comparison, the alpha diversity should be left blank. > > Kindly Have a look at the confounders@Aleru DivineFrom here: “Abundances of nine genera significantly follow the lifestyle gradient. The relative abundances of nine genera significantly follow the lifestyle gradient via a Jonckheere-Terpstra test followed by Benjamini–Hochberg correction (adjusted p < 0.05).” > > “We also implemented an alternative approach for identifying which taxa were following the lifestyle gradient by performing the Jonckheere-Terpstra test for all genera and correcting for multiple tests. We find that nine genera significantly followed the lifestyle gradient, including the two that were also identified using ALDEx2.” > > “We observe that 2 of the 111 oral genera (1.8%) were significantly differentially abundant after accounting for multiple tests, namely Streptobacillus and an unclassified Porphyromonadaceae genus” > > I believe the other 7 taxa are also significant and should still be curated. 2 different tests were specified and 9 genera was also significant after multiple testing. I await other opinionsIn a normal scenario, the two tests would be curated as different expeirments but in this case as they are both not permissible. Curation as Kruskal Wallis is good but writing a note indicating the exact two tests mentioned for that exact experiment (Figure 4) can help with further clarification.I would leave brachymonas as it is. I intend to curate just taxa with p adjusted values as Chloe mentioned. > > Thank you for your checking out the study

Kate Rasheed (02:54:25) (in thread): > @Adeshile OluwatosinUnder the additional information, the significant 9 genera used linear models while the 2 significant genera from ALDEX used Kruskal-Wallis. > > Signature sources would still be figure 4

Kate Rasheed (02:58:37) (in thread): > Confounder for experiment 1 and the new experiment is sex alone. > > See this: “Oral microbiome genera tested for differential abundance across lifestyle with age and sex as covariates. Due to the lack of age data for the American Industrialists, only sex was included in the model tested with all individuals, whereas both sex and age were included in the model tested across the Nepali individuals.”

Adeshile Oluwatosin (02:59:24) (in thread): > Hello@Kate RasheedI’mcurrently going through the study for the mention of linear model to Jonckheere test

Adeshile Oluwatosin (03:00:02) (in thread): > Confounder for experiment 1 is geographical area and technical variability. > > The above mentioned is a confounder for atablewhich is not curatable.

Kate Rasheed (03:04:59) (in thread): > They are similar even if the table isn’t curatable. If you check the paper, you would see the tables were referenced. > > See this: “By focusing on individuals across a range of lifestyles within a confined geographic region, our study aims to discern oral microbial signatures of lifestyle without the confounding effects of geography, climate, and technical factors.” > > If you check above Fig. 4, you would see that sex and age were covariates. However , for American industrialization, age wasn’t used.

Adeshile Oluwatosin (03:12:39) (in thread): > In the case of the 9 genera: I would curate two experiments seperately for Jonckheere-Terpstra test and ALDEx2

Kate Rasheed (03:13:00) (in thread): > The confounders for experiment 2, 3 and 4 are sex and age

Adeshile Oluwatosin (03:25:55) (in thread): > This study hmmm > > Importantly, we are able to isolate the role of lifestyle from confounders, as geographical and technical variability are controlled for in the study with the inclusion of multiple lifestyles solely from Nepal.

Kate Rasheed (03:32:06) (in thread): > The confounders you used was for Nepal study alone. This one is for Nepal and USA:smile:.

Svetlana Ugarcina Perovic (03:41:16): > :teapot:Good morning, how are you today?:coffee:What did you grasp from two months of BugSigDB-ing?

Adeshile Oluwatosin (03:46:00) (in thread): > I’llgo over the study again:joy:

Joy (03:48:45) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing

Kate Rasheed (04:12:48) (in thread): > Good morning@Svetlana Ugarcina Perovic. I’m fine thank you for asking. Tea please:smile:. > > From two months of BugSigDB-ing, I’ve learnt to ask questions for clarity, and not assume. > > I’ve also learnt to ask for help and render help(I see this as the primary goal of the community). > > Finally, no one knows it all, hence, the need to collaborate and engage in discussions. > > Thank you for this amazing community:hugging_face:. > > PS. I was intrigued to find out that Bacteria is No. 2 under NCBI taxonomy browser:smile:.

Aleru Divine (04:14:08) (in thread): > I understand your point@Kate Rasheedthis kind of happens a lot.:sweat_smile:Thisexcerptis still describing a longitudinal study.

Aleru Divine (04:19:19) (in thread): > Thank you@Kate Rasheed@Adeshile OluwatosinI’llgo throughagaincarefully to confirm the confounders.

Adeshile Oluwatosin (04:27:15) (in thread): > Good morning@Svetlana Ugarcina Peroviccoffee today. > I need to be awaken:hugging_face:For the past two months of curating. I’ve learnt how important communicating is and how it’s a continuous learning process. > > I’ve been able to work on way more articles, learn on diseases, methods, what causes them, and sometimes I dive into finding out if there’s a cure for these diseases. > > As a biochemist, I really enjoy anything related to research about human health and curating has expanded my knowledge in this area. > > Thank youagainfor the opportunity.

Adeshile Oluwatosin (04:28:09) (in thread): > Thank you my darlingIactually appreciate@Aleru Divinel

Joy (04:43:30) (in thread): > Good morning@Svetlana Ugarcina Perovic!:coffee:I’m doing well, thank you! > From two months of BugSigDB-ing, I’ve grasped the importance ofmeticulous data curationin identifying microbial signatures, the role of robust metadata in enhancing research reproducibility, and how microbial shifts connect to human health and disease. It’s been a rewarding dive into bioinformatics and scientific collaboration!:star2:

Aleru Divine (05:08:22) (in thread): > Good morning@Svetlana Ugarcina Perovic:coffee:I’m very well, thank you! I hope you are too. > > Over the past two months and beyond, I’ve learned to communicate better, ask for help when I’m stuck, and learnedto collaborate more. I’ve also gotten more comfortable reaching out and offering help on studies. > > The most fascinating part for mein all of this isactually reading the papers and understanding how disease conditions, medications, diet, anda lot offactors can alter the human microbiome (even before I start the curation process). It’s amazing how some things can have such a big impact. > > One of the plenty remarkable things I’ve learned is how certain bacteria can predict if you’re at risk of developing a disease. One of the studies I curated tried to predict cardiometabolic risk using the presence of some bacteria in the gut as biomarkers and also checked if the oral microbiome can be used for such predictions. It is absolutely incredible to see these connections across a lot of curated studies in BugSigDB. > > This work is very inspiring, and I’m really proud to be part of this community.

Cynthia Iwuoha (05:34:30) (in thread): > Good morning@Svetlana Ugarcina Perovic, I’m doing great, trust you’re good too. Tea please. > > From my two months of engaging with BugSigDB, I’ve gained invaluable insights into the significance of effective communication within a community. Curating articles has not only enhanced my understanding of various bacterial diseases but has also deepened my knowledge about the complex of scientific curation. > This experience has taught me the importance of sharing accurate information, collaborating with others, and advancing my understanding of microbiology. > My time with BugSigDB has been enriching, fostering both personal and opportunity for professional growth in the field of bacterial research. > I am grateful for this opportunity

Mildred Anashie (05:41:15) (in thread): > Good morning@Svetlana Ugarcina Perovic:coffee:I’mdoing well today, Thank you:blush:The past two months has been an incredible journey of learning, unlearning and relearning. > > One of the things that fascinates me always, has to be the numerous microorganisms out there and how they affect the gut microbiota, and to think that so many are still unidentified:face_with_open_eyes_and_hand_over_mouth:.I’vealso understood the power in collaboration, and the need to always double check (most times triple check:smile:) before making conclusions. > > The importance of team work and being a part of a team > > BugSigdb-ing has truly enhanced my knowledge in research and I’m grateful for this community

Adeshile Oluwatosin (06:21:51) (in thread): > @Aleru DivineI’mstill awaiting a response

Adeshile Oluwatosin (06:24:49) (in thread): > @Aleru DivineI’mstill awaiting a response:pleading_face:

Rahila-me (07:16:01) (in thread): > Good morning! I’m doing well, thank you—how about you?:coffee:Please > From two months of contributing to BugSigDB, I gained valuable insights into managing open-source projects, particularly in the field of research-based datasets. Here are my key takeaways: > 1. Domain Understanding: I developed a deeper understanding of the relationship between microbial signatures and diseases, which expanded my perspective on bioinformatics. > 2. Collaboration: Being part of a collaborative effort improved my teamwork and communication skills, especially in interdisciplinary fields. > 3. Version Control and Documentation: Managing contributions taught me the importance of thorough documentation and using Git effectively for collaborative coding.

Ebuka Chinwuba (07:40:51) (in thread): > I’m Fine Thank you@Svetlana Ugarcina PerovicI grasped a whole lot, Firstly, I Understood the role of BugSigDB, that it serves as a critical repository for organizing microbiome signatures, making it easier to study microbial patterns associated with specific conditions or environments. > > I Learned how to identify and interpret microbiome signatures across various datasets and gained knowledge about how microbiome signatures are associated with specific conditions or environmental factors. > > Also I enhanced my critical thinking by cross-referencing studies to ensure data accuracy and reliability. Asking questions and doing a collaborating work. > > Lastly, connecting theoretical knowledge to real-world applications, particularly how curated data supports further research into microbiome-associated diseases or conditions. I appreciate the collaborative aspect of contributing to a resource that supports global microbiome research. Experiencing how community contributions, like those on BugSigDB, support larger scientific efforts.

Aleru Divine (07:56:34) (in thread): > My apologies@Adeshile OluwatosinI was a bit occupied.I’ll go through this now

Yoko C (08:02:51) (in thread): > Good morning all! Most recently I was captivated by the effort that goes into shareable and usable information at a large scale, for example the ontologies, vocabularies, organism IDs, pathways, databases, updates, software, mentorship, ect. Of course producing information that can be used by others has always been a focus of science but seeing it “behind the scenes” was very interesting. Some things that have taken a “grasp of me” are thinking about how hard it is to not jump to conclusions, be it from reading a paper and its amazing results or from assumptions made on what one thinks they know. I really enjoyed the process of making questions, revisiting details, communicating.

Yoko C (08:21:12) (in thread): > Hello. So, talking about confounders something that I am confounded on:upside_down_face:is if we add confounders that were used for the overall paper or section of the paper, or if we add the ones used for the specific test. In this study there are several experiments that come from T-tests, which to my understanding, is a type of test where you can’t really include confounders. Of course, before the test you can separate by groups, stratify by age, ect, but the test itself doesn’t include confounders. I have seen reviewed studies where confounders are included in the experiment even though the test was Mann-whitney, so I am quite uncertain about the specific way we should curate them.

Aleru Divine (08:31:05) (in thread): > You made a lot of sense@Yoko C:pleading_face:I’ve seen some studies control for specific confounders in particular tests or comparisons, while some do adjustments for confounders across the whole study,so we gotta be careful with identifying and curating them.I’mstill going through this study andhaven’tcome to a conclusion yet.

Adeshile Oluwatosin (08:35:29) (in thread): > Thank you@Yoko Cfor your response. > > I’ve had to read through the study over and over again on specifying the confounders. Thank you for your input > > I totally get what you are saying as well

Mildred Anashie (09:47:34) (in thread): > Hi@Adeshile OluwatosinI know this curation is already done but based on the confounders and experiments this are my observations. I apologize this is coming late:pray: > * So I believe Fig 4 might have two experiments because the figure legend seems to be reporting results for both ALDEX2 and Jonckheere-Terpstra. I do not see covariates or confounders for those. Also, you might have to leave alpha diversity blank as I do not see alpha diversity for one against all experiments (But sup fig 5 might be pointing to this, if that is right then they would all be unchanged). > * Table S4 and Fig 4 are showing the same taxa that are significant for Jonckheere-Terpstra while Table S2 is showing the ALDEX2 results in Fig 4. > * The covariates (sex and age) are accounted for in Table S3 and the results are differential abundance and I’m still unsure how you would curate but you would focus on the columns with BH at the end e.g lifestyle2.Recently Settled:pval.BH. The statistical test is Generalized Linear Model. > * Also see the Table Legend that explains what was done but the contrasts are unclear “Oral microbiome genera tested for differential abundance across lifestyle with age and sex as covariates.Due to the lack of age data for the American Industrialists, only sex was included in the model tested with all individuals, whereas both sex and age were included in the model tested across the Nepali individuals. The glm module was utilized andp-value correction was applied using the Benjamini-Hochberg method. Both unadjusted (kw.ep) and adjustedp-values (kw.eBH) are shown, and adjustedp-value < 0.05 is the threshold for significance.Tab 1 shows the output for the glm model withno covariates and all individuals.Tab 2shows the output for the glm modelwith sex as a covariate and all individuals.Tab 3shows the output for the glm modelwith no covariates and only Nepali individuals.Tab 4shows the output for the glm modelwith both sex and age as covariates and only Nepali individuals.” > * Also see this from the Differential abundance section ‘To validate that our findings are robust to the inclusion of sex and age as covariates, the GLM module was used. Because the outputs for the two modules differ, the data was reanalyzed with and without covariates for comparison purposes. Furthermore, because we are missing age data for the American industrialists, this comparison was conducted twice: once with all individuals and sex as the only covariate, and once with the Nepali individuals and both sex and age as the covariates. To account for multiple tests, the Benjamini–Hochberg method forp-value correction was applied. Adjustedp-values < 0.05 were considered significant’. > * Finally, I think just Sex and age were confounders controlled for and not in all the experiments. I saw this for the other confounders mentioned “By focusing on individuals across a range of lifestyles within a confined geographic region, our study aims to discern oral microbial signatures of lifestyle without the confounding effects of geography, climate, and technical factors’. So I believe by grouping based on lifestyles in the populations they didn’t have to control for the other confounders they mentioned.

Aleru Divine (09:58:35) (in thread): > @Adeshile Oluwatosinhaving gone through this again, please change the location of subjects for experiments 2, 3 and 4 to Nepal since these experiments involved studying populations within Nepal.Thank you for the feedback@Mildred AnashieI agree with these confounders too. > > And I understand thatage and sexwere the confounders controlled for in experiments 2, 3 and 4 (Nepal populations) while onlysexwas controlled for in the comparisons across all populations.

Adeshile Oluwatosin (09:58:51) (in thread): > Hello@Mildred AnashieThank you for properly looking through the study, > > Yes, Figure 4 was curated as 2 experiments. > Alpha diversity as well is also curated to be left blank now, there’s actually no direct comparisons between the two groups stated for experiment 1. > > The supplementary information gave more details on confounders. > And from most of the references. I see that Experiment1,5 and 6 has sex as a confounder. Experiment 2,3,4 has sex and age as a confounders

Adeshile Oluwatosin (10:01:59) (in thread): > @Aleru DivineThanks for pointing that out. > > The curation is accurate now. > > Thank you guys for always

Mildred Anashie (11:31:02): > Congratulations@Aleru Divineand@Kate Rasheed:confetti_ball::tada:

Adeshile Oluwatosin (11:32:19): > Congratulations@Kate Rasheed@Aleru DivineWell done

Aleru Divine (11:39:44) (in thread): > Thank you so much@Mildred Anashie:heart:

Aleru Divine (11:40:13) (in thread): > Thank you so much@Adeshile Oluwatosin:heart:

Kate Rasheed (11:40:56) (in thread): > Thank you so much@Mildred Anashie

Kate Rasheed (11:41:08) (in thread): > Thank you so much@Adeshile Oluwatosin

Samuel Nnanna (11:47:54): > Ayeeee:champagne::confetti_ball::confetti_ball:congratulations@Kate Rasheedand@Aleru DivineAnd a big thank you to everyone on here. I really did learn a lot and the short time here made my goals a bit more defined; merging health and tech. > > Looking forward to whatI’dachieve with the knowledge from here. > Thank you to the mentors@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Esther AfuapeOnce again, congratulations to you guys:confetti_ball::confetti_ball:

Aleru Divine (11:50:07) (in thread): > Thank you so much@Samuel Nnanna:heart:

Kate Rasheed (11:50:51) (in thread): > Thank you so much@Samuel Nnanna

Kate Rasheed (11:59:58): > Good evening people:star-struck:. I am quite short of words but I’ll release the short words:smile:. > > Congratulations to@Aleru Divine. I remember your introduction statement and I’m really glad the third time was the charm for you. This is a victory well deserved. You’ve really worked hard. > > To my mentors@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Esther Afuape@Peace Sandy@Chioma Onyido@Scholastica Urua, thank you for finding me worthy of this internship and giving me the platform to nurture my newly found passion for Microbiome curation. I believe I won’t let you down. > > To my fresh eyes and responders@Mildred Anashie@Adeshile Oluwatosin@Yoko C. I’m really really grateful. You’ve made me learn so much about curation. > > Congratulations to everyone who has contributed in this phase. Putting up your papers for peer-review has made me explore different Microbiome articles and I’ve really learnt from them all. Your dedication will pay-off. > > Let’s BugSigDB to the sky:sparkles::sparkles:.

Chris Awoke (12:57:24): > Woohoo:tada:Big congratulations to@Aleru Divineand@Kate RasheedWell done:+1:

Scholastica Urua (13:14:22): > Congratulations@Kate Rasheedand@Aleru Divine:tada:

Chinwendu Joy Enyidiegwu (13:28:36) (in thread): > wowww, congratulations@Kate Rasheed@Aleru Divine

Chinwendu Joy Enyidiegwu (13:29:40): > big congratulations@Aleru Divine@Kate Rasheed

Aleru Divine (13:35:31) (in thread): > Thank you so much@Chris Awoke:relaxed:

Rahila-me (13:35:36): > Congratulations@Aleru Divineand@Kate Rasheed:tada::tada:

Aleru Divine (13:36:09) (in thread): > Thank you so much@Scholastica Urua:relaxed:

Aleru Divine (13:36:43) (in thread): > Thank you so much@Chinwendu Joy Enyidiegwu:hugging_face:

Aleru Divine (13:36:57) (in thread): > Thank you so much@Rahila-me:hugging_face:

Aleru Divine (13:44:48) (in thread): > Thank you so much@Chinwendu Joy Enyidiegwu

Cynthia Iwuoha (13:51:06): > Congratulations@Aleru Divine@Kate Rasheed:tada::tada:

Kate Rasheed (14:28:08) (in thread): > Thank you so much@Chris Awoke

Kate Rasheed (14:28:36) (in thread): > Thank you so much my mentor:heart:.

Kate Rasheed (14:28:54) (in thread): > Thank you so much sis

Kate Rasheed (14:29:04) (in thread): > Thank you so much Liza

Rahila-me (14:30:44) (in thread): > Urw

Kate Rasheed (14:31:59) (in thread): > Thank you so much Cynthia

Kate Rasheed (14:32:49) (in thread): > Thank you so much@Chinwendu Joy Enyidiegwu

Aleru Divine (14:52:27) (in thread): > Thank you so much@Cynthia Iwuoha

Aleru Divine (14:58:42): > Hello and good evening, everyone! > I am super duper excited and filled with gratitude to have made it through the contribution period to become an intern! The joy I feel is beyond words. This feels surreal and I’m still a bit overwhelmed with excitement. Oh my days!!!:pleading_face:This journey has been nothing short of amazing, and I owe it all to the incredible mentors, fellow applicants, and community for the support every step of the way. > > My heartfelt thanks to the mentors@Svetlana Ugarcina Perovic,<@UBNSEMS3S>,<@U1LCB8WEA>,@Chioma Onyido,@Peace Sandy,@Esther Afuape,@Scholastica Urua, for recognizing my potential and giving me with this opportunity. Your guidance and support have been invaluable, and I’m honored to learn and grow under you. > > To my peers, I cannot express enough just how much I value your support. From peer reviews and feedback to our collaborations, you have made this journey not just easier but also incredibly fulfilling. I have learned so much from each of you, and your dedication and passion continue to inspire me. > > I also want to give a huge shoutout to@Kate Rasheed, for making it through as well! Congratulations on this well-deserved accomplishment!:clap::partying_face:I am super excited to embark on this internship journey with you. > > As I enter this new phase, I’m excited and hopeful for an amazing internship experience. With such an incredible community, I know it will be memorable. I look forward to more collaborations and learning from each one of you. > > Thank you so much and cheers to more BugSigDB-ing:relieved:

Kate Rasheed (15:20:36) (in thread): > Congratulations@Aleru Divine. You’ve done really well.

Aleru Divine (16:32:32) (in thread): > Thank you@Kate Rasheed:hugging_face:

Aleru Divine (16:33:23) (in thread): > Aww! Thank you@Kate Rasheedand congratulations:tada::clap:

Aaishah Mahadeo (23:57:35): > Hello everyone, I have a question about this articlehttps://journals.sagepub.com/doi/full/10.3233/JAD-190587. Do I need to curate Figures 3 and 4C?

2024-11-29

Peace Daniel (00:48:03) (in thread): > Congratulations girlie:heart_hands::heart:

Kate Rasheed (01:06:54) (in thread): > Good morning@Aaishah Mahadeo. Yes you would curate figures 3 and 4C.

Aleru Divine (01:48:16) (in thread): > Hi@Aaishah Mahadeo, yesI agree,you’d curate figure 3, 4A and 4C, these figures show differential abundance results.

Aleru Divine (01:48:44) (in thread): > Thank you so much@Peace Daniel

Svetlana Ugarcina Perovic (03:07:34): > Good morning:potted_plant:Our community’s doors stay open for your future contributions.We truly value your curation effort and > hope you’ll continue being part of our community. > > Happy Friday! Happy BugSigDB-ing!

Precious Orakwe (04:23:32) (in thread): > Congratulations

Samuel Nnanna (08:05:36) (in thread): > Thanks@Svetlana Ugarcina Perovic:grinning:I’ll be there

Aleru Divine (08:09:16): > Hello and good afternoon everyone,   > > Thank you so much for your kind messages. I genuinely appreciate all of you.:blush:I know how hard it can be to deal with the disappointment of not being selected right now. I have been there myself twice. I know it is not very easy, and it is okay to feel the way you do now. But I want to encourage you to keep going.   > > It took me some time to feel less devastated when I was not selected. But in all of this, I found comfort in this supportive community filled with people who genuinely want to see each other succeed. This support gave me the strength to continue contributing.  > > There is so much you have learned already and so much you can still learn and achieve. I encourage you to keep contributing to the community, grow and better your skills, and reapply as early as possible when applications open again. I will be rooting for you every step of the way, and I know that the mentors will be too.  > > Please don’t be discouraged, you do belong here, every one of you. I believe that your value to this community is not tied to a selection process. I was shown so much support from the mentors, it was very encouraging and I am glad I found the courage to not give up. > > Not getting selected is not the end of the road, and there is still so much ahead for you.Keep pushing forward, and I cannot wait to see what you achieve!   > Thank you so much!:heart:

Samuel Nnanna (08:13:54) (in thread): > Thanks for your kind and very encouraging words@Aleru DivineAnd to the rest of the team, I just want to say y’all did good. This was an awesome experience for me, thanks to you guys. > > Do not let the odd feelings fester, yeah it’s okay to feel odd atm but please be kind to yourselves.

Precious Orakwe (08:52:34) (in thread): > Thank you

Kate Rasheed (09:20:49) (in thread): > Thank you so much for this encouraging words.

Aaishah Mahadeo (09:22:53) (in thread): > Okay, thank you!

Mary Agekameh (14:35:15) (in thread): > Congratulations@Aleru DivineThank you for the kind words!

Aaishah Mahadeo (19:58:40): > Hello, I am having difficulty finding the supplemental material for these articles: (1)https://journals.sagepub.com/doi/10.3233/JAD-190587?icid=int.sj-full-text.citing-articles.8and (2)https://journals.sagepub.com/doi/10.3233/JAD-201497?icid=int.sj-abstract.similar-articles.5I would appreciate some assistance, thank you.

2024-11-30

Kate Rasheed (04:15:03) (in thread): > Good morning@Aaishah Mahadeo. I believe there are no supplementary material in the papers. > > No supplementary table or figure was referenced all through the paper and I checked the PDF (for the first article), there was no mention of supplementary article.

Aleru Divine (08:43:18) (in thread): > Hi@Aaishah MahadeoI went through the papers too.They only referenced a supplementary material in the second paper.But the link still goes back to the paper sadly.Idon’tknow how we can get that.I believe the mentors can help with getting the material but this will probably be on Monday.My apologies:pray:

BOLARINWA AISHAT (13:58:25) (in thread): > Thank you so much for your kind words@Aleru DivineI wish you all the best:smiling_face_with_3_hearts::hugging_face:

2024-12-01

PATIENCE ONAH (13:10:16) (in thread): > Congratulations@Aleru Divine. Well deserved

Svetlana Ugarcina Perovic (14:19:39) (in thread): > In this case, we are kindly asking the authors via email (already sent, you will see it in your inbox) for the supplementary material. Usually they are willing to share it without any problem, especially because often they are not aware that the journal platform skipped that part of their paper…

Kate Rasheed (14:21:52) (in thread): > Ohhh. Well noted@Svetlana Ugarcina Perovic. Thank you.

Svetlana Ugarcina Perovic (14:23:57) (in thread): > Here is an email template that we are using for communication:https://bugsigdb.org/Requests#Template_Email_to_Corresponding_Authors - Attachment (BugSigDB): Requests > …

Aleru Divine (14:37:44) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Aaishah Mahadeo (14:52:56) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (15:01:30): > Free registration for delegates from LMICs!Applied Bioinformatics & Public Health Microbiology (21-23 May 2025) is open for registrations. > Public health genomics, equity in public health, scaling bioinformatics: industry and infrastructure, and much more.https://coursesandconferences.wellcomeconnectingscience.org/event/applied-bioinformatics-public-health-microbiology-20250521/ - Attachment (Wellcome Connecting Science Courses and Conferences): Applied Bioinformatics & Public Health Microbiology — 20250521 > The implications of data-driven genomics approaches in public health settings

2024-12-02

Svetlana Ugarcina Perovic (03:52:10): > Good morning! > > This week we DO NOT HAVE our team meeting,we will be at MVIF and you are more than welcome to join us.https://cassyni.com/s/mvif-34cc<@UBNSEMS3S><@U1LCB8WEA> - Attachment (Cassyni): MVIF 34 - with keynote talk by Prof. Sean Gibbons - seminars · Cassyni > Microbiome Virtual International Forum (MVIF) is a recurring bite-sized alternative to multi-day microbiome conferences: Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference. > > Forum n. 34 is a Pacific-first event, with live talks starting 4th December 2024, 9:30 am Tokyo time (see what time it is where you are here and add to your calendar here). Professor Sean Gibbons will be the keynote speaker for this event. > > For Atlantic time zones, recorded talks with live hosting and discussion will start on 5th December at 8:30 am New York time (see what time and date it is where you are here and add to your calendar here). > > MVIF is a non-profit association registered in Italy > If you’d like to support MVIF, you can donate to our crowdfunding campaign . > > Thanks to our co-organizing non-commercial partners the Seerave Foundation and CUNY Graduate School of Public Health & Health Policy and our Gold Sponsor Roche for their support. > > Matanu!

Aleru Divine (04:06:51) (in thread): > Good morning@Svetlana Ugarcina Perovicand thank you for the reminder:blush:

Mildred Anashie (04:35:39) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (05:11:12) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kate Rasheed (05:29:31) (in thread): > Thank you for the reminder.

Peace Daniel (07:56:55): > Hi:wave:I need help determining the sample sizes for thisstudy, take a look at table 1 and excerpt attached - Attachment (Frontiers): Frontiers | Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain > A link between the gut microbiome and Parkinson’s disease (PD) has been intensively studied, and more than 100 differential genera were identified across the…

Peace Daniel (07:57:20) (in thread): > A total of 16 studies, including ten for feces, one for blood, and five for the brain, with 2,883 participants were included in this study before data cleaning. All the Project IDs and details of metadata were provided in Table 1 (Supplementary Table 1 and Supplementary Data 2). Genera reported as potential contaminants and non-detectable in fecal microbiome were termed as “pan-contaminants” and were removed before microbiota analysis. For the feces, 311 genera were identified across 2,252 individual samples. After removing contaminants (Supplementary Data 3), 197 genera retained and 28 genera had an average relative abundance greater than 0.5% across all samples (Figure 2A). For the blood, 328 genera were identified across 86 individual samples with 100 retained after excluding pan-contaminants (Supplementary Data 4), and 14 genera had an average relative abundance greater than 0.5% across all samples (Supplementary Figure 1A). For the brain, 1,197 genera were identified across 376 individual samples with 116 retained after removing pan-contaminants (Supplementary Data 5), and 18 genera had an average relative abundance greater than 0.5% across all samples (Supplementary Figure 1B). For fecal studies, samples overlapping between PRJEB14674 and PRJNA601994 were de-duplicated, and 1,914 samples were finally included. There were four replicated runs of each sample in PRJNA557205, and the RNA-Seq data from the first run (run accession IDs) of each sample were used in both microbiota analysis and transcriptome analysis (Li et al., 2020).

Kate Rasheed (07:57:33) (in thread): > Welldone@Peace Daniel. I’ll take a look.

Peace Daniel (07:57:36) (in thread): > The numbersdon’tadd to me, maybeI’mmissing something

Yoko C (09:24:36) (in thread): > Hello, I think I see what you mean, they mention 16 studies and the tables show 15 and 9 studies, and the numbers don’t add up to what the text says. Maybe going by the number of samples mentioned in the text is the best option here?

Peace Daniel (09:35:01) (in thread): > Not quite sure as I need numbers of both control and Pd for feces, blood and brain samples

Yoko C (11:03:38) (in thread): > Right! after double checking I realized the table does have 16 studies but doesn’t add up to the 2883 participants from the text anyways, the 9 other studies are for microarray, and the text doesn’t mention number of participants in different groups either. Hopefully somebody has a better idea if you can go ahead with the tables removing the duplicates.

Yoko C (11:41:15): > Hello, thought this might be relevant, these PMIDs have duplicate studies: > 23032991 “Study 82” “Study 83” “Study 84” > 29234019 “Study 10” “Study 11” > 30497517 “Study 38” “Study 39” These PMIDs aren’t duplicated on the website but show up as duplicated on the downloadable database 30366118 “Study 149” “Study 345” > 28018325 “Study 62” “Study 63”

Kate Rasheed (11:48:19) (in thread): > I agree@Yoko C. It’s better@Peace Danielleaves the sample sizes blank since it doesn’t add up.

Peace Daniel (12:58:21) (in thread): > I might have to wait till the next office hour

2024-12-03

Svetlana Ugarcina Perovic (06:10:29) (in thread): > Thanks for this, Yoko! > I will check them all out.

Svetlana Ugarcina Perovic (06:42:55) (in thread): > https://bugsigdb.org/Study_82https://bugsigdb.org/Study_83https://bugsigdb.org/Study_84@Victoria (Burah) Poromonplease check this out and inform which one to keep. Thank you!

Svetlana Ugarcina Perovic (06:44:28) (in thread): > https://bugsigdb.org/Study_10https://bugsigdb.org/Study_11@Victoria (Burah) Poromon@Chioma Onyidoplease check this out and inform which one to keep. Thank you!

Svetlana Ugarcina Perovic (06:49:45) (in thread): > <@UBNSEMS3S>could you please check this out: > Yoko noticed that two PMIDs aren’t duplicated on the website but show up as duplicated when downloaded: > > PMID: 30366118https://bugsigdb.org/Study_149https://bugsigdb.org/Study_345PMID: 28018325https://bugsigdb.org/Study_62https://bugsigdb.org/Study_63

Victoria (Burah) Poromon (07:09:24) (in thread): > Hi@Svetlana Ugarcina PerovicThe studies arenot exactly duplicates, they areall related.Theresults in study 83 should be in study82 as Experiment 2, and study 84 is Experiment 3.

Svetlana Ugarcina Perovic (07:12:15) (in thread): > Is there a reason why they are separated per study?

Svetlana Ugarcina Perovic (07:12:49) (in thread): > I see, they differ in study design….

Victoria (Burah) Poromon (07:14:05) (in thread): > Yes they differ in study design, but two are actually case-control

Svetlana Ugarcina Perovic (07:17:01) (in thread): > There should be a reason why they are separated. They are all reviewed. Is there any note in discussion page?

Victoria (Burah) Poromon (07:19:06) (in thread): > No notes in discussion

Svetlana Ugarcina Perovic (07:26:37): > I did not try it yet, but sounds promising. > > An early version of the research app for anyone looking for a new way to organize and read research papers. Try the beta and download the app athttps://un.ms/research - Attachment (un.ms): Research by UNMS > Desktop app for reading, understanding and organizing research, with AI.

Aleru Divine (07:35:10) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:pray:I signed up but haven’t been able to verify my email yet. It might be a network issue so I’ll try again a little later.

Kate Rasheed (11:07:40) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic@Aleru DivineI have been able to sign up and verify my mail.

Aleru Divine (12:24:26) (in thread): > Thank you@Kate RasheedI’lltry again now

2024-12-04

Joy (03:30:13) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing

Svetlana Ugarcina Perovic (09:11:49) (in thread): > UPDATE: it’s not free, just tried it out…

Svetlana Ugarcina Perovic (10:05:13) (in thread): > See you tomorrow at MVIF!

2024-12-05

Aaishah Mahadeo (15:10:20): > Hi, I hope everyone is doing well. I have a few questions about this article:https://www.frontiersin.org/journals/neuroscience/articles/10.3389/fnins.2021.619051/full#S11In Figure 3, is the figure above the LFfSe curatable? Also, is the supplementary table 4 curatable? Thank you! - Attachment (Frontiers): Frontiers | APOE-ε4 Carrier Status and Gut Microbiota Dysbiosis in Patients With Alzheimer Disease > BackgroundAlternations in gut microbiota and a number of genes have been implicated as risk factors for the development of Alzheimer disease (AD). However, t… - File (Excel Spreadsheet): Table_4_APOE-ε4 Carrier Status and Gut Microbiota Dysbiosis in Patients With Alzheimer Disease.XLSX

Kate Rasheed (15:12:04) (in thread): > Hi@Aaishah Mahadeo. I’ll look through

Kate Rasheed (15:17:42) (in thread): > For Figure 3, the cladogram is curatable. Some taxa like Aerostipes and Ruminococcaceae should be added to the signatures you have. > > Please note that the cladogram is also LEfSe result.

Samuel Nnanna (15:17:52) (in thread): > Hi@Aaishah MahadeoFigure 3 in the study is curatable. It is a LEfSe cladogram showing differential abundance between patients with Alzheimer disease and healthy subjects. The gray bars represent signatures abundant in Alzheimer disease patients and the reds are for the healthy control

Samuel Nnanna (15:19:07) (in thread): > The table doesn’t seem to be curatable as it doesn’t exactly show what’s being compared or signatures

Kate Rasheed (15:23:08) (in thread): > I agree with@Samuel Nnannathat Supplementary table 4 is not curatable.

Aaishah Mahadeo (15:23:29) (in thread): > For figure 3, can I curate both under the same signature?

Kate Rasheed (15:24:19) (in thread): > Yes@Aaishah Mahadeo. Some of the taxa in the cladogram are repeated in the bar graphs.

Aaishah Mahadeo (15:25:18) (in thread): > Ok, thank you so much. Do you mind explaining how to interpret the cladogram? How do I know if a bacterial taxa increased or decreased?

Kate Rasheed (15:26:26) (in thread): > The red color is for the healthy controls while the grey is for the case group. > > Taxa with grey would be increased while those with red would be decreased. > > Just as we have in the bars@Aaishah Mahadeo

Kate Rasheed (15:28:42) (in thread): > Ignore the image and focus on the listed legend

Aaishah Mahadeo (15:29:47) (in thread): > Thank you so much@Kate Rasheedand@Samuel NnannaI appreciate all the help.

Aaishah Mahadeo (16:16:16): > Hi, for this paper,https://alz-journals.onlinelibrary.wiley.com/doi/10.1016/j.jalz.2019.07.002, how can I curate Table 2 and the attached supplementary tables S1 and S2? - File (Word Document): alzjjalz201907002-sup-0001 (1).docx

2024-12-06

Adeshile Oluwatosin (01:25:19) (in thread): > Hello@Aaishah MahadeoTable 2 is curatable. > Group 0; normal controls > Group 1: patients with AD > MHT: yes > > Taxa with positive b value (increased abundance in Group 1). > Taxa with negative value (decreased abundance in Group 1). > “The positive b value indicated the taxa were associated with AD patients, and negative number indicated the taxa were associated with the normal controls.”Different body sites = different experiments

Kate Rasheed (02:14:38) (in thread): > @Aaishah MahadeoI believe Table S1 and S2 is curatable. You would pay attention to the SD value of AD, NC > > If the SD of AD is greater than NC in any of the taxa, it would be increased and vice versa. > > Table S2 would be curated as separate experiments since it’s a different body site. > > Experiments would be AD vs NC

Kate Rasheed (02:17:42) (in thread): > Table 2 made use of linear regression model as the statistical test so it would be a different experiment.

Adeshile Oluwatosin (03:00:20) (in thread): > Hmmmm@Kate RasheedWas referencing this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1732694740845139?thread_ts=1732687011.259369&channel=C04RATV9VCY&message_ts=1732694740.845139 - Attachment: Attachment > @Adeshile Oluwatosin If the tables aren’t showing taxa that is increasing or decreasing then we shouldn’t curate it. > > I’ve looked through S2, S3 and S8 and I don’t think they should be curated.

Kate Rasheed (03:44:28) (in thread): > @Adeshile OluwatosinFor the table you referenced, there was no value on either of the groups that’s why it’s not curatable.@Aaishah MahadeoWould curate all the taxa but the experiment would just be for AD vs NC because the p-value for AD vs MCI is above the threshold.

Kate Rasheed (03:50:20) (in thread): > @Adeshile OluwatosinThe taxa in table 2 is similar to the supplementary table. From there we can see that attention should be paid to the SD instead of Mean.

Adeshile Oluwatosin (04:00:26) (in thread): > Pay attention@Aaishah Mahadeowell done

Aaishah Mahadeo (11:41:15) (in thread): > @Kate Rasheed@Adeshile OluwatosinThank you so much for all the help

Adeshile Oluwatosin (11:41:58) (in thread): > You are welcome@Aaishah Mahadeokindly notify, if stuck on anything else

Yoko C (15:43:27) (in thread): > Hello@Aaishah Mahadeo, just wanted to add an observation for the supplementary tables, SD is probably standard deviation, which usually does not imply increase or decrease, I would use the mean instead. You can also see that below each the supplementary tables they give you the info for what pa and pb are. For example S1 says: “a Comparison between AD and cognitively normal controls”, > “b Comparison between AD and MCI”. So that would mean you have two different experiments for table S1. Filter the values for column pa below 0.05 to get significant taxa and same for pb.

Yoko C (15:47:36) (in thread): > I’m not sure what statistical test was used for these though.

Kate Rasheed (15:49:17) (in thread): > @Yoko CPb do not have significant values based on what I saw. > > I believe the statistical test was linear regression too.

Yoko C (15:59:00) (in thread): > @Kate Rasheedthey mention kruskal wilcox (type-o?) for all levels and glm for genera sequence counts, so that is confusing to me:sweat_smile:

Aaishah Mahadeo (17:45:26) (in thread): > @Svetlana Ugarcina PerovicWe are not sure how Tables S1 and S2 should be curated. Should the Mean or SD be used? Also, what statistical test was used? Thank you!

2024-12-07

Kavya Ayalasomayajula (18:28:58): > Hi all, had a question about graph interpretation. Wondering what the solid bars at the top of each graph mean. Also wondering what the starsabove themmean and 1vs 2 stars. Thank you - File (JPEG): IMG_2971

Mildred Anashie (21:14:27) (in thread): > Hi@Aaishah MahadeoI agree with@Yoko CUse the mean to curate and I think there should be two experiments but P b seems to not be significant soyou’dfocus on Pa onlyI’lllook through for the statistical test

Mildred Anashie (21:19:15) (in thread): > Hi@Kavya Ayalasomayajulathe stars (asterisk) indicates significance, I.e showing you wherethere’sa significance while the bars shows what groups/contrasts has the significance. > > For example, looking at 5D we can see that there is a contrast showing significance between Good and HC. You can interpret the rest using that

Kavya Ayalasomayajula (21:56:04) (in thread): > @Mildred Anashiethank you, do you happen to know what two asterisks signify ? Is it different than one asterisk?

2024-12-08

Kavya Ayalasomayajula (00:54:02) (in thread): > @Aleru Divine@Mildred Anashie@Kate Rasheed@Yoko C@Adeshile OluwatosinThanks everyone for this extremely informative feedback! This was a tough study so I am still working on edits, but working through all of your comments and recommendations

Aleru Divine (03:43:08) (in thread): > Good morning@Kavya Ayalasomayajulatwo asterisks also signify significance.Using this for example “P < 0.05; P < 0.01; *****P < 0.0001”this is from another paper but can be applied to thisP < 0.05 means there was statistical significance, meaning there is less than a 5% probability that the observed result occurred by chance. The (* P < 0.01) means higher significance, meaning less than a 1% probability that the result occurred by chance. > And the (******** P < 0.0001) means extremely high significance, meaning less than a 0.01% probability that the result occurred by chance.

Mildred Anashie (04:28:21) (in thread): > Yea@Kavya AyalasomayajulaTwo asterisks also indicate significance, just as@Aleru Divinehas mentioned > > It could mean a stricter threshold than 0.05 was used. It could be 0.01, 0.001 etc.

Kavya Ayalasomayajula (09:43:28) (in thread): > @Aleru Divine@Mildred Anashiegreat explanations, thank you!

2024-12-09

Rahila-me (04:54:51) (in thread): > @Kavya Ayalasomayajulacame late to the party, well and detailed explained by@Mildred Anashieand@Aleru Divine

Kavya Ayalasomayajula (20:31:17): > Hi all, have some questions about what is curatable in this study. I was originally planning to curate Figure 1, as I assumed the figure had to do with relative abundance of species. However, it seems like the displayed taxa have to do with a machine learning model the authors created and which taxa contribute to the model’s predictions. I am not very familiar with these techniques, so I was wondering if this is still curatable. Additionally, I am having trouble determining if figure 3 is curatable. It seems it maps out the association between taxa and inflammation markers, but I am unsure if I can use it to compare taxa between groups. I know this is a busy time of year so I appreciate your feedback and time. Supplementary table 1 mentions relative abundance but I am once again having difficulty interpreting this spreadsheet, and if it is curatable at all. - File (PDF): Higher levels of Bifidobactera and tumor necrosis factor in children with drug-resistant epilepsy.pdf

2024-12-10

Kate Rasheed (00:51:01) (in thread): > Good morning@Kavya Ayalasomayajula. > > Figure 1 is curatable. Look at the caption: > “A)Comparing all patients before vs during > *****KD and B) responders vs. non-responders before KD***” > Patients before(bars to the right), patients during KD(bars to the left). Same pattern for responders. > > Figure 3 and Supplementary Table 1 are not curatable. > > Weldone Kavya.

Rahila-me (01:09:03) (in thread): > @Kavya Ayalasomayajulataxa and inflammation markers for figure 3 can’t be curated also S table1 as for figure 1 it is very much curatable. Good morning

Kate Rasheed (03:08:50): > Good morning people. Happy Tuesday:sparkles:. > > Please I would appreciate your thoughts on how to curate Table S7. > > I’m thinking apairwise comparisonwould be preferable to determine the abundance direction instead of aone-against-the restanalysis. > > Here is the link:https://www.nature.com/articles/s41598-020-69111-xWhat do you think please? - Attachment (Nature): Changes in the vaginal microbiota across a gradient of urbanization > Scientific Reports - Changes in the vaginal microbiota across a gradient of urbanization

Adeshile Oluwatosin (03:15:17) (in thread): > Good morning@Kavya AyalasomayajulaFigure 1aand b is curatable. > > Figure 3 and sTable1 is not curatable. > There’s no differential abundance analysis.

Adeshile Oluwatosin (03:15:54) (in thread): > Hello@Kate RasheedI would have a look

Adeshile Oluwatosin (03:17:51) (in thread): > So you have two experiments from figure 1

Adeshile Oluwatosin (03:18:59) (in thread): > Ohhhit’smy curation:joy:I shared my thoughts with you already. > Awaiting other opinions

Aleru Divine (03:24:31) (in thread): > Good morning@Kate RasheedI’llhave a look at this:blush:

Aleru Divine (03:52:02) (in thread): > Well done on your curation@Kavya Ayalasomayajula! I agree on Figure 1 being curatable too. > > 1A shows feature importance of taxa positively or negatively associated with KD and B. Increased signatures (1) are the bars to the right (greater than 0) and decreased signature (2) are the bars to the left (less than 0). > The same interpretation should be applied to 1B > > I also agree that Figure 3 is not curatable. The results described in figure 3 does not directly mean differential abundance instead, it represents associations between inflammation markers and gut microbes identified through a multivariate modeling approach. > > Supplementay table 1 (I got lost for a moment) is also not curatable I agree. the table shows relative abundance resullts of individual taxonomic profiles not comparisons between groups, so it does not represent differential abundance.

Aleru Divine (04:02:25) (in thread): > @Kate RasheedI agree with pairwise comparison being appropriate in this context. > I also noticed a lot of the signatures do not show significant differences in the samples from the cervicovaginal site, and none of the signatures were identified as significantly different in the samples from the introitus. > That is a lot:sweat_smile:

Kate Rasheed (04:48:44) (in thread): > Thank you so much@Aleru Divine

Yoko C (08:14:04) (in thread): > Hi, I don’t think its curatable ssince s7 is about prevalence

Yoko C (08:24:33) (in thread): > Hello, I think you are right about fig 1 not being curatable. Figure 1 is about feature importance. This doesn’t necessarily mean abundances were involved but more what bacteria were important for the models to distinguish between types of patients.

Kate Rasheed (08:36:49) (in thread): > @Yoko CHi:hugging_face:. Chloe and Svetlana mentioned that it’s curatable. > > Prevalence also mean abundance.

Yoko C (08:42:38) (in thread): > @Kate Rasheedoh, yes it is a type of abundance but I remember reading somewhere prevalence isn’t curatable. But if they said it is, than I think you have two comparisons, one between urbanization groups and another between ethnicities.

Yoko C (11:43:36): > Hello, I need some help deciding if I should curate a full table (supplementary table 4) or only the highlighted genera. Initially I was curating all genera for two groups, hABX and hCTRL samples and only highlighted genera for FMT-ABX and FMT-C groups (as the table states). However after re-reading this: “To limit the number of tests carried out when studying differentially abundant species, the species detected in at least two samples, per sample type, with mean relative abundances higher than 0.1% were selected, resulting in 105 species being tested in distal colon content samples. To account for multiple tests the Benjamini – Hochberg procedure was applied (FDR < 0.05).” I realized the table might include all genera found without necessarily meaning all are found in the 4 different groups. So I think I should go with the text in the results along with the highlighted taxa. This is the studyhttps://www.tandfonline.com/doi/full/10.1080/19490976.2024.2377570#d1e549

Kate Rasheed (11:51:35) (in thread): > @Yoko CWelldone on this. > > See what I found: > > “Genus among significantly different species detected in DC content between FMT-ABX and FMT-C groups” > > Genera with blue color are to be curated as they are showing significantly differential abundance between FMT-ABX and FMT-C

Yoko C (11:59:19) (in thread): > @Kate Rasheed, thanks. I think this table has information for 4 groups where samples were taken from feces (for humans) or DC (mice distal colon). So I am not sure if I should take all information in the table or only the highlighted genera, green for humans and light blue for mice. The reason I think this table also has information for humans is this: “Analysis of gut microbial composition at genus level revealed several significantly different genera between hABX and hCTRL samples, includingBacteroides,Phocaeicola, Parabacteroides, Blautia, Clostridium, andAkkermansiaamong others (p< 0.05, ,Supplementary Table S3).” I think S3 is a typo and they meant s4 because s3 is for antibiotics.

Yoko C (12:00:05) (in thread): > So initially I was including all the genera in the table but now I am thinking it should only be highlighted info

Kate Rasheed (12:10:45) (in thread): > Yes that’s right. Highlighted blue for mice while the rest for humans

Yoko C (12:14:15) (in thread): > So you think all for humans, or just green for humans?

Aleru Divine (13:54:19) (in thread): > Hi@Yoko CIsee your point andI’llhave a look at the study.

Kate Rasheed (14:43:00) (in thread): > See what the green stands for “****p< 0.05 & more than 1% rel abundance in at least one group***” > > The significant genera stops at 62 that’s why there’s a broken line after 62@Yoko C

Aleru Divine (15:52:19) (in thread): > @Yoko CI’ve gone through this and I think you should curate only the highlighted signatures. > > From this “Analysis of gut microbial composition at genus level revealed several significantly different genera between hABX and hCTRL samples, includingBacteroides,Phocaeicola, Parabacteroides, Blautia, Clostridium, andAkkermansiaamong others (p< 0.05,Figure 1(d),Supplementary Table S3)” I think they meant S4 too > > Also, it looks to me like this table only shows relative abundance results for hABX and hCTRL because from the excerpt above, Blautia for example is highligted in blue, Phocaeicola is highlighted in green and Parabacteroides is highlighted in both green and blue. But the excerpt above is for hABX and hCTRL. > > I may have missed it, but can you show me where describes the ones highlighted in blue as showing significantly differential abundance between FMT-ABX and FMT-C. I honestly can’t find it although I am still looking. > > Where I actually see differential abundance results for**** FMT-ABX and FMT-C groups ****is in figure 4E

Kate Rasheed (15:56:09) (in thread): > @Aleru DivineScroll to the right of the table. You would find the description of the highlighted figures.

Aleru Divine (15:57:28) (in thread): > Oh! Thank you Kate! > Seen!

Aleru Divine (16:00:16) (in thread): > In addition to the ones highlighted in blue, figure 4E also shows species differential abundance results for FMT-ABX and FMT-C

Aleru Divine (16:10:57) (in thread): > Now I understand youwon’tbelieve I was looking at this for hours:sob:here’smy interpretation@Yoko C@Kate Rasheed > 1. Signatures that are not highlighted in either green or blue are not statistically significant. > 2. Signatures highlighted in blue are significantly different between the FMT-ABX and FMT-C groups.(Mice) > 3. Signatures highlighted in green are statistically significant for hABX and hCTRL.(Humans)

Kate Rasheed (16:17:59) (in thread): > @Aleru DivineFor number 1, there are signatures not highlighted but they are significant. > > Check out their p-values.

Yoko C (17:50:15) (in thread): > @Kate Rasheedand@Aleru Divinethank you both for looking at this, I think I will only curate highlighted (green or blue) signatures, because it’s not clear what group the other signatures are from (mice or humans). Really appreciate it!

Kate Rasheed (18:31:28) (in thread): > @Yoko CFrom what I can interpret from the table, all taxa(green and blue) from 2-62 are significant between hABX and hCTRL. > > The blue highlighted taxa are also significant between FMT-ABX and FMT-C. > > Please look at the description of the blue and green, so you can verify this. > > Also look at the broken line after 62, from 63 downwards, the taxa are insignificant, hence, the broken line.

2024-12-11

Aleru Divine (01:09:08) (in thread): > Replying to this “For number 1, there are signatures not highlighted but they are significant. > > Check out their p-values.”@Kate Rasheedthere no p-values indicated in the table:thinking_face:that is why I think those aren’t significant.

Yoko C (01:21:08) (in thread): > @Aleru Divine, column E = ANCOMBC_pval

Yoko C (01:36:05) (in thread): > @Kate Rasheed, initially I curated the table in that way. But now I realized the description for green doesn’t specify if it’s for humans or mice. I think I just assumed it was for humans because it overlaps with what is reported in results. Also, there are blue highlights that have a p value above 0.05. Re-reading the description, what I think this means is that within that highlighted genus there are species that are significantly different but the whole genus isn’t significant. I am now rethinking about curating the table at all:scream_cat:because the information isn’t clear.

Aleru Divine (02:23:15) (in thread): > @Yoko Csince they indicated that the signatures highlighted in blue are genus among significantly different species detected in DC content between FMT-ABX and FMT-C groups I think only those are for mice.There are ones highlighted in both green and blue, that would mean both mice and human I think.:thinking_face:also,what about this? > “*p< 0.05 & more than 1% rel abundance in at least one group” > > Either this means they only considered the signatures that had more than 1% relative abundance in one group as significant or they’re just telling us “hey look, these are the signatures with more than 1% relative abundance in at least one group” > > If it’s the latter, then I think you’d curate all from 2-62.@Yoko CAlso, whywouldn’tthey just say?:sob:

Kate Rasheed (02:29:51) (in thread): > @Aleru DivineI believe it’s the latter.@Yoko CYou should curate the table the way you did.

Kate Rasheed (02:41:24) (in thread): > For the genus with blue. It doesn’t say they are all significantly different. It saysgenusamong. > *****Th***ose above the broken line are the significant ones.@Yoko C@Aleru Divine. What do you think?https://community-bioc.slack.com/archives/C04RATV9VCY/p1733849495887459?thread_ts=1733849016.726519&cid=C04RATV9VCY - Attachment: Attachment > @Yoko C Welldone on this. > > See what I found: > > “Genus among significantly different species detected in DC content between FMT-ABX and FMT-C groups” > > Genera with blue color are to be curated as they are showing significantly differential abundance between FMT-ABX and FMT-C

Aleru Divine (02:45:00) (in thread): > I agree@Kate Rasheed

Svetlana Ugarcina Perovic (10:40:03): > Tomorrow (Thursday) isour weekly team meeting and office hours at 9 AM EDT. Bring your questions up. > cc<@UBNSEMS3S>

Aleru Divine (12:21:31) (in thread): > Thanks for the reminder@Svetlana Ugarcina PerovicLooking forward to it!:blush:

Aaishah Mahadeo (14:52:42) (in thread): > For table 2, what would the data transformation and statistical test be?

Kate Rasheed (15:12:10) (in thread): > @Aaishah Mahadeohttps://community-bioc.slack.com/archives/C04RATV9VCY/p1733469462961299?thread_ts=1733433376.541959&cid=C04RATV9VCYThe data transformation should be relative abundance - Attachment: Attachment > Table 2 made use of linear regression model as the statistical test so it would be a different experiment.

Aaishah Mahadeo (15:13:16) (in thread): > Thank you so much@Kate Rasheed

Alisha Mahadeo (16:05:47): > Hello everyone! I have a question about this article:https://www.tandfonline.com/doi/full/10.1080/19490976.2020.1747329. Is the attached supplementary tables curatable? I have attached a Word document which describes what the supplementary tables S3 and S4 shows. Thank you so much for your help! - File (Word Document): Supplementary online material.docx - File (Excel Spreadsheet): Table S3TD VS ASD.xlsx - File (Excel Spreadsheet): Table S4 Supplement 16S TD VS NC-ASD -20-2-20.xlsx

Kate Rasheed (16:09:33) (in thread): > @Aaishah MahadeoHello:hugging_face:. Yes the tables are curatable and you should use the mean for this one.

Alisha Mahadeo (16:10:28) (in thread): > Hi! Thank you so much!

U1LCB8WEA (16:57:15): > Hi all, would anyone who is curious please take a look at an experimental feature (implemented by<@U01NWEPKPRD>) to identify similar signatures to any signature in BugSigDB. Go to a random signature athttps://bugsigdb-staging.wikiworks.com/Special:RandomInCategory/Studiesand click on the “Look for similar signatures” link. Please go ahead an play with the similarity app, let me know if you find it intuitive or not, and report any problems you have. (note:https://bugsigdb-staging.wikiworks.comis a testing site so any edits there would be lost! It’s separate from the realbugsigdb.org)

Kate Rasheed (18:16:10) (in thread): > This is really amazing. It was intuitive indeed. > > The laid down steps under “Getting Started” made the app easy to understand.

2024-12-12

Aleru Divine (01:50:11) (in thread): > Oh wow, I think I must have said wow at least a dozen times. > > The interface is intuitive. The “Getting Started” section is a great touch, but honestly, everything is easy to follow. > > I didn’t run into any problems at all. > Amazing work@Samuel Gamboawell done!

Chioma Onyido (02:28:58): > Hello all,:wave::skin-tone-5:If you’re a fan of Research code writing or generally curious about how to publish your codes, then thisdiscussionis one you don’t want to miss.I’ll be presenting in the next hour! (9:30am WAT). > > Thank you so much@Svetlana Ugarcina Perovicand@Levi Waldronfor your continuous guidance and incredible support!:smile::100:https://us06web.zoom.us/meeting/register/tZErcOqsrDssHNV-TY6OG89MZkwOtXs-oNF_#/registration - File (PNG): IMG_9370

Kate Rasheed (02:29:53) (in thread): > :dancer:I will be there. Welldone@Chioma Onyido

Aleru Divine (02:32:08) (in thread): > Make that two@Kate Rasheed:relieved:Won’tmiss it@Chioma Onyido:hugging_face:

Kavya Ayalasomayajula (03:11:58) (in thread): > Thank you everyone for your input. I am leaning towards curating now, may ask during the meeting just to confirm

Adeshile Oluwatosin (03:33:08) (in thread): > Thanks for the reminder@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (03:38:07) (in thread): > Thank you for this > I would try it out now

Adeshile Oluwatosin (03:39:15) (in thread): > Joining the session:relaxed:

Svetlana Ugarcina Perovic (03:45:54): > RIGHT NOW@Chioma Onyidois rocking! - File (PNG): Chioma_RSSE.png

Adeshile Oluwatosin (03:46:24) (in thread): > :relaxed::relaxed::relaxed:

Kate Rasheed (05:03:05) (in thread): > What a session! Thank you so much for the invite@Chioma Onyido. I really really learnt a lot. > > Yet again, I was reminded of the importance of documentation in open source. > > Open science really rocks.

Adeshile Oluwatosin (05:06:38) (in thread): > Thank you for this session > > I have access to a whole lot now. I documented the links dropped in the chat box.:blush::blush::blush:@Chioma Onyidoit was nice to hear you speak

Aleru Divine (05:06:40) (in thread): > Amazing discussion indeed! Thank you and well done@Chioma OnyidoI’mglad Ididn’tmiss this.

Joy (05:18:46) (in thread): > Thank you@Levi Waldron,I’ll try it out.

Chioma Onyido (05:22:05) (in thread): > Thank you all so much! I’m really glad to see this.:grinning_face_with_star_eyes:

Kate Rasheed (06:01:43) (in thread): > I@Adeshile OluwatosinPlease share the links

Adeshile Oluwatosin (06:02:15) (in thread): > https://carpentries.org/ - Attachment (The Carpentries): Home > The Carpentries is a fiscally sponsored project of Community Initiatives, a registered 501(c)3 non-profit organisation based in California, USA. We are a global community teaching foundational computational and data science skills to researchers in academia, industry and government.

Adeshile Oluwatosin (06:02:23) (in thread): > https://chaoss.community/

Adeshile Oluwatosin (06:02:38) (in thread): > https://cran.r-project.org/

Adeshile Oluwatosin (06:02:50) (in thread): > https://osf.io/

Adeshile Oluwatosin (06:03:09) (in thread): > https://www.dontusethiscode.com/

Adeshile Oluwatosin (06:03:16) (in thread): > https://science.nasa.gov/open-science/tops/ - Attachment (science.nasa.gov): Transform To Open Science - NASA Science > Transform to Open Science is a NASA initiative designed to transform agencies, organizations, and communities to a culture of Open Science.

Aleru Divine (06:05:03) (in thread): > @Kate Rasheed@Adeshile OluwatosinHere’s the comprehensive resource sheet shared during the session.Incase you missed any.https://docs.google.com/document/u/0/d/1f6B_AUNLoO0HjOFTXICoWK_lGXVJgGpiMk2PsUnj-pM/mobilebasic#heading=h.kjwacfyiri6w

Kate Rasheed (06:10:35) (in thread): > Thank you so much@Adeshile Oluwatosin@Aleru Divine

Kate Rasheed (06:11:45) (in thread): > I was hearing Kate Kate; and in my mind, I was like who please:sweat_smile:

Aleru Divine (06:13:26) (in thread): > :sweat_smile::sweat_smile:girrrrrl:smiling_face_with_smiling_eyes_and_hand_covering_mouth:I also saw “please share the link Kate” and all I thought was you:sweat_smile:

Adeshile Oluwatosin (06:53:41) (in thread): > The lecturer in linguistics I think, is alsobearingKate lol

Aaishah Mahadeo (06:58:50): > Good morning everyone, I hope all is well. For the article attached, are figures 3 and 4 the only figures that can be curated? Can any other figures in the paper or supplemental material (also attached) be curated? - File (PDF): Profiling the oral microbiomes in patients with Alzheimer’s disease(1).pdf - File (Word Document): Profiling the oral microbiomes in patients with Alzheimer’s disease (supplementary).docx

Kate Rasheed (07:04:09) (in thread): > Hello@Aaishah Mahadeo. Figure 5a-d is curatable. > > Supplementary figure 2a-b and 3d are curatable.

Kate Rasheed (07:09:14) (in thread): > Supplementary Figure 3d made use of Mann-whitney. I’m not sure of the statistical test for 2a-b

Kate Rasheed (07:12:58) (in thread): > Figure 5 and Supplementary Figure 2a-b uses STAMP analysis. I don’t know how it would be curated in BugSigDB. > > You can ask during office hours today@Aaishah Mahadeo

Aaishah Mahadeo (07:13:50) (in thread): > Ok, thank you so much@Kate Rasheed

Aleru Divine (07:43:28) (in thread): > Hi@Aaishah Mahadeo, well done on your curation.I agree with@Kate RasheedI found this “Moreover, significant features among the groups were detected by STAMP using Welch’s t test between two groups and analysis of variance among more than two groups (p value filter: 0.05).” > > This implies > 1. Welch’s t test was the statistical test used for figure 5(a-b) and supplementary Figure 2(a-b). > 2. ANOVAwas the statistical test used for figure 5(c-d).

Aleru Divine (07:46:59) (in thread): > Also to add again, LEfSe is the statistical test used for figure 3b and 4b.It just utilized Kruskal-Wallis.

Aaishah Mahadeo (08:03:56) (in thread): > Thank you so much@Aleru DivineDo you know how Figures 2 and 5 can be curated?

Aleru Divine (08:07:11) (in thread): > Do you mean figure 5 and supplementary figure 2?

Aaishah Mahadeo (08:07:27) (in thread): > Yes

Kate Rasheed (08:10:21) (in thread): > For supplementary figure 2, if the purple box is longer than the orange, that would be increased in CS and vice versa.

Kate Rasheed (08:15:44) (in thread): > For Figure 5a, if the red box is longer than the purple, that would be increased in NAS and vice versa.

Kate Rasheed (08:17:30) (in thread): > For Figure 5b, if the turquoise green box is longer than the light green, that would be increased in NAG and vice versa.

Aleru Divine (08:21:34) (in thread): > @Aaishah MahadeoFigure 5a shows differential abundance results between 2 groups EAS and NAS.Soyou’dgroup according to severity and in this caseyou’dhaveEAS-early-onsetAlzheimer’s disease patients -red barsGroup 0 > NAS-late-onsetAlzheimer’s disease patients -purple barsGroup1.Signature 1 (increased in NAS) > Signature 2(decreased in NAS) > > Same thing with 5b

Aleru Divine (08:28:10) (in thread): > Figure 5C and 5D are pairwise comparison > > For 5C has the following comparisons > LAS vs NAS > LAS vs SAS > MAS vs SAS > > you can use this for figure 5D

Yoko C (08:33:37) (in thread): > Hello, for figure 5c and 5d, how would the different abundance sets be curated though?

Aleru Divine (08:37:12) (in thread): > 5C and 5D are both pair wise figures

Aaishah Mahadeo (09:50:03) (in thread): > Thank you so much

Aaishah Mahadeo (09:50:57) (in thread): > How do I curate Figure 6 a and c?@Kate Rasheed@Aleru Divine

Svetlana Ugarcina Perovic (10:01:29): > THANKS for great questions today! Feel free to post your pending questions here in Slack. Next meeting we will talk about how to curate results from meta-analysis. > > Do not miss the last team meeting in 2024next Thursday (Dec 19)! The first team meeting in 2025 will be on January 9. > > cc<@UBNSEMS3S>

Aleru Divine (10:02:26): > Thank you for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina PerovicThanks everyone for all the questions!

Aaishah Mahadeo (10:03:48): > Hi, for this study,https://journals.asm.org/doi/full/10.1128/mbio.00632-19How would I curate the figures? For Figure 2, will it be AD vs NO, AD vs Other and Other vs NO? Also, can any of the supplemental materials be curated?

Aleru Divine (10:03:59) (in thread): > Already looking forward to the next meeting:grinning_face_with_star_eyes:Thank you@Svetlana Ugarcina Perovic<@UBNSEMS3S>

Alisha Mahadeo (10:07:53): > Hello, how would I begin my analysis for my studies curated during my fieldwork. For example, creating a table of studies and a table of the frequencies of occurrence of each taxon reported in the curated signatures.

Aleru Divine (10:10:26) (in thread): > Hi@Aaishah MahadeoThe description in Figure 2 suggests that the comparisons focus on: > > AD vs. NO > Other vs. NO > > This is implied from this excerpt > > “Genera with greater than 0.1% mean relative abundance were significantly associated with Alzheimer’s disease (AD) or other dementia types (Other) in comparison to elders without dementia (NO).”

Aaishah Mahadeo (10:11:12) (in thread): > Okay thank you so much@Aleru Divine

Victoria (Burah) Poromon (10:11:33): > Hi<@UBNSEMS3S>About these duplicate studies that were foundhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1733157675134569I looked at them and I found outthey’renot exactly duplicates but different experiments from the same research. > > Is it okay to merge them together into one experiment? Or leave them as they are? - Attachment: Attachment > Hello, thought this might be relevant, these PMIDs have duplicate studies: > 23032991 “Study 82” “Study 83” “Study 84” > 29234019 “Study 10” “Study 11” > 30497517 “Study 38” “Study 39” These PMIDs aren’t duplicated on the website but show up as duplicated on the downloadable database 30366118 “Study 149” “Study 345” > 28018325 “Study 62” “Study 63”

Aleru Divine (10:11:49) (in thread): > Checking the supplementary materials now.

Joy (10:13:13): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor the office hour today. Looking forward to next one to learn how to curate meta-analysis. Thank you all, your questions were helpful in my curation to get better.

Peace Daniel (10:13:35) (in thread): > Thank you@Svetlana Ugarcina PerovicHere’sthelinkto the study I asked questions on<@UBNSEMS3S> - Attachment (Frontiers): Frontiers | Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain > A link between the gut microbiome and Parkinson’s disease (PD) has been intensively studied, and more than 100 differential genera were identified across the…

Joy (10:15:09): > https://www.nature.com/articles/s41467-024-49093-4My second question was: Since@Chloesaid fig 1 was not curatable, which of the tables in this study is curatable and how many experiments will I have in this study? Waiting patiently to hear from you all. - Attachment (Nature): Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice > Nature Communications - Here, in, the authors investigate the relationship between fecal microbiota and nutritional status in a trial on 380 Cambodian schoolchildren, establishing a correlation…

Aleru Divine (10:17:38) (in thread): > @Aaishah MahadeoIdon’t think any of the supplementary materials are curatable.@Yoko C@Kate Rasheedcan you have a look please.Thanks!

Kate Rasheed (10:18:17) (in thread): > Welldone@Joy. Fig. 2 is curatable and it has four experiments.

Aleru Divine (10:18:45) (in thread): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic@Chioma Onyido

Kate Rasheed (10:19:53) (in thread): > Fig. 4 is curatable UR original vs UR improved. Statistical test is MaAsLin with MHT correction

Kate Rasheed (10:21:19) (in thread): > Supplementary Figure 2 is curatable with four experiments

Kate Rasheed (10:23:05) (in thread): > In total, you have 9 experiments

Kate Rasheed (10:36:13) (in thread): > Table S1 and S2 seems curatable. They are the summarized taxa in Figure 3 and 4.

UBNSEMS3S (10:36:17): > Thank you to everyone who attended today’s office hours. Here’s the recording. - File (MPEG 4 Video): Video1392393038.mp4

Aleru Divine (10:36:37) (in thread): > Hi@JoyI agree with@Kate Rasheedfigure 2 is curatable, figure 4 too and supplementary figure 2.

Kate Rasheed (10:37:58) (in thread): > Table S1 is based on frailty and nutrition clinical measures for Alzheimer disease.@Aleru Divine

Kate Rasheed (10:38:34) (in thread): > Thank you for the clarifications.

Aleru Divine (10:41:25) (in thread): > What do they mean by summarized? > How would these be curated?

Kate Rasheed (10:50:22) (in thread): > It says decreased and increased abundance in column two. That’s why it was referenced alongside the figure.

Kate Rasheed (10:52:09) (in thread): > By summarized they mean, the taxa showing increased in the figures is showing increased abundance in the second column of each table. > > Plus they grouped it to show the exact type of species:smile:

Aleru Divine (10:54:11) (in thread): > The signatures, abundance directions, and statistical tests are same compared to figure 3 and 4. The tables appears to serve as a summary, and how I understand it is, it is highlighting associations with butyrate-producing species, Alzheimer’s disease, inflammation, and related factors. > Curating it again would likely be redundant.

Yoko C (10:55:48) (in thread): > Hello, but do Fig 3 and 4 or the tables inform about being statistically significant?

Aleru Divine (10:58:09) (in thread): > That was super fast! Thank you<@UBNSEMS3S>:blush:On my end, the connection lagged quite a bit due to my network issues, so having this recording means so much to me:pray:

Kate Rasheed (11:00:51) (in thread): > Yes I see what you mean now@Aleru Divine. I thought since they made reference to it, then she can add it.

Aleru Divine (11:01:58) (in thread): > @Yoko C:thinking_face:I don’tsee anything on this.:fearful:

Kate Rasheed (11:10:12) (in thread): > Looking at it again, I don’t think Fig. 3, 4 and the supplementary tables should be curated since they are features from random forest and based on what Chloe said today, we don’t curate feature abundance unless there is no other curatable figure/table. > > Since figure 2 is curatable with mixed-effects model as the statistical test, figure 3, 4 and the supplementary tables shouldn’t be curated.@Aaishah Mahadeo

Aaishah Mahadeo (11:11:06) (in thread): > So should I only curate Figure 2 for this study?@Kate Rasheed

Kate Rasheed (11:11:48) (in thread): > Yes@Aaishah Mahadeo

Aleru Divine (11:12:00) (in thread): > YeahI agree@Kate Rasheed

Aaishah Mahadeo (11:12:26) (in thread): > Okay, thank you so much@Kate Rasheed@Aleru Divine

Kate Rasheed (11:50:37) (in thread): > @Peace DanielCan you post your question outside this thread?

UBNSEMS3S (12:14:46) (in thread): > https://github.com/waldronlab/bugSigSimpleStart here. I am actively working on making updates to this package but it’s the best place to get started with your analysis. In particular, I’d take a look at the vignette that Mary made for her capstone master’s essay.

UBNSEMS3S (12:18:51) (in thread): > A lot of these early studies (< study 100) should stay as-is). I’m reviewing the others.

UBNSEMS3S (12:19:53) (in thread): > Study 149 and 345 appear to be different studies with different PMIDs. Not sure why they are showing up as the same PMID.

Victoria (Burah) Poromon (12:22:42) (in thread): > Okay, Thank you.

Adeshile Oluwatosin (13:39:45) (in thread): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (13:40:35) (in thread): > Thank you<@UBNSEMS3S>had network issues. > I would need to rewatch

UBNSEMS3S (14:17:44) (in thread): > I did once investigate if Zoom offered the option to use a data center closer to Africa since we have so many BugSigDB contributors from the continent and it might resolve some of the network issues, but it seems like they don’t have one. - File (PNG): image.png

Adeshile Oluwatosin (14:20:57) (in thread): > It would have been a great relief > Thank you for checking it out > I would make use of my wifi next time

Kate Rasheed (14:21:55) (in thread): > @Aleru Divine@Adeshile OluwatosinShould we migrate to Germany:thinking_face:

Aleru Divine (14:21:59) (in thread): > Oh wow! Thanks for looking into that.<@UBNSEMS3S>It’s quite unfortunate though:white_frowning_face:thiswould’vebeen a lot helpful.

Aleru Divine (14:22:19) (in thread): > Girrrrrrl:pleading_face::pleading_face:Letssssssssssss!!!

Adeshile Oluwatosin (14:44:18) (in thread): > @Kate Rasheed:joy:

Joy (15:54:11) (in thread): > Thank you@Kate Rasheedand@Aleru Divine

Alisha Mahadeo (16:53:23) (in thread): > Sounds good! Thank you so much for your help!

Aaishah Mahadeo (18:16:16): > Hi, for the study attached, is Supplementary Figure 2 the only figure that can be curated? - File (PDF): Classifying dementia progression using microbial profiling of saliva .pdf

2024-12-13

Adeshile Oluwatosin (02:13:07) (in thread): > Hello@Aaishah Mahadeocheck figure 1C-E. > > The description states that there is significance in the taxa listed.

Adeshile Oluwatosin (02:25:42) (in thread): > “C) L. wadei and F. villosus diverge significantly in CNr, MCI, and AD as compared to CNh. D) P. gingivalis is reduced in MCI as compared to CNh. E) P. tannerae, F. alocis, and C. valvarum are significantly changed in AD as compared to CNh and tend to diminish in CNr and MCI.” > > Logistic regression seems like the test used here, so it’s a seperate expeirment.

Adeshile Oluwatosin (02:37:16) (in thread): > From this: “logistic regression analysis (LRA) was employed to identify taxa that varied in abundance among patient groups.”

Svetlana Ugarcina Perovic (03:01:55): > One email made my whole week. (see my LinkedIn post below) > > What is your highlight for this week?Happy Friday!https://www.linkedin.com/posts/svetlana-ugarcina-perovic_this-week-i-received-a-very-[…]941541220353-Fx6Z?utm_source=share&utm_medium=member_desktop - Attachment (linkedin.com): Svetlana Ugarcina Perovic on LinkedIn: This week I received a very nice cold email (sharing it w/ :grinning:’s… > This week I received a very nice cold email (sharing it w/ :grinning:'s permission) > :grinning:asked: > What does your daily work involve? > What skills do you think are most…

Kate Rasheed (03:04:27) (in thread): > My highlight for this week is my first ever blog post:smile::https://tinyurl.com/yck4wdbc - Attachment (Kate Rasheed): Outreachy reached out :dancer::dancer::dancer: > The news :heart_eyes: Yepeee!!! On the 28th of November, my joy knew no bounds when the most-sought after internship reached out to me and accepted me as an Outreachy intern working on the BugSigDB Microbiome…

Aleru Divine (03:31:13) (in thread): > Makes the two of us@Kate RasheedThis is definitely the week of 2024 for me:smiling_face_with_3_hearts:And here’s thelinkto mine:smiling_face_with_smiling_eyes_and_hand_covering_mouth: - Attachment (Divine Aleru’s Blog): A New Chapter with Outreachy > Dearest gentle reader *winks in Bridgerton, It is with great delight and a touch of nervous excitement that I share with you the news that I have been selected as an Outreachy intern to work in the Bioconductor community on the BugSigDB Microbiome St…

Samuel Nnanna (04:38:25) (in thread): > @Aaishah MahadeoI agree with@Adeshile OluwatosinSo Figure S2 (supplementary Figure 2) and Figure 1 C-E are curatable.

Aaishah Mahadeo (08:51:21) (in thread): > Thank you so much@Adeshile Oluwatosin@Samuel Nnanna

Aaishah Mahadeo (09:14:16) (in thread): > @Adeshile Oluwatosin@Samuel NnannaFor Figure 1 C-E, will there be 3 experiments? Experiment 1: CNr vs CNh, Experiment 2: MCI vs CNh, Experiment 3: AD vs CNh

Aaishah Mahadeo (10:04:47) (in thread): > @Kate Rasheed@Aleru DivineCan you please have a look at this too? Thank you!

Aleru Divine (10:05:53) (in thread): > Sure thing@Aaishah Mahadeo

Kate Rasheed (10:09:43) (in thread): > @Aaishah MahadeoThe experiment you listed are very correct.

Aaishah Mahadeo (10:11:59) (in thread): > How do I know if it is significant or not?

Aleru Divine (10:14:10) (in thread): > My internet is very slow@Aaishah MahadeosoI haven’tlooked at the supplementary materials.But figure 1(c-e) are curatable.And a total of 3 experiments.The comparisons you shared above are correct.:thumbsup:

Kate Rasheed (10:14:51) (in thread): > They are all significant.

Aleru Divine (10:17:01) (in thread): > @Aaishah Mahadeoread the text above the figure.The p-values are included.Andthey’reall significant.

Aaishah Mahadeo (10:17:11) (in thread): > For figure 1e, F. alocis increased or decreased in AD?

Aleru Divine (10:18:20) (in thread): > Decreased in AD compared to CNh

Aaishah Mahadeo (10:19:18) (in thread): > Thank you so much!@Aleru Divine@Kate Rasheed

Aleru Divine (10:22:15) (in thread): > Okay, nothing else except supplementary figure 2 is curatable from the supplementary materials.:thumbsup:

Aaishah Mahadeo (10:22:58) (in thread): > Okay, thank you!

Peace Daniel (11:33:03) (in thread): > This is a fun mail and beautiful posts@Aleru Divine@Kate Rasheed:clap::heart:

Kate Rasheed (11:33:33) (in thread): > Thank you so much@Peace Daniel

Peace Daniel (11:34:03) (in thread): > I’dmade a post earlierhere@Kate Rasheed - Attachment: Attachment > Hi :wave::skin-tone-4:
> I need help determining the sample sizes for this study, take a look at table 1 and excerpt attached

Kate Rasheed (11:42:53) (in thread): > @Aleru DivineLooking at this again. It can work as a one-against-the-rest analysis. There would be one experiment. > 2 signatures are increased while the rest are decreased. > > PS. That’s if@Aaishah Mahadeohasn’t curated the three experiments:smile:

Aleru Divine (11:43:18) (in thread): > Thank you so much@Peace Daniel:blush:

Aleru Divine (11:46:21) (in thread): > Yeah@Kate Rasheedthat works.Yikes! Omdsss

UBNSEMS3S (11:49:07) (in thread): > I can take a look later today. Ping me if you don’t hear from me in the next few hours.

Kate Rasheed (11:52:16) (in thread): > @Adeshile OluwatosinThank you for bringing this up

Adeshile Oluwatosin (11:54:10) (in thread): > You are welcome@Kate RasheedAnytime

2024-12-14

Aaishah Mahadeo (00:03:53) (in thread): > Hi@Kate Rasheed, I haven’t curated the three experiments yet

Aaishah Mahadeo (00:14:19) (in thread): > Will it be group 0: CNh and group 1: AD, MCI and CNr?

Yoko C (01:07:39) (in thread): > Hello, I think I don’t agree with the overall opinion here, but I might be wrong and over complicating things. I think figure 1C uses ANOVA while 1D and 1E use Mann-Whitey. This is because the “Results” give this type of info: ” (F 3,74 = 3.5, P < 0.05)“, F is usually used when you preformed an ANOVA, which tells you there is a difference in the groups but doesn’t tell you where the difference is. For D and E it gives you a U value, for example”(U = 376, P < 0.001)“. U is usually used when a Mann-Whitey test is done, which compares groups of 2. I would only record the comparisons from D and E given in the Results text and from Figure 1 description text. The graph itself doesn’t tell you which groups are significantly different.

2024-12-16

Aleru Divine (04:30:08) (in thread): > Hi@Yoko C, I think you make a great point. > Figure 1C-E aren’t lefse results. The lefse reference was for supplementary figure 2. > “The linear discriminant analysis effect size (LEfSe) shows a depletion of bacterial taxa in MCI as compared to the other conditions (Figure S2B, D, and F)” > > And you are correct on these statistical tests. The study did not have any info on the statistical tests used apart from LEfSe hence the assumption, but you make a really great point. And I agree. > > Also, from figure description, I think 1C should be curated, the description does tell us where the difference is. > “C)L. wadeiandF. villosusdiverge significantly in CNr, MCI, and AD as compared to CNh.” > > Keyword: Diverge means different, differs… > > Is there any particular reason why?

Kate Rasheed (04:34:10) (in thread): > Thank you for this explanation@Aleru Divine. I totally agree. > > Logistics regression was used for predictive analysis.

Svetlana Ugarcina Perovic (05:15:05): > :drum_with_drumsticks:NEW BUGSIGDB MEMBER > > Please welcome@Karima Diafi(https://www.linkedin.com/in/ka-di/) > > Karima, feel free to ask any BugSigDB question here and join our discussions.Happy Monday, everyone!

Aleru Divine (05:17:38) (in thread): > @Aaishah Mahadeoplease curate all comparisons seperately. > > Also take note that figure 1C uses ANOVA while 1D and 1E use Mann-Whitey. > > This would mean a total of 6 experiments from this figure:For ANOVA (1c)1: CNr vs CNh, > 2: MCI vs CNh, > 3: AD vs CNhFor Mann-Whitey (1D and 1E)1: CNr vs CNh, > 2: MCI vs CNh, > 3: AD vs CNh

Aleru Divine (05:22:41) (in thread): > Welcome:hugging_face:@Karima DiafiNice to have you here.Looking forward to collaborating with you.Happy Monday to you too@Svetlana Ugarcina Perovicand everyone:sunflower:

Kate Rasheed (05:32:32) (in thread): > Welcome@Karima Diafi. It’s great to have you here:relaxed:.

Adeshile Oluwatosin (05:53:01) (in thread): > Welcome@Karima DiafiNice to meet you

Svetlana Ugarcina Perovic (06:17:26): > :bouquet:**** a BIG shout-out to (in alphabetical order):****@Adeshile Oluwatosin@Aleru Divine@Joy@Kate Rasheed@Mildred Anashie@Peace Daniel@Samuel Nnanna@Victoria (Burah) Poromon@Yoko Cfor HUGE reviewing curation efforts!

Adeshile Oluwatosin (06:21:12) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Aleru Divine (07:17:46) (in thread): > Thank you so much for the shout-out@Svetlana Ugarcina Perovic:blush:

Kate Rasheed (07:18:03) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Karima Diafi (07:25:52) (in thread): > Thank you all so much for the warm welcome!:blush:I’m excited to be here and look forward to collaborating and learning from everyone here. Happy Monday!:star2:

Victoria (Burah) Poromon (07:58:30) (in thread): > Thank youuu:blush:@Svetlana Ugarcina Perovic

Joy (08:13:28) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (08:14:57) (in thread): > Welcome@Karima DiafiNice to have you here!

Joy (08:41:30): > Greetings great curators, especially@Kate Rasheedand@Aleru DivineI would appreciate a peer review of this study I am working on.1.In Fig 2D, the condition which isstuntingcould not be found among the conditions listed so I inputed “nutrirional deficiency `` 2.I want to be sure the data transformation I am using is correct :log transformationis correct3.I included the Alpha diversityFaithbecause it was in the supplementary Fig 24.For each experiment, I added all the Matched ons in the study. Is that appropriate? Waiting patiently to hear from you all . P.S (I am still inputting the taxa)https://bugsigdb.org/Study_1260https://www.nature.com/articles/s41467-024-49093-4#Fig2 - Attachment (BugSigDB): Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice - BugSigDB > Faecal microbiota plays a critical role in human health, but its relationship with nutritional status among schoolchildren remains under-explored. - Attachment (Nature): Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice > Nature Communications - Here, in, the authors investigate the relationship between fecal microbiota and nutritional status in a trial on 380 Cambodian schoolchildren, establishing a correlation…

Kate Rasheed (09:14:24) (in thread): > I’ll look through. Welldone@Joy

Aaishah Mahadeo (09:15:12) (in thread): > Thank you so much for all the help@Aleru Divine@Kate Rasheed

Samuel Nnanna (09:17:43) (in thread): > thank you@Svetlana Ugarcina Perovic:grin:

Aleru Divine (09:35:41) (in thread): > Also supplementary figure 2 has 3 experiments. Just making sure. Those should be curated separately as well. > > Making a total of 9 experiments for this study@Aaishah Mahadeo

Kate Rasheed (09:38:45) (in thread): > There are no matched-on variables mentioned in the article. > For the confounders, I only see age and sex. > > For LEfSe results, the data transformation is relative abundance while MaAsLin uses arscine square root.@Joy

Kate Rasheed (09:41:38) (in thread): > For experiment 1, please leave the condition as Anaemia alone. > > The condition in Fig. 2D can begrowth delay

Aleru Divine (09:42:30) (in thread): > Hi@JoyI’ll give this a review as well.Well done

Aaishah Mahadeo (12:51:25) (in thread): > Thank you!@Aleru Divine

Mildred Anashie (13:57:18) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:

Karima Diafi (14:59:40) (in thread): > Thank you@Joy, I appreciate it:blush:

Joy (16:10:03) (in thread): > Thank you@Kate Rasheed

Joy (16:11:10) (in thread): > @Aleru DivineI’ll be waiting for your feedback as well

Aaishah Mahadeo (22:02:49): > Hi, I have to do my analysis for my curations for my final fieldwork assignment. I downloaded one of the student’s samples from GitHub and I am trying to run it but I am having difficulty installing the ‘waldronlab/bugSigSimple’ package.<@UBNSEMS3S>@Svetlana Ugarcina Perovic

2024-12-17

Svetlana Ugarcina Perovic (03:01:06): > Good morning, what a great and important topic of the Outreachy week 2Everyone struggles!I love that they mentioned –> “Rubber duck debuggingis a method of debugging code by articulating a problem in spoken or written natural language.” Explaining code OR any other problem to a rubber duck i.e. your colleague can actually solve problems! > > To me this happens so many times, especially when I am new in the team or to the project. Usually when I can’t see direction to the solution of my current challengewithin max 30 minI’m writing to my team mate. I see that the Outreachy advised “If you’re stuck for morethan 1 to 3 hours, ask your mentor”. In my opinion, you should not wait hours to pass, feel free to ask when you feel stuck earlier than that! > > Greetings from my local cafeteria - Attachment (X (formerly Twitter)): Svetlana U. Perović (@svetlana_up) on X > @MikeNeug @CIBIO_UniTrento Good working morning, Mike! > > (A whole cafeteria only for me; and @fasnicar will join me soon online :coffee: )

Svetlana Ugarcina Perovic (03:06:18) (in thread): > Hi@Aaishah Mahadeo, what’s the error message?

Svetlana Ugarcina Perovic (03:29:15) (in thread): - File (PNG): Screenshot 2024-12-17 at 09.28.06.png

Aleru Divine (03:40:32) (in thread): > Good morning@Svetlana Ugarcina Perovicawesome coffee greeting thread by the way.:star-struck:Oh Ilovetherubber duck debuggingmethod, explaining a problem out loud or just asking myself a question over and over again works like magic. And you’re right, asking for help sooner is always better. I’m still learning to not always keep to myself andI thinkI’m making good progress:heart_hands:

Aleru Divine (03:41:50) (in thread): > On it! I was a bit exhausted yesterday so Icouldn’tget to it

Kate Rasheed (05:05:42) (in thread): > It’s the picture for me:star-struck:. I agree to always asking for help and not always trying to debug on your own (especially when it’s complex).

Joy (05:20:53) (in thread): > Good morning@Svetlana Ugarcina Perovicthe pictures are inviting. The rubber duck debugging does help and you can loop your way out of a problem. Thanks

Joy (05:22:32): > Good morning curators, how do we curateunknowntaxon?

Kate Rasheed (05:35:24) (in thread): > Good morning@Joy. We curate asUnidentified

Karima Diafi (05:35:49): > Hello everyone:blush:, I am preparing to curate my first article and would appreciate your guidance. After reviewing several studies, I have selected this one as a starting point(https://pubmed.ncbi.nlm.nih.gov/36719617/). Should I proceed with curating it directly, or would it be better to first discuss it with a team member? I would also appreciate any feedback on whether this study is a suitable choice or if I should consider exploring further. Thank you for your support! - Attachment (PubMed): Altered gut microbiota in patients with idiopathic Parkinson’s disease: an age-sex matched case-control study - PubMed > We observed differences in gut microbiota composition between PD patients and their healthy spouses. Our findings suggest that disease duration influenced microbiota composition, which in turn influenced development of non-motor symptoms in PD. This study is the first in terms of both gut microbiota …

Joy (05:38:26) (in thread): > Duly noted. thanks@Kate Rasheed

Joy (05:46:13) (in thread): > Hello@Karima Diafi!:blush:That’s great to hear—you’re off to a strong start! > To ensure a smooth curation process, it’s a good idea to discuss the study with a team member first. This way, you can confirm its relevance and align on key aspects before proceeding. Your chosen study looks promising, but getting feedback from others will help ensure it’s a suitable choice. > Looking forward to seeing how your first curation turns out—great job taking the initiative!:clap:

Victoria (Burah) Poromon (06:09:27) (in thread): > Hi@Karima DiafiWell done! > > I wasn’t able to access the full articlefrom my end, but I think this is a great first choice. > > Discussing it before curating is fine, this will help with understanding what informationyou’relooking to get from the paper. But you can also go ahead and curate directly if you feel comfortable. > > You can also ask for peer reviews at any point if you feel stuck, and also afteryou’redone curating. > Have fun!:blush:

Svetlana Ugarcina Perovic (06:51:09) (in thread): > @Karima Diafi, great start! > > First check if the study is already curated by searching the PMID in “Search BugSigDB” (right upper corner)https://bugsigdb.org/w/index.php?title=+Special%3ASearch&search=36719617&go=GoThen, check if someone already opened the issue for it i.e. if it’s already put up for curation:https://github.com/waldronlab/BugSigDBcuration/issuesI checked both: > there is no curation done > there is no open GitHub issue > so I opened it:https://github.com/waldronlab/BugSigDBcuration/issues/545Now, please make a comment there that you would like to curate it, and I will assigned this paper to you.Enjoy! And, come back here when you are stuck :)

Svetlana Ugarcina Perovic (07:02:15) (in thread): > Go step by step following this video:https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=7Try to fill in all the information. Do not worry about mistakes, there is edit option:slightly_smiling_face:and we will fix it together if needed. - Attachment (YouTube): Adding a study to bugsigdb.org

Svetlana Ugarcina Perovic (07:02:58) (in thread): > By the way, excellent choice for the very first curation:clap:

Aaishah Mahadeo (07:12:23) (in thread): > Hi@Svetlana Ugarcina Perovic, I have attached screenshots of the code chunk and error messages - File (PNG): Screen Shot 2024-12-17 at 7.03.04 AM.png - File (PNG): Screen Shot 2024-12-17 at 7.08.29 AM.png - File (PNG): Screen Shot 2024-12-17 at 7.08.47 AM.png

Aaishah Mahadeo (07:13:07) (in thread): > @Svetlana Ugarcina PerovicWhen I tried to load it, this is the error message I am getting - File (PNG): Screen Shot 2024-12-17 at 7.09.08 AM.png

Aleru Divine (07:15:09) (in thread): > Hi@JoyMy apologies for the delay. > > I think “growth abnormality” works better for “stunting” than nutritional deficiency. This is because stunted growth is a type of growth abnormality. > > I agree with Kate, age and sex were confounders controlled for and not matched-on factors.Experiment 1,For antibiotics exclusionThe most helpful entry would be the number of days, weeks, months, rather than a full sentence describing it. So it would be “30 days” for your study****. *******For group 1 definition:***This works to simplify and make the definition more understandable. “This group includes children diagnosed with anemia, with hemoglobin levels below the threshold (typically less than 11 g/dL).” > > There’s no MHT correction for Figure 2 and S2, this applies to experiments 1-8. > “The differences were identified using Linear discriminant analysis Effect Size (LEfSe) analysis with an unadjustedP-value < 0.05, and a logarithmic LDA (linear discriminant analysis) score of > 2.” > > Alpha diversity: The direction of the change is indicated by “<”. If that is the case. Wouldn’t that mean they’re decreased for all group 1. Or I am misinterpreting the table. > > Please ensure to curate all signatures. Usually I finish before I move on to the next experiment so none is omitted by accident. > > Thank you so much!

Aaishah Mahadeo (07:16:52) (in thread): > This analysis is due today for me

Yoko C (12:21:44): > Hey there everyone, i want to opinions on Figure 4 forhttps://www.mdpi.com/2079-7737/13/6/363, I was going to go for a paired comparison based on the colors, but they describe the colors as “correlation” and I’m not sure I fully understand what that implies. So now I am thinking it’s better to go off the text: “A total of 22 genera exhibited differential abundance among these bat species (Figure 4); seven in nectarivorous bats (Clostridium_ss_1, Enterobacteriaceae_unclassified, Ureaplasma, …” and do one signature per group. Another doubt I have is about table s4, which is for unique taxa within each group. Since these taxa are only found in one group, that would make them different between groups but maybe not differentially abundant different, so not sure if that should be curated or not.

Kate Rasheed (14:02:55) (in thread): > @Yoko CI think you should do a one-against-the-rest analysis and use the “in-text result from Microbial composition” as your signature source. This would mean one signature per group

Kate Rasheed (14:06:24) (in thread): > Table S4 is the list of taxa found in a particular group. It’s not saying which of the taxa is increased or decreased. > > To me, it’s not curatable

Karima Diafi (14:19:13) (in thread): > Well understood:+1:.. Thank you@Joy@Victoria (Burah) Poromon@Svetlana Ugarcina Perovicfor the clear guidance! I’ll proceed accordingly.

Yoko C (14:32:00) (in thread): > thanks Kate, I’ll go with the text than! About the table, because its about taxa unique to a group, it means all other groups have 0 abundance (decreased) by default, this is why I was doubting. Thanks you:heart:

Karima Diafi (15:54:31): > Hello again everyone:blush:, I’ve added the study as instructed, but the information didn’t autofill since it’s not indexed in PubMed and doesn’t have a PMID. Should I proceed by filling it in manually, or is a PMID required to move forward? - File (PNG): Screenshot 2024-12-17 213750.png - File (PNG): Screenshot 2024-12-17 213803.png

Aleru Divine (15:57:54) (in thread): > HI@Karima DiafiFor the study information to fill automatically, you have to use the PMID.The PMID is directly above the DOI. - File (JPEG): IMG_1864

Karima Diafi (16:04:45) (in thread): > Thank you@Aleru Divine. I realize now that searching directly using the DOI was not a good idea. - File (PNG): image.png

Aleru Divine (16:23:03) (in thread): > You can use the DOI on any search engine. But use the study title or PMID on PubMed.

Karima Diafi (16:36:33) (in thread): > Got it, thank you for the clarification!

Karima Diafi (16:36:44) (in thread): > I want to leave the statistical analysis and alpha diversity for later; if I save it as complete, can I modify it afterward, right?

Aleru Divine (16:44:52) (in thread): > Yes you can.

Joy (17:34:46) (in thread): > Thank you@Aleru Divine

2024-12-18

Svetlana Ugarcina Perovic (10:36:51) (in thread): > Your must read today:https://katerasheed1.wordpress.com/2024/12/18/struggles-stretchers-and-yardsticks-for-growth/:clap:@Kate Rasheedshared her struggles (and solutions too) - Attachment (Kate Rasheed): Struggles: Stretchers and Yardsticks for Growth. > In every journey, there are struggles encountered and growth enhanced. Struggles are stretchers and yardsticks for growth. Babies struggle as well while trying to reach a milestone. Source: Google …

Svetlana Ugarcina Perovic (10:42:02): > TOMORROW atour weekly team meeting and office hours at 9 AM EDT (>>3:00 PM<<**** ****in Europe, Nigeria, etc.).https://us02web.zoom.us/j/2737200499<@UBNSEMS3S>will talk about how to curate results from meta-analysis. > > Do not miss the last team meeting in 2024next Thursday (Dec 19)! The first team meeting in 2025 will be on January 2.

Adeshile Oluwatosin (10:51:32) (in thread): > I will be there:blush:

Aleru Divine (16:19:47) (in thread): > Looking forward to it!:blush:

2024-12-19

Aaishah Mahadeo (00:09:29) (in thread): > Hi,<@UBNSEMS3S>and I were able to resolve this issue. For anyone who encounters this issue in the future while attempting to download the bugSigSimple package, make sure that you have the latest software update on your Mac (I am not sure about Windows) and then update R and RStudio. Also, make sure the ‘curl’ and ‘curatedMetagenomicData’ packages are installed.

Karima Diafi (04:48:14): > Hello everyone:blush:, I hope this message finds you well. I’ve just completed my first curation and am looking forward to receiving the review. Thank you in advance. Wishing you all a great day!:star2:

Aleru Divine (04:49:06) (in thread): > Well done!:clap::clap:

Karima Diafi (04:49:25) (in thread): > Thank you!

Kate Rasheed (04:54:25) (in thread): > Wooooshhhhhh:dancer:. Congratulations@Karima Diafi. I’m so happy for you.

Karima Diafi (04:55:30) (in thread): > Thank you@Kate Rasheed, I appreciate it.:innocent:

Svetlana Ugarcina Perovic (06:30:17) (in thread): > THANKS for sharing the solution!

Svetlana Ugarcina Perovic (06:31:01) (in thread): > Wooow, that was fast!@Kate Rasheedcould you please review it.

Kate Rasheed (07:06:53) (in thread): > Yes please@Svetlana Ugarcina Perovic

Peace Daniel (09:01:52) (in thread): > Good job@Karima Diafi

Svetlana Ugarcina Perovic (10:01:31): > @Kate Rasheedasked: When taxa has slashes, do we curate them individually or together as stated in the paper. For example: Eggetherlla lenta/Clostridiodes difficile, Bacteroides ovatus/vulgatus. > > We curate them together as they representclosely related species.

Svetlana Ugarcina Perovic (10:02:04): > <@UBNSEMS3S>, thanks for meta-analysis explanation!

Svetlana Ugarcina Perovic (10:02:19): > How to curate meta-analysis study: - File (PNG): Screenshot 2024-12-19 at 15.26.15.png

Kate Rasheed (10:03:16) (in thread): > Thank you so much.

Kate Rasheed (10:05:00): > Thank you<@UBNSEMS3S>for today’s session. I learnt a lot from the explanation on meta-analysis study curation. > > Thanks to everyone that asked questions too. > > Happy holidays everyone:hugging_face:.

Aleru Divine (10:06:53): > Thank you for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina Perovic:blush:

UBNSEMS3S (10:07:29): > As per our discussion during today’s meeting of the “Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease toBlautiaGenus: Evidence From Feces, Blood, and Brain” paper, RNA-seq is a method for measuring gene expression and so I feel fairly confident saying those studies were not included in the microbiome differential abundance analysis.

Karima Diafi (10:12:30) (in thread): > Thank you@Peace Daniel:blush:@Kate RasheedI just noticed that I added a fig1.A signature but it wasn’t showed up on the study page.. does this mean we can add a maximum of two signatures?

Yoko C (10:15:05): > Hello, I am reviewing the study forhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01820-1I wanted to check which sample size should be used. The sample size is provided in Figure 5A and Figure 6A but the numbers in these graphs do not add up to the numbers provided by the abstract and results. Results mention the experiment started with 48 mice, but a second part of the study was only carried out with 46 mice, 22 mice euthanized before the end of the study (FVT-SDT 0, FVT-UnT 2, and FVT-ChP 3, FMT 5, FVT-PyT 7, and saline 5) 24 survived to the end of the study (FVT-SDT 8/8, FVT-UnT 5/7 mice, FVT-ChP 5/8, FVT-PyT 1/8, FMT 3/8 mice, saline 2/8) adding up to 46. The graphs on the other hand list 23 euthanized and 24 survived, and 21 and 24, which aren’t consistent with each other and don’t add up to 46. We were wondering if the sample sizes should come from the figures or the results? Figure 4 also gives sample sizes for mice that survived to termination but these add up to 25.

Samuel Nnanna (10:15:57): > Thank you@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovicfor the office hour session today

Kate Rasheed (10:16:13) (in thread): > @Karima DiafiEach experiment has a maximum of two signatures. One for increased and the other for decreased. > > I’ll look through your study and give feedback on GitHub.

Peace Daniel (10:21:18) (in thread): > Okay,thank you

Peace Daniel (10:24:28) (in thread): > Does that mean this tableshouldn’tbe curated<@UBNSEMS3S>? - File (JPEG): IMG_3850

Karima Diafi (10:25:11) (in thread): > Thank you@Kate Rasheedfor taking the time to provide feedback. I do have a question related to the study, but I’ll hold off until after the review.

UBNSEMS3S (10:25:18) (in thread): > Were all of them from RNA-seq studies?

UBNSEMS3S (10:25:26): > Today’s recording. Thank you everyone who atttended. - File (MPEG 4 Video): bugsigdb-2024-12-19.mp4

Peace Daniel (10:26:02) (in thread): > Yes, all studies on the brain was RNA-seq

UBNSEMS3S (10:26:47) (in thread): > Hmmm ok yet they got DA results. Perhaps they are confusing shotgun with RNA-seq? I am investigating further.

UBNSEMS3S (10:33:49) (in thread): > I think they used RNA-Seq data but prepared it like shotgun dataset. I would treat these like they were shotgun metagenomic analysis.

Peace Daniel (10:35:01) (in thread): > Okay, thank you so much

Aleru Divine (11:24:01): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>please what is the data Transformation for ANCOM-BC?

Mildred Anashie (11:24:38) (in thread): > Hi@Aleru DivineI believe its centered log ratio

Aleru Divine (11:25:10) (in thread): > That is for ANCOM@Mildred Anashie:smiling_face_with_tear:

Svetlana Ugarcina Perovic (11:26:39) (in thread): > To my knowledge. ANCOM-BC performs CLR (Centered Log-Ratio) transformation

Aleru Divine (11:27:21) (in thread): > Okay, thank you so much@Svetlana Ugarcina Perovic@Mildred Anashie:pray:

Svetlana Ugarcina Perovic (11:27:46) (in thread): > BUT

Svetlana Ugarcina Perovic (11:27:52) (in thread): > I am not right maybehttps://forum.qiime2.org/t/interpretation-of-log-fold-change-in-ancom-bc/28130/5 - Attachment (QIIME 2 Forum): interpretation of log-fold change in ANCOM-BC > Hi @lizgehret, Thanks a lot! I would like to confirm that ‘centered’ log transformation is applied in this method also. After centered log transformation, values greater than 1 may not be greater than zero after transformation, because a certain shift of the center value is applied. Am I right?

Svetlana Ugarcina Perovic (11:28:01) (in thread): - File (PNG): Screenshot 2024-12-19 at 17.27.38.png

Svetlana Ugarcina Perovic (11:28:33) (in thread): > Check out this paperhttps://www.nature.com/articles/s41467-020-17041-7 - Attachment (Nature): Analysis of compositions of microbiomes with bias correction > Nature Communications - Differential abundance analysis of microbiome data continues to be challenging due to data complexity. The authors propose a method which estimates the unknown sampling…

Aleru Divine (11:29:10) (in thread): > Thank you so much!@Svetlana Ugarcina PerovicChecking it right away!

Svetlana Ugarcina Perovic (11:30:47) (in thread): > ok, please do let us know here what you concluded

Aleru Divine (12:23:50) (in thread): > Thank you for sharing the paper@Svetlana Ugarcina PerovicWhat I understand is that ANCOM-BC doesn’t exactly apply a data transformation like CLR for example. Instead, it uses a linear regression framework with a built-in normalization technique that kind of corrects the usual biases.
> > I think it still relieson relative abundance because microbiome data is compositional. > > So my opinion is relative abundance or leave blank.

Mildred Anashie (12:28:08) (in thread): > I agree with you@Aleru DivineI went through the paper a bit and it seems to point to relative abundance > > > Thank you for sharing@Svetlana Ugarcina Perovic

Yoko C (15:35:48) (in thread): > Hi, the paper mentions a log scale is used, so would that imply a log transformation?

Joy (17:59:19): > Thank you<@UBNSEMS3S>for the office hour session today!

2024-12-20

Kate Rasheed (06:33:46) (in thread): > @Yoko CGood afternoon. Are you sure you shared the right article? I can’t see what you are talking about in this article.

Yoko C (06:36:31) (in thread): > Thanks Kate! I edited with the correct article nowhttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01820-1

Kate Rasheed (07:02:10) (in thread): > Fig. S5A gives a total of 22 euthanized and 24 survived. > > Fig. S5C gives a total of 23 euthanized and 21 survived. > > I’ll go with choosing sample size from the result. It means the alpha diversity will be curated from Fig. S5A which is consistent with the result.@Yoko C

Svetlana Ugarcina Perovic (07:38:57) (in thread): > The data transformation for ANCOM-BC involves**** a linear regression frameworkthat incorporates a sample-specific offset term to account for the sampling fraction. This transformation** is analogous to log-ratio transformation**, which is commonly used to handle the compositionality of microbiome data.

Svetlana Ugarcina Perovic (07:39:28) (in thread): > We are full of doubts, leave it blank but also a note with this paper that we just discussed.

Svetlana Ugarcina Perovic (07:39:44) (in thread): > <@UBNSEMS3S>any thoughts on this? Thanks!

Svetlana Ugarcina Perovic (07:42:50) (in thread): > My answer is: No, the centered log ratio (CLR) transformation is not used in ANCOM-BC. Instead, ANCOM-BC employs a linear regression framework. The linear regression framework used in ANCOM-BC is based on modeling the log-transformed operational taxonomic unit (OTU) counts data.

Aleru Divine (07:50:33) (in thread): > Thank you for the clarification@Svetlana Ugarcina Perovic

Karima Diafi (10:35:57): > Thank you,@Kate Rasheed, for your valuable feedback:blush:. I greatly appreciate it and would like to ask a few questions regarding your comments, if you don’t mind.

Kate Rasheed (10:36:39) (in thread): > Please ask your questions. We would really appreciate it.@Karima Diafi

Karima Diafi (10:44:41) (in thread): > Those are the change I made after your review : > 1. I changed the antibiotics exclusion to “3 months”. > 2. I added age and sex under matched-on. > 3. I tick “yes” for the MHT correction. > 4. I added “unchanged” to richness. > 5. For signature 2 under experiment 1, I changed : > -Coriobacteriales incertae cedis to Coriobacteriaceae incertae sedis. > -Firmicutes to Bacillota. > -Verrucomicrobiae to verrucomicrobia > -Lactobacillaceae to Lactobacillaceae (33958) > I didn’t find the ID: > -Lachnospiraceae_ND3007_group, > -Eubacterium_hallii group > 6. I populate the information in experiment 1 under experiment 2. > > > I am still try to figure out how to curate the rest figures.

Karima Diafi (10:46:28) (in thread): > Concerning the questions : > * Can you please tell me why the significance threshold to 0.25 instead the p-value threshold=0.05? > * For : Ruminococcus gauvreauii_group can I add it as : Ruminococcus gauvreauii?

Kate Rasheed (10:48:26) (in thread): > Eubacterium hallii has a new name “Anaerobutyricum hallii” with this tax id: 39488 > > Lachnospiraceae ND3007 group has not been found in NCBI. You don’t need to change it.@Karima Diafi

Kate Rasheed (10:49:52) (in thread): > For the significance threshold as 0.25, there was a multiple hypothesis correction done that adjusted the p-value to a q-value threshold of 0.25. > > If we leave the threshold at 0.05, it means there was no MHT correction done.

Kate Rasheed (10:50:40) (in thread): > Ruminococcus gauvereauii is correct.

Karima Diafi (10:52:56) (in thread): > Understood, thank you for clarifying.

UBNSEMS3S (11:04:31) (in thread): > ANCOM uses CLR, ANCOM-BC does not according to the discussion here:https://forum.qiime2.org/t/interpretation-of-log-fold-change-in-ancom-bc/28130/3

Kate Rasheed (11:27:18): > Good evening everyone. Please I would like to seek your thoughts on Fig. 3C of this article:https://www.nature.com/articles/s41598-023-47748-8It doesn’t seem curatable to me. What do you think please? - Attachment (Nature): Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits > Scientific Reports - Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits

Aleru Divine (11:38:58) (in thread): > Thank you@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Mildred Anashie@Yoko CSuper helpful thread:pleading_face::pray:

Svetlana Ugarcina Perovic (16:40:05) (in thread): > Here is a thread that discussed it:https://community-bioc.slack.com/archives/C04RATV9VCY/p1730389297809379 - Attachment: Attachment > Hello everyone and @UBNSEMS3S, in the meeting you mentioned that some heatmaps aren’t clear enough to be curatable, which made me doubt on a heatmap I was working on https://www.nature.com/articles/s41598-023-47748-8/figures/3. So the way I curated the heatmap is based on the cluster P+, P- orange and blue bottom bar (because it is the most clear). Now I think maybe I shouldn’t curate it. But if it is curatable, I have another question. Since this heatmap was made through SIAMCAT, and they say one of their tools is LASSO logistic regression, is that the test used ? Thanks

Svetlana Ugarcina Perovic (16:48:34) (in thread): > @Yoko Ccould you please explain how in the end you curated Fig 3C? Thanks!

Peace Daniel (17:55:36): > Hi:wave:I’d love assistance in sourcing the NCBI ID’s of the following in thisstudyif possible > * cc_115 > * 1-68 > * ph2 > * rc4-4 > There was no mention of these in the study soI’mnot sure. Would love a second opinion - Attachment (Frontiers): Frontiers | Integrated Microbiome and Host Transcriptome Profiles Link Parkinson’s Disease to Blautia Genus: Evidence From Feces, Blood, and Brain > A link between the gut microbiome and Parkinson’s disease (PD) has been intensively studied, and more than 100 differential genera were identified across the…

2024-12-21

Kate Rasheed (01:31:39) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Kate Rasheed (01:32:45) (in thread): > Good morning@Peace Daniel. I’ve checked and didn’t see these taxa. I guess you would curate it that way.

Kavya Ayalasomayajula (01:34:08): > Hi all, I am reviewing an old study I curated. I curated a table in which authors compared relative abundanceat the genus level between groups. I found they had a separate table which compared relative abundance at the phylum level as well. Is it worth it to go back and curate an experiment for the phylum level?I’mnot sure if this would be helpful. Thanks in advance

Kate Rasheed (01:41:09) (in thread): > Good morning@Kavya Ayalasomayajula. If a different statistical test was used, then you should curate a separate experiment. If it’s the same statistical test, just add the phylum taxa to previously curated signatures.

Peace Daniel (03:13:33) (in thread): > Yeah, I did > Thanks for your response

Yoko C (11:12:58) (in thread): > Hi, I I curated the heatmap based on the orange and blue bars.

Kavya Ayalasomayajula (11:14:38) (in thread): > Thanks!

2024-12-22

Svetlana Ugarcina Perovic (05:56:51) (in thread): > Yes yes, that’s clear from the previous thread, but how you defined decrease/increase, please give 2-3 examples to understand it better. Thanks!

Yoko C (15:02:42) (in thread): > Oh, I didn’t really do this in a methodical way, or rather my method was just using the “Relative abundance” color scale included in the graph and doing a rough estimation. This is why I initially doubted if I should curate it or not. There is a table linked to this graph but I remember I didn’t see it provided a direction for the change so I didn’t use it, but maybe it does and that would be a better way to curate it.

Yoko C (15:10:22) (in thread): > I think this study also has prevalence information that could be curated but I didn’t curate it because at the time I thought that was a type of abundance that was not expected to be curated, so that would be another thing to check.

2024-12-23

Svetlana Ugarcina Perovic (03:49:18) (in thread): > @Aleru Divine@Mildred Anashieplease check our doubts here, thanks!

Svetlana Ugarcina Perovic (03:52:25) (in thread): > @Yoko Ctwo things to note:slightly_smiling_face: > 1. we do not do “a rough estimation” of results, if the figure is not crystal clear for curation than it’s not curatable > 2. we do not curate “prevalence information” > Please stay in the thread, and let’s hear from@Aleru Divine@Mildred Anashiewhat they think.Happy Monday, ALL!

Aleru Divine (04:02:06) (in thread): > Thank you@Svetlana Ugarcina PerovicI’mtaking a look right away

Svetlana Ugarcina Perovic (04:43:08): > :drum_with_drumsticks:NEW BUGSIGDB MEMBER > > Please welcome@Ouma RonaldOuma, feel free to ask any BugSigDB question here and join our discussions.

Ouma Ronald (04:45:05): > Greetings everyone here. Am more than excited to be here . I’m Ouma Ronald, in my 3rd year in software engineering at Bugema University. I’m excited to contribute to this project and collaborate with the team thus learning more skills.Happy holidays and a prosperous new year. Thank you@Svetlana Ugarcina Perovic, am so happy to meet the team.

Samuel Nnanna (05:22:10): > Welcome@Ouma RonaldGlad to have you here > Feel free to ask any questions and trust you’ll get the support you need. > Looking forward to working and learning with you

Ouma Ronald (05:24:22) (in thread): > Thank you so much@Samuel Nnanna. am humbled

Kate Rasheed (06:26:48) (in thread): > Hello@Ouma Ronald. So glad to have you here and I’m looking forward to collaborating with you too.

Joy (07:00:11) (in thread): > Hi@Ouma RonaldIt’s nice to have you here. Welcome to the community.:rocket:

Ouma Ronald (07:19:43) (in thread): > I am humbled to be part of this team . Thank you for the love and kindness

Adeshile Oluwatosin (07:48:24) (in thread): > Hello@Ouma RonaldWelcome to the community. Feel free to ask questions when stuck

Adeshile Oluwatosin (07:52:42) (in thread): > Hello everyone, > Dropping my two cents > I checked out figure 3C. Although there was mention of significant different relative abundance between two clusters. > The figure itself is not clear enough to curate.

Adeshile Oluwatosin (07:56:16) (in thread): > Noted@Svetlana Ugarcina Perovic

Aleru Divine (09:33:31) (in thread): > Hello:wave:@Ouma RonaldGood to have you here! Looking forward to collaborating with you and happy holidays:blush:

Yoko C (10:13:02) (in thread): > @Svetlana Ugarcina Perovicthank you for clarifying for both the figure and prevalence not being curatable.

Svetlana Ugarcina Perovic (11:36:45) (in thread): > @Adeshile Oluwatosinedit the tag:wink:

Adeshile Oluwatosin (13:57:45) (in thread): > Done@Svetlana Ugarcina PerovicIdidn’teven notice:smile:

Ouma Ronald (14:53:23) (in thread): > Thank you all for the warm welcome.I’mtouched on . > Thanks for the love. > > Happy I am to meet this beautiful family

Mildred Anashie (15:53:48) (in thread): > Okay@Svetlana Ugarcina PerovicI believe it’s a difficult one to curate as I stated in the previous thread, because I can’t tell increase and decrease easily from the figure > > > I keep wondering ifI’mmissing something:thinking_face:I’llgive it another look

Kavya Ayalasomayajula (23:02:47): > Hi all, I curated this studyhttps://bugsigdb.org/Study_1256from this paper using supplemental digital content 4. However, I am unsure if I can curate supplemental digital content 5 (correlation analysis between taxa and a categorical variable) or supplemental digital content 9 (SIMPER analysis–not sure how to interpret this or if it is curatable). Thanks and happy holidays! - Attachment (BugSigDB): Ketogenic Diets in Children With Intractable Epilepsy and its Effects on Gastrointestinal Function, Gut Microbiome, Inflammation, and Quality of Life - BugSigDB > OBJECTIVES: The ketogenic diet (KD) is a treatment for children with intractable epilepsy (IE), can cause gastrointestinal symptoms, and have an adverse effect on growth, nutrition and quality of life (QOL). - File (PDF): J pediatr gastroenterol nutr - 2023 - Menzies - Ketogenic Diets in Children With Intractable Epilepsy and its Effects on.pdf

2024-12-24

Kate Rasheed (00:45:46) (in thread): > Good morning@Kavya Ayalasomayajula. You’re right with the curation. Just supplemental digital content 4 is curatable.

Aleru Divine (01:57:12) (in thread): > Hi@Kavya AyalasomayajulaI checked this out too andIalso agree that S5 and S9aren’tcuratable.Happy holidays!

Svetlana Ugarcina Perovic (07:48:54): > Check this opportunity out:https://www.linkedin.com/posts/bioconductor_index-activity-7277231869555818496-Z6S4 - Attachment (linkedin.com): Bioconductor on LinkedIn: Bioconductor Course | Nairobi, Kenya | March 2025 > :earth_africa: Exciting news! Join us for a Bioconductor workshop in Nairobi, Kenya, from March 24–28, 2025! This week-long, in-person course will cover genomic data…

Aleru Divine (07:55:43) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:hugging_face:

Adeshile Oluwatosin (07:59:04) (in thread): > Thank you@Svetlana Ugarcina Perovic

Kate Rasheed (08:08:24) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Joy (09:32:12) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing

Kavya Ayalasomayajula (11:24:53) (in thread): > Thank you!

Samuel Nnanna (22:48:52) (in thread): > Thank you@Svetlana.

Samuel Nnanna (22:49:56): > Merry Christmas and Happy Holidays:champagne::champagne::confetti_ball::confetti_ball:<!here>Take some time to rest:grin::grin:Be kind to yourselves:clinking_glasses::clinking_glasses:

2024-12-25

Aleru Divine (03:18:23) (in thread): > Thank you@Samuel NnannaMerry Christmas everyone:christmas_tree:

Svetlana Ugarcina Perovic (03:22:57): > :christmas-parrot:**** Happy holidays and happy New Year!****:christmas-parrot::question:How do you say this greeting in your native language:question:I will go first:Срећни празници и срећна Нова година!

Aleru Divine (03:25:25) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy holidays:partying_face:Idon’tknow how to say it in my language:grimacing:might have to ask my mom:face_with_open_eyes_and_hand_over_mouth:

Kate Rasheed (03:26:31) (in thread): > @Aleru DivineWe are on the same page:smile:

Chioma Onyido (03:33:28) (in thread): > Thank youuu Svet.Ekeresimesi oma* na Afa ofu oma diri anyi n’ile*!:christmas_tree::heart_hands::skin-tone-5:

Adeshile Oluwatosin (04:23:50) (in thread): > Merry Christmas:blush:

Kate Rasheed (04:35:56) (in thread): > This is it in my language:smile:. Thank you so much@Chioma Onyido.@Aleru DivineI’m no longer on the same page with you:sweat_smile:.

Chioma Onyido (04:36:28) (in thread): > Yess! Just updated it@Kate Rasheed, added happy new year.:smile:

Samuel Nnanna (07:00:59) (in thread): > And here I was thinking about how to type mine > Thank you@Chioma Onyido:joy::joy::joy:

Joy (15:08:53) (in thread): > Thank you@Svetlana Ugarcina PerovicMerry Christmas!:mx_claus:

2024-12-26

Ouma Ronald (04:30:14) (in thread): > mbaagaliza kulisimansi ennungi wamu n’omwaka omugya ogwemirembe

Yoko C (10:55:01) (in thread): > Felices fiestas y feliz año nuevo, or kusisitaw fiestanaka uqat machaq mara

Yoko C (10:57:45): > Hey everyone, so I was going over a the curation policy and for this part “If signatures are reported using two different statistical tests and they are overlapping, use the test that reports a larger number of signatures. Curate as two different experiments when results are very different between the tests.” I am wondering what “very different” would mean, would it be like 1 or 2 taxa from the test with less signatures not included in the test that reports a larger number of signatures?

2024-12-27

Svetlana Ugarcina Perovic (04:00:56) (in thread): > <@UBNSEMS3S>we should revise this. I would say: If signatures are reported using two different statistical tests and they areFULLY overlapping,~use the test that reports a larger number of signatures~. record one experiment and note about two tests performed. Curate as two different experiments when results are~very different~different (not fully overlapping) between the tests.

Svetlana Ugarcina Perovic (04:01:09) (in thread): > Thanks@Yoko Cfor bringing this up!

Karima Diafi (06:25:05): > Hello everyone, I keep adding signatures, but they don’t appear on the study page!

Tino (06:35:32) (in thread): > Muve ne Christmas yakanaka negore dzva!! (It’s the Shona language in Zimbabwe):relaxed:

Tino (06:38:33): > Hello@Svetlana Ugarcina Perovicplease delete experiment 3 fromHttps://bugsigdb.org/Study_1216 - Attachment (BugSigDB): Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing - BugSigDB > Understanding the violence behaviors in schizophrenia patients has always been the focus of forensic psychiatry.Although many studies show gut microbiota could regulate behavior, to our knowledge, no studies have profiled the gut microbiota structure in schizophrenia patients with violence.

Aleru Divine (06:50:19) (in thread): > Thank you@Svetlana Ugarcina Perovic

Aleru Divine (06:51:41) (in thread): > Sorry about this@Karima DiafiThis is a general issuethat happens sometimesI usually mark my study as incomplete/complete a few times and it all comes up.I refresh the page too (this doesn’t work all the time)Can you try thistrick from@Svetlana Ugarcina Perovichttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Tino (07:03:57): > Hello everyone and@Kate RasheedI am doing corrections on a paper I curated beforehttps://github.com/user-attachments/files/17643426/s00414-020-02439-1.pdfI need a peer review especially on Experiment 2 of this studyhttps://bugsigdb.org/Study_1216@Kate Rasheedplease delete experiment 3 fromhttps://bugsigdb.org/Study_1216 - Attachment (BugSigDB): Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing - BugSigDB > Understanding the violence behaviors in schizophrenia patients has always been the focus of forensic psychiatry.Although many studies show gut microbiota could regulate behavior, to our knowledge, no studies have profiled the gut microbiota structure in schizophrenia patients with violence.

Kate Rasheed (07:07:02) (in thread): > @TinoWelldone on this correction. I see experiment 2 has about 5 signatures which shouldn’t be. An experiment should have just two signatures (increased and decreased). All taxa with decreased abundance should be added to signature 2 while those with increased abundance should be added to signature 1. > > You can request that other signatures be deleted. Thank you so much.

Kate Rasheed (07:10:13) (in thread): > I’m guessing you separated the signatures because of their taxonomic rank. This shouldn’t be. All taxa irrespective of their rank should be curated together, as long as it’s the same statistical test and experiment.

Tino (07:16:59) (in thread): > @Kate Rasheedthanks! Yes I had separated the signatures because of their taxonomic rank! That’s what was tripping me up. Thank you, lesson learned!:grin:

Kate Rasheed (07:18:28) (in thread): > You’re welcome@TinoPlease tag@Svetlana Ugarcina Perovicfor the deletion of experiment 2 - signatures 3-5 and experiment 3:hugging_face:

Tino (07:21:34) (in thread): > hello@Svetlana Ugarcina Perovicplease delete experiment 2: signatures 3, 4 and 5. And also delete experiment 3 > from this study httpshttps://bugsigdb.org/Study_1216 - Attachment (BugSigDB): Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing - BugSigDB > Understanding the violence behaviors in schizophrenia patients has always been the focus of forensic psychiatry.Although many studies show gut microbiota could regulate behavior, to our knowledge, no studies have profiled the gut microbiota structure in schizophrenia patients with violence.

Svetlana Ugarcina Perovic (08:57:56) (in thread): > Experiment_2/Signatures_3, 4 and 5 > Experiment_3 > deleted. > > And documented herehttps://github.com/waldronlab/BugSigDBcuration/issues/420 - Attachment: #420 Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing > Profiling the differences of gut microbial structure between schizophrenia patients with and without violent behaviors based on 16S rRNA gene sequencing – Xiacan Chen et al. – International Journal of Legal Medicine
> https://link.springer.com/article/10.1007/s00414-020-02439-1 > > PDF to download:
> s00414-020-02439-1.pdf > > Electronic supplementary material to download:
> 414_2020_2439_MOESM1_ESM.docx

Adeshile Oluwatosin (09:00:11) (in thread): > Noted@Svetlana Ugarcina Perovic

Joy (09:09:13) (in thread): > Thank you@Svetlana Ugarcina Perovic

Karima Diafi (09:34:40) (in thread): > Okey, I will try this trick.. thank you@Aleru Divine

Karima Diafi (10:02:05) (in thread): > Hello@Kate Rasheed, I hope your doing fine.. > I have a question regarding this experiment: Patients with RBD vs Patients without RBD > what should I write in the group 0? > additionally, if I want a signature to be deleted should I requested it on GitHub or slack ? - File (PNG): image.png

Kate Rasheed (10:03:27) (in thread): > Group 0 would be Patients without RBD. > > You can request on GitHub

Karima Diafi (10:03:51) (in thread): > Thank you@Kate Rasheed:blush:

2024-12-28

Karima Diafi (04:46:21) (in thread): > Hello@Svetlana Ugarcina Perovic, I was struggling with the signatures not shwing up after saving, I found a workground.. If I go back to the experiment, make any modification and save it again, the signatures appear.. it seems that editing something in the experiment triggers the signatures to show up..

Karima Diafi (05:21:02) (in thread): > Hello@Kate Rasheed, I am finalizing the correction and have this two taxa that I couldn’t find on NCBI, what should I do in this case? > additionally for : Eubacterium_ventriosum_group, I listed it as Eubacterium ventriosum.. - File (PNG): Screenshot 2024-12-28 092347.png - File (PNG): Screenshot 2024-12-28 111547.png

Kate Rasheed (05:25:40) (in thread): > The first one is resolved asClostridiumwhile the second isFirmicutes bacterium CAG:56@Karima Diafi

Karima Diafi (05:29:54) (in thread): > Thank you@Kate Rasheed

Svetlana Ugarcina Perovic (07:00:13) (in thread): > @Karima Diafigreat that you found a solution! Please share it herehttps://github.com/waldronlab/BugSigDB/issues/248so the team can learn more from it. Thanks! - Attachment: #248 Incomplete display of Study 1103 > I entered this study and entered 3 experiments. After refreshing a couple of times, I was still only seeing 2 experiments. Then the 3rd appeared. I also entered signatures but they are not showing.

2024-12-30

Joy (06:16:36): > Good morning everyone, I trust we are enjoying the holidays. I’d like to request a peer review of this study I curated. I’m looking forward to hearing from you.https://bugsigdb.org/Study_1260https://www.nature.com/articles/s41467-024-49093-4#Fig2 - Attachment (BugSigDB): Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice - BugSigDB > Faecal microbiota plays a critical role in human health, but its relationship with nutritional status among schoolchildren remains under-explored. - Attachment (Nature): Faecal microbiota of schoolchildren is associated with nutritional status and markers of inflammation: a double-blinded cluster-randomized controlled trial using multi-micronutrient fortified rice > Nature Communications - Here, in, the authors investigate the relationship between fecal microbiota and nutritional status in a trial on 380 Cambodian schoolchildren, establishing a correlation…

2025-01-02

UBNSEMS3S (08:56:08): > Our weekly team meeting will be in 5 minutes athttps://us02web.zoom.us/j/2737200499! We will check in as we start the new year.

Adeshile Oluwatosin (09:01:28) (in thread): > Noted > Happy new year:fireworks:

Joy (09:23:36) (in thread): > Duly noted!

UBNSEMS3S (09:30:47): > Thank you everyone who attended our short meeting this morning. Here is the recording. We’ll have a larger, longer meeting next week I’m sure. - File (MPEG 4 Video): video1267807659.mp4

Adeshile Oluwatosin (09:32:01) (in thread): > Thank you

UBNSEMS3S (11:05:52) (in thread): > I will update it next week. Thank you for bringing it to my attention. Some of the curation policy is outdated or poorly written.

Aleru Divine (11:10:47) (in thread): > Thank you so much!<@UBNSEMS3S>

Svetlana Ugarcina Perovic (13:45:46): > Have you seen the longest list of taxa in signatures? Check thishttps://bugsigdb.org/Study_1218out!:clap:@Kate Rasheed@Aleru Divine:boom:https://bugsigdb.org/Study_1218/Experiment_6/Signature_2 - Attachment (BugSigDB): Study 1218/Experiment 6/Signature 2 > Source: Supplementary Data 11 Description: Differentially abundant taxa in oral samples between Autism Spectrum Disorders children with Lower SCQ and Upper SCQ…

Peace Daniel (13:58:49) (in thread): > Wow,that’sa lot:smiling_face_with_tear:

Kate Rasheed (14:28:58) (in thread): > It was really a lot:sweat_smile:

Samuel Nnanna (22:21:14) (in thread): > Oh Lord……welldone@Kate Rasheed@Aleru Divine

2025-01-03

Adeshile Oluwatosin (01:16:41) (in thread): > Amazing:blush:

Adeshile Oluwatosin (01:19:22) (in thread): > Experiment 6/signature 2:joy:

Joy (04:51:20) (in thread): > Wow, thats alot! welldone@Kate Rasheed@Aleru Divine!

2025-01-04

Joy (09:07:41): > Hi@Svetlana Ugarcina Perovickindly delete signature 3. thanks

Joy (09:50:10): > My apologies@Svetlana Ugarcina Perovic, this is the study, thankshttps://bugsigdb.org/Study_1163 - Attachment (BugSigDB): Differential effects of antiretrovirals on microbial translocation and gut microbiota composition of HIV-infected patients - BugSigDB > INTRODUCTION: Increased bacterial translocation and alterations to gut microbiota composition have been described in HIV infection and contribute to immune activation and inflammation.These effects persist despite combined antiretroviral therapy (cART).

Ndukauba Oluchi (11:06:34): > Hello everyone and Happy New year:confetti_ball:. My name is Ndukauba Oluchi, I have a bachelor’s degree in Biochemistry and I’m excited to contribute to this project and collaborate with this team to learn and grow. > Thank you:pray:

Peace Daniel (14:00:48) (in thread): > Welcome, happy new year to you

2025-01-05

Svetlana Ugarcina Perovic (06:42:41) (in thread): > Welcome to the community!

Svetlana Ugarcina Perovic (06:43:20) (in thread): > Deleted.

Aleru Divine (12:18:07) (in thread): > Welcome@Ndukauba Oluchi:hugging_face:Looking forward to collaborating with you

Kavya Ayalasomayajula (15:22:24): > Hi all, I hope everyone had a happy holidays! I wanted to ask for some clarifications in our curation policy. “Sometimes papers report an unclassified species, but provide classification up to the genus level. Such unclassified species should be excluded from the curation as opposed to curating the taxon up to the genus level. In general, differential abundance of a certain species does not necessarily imply differential abundance of the corresponding genus. (Note that this equally applies to the case of unclassified higher taxonomic levels such as the case of an unclassified genus where classification is provided up to the family level).” My study lists unclassified Blautia at the species level. I am confused as to whether I should completely exclude this in the curation, or list as “unclassified Blautia” (no rank) or “Blautia sp.” (which is listed under unclassified Blautia). Similarly, what about when the plot lists unclassified Peptococcaceae (mentioned separately at both genus and family level). Would I curate the family level taxa as “unclassified Peptococcaceae” and leave out the genus level taxa? Let me know if this makes sense. I am having a trouble with many “unclassified” species in this plot. - File (PNG): Screenshot 2025-01-05 at 2.21.29 PM.png

Sergius Nyah (15:48:25): > Greetings everyone, > My name is Sergius Justus, a final year Computer Science student. I’m humbled to contribute my skills to this project and learn as well from everyone here. > Please feel free to reach out. Would love to know what’s happening!

Joy (16:02:39) (in thread): > Hi@Kavya Ayalasomayajulawelldone on this curation, I think you only curate taxa as"sp."if explicitly named in the study (e.g.,"Blautia sp.")., as for “Unclassified Peptococcaceae” Only curate genus-level taxa that are explicitly identified and resolved.

Kavya Ayalasomayajula (17:04:44) (in thread): > Thank you@Joywould it be best to curate as unclassified Blautia or leave that portion out?

Joy (17:21:47) (in thread): > * As for me, I will not curate as"Unclassified Blautia"(as this implies genus-level abundance, which is not the same). > Reasoning: The study lacks enough resolution to link differential abundance at the species level to the genus level with confidence.

Kavya Ayalasomayajula (18:01:07) (in thread): > Thank you!

2025-01-06

Yoko C (12:10:53) (in thread): > Hello, I think the curation policy is confusing regarding what to do in these cases. But because your graph does specify it is at species level, s_unclassified Blautia, I would go forBlautia sp, and sp for the rest of the cases where you have s_unclassified. Regarding the unclassified Peptococcaceae genus and family, maybe just unclassified Peptococcaceae and a note mentioning these were two ranks? If possible, maybe check during office hours.

Aleru Divine (13:02:20) (in thread): > Welcome@Sergius Nyah:hugging_face:Looking forward to collaborating with you

Sergius Nyah (13:05:57) (in thread): > Sure!!!:blush:

Kavya Ayalasomayajula (13:55:31) (in thread): > @Yoko Cthank you for this input. Yes, I might ask during office hours for additional clarification

Peace Sandy (13:58:14) (in thread): > Nice Article@Kate Rasheed

Adeshile Oluwatosin (14:38:49) (in thread): > @Aleru DivineHere you go

Adeshile Oluwatosin (14:39:11) (in thread): > Another discussion here as well@Aleru Divine

Kate Rasheed (14:52:25) (in thread): > Thank you so much@Peace Sandy

2025-01-08

Peace Daniel (07:49:42) (in thread): > @Kate Rasheed

2025-01-09

UBNSEMS3S (09:01:35): > Sorry for the late notice but we will be meeting right now

Kate Rasheed (09:33:23): > Here is the discussion page<@UBNSEMS3S>where Ruminococcaceae UCG -014 was resolved as Uncultured Oscillospiraceae bacterium.https://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID#%22CHLOROPLAST%22_An_Organelle - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

UBNSEMS3S (10:01:57): > Posting a slightly updated version of my Regression info because I had the link/transformation for Poisson and Negative Binomial Regression incorrect. They use alog transformation. - File (PNG): image.png

Kate Rasheed (10:03:17) (in thread): > Thanks for this.

UBNSEMS3S (10:10:15) (in thread): > Per some discussion long ago, this is the correct solution. Levi wrote: > > The first row I added to this table was UCG, which stands for “Uncultured genus-level group”, and has the example ofRuminococcaceae UCG-014 spwith the following resolution: “This example can be treated as an uncultured Ruminococcaceae bacterium, which is listed in NCBI under a heterotypic synonymuncultured Oscillospiraceae bacterium. This is good because it has the correct rank (species) and identifies the finest-known level of taxonomy (family Oscillospiraceae / Ruminococcaceae)” and link for more information:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6407505/ - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (PubMed Central (PMC)): Improved taxonomic assignment of rumen bacterial 16S rRNA sequences using a revised SILVA taxonomic framework > The taxonomy and associated nomenclature of many taxa of rumen bacteria are poorly defined within databases of 16S rRNA genes. This lack of resolution results in inadequate definition of microbial community structures, with large parts of the …

Kate Rasheed (10:12:00) (in thread): > Thank you so much.@Aleru Divine

Aleru Divine (10:13:54) (in thread): > Thank you<@UBNSEMS3S>

Aleru Divine (10:14:33) (in thread): > Thank you so much for the explanation today<@UBNSEMS3S>:blush:

2025-01-10

Adeshile Oluwatosin (06:40:30) (in thread): > Thank you<@UBNSEMS3S>

Svetlana Ugarcina Perovic (09:58:10): > :drum_with_drumsticks:Latest stories from@Kate Rasheed@Aleru Divine:drum_with_drumsticks:“Ask questions, don’t assume – Whenever you are unsure, ask questions. There is nothing like foolish question.”https://katerasheed1.wordpress.com/2025/01/07/microbiome-study-curation-walk-with-me/“Asking for help isn’t a weakness, it’s a strength.”https://alerudivine.hashnode.dev/im-learning-to-ask-for-helpSo far, my favorite blog posts from Kate and Divine! - Attachment (Kate Rasheed): Microbiome Study Curation : Walk with me > Hello people! Are you aspiring to become an Outreachy intern? Or you’re looking for a project to contribute to? In my first blog post, I mentioned that I am an Outreachy intern; who is workin… - Attachment (Divine Aleru’s Blog): I’m Learning to Ask for Help > If there’s one thing I wish I had learned earlier in life, it would be how to ask for help. Growing up, I was often the kid who always had answers, so it was assumed I had everything under control. And for a long time, I did or at least I thought I d…

Kate Rasheed (09:59:17) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Aleru Divine (11:03:46) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:blush:

Yoko C (13:34:52): > Hello, I’m a little confused on how to compare boxplots. I generally use the median to compare, but I was recently advised on using the “dots” above the boxes. I’m now doubting when to use “dots” and when to use the median? Should data points be used when we are comparing boxplots linked to Wilcoxon? Are there any resources that explain when to use medians or quartiles or the data points? For the following graph, I’m uncertain on some comparisons:https://www.nature.com/articles/s41598-023-47748-8/figures/3For example: Akkermansiaceae: Car vs Adadle. For Succinivibrionaceae: Industrial vs Transitional. For Erysipelatoclostridiaceae: Industrial vs Traditional. For Lactobacillaceae: CAR vs Madagascar.

UBNSEMS3S (17:27:14) (in thread): > Use the median. I think maybe there was a bit of telephone. The 1, 2, or 3 stars above the horizontal lines indicate the statistical significance. - File (PNG): image.png

2025-01-11

Ndukauba Oluchi (08:32:08): > Happy birthday@Aleru Divine:tada::tada::tada::tada::tada::tada:

2025-01-13

Aleru Divine (00:32:01) (in thread): > Thank you so much!@Ndukauba Oluchi

Svetlana Ugarcina Perovic (02:37:20): > A new preprint by Paul Jensen showed:74% of all known microbial species remain unstudied (https://www.biorxiv.org/content/10.1101/2025.01.04.631297v1.full.pdf) > Nature already discussed it herehttps://www.nature.com/articles/d41586-025-00038-xAlso there is a nice thread by Justine Debelius where she mentioned the BugSigDB (see also a screenshot):https://bsky.app/profile/jwoodelius.bsky.social/post/3lezaprwym22yHappy Monday! - File (PNG): Screenshot 2025-01-10 at 13.51.06.png - File (PNG): Screenshot 2025-01-13 at 08.35.29.png - File (PNG): Screenshot 2025-01-13 at 08.35.40.png

Svetlana Ugarcina Perovic (03:40:58) (in thread): > https://gtdb.ecogenomic.org/is the database mentioned by Justine > > cc@Kate Rasheed - Attachment (gtdb.ecogenomic.org): GTDB - Genome Taxonomy Database > The Genome Taxonomy Database (GTDB) is an initiative to establish a standardised microbial taxonomy based on genome phylogeny.

Ouma Ronald (04:31:14): > Warm greetings @everyone here. I am currently experimenting with the API sandbox however, I am afraid according to my findings. The API is connected to live data where sample interactions might cause unwanted modification to the live data > but am doing my best. Also i want to find out if there is a way i can set up the API locally to avoid interference of live data. Also another issue , I can’t signin tohttps://bugsigdb-staging.wikiworks.com/. Any help about this please??:pray:

Svetlana Ugarcina Perovic (04:36:29) (in thread): > cc<@UBNSEMS3S><@U1LCB8WEA>

U1LCB8WEA (08:14:46) (in thread): > Ouma and I had a huddle about it this morning

Svetlana Ugarcina Perovic (08:47:58) (in thread): > Great, thanks<@U1LCB8WEA>!

Adeshile Oluwatosin (10:40:32): > Hello<@UBNSEMS3S>I would appreciate the recording of last week office hour. Thank you so much

UBNSEMS3S (11:02:38): > Ah sorry I knew I forgot something. Here it is. - File (MPEG 4 Video): bsdb meeting 2025_01_09.mp4

Adeshile Oluwatosin (11:39:02) (in thread): > Thank you

Princess Rehoboth Asuelimen (12:30:45): > @Princess Rehoboth Asuelimen has left the channel

2025-01-14

Svetlana Ugarcina Perovic (05:41:22): > ConferenceMay 19 > > Harvard Chan Microbiome in Public Health Center (HCMPH) symposium > > Virtual registration continues to be free and is available [HERE] - Attachment (Harvard T.H. Chan School of Public Health): HCMPH Symposium | Harvard Chan Microbiome in Public Health Center | Harvard T.H. Chan School of Public Health > We are delighted to invite everyone to the seventh annual Harvard Chan Microbiome in Public Health Center (HCMPH) symposium on May 19, 2025. We are happy to

Joy (07:48:50): > Hi everyone, > I am working on curating a study that mentionsγ-Proteobacteria and δ-Proteobacteria( subclasses of Proteobacteria) as a taxonomic group with significant changes in abundance. However, I noticed thatγ-Proteobacteria and δ-Proteobacteriacannot be found in the NCBI Taxonomy Browser. > Could you please guide me on how to proceed with curating this taxon? Should I: > 1. Use a broader taxonomic rank (e.g., Proteobacteria)? > 2. Enter “γ-Proteobacteria” as plain text without an NCBI Taxonomy ID? > 3. Exclude it from curation altogether? > Any advice or best practices for handling such cases would be greatly appreciated! > Thank you for your help.@Kate Rasheed@Aleru Divine<@UBNSEMS3S>https://onlinelibrary.wiley.com/doi/10.7448/IAS.20.1.21526

Mildred Anashie (08:16:30) (in thread): > Hi@JoyWell done on your curation > As you rightly mentioned, γ-Proteobacteria and δ-Proteobacteria are classes of Proteobacteria. > > I believeγ-Proteobacteriastands forGammaProteobacteriaandδ-Proteobacteriastands forDeltaProteobacteriawith NCBI Id’s (1236and28221respectively).I’ll try to go through the paper to confirm this

Joy (08:22:38) (in thread): > Thank you@Mildred Anashie

Aleru Divine (10:55:49) (in thread): > Thank you for clarifying this,@Mildred Anashie. > > To elaborate,@Joy, both are classes within theProteobacteria(Pseudomonadota) phylum and should be curated separately asGammaproteobacteriaandDeltaproteobacteria. > > While going through the paper, specifically Table 2 (Relative abundance of major phyla present in the gut in control and HIV-infected patients), I noticed β-Proteobacteria listed. This isBetaproteobacteria, which should also be curated differently also.

Joy (11:40:54) (in thread): > I appreciate@Aleru Divine

Yoko C (12:07:31): > Hello, I have some curation issues with nomenclature.The paperlists Lachnospiraceae NK4A136 group (genus) (ASV_53_Lachnospiraceae_NK4A136_group) and I was advised to change this to Lachnospiraceae bacterium NK4A136 (NCBI 877420) (species), is that ok? Same for [Eubacterium] coprostanoligenes group, this is a genus,the paper(figure s6) actually compared bacterial families, so is it ok to change this to Eubacterium coprostanoligenes (species). Another correction I was given is “Coprococcus 3 should be curated as Coprococcus while Coprococcus 3 comes should be Coprococcus comes”. > From my understanding, this type of nomenclature was established inhttps://pmc.ncbi.nlm.nih.gov/articles/PMC6407505/. Where they assigned “taxonomic designations down to genus-equivalent level” and “Clusters that did not also contain sequences of described species were named to the lowest taxonomic level … identifier included in the name as appropriate.” Here they provide the nomenclature used by other databases as well, so I’m not sure if I could use that, for example: g_[Eubacterium] rumcoprostanoligenesgroup (Silva 119Rum) is part of f_Ruminococcaceae in Silva 119. Or Coprococcus 3 (Silva 119Rum) is Coprococcus in Greengenes and Silva 119. I thought it was best to leave the nomenclature used on the paper but not sure, since for example we can change Ruminococcaceae UCG 0x sp to Oscilospiraceae sp.

Yoko C (12:11:09): > I have also been asked to curate this graphhttps://www.nature.com/articles/s41467-020-17541-6/figures/5as a mixed linear model, but it is described as coming from an LDA analysis, so I’m not sure if it is actually a mixed linear model or not? If it isn’t should I leave the test as blank?

Yoko C (12:20:54): > Finally, I have an experiment where I have Bacillales Family XI. Incertae Sedis, and Gemellaceae, increasing and decreasing signatures respectively. Bacillales Family XI. Incertae Sedis is the heterotypic synonym for Gemellaceae, so Gemellaceae ends up being on both increasing/decreasing. I was asked to only leave Gemellaceae as decreasing. Should I remove one or keep both? I have a similar case with two different ASV’s for the genus Subdoligranulum on increasing and decreasing sides.

Aleru Divine (12:34:02) (in thread): > Hi@Yoko CI believe what you’ve curated is 5C which is a tree-based LDA algorithm and it is neither a linear regression model nor a logistic regression model. It is a classification model and it has classified the groups and identified the features that differ between them as seen. > > The linear mixed-effects regression was referring to 5b.It’sbest to leave this blank for now until we get an answer/clarification.Because I may be wrong:grimacing::disappointed_relieved:

Aleru Divine (12:41:00) (in thread): > @Yoko CI’d saycurateboth.Thereason is, sinceGemellaceaeis at the family level, the signatures for both increasing and decreasing abundance may be referring to different species or strains within the family, which were only identified at the family level. > > The same applies toSubdoligranulum.

Yoko C (13:53:50) (in thread): > @Aleru Divinethanks, yes it is 5c and was left as blank. Could the test be added to the options?

Aleru Divine (15:29:57) (in thread): > We’ll bring this up during the office hours@Yoko C

Aleru Divine (15:30:18) (in thread): > Also thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1736874451928209 - Attachment: Attachment > Hello, I have some curation issues with nomenclature. The paper lists Lachnospiraceae NK4A136 group (genus) (ASV_53_Lachnospiraceae_NK4A136_group) and I was advised to change this to Lachnospiraceae bacterium NK4A136 (NCBI 877420) (species), is that ok? Same for [Eubacterium] coprostanoligenes group, this is a genus, the paper(figure s6) actually compared bacterial families, so is it ok to change this to Eubacterium coprostanoligenes (species). Another correction I was given is “Coprococcus 3 should be curated as Coprococcus while Coprococcus 3 comes should be Coprococcus comes”. > From my understanding, this type of nomenclature was established in https://pmc.ncbi.nlm.nih.gov/articles/PMC6407505/ . Where they assigned “taxonomic designations down to genus-equivalent level” and “Clusters that did not also contain sequences of described species were named to the lowest taxonomic level … identifier included in the name as appropriate.” Here they provide the nomenclature used by other databases as well, so I’m not sure if I could use that, for example: g_[Eubacterium] rum_coprostanoligenes_ group (Silva 119Rum) is part of f_Ruminococcaceae in Silva 119. Or Coprococcus 3 (Silva 119Rum) is Coprococcus in Greengenes and Silva 119. I thought it was best to leave the nomenclature used on the paper but not sure, since for example we can change Ruminococcaceae UCG 0x sp to Oscilospiraceae sp.

2025-01-15

Peace Daniel (04:31:24): > Hi:wave:I have a question, do you get better at curating when reviewing someone’s curation or when curating a new study?

Svetlana Ugarcina Perovic (04:32:05) (in thread): > What a great question!!!

Kate Rasheed (04:33:56) (in thread): > Good morning@Peace Daniel. For me, you get better at both:sweat_smile:. This is because while reviewing and curating studies, you explore a wide range of conditions with different statistical test and all. > > For example, while reviewing a study, I came across Corncob which uses Beta Binomial Regression. I’ve never seen this statistical test while curating a new study.

Kate Rasheed (04:35:15) (in thread): > Moreso, in reviewing and curating a study, you will likely come across something you haven’t seen before. This would prompt you to ask questions to know more. > > In asking questions, you get better at curation.

Peace Daniel (04:36:25) (in thread): > Good morning!@Kate RasheedYou do have a point, I feel as though one would be more attentive while reviewingsomeone’scuration.You’reright, asking questions is whatI’lllearn this year:sweat_smile:

Peace Daniel (04:37:30) (in thread): > Can you share the study with corncob please? First time seeing it as well

Kate Rasheed (04:46:38) (in thread): > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-023-01671-2#Tab2@Peace Daniel. This is the second article on Corncob:smile: - Attachment (BioMed Central): A comprehensive analysis of gut and skin microbiota in canine atopic dermatitis in Shiba Inu dogs - Microbiome > Background Like its human counterpart, canine atopic dermatitis (cAD) is a chronic relapsing condition; thus, most cAD-affected dogs will require lifelong treatment to maintain an acceptable quality of life. A potential intervention is modulation of the composition of gut microbiota, and in fact, probiotic treatment has been proposed and tried in human atopic dermatitis (AD) patients. Since dogs are currently receiving intensive medical care, this will be the same option for dogs, while evidence of gut dysbiosis in cAD is still missing, although skin microbial profiling in cAD has been conducted in several studies. Therefore, we conducted a comprehensive analysis of both gut and skin microbiota in cAD in one specific cAD-predisposed breed, Shiba Inu. Additionally, we evaluated the impact of commonly used medical management on cAD (Janus kinase; JAK inhibitor, oclacitinib) on the gut and skin microbiota. Furthermore, we genotyped the Shiba Inu dogs according to the mitochondrial DNA haplogroup and assessed its association with the composition of the gut microbiota. Results Staphylococcus was the most predominant bacterial genus observed in the skin; Escherichia/Shigella and Clostridium sensu stricto were highly abundant in the gut of cAD-affected dogs. In the gut microbiota, Fusobacteria and Megamonas were highly abundant in healthy dogs but significantly reduced in cAD-affected dogs. The abundance of these bacterial taxa was positively correlated with the effect of the treatment and state of the disease. Oclacitinib treatment on cAD-affected dogs shifted the composition of microbiota towards that in healthy dogs, and the latter brought it much closer to healthy microbiota, particularly in the gut. Additionally, even within the same dog breed, the mtDNA haplogroup varied, and there was an association between the mtDNA haplogroup and microbial composition in the gut and skin. Conclusions Dysbiosis of both the skin and the gut was observed in cAD in Shiba Inu dogs. Our findings provide a basis for the potential treatment of cAD by manipulating the gut microbiota as well as the skin microbiota. Video Abstract

Aleru Divine (04:49:05) (in thread): > Hi@Peace DanielI never thought about this until now:sweat_smile:I think both are equally helpful, and I agree with@Kate Rasheedthey both equally expose you to different study designs and methods. I see reviewing as a form of curating, with more attention because now, itissort of in your hands to make sure the paper is completely accurate and that is a huge responsibility. Butgenerallyyou do get better at curating bydoing both.

Peace Daniel (04:53:32) (in thread): > I agree@Aleru DivineI’ve had this question in mind since I woke up this morning and yes, this is my perspective when reviewing.

Svetlana Ugarcina Perovic (07:58:30): > A great podcast ep with Ameet Pinto, an expert indrinking water microbiome(and one of my postdoc mentors back in 2014)https://www.youtube.com/watch?v=JDAUDyeJ6AM - Attachment (YouTube): Matters Microbial #72: Who is in Your Water?

Svetlana Ugarcina Perovic (08:04:01): > Also, there is another very interesting podcast ep, Kevin Libuit and Andrew Page had a great chat about theirjob hunting experiences, the importance of professional networks and making genuine connection: https://www.youtube.com/watch?v=k6KWu1Reuik - Attachment (YouTube): The Job Hunt Experience

Victoria (Burah) Poromon (08:24:17) (in thread): > Ah:sweat_smile:This is a wonderful question. > I’d say both! > > But if I had to choose between them, I’d say curating a new study:sweat_smile:Most times you come across a perfectly curated study, everything is as it should be. You don’t get to spendsomuch time reviewing it. But when you’re curating a new study, no matter how straightforward it is, you still spend a lot of time on it. > > And i have this belief that the more time you spend doing something, the better you get at doing it.

Kate Rasheed (08:30:37) (in thread): > This belief is quite true though:sweat_smile:@Victoria (Burah) Poromon

Peace Daniel (09:34:40) (in thread): > Absolutely@Victoria (Burah) Poromon

Svetlana Ugarcina Perovic (10:55:39) (in thread): > corncob spotted:smile:https://github.com/waldronlab/BugSigDBcuration/issues/553cc@Kate Rasheed@Peace Daniel - Attachment: #553 Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function > Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function – Audrey Byrne – Microbiome
> https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-024-01973-z

Peace Daniel (11:30:00) (in thread): > I’mtempted:see_no_evil:thank you for sharing@Svetlana Ugarcina Perovic

Yoko C (12:24:05) (in thread): > For me, it depends what stage you are on. I learned what was expected from curations by going over already reviewed curations using the “Random page” option. Once I got the hang, I started doing my own curations and realized that even simple things can become complicated. Reviewing other’s curations helped me learn about different ways people approach problems and apply these to my own curations or notice similar mistakes I made. This led to feel motivated to curate more and so on. It’s kind of like a cycle of think.

Peace Daniel (12:39:42) (in thread): > Your perspective is refreshing@Yoko CHow exactly do you learnpeople’sapproach from curations? I feel like an in-depth observation would be put in place for this

Yoko C (13:26:03) (in thread): > @Peace Danielthanks. Well, for example, I have issues with group and figure descriptions, I always wonder if I was a researcher using BugSigDB, would it be too long or too short, would I need to go back to the paper? So I always like to see how people manage to succinctly and accurately describe groups. Or specially when I was just learning, seeing how a contrast with more than two groups was approached was very needed, since we should only do two signatures per experiment. It’s basically comparing how I would curate something to how somebody else did it, and either validating my approach or realizing it was incorrect/incomplete and I needed to find out more about the issue (like transformations) or read the paper more carefully to realize how they came to a conclusion.

Peace Daniel (13:52:16) (in thread): > Valid, thank you for sharing!

UBNSEMS3S (19:00:02): > Our weekly team meeting will be tomorrow at 9 AM EST athttps://us02web.zoom.us/j/2737200499! I’m excited, as always, to see you all and to ramble about some statistical topic for 20-30 minutes.

2025-01-16

Svetlana Ugarcina Perovic (04:43:25): > :clap:**** Week 6 of Outreachy internships:****111 curations (curated during contribution months) have been reviewed by@Kate Rasheedand@Aleru Divinewith the community support! > > Also, Kate and Divine started their own project of interest. You can share it briefly in comments here:slightly_smiling_face:

Peace Daniel (05:03:08) (in thread): > Good job@Kate Rasheed@Aleru Divine

Aleru Divine (05:07:35) (in thread): > Thank you@Svetlana Ugarcina Perovic@Peace DanielI’ve been searching and reviewing research papers on hypoglycemia/hyperglycemia (low/high(excess)blood glucose)and hypotension/hypertension(low/highblood pressure) for curation. The aim is to make the BugSigDB more comprehensive and valuable for researchers exploring these conditions which is currently underrepresented. > > If you come across any such papers, please do share with me. I’d be very happy to curate them. > > Thank you so much!

Aleru Divine (05:08:11) (in thread): > Yay!!! Looking forward to it!:blush:

Kate Rasheed (05:27:26) (in thread): > Thank you@Svetlana Ugarcina Perovic@Peace Daniel. > > I’m working on a comparison between Paul Jensen’s analogy of species and the BugSigDB curated signatures; to see the most frequently recorded microbes in the whole of BugSigDB database. > > From the articles shared here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1736753840862999?thread_ts=1736753840.862999&cid=C04RATV9VCYPaul Jensen says: “More than 90% of all bacteriology articles study fewer than 1% of the species, creating a “long tail” of understudied microbes.” > > Hence, the goal of this project is to see how well BugSigDB covers (or not cover) the bacterial species diversity. - Attachment: Attachment > A new preprint by Paul Jensen showed: 74% of all known microbial species remain unstudied (https://www.biorxiv.org/content/10.1101/2025.01.04.631297v1.full.pdf) > Nature already discussed it here https://www.nature.com/articles/d41586-025-00038-x > > Also there is a nice thread by Justine Debelius where she mentioned the BugSigDB (see also a screenshot): https://bsky.app/profile/jwoodelius.bsky.social/post/3lezaprwym22y > > Happy Monday!

Peace Daniel (05:32:48) (in thread): > This looks tasking@Kate RasheedI’dlove to see your conclusion, well done!

Kate Rasheed (05:32:49) (in thread): > A really interesting project@Aleru Divine.

Svetlana Ugarcina Perovic (06:25:49): > INVITATION:We would be happy if you can join us next week for the first MVIF this year - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Mildred Anashie (07:51:33) (in thread): > Great job@Aleru Divineand@Kate Rasheed:clap:

Joy (08:48:57) (in thread): > Good job@Kate Rasheedand@Aleru Divine!:rocket:

Ndukauba Oluchi (08:59:56) (in thread): > I’d love to attend this:hearts:

Adeshile Oluwatosin (09:02:08) (in thread): > Well done@Aleru Divineand@Kate Rasheed

Mildred Anashie (10:01:39): > Hi<@UBNSEMS3S>Thank you for the questions answered, these are the ones that youcouldn’tget to….I apologize for the many questions:pray:I’m also reviewing an already curated study and I need some clarifications on the following to complete my review, > 1. Is Fig 5 and 6 curatable and how can it be interpreted? > 2. ⁠Also the paper says MaAslin didn’t reach statistical significance after adjusting for MHT and Supp table 5, 9 and 11 shows that, however Table 3 shows significant results but doesn’t show if MHT was done should this be curated regardless of what it says about the test? > 3. I see different LDA scores for the LEfSe results in the supplemental tables, but the paper states 4.27 to be LDA for the 2group analysis and 4.47 for the 4group analysis. What should be done in this case? > > Link to article:https://pubmed.ncbi.nlm.nih.gov/38658841/ - Attachment (PubMed): Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study - PubMed > Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers ag …

Joy (10:02:30): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor the office hours today!

Aleru Divine (10:15:07): > Thank you for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:17:03) (in thread): > Reminder:arrow_up:why sometimes studies have some species in the results/signatures listed together

Yoko C (10:27:17) (in thread): > <@UBNSEMS3S>, I hope it’s ok that I re-ask this. I had asked about this last office hours and you had mentioned it would be a good idea to see the articles. Thanks.

UBNSEMS3S (10:47:39): > Meeting recording. Thank you everyone who attended for your excellent questions. - File (MPEG 4 Video): bsdb meeting 2025_01_16.mp4

Yoko C (11:11:02) (in thread): > @Svetlana Ugarcina Perovicthank you. I think I might have curated signatures in a similar format incorrectly and would like to check if I should change them. I did leave a note on the red globe “Needs Review” option with how it was originally listed in the paper. For examplehttps://bugsigdb.org/Study_1174#Experiment_6:* - Streptococcus sp. [C equinus/infantarius/lutetiensis] was entered as Streptococcus sp. Because previously these species were part of theStreptococcus bovis/Streptococcus equinus Complex. ** - Streptococcus sp. [C equinus/gallolyticus/macedonicus/pasteurianus]entered asStreptococcus gallolyticussubsp.Macedonicus. Formerly bovis biotype 1 based onhttps://pmc.ncbi.nlm.nih.gov/articles/PMC6386949/. - Bifidobacterium sp. [C catenulatum/kashiwanohense]entered asBifidobacterium catenulatum subsp. Kashiwanohense . - Bacteroides sp. [C dorei/vulgatus] entered asPhocaeicola sp. Bacteroides dorei listed asPhocaeicola doreiandvulgatusasPhocaeicola vulgatus. *And a few others. Please let me know if I should change back to the original format. Thank you.

Svetlana Ugarcina Perovic (11:18:02) (in thread): > @Yoko Cplease correct them in a single record [e.g.C. equinus/infantarius/lutetiensis] not separated nor as an sp group. Thanks!

Svetlana Ugarcina Perovic (11:23:28): > If you are up to more than curating and reviewing or just want to try something else to contribute, feel free to check outhttps://bugsigdb.org/Help:Contents#TODO_for_reviewerssection. > > cc<@UBNSEMS3S> - Attachment (BugSigDB): Help:Contents > …

UBNSEMS3S (15:47:30): > treeDA is now a statistical test option in BugSigDB

UBNSEMS3S (15:53:18) (in thread): > 1. Figure 5 is from an RF analysis. This is not quite the same thing as a DA analysis. No need to curate. The in-text description for Figure 6 says there were no significant results. > 2. The taxa in Figure 2 that are significant are unadjusted p-values. This is stated in the text: “a total of 16 nominally significant species (p < .05) but none of them surpassed the multiple testing.” > 3. This appears to be results from two different analyses. One is 2 group and one is 4 group. The 4 group analysis would be a one against the rest analysis while the 2 group is group 1 vs group 0.

Joy (15:57:48) (in thread): > Thank you<@UBNSEMS3S>for this information.

Kate Rasheed (16:13:19) (in thread): > Thank you so much for this<@UBNSEMS3S>

Kate Rasheed (16:13:57) (in thread): > Please use treeDA as the statistical test@Yoko C

UBNSEMS3S (16:21:36) (in thread): > This has been updated. I am making further updates to the curation policy.

2025-01-17

Svetlana Ugarcina Perovic (02:49:16): > Friday morning::coffee:️ and:radio:the Coffee literature review podcast episode with Nicola Segata > hosted by Christopher Hendon & Doran PenningtonHappy Friday!https://www.youtube.com/watch?v=WyE5NY2bCUw&list=PL4qcpXTWaD0W_SooIewS0LN4Kq80SYtPn&index=5 - Attachment (YouTube): Ep18. Coffee affects your microbiome with Prof. Nicola Segata

Mildred Anashie (03:47:22) (in thread): > Okay > > Thank you > > Just to confirm No 2 refers to Table 3 and Not Figure 2 right?

UBNSEMS3S (11:01:25) (in thread): > Correct.

2025-01-18

Kate Rasheed (04:58:04): > Good morning<@UBNSEMS3S>. I tried running this script on Rhttps://github.com/waldronlab/BugSigDBStats/blob/main/vignettes/BugSigDBStats.RmdBut I’m currently stuck in pubyear3 as the API cannot retrieve data from some of the PMID’S. > > Here is the error message: > > pubyear3 <- pmid2pubyear(pmids[711:length(pmids)]) > Warning: cannot open URL ’https://www.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?tool=bioconductor&rettype=xml&retmode=text&db=PubMed&id=31200089%2c33085540%2c32161568%2c27562258%2c34592155%2c31076212%2c29920927%2c35719348%2c36803646%2c36216843%2c31672155%2c33996618%2c36894986%2c24629344%2c33614635%2c23491408%2c32807798%2c36198385%2c31063846%2c35035709%2c34650532%2c26179554%2c36442206%2c32073296%2c36376318%2c35615912%2c26408641%2c36203175%2c32169076%2c29685174%2c30405010%2c34505401%2c25283067%2c33557896%2c25278091%2c37586456%2c24370189%2c32931939%2c36678227%2c35657343%2c31463790%2c29196767%2c29172724%2c35171931%2c32152391%2c35133187%2c37597851%2c37762390%2c32106294%2c33178173%2c21957459%2c36573834%2c36631533%2c29230385%2c37507685%2c32591968%2c37468867%2c36760344%2c36869345%2c37438797%2c35692191%2c37605183%2c35305613%2c32630754%2c35642922%2c35888992%2c33184260%2c30631088%2c37604954%2c36389150%2c37658443%2c35083314%2c37091735%2c35722326%2c36790203%2c37587195%2c32320621%2c37220908%2c37483698%2c367[… truncated]

2025-01-19

Yoko C (10:34:11): > Hello everyone, when I enter signatures in a format including [ ], e.g. Bifidobacterium sp. [C catenulatum/kashiwanohense], this seems to break the page a little. Picture attached of how it shows, when I click the link I get the message “The requested page title contains invalid characters:”[“.” . This is for this experimenthttps://bugsigdb.org/Study_1174#Experiment_6. Wondering if I should remove the brackets or if this is a bug. - File (PNG): Screenshot 2025-01-19 at 11-21-40 Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits - BugSigDB.png

Peace Daniel (10:35:46) (in thread): > I think you should remove the []signatures aren’tusually entered that way

Peace Daniel (10:37:42) (in thread): > You can add a review with the other information

Yoko C (10:39:18) (in thread): > @Peace DanielI think it might be the best option, but checking because I was asked to enter them like that.

Yoko C (10:41:42) (in thread): > Signatures can include brackets, but I think it’s usually the genus. It seems the issue here is they come after something else.

Peace Daniel (10:45:50) (in thread): > Can you explain which is the genus and specie in the first taxa you curated and whyyou’recurating it that way?

Peace Daniel (10:46:22) (in thread): > I think you might have to wait for another opinion if you were asked to curate it that way@Yoko C

Kate Rasheed (10:52:13) (in thread): > @Yoko CCan you try replacing the square brackets with parenthesis (round bracket)?

Yoko C (11:15:40) (in thread): > @Peace Daniel, this is how it is presented in the paper. Regarding which is the genus, for Actinomyces sp [oral taxon181/ph3], the genus is Actinomyces the species is a complex of species, 1 species is oral taxon 181 and the other is ph3. The way I interpret this (and I might be wrong) is the brackets mean that part of the nomenclature is still “waiting” to be officially named. The C and slash mean this is a complex of species, they are closely related species and might only be one or you can’t tell which it is, or it might be all. For some of these I found they are considered a species and subspecies. Anyways, as you suggest I’ll wait for another answer. Thanks.

Peace Daniel (11:18:06) (in thread): > Okay I understand, my suggestion would be entering Actinomyces sp as the taxa and oral taxon 181/ph3 in reviews

Yoko C (11:23:32) (in thread): > @Peace Danielthat’s exactly what I did after seeing that the first curation with the original format caused this. But there is a thread on here where Svetlana discusses a similar format should be curated as is, so I checked and it was recommended I revert to the original curation with this format.

Yoko C (11:24:16) (in thread): > @Kate RasheedThat works, but not sure if it’s ok to change the nomenclature like that. If it is than I will apply this change. Thanks

Peace Daniel (11:27:54) (in thread): > Okay, hopefulthere’ll bea resolution soon@Yoko C

2025-01-20

Ndukauba Oluchi (02:40:39): > Good morning everyone, please I have a question. I am trying to create a Study(my first contribution:grin:) . In the study design, how do I get a paper to work on? Do I search for studies on the Internet or is there like a page where I can see different studies and just pick one to curate?

Kate Rasheed (02:44:24) (in thread): > Good morning@Ndukauba Oluchi. Click on the link below, you would see the list of papers to curate. Click on one of the papers and signify interest.https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue+is%3Aopen+label%3A%22paper+to+curate%22

Ndukauba Oluchi (02:46:58) (in thread): > Alright, Thank you@Kate Rasheed

Svetlana Ugarcina Perovic (03:40:07) (in thread): > @Ndukauba Oluchiassignedhttps://github.com/waldronlab/BugSigDBcuration/issues/537#issuecomment-2601687887! > > Enjoy and come back here:slightly_smiling_face:when stuck or have any questions. > > When you finish your curation, just comment in the GitHub issue “{link to the bugsigdb study curated} ready for review.” - Attachment: Comment on #537 Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism > Good morning @SvetlanaUP
> I am Ndukauba Oluchi. I would love to curate this paper > > Thank you so much.

Svetlana Ugarcina Perovic (03:45:05) (in thread): > See you tomorrow at MVIF!

Svetlana Ugarcina Perovic (03:46:10) (in thread): > What a great start of the week!****“my first contribution ****:grin:****” ****GO GO GO,@Ndukauba Oluchi! > And enjoy ;)

Ndukauba Oluchi (09:50:50): > Hello everyone, please how do i find the CONDITION of this paper. i am finding it difficult, i need some helphttps://github.com/waldronlab/BugSigDBcuration/issues/537 - Attachment: #537 Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism > Mobile genetic elements from the maternal microbiome shape infant gut microbial assembly and metabolism – Tommi Vatanen – Cell
> https://www.cell.com/cell/fulltext/S0092-8674(22)01467-2

Kate Rasheed (10:07:10) (in thread): > Hi@Ndukauba Oluchi. For me,Pregnancycan be used as the condition but let’s hear what others have to say.

U1LCB8WEA (10:45:25) (in thread): > Hi@Ouma RonaldI just asked@Sergius Nyahto work on testing and documenting the API with you. I hope you two will discuss and that we can catch up on everything at lab meeting on Thursday.

Ouma Ronald (11:20:39) (in thread): > Sure@Levi Waldron. I hope we can share my findings together as i have some findings.Am looking forward to working with him

Ndukauba Oluchi (11:33:04) (in thread): > I Don’t mean to bombard with questions but please where do I find details for lab analysis , statistical analysis and alpha diversity in this paperhttps://github.com/waldronlab/BugSigDBcuration/issues/537

Yoko C (11:33:27) (in thread): > Hello, each experiment will have a different condition. An easy way to find the condition is looking at the description of the graph or table you are curating. This page also helps you on deciding what the condition can behttps://bugsigdb.org/Curation_Policy#Condition - Attachment (BugSigDB): Curation Policy > .

Ndukauba Oluchi (11:34:36) (in thread): > @Yoko Cthank you found it.

Ndukauba Oluchi (11:35:02) (in thread): > @Yoko CI Don’t mean to bombard with questions but please where do I find details for lab analysis , statistical analysis and alpha diversity in this paperhttps://github.com/waldronlab/BugSigDBcuration/issues/537

Yoko C (11:36:05) (in thread): > The methods section will usually provide you with lab analysis and statistical information. The results section will have the alpha diversity and will probably further describe what statistical tests were used for the experiments

Yoko C (11:38:33) (in thread): > It seems like this paper doesn’t provide information on alpha diversity.

Ndukauba Oluchi (11:39:14) (in thread): > it doesn’t:sob:

Ndukauba Oluchi (11:39:48) (in thread): > do you see the sequencing type, is itpermanova analysis?

Yoko C (11:44:50) (in thread): > Metagenomic libraries were sequenced on the Illumina HiSeq 2500 platform

Yoko C (11:44:58) (in thread): > That is the sequencing information

Yoko C (11:45:35) (in thread): > Its under the section: Method details > Metagenome library construction and sequencing

2025-01-21

Michael Hungbo (06:26:50): > Hello everyone! > My name is Michael Hungbo. I’m a recent graduate of Animal Breeding and Genetics, a software developer, and technical writer. My passion for science and open-source software led me to BugSigDB. I’m looking forward to contributing to the project and collaborating with you all!

Svetlana Ugarcina Perovic (06:31:59) (in thread): > Welcome to the team, Michael!Please go through this intro material: > * BugSigDB project information, estimated time: 15 minutes (https://bugsigdb.org/Project:About) > * Reading materials on the human microbiome, estimated time: 2 hours (https://docs.google.com/document/d/1cpY8RoOHjJ_oxkDRGwlpqL-I29IN9B5BifhZIlqTjhE/edit?tab=t.0) > * Step-by-step guidance on how to document a signature in BugSigDB: 5 minutes (https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=6) > * View examples of completed BugSigDB curations, estimated time: 15 minutes (https://bugsigdb.org/Study_600) > * Video trainings on BugSigDB curation (https://www.youtube.com/playlist?list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq) > And open your bugisgdb accounthttps://bugsigdb.org/Main_PageFor any questions, do not hesitate to ask here.

Michael Hungbo (06:44:37) (in thread): > Thank you,@Svetlana Ugarcina Perovic! I’ll check these out.:slightly_smiling_face:

Aleru Divine (06:54:34) (in thread): > Welcome@Michael Hungbo:blush:

Ouma Ronald (07:03:10) (in thread): > nice to meet you@Michael Hungbo.Welcome to the home away from home

Michael Hungbo (07:16:11) (in thread): > Thank you all!:blush:

Ndukauba Oluchi (12:18:09): > Hello everyone, I don’t think my paper has Alpha diversity in it. What do I do please.https://www.cell.com/cell/fulltext/S0092-8674(22)01467-2

Svetlana Ugarcina Perovic (13:23:59) (in thread): > Q: Is it possible for a study not to have alpha diversity > A: Yes, the authors might not have been interested in alpha diversity.

Ndukauba Oluchi (13:28:38) (in thread): > Okay noted. So should I just go on with curating the signatures and leave the alpha diversity as UNCHANGED?

Kate Rasheed (14:50:21) (in thread): > @Ndukauba OluchiYou would leave the alpha diversity blank.

Ndukauba Oluchi (15:04:04) (in thread): > Okay, thank you@Kate Rasheed

2025-01-22

Ndukauba Oluchi (10:18:36) (in thread): > Welcome@Michael Hungbo

Ndukauba Oluchi (10:18:57) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:35:38): > Reminder for our weekly team meeting:tomorrow at 9 AM EST athttps://us02web.zoom.us/j/2737200499cc<@UBNSEMS3S>

Joy (10:36:59) (in thread): > Duly noted, thanks@Svetlana Ugarcina Perovic

Kate Rasheed (10:37:07) (in thread): > Well noted with thanks.

2025-01-23

Svetlana Ugarcina Perovic (09:15:38): > .<@UBNSEMS3S>just shared some resources for learning R: > * https://www.datacamp.com/courses/free-introduction-to-r > * https://r4ds.hadley.nz/

Chioma Onyido (09:19:16) (in thread): > In the waiting room.:pray:

UBNSEMS3S (09:25:23) (in thread): > > pmids <- pmids[!is.na(pmids)] > pubyear1 <- pmid2pubyear(pmids[1:361]) > pubyear2 <- pmid2pubyear(pmids[362:710]) > pubyear3 <- pmid2pubyear(pmids[711:1000]) > pubyear4 <- pmid2pubyear(pmids[1001:length(pmids)]) > pubyear <- c(pubyear1, pubyear2, pubyear3, pubyear4) > head(cbind(pmids, pubyear)) >

Aleru Divine (09:45:27): > Thank you so much for the incredibly enlightening Office Hours session,<@UBNSEMS3S>@Svetlana Ugarcina Perovic!:blush:

Adeshile Oluwatosin (09:47:45): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina PerovicI appreciate

Mildred Anashie (09:50:48) (in thread): > I’ll definitely explore this resources > Thank you@Svetlana Ugarcina Perovic<@UBNSEMS3S>:pray:

Joy (10:07:19) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing the resources!

2025-01-24

Kate Rasheed (03:59:04): > Good morning<@UBNSEMS3S>. Thanks for the office hour session yesterday and fixing the error. > > I’ve made progress in running the R script. I’m currently stuck in themicrobe co-occurenceas the microbeHeatmap isn’t displaying the output. > > At first I got an error concerning the “safe” package which I later installed. > > Now the heatmap can’t display the output because the rows and columns aren’t having the same matrix. > > Here is the error: > > Loading required namespace: safe > Error: number of observations in top annotation should be as same as ncol of the matrix.

Joy (05:11:05): > Good morning@Svetlana Ugarcina Perovic, Could you delete Experiment 1,Signature 2and Experiment 2,Signature 2. Thank you.https://bugsigdb.org/Study_1230 - Attachment (BugSigDB): Longitudinal analysis of the gut microbiota during anti-PD-1 therapy reveals stable microbial features of response in melanoma patients - BugSigDB > Immune checkpoint inhibitors (ICIs) improve outcomes in advanced melanoma, but many patients are refractory or experience relapse.The gut microbiota modulates antitumor responses.However, inconsistent baseline predictors point to heterogeneity in responses and inadequacy of cross-sectional data.

Svetlana Ugarcina Perovic (07:48:48) (in thread): > Deleted.

Joy (07:50:43) (in thread): > Thank you!

UBNSEMS3S (09:32:00) (in thread): > Yeah I ran into this same issue yesterday. I am investigating it and hopefully will have a solution soon.

Kate Rasheed (10:35:26) (in thread): > Okay. Thank you so much.

UBNSEMS3S (10:35:46): > Office hours recording. Thank you everyone who attended. - File (MPEG 4 Video): BSDB 2025_01_23.mp4

Kate Rasheed (11:45:05): > Good evening everyone. Please I have a question concerning ALDEx2 package that was used in thisarticleas the statistical test. > > From the supportinglinkattached to ALDEx2, I discovered that Welch’s t-test and Wilcoxon was used. I don’t know if I should record the statistical test as Welch’s t-test and Wilcoxon as seen inBioconductor. - Attachment (SpringerLink): Unifying the analysis of high-throughput sequencing datasets: characterizing RNA-seq, 16S rRNA gene sequencing and selective growth experiments by compositional data analysis - Microbiome > Background Experimental designs that take advantage of high-throughput sequencing to generate datasets include RNA sequencing (RNA-seq), chromatin immunoprecipitation sequencing (ChIP-seq), sequencing of 16S rRNA gene fragments, metagenomic analysis and selective growth experiments. In each case the underlying data are similar and are composed of counts of sequencing reads mapped to a large number of features in each sample. Despite this underlying similarity, the data analysis methods used for these experimental designs are all different, and do not translate across experiments. Alternative methods have been developed in the physical and geological sciences that treat similar data as compositions. Compositional data analysis methods transform the data to relative abundances with the result that the analyses are more robust and reproducible. Results Data from an in vitro selective growth experiment, an RNA-seq experiment and the Human Microbiome Project 16S rRNA gene abundance dataset were examined by ALDEx2, a compositional data analysis tool that uses Bayesian methods to infer technical and statistical error. The ALDEx2 approach is shown to be suitable for all three types of data: it correctly identifies both the direction and differential abundance of features in the differential growth experiment, it identifies a substantially similar set of differentially expressed genes in the RNA-seq dataset as the leading tools and it identifies as differential the taxa that distinguish the tongue dorsum and buccal mucosa in the Human Microbiome Project dataset. The design of ALDEx2 reduces the number of false positive identifications that result from datasets composed of many features in few samples. Conclusion Statistical analysis of high-throughput sequencing datasets composed of per feature counts showed that the ALDEx2 R package is a simple and robust tool, which can be applied to RNA-seq, 16S rRNA gene sequencing and differential growth datasets, and by extension to other techniques that use a similar approach. - Attachment (Bioconductor): ALDEx2 > A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch’s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.

2025-01-25

Peace Daniel (03:50:05): > Hello everyone, > I’d love to confirm the data transformation and statistical test in thisstudyI see AlDEx and relative abundance but I think CLR was used for the comparison between fast vs slow - Attachment (PubMed Central (PMC)): The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies > Altered gut microbiome (GM) composition has been established in Parkinson’s disease (PD). However, few studies have longitudinally investigated the GM in PD, or the impact of device-assisted therapies. To investigate the temporal stability of GM …

Peace Daniel (03:53:16) (in thread): > I’m fig 2B caption, it says volcano plots and log fold change which I’ll be curating. > Also figures 4,7

Yoko C (11:33:30) (in thread): > Hello, the data analysis says this: ” ALDEx2 was used to generate 128 Dirichlet Monte Carlo instances using raw sequence counts. Monte Carlo instances were transformed using the center-log ratio transformation and the Wilcoxon signed-rank test, followed by a Benjamini-Hochberg false-discovery rate (FDR) correction.” So I think here they used the Wilcoxon test report from Aldex2. If there is a supplementary table maybe there they specify the test?

Yoko C (11:45:57) (in thread): > Hi, I agree this is centered log transformation, I think in many cases they use log-fold for the graph but the test might be preformed with another transformation. Aldex2 uses Welch’s t or Wilcoxonhttps://microbiomejournal.biomedcentral.com/articles/10.1186/2049-2618-2-15/tables/1so you’d have to see if they mention anything further on that. Hopefully somebody can further clarify on this.

Peace Daniel (14:31:35) (in thread): > Thank you so much.I’llread the article you attached.

Kate Rasheed (14:43:59) (in thread): > Thank you so much@Yoko C

2025-01-27

Joy (03:31:34): > Good morning<@UBNSEMS3S>I want to request that theTukey-Kramer testbe added to BugSigDB as one of the statistical tests. It was utilized alongside the ANOVA test in this study I am reviewing, and I believe its inclusion would enhance the database’s representation of statistical methods used in microbiome research. Thanks.https://www.frontiersin.org/journals/immunology/articles/10.3389/fimmu.2021.710513/full#B1 - Attachment (Frontiers): Frontiers | Parasite-Derived Excretory-Secretory Products Alleviate Gut Microbiota Dysbiosis and Improve Cognitive Impairment Induced by a High-Fat Diet > High-fat (HF) diet-induced neuroinflammation and cognitive decline in humans and animals have been associated with microbiota dysbiosis via the gut-brain axi…

Mildred Anashie (03:35:35): > Happy Monday EveryoneI’m working on curating thispaperand I’ll appreciate your opinions > > Figure 3 and Supp Figure 7b potentially has 4 experiments with signatures. During one of the recent office hours I brought the question and Chloe said it can be curated but since the direction of significance is not clear it should be left out. > > I’m posting this here Incase anyone has an idea how to tell the increase and decrease in this figures, before I request to delete the already curated experiments on this. > > Also, I need help with the study design. > > Thank you for your help:pray: - Attachment (BioMed Central): Changes in social environment impact primate gut microbiota composition - Animal Microbiome > Background The gut microbiota (GM) has proven to be essential for both physical health and mental wellbeing, yet the forces that ultimately shape its composition remain opaque. One critical force known to affect the GM is the social environment. Prior work in humans and free-ranging non-human primates has shown that cohabitation and frequent social interaction can lead to changes in GM composition. However, it is difficult to assess the direction of causation in these studies, and interpretations are complicated by the influence of uncontrolled but correlated factors, such as shared diet. Results We performed a 15-month longitudinal investigation wherein we disentangled the impacts of diet and social living conditions on GM composition in a captive cohort of 13 male cynomolgus macaques. The animals were in single housing for the first 3 months of the study initially with a variable diet. After baseline data collection they were placed on a controlled diet for the remainder of the study. Following this diet shift the animals were moved to paired housing for 6 months, enabling enhanced social interaction, and then subsequently returned to single housing at the end of our study. This structured sequencing of diet and housing changes allowed us to assess their distinct impacts on GM composition. We found that the early dietary adjustments led to GM changes in both alpha and beta diversity, whereas changes in social living conditions only altered beta diversity. With respect to the latter, we found that two particular bacterial families — Lactobacillaceae and Clostridiaceae — demonstrated significant shifts in abundance during the transition from single housing to paired housing, which was distinct from the shifts we observed based on a change in diet. Conversely, we found that other bacteria previously associated with sociality were not altered based on changes in social living conditions but rather only by changes in diet. Conclusions Together, these findings decouple the influences that diet and social living have on GM composition and reconcile previous observations in the human and animal literatures. Moreover, the results indicate biological alterations of the gut that may, in part, mediate the relationship between sociality and wellbeing.

Svetlana Ugarcina Perovic (03:45:37): > Interesting read:https://erictopol.substack.com/p/how-our-gut-microbiome-can-driveIf your gut bacteria could talk, what might they be whispering to your brain?:broccoli:“Psst… grab that broccoli”:lollipop:“Hey brain, send them to the candy aisle… NOW!” > > HAPPY MONDAY! - Attachment (erictopol.substack.com): How Our Gut Microbiome Can Drive Sugar Cravings > More Evidence for Our Gut Taking Center Stage for What We Eat

Mildred Anashie (03:48:29) (in thread): > Good morning@JoyI believe Chloe would better explain this, > But from what I know,Tukey Kramer is not a standalone statistical test(I hope I am not wrong). It is a post hoc test used after performing ANOVA (Analysis of Variance) when you need to determine which specific group means are significantly different from each other. > After performing ANOVA to check if there is a significant difference among group means. A post hoc test such as Tukey-Kramer test is then used to identify thespecific groupswith these significant differences. > > The paper you shared also clearly says “After data were tested for normality, the differences among the intervention groups were determined using one-way analysis of variance (ANOVA)******followed by the post hoc******Tukey-Kramer test”. > > This test typically follows ANOVA. So you should record ANOVA as the statistical test.You canwait for Chloe’s response on this, Incase I am mixing up things or I am wrong on something.

Peace Daniel (03:50:25) (in thread): > Not the broccoli:tired_face:Happy Monday@Svetlana Ugarcina Perovic

Joy (04:35:56) (in thread): > Thank you@Mildred Anashie, I’ll also be waiting for<@UBNSEMS3S>response.

Kate Rasheed (05:31:22) (in thread): > This point is correct@Mildred Anashie. Chloe explained this two weeks ago during office hour.

Aleru Divine (06:48:18) (in thread): > Happy Monday to you too@Mildred AnashieLooked at the figures again and still got nothing.:pleading_face:As for the study design, this is a longitudinal study as described in Figure 1A.

Mildred Anashie (06:49:26) (in thread): > Okay@Aleru DivineThank you > Needed to confirm that

Aleru Divine (07:16:22) (in thread): > Happy Monday!@Svetlana Ugarcina PerovicThis was an interesting read. Thanks for sharing!

Peace Daniel (08:35:53): > Am I the only one having difficulty entering signatures on BugSigdb? It loads very slowly and sometimes just hangs,it’seven worse on laptop

Ndukauba Oluchi (08:37:04): > I noticed that too@Peace DanielI also noticed that when you enter more than 1 experiment, it takes time for it to reflect on your study page too.

Peace Daniel (08:39:34) (in thread): > Oh, I thought it was a network issue.

Adeshile Oluwatosin (11:45:21) (in thread): > Hello@Peace DanielIt could be the network > Or simply refreshing your browser could work

Peace Daniel (11:59:29) (in thread): > I don’tthink so, other sites seem to be working fine…Figma too

UBNSEMS3S (13:07:59) (in thread): > Since there are a ton of potential post-hoc ANOVA tests, I am thinking maybe we just add “post-hoc pairwise test” as an option. Any thoughts on this<@U1LCB8WEA>?

U1LCB8WEA (16:10:47) (in thread): > I don’t see how the fact it’s post-hoc is important; e.g. if they do an ANOVA followed by post-hoc t-test, I would just record it as t-test. After all, it’s the t-test that produced the signature between the two groups.

U1LCB8WEA (16:17:40) (in thread): > Actually, we could have a “Tukey’s Range Test” that would include both HSD and Tukey-Kramer. It is a bit different than t-test and includes a multiple testing correction.

U1LCB8WEA (16:18:09) (in thread): > But ANOVA isn’t wrong, either…

U1LCB8WEA (16:18:57) (in thread): > I just re-read Chloe’s point, “post-hoc pairwise test” would be better than “Tukey’s Range Test”

2025-01-28

Taofeecoh Adesanu (03:01:44): > Hello everyone. My name is Taofeecoh Adesanu, a graduate of Physiology looking to build a career in Bioinformatics. On the side, I do projects on Data Analysis with Python and R . > I discovered BugSigDB project via outreachy while combing the net to learn about Bioinformatics, and found it really interesting. > > Going forward, I’d like to contribute to the database as much as I can and also get familiar in preparation for my application as a prospective Outreachy Intern. > > I look forward to working with you all. > Thank you.

Svetlana Ugarcina Perovic (03:25:30) (in thread): > Welcome to the team, @Taofeecoh Adesanu****!****Please go through this intro material: > * BugSigDB project information, estimated time: 15 minutes (https://bugsigdb.org/Project:About) > * Reading materials on the human microbiome, estimated time: 2 hours (https://docs.google.com/document/d/1cpY8RoOHjJ_oxkDRGwlpqL-I29IN9B5BifhZIlqTjhE/edit?tab=t.0) > * Step-by-step guidance on how to document a signature in BugSigDB: 5 minutes (https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=6) > * View examples of completed BugSigDB curations, estimated time: 15 minutes (https://bugsigdb.org/Study_600) > * Video trainings on BugSigDB curation (https://www.youtube.com/playlist?list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq) > And open your bugisgdb accounthttps://bugsigdb.org/Main_PageFor any questions, do not hesitate to ask here. - Attachment (BugSigDB): Project:About > … - Attachment (YouTube): Adding a study to bugsigdb.org - Attachment (BugSigDB): Alteration of the fecal microbiota in Chinese patients with Parkinson’s disease - BugSigDB > Emerging evidences suggest that gut microbiota dysbiosis plays a role in Parkinson’s disease (PD).However, the alterations in fecal microbiome in Chinese PD patients remains unknown.This case-control study was conducted to explore fecal microbiota compositions in Chinese PD patients. - Attachment (YouTube): BugSigDB HOWTO videos > Videos describing the functionality and purpose of BugSigDB.org

Taofeecoh Adesanu (04:05:57) (in thread): > Thank you@Svetlana Ugarcina Perovic. > I have requested an account, now going through the shared resources once again.

Svetlana Ugarcina Perovic (05:10:22): > Do NOT miss this webinar!:clap:@Chioma Onyidohttps://www.linkedin.com/posts/academic-grant-writing-enclave-age_bioinformatics-geno[…]909171720192-jQ3x - Attachment (linkedin.com): Academic & Grant Writing Enclave (AGE) on LinkedIn: #bioinformatics #genomics #researchinnovation #africanacademies… > In recent years, Bioinformatics has emerged as a game-changer in research, blending computational tools with biological data to drive breakthroughs. From revolutionizing disease diagnostics and personalized medicine to advancing drug discovery and agricultural innovation, the possibilities are endless. > > :star2: For instance: > Global funding for bioinformatics is projected to surpass $21 billion by 2026, highlighting its growing significance in research. > > In Africa, bioinformatics is shaping the fight against diseases like malaria and cancer through genomic studies, making it a cornerstone of precision medicine. > > Want to learn how YOU can leverage these trends? > Join the Academic & Grant Writing Enclave (AGE) for an exclusive webinar on: > 𝗧𝗵𝗲 𝗣𝗼𝘁𝗲𝗻𝘁𝗶𝗮𝗹 𝗮𝗻𝗱 𝗙𝘂𝘁𝘂𝗿𝗲 𝗼𝗳 𝗕𝗶𝗼𝗶𝗻𝗳𝗼𝗿𝗺𝗮𝘁𝗶𝗰𝘀 𝗶𝗻 𝗥𝗲𝘀𝗲𝗮𝗿𝗰𝗵: 𝗢𝗽𝗽𝗼𝗿𝘁𝘂𝗻𝗶𝘁𝗶𝗲𝘀 𝗳𝗼𝗿 𝗔𝗳𝗿𝗶𝗰𝗮𝗻 𝗔𝗰𝗮𝗱𝗲𝗺𝗶𝗲𝘀. > > 𝗪𝗲𝗯𝗶𝗻𝗮𝗿 𝗗𝗲𝘁𝗮𝗶𝗹𝘀: > 𝗗𝗮𝘁𝗲: Saturday, 15th February 2025 > 𝗧𝗶𝗺𝗲: 10:00 AM (WAT) > 𝗙𝗮𝗰𝗶𝗹𝗶𝘁𝗮𝘁𝗼𝗿: Ms. Chioma Onyido (Bioconductor, Covenant University, Lagos State, Nigeria) > > 𝗥𝗲𝗴𝗶𝘀𝘁𝗿𝗮𝘁𝗶𝗼𝗻 𝗟𝗶𝗻𝗸: > https://lnkd.in/eS6EJWU9 > > Don't miss this opportunity to explore how Bioinformatics is transforming research in Africa and beyond. > > #Bioinformatics > #Genomics > #ResearchInnovation > #AfricanAcademies > #AcademicEnclave > > © 𝗔𝗰𝗮𝗱𝗲𝗺𝗶𝗰 𝗮𝗻𝗱 𝗚𝗿𝗮𝗻𝘁 𝗪𝗿𝗶𝘁𝗶𝗻𝗴 𝗘𝗻𝗰𝗹𝗮𝘃𝗲

Aleru Divine (05:11:53) (in thread): > Welcome to the team@Taofeecoh Adesanu:blush:

Kate Rasheed (05:14:29) (in thread): > Thank you for sharing.

Adeshile Oluwatosin (05:19:07) (in thread): > Welcome@Taofeecoh Adesanu

Aleru Divine (05:19:20) (in thread): > Registered to attend! Thank you for sharing@Svetlana Ugarcina PerovicLooking forward to it:blush:

Chioma Onyido (05:21:40) (in thread): > Thank you so much for sharing Svet!:blush::sparkles:

Mildred Anashie (07:11:43): > Hi@Svetlana Ugarcina PerovicKindly delete Experiment 2 in this studyhttps://bugsigdb.org/Study_1241Thank you

Svetlana Ugarcina Perovic (07:27:12) (in thread): > Deleted.

Taofeecoh Adesanu (08:23:12) (in thread): > Thank you@Aleru Divine@Adeshile Oluwatosin:slightly_smiling_face:

Joy (09:03:57) (in thread): > Welcome to the community@Taofeecoh Adesanu!:handshake:

Joy (09:04:45) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing. I can’t wait!

Joy (09:08:29): > Hi everyone, > > I’m working on curating the taxon 0319_6G20 at the genus and family level for Figure 3D for this study:https://www.nature.com/articles/s41598-022-25041-4#Fig3, but I’ve hit a roadblock. This specific taxon cannot be found in the NCBI Taxonomy Browser. What I did find is uncultured bacterium #0319-6G20. > > How should I proceed in such cases where the exact taxon isn’t available? Should I map it to the closest match (uncultured bacterium #0319-6G20) or classify it as “unknown” for genus and family? I’d appreciate any guidance or best practices for handling this situation. > > Thanks in advance!

Peace Daniel (10:04:28): > Hello everyone > I’d like to confirm if fig 7 in thisstudyshould be curated, there was no indication of a significant p value and this statement at the end of the caption >
> “Although a notable trend of overrepresentation of Roseburia was seen during the (t = 0 to t = 12) interval, although not quite reaching statistical significance, p = 0.051.” - Attachment (PubMed Central (PMC)): The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies > Altered gut microbiome (GM) composition has been established in Parkinson’s disease (PD). However, few studies have longitudinally investigated the GM in PD, or the impact of device-assisted therapies. To investigate the temporal stability of GM …

Adeshile Oluwatosin (10:26:01) (in thread): > Hello@JoyI advice to state exactly as written in the paper. > I checked NCBI and “uncultured bacterium 0319-6G20” is at the species level. > > But Figure 3D indicates thatit is atgenus and family level. > Thank you

Joy (10:27:27) (in thread): > Thank you@Adeshile Oluwatosin:pray:

Adeshile Oluwatosin (10:29:41) (in thread): > Indicate when curating as > “g_0319_6G20 and f_0319_6G20”

Svetlana Ugarcina Perovic (10:34:54): > SAVE THE DATE: February 5https://www.linkedin.com/posts/svetlana-ugarcina-perovic_foss-opensource-openscience-[…]827339431936-V8-v - Attachment (linkedin.com): Svetlana Ugarcina Perovic on LinkedIn: Next week, on February 5, I’ll be sharing my experience mentoring with… > Next week, on February 5, I'll be sharing my experience mentoring with Outreachy. See you at :coffee: chat! > > P.S. Thanks to Bioconductor, Segata Lab, Levi Waldron and HUGE BugSigDB community I have a lot to share.

Ndukauba Oluchi (11:01:37): > hello everyone, I have a question > when inputting signatures in bugsigdb, in my study I sawROTHIA , but on bugsigdb what I saw wasRothia with numbers beside it (Rothia 32207)in this case, what do I do?

Peace Daniel (11:05:47) (in thread): > Hi, check onNCBIto confirm if it’s the same taxonomic hierarchy as the one in the paper you’re curating from. If it is, you can curate with the number - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Ndukauba Oluchi (11:06:51) (in thread): > hello peace, I am not sure it can be curated because I am seeing -log(p-value) which might indicate negative values and you know we don’t curate for negative values. but lets see what others have to say though.

Ndukauba Oluchi (11:07:57) (in thread): > thank you@Peace Daniel

Aleru Divine (11:17:12) (in thread): > @Peace DanielI think it was only referring to Roseburia.:thinking_face:

Adeshile Oluwatosin (11:20:05) (in thread): > Hello@Peace DanielFigure 7 is very much curatable. > ALDEX2 being the statistical test. > I can see differential abundant taxa for DBS and LCIG participants at different time intervals specified in the text both at genus and family levels. > > Comparisons between different time intervals = different experiments. > > I’m thinking curate over representation as increase and under representation as decreased signatures. > As for roseburia, don’t curate that.

Adeshile Oluwatosin (11:25:07) (in thread): > @Ndukauba OluchiRothia 32207 isat genus level > Confirm ifit’ssame in your study.

Ndukauba Oluchi (11:26:17) (in thread): > @Adeshile Oluwatosinwhat I can see in my study is just Rothia without any number as a suffix.

Adeshile Oluwatosin (11:27:26) (in thread): > Can you kindly send a link or screenshot.

Adeshile Oluwatosin (11:29:40) (in thread): > @Ndukauba OluchiYes, it could be like that sometimes > Be careful not to duplicate same experiments in cases like this.

Adeshile Oluwatosin (11:43:54) (in thread): > @Ndukauba OluchiRothia 32207 is to be curated.The numbers showing is totally fine.As “508215” is a genus of eudicots (plants) and is unrelated to bacterial taxa.

Adeshile Oluwatosin (11:44:23) (in thread): > But actually confirm which correlates with your study. Thanks

Peace Daniel (11:45:06) (in thread): > Yh, I was referring to the p value > ALDEx2 is not in BugSigdb, another discussion for Thursday

Adeshile Oluwatosin (11:46:11) (in thread): > I checked on it and didn’t see that as well. > You can confirm at the office hour.

Peace Daniel (11:46:14) (in thread): > Right@Aleru DivineWhat about the p value not stated, although most in the study was 0.01

Aleru Divine (11:49:23) (in thread): > It’s0.05that’swhy the paper isemphasizing that Roseburia was not significant at 0.051.

Peace Daniel (11:51:38) (in thread): > I mean the p value for fig 7, I initially had plans to curate it but I need t confirm it first soI don’tmake a mistake

Aleru Divine (11:53:47) (in thread): > I believe signatures with p<0.05 were considered significant.That’swhy they emphasized that the one with p>0.05 was not significant.

Peace Daniel (12:01:16) (in thread): > My emphasis would be on the p value to curate for fig 7, I do agree it can be curated and we just resolved the issue of the taxas being statically significant. Do I record 0.01 which was used in the study or 0.05 default?

Aleru Divine (12:04:27) (in thread): > 0.01 I believe:sweat_smile:

Peace Daniel (12:05:37) (in thread): > Ahha gotcha, I just have to confirm these things. Thank you

Aleru Divine (12:07:18) (in thread): > Okay! Looking forward to it!:crossed_fingers:

Adeshile Oluwatosin (12:07:30) (in thread): > @Aleru DivineI also thought it was 0.05 > Butdidn’twant to assume, lol

Peace Daniel (12:07:55) (in thread): > Nah I meant, you just confirmed it > > Omg thank you:sweat_smile:

Peace Daniel (12:08:46) (in thread): > I don’tthink it would be 0.05@Adeshile Oluwatosinall the p values used was 0.01 which indicated statistical significance

Adeshile Oluwatosin (12:09:01) (in thread): > Maybe you should also check for other taxa thatwouldn’tmeet the significant threshold if you are using 0.01.

Adeshile Oluwatosin (12:09:10) (in thread): > Alright then@Peace Daniel

Aleru Divine (12:11:28) (in thread): > @Peace DanielOkay.:sweat_smile:It is 0.01 in the paper.

Ndukauba Oluchi (12:49:54) (in thread): > here it is@Adeshile Oluwatosinhttps://www.nature.com/articles/s41522-024-00622-5#Fig1 - Attachment (Nature): The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment > npj Biofilms and Microbiomes - The blood pressure lowering effect of beetroot juice is impaired in periodontitis and recovered after periodontal treatment

Ndukauba Oluchi (12:51:11) (in thread): > I have two tables in my paperone for Generaandone for species please which do i curate for my signatures

Peace Daniel (12:57:28) (in thread): > I believe we curate both,@Aleru Divinecan you confirm?

Adeshile Oluwatosin (13:00:59) (in thread): > You are to curate both@Ndukauba Oluchi

Ndukauba Oluchi (13:02:09) (in thread): > So I’m going to have like 10 signatures:joy:Got it:+1:

Adeshile Oluwatosin (13:08:18) (in thread): > In Figure 6A-E is curatable. > “Rothia dentocariosa” was mentioned with Taxonomy ID: 2047

Aleru Divine (13:14:00) (in thread): > @Ndukauba Oluchi, whenwe are dealing with different tables or figures, all taxonomic levels should be curated. But, if they are on the same table(onerow)only the lowest taxonomic rank should be curated.

Peace Daniel (13:14:46) (in thread): > @Ndukauba Oluchiwhere did you see taxas with genus rank level, I believe it’s species I see

Adeshile Oluwatosin (13:19:53) (in thread): > Supplementary Figure 1and 2@Peace Daniel

Peace Daniel (13:22:00) (in thread): > Idon’tthink suppl fig 1 should be curated

Adeshile Oluwatosin (13:32:10) (in thread): > Relative abundances between two or more groups can also be curated either as combination or pairwise analysis.

Peace Daniel (13:44:22) (in thread): > How do you read the increase and decreased taxas in that?

Adeshile Oluwatosin (14:05:37) (in thread): > In the case of Figure 5 and supplementary Figure 1. They should not be curated. It’s not comparing the abundances between the groups. The abundant species in each groups was only mentioned.@Peace Daniel

Adeshile Oluwatosin (14:10:10) (in thread): > I only made the intial statement for future reference.

Peace Daniel (14:11:47) (in thread): > Alright, youshould’veadded that as I was talking about the fig 1 in this study. All good:thumbsup:

2025-01-29

Svetlana Ugarcina Perovic (04:10:13): > UPDATE about currently open tasks:@Kate Rasheedand@Aleru Divine, supported by YOU, reviewed >100 curations. ONLY 18 studies left to be reviewed.Please see list of “NEEDS REVIEW” curations: https://github.com/waldronlab/BugSigDBcuration/issues?q=is%3Aissue%20state%3Aopen%20label%3A%22needs%20review%22%20%20sort%3Acreated-descand feel free to review some (just tag me and request a review). While reviewing you are more than welcome to clarify here your doubts as a reviewer. > Earlier@Peace Danielopened a good discussion on curating vs reviewing. Check it out:https://community-bioc.slack.com/archives/C04RATV9VCY/p1736933484366199If you are up to more than curating and reviewing or just want to try something else to contribute, feel free to check outhttps://bugsigdb.org/Help:Contents#TODO_for_reviewerssection > ANDhttps://github.com/waldronlab/BugSigDB/issuesAlso, you can add papers for curation herehttps://github.com/waldronlab/BugSigDBcuration/issuesJust make sure that they are curatable (with significant differential abundance results) and they have not been already added as “paper to curate” or already curated. Please tag me to approve it. > > AND, finally your main task and always open:ENJOY!Greetings from<@U1LCB8WEA><@UBNSEMS3S>and@Svetlana Ugarcina Perovic! - Attachment: Attachment > Hi :wave::skin-tone-4:
> I have a question, do you get better at curating when reviewing someone’s curation or when curating a new study?

Joy (05:55:41) (in thread): > Thank you@Levi Waldron. Well explained. My bad, I just came across this response after a day. I was deep neck into curating other studies. I truly appreciate.

Svetlana Ugarcina Perovic (09:41:41): > Reminder for our weekly team meeting:tomorrow at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions! ALL are welcome to join, especially**** new members**. > > cc<@UBNSEMS3S>

2025-01-30

Kate Rasheed (02:40:09) (in thread): > Good morning<@UBNSEMS3S>. I would like to followup on this to know if there is a solution yet. > > Thank you so much.

Svetlana Ugarcina Perovic (05:01:51): > :question:Quiz time:thinking_face:just to warm your curation uphttps://www.amnh.org/explore/ology/microbiology/what-do-you-know-about-the-human-microbiome

Kate Rasheed (05:10:14) (in thread): > 7 out of 10:smile:. > > I’m happy to find out that most of the bacteria that live on the skin are found in the knee:smile:. > > Why is this so?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:13:56) (in thread): > They provided explanation: “On the cool and dry skin of your knee, the bacteria are fewer butmore diverse, with hundreds of kinds that come and go.”@Kate Rasheedquestion was about**** the diversity ****not about the abundance: “Which area has the greatest diversity of microbes?”

Aleru Divine (05:17:45) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic

Kate Rasheed (05:19:08) (in thread): > Ohhhh. More diverse. This is well noted.

Aleru Divine (05:25:03) (in thread): > This was fun! Thank you@Svetlana Ugarcina Perovic:sweat_smile:I got a 9/10. Can’t believe I failed the very first question.What was I thinking “humans are the smartest organisms on Earth”:face_with_peeking_eye:

Peace Daniel (05:41:19) (in thread): > This was fun, I had an 8/10. > I most especially liked the sound after getting it correctly:sweat_smile:

Peace Daniel (05:42:38) (in thread): > Lol@Aleru Divinewe’rethe smartest tho

Ndukauba Oluchi (05:50:26) (in thread): > I got a 6/10 that’s a nice try:+1::joy:

Taofeecoh Adesanu (06:52:33) (in thread): > An interesting break from my tasks:grin:; got a 9 after making a silly guess on one question.

Joy (07:27:34) (in thread): > A fun way to learn. I got 10/10. Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (09:08:56) (in thread): > Next Wednesday:arrow_up:cc<@UBNSEMS3S><@U1LCB8WEA>

Svetlana Ugarcina Perovic (09:44:09): > First time seeing this error message! - File (PNG): Screenshot 2025-01-30 at 15.42.38.png

Adeshile Oluwatosin (09:46:44) (in thread): > I’mhaving same issues on GitHub, thought it was my network .

Ndukauba Oluchi (09:59:26): > Thank you<@UBNSEMS3S>

Aleru Divine (09:59:30) (in thread): > I got this error message today.But it disappeared when I refreshed my page.

Aleru Divine (10:00:10): > Thank you for the office hours session<@UBNSEMS3S>@Svetlana Ugarcina PerovicAnd everyone, for all the questions:blush:

Svetlana Ugarcina Perovic (10:02:01): > Reminder:If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format:https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Joy (10:04:06) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing this!

Svetlana Ugarcina Perovic (10:05:03) (in thread): > @Taofeecoh Adesanuit seems now is displaying all > > but anyway I made a comment inhttps://github.com/waldronlab/BugSigDBcuration/issues/543 - Attachment: #543 Gut microbiome in PCOS associates to serum metabolomics: a cross-sectional study > Gut microbiome in PCOS associates to serum metabolomics: a cross-sectional study > > Link to study: https://www.nature.com/articles/s41598-022-25041-4

Joy (10:05:24): > Thank you<@UBNSEMS3S>and@Svetlana Ugarcina Perovicfor the office hours session and the clarity on the questions today.

Svetlana Ugarcina Perovic (10:09:41) (in thread): > I have an idea, since this is a very first task for@Taofeecoh Adesanuand you@Joyare already experienced curator, could you two meet and go over this curation together? While explaining how you curated the study, you can both spot what should be corrected. What do you think?

Joy (10:11:57) (in thread): > Duly noted@Svetlana Ugarcina PerovicI’ll do just that. I have sent@Taofeecoh Adesanua message.

Svetlana Ugarcina Perovic (10:12:44) (in thread): > Excellent! Enjoy a teamwork!

Taofeecoh Adesanu (10:16:34) (in thread): > @Svetlana Ugarcina PerovicA heart warming idea, as I could really make use of some help. > Thank you once again.

Svetlana Ugarcina Perovic (10:30:44) (in thread): > @Taofeecoh AdesanuI am pretty sure this will be a great experience, and ask anything to@Joy(:face_with_finger_covering_closed_lips:she has been curating a lot with us, seehttps://bugsigdb.org/Special:Contributions/Joiejoie) - Attachment (BugSigDB): Special:Contributions/Joiejoie

Svetlana Ugarcina Perovic (10:39:23): > I need YOUR HELP. > > To prepare myself better for the next Wednesday Outreachy coffee chat (https://www.youtube.com/watch?v=PiOm6nqzTVQ), I would really like to knowwhat qualities or support do you value most from a mentor when working to complete a task? It does not need to be only from your bugsigdb experience, but could you please point out some good and bad examples from your bugsigdb experience if there is any.

Peace Daniel (11:19:08) (in thread): > Personally, I prefer to be in an environment where I feel welcome, my contributions are acknowledged and I can get all the support I need without feeling like I’m asking too much. > > I’ve had fair experiences while contributing to open source and I love BugSigdb because everyone’s contributions are appreciated, I mean yes I know I’m volunteering but it feels good to be acknowledged. > Some open-source communities are really difficult to navigate, mentors aren’t very active and your questionsmightn’tget resolved.

Joy (11:23:37) (in thread): > Thank you@Svetlana Ugarcina Perovic, these are the good quality examples from My BugSigDB Experience:white_check_mark:Encouraging Independence: I appreciated when the mentors here encouraged interns to investigate solutions before stepping in with direct answers. This approach helped develop problem-solving skills.:white_check_mark:Timely Responses: When mentors provided timely feedback on studies being reviewed and our progress on Github, it helped keep things on track.:white_check_mark:Detailed Explanations: Mentors gave in-depth explanations on statistical tests, explaining Meta analysis etc when these questions came up, which made understanding complex tasks easier.

Ndukauba Oluchi (11:34:03) (in thread): > @Peace Danieland@Joyhave said it all!:clap:

Peace Daniel (16:19:32): > Hello@Svetlana Ugarcina PerovicPlease delete signatures 1 & 2 in experiment 5 of this study > Also Experiment 8 in thisstudy - Attachment (BugSigDB): The Gut Microbiome in Parkinson’s Disease: A Longitudinal Study of the Impacts on Disease Progression and the Use of Device-Assisted Therapies - BugSigDB > BACKGROUND: Altered gut microbiome (GM) composition has been established in Parkinson’s disease (PD).However, few studies have longitudinally investigated the GM in PD, or the impact of device-assisted therapies.

UBNSEMS3S (16:32:55): > Recording of our meeting today. Thank you for attending. - File (MPEG 4 Video): bsdb meeting 2025_01_30.mp4

UBNSEMS3S (16:44:04): > I investigated this paper:https://journals.asm.org/doi/10.1128/spectrum.01387-21that@Kate Rasheedshared during the meeting today. While I do think the analyses done in this paper are theoretically curatable, I don’t think they are practically. There are over 10,000 distinct significant differential abundance results in their raw DESeq2 with over 100 experiments potentially. > > I think, given the nature of this paper, it is beyond the scope of BSDB to curate at this time.

Aleru Divine (16:49:34) (in thread): > I agree@Peace Daniel@JoyOne of the things I value most from a mentor is feedback. It helps me improve and see things from different perspectives. But beyond just giving feedback, how it is delivered matters a lot. I really appreciate when it is clear, constructive, and helps me understand what went well and what needs to be improved. > > Another one is empathy in feedback. And I don’t mean sugarcoating things, but having a supportive tone, especially when something is challenging. It makes a huge difference when a mentor corrects or guides with patience rather than frustration. It creates a space where I feel comfortable asking questions and not just trying to “get things right” out of fear of messing up.” > > All of this is very evident in the BugSigDB community, and it is one of the reasons I believe it is one of the best open-source communities that I have had the opportunity to contribute to.:heart_hands:

2025-01-31

Kate Rasheed (01:19:51) (in thread): > Good morning. Thank you so much for this<@UBNSEMS3S>.

Mildred Anashie (04:15:15) (in thread): > For me, just like Divine, qualities like patience, creating a safe space to ask questions openly, and providing constructive feedback are what I value most in a mentor. I also appreciate when mentors create a collaborative environment, encouraging teamwork with other contributors, which leads to shared learning and growth. These also makes up my good experiences within this community. > Clarity in feedback and communicationbased on expectationsis also important.Overall, BugSigdb is one of the open source communities I have contributed to that prioritizes inclusion and collaboration,my little contributions are being noticed andI’msure appreciated,which isabsolutelygreat.Thank you@Svetlana Ugarcina Perovic, Thank you everyone:blush:

Svetlana Ugarcina Perovic (04:37:40) (in thread): > Deleted.

Svetlana Ugarcina Perovic (04:38:09) (in thread): > Deleted with a commenthttps://github.com/waldronlab/BugSigDBcuration/issues/297 - Attachment: #297 Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns > Standard Sample Storage Conditions Have an Impact on Inferred Microbiome Composition and Antimicrobial Resistance Patterns – Casper Sahl Poulsen – Microbiology Spectrum
> https://journals.asm.org/doi/10.1128/spectrum.01387-21

Taofeecoh Adesanu (05:22:25): > Hello everyone! > > The methods’ section describes the sample/body site as thus:“Collection of peripheral venous blood and stool samples. All subjects’ peripheral venous blood was****collected on the third day of the menstrual cycle and the levels of sex hormones (luteinizing hormone (LH), follicle****stimulating hormone (FSH), and testosterone (T)) were determined to ensure that no abnormalities were****present. Stool samples were obtained from the participants 3–5 days after menstruation. Sterile plastic spoons****and plastic tubes were used by each subject to collect about 10 g of fresh stool samples. The blood and fecal samples****were transported within 2 h and preserved at − 80 °C until further processing.”However, Non-targeted metabolomics analysis was done on the blood while 16S rRNA-seq was done on stool. According to the curation policy, there are mainsequencing types,does that mean only the stool gets recorded as body site since 16S sequencing was done on it?**** and not the blood**

Kate Rasheed (05:24:17) (in thread): > Good morning@Taofeecoh Adesanu. Please share the link to the paper

Svetlana Ugarcina Perovic (05:25:03) (in thread): > @Taofeecoh Adesanuyou are recording only samples that were sent to sequencing.

Svetlana Ugarcina Perovic (05:25:53) (in thread): > We are recording onlysequencing results.

Ndukauba Oluchi (05:26:10) (in thread): > @Taofeecoh AdesanuFrom this, feaces is to be recorded as the sample

Taofeecoh Adesanu (05:26:45) (in thread): > @Kate RasheedGood morninghttps://bugsigdb.org/Study_1271 - Attachment (BugSigDB): Gut microbiome in PCOS associates to serum metabolomics: a cross-sectional study - BugSigDB > The association between gut microbiome and chronic metabolic disease including polycystic ovary syndrome (PCOS), is well documented, however, the relationship between the gut microbiota and serum metabolites remains unknown.

Svetlana Ugarcina Perovic (05:27:24) (in thread): > @Joydid a good job: recordingBody site : Feces

Taofeecoh Adesanu (05:27:50) (in thread): > Okayyy, thank you.@Svetlana Ugarcina Perovic@Ndukauba Oluchi

Svetlana Ugarcina Perovic (05:28:38) (in thread): > Feel free to ask whenever you have doubt!From your questions the other curators are learning as well.

Peace Daniel (06:02:35) (in thread): > Thank you

Ndukauba Oluchi (06:14:19): > Hello everyone, i have a question. > when i see something like this for alpha diversity“There were******* significant differences****** when comparing healthy individuals with periodontitis patients at baseline” does it meanINCREASED ?***

Svetlana Ugarcina Perovic (06:17:16) (in thread): > NOT necessarily, check for the Figure or Table (sometimes it is in the supplementary material) where alpha diversity results are reported.

Ndukauba Oluchi (06:20:21) (in thread): > alright@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (06:26:43): > FEEDBACK welcome.What do you think abouthttps://bugsigdb.org/Main_Pagefunctionality? > The question goes more into direction on how to increase the functionality of the site for researchers looking for information on bugs or diseases. > Imagine that you want to extract some specific microbiome information from already curated studies… > > Thanks!

Ndukauba Oluchi (07:03:34) (in thread): > Great question!@Svetlana Ugarcina Perovichttps://bugsigdb.org/Main_Pagesite is an indispensable resource for Microbiome research, To further enhance it’s usability and impact, particularly for researchers looking for microbial-disease insight, for me, I would like these to be added to its functionality:white_check_mark:Natural Language Processing search: A situation where I can ask questions in bugsigdb site search bar like “How many Microbes are in the saliva” or “what Microbes are associated with PCOS” just for information.:white_check_mark:User Interface(UI): what if we make the homepage more intuitive and increase the visual appeal of the site so that there will be easy navigation for new researchers and users, because when I logged into Bugsigdb for the first time(as a first timer) it was a little difficult for me to navigate through the site without help.:white_check_mark:Personally I Love Dark mode, it would be nice if we have an icon for changing to dark themes:blush::grin:Thank you:blush:

Yoko C (07:47:48) (in thread): > Hello, some suggestions I have are that the option to export data is more visible. For example when you use “Filter taxa”, the option to export the results as a CSV isn’t there, but there is an option in the “Drill down page” which you don’t see unless you go to the bottom of the page. Also where it says “Browse all studiesby Host species | Body site | Condition | Taxa | Location of subjects” that those options are clickable. Something that might be interesting is grouping the hosts for example insects, bats, etc. I think a category that might also be interesting is adding the database used in the Study (Silva, Greengenes ect) although that might complicate things retrospectively.

Ndukauba Oluchi (08:04:05): > please I have a question > 1. When curating signatures and I see something like “*********ACTINOMYCES NA**********”, this cannot be found on bugsigdb, and the study says “**********Organisms marked with NA indicate that they could not be assigned at the species level” ****what do I do? > 2. while curating for signatures, I sawactinomyces odontolyticus***in the paper but it’s not on bugsigdb, I inputted it on the NCBI taxonomy browser search bar and this was what I got. can someone please explain to me - File (PNG): ncbi.png

Peace Daniel (08:35:19) (in thread): > I think you could curate as unclassified actinomyces and add a note, but let’s hear what others say > > When you click on schaalia odontolyticus and read through, you’d see it’s another name for actinomyces odontolyticus. So, curate it with the NCBI Id 1660

Ndukauba Oluchi (08:57:37) (in thread): > Where did you see the NCBI id 1660

Peace Daniel (09:02:10) (in thread): > When you click on the taxa, read the content there. The NCBI Id is at the top part

Ndukauba Oluchi (09:03:35) (in thread): > oh! i am really learning well. thank you so much@Peace Daniel

UBNSEMS3S (13:09:50): > Thanks to the hardwork of@Aleru Divine, the BugSigDB Stats page is now updating for the first time in years

Aleru Divine (13:22:41) (in thread): > Thank you!<@UBNSEMS3S>:blush:Glad I could help!

Joy (13:44:47) (in thread): > Waoh that’s good to know<@UBNSEMS3S>, good work@Aleru Divine!

Taofeecoh Adesanu (19:27:16): > Thanks to@Joyfor the guide while reviewing this:raised_hands:.@Svetlana Ugarcina PerovicFor signature 2 of this study, the last two taxa could not be found neither in BugSigDb nor the Taxonomy browser; however“Clostridium sp. CAG:352”was found. > * Is it safe to conclude that“g_CAG_352”is the same as“Clostridium sp. CAG:352”? > * “Faecalibacterium” originally documented as* “g_Faecalibacterium” in the study paper flagged an error in BugSigDB. Again, can”Faecalibacterium sp.” *replace“Faecalibacterium”? > Thank you. - File (PNG): image.png

Adeshile Oluwatosin (20:37:13) (in thread): > Hello@Taofeecoh Adesanug_CAG_352 and “Clostridium sp. CAG:352” taxonomical rank is different so leave it as it is, > The first is genus, the second is of species level. > > Kindlycheck if the rank is same before you curate,

2025-02-01

Taofeecoh Adesanu (02:14:35) (in thread): > Thank you@Adeshile Oluwatosin

Peace Daniel (02:37:22) (in thread): > Exactly what@Adeshile Oluwatosinsaid,it’sokay not to find all taxas on BugSigdb. You just curate as it is

2025-02-02

Svetlana Ugarcina Perovic (07:55:15) (in thread): > “g” in the beginning stands for “genus” > “sp” stands for “species” > when curating keep that in mind.

Svetlana Ugarcina Perovic (07:57:18) (in thread): > Faecalibacterium genus should be availablehttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216851&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Joy (08:01:57) (in thread): > Duly noted. Thank you@Svetlana Ugarcina Perovicfor this piece of information, I don’t know why it was flagged, maybe I ’ll delete it and curate it again if it is ok by doing that.

2025-02-03

Svetlana Ugarcina Perovic (02:56:36): > This is brillianthttps://waldronlab.io/BugSigDBStats/articles/BugSigDBStats.html(thanks again@Aleru Divinefor making this working daily) > > What I have noticed, some changes should be made in curations withAntibiotics exclusionnot uniformly defined. > > And Condition: Gut microbiome measurement should be more specifically defined i.e. underwhich condition ”Gut microbiome measurement” was performed is more specific that we would like to define for the curation. > > Antibiotics exclusion: > "None", "none", "N/A", "No", "Unknown" -> leave it empty > "4 weeks", "30 days" -> change it to 1 month > > > > Condition: > "Gut microbiome measurement" -> condition under which gut microbiome measurement was performed OR condition of the study > > If someone is up to work on this, leave your comment below. Thanks! > Also, take your time to have a look at these beautiful stats, and if you notice something to improve, just let us know here. > > AND,Happy Monday!UPDATE:We have two leaders:drum_with_drumsticks:@Samuel Nnanna@Aleru Divinecontact them respectively to join > Antibiotic exclusion task > Condition task

Samuel Nnanna (03:13:58) (in thread): > Good morning@Svetlana Ugarcina PerovicThanks for your observation and I would like to work on uniformly defining the antibiotic exclusions as requested.

Aleru Divine (03:20:22) (in thread): > Thank you so much@Svetlana Ugarcina Perovic:blush:I’d love to work on thecondition. > I am open to collaborating if anyone wants to join me to work on this.:hugging_face:

Svetlana Ugarcina Perovic (03:20:52) (in thread): > Excellent@Samuel Nnanna! Feel free to team up with someone who is also maybe interested.

Svetlana Ugarcina Perovic (03:23:37) (in thread): > <@UBNSEMS3S>actually the unit(s) for Antibiotic exclusion should be better defined. Now it says in the description: “InformationNumber of days **without antibiotics usage…” > > and also there should be a note to leave it blank when there is no exclusion. > > number of months is the most frequent measure, and then when is less then a month we can record days, what do you think?

Adeshile Oluwatosin (03:40:23) (in thread): > Hi@Aleru DivineDo you mind teaming up to work on the condition.

Adeshile Oluwatosin (03:56:13) (in thread): > @Svetlana Ugarcina PerovicAre we permitted to make changes directly even to already reviewed curations. > Also, where should all the changes be reported

Svetlana Ugarcina Perovic (04:04:08) (in thread): > Yes, directly and to already reviewed curations. > It’s up to@Aleru Divineand you where you track your work/changes i.e. how you split the work. > Changes on the platform will be automatically recorded. (there is History option)

Adeshile Oluwatosin (04:08:11) (in thread): > Okay, thank you

Samuel Nnanna (04:08:46) (in thread): > @Svetlana Ugarcina Perovicfor the antibiotics exclusion, we have to find papers already curated and also already reviewed with such conditions and correct them? > And for those already reviewed, request for it to be opened to be corrected if said conditions are seen?

Adeshile Oluwatosin (04:09:37) (in thread): > Is there need to request for the papers to be opened before making changes?

Svetlana Ugarcina Perovic (04:11:14) (in thread): > There is no need for any special request.

Samuel Nnanna (04:11:57) (in thread): > @Svetlana Ugarcina Perovicthanks for clarifying

Adeshile Oluwatosin (04:12:28) (in thread): > Noted

Joy (04:12:36) (in thread): > Thank you@Svetlana Ugarcina Perovicfor these tasks, I’ll like to team up with@Samuel Nnannafor his task, is that ok with you@Samuel Nnanna?

Svetlana Ugarcina Perovic (04:12:37) (in thread): > ****“Gut microbiome measurement” OR “Microbiome measurement” ****papers are listed here:https://bugsigdb.org/Special:RunQuery/Drill?Drill=Taxon%255Bis_list%255D%3D1%26Loca[…]ndition+logic%5D=OR&Drill%5BNCBI%5D=&wpRunQuery=&pf_free_text= - Attachment (BugSigDB): Special:RunQuery/Drill

Aleru Divine (04:13:40) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy to collaborate@Adeshile Oluwatosin:blush:

Samuel Nnanna (04:14:07) (in thread): > @Joyyes let’s work on it together. > > Anyone else who would like to assist is also very welcome to. We’d need all the help to get this done

Joy (04:15:03) (in thread): > @Samuel NnannaGreat. Thanks

Svetlana Ugarcina Perovic (04:16:05) (in thread): > For Antibiotics expulsion you have to do a simple search:https://bugsigdb.org/w/index.php?title=_Special:Search&search=Antibiotics+exclusions%3A+none&go=Go&searchToken=47vbgn93gj6ubwbsv2vrqbq0j - Attachment (BugSigDB): Special:Search

Samuel Nnanna (04:26:04) (in thread): > Thank you for this@Svetlana Ugarcina PerovicI am compiling a list of Paper that need the Antibiotics Exclusion correction

Samuel Nnanna (04:26:34) (in thread): > This list would be in 10s

Samuel Nnanna (04:26:49) (in thread): > I hope it helps make the search easier

Samuel Nnanna (04:43:35) (in thread): > > Antibiotics exclusion: > "None", "none", "N/A", "No", "Unknown" -> leave it empty > "4 weeks", "30 days" -> change it to 1 month > > Just to be sure, where there is “none”, should be left empty?@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (04:47:40) (in thread): > Yes@Samuel Nnanna

Samuel Nnanna (04:48:07) (in thread): > Thanks@Adeshile Oluwatosin

Samuel Nnanna (04:49:23) (in thread): > Here’s a list of Curations that have such conditions;https://bugsigdb.org/Study_717https://bugsigdb.org/Study_300https://bugsigdb.org/Study_321https://bugsigdb.org/Study_321https://bugsigdb.org/Study_715https://bugsigdb.org/Study_1014https://bugsigdb.org/Study_715https://bugsigdb.org/Study_170https://bugsigdb.org/Study_1062https://bugsigdb.org/Study_963https://bugsigdb.org/Study_93https://bugsigdb.org/Study_715https://bugsigdb.org/Study_843https://bugsigdb.org/Study_91https://bugsigdb.org/Study_93https://bugsigdb.org/Study_562https://bugsigdb.org/Study_678https://bugsigdb.org/Study_326https://bugsigdb.org/Study_306

Samuel Nnanna (04:50:34) (in thread): > Still compiling more as I am still checking, but I hope this helps.@Adeshile Oluwatosin@Joy

Joy (04:52:52) (in thread): > Sure, It does help@Samuel Nnanna

Kate Rasheed (04:54:44) (in thread): > @Samuel Nnanna. Welldone on this. I’ll work with you and joy to make these changes

Taofeecoh Adesanu (04:58:09) (in thread): > @Aleru Divine@Samuel NnannaWell done.

Taofeecoh Adesanu (04:59:43) (in thread): > @Aleru Divinedo you mind I collaborate with you and@Adeshile Oluwatosin?

Aleru Divine (05:00:44) (in thread): > Idon’tmind at all@Taofeecoh Adesanu:blush:

Samuel Nnanna (05:18:09) (in thread): > https://bugsigdb.org/Study_584https://bugsigdb.org/Study_850https://bugsigdb.org/Study_536https://bugsigdb.org/Study_672https://bugsigdb.org/Study_955https://bugsigdb.org/Study_528https://bugsigdb.org/Study_715https://bugsigdb.org/Study_1062https://bugsigdb.org/Study_629https://bugsigdb.org/Study_835https://bugsigdb.org/Study_788https://bugsigdb.org/Study_279https://bugsigdb.org/Study_927https://bugsigdb.org/Study_1044https://bugsigdb.org/Study_1077https://bugsigdb.org/Study_983https://bugsigdb.org/Study_926https://bugsigdb.org/Study_1075https://bugsigdb.org/Study_1056https://bugsigdb.org/Study_551https://bugsigdb.org/Study_844here’s more.@Joy@Adeshile Oluwatosin@Kate Rasheed - Attachment (BugSigDB): Fecal Microbiota Characteristics of Patients with Colorectal Adenoma Detected by Screening: A Population-based Study - BugSigDB > BACKGROUND: Screening for colorectal cancer (CRC) and precancerous colorectal adenoma (CRA) can detect curable disease.However, participation in colonoscopy and sensitivity of fecal heme for CRA are low. - Attachment (BugSigDB): Geography, niches, and transportation influence bovine respiratory microbiome and health - BugSigDB > Bovine respiratory disease (BRD), one of the most common and infectious diseases in the beef industry, is associated with the respiratory microbiome and stressors of transportation. - Attachment (BugSigDB): Short- and long-term impacts of azithromycin treatment on the gut microbiota in children: A double-blind, randomized, placebo-controlled trial - BugSigDB > BACKGROUND: Macrolides are commonly prescribed for respiratory infections and asthma-like episodes in children.While their clinical benefits have been proved, concerns regarding the side-effects of their therapeutic use have been raised. - Attachment (BugSigDB): Factors Associated With the Microbiome in Moderate-Late Preterm Babies: A Cohort Study From the DIAMOND Randomized Controlled Trial - BugSigDB > The gut microbiota of preterm infants is affected by perinatal factors and, in turn, may impact upon infant health. - Attachment (BugSigDB): The alteration of intestinal mucosal α-synuclein expression and mucosal microbiota in Parkinson’s disease - BugSigDB > Parkinson’s disease (PD) is the second most common neurodegenerative disease but still lacks a preclinical strategy to identify it.The diagnostic value of intestinal mucosal α-synuclein (αSyn) in PD has not drawn a uniform conclusion.

Samuel Nnanna (05:55:53) (in thread): > I got a very insightful suggestion from@Kate RasheedThank you so much > > I have prepared an excel sheet where i’ll be updating the study links, to make things easier for us all, whoever picks a study could also update there as well. This would help us track our progress

Samuel Nnanna (05:55:57) (in thread): > https://docs.google.com/spreadsheets/d/13Yl8E4fDtB6e7gppIGbQ94VJ9CcJboc_0GXERG9z4Wc/edit?usp=sharing

Samuel Nnanna (05:58:06): > Hi everyone, I hope y’all doing okay. > In regards to the Antibiotics Exclusion Task, below is a link that could help us track our progress > Please update as we progress, thank youhttps://docs.google.com/spreadsheets/d/13Yl8E4fDtB6e7gppIGbQ94VJ9CcJboc_0GXERG9z4Wc/edit?usp=sharing

Mildred Anashie (06:58:04) (in thread): > Happy to help@Samuel Nnanna

Kate Rasheed (07:08:57) (in thread): > Thanks for this.

Adeshile Oluwatosin (07:16:24) (in thread): > Noted

Kate Rasheed (07:27:41) (in thread): > @Adeshile OluwatosinI see that you have worked on some of the studies on the list. Kindly update the ones you’ve worked on with completed

Adeshile Oluwatosin (07:59:25) (in thread): > Okay@Kate Rasheed

Svetlana Ugarcina Perovic (08:02:16): > When they ask me:What is/are your proudest moment as an Outreachy mentor?@Svetlana Ugarcina Perovic: Teamwork seen just above this message:arrow_up:AND curations-reviews like this one by@Yoko C@Adeshile Oluwatosinhttps://github.com/waldronlab/BugSigDBcuration/issues/540THANK YOU for making me proud every day!

Adeshile Oluwatosin (08:16:23) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Joy (10:52:50): > Good afternoon@Svetlana Ugarcina Perovickindly delete the following:Signatures 1 and 2for Experiment 1Signatures 1 and 2for Experiment 2Signatures 1 and 2for Experiment 3Signatures 1 and 2for Experiment 4 andSignature 2for Experiment 5https://bugsigdb.org/Study_1193Thanks

Yoko C (11:05:40) (in thread): > Thank you! Both@Svetlana Ugarcina Perovicand@Adeshile Oluwatosin:heart:

Samuel Nnanna (12:59:26) (in thread): > Welldone@Adeshile Oluwatosin@Joy@Kate Rasheed@Mildred AnashieI’ll start compiling Papers withAntibiotics exclusion: NAsoon. > > Anyone who wishes to assist is welcome. So far, papers withAntibiotics exclusion: nonehave been worked on > You can add papers with such conditions here;https://docs.google.com/spreadsheets/d/13Yl8E4fDtB6e7gppIGbQ94VJ9CcJboc_0GXERG9z4Wc/edit?gid=1528686316#gid=1528686316Thank you

Mildred Anashie (13:04:41) (in thread): > Well done@Samuel Nnanna@Kate Rasheed@Adeshile Oluwatosin@Joy

Kate Rasheed (14:45:49) (in thread): > Welldone@Samuel Nnanna@Mildred Anashie@Joy@Adeshile Oluwatosin

Joy (15:45:07) (in thread): > :bioc:

2025-02-04

Adeshile Oluwatosin (01:29:17) (in thread): > @Samuel NnannaThere are curations with “NA” as well curated for antibiotics Exclusion.Let’stake note

Adeshile Oluwatosin (01:29:20) (in thread): > Good morning

Adeshile Oluwatosin (01:32:20) (in thread): > Ohhh you’ve noticed great:+1:sothere’s“NA” and “N/A”

Adeshile Oluwatosin (01:40:09) (in thread): > I also think we should check them out with small letters as well.

Samuel Nnanna (04:29:41) (in thread): > @Svetlana Ugarcina PerovicGood morning > In situation where the Antibiotics exclusion is 6 weeks, should it be left as 6 weeks or reported as 1 month and 2 weeks. > > I think 6 weeks is a bit more simplified but then given the uniformity we’re trying to achieve, I don’t know which is preferable.

Samuel Nnanna (04:40:15) (in thread): > Good morning y’all, Trust you had a great night’s rest. > I have added more papers{Antibiotics exclusion: NA}I’ll check for those withN/Aas well and add them. > > Also i noticed some had extra details. eg: > “use of antibiotics or probiotics for 2 weeks before or after delivery, resulted in being excluded from the study” > > I think the above should just be “2 weeks” > What do you think?

Mildred Anashie (04:43:02) (in thread): > @Samuel Nnannajust 2 weeks works > > Well done, I just started working onsome ofthe ones you added

Samuel Nnanna (04:44:51) (in thread): > @Mildred Anashieaahhhhh I think so too. Thank you. > Also Thank you for all the help with the task.

Joy (04:49:23) (in thread): > Welldone@Samuel Nnanna, good job! Thanks@Mildred Anashie@Kate Rasheed@Adeshile Oluwatosinfor all the encouragement and support.

Adeshile Oluwatosin (04:57:03) (in thread): > Let’s go:relieved:

Adeshile Oluwatosin (04:57:20) (in thread): > 6 weeks is cool@Samuel NnannaShe mentioned specifically for 4 weeks = 1 month. > So I’m thinking 8 weeks = 2 month. > 12 weeks = 3 months

Samuel Nnanna (05:00:15) (in thread): > https://bugsigdb.org/Study_1First BugSigDB curation i guess > > In the curation I saw this for Antibiotics exclusion > “NYU included who had not been on long-term antibiotic treatment” > > I scanned through the paper and in the sensitivity section I saw this > “We also conducted our main analysis excluding participants who had taken antibiotics within 30 days prior to sample collection (n= 19 from the NYU study), in order to ensure results were not biased by effects of antibiotics on the microbiota (antibiotic usage information was not available in the CDC study) (Additional file1: Table S9). Excluding these participants groups did not substantially impact findings.” > > What do you guys think? - Attachment (BioMed Central): The gut microbiota in conventional and serrated precursors of colorectal cancer - Microbiome

Samuel Nnanna (05:03:36) (in thread): > Okay thanks@Adeshile Oluwatosin

Adeshile Oluwatosin (05:08:42) (in thread): > I’m trying to check in the study if there are comparisons/contrast specific to NYU study and some just for CDC. In this case, 1 month would be curated only for experiments whose comparison is related to NYU. But I’m still scanning through@Samuel Nnanna

Svetlana Ugarcina Perovic (05:10:35) (in thread): > Deleted.

Adeshile Oluwatosin (05:12:33) (in thread): > But in the case where for the contrast,there’sno specification. I think 1 month (NYU) is good enough for the antibiotics exclusion. My opinion

Svetlana Ugarcina Perovic (05:13:02) (in thread): > Yes 6 weeks is ok

Joy (05:13:06) (in thread): > Thank you@Svetlana Ugarcina Perovic.

Joy (05:40:20) (in thread): > I’ll go with 1 month because the study explicitly mentions excluding participants who took antibiotics within 30 days before sample collection

Samuel Nnanna (06:09:22) (in thread): > Thanks guys for the inputs and I agree, since we’re looking at Antibiotics exclusion and some participants were excluded based on that

Samuel Nnanna (10:18:22) (in thread): > @Svetlana Ugarcina PerovicHello:wave:,we’vecome across some papers while on the task where the reported value for antibiotics exclusion is wrong and another paper where some datawasn’treported but they already have the “reviewed” status > > In such situations, do we correct all errors and add missing curation data, basically“re-review” ?

Svetlana Ugarcina Perovic (10:19:44) (in thread): > Please report them here: bugsigdb study link and corrections and tag me please, thanks!

Samuel Nnanna (10:23:30) (in thread): > Okay thank you@Svetlana Ugarcina Perovic@Adeshile Oluwatosinand@Mildred Anashieplease send thestudylinksofthecurationwith such cases here > Thank you > > Anyone else that comes across aforementioned cases, please send the study link and corrections here:pray::pray:

Svetlana Ugarcina Perovic (10:24:43) (in thread): > Not papers, please specific bugsigdb study links, thanks!

Adeshile Oluwatosin (11:09:41) (in thread): > https://bugsigdb.org/Study_305corrected from “course of study” to “1 month” > Table S2 reports 4 weeks.

Adeshile Oluwatosin (11:13:59) (in thread): > @Svetlana Ugarcina Perovic

Mildred Anashie (11:46:41) (in thread): > @Adeshile OluwatosinI see you correctedthe Antibiotic exclusion forthisstudyalready. > I was going through the study and realized the things that weren’t recorded that’s why I paused on it, In my opinion a few corrections need to be added and changed in this study. > * Supplementary figure 2 was curated alongside signature 1 in Experiment 1 but it should be recorded differently, as it’s a different statistical test from Fig 3a. > * I’m unsure if Fig 1a should be curated, but Fig 1b looks curatable and appears to be the same statistical test as figure S2. > * Also, Fig 3b has an experiment that wasn’t recorded. > * Fig 4 looks like LEfSe as well from what the paper says “******Manual inspection of the abundance profiles for selected discriminatory OTUs revealed that the abundance patterns were consistent for the majority of samples (as opposed to few outliers) confirming that the LEfSe was robust (Figure 4).” ****And this should be curated alongside Fig 3a. > * All the alpha diversity for the first experiment recorded are increased and Faith should have been recorded instead of Richness. > This are the few things I have identified for now, I’ll look through again@Svetlana Ugarcina Perovic - Attachment (BugSigDB): Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women - BugSigDB > BACKGROUND: While the importance of commensal microbes in vaginal health is well appreciated, little is known about the effects of gynecological cancer (GynCa) and radiation therapy (RT) on the vaginal microbiome (VM) of postmenopausal women.

Adeshile Oluwatosin (11:57:15) (in thread): > @Mildred AnashieIdidn’tdo a general review of the study, just the antibiotic exclusion. I would have a look at it as well.

2025-02-05

Svetlana Ugarcina Perovic (03:35:13) (in thread): > @Mildred Anashie@Adeshile OluwatosinI openedhttps://github.com/waldronlab/BugSigDBcuration/issues/580please do review there and list your corrections. Good job for spotting all missed details. - Attachment: #580 Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women > Comparison of vaginal microbiota in gynecologic cancer patients pre- and post-radiation therapy and healthy women > > Corrections to https://bugsigdb.org/Study_305

Svetlana Ugarcina Perovic (03:37:13): > Good morning:coffee::teapot:See you today at the Outreachy coffee chat (https://www.youtube.com/watch?v=PiOm6nqzTVQ). - Attachment (YouTube): Coffee Chat with Outreachy Mentor

Joy (04:15:02): > Thanks for the reminder@Svetlana Ugarcina Perovic. I will be there!

Mildred Anashie (04:16:03) (in thread): > Okay@Svetlana Ugarcina PerovicThank you:pray:

Mildred Anashie (04:16:31) (in thread): > I figuredWell done@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (04:23:57) (in thread): > https://waldronlab.io/BugSigDBStats/articles/BugSigDBStats.htmlCan we have here options to jump to the section of interest rather than scrolling and searching for it. Also it would be very convenient to have in the end “return to the top” option.

Adeshile Oluwatosin (04:38:51) (in thread): > Okay, noted@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (04:47:26) (in thread): > Thank you all for your feedback on mentoring! > > I’m happy that you recognized our efforts inensuring effective communication and accommodating the varying learning paces of each contributor.What I will definitely continue doing is, at the same time, encouraging independence (not relying on the mentors directions) and pairing contributors to work collaboratively on specific tasks. These are the points when we grow more:potted_plant:

Adeshile Oluwatosin (06:31:58) (in thread): > @Svetlana Ugarcina PerovicPlease delete:https://bugsigdb.org/Study_928/Experiment_2/Signature_3It’s a duplicate of signature 1. - Attachment (BugSigDB): Study 928/Experiment 2/Signature 3 > Source: Fig. 2G Description: Comparison of microbiome signatures between patients with CGD (without a history of IBD) VS Healthy individuals using LEfSe Abundance…

Adeshile Oluwatosin (07:07:03) (in thread): > @Svetlana Ugarcina PerovicNo antibiotics exclusion in the study (No changes has been made yet)https://bugsigdb.org/Study_928 - Attachment (BugSigDB): Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease - BugSigDB > BACKGROUND: Chronic granulomatous disease (CGD) is caused by defects in any 1 of the 6 subunits forming the nicotinamide adenine dinucleotide phosphate oxidase complex 2 (NOX2), leading to severely reduced or absent phagocyte-derived reactive oxygen species production.

Adeshile Oluwatosin (07:22:15) (in thread): > @Svetlana Ugarcina Perovic > * Exp 1: Group 0/1 names are same. > * Exp 2/3/4 in this study has no Group 0 name. > * Antibiotics exclusion: inconsistency (3 weeks and 4 weeks) was mentioned. See Materials and Methods/Participant characteristics. > No corrections has been made to study.https://bugsigdb.org/Study_814 - Attachment (BugSigDB): Gastrointestinal tract involvement in systemic sclerosis: The roles of diet and the microbiome - BugSigDB > BACKGROUND: Alterations in gastrointestinal (GI) microbial composition have been reported in patients with systemic sclerosis (SSc).However, it is unclear to what degree these alterations and/or dietary changes contribute to the SSc-GI phenotype.

Adeshile Oluwatosin (07:50:10) (in thread): > @Svetlana Ugarcina PerovicIdon’thave access to this paper to confirmhttps://bugsigdb.org/Study_514 - Attachment (BugSigDB): Molecular detection of microbial colonization in cervical mucus of women with and without endometriosis - BugSigDB > PROBLEM: Intrauterine microbial colonization and its association with the pathogenesis of endometriosis via an innate immune cascade have been reported.As a potential source of microbial transmission, information on microbial colonization in cervical mucus is unknown.

Taofeecoh Adesanu (08:56:04): > Hello everyone! > In experiment 3 of this study:https://bugsigdb.org/Study_1016, the condition is “response to chemoradiotherapy”; however I can’t find an exact match in the dropdown or EFO, rather I found “response to immunochemotherapy” and “response to combination chemotherapy”, what do I do please? > I don’t want to assume. > > Thank you. > > cc:@Svetlana Ugarcina Perovic

Peace Sandy (09:08:52) (in thread): > Looking forward to it

Joy (09:12:34): > Hi@Taofeecoh Adesanuthe condition “Gut microbiome measurement”

Adeshile Oluwatosin (09:22:13) (in thread): > Hello@JoyWe no longer curate “gut microbiome measurement” or “microbiome measurement” in bugsigdb.

Adeshile Oluwatosin (09:22:41) (in thread): > Conditions are almost never that as updated in the curation policy

Taofeecoh Adesanu (09:27:06) (in thread): > Curated studies with “Gut microbiome measurement” as the condition is what@Aleru Divine,@Adeshile Oluwatosinand I are reviewing as noted by@Svetlana Ugarcina Perovic. > Hence, the condition, going forward won’t / can’t be “gut microbiome measurement”.

Svetlana Ugarcina Perovic (09:33:44) (in thread): > “Treatment” works.

Taofeecoh Adesanu (09:34:37) (in thread): > Alright. > Thank you:heart_hands:

Taofeecoh Adesanu (09:35:26) (in thread): > @JoyYour initial suggestion of “treatment” was right. > Thank you.

Svetlana Ugarcina Perovic (11:20:05): > It was an awesome chathttps://www.youtube.com/live/PiOm6nqzTVQI enjoyed it a lot! - Attachment (youtube.com): - YouTube > Enjoy the videos and music you love, upload original content, and share it all with friends, family, and the world on YouTube.

Taofeecoh Adesanu (11:26:21): > Hello everyone! > > What would be the suitable condition for this study in your opinion?https://bugsigdb.org/Study_1077Thank you for your help once again.:heart_hands:cc:@Svetlana Ugarcina Perovic - Attachment (BugSigDB): Comparison of Co-housing and Littermate Methods for Microbiota Standardization in Mouse Models - BugSigDB > The intestinal microbiota is a fundamental factor that broadly influences physiology.Thus, studies using transgenic animals should be designed to limit the confounding effects of microbiota variation between strains.

Joy (11:42:16): > I am thinking Phenotype will do

Taofeecoh Adesanu (11:45:03): > Yes, I thought so too. As a matter of fact, I’m in a bind between phenotype/genotype variation:confused:

Joy (11:45:04): > This is because the study investigates the impact of gut microbiota variability onmouse phenotypes in genetic studies,particularly in knockout (KO) versus wild-type (WT). comparisons

Taofeecoh Adesanu (11:47:57): > Thank you@Joy, I’d just keep it to phenotype.

Svetlana Ugarcina Perovic (15:00:26) (in thread): > @Adeshile Oluwatosinhttps://bugsigdb.org/Study_928/Experiment_2/Signature_3deleted.

Svetlana Ugarcina Perovic (15:01:39) (in thread): > https://bugsigdb.org/Study_928here it can stay a specific note on Antibiotics exclusion

Svetlana Ugarcina Perovic (15:03:41) (in thread): > Forhttps://bugsigdb.org/Study_814I reopenedhttps://github.com/waldronlab/BugSigDBcuration/issues/101Please make comments there and eventually corrections.

Svetlana Ugarcina Perovic (15:08:36) (in thread): > Here is a paper of this curationhttps://bugsigdb.org/Study_514 - File (PDF): 10.1111@aji.13147.pdf

Svetlana Ugarcina Perovic (15:14:04): > Reminder for our weekly team meeting:tomorrow at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions! > > Please@Samuel Nnanna@Aleru Divineprepare a short summary on the task status: Antibiotics exclusion and Condition editinghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1738569396368029cc<@UBNSEMS3S>(edited) - Attachment: Attachment > This is brilliant https://waldronlab.io/BugSigDBStats/articles/BugSigDBStats.html (thanks again @Aleru Divine for making this working daily) > > What I have noticed, some changes should be made in curations with Antibiotics exclusion not uniformly defined. > > And Condition: Gut microbiome measurement should be more specifically defined i.e. under which condition “Gut microbiome measurement” was performed is more specific that we would like to define for the curation. > > Antibiotics exclusion: > "None", "none", "N/A", "No", "Unknown" -> leave it empty > "4 weeks", "30 days" -> change it to 1 month > Condition: > "Gut microbiome measurement" -> condition under which gut microbiome measurement was performed OR condition of the study > If someone is up to work on this, leave your comment below. Thanks! > Also, take your time to have a look at these beautiful stats, and if you notice something to improve, just let us know here. > > AND, Happy Monday! > > UPDATE: > We have two leaders :drum_with_drumsticks: @Samuel Nnanna @Aleru Divine contact them respectively to join > Antibiotic exclusion task > Condition task

2025-02-06

Aleru Divine (04:00:43) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you for the office hours reminder! > > For the conditions, we borrowed the idea from@Samuel Nnannaand@Kate Rasheedand also put together a spreadsheet summarizing the list of studies with conditions that need changes and additional columns for the reviewer and the status. > > So far, we’ve listed all the studies, and there are about 10 more corrections left to make. > > Here’s thelinkto the conditions review spreadsheet.

Svetlana Ugarcina Perovic (04:05:40) (in thread): > Good job!!!@Aleru Divine@Taofeecoh Adesanu@Adeshile Oluwatosin

Samuel Nnanna (04:11:16) (in thread): > Good Morning@Svetlana Ugarcina PerovicThe Antibiotics Exclusion Task is still in progress. We devised a progress tracking mechanism using a spreadsheet and so far we’ve corrected over 90 studies. > > Compilations of studies with the Task situations is still being done. We have exhausted papers with “none” and “na” tags, currently working on those with “n/a”. > > We would need to explore other ways to find papers with task situations as there are studies that need corrections outside of the search tags (n/a, na, none) > Here’s thelinkto the spreadsheet.

Svetlana Ugarcina Perovic (04:16:07) (in thread): > Good job!!!@Samuel Nnanna@Adeshile Oluwatosin@Kate Rasheed@Joy@Mildred Anashie

Adeshile Oluwatosin (04:19:02) (in thread): > All noted@Svetlana Ugarcina PerovicFor:https://bugsigdb.org/Study_928I’m saying the note stated does not seem like the antibiotic exclusion. There are several papers with notes and wasn’t corrected as that’s what was reported in the paper. > Kindly have a look.

Svetlana Ugarcina Perovic (04:25:17) (in thread): > ok@Adeshile OluwatosinI reopened the issuehttps://github.com/waldronlab/BugSigDBcuration/issues/199please communicate with@Chioma Onyidoto fix it, thanks! - Attachment: #199 Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease > Intestinal microbiome and metabolome signatures in patients with chronic granulomatous disease – Prabha Chandrasekaran et al. – J Allergy Clin Immunol
> https://www.jacionline.org/article/S0091-6749(23)01101-6/fulltext

Adeshile Oluwatosin (04:27:12) (in thread): > Okay, noted@Svetlana Ugarcina Perovic

UBNSEMS3S (09:02:23): > Having some zoom login issues. 2 minutes.

Aleru Divine (09:48:58): > Thank you for the office hours session today<@UBNSEMS3S>@Svetlana Ugarcina Perovicand everyone for the questions asked:blush:

Svetlana Ugarcina Perovic (09:50:18): > @Ndukauba Oluchiwhat helps when you do not have NCBI ID match is to check out how taxon has been recorded in other reviewed curations, seehttps://bugsigdb.org/w/index.php?title=_Special:Search&search=Rikenellaceae+RC9&go=Go&searchToken=7ljdk85fot0509le7zjcxzv1b - Attachment (BugSigDB): Special:Search

Joy (09:52:27) (in thread): > Thank you@Svetlana Ugarcina Perovicfor this!

Taofeecoh Adesanu (09:54:33) (in thread): > Sincerely, thank you!:heart_hands:I did learn a lot.:slightly_smiling_face:

Ndukauba Oluchi (09:59:11) (in thread): > Wow:astonished:, thank you@Svetlana Ugarcina Perovicfor this

Ndukauba Oluchi (11:22:15) (in thread): > hello@Samuel Nnannahow do i join the antibiotics exclusion tasks? would love to collaborate with you.

Aleru Divine (11:33:42) (in thread): > Hi everyone! > > I need help with antibiotics exclusion in thispaper.Participants were excluded if they had a history of antibiotics consumption in the last 6-8weeks.I have curated the antibiotics exclusion: 6-8weeks.I’d like to know if this is acceptable in this case or if you have any suggestions on what to do.Thank you for your help:blush:

Taofeecoh Adesanu (11:38:13) (in thread): > May be curating it as a 6 weeks?:thinking_face:Since that is the minimum timeline of exclusion.

Aleru Divine (11:42:24) (in thread): > Thank you@Taofeecoh AdesanuThis makes sense.But I was also thinking maybethere’sa reason theydidn’tjust say 6 weeks.:sob:IDK!

Ndukauba Oluchi (11:42:41) (in thread): > Good job!@Aleru Divinei would say you use 2 months so we can have an exact number.

Taofeecoh Adesanu (11:42:44) (in thread): > Hello@Samuel Nnanna, > I was hoping I could help out with this review but I can’t find a new link flagged “uncompleted” in the tracker.

Ndukauba Oluchi (11:43:43) (in thread): > just like to sum everything up, i don’t know if you understand me? because 8weeks is 2months

Ndukauba Oluchi (11:44:01) (in thread): > we don’t want something in-between

Aleru Divine (11:46:03) (in thread): > Thank you@Ndukauba OluchiI understand, butI’malso considering that they included 6 weeks that means somewereexcluded if they took antibiotics at 6 weeks (1 month and 2 weeks) and some at 8 weeks(2 months).It’snot linear:smiling_face_with_tear:

Taofeecoh Adesanu (11:46:08) (in thread): > @Ndukauba Oluchi, that works too but we’ve had studies with Antibiotic Exclusion of 6 weeks; I don’t think the uniformity we aim to have is still compromised:thinking_face:

Ndukauba Oluchi (11:50:33) (in thread): > oh! i just read it now from materials and methods@Aleru Divine@Taofeecoh AdesanuAfter eliminating subjects with a history of consumption of antibiotics in the last 6–8 weeks. you are right, i think it should be left as 6-8weeks.

Aleru Divine (11:54:17) (in thread): > Maybe this might be an exception@Taofeecoh Adesanu@Ndukauba OluchiI once had a study that had different antibiotics exclusion criteria for the cases and the controls.It was advised to curate both.So maybe leaving this as reported in the paper.

UBNSEMS3S (12:09:54): > Office hours recording. Thank you everyone who attended. - File (MPEG 4 Video): bsdb meeting_2025_02_06.mp4

UBNSEMS3S (12:26:04): > BugSigDBStats now has a working sidebar for navigation:http://waldronlab.io/BugSigDBStats/articles/BugSigDBStats.htmlPlease let me know of other improvements you’d like to see.

Samuel Nnanna (12:46:25) (in thread): > Hello@Aleru DivineI think it’s best to report as 1-2 months, then maybe a note (discussion pages) where you would properly explain the timeline as seen in the paper. This is to maintain consistency with the new report convention where 4 weeks is 1 month > what do you think@Mildred Anashie@Adeshile Oluwatosin@Joy

Samuel Nnanna (12:48:20) (in thread): > Hello@Taofeecoh Adesanuwe would love to have you onboard. > I’ll b adding more papers to the tracker soon and i’ll update as soon as its added.

Samuel Nnanna (12:51:08) (in thread): > @Ndukauba OluchiApologies for the late response. More papers would be added to the tracker soon, as soon as it is, i’ll update here as well. > > We’re looking forward to your contributions and we appreciate the assistance.:blush:

Aleru Divine (13:26:43) (in thread): > Thank you for all your inputs@Samuel Nnanna@Taofeecoh Adesanu@Ndukauba Oluchi

Mildred Anashie (13:50:33) (in thread): > @Aleru Divinewell done on this@Samuel NnannaI’m thinking the antibiotic exclusion might be recorded as stated, because the paper doesn’t say if one is relative to a particular group > > or recorded as 2 months since it seems like a general statement was made and 2 months is the final timeline the antibiotic exclusion covers:thinking_face:

Samuel Nnanna (14:02:54) (in thread): > Ahhh this is the tricky part > Well I guess there could be exceptions where completely necessary > > And yes I thinkyouhave a good point@Mildred Anashie.Since theyweren’tspecific

Aleru Divine (14:05:39) (in thread): > I’vecurated as 6-8weeks and I hope to get feedback from the mentors on this.Thanks everyone!

Aleru Divine (16:26:50) (in thread): > Thank you so much!:blush:

2025-02-07

Svetlana Ugarcina Perovic (01:47:43) (in thread): > It’s ok in this case to record 6-8 weeks.

Samuel Nnanna (02:24:56) (in thread): > Good morning guys > I trust everyone slept good:relieved:I have added more papers to the tracker > Welldone guys and I appreciate the efforts and teamwork > Have a great day

Ndukauba Oluchi (02:32:33) (in thread): > Great Job!@Samuel Nnanna

Kate Rasheed (02:41:27) (in thread): > Good morning@Samuel Nnanna. Welldone on this addition. > > However, I’ve refreshed the sheets and I can’t find the populated links (it stopped at 151 from my end)

Mildred Anashie (02:43:49) (in thread): > I can see up to 170@Kate RasheedIs that correct?@Samuel Nnanna

Samuel Nnanna (02:43:58) (in thread): > https://docs.google.com/spreadsheets/d/13Yl8E4fDtB6e7gppIGbQ94VJ9CcJboc_0GXERG9z4Wc/edit?usp=sharingplease check again@Kate Rasheed

Kate Rasheed (02:44:57) (in thread): > Yes yes. Saw it now. 170

Joy (02:46:41) (in thread): > Good job@Samuel Nnanna!

Ndukauba Oluchi (03:26:35): > Hello everyone:hugging_face:, How are we doing? > I want to ask if it is possible that I add papers to Bugsigdb, and how do I add them if I find one?

Ndukauba Oluchi (03:35:44): > Also in a case where you have 2 antibiotics exclusion for example as stated in my paperParticipants were excluded if (i) they had used antibiotics or immunosuppressants in the past 6 months; (ii) they had used local antibiotics in the past 7 days; > How do I curate? 6months and 1 week?

Peace Daniel (03:45:00) (in thread): > First search BugSigdb if the paperisn’tcurated and also GitHub. If it hasn’t and the paper is curatable (alpha diversity, differential abundance) you can add it on GitHub and notify@Svetlana Ugarcina Perovic

Peace Daniel (03:47:20) (in thread): > I think you’d record both, probably 6 months and then 7 days local antibiotics

Ndukauba Oluchi (03:58:26) (in thread): > Okay

Ndukauba Oluchi (03:59:04) (in thread): > Okay, thank you@Peace Daniel

Aleru Divine (04:02:24) (in thread): > Thank you@Svetlana Ugarcina Perovic

Ndukauba Oluchi (05:30:39) (in thread): > Hello everyone, I have just assisted@Samuel Nnannato add more papers to the tracker. we can check it out. > Also while adding papers, I found out that some papers have up to 11 experiments with different antibiotics exclusions, so when correcting, we have to check thoroughly to avoid mistakes. > Great Job guys!:heart:and thank you for your efforts.

Peace Daniel (06:05:26) (in thread): > Hi@Aleru Divine@Samuel NnannaDo any of you need more hands? I’ll be happy to help

Aleru Divine (06:13:13) (in thread): > Hello@Peace Daniel, I believe we have completed the conditions task as there aren’t any more left to correct. > > As for the antibiotics task, please read through this thread and check this spreadsheet to help with correcting the antibiotics exclusion. I’ll be joining in on this task soon:blush:https://docs.google.com/spreadsheets/d/13Yl8E4fDtB6e7gppIGbQ94VJ9CcJboc_0GXERG9z4Wc/edit?usp=sharing

Joy (06:38:41) (in thread): > Well done@Ndukauba Oluchi!

Svetlana Ugarcina Perovic (07:50:38) (in thread): > @Ndukauba Oluchiyou are recording it as “6 months”

Svetlana Ugarcina Perovic (07:51:19) (in thread): > because those 7 days are included in the last 6 months

Svetlana Ugarcina Perovic (07:51:38) (in thread): > you can leave a special note to it

Ndukauba Oluchi (07:51:52) (in thread): > Okay, thank you so much!@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:24:05): > :drum_with_drumsticks:@Taofeecoh Adesanuput her first curation up for a reviewhttps://github.com/waldronlab/BugSigDBcuration/issues/570If you want to review it, just make a comment in the GitHub issue.

Kate Rasheed (10:25:42) (in thread): > :dancer::dancer:Go@Taofeecoh Adesanu

Taofeecoh Adesanu (11:02:20) (in thread): > Thank you all. > I look forward to learning from your inputs.:slightly_smiling_face:

Peace Daniel (11:08:52) (in thread): > Good job@Taofeecoh Adesanumany more to come:heart:

Joy (11:27:52) (in thread): > Nice one@Taofeecoh Adesanu!:ok_hand:

2025-02-08

Svetlana Ugarcina Perovic (05:05:45): > Welcome to the #bugsigdb**** community, ****@Akriti****!****Feel free to introduce yourself here. > > Here is your first curationhttps://github.com/waldronlab/BugSigDBcuration/issues/555Feel free to ask any question here while curating and ENJOY! - Attachment: #555 Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study > Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study – Luigi Sacchettino – PlosOne
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315374

Peace Daniel (05:47:10) (in thread): > Welcome@Akriti

Akriti (06:37:27) (in thread): > Thank you@Peace Daniel:slightly_smiling_face:

Joy (07:03:29) (in thread): > Welcome@Akriti!

Adeshile Oluwatosin (12:16:01) (in thread): > Welcome@Akriti

Taofeecoh Adesanu (12:20:11) (in thread): > Welcome to the community@Akriti:tada::tada:

2025-02-09

Akriti (03:37:50) (in thread): > Thank you@Adeshile Oluwatosin,@Taofeecoh Adesanu

Akriti (04:03:01): > Hello Mam@Svetlana Ugarcina Perovicmay I get to know more about my issue on which I am working .Will really helpful for me

Adeshile Oluwatosin (05:23:45) (in thread): > Hello@AkritiGo through this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1738052730140509?thread_ts=1738051304.239889&channel=C04RATV9VCY&message_ts=1738052730.140509 - Attachment: Attachment > Welcome to the team, @Taofeecoh Adesanu! > > Please go through this intro material: > • BugSigDB project information, estimated time: 15 minutes (https://bugsigdb.org/Project:About) > • Reading materials on the human microbiome, estimated time: 2 hours (https://docs.google.com/document/d/1cpY8RoOHjJ_oxkDRGwlpqL-I29IN9B5BifhZIlqTjhE/edit?tab=t.0) > • Step-by-step guidance on how to document a signature in BugSigDB: 5 minutes (https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=6) > • View examples of completed BugSigDB curations, estimated time: 15 minutes (https://bugsigdb.org/Study_600) > • Video trainings on BugSigDB curation (https://www.youtube.com/playlist?list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq) > And open your bugisgdb account https://bugsigdb.org/Main_Page > > For any questions, do not hesitate to ask here.

Taofeecoh Adesanu (05:31:12) (in thread): > Hello@Akriti! > In addition to what@Adeshile Oluwatosinshared: please go through this toothe curation policy. > > You will find it really helpful:slightly_smiling_face: - Attachment (BugSigDB): Curation Policy > .

Aleru Divine (06:06:02) (in thread): > Welcome@Akriti:hugging_face:

Aleru Divine (06:10:42) (in thread): > Well done@Taofeecoh Adesanu:clap:I requested to review this:blush:

Akriti (06:22:24) (in thread): > ok thank you for sharing@Taofeecoh Adesanu

Taofeecoh Adesanu (06:34:47) (in thread): > @Aleru DivineI’m honored:slightly_smiling_face:, thank you. > I look forward to your corrections.

2025-02-10

Karima Diafi (05:46:16): > Good morning everyone:sun_with_face:, I hope that you’re doing great.. I am currently curating this paper, however,it does not specify any sequencing technology or methodology.Should I proceed with data curation based on the available information, or would it be more appropriate to clarify with the authors before moving forward? > Have a nice day:blush: - Attachment (SpringerOpen): Gut microbiota in Parkinson’s disease patients: hospital-based study - The Egyptian Journal of Neurology, Psychiatry and Neurosurgery

Peace Daniel (05:49:18) (in thread): > I’lltake a look@Karima Diafi

Peace Daniel (05:50:48): > @Svetlana Ugarcina Perovic@Samuel NnannaThisstudydoes not include the time for antibiotic exclusion,what’sthe best course of action for updating the data on antibiotic exclusion? - Attachment (BugSigDB): A Walnut-Enriched Diet Affects Gut Microbiome in Healthy Caucasian Subjects: A Randomized, Controlled Trial - BugSigDB > Regular walnut consumption is associated with better health.We have previously shown that eight weeks of walnut consumption (43 g/day) significantly improves lipids in healthy subjects.In the same study, gut microbiome was evaluated.

Peace Daniel (05:59:01) (in thread): > I believe a qPCR was used for quantification, take a look at this > > “ The Bacterial abundance was quantified by qPCR using SYBR Green qPCR in a Rotor gene 3000 (Corbett Life Science, Australia) using 16S rRNA group specific primers as this is the available in our lab.”

Adeshile Oluwatosin (06:07:42) (in thread): > I suggest Leave empty@Peace Daniel

Peace Daniel (06:08:51) (in thread): > For this, I think using 2 months would be best. What do you suggest? > > 4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents > > This@Svetlana Ugarcina Perovic

Peace Daniel (06:10:29) (in thread): > I think so too, just need a confirmation@Adeshile OluwatosinAlthough@Svetlana Ugarcina Perovicdid say unknown should be left empty

Svetlana Ugarcina Perovic (06:11:29) (in thread): > We are recording only what’s written.

Svetlana Ugarcina Perovic (06:11:54) (in thread): > We are not guessing number of months/weeks..

Svetlana Ugarcina Perovic (06:14:08) (in thread): > Leave it empty. Usually participants with any ongoing antibiotic treatment are not even invited for the study, only in the case of studying a specific antibiotic treatment.

Adeshile Oluwatosin (06:14:23) (in thread): > @Peace DanielI have made changes to ’2 months” for the other question

Svetlana Ugarcina Perovic (06:14:58) (in thread): > @Adeshile Oluwatosinwhich question? Please be more clear.

Peace Daniel (06:14:59) (in thread): > Okay@Svetlana Ugarcina Perovic

Karima Diafi (06:15:03) (in thread): > Thank you@Peace Daniel, It looks like they targeted specific bacterial taxa using qPCR, so sequencing was not required.”

Samuel Nnanna (06:15:16) (in thread): > @Svetlana Ugarcina Perovicthank you for the clarification

Adeshile Oluwatosin (06:16:23) (in thread): > I have made changes to this studyhttps://bugsigdb.org/Study_440To report as 2 months. Since 4 weeks is inclusive of 8 weeks here “4 weeks for topical antibiotics, corticosteroids, and other anti-inflammatory medications, within 8 weeks for systemic antibiotics, corticosteroids, and other immunosuppressive agents” - Attachment (BugSigDB): Characterization and Analysis of the Skin Microbiota in Rosacea: A Case-Control Study - BugSigDB > BACKGROUND: The efficacy of antibiotics in rosacea treatment suggests a role for microorganisms in its pathophysiology.Growing concern over the adverse effects of antibiotic use presents a need for targeted antimicrobial treatment in rosacea.

Svetlana Ugarcina Perovic (06:17:18) (in thread): > @Adeshile Oluwatosinplease do not mix questions and answers, keep them in separate threads. This is important to avoid confusions.

Adeshile Oluwatosin (06:19:23) (in thread): > Okay, noted@Svetlana Ugarcina Perovicthank you so much. > > I only responded in this thread because peace asked both questions in same thread

Peace Daniel (06:20:20) (in thread): > Just ask in a separate thread@Adeshile OluwatosinI was also seeking clarification before you wrote you had already made the change

Adeshile Oluwatosin (06:21:01) (in thread): > I was not asking a question. I was actually responding to you. > But it is fine@Peace Daniel

Svetlana Ugarcina Perovic (06:27:41) (in thread): > No worries, just pay attention to separate discussion threads to avoid future confusion and to be more clear to other readers of your comments. Thanks!

Adeshile Oluwatosin (06:28:34) (in thread): > To clarify@Peace DanielThe initial question for this thread leave empty.

Adeshile Oluwatosin (06:29:03): > @Peace Danielhttps://bugsigdb.org/Study_440Record as 2 months for this study. > Thank you

Peace Daniel (06:29:49) (in thread): > Yes@Adeshile Oluwatosinyou’veeffected the change > Noted@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (06:29:52) (in thread): > Thank you@Svetlana Ugarcina Perovic

Peace Daniel (06:30:36) (in thread): > You’vedone that:white_check_mark:

Svetlana Ugarcina Perovic (06:31:29) (in thread): > Ok, I see now. Next time we should communicate better and agree first before we make changes.

Svetlana Ugarcina Perovic (06:32:14) (in thread): > Sorry for my additional question, I had to clarify it.

Samuel Nnanna (06:33:35) (in thread): > Hello Everyone, Trust we’re having a good day. > I want to say thank you for all the contributions and efforts. > > A reminder; > When you pick a paper to work on, please add your name and select the appropriate status (“in progress” while working on it and “completed” when you’re done. > > This is to prevent someone else from working on a paper while you’re on it as well. > > Thank you!

Adeshile Oluwatosin (06:34:35) (in thread): > I already made changes before she asked on the group as I was working on antibiotics exclusion > I responded prior to her asking. > Thank you once again@Svetlana Ugarcina Perovic

Peace Daniel (06:35:40) (in thread): > Oh, I get the confusion@Adeshile OluwatosinPlease add the status next time, thank you:blush:

Svetlana Ugarcina Perovic (06:36:06) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1739187215732729?thread_ts=1738580286.272219&cid=C04RATV9VCY - Attachment: Attachment > Hello Everyone, Trust we’re having a good day. > I want to say thank you for all the contributions and efforts. > > A reminder; > When you pick a paper to work on, please add your name and select the appropriate status (“in progress” while working on it and “completed” when you’re done. > > This is to prevent someone else from working on a paper while you’re on it as well. > > Thank you!

Svetlana Ugarcina Perovic (06:37:58) (in thread): > No worries, these communication issues happen all the time when working online, just remember next time to register/record all your ongoing activities. And keep asking questions, please do not change that:smile:

Svetlana Ugarcina Perovic (06:38:29) (in thread): > Keep on talking to each other!

Peace Daniel (06:38:30) (in thread): > Absolutely, thank you@Svetlana Ugarcina Perovic@Adeshile Oluwatosin

Peace Daniel (06:42:56): > Another question@Svetlana Ugarcina PerovicFor thisstudy“use of antibiotics between 2 weeks prior to delivery and 2 weeks after delivery, for any reason except for prophylactic use” > > Do I record as 1 month and add a note? - Attachment (BugSigDB): Early-Life Events, Including Mode of Delivery and Type of Feeding, Siblings and Gender, Shape the Developing Gut Microbiota - BugSigDB > Colonization of the infant gut is believed to be critically important for a healthy growth as it influences gut maturation, metabolic, immune and brain development in early life.

Samuel Nnanna (06:49:28) (in thread): > @Peace Danielreport as seen in the paper > 2 weeks prior to delivery > 2 weeks after delivery

Svetlana Ugarcina Perovic (06:49:31) (in thread): > Record: 2 weeks prior to delivery and 2 weeks after delivery

Peace Daniel (06:49:58) (in thread): > Okay, I thought it was similar to thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1738917344139929 - Attachment: Attachment > Also in a case where you have 2 antibiotics exclusion for example as stated in my paper > Participants were excluded if (i) they had used antibiotics or immunosuppressants in the past 6 months; (ii) they had used local antibiotics in the past 7 days; > > How do I curate? 6months and 1 week?

Svetlana Ugarcina Perovic (06:50:05) (in thread): > Because this is not any 1 month, it’s specific to the study condition

Peace Daniel (06:50:28) (in thread): > Noted@Svetlana Ugarcina Perovic

Peace Daniel (07:17:52): > For thisstudy@Svetlana Ugarcina PerovicI can’t access the full material but I observe that two statistical tests were used, just the first experiment has an antibiotic exclusion and data transformation while the second doesn’t. - Attachment (BugSigDB): Alterations of gut microbiome in autoimmune hepatitis - BugSigDB > OBJECTIVE: The significance of the liver-microbiome axis has been increasingly recognised as a major modulator of autoimmunity.

Ndukauba Oluchi (07:56:37): > Hi@Peace DanielI suggest you record antibiotics exclusion for the first experiment only and leave the second one blank.

Ndukauba Oluchi (07:57:29) (in thread): > Good Job!@Samuel Nnannayou are doing well!

Peace Daniel (07:58:28) (in thread): > I need to read the paper to confirm, it was the same experiment but different statistical tests

Ndukauba Oluchi (08:02:42) (in thread): > Alright@Peace Daniel

Joy (08:33:29): > Hi@Svetlana Ugarcina Perovic, for thisStudy, will it be ok to curate the antibiotic exclusion as 6 months? It has the following text in the antibiotic exclusion box:****“proof of extensive antibiotic therapy for 1+ week in previous 6 months. also, prior treatment of systemic antituberculous therapy for more than 1 week.”**** - Attachment (BugSigDB): Predominance of Escherichia-Shigella in Gut Microbiome and Its Potential Correlation with Elevated Level of Plasma Tumor Necrosis Factor Alpha in Patients with Tuberculous Meningitis - BugSigDB > Tuberculous meningitis (TBM), the most lethal and disabling form of tuberculosis (TB), may be related to gut microbiota composition, warranting further study.

Ndukauba Oluchi (09:29:13): > Hello@JoyFrom your paper,Exclusion criteria includes: (iii) receipt of treatment with extensive antibiotic therapy for more than 1 week during the previous 6 months;I think it should be curated as 6 months, because they are excluding people who have taken antibiotics for more than 1 week in the last 6 months > Do you understand?

Ndukauba Oluchi (09:37:11): > A systemic antituberculous therapy simply means treatment(drugs) for tuberculosis (I searched Google), so since they didn’t mention or specify any antibiotic, I think it shouldn’t be curated.

Samuel Nnanna (09:44:39) (in thread): > Hello@Joyand@Ndukauba OluchiWelldone on your efforts.@JoyI think you should go ahead and curate 6 months since it was mentioned in the paper@Ndukauba OluchiTuberculosis is caused by the bacteriumMycobacterium tuberculosiswhich means taking an antituberculosis is taking an antibiotic. They don’t have to mention the particular Antibiotics taken.

Ndukauba Oluchi (09:45:53) (in thread): > Alright@Samuel NnannaNoted. > Thank you.

Joy (11:37:56) (in thread): > Duly noted@Ndukauba Oluchi, thank you

Joy (11:41:46) (in thread): > Thank you@Samuel Nnanna

Peace Daniel (12:09:19) (in thread): > Pls comment in the thread soit’smore organized

Svetlana Ugarcina Perovic (13:39:30) (in thread): > Please record 6 months.

Svetlana Ugarcina Perovic (13:41:54) (in thread): > Here you go: - File (PDF): 10.1136@gutjnl-2018-317836.pdf

Svetlana Ugarcina Perovic (13:43:46) (in thread): > <@UBNSEMS3S>do you have maybe access to the supplementary materialhttps://gut.bmj.com/content/69/3/569.full?

Peace Daniel (13:46:22) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (14:10:33) (in thread): > Duly noted. Thanks@Svetlana Ugarcina Perovic

Ndukauba Oluchi (14:15:45) (in thread): > Oh! Duly noted@Peace Daniel

Peace Daniel (15:08:22) (in thread): > Hi again@Svetlana Ugarcina PerovicI believe the data transformation for logistic regression should be a log transformation but then it wasn’t clearly stated which cohort it was performed on, I assume it was same as experiment 1 because the group numbers are the same but please provide more clarity. Thank you! > > First, we performed a cross-sectional study of 91 steroid-naïve patients with AIH and 98 age, gender and BMI matched healthy controls. Subsequently, an independent cohort with 28 steroid- naïve patients and 34 controls was used to verify the results. > > We applied linear discriminant analysis effect size (LEfSe) analysis to identify taxa or pathways differentially abundant between cases and controls. This method first uses the non-para- metric factorial Kruskal-Wallis sum-rank test to detect features with significant differential abundance and then uses linear discriminant analysis (LDA) to calculate the effect size of each feature. Multivariate Association with Linear Models algorithm (MaAsLin) was used for association testing of the covariates versus the abundance of microbial taxa or pathway with default parameters, to deconfound the effects of age, gender, BMI, anti- biotic and UDCA exposure.24 > Statistical analyses were performed with R (V.2.15.3). The relative taxa abundance was arcsine square root transformed before regression tests (glm function). We employed multivari- able stepwise logistic regression analysis to identify the genera that best discriminate AIH from controls using the caret package. The input features consisted of the 11 AIH-associated genera and then a feature elimination step was performed with glmSte- pAIC method to select the top features and optimise the model.

2025-02-11

Peace Daniel (03:26:52): > Hello everyone@Svetlana Ugarcina PerovicShould figure 3E-H be curated in thispaper.I’d loveopinions please, thank you!It says here, “To assess whether the differentially abundant phages impact gut bacteria composition, we predicted their hosts using iPHoP [44]. The predicted hosts for Peeveelvirus were Staphylococcus aureus and Staphylococcus agnetis. Similar hosts were predicted for Biseptimavirus (Table S3). Predicted hosts for Peduovirus were Escherichia coli, Escherichia fergusonii, and Escherichia albertii, like those for Alegriavirus (Table S3). E. coli, E. albertii, E. fergusonii, and S. aureus were all significantly elevated in nHEU compared to nHU (p = 0.0078, 0.0117, 0.0116, and 0.0491 respectively, Fig. 3E–H).” - Attachment (BioMed Central): Neonates exposed to HIV but uninfected exhibit an altered gut microbiota and inflammation associated with impaired breast milk antibody function - Microbiome > Background Infants exposed to HIV but uninfected have altered immune profiles which include heightened systemic inflammation. The mechanism(s) underlying this phenomenon is unknown. Here, we investigated differences in neonatal gut bacterial and viral microbiome and associations with inflammatory biomarkers in plasma. Further, we tested whether HIV exposure impacts antibody-microbiota binding in neonatal gut and whether antibodies in breast milk impact the growth of commensal bacteria. Results Neonates exposed to HIV but uninfected (nHEU) exhibited altered gut bacteriome and virome compared to unexposed neonates (nHU). In addition, HIV exposure differentially impacted IgA-microbiota binding in neonates. The relative abundance of Blautia spp. in the whole stool or IgA-bound microbiota was positively associated with plasma concentrations of C-reactive protein. Finally, IgA from the breast milk of mothers living with HIV displayed a significantly lower ability to inhibit the growth of Blautia coccoides which was associated with inflammation in nHEU. Conclusion nHEU exhibits profound alterations in gut bacterial microbiota with a mild impact on the enteric DNA virome. Elevated inflammation in nHEU could be due to a lower capacity of breast milk IgA from mothers living with HIV to limit growth the of gut bacteria associated with inflammation. Video Abstract

Mildred Anashie (03:40:05) (in thread): > Hi@Peace DanielIhaven’tlooked through the rest of the paper but I believe it should be curated > > However, the statistical used for itisn’tso clear, you might have to look through to confirm what test was used as Idon’tthink iPHoP is a statistical test.

Peace Daniel (03:41:55) (in thread): > Would appreciate if you could take a closer look, thank you@Mildred AnashieStatistical test is Deseq2 and corncob

Svetlana Ugarcina Perovic (04:36:39) (in thread): > @Aleru Divinecould you please take a look at this issue:arrow_up:

Aleru Divine (04:46:43) (in thread): > Yes, on it!

Svetlana Ugarcina Perovic (04:47:23) (in thread): > @Aleru Divineplease help in here, thanks!

Svetlana Ugarcina Perovic (04:57:29) (in thread): > It’s good to bring such questions, more complex, to the team meeting, because we all can discuss them and learn from them.

Peace Daniel (04:59:23) (in thread): > Noted@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (04:59:54) (in thread): > Keep up the good work!

Mildred Anashie (05:10:58) (in thread): > Okay@Peace DanielI’llgive it a look and revert back

Aleru Divine (05:46:40) (in thread): > I’vecarefully reviewed this@Svetlana Ugarcina PerovicRelative abundance can have an additional transformation appliedas we know itand it was done in this case. From the description of the figure that has results from the logistic regression analysis (3C), the relative abundance is plotted on a logarithmic scale which is implying that the data was transformed to log values before plotting.Additionally suggestions:Figure 3C needs to be curated for experiment 2. The sample sizes and antibiotics exclusion should be the same as experiment 1 as they are both from the exploration data.Regardingconfounders, the study controls for five variables using MaAsLin (age, gender, BMI, antibiotics, and ursodeoxycholic acid(UDCA)), but only four have been curated so far. > > It seems these confounders were used to further validate the results from the initial differential abundance analysis (LEfSe), meaning they weren’t controlled for in the first experiment (LEfSe), only in the second (logistic regression). See page 4 for reference. > > Lastly, Figure 2C should be curated as part of Experiment 1. The only difference is the LDA score (4.15), which still meets the LDA > 2.0 threshold. So, it should either be added to Experiment 1 I believe.

Peace Daniel (05:48:26) (in thread): > Thank you@Aleru DivineSo, experiment 2 should be log transformation with the other points you noted yh?

Aleru Divine (05:50:50) (in thread): > Yes@Peace Daniel

Peace Daniel (05:51:49) (in thread): > Okay, can i effect these corrections?@Svetlana Ugarcina Perovic

Mildred Anashie (07:31:20) (in thread): > Heeewwww,I’vetaken a look@Peace Daniel:smile:It isatrickyoneand I still couldn’t identify the statistical test, the only method they pointed towards was usingiPHOp, which integrates BLAST-based homology searches along with other factors to predict which bacterial hosts are associated with the identified phages.You should bring this up,let’slearn more on this as@Svetlana Ugarcina Perovicadvised > > You might have to leave out the figure though, butlet’swait for clarification on what to do > Well done:clap:

Peace Daniel (07:37:09) (in thread): > Thank you girl@Mildred Anashie:heart_hands:I’llbring this up in the next meeting

Svetlana Ugarcina Perovic (08:13:48) (in thread): > Yes please@Peace DanielThanks@Aleru Divinefor your thorough feedback!

Aleru Divine (08:22:03) (in thread): > Missed this notification butI’llhave a look:pray:

Svetlana Ugarcina Perovic (08:36:38) (in thread): > Fig 3E-H are results based oniPHoP(Integrated Phage HOst Prediction) analysis for computational prediction of host taxonomy from phage (viruses of bacteria) genomes. These results are not significant differentially abundant results to curate.

Peace Daniel (08:50:04) (in thread): > Thank you so much@Svetlana Ugarcina PerovicCc@Kate Rasheed

Svetlana Ugarcina Perovic (08:59:44) (in thread): > cc@Aleru Divine

Aleru Divine (09:01:49) (in thread): > Thank you so much for clarifying this@Svetlana Ugarcina Perovic:blush:

Kate Rasheed (09:06:41) (in thread): > Thank you so much for clarifying@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (09:56:37) (in thread): > @Akritihow are you doing? We are here for any doubt :)

Akriti (09:58:50) (in thread): > Yes mam I am working on it and facing some issue

Akriti (09:59:58) (in thread): > like there is no codeset and only have a readme file so I am facing issue what part I should change and like where ot start

Akriti (10:00:31) (in thread): > and is it completly documenting issue?

Akriti (10:00:40) (in thread): > Thank you:)

Svetlana Ugarcina Perovic (10:01:23) (in thread): > Have you read the intro material? We are not dealing directly with code, we are curating microbiome results from the paper to the bugsigdb online platform.

Svetlana Ugarcina Perovic (10:05:38) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1739096625357919?thread_ts=1739091781.076049&cid=C04RATV9VCY - Attachment: Attachment > Hello @Akriti Go through this: > https://community-bioc.slack.com/archives/C04RATV9VCY/p1738052730140509?thread_ts=1738051304.239889&channel=C04RATV9VCY&message_ts=1738052730.140509

Akriti (10:44:30) (in thread): > Thank you for providing helpful resources mam

Yoko C (11:18:59): > Hello everyone, what is the wording being used for participants currently not on antibiotics?

Peace Daniel (12:46:05) (in thread): > Antibiotics exclusion?

Svetlana Ugarcina Perovic (15:51:11) (in thread): > @Yoko CI am always surprised (positively) by your unique questions! What you are trying to define? We need more context.

Svetlana Ugarcina Perovic (15:54:27) (in thread): > @Samuel Nnannaha1Month should be 1month - Attachment (BugSigDB): Gut bacteria identified in colorectal cancer patients promote tumourigenesis via butyrate secretion - BugSigDB > Emerging evidence is revealing that alterations in gut microbiota are associated with colorectal cancer (CRC).However, very little is currently known about whether and how gut microbiota alterations are causally associated with CRC development.

Svetlana Ugarcina Perovic (15:58:46) (in thread): > @Samuel Nnannawe need uniform wording for “currently on antibiotics” and similar, see herehttps://bugsigdb.org/w/index.php?title=+Special%3ASearch&search=currently+on+antibiotics&go=Go - Attachment (BugSigDB): Special:Search

Svetlana Ugarcina Perovic (15:59:51) (in thread): > Oh, now I get it, you are asking for Antibiotics exclusion

Ndukauba Oluchi (16:00:45) (in thread): > Hey@Svetlana Ugarcina Peroviccan I also join@Samuel Nnannato make this changes?

Svetlana Ugarcina Perovic (16:00:54) (in thread): > I already tagged@Samuel Nnannaon this issue > We need uniform wording for “currently on antibiotics” and similar, see herehttps://bugsigdb.org/w/index.php?title=+Special%3ASearch&search=currently+on+antibiotics&go=GoThey are all arbitrary defined.Any suggestions?

Svetlana Ugarcina Perovic (16:01:14) (in thread): > Sure!

Samuel Nnanna (16:01:15) (in thread): > Thanks for the clarification forhttps://bugsigdb.org/Study_624

Svetlana Ugarcina Perovic (16:02:24) (in thread): > That example shows that we should check also such typos… capital letters…

Samuel Nnanna (16:05:19) (in thread): > Lets stick with “currently on antibiotics” removing all the extras@Svetlana Ugarcina Perovicjust like we do for “1 month” where original curation was “participants were excluded if they had taken antibiotics 1 month prior to sample collection” > > And yes I’ll be doing a thorough check for already reviewed papers

Svetlana Ugarcina Perovic (16:06:35) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1739307919555409?thread_ts=1738580286.272219&cid=C04RATV9VCY - Attachment: Attachment > Lets stick with “currently on antibiotics” removing all the extras@Svetlana Ugarcina Perovic > just like we do for “1 month” where original curation was “participants were excluded if they had taken antibiotics 1 month prior to sample collection” > > And yes I’ll be doing a thorough check for already reviewed papers

Svetlana Ugarcina Perovic (16:07:17) (in thread): > I agree. “currently on antibiotics”

Svetlana Ugarcina Perovic (16:07:32) (in thread): > Thanks@Samuel Nnanna!

Svetlana Ugarcina Perovic (16:11:49) (in thread): > :thinking_face:but@Yoko Cis asking for “currently**** not**on antibiotics”

Svetlana Ugarcina Perovic (16:12:34) (in thread): > We need more info here@Yoko C…

Samuel Nnanna (16:13:40) (in thread): > @Yoko Cplease share the study link > If they’re not on antibiotics, doesn’t it mean no antibiotics exclusion was done?

Mildred Anashie (16:14:50) (in thread): > @Svetlana Ugarcina PerovicI agree > We need more information@Yoko CCurrently not on antibiotics indicates an exclusion was done butdoesn’tstate the duration, if nothing else was stated in the paperI’mthinking leaving it blank:thinking_face:

Samuel Nnanna (16:17:26) (in thread): > Hello everyonePlease note that after a number, the following word should be in lowercase.eg. 1 “Month” should be 1 “month”Also, for the correction, we’ll work in pairs to make it easier for us all. So pair up > > Please leave a note on the sheet where confused and ask questions in the channel for clarity. > Thanks

Svetlana Ugarcina Perovic (16:17:39) (in thread): > Currently not on antibiotics indicates no antibiotics exclusion.

Mildred Anashie (16:29:31) (in thread): > Noted@Svetlana Ugarcina Perovic

Yoko C (18:15:26) (in thread): > Hello, this is what thepapersays: “Other exclusion criteria included use of antibiotics,” and “…we had two participants, one in each group, taking antibiotics…These participants were excluded from the analysis.”

Adeshile Oluwatosin (19:47:46) (in thread): > @Yoko Csee this “Other exclusion criteria included use of antibiotics or laxatives within the last three months”in Eligibility and recruitment part of the article.

Yoko C (20:41:55) (in thread): > Thank you@Adeshile Oluwatosin, not sure why I skipped the 3 months. Its settled then.

Adeshile Oluwatosin (21:01:06) (in thread): > Welcome:hugging_face:@Yoko C

2025-02-12

Svetlana Ugarcina Perovic (01:55:48): > Reminder for our weekly team meeting:tomorrow at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions!

Adeshile Oluwatosin (01:56:14) (in thread): > Noted:relieved:

Svetlana Ugarcina Perovic (02:02:42) (in thread): > @Adeshile Oluwatosingood job!

Svetlana Ugarcina Perovic (02:26:30): > :drum_with_drumsticks:NEW BUGSIGDB MEMBER > > Please welcome@Juliana Kentomahun MautinJuliana, feel free to introduce yourself here. For any BugSigDB question we are here and please do join our discussions. > > Welcome material:https://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Svetlana Ugarcina Perovic (02:31:31): > Hello everyone, I just (re)created a canvashttps://community-bioc.slack.com/canvas/C04RATV9VCYas our Welcome material. > > Please leave comments here if you spot something to be added or improved. Thanks!

Adeshile Oluwatosin (02:32:41) (in thread): > Welcome to the community@Juliana Kentomahun Mautin

USLACKBOT (02:39:08): > svetlana_up made updates to a canvas tab:[canvas content]

Joy (03:24:30) (in thread): > Good job@Svetlana Ugarcina Perovicon this creation, the canvas looks great and it’s detailed.

Svetlana Ugarcina Perovic (05:25:02): > TOMORROW@Chioma Onyidotalks about Computational Biology conceptshttps://www.linkedin.com/posts/g-ihub_computationalbiology-machinelearning-healthtech[…]064508637184-_awG - Attachment (linkedin.com): #computationalbiology #machinelearning #healthtech #bioinformatics… | G-iHub > Are you curious about Computational Biology but unsure where to start? > Do you wonder how machine learning, data science, and biology come together to solve real-world health challenges? > > Join us on this journey into Computational Biology, where we’ll break down complex concepts into simple, practical steps. > > :rocket: In our upcoming session, you'll learn: > :white_check_mark: How different backgrounds—biology, math, computer science—fit into the field. > :white_check_mark: The key role of machine learning in bioinformatics and algorithm development. > :white_check_mark: The difference between computational biology and bioinformatics and how they work together. > :white_check_mark: Real-world applications in genomics, drug discovery, and systems biology. > > :spiral_calendar_pad: Date: 13th February,2025 > :alarm_clock: Time: 3pm-5pm GMT > :mortar_board: Includes a FREE! Roadmap resource > > Don’t miss this opportunity to gain valuable insights that can shape your career in health tech! > LIMITED SPOT AVAILABLE! > Register now at > https://lnkd.in/e7CXe8Dn > > #ComputationalBiology #MachineLearning #HealthTech #Bioinformatics #DataScience

Taofeecoh Adesanu (07:01:21) (in thread): > You are welcome to the community@Juliana Kentomahun Mautin:tada:

Svetlana Ugarcina Perovic (09:08:31): > Some time ago@Joan C. Chukwuemekamade this helpful video on resolving GTDB taxa IDs to NCBI IDs (ones that we are recording in BugSigDB):https://community-bioc.slack.com/archives/C04RATV9VCY/p1698448487133659cc@Aleru Divine@Taofeecoh Adesanu - Attachment: Attachment > After curating signatures for a study experiment, a couple of them were marked “red” due to missing NCBI ID. I didn’t see them in NCBI initially, however, I recalled that the study mentioned Genome Taxonomy Database (GTDB) > > So I googled it and searched for the taxa names. Interestingly, it shows taxon history (which is helpful for obsolete names) and also the corresponding name in NCBI. > > Here’s a video example of how I resolved them, using one of the signatures as an instance. > > @UBNSEMS3S @U1LCB8WEA @Svetlana Ugarcina Perovic Please, would want to check if this step I took is okay and still in line with the required “detective” approach:blush: to resolving Missing NCBI ID issues?

Adeshile Oluwatosin (09:10:11) (in thread): > Thank you@Svetlana Ugarcina Perovicthis would be helpful

Aleru Divine (09:22:36) (in thread): > Thank you so much for sharing@Svetlana Ugarcina Perovic:blush:

Taofeecoh Adesanu (09:29:29) (in thread): > Thank you for sharing this resource@Svetlana Ugarcina Perovic. The issue is that this is not as straightforward for signatures in this study:https://bugsigdb.org/Study_1281. > > For some signatures, the GT Database returned hundreds of rows of different Accession numbers and NCBI Taxonomy matching the same species:disappointed_relieved:, and I guess this is the reason they reported the Taxa ID as “unclassified” in the document. - Attachment (BugSigDB): Expanding the human gut microbiome atlas of Africa - BugSigDB > Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors.

Taofeecoh Adesanu (09:55:06): > Hello everyone, > > So while working on thisstudy, I observed that some signatures exist in NCBI Taxonomy browser but could not be matched in BugSigDB, either on ID or names. > > For instance , I couldn’t find any match for Taxonomy IDs starting with 129 or 126 in BugSigDB. > > Anyone else experiencing or experienced this? > Thank you. > > cc:@Svetlana Ugarcina Perovic<@UBNSEMS3S> - Attachment (BugSigDB): Expanding the human gut microbiome atlas of Africa - BugSigDB > Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors.

Yoko C (11:22:01) (in thread): > Hello, I was able to save some using the NCBI ID. I didn’t test for all. - File (JPEG): Untitled.jpg

Peace Daniel (12:42:35) (in thread): > Well detailed@Svetlana Ugarcina PerovicWas wondering if you could also add q value as some papers report this instead and also adding Benjamin-Hochberg as something to look out for when checking for MHT correction. > > Great job so far:clap:

Peace Daniel (12:45:02) (in thread): > Hi@Taofeecoh Adesanufrom my experience if you input a signature using the NCBIId, BugSigdbupdatesitself and you can input that signature again using the name

Peace Daniel (12:47:35) (in thread): > also you might want to check your group definition and sample size, good job@Taofeecoh Adesanu

Chioma Onyido (14:11:09) (in thread): > Thanks a bunch for sharing Svet. Looking forward to seeing some of you there!:star-struck:

Taofeecoh Adesanu (15:09:24) (in thread): > @Peace DanielThank you for the observation, it has been corrected. Also, I noticed the update when I tried to input the same signature again, it didn’t flag as needing review and that made perfect sense. After all, that is one of the purposes of BugSigDB:slightly_smiling_face:.

Taofeecoh Adesanu (15:11:20) (in thread): > @Yoko CThank you, I tried again.

2025-02-13

Peace Daniel (02:14:59) (in thread): > I also noticed three alpha diversity but only two were reported in exp 1@Aleru DivineStill confused about this statement here especially if we’re to take out confounders from experiment 1 > > “Subsequently, an independent cohort with 28 steroid- naïve patients and 34 controls was used to verify the results. The division of the discovery and validation cohorts was done prior to data analysis.” > > If experiment 2 was the validation test and cohort which had confounders, does this not mean the sample size were different from the first? Also take a look at the caption for fig 3A, 3B > > Lastly, I’d like to confirm if Clostridiales Unknown was increased in control. Thank you

Svetlana Ugarcina Perovic (03:57:02): > :arrow_up::drum_with_drumsticks:@Taofeecoh Adesanu’s first curation reviewed:white_check_mark:by@Aleru Divinehttps://github.com/waldronlab/BugSigDBcuration/issues/570Congrats, Taofeecoh! This was an excellent first curation, how was your experience? What did you learn that you would apply in your next curation?

Svetlana Ugarcina Perovic (04:04:05) (in thread): > Updated. Thanks!

Svetlana Ugarcina Perovic (04:11:33): > TODAY:https://community-bioc.slack.com/archives/C04RATV9VCY/p1739343348961179 - Attachment: Attachment > Reminder for our weekly team meeting: tomorrow at 9 AM EST at https://us02web.zoom.us/j/2737200499 > > Bring your questions!

USLACKBOT (04:15:19): > svetlana_up made updates to a canvas tab:[canvas content]

Adeshile Oluwatosin (05:02:49) (in thread): > Thank you for this@Svetlana Ugarcina Perovic > * I think T-test should be mentioned for relative abundance as well. > * Also, antibiotics exclusionmention of curating “4 weeks” as 1 month, 8 weeks as 2 months etc. Should be mentioned. > * I also think an instance should be given for when the disease itself should be used as condition (it could be as short as possible so it’s not bulky). > I believe adding this will make it easier for a new curator to get familiar with curating. > Thank you once again.

Taofeecoh Adesanu (05:06:09) (in thread): > Thank you@Svetlana Ugarcina Perovic@Aleru Divine! > > It was quite overwhelming at first but thanks to@Aleru Divineand@Kate Rasheedencouraging words, I was able to take my time in feeling comfortable before delving into it fully. > I was able to customize my workflow in a way to make tasks less daunting. > A major lesson I learnt is how to handle input of signatures better; even though it was stated in the curation policy, I guess~some~all things are best learned with application and experience. > This would definitely stick with me in my subsequent curations. > > Thank you all, I’m grateful:hugging_face:

Akriti (06:17:10) (in thread): > Hello Mam

Akriti (06:18:15) (in thread): > I am workingon the issue I wanna ask I have a single Readme file in code so I should make changes in that

Akriti (06:18:44) (in thread): > like I have attack any kind of links related to my solution?

Svetlana Ugarcina Perovic (06:19:10) (in thread): > We are not curating microbiome data in a Readme file. We do all our work herehttps://bugsigdb.org/Main_Page - Attachment (BugSigDB): Main Page > …

Svetlana Ugarcina Perovic (06:19:45) (in thread): > * Step-by-step guidance on how to document a signature in BugSigDB: 5 minutes (https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=6) - Attachment (YouTube): Adding a study to bugsigdb.org

Akriti (06:20:21) (in thread): > ok ok got it mam

Akriti (06:20:30) (in thread): > Thank you:slightly_smiling_face:

Peace Daniel (06:24:45) (in thread): > Hi there@AkritiI’mavailable for a hurdle if you still experience any difficulty. Well done:heart:

Akriti (06:35:16) (in thread): > Thank you for the asking@Peace Daniel

Akriti (06:36:02) (in thread): > May we have any another day as I am unavailable today:slightly_smiling_face:

Peace Daniel (06:38:22) (in thread): > Ofc, just send me a message

Aleru Divine (09:05:05) (in thread): > Great job@Taofeecoh Adesanu:blush::blush:

Akriti (09:38:19) (in thread): > yeah thank you :)

Anushka Paharia (09:44:02): > I have installed R and bioconductor. What are the prerequisites to contributing further than that? Should I improve on my tech stack proficiency?

Svetlana Ugarcina Perovic (09:44:55): > INVITATION:We would be happy if you can join us next week at MVIF - Attachment (microbiome-vif.org): WELCOME TO MICROBIOME VIRTUAL INTERNATIONAL FORUM (MVIF) > A recurring bite-sized alternative to multi-day microbiome conference: regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference!

Svetlana Ugarcina Perovic (09:45:47) (in thread): > https://community-bioc.slack.com/archives/C36B0HK7W/p1739456940569049 - Attachment: Attachment > Hello everyone, > I am Anushka, a cs undergrad from India. I am enthusiastic about Data Science and open source. I’m hoping to participate in this cohort of Outreachy. I wanna know what kind of prior skills I should have before I dive into the contribution phase. I have done data science projects and programming in R. Thankyou.

Svetlana Ugarcina Perovic (09:46:39) (in thread): > Hi Anushka, welcome to the team, please check out ourwelcome material - File (Canvas): Welcome material

Adeshile Oluwatosin (09:48:31) (in thread): > Welcome to the community@Anushka PahariaIf you have any issues/questions. Feel free to ask

Adeshile Oluwatosin (09:48:54) (in thread): > Will definitelyjoin:+1:

Peace Daniel (09:53:22) (in thread): > <@UBNSEMS3S>

Adeshile Oluwatosin (09:55:00) (in thread): > Seen this yet@Svetlana Ugarcina Perovicwhat do you think?

Chioma Onyido (09:57:38) (in thread): > We’re on

Svetlana Ugarcina Perovic (09:58:05) (in thread): > Ok, I will updated it, 2nd point you mean Antibiotics exclusion?

Adeshile Oluwatosin (09:59:57) (in thread): > The three points stated

Svetlana Ugarcina Perovic (10:00:40) (in thread): > Sorry I do not understand it: Also,**** alpha diversity**mention of curating “4 weeks” as 1 month, 8 weeks as 2 months etc. Should be mentioned.

Peace Daniel (10:01:52) (in thread): > Should be antibiotic exclusion

Adeshile Oluwatosin (10:02:10) (in thread): > Antibiotics exclusion I mean

Taofeecoh Adesanu (10:04:34) (in thread): > Welcome to the community@Anushka Paharia!

Peace Daniel (10:05:39) (in thread): > @Svetlana Ugarcina PerovicI thinkit’sbest to delete Experiment 2 based on what Chloe said, if the signatureshouldn’tbe curated and the sample size should be combined..What are your thoughts please?

Svetlana Ugarcina Perovic (10:13:06) (in thread): > Experiment 2 deleted.

Svetlana Ugarcina Perovic (10:13:20) (in thread): > Updated. Thanks!!

USLACKBOT (10:16:43): > svetlana_up made updates to a canvas tab:[canvas content]

Svetlana Ugarcina Perovic (10:41:18): > Stay strong@Chioma Onyido - File (PNG): Screenshot 2025-02-13 at 16.40.40.png

Svetlana Ugarcina Perovic (10:48:32) (in thread): > You are doing great!!!

Ndukauba Oluchi (11:24:32) (in thread): > @Anushka Pahariayou are welcome

Aleru Divine (12:15:39): > Good evening@Svetlana Ugarcina PerovicI’dlike to delete this study.I missed a number when entering the PMID.https://bugsigdb.org/Study_1294Thanks! - Attachment (BugSigDB): Differential inactivation of soluble reticulocyte transfer factors with N-ethylmaleimide - BugSigDB > .

Chioma Onyido (12:29:41) (in thread): > Thank youu Svet:face_holding_back_tears:

Chioma Onyido (12:30:06) (in thread): > Thank you all so much for showing up!

Chioma Onyido (12:31:00) (in thread): > @Mildred Anashie!:clap: - File (JPEG): IMG_0922

Anushka Paharia (15:01:48): > Hello@Svetlana Ugarcina Perovic, I went through the intro material. In the video tutorials //BiocManager :: install(“bugsigdbr”)// is mentioned, but it’s not working on my system. What might be the reason for that? Is that an old library?

Svetlana Ugarcina Perovic (15:06:06) (in thread): > deleted.

2025-02-14

Svetlana Ugarcina Perovic (02:34:46) (in thread): > Good morning, Anushka! For the Microbiome Study Curation Outreachy task you do not need anything to install. We do all curation inhttps://bugsigdb.org/Main_Pageplease seehttps://community-bioc.slack.com/canvas/C04RATV9VCY - Attachment (BugSigDB): Main Page > … - File (Canvas): Welcome material

Kate Rasheed (03:25:12): > Good morning<@UBNSEMS3S>. Thank you for yesterday’s office hour. I would be looking forward to the recording. > > For the article that uses centered-log ratio as the data transformation for DeSeq2, below is the PDF. > > Thank you so much - File (PDF): nyangahu2020 (1).pdf

Victoria (Burah) Poromon (04:01:13): > Hi everyone, Good morning. > So I am putting my recent curation up for peer review. > > Study link:https://bugsigdb.org/Study_1277GitHub link:https://github.com/waldronlab/BugSigDBcuration/issues/544Please leave your kind feedback/suggestions on GitHub.:pray:Thank you so much!:tulip: - Attachment (BugSigDB): Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet - BugSigDB > OBJECTIVES: The ketogenic diet (KD) is recommended to improve polycystic ovary syndrome (PCOS); however, its mechanisms of action are unclear. - Attachment: #544 Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet > Effect of the ketogenic diet on gut microbiome composition and metabolomics in polycystic ovarian syndrome rats induced by letrozole and a high-fat diet > > Link to study: https://www.sciencedirect.com/science/article/pii/S0899900723001569

Taofeecoh Adesanu (04:45:14) (in thread): > Hi@Anushka Paharia, if you’ve gone through the intro materials and still unclear, please send me a dm, I could hop on a call with you to help with onboarding.

UBNSEMS3S (10:51:07) (in thread): > I see the confusion. They specify that they used the CLR-transformation for some of the microbiome analysis: > > Due to the compositional nature of microbiome data, data were normalized by centred log-ratio (clr) prior to plotting the Euclidean distance, principal component analysis and alpha diversity plots. > Note that they do not say that they used CLR-transformation prior to DESeq2.

USLACKBOT (15:49:38): > svetlana_up made updates to a canvas tab:[canvas content]

Svetlana Ugarcina Perovic (16:01:16): > All accounts approved, all direct messages answered.If you have any questions, please post them in this channel so that all curators can participate in and benefit from the discussion.Plus, if the mentors are not available to answer you immediately, there’s a big chance that your answer could be answered by other community member/curator here since for example they already experienced the same issue, or we already discussed the issue etc.Have a nice weekend, all!

2025-02-15

Anushka Paharia (02:54:04): > For this article,https://www.nature.com/articles/s41551-024-01318-z#citeas, as the experiment is done on a replication of human gut, should the host species and body site be left blank or filled as homo sapiens, feces? - Attachment (Nature): A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma > Nature Biomedical Engineering - A gut-on-a-chip incorporating peristaltic-like movements and faecal samples from patients with melanoma recapitulates microbiome–host interactions and predicts…

Adeshile Oluwatosin (04:56:19) (in thread): > Hello@Anushka PahariaKindly curateThe host speciesasHomo sapiens and the Body site-feces. > Host species and body site should not be left blank.

2025-02-16

Svetlana Ugarcina Perovic (11:47:19) (in thread): > “Freshfaecal samples from**** patients**with melanoma were submitted for Shotgun metagenomic sequencing” thus: > host species: Homo sapiens > Body site: feces

Svetlana Ugarcina Perovic (12:13:06) (in thread): > @Adeshile Oluwatosinin our answers we try to be precise as much as we can. In this case, you left outthe reason why to “kindly curate…” and “should not be left blank.” Only that way, we could learn it and record it for the next time.

Adeshile Oluwatosin (12:14:12) (in thread): > Thank you Svetlana for pointing this out to me. > Duly noted@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (12:17:15) (in thread): > By the way@Anushka Pahariathis is an excellent question. When curating a study, we are focused on everything aroundsequencingdone in a study which can include other type of analysis, beside sequencing, other type of samples etc.

2025-02-17

Svetlana Ugarcina Perovic (06:38:58): > Happy Monday!While BugSigDB is under upgrading process, you could review already curated studies:make notes and your feedback in their corresponding github issue:https://github.com/waldronlab/BugSigDBcuration/labels/needs%20reviewThank you for your patience. - File (PNG): Screenshot 2025-02-17 at 12.36.27.png

Adeshile Oluwatosin (06:42:10) (in thread): > Happy Monday@Svetlana Ugarcina PerovicI tried reviewing studies but not all signatures are reflecting.I’vechecked andit’ssame across different studies. - File (JPEG): IMG_3606

Svetlana Ugarcina Perovic (06:45:24) (in thread): > “make notes and your feedback in their corresponding github issue” > I did not mention any editing :)

Adeshile Oluwatosin (06:47:14) (in thread): > I understand, I always look through the signatures as well while reviewing.

Svetlana Ugarcina Perovic (06:48:19) (in thread): > Since upgrading is ongoing, just make notes to the original curator what should be corrected and/or rechecked. Thanks!

Adeshile Oluwatosin (06:49:28) (in thread): > Okay, thank you

Svetlana Ugarcina Perovic (06:51:38) (in thread): > AND why! Do not forget to clarify why something should be corrected and/or rechecked.

Adeshile Oluwatosin (06:52:23) (in thread): > All points noted. > Thank you mentor

Samuel Nnanna (07:36:51) (in thread): > https://bugsigdb.org/Study_170Hello@Svetlana Ugarcina PerovicI need help with getting free access to the paper for the study above

Svetlana Ugarcina Perovic (07:38:24): > TWO microbiome events this weekOn Wednesday MVIF 36 with talks on the latest microbiome studies:https://www.microbiome-vif.org/en-USOn Thursday “MaAsLin 3 for Microbiome Statistics and Epidemiology” webinarhttps://www.linkedin.com/events/webinar-maaslin3formicrobiomest7291097714736427008/Curtis Huttenhowerwill talk about: > * the science behind MaAsLin 3 > * key features and real-world applications > * how it’ll empower microbiome research across disciplines

Svetlana Ugarcina Perovic (07:43:57) (in thread): > @Samuel NnannaHere you go: > Do not skip Supporting information! - File (PDF): liu2017.pdf

Samuel Nnanna (07:44:36) (in thread): > Thank you:pray:

2025-02-18

Juliana Kentomahun Mautin (05:59:14): > Good morning everyone, I’m excited to be here, looking forward to learn, connect and grow:heart_eyes::relaxed::heart_eyes:

Svetlana Ugarcina Perovic (05:59:39) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1739345190710579

Juliana Kentomahun Mautin (06:00:12) (in thread): > Thank you@Adeshile Oluwatosin@Taofeecoh Adesanu

Juliana Kentomahun Mautin (06:01:49) (in thread): > Thank you@Svetlana Ugarcina Perovic

Peace Daniel (06:24:59) (in thread): > Welcome@Juliana Kentomahun Mautin

Juliana Kentomahun Mautin (07:15:52) (in thread): > Thank you@Peace Daniel

Akriti (08:29:37) (in thread): > Hello mam

Akriti (08:30:27) (in thread): > I am trying to complete my task but it showing this > This wiki is currently being upgraded to using PMID as study page name. Meanwhile, it is in a read-only mode. Please check back in a couple of days. > > what is this mam and how can i solve it

Svetlana Ugarcina Perovic (08:32:16) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1739792338699759 - Attachment: Attachment > Happy Monday! > > While BugSigDB is under upgrading process, you could review already curated studies: make notes and your feedback in their corresponding github issue: https://github.com/waldronlab/BugSigDBcuration/labels/needs%20review > > Thank you for your patience.

Svetlana Ugarcina Perovic (08:32:51) (in thread): > @Akriti

Akriti (08:38:13) (in thread): > but mam i m working on it

Akriti (08:38:24) (in thread): > it’s not complete yet from my sire

Svetlana Ugarcina Perovic (08:41:25) (in thread): > @AkritiI understand that your curation is incomplete i.e. under curation. The suggestion above is directed to curations already completed by other curators that are awaiting for the review.

Akriti (08:43:18) (in thread): > yes mam curation part is compeleted and it’s showing need review but experiment section still incompleted

Akriti (08:43:28) (in thread): > I am asking for that

Svetlana Ugarcina Perovic (08:45:02) (in thread): > “Meanwhile, it is in**** a read-only mode**.” means we can not do any editing. Thank you for your patience.

Akriti (08:45:38) (in thread): > ok got it mam

Akriti (08:46:10) (in thread): > so should i need to pull it on github as it is

Svetlana Ugarcina Perovic (08:49:58) (in thread): > No, we are waiting for the bugsigdb platform to be back, on an edit mode. And finalize it when all is ready for use. > > While waiting, you could go over already curated and reviewed curation:https://github.com/waldronlab/BugSigDBcuration/issues?q=label%3Areviewed%20

Akriti (08:52:13) (in thread): > ok mam got it

Akriti (08:52:43) (in thread): > thank you for the help mam

Karima Diafi (10:29:52): > @Karima Diafi has left the channel

Svetlana Ugarcina Perovic (10:53:12) (in thread): > https://bugsigdb.org/Main_Pageis back and ready for your editing. - Attachment (BugSigDB): Main Page > .

Adeshile Oluwatosin (10:55:14) (in thread): > Great:blush:

Akriti (11:40:20) (in thread): > ok finally

Shahenda Soliman (21:14:55): > Good morning All, I’m happy to be among you:blush:I’m Shahenda Soliman from Egypt. I have submitted an initial application to Outreachy & I’m looking forward to learning, growing and giving back. > While I’m anxiously waiting for the initial application results, I wonder if there’s anything that I can do in the meantime to be (hopefully:face_holding_back_tears:) in this beautiful community. > My bachelor’s degree was in Microbiology so this project interests me a lot. In addition to me checking the pinned messages, I just need to be assured on somethings:point_down::star-struck:Should I be profitient in R/RStudio? > What skills should I prepare myself for in order to contribute to BugsigDB? I know some but I’m willing to know more please.:cherry_blossom:I’m open to any advice:hugging_face:

2025-02-19

Taofeecoh Adesanu (04:05:45) (in thread): > Hello@Shahenda Soliman! Welcome to the community, we are glad to have you. > Short answer to your question: No you do not need to be proficient in R/RStudio to contribute to BugSigDb.

Svetlana Ugarcina Perovic (04:06:08) (in thread): > Hi, Shahenda! Welcome to our community! > > First, to answer your question: NO, you do not need to be a pro in R. > > Second, please go through our Welcome material:https://community-bioc.slack.com/canvas/C04RATV9VCYFor any BugSigDB question we are here to help you and please do join our discussions. - File (Canvas): Welcome material

Svetlana Ugarcina Perovic (04:39:21): > A must read for today:https://www.biorxiv.org/content/10.1101/2025.02.13.638109v1 - Attachment (bioRxiv): Commonly used compositional data analysis implementations are not advantageous in microbial differential abundance analyses benchmarked against biological ground truth > Previous benchmarking of differential abundance (DA) analysis methods in microbiome studies have employed synthetic data, simulations, and “real data” examples, but to the best of our knowledge, none have yet employed experimental data with known “ground truth” differential abundance. A key debate in the field centers on whether compositional methods are necessary for DA analysis, which is challenging to answer due to the lack of ground truth data. To address this gap, we created the Bioconductor data package MicrobiomeBenchmarkData, featuring three microbiome datasets with established biological ground truths: 1) diverse oral microbiomes from supragingival and subgingival plaques, expected to favor aerobic and anaerobic bacteria, respectively, 2) low-diversity microbiomes from healthy vaginas and bacterial vaginosis, conditions that have been well-characterized through cell culture and microscopy, and 3) a spike-in dataset with constant, known absolute abundances of three bacteria. We benchmarked 17 DA approaches and demonstrated that compositional DA methods are not beneficial but rather lack sensitivity, show increased variability in constant-abundance spike-ins, and, most surprisingly, more frequently produce paradoxical results with DA in the wrong direction for the low-diversity microbiome. Conversely, commonly used methods in microbiome literature, such as LEfSe, the Wilcoxon test, and RNA-seq-derived methods, performed best. We conclude that researchers continue using widely adopted non-parametric or RNA-seq DA methods and that further development of compositional methods includes benchmarking against datasets with known biological ground truth. > > ### Competing Interest Statement > > The authors have declared no competing interest.

Taofeecoh Adesanu (05:02:14) (in thread): > Good morning@Svetlana Ugarcina Perovic, is theadd study pageback together with the main_page? > > From my end, it doesn’t look like it. - Attachment (BugSigDB): Special:FormEdit/Study - File (PNG): image.png

Svetlana Ugarcina Perovic (05:04:10): > TODAY:https://cassyni.com/s/mvif-36Our team will be supporting this event in various roles:@Victoria (Burah) Poromonwill handle the opening and Q&A moderation@Kate Rasheed, Victoria and I will manage the live social media coverage@Adeshile Oluwatosinwill provide technical support to ensure everything runs smoothly > > You’ll also have the opportunity to connect with<@UBNSEMS3S><@U1LCB8WEA>in the audience. > > See you at MVIF! - Attachment (Cassyni): MVIF 36 - with keynote talk by Prof. Ruixin Liu - Schedule of sessions · Cassyni > Microbiome Virtual International Forum (MVIF) is a recurring bite-sized alternative to multi-day microbiome conferences: Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference. > > Forum n. 36 is a Pacific-first event, with live talks starting 18th February 2025, 9:30 am Tokyo time (see what time it is where you are here and add to your calendar here). Professor Ruixin Liu will be the keynote speaker for this event. > > For Atlantic time zones, recorded talks with live hosting and discussion will start on 19th February at 8:30 am New York time (see what time and date it is where you are here and add to your calendar here). > > MVIF is a non-profit association registered in Italy > If you’d like to support MVIF, you can donate to our crowdfunding campaign . > > Thanks to our co-organizing non-commercial partners the Seerave Foundation and CUNY Graduate School of Public Health & Health Policy and our Gold Sponsor Roche for their support. > > Matanu!

Svetlana Ugarcina Perovic (05:05:48) (in thread): > It seems it is still under some kind of test. Let’s check with<@UBNSEMS3S>

Adeshile Oluwatosin (05:31:37) (in thread): > Welcome to the community@Shahenda Soliman

Adeshile Oluwatosin (05:34:27): > <@UBNSEMS3S>Could you please share the recording of last week’s meeting? Thank you so much

Anushka Paharia (06:19:32): > Hello everyone, Good Morning. I have curated my first study. > Study link:https://bugsigdb.org/39939548Github link:https://github.com/waldronlab/BugSigDBcuration/issues/591Please review it and provide feedback and suggestions, and also what I have done wrong, Thankyou so much! > Also, I added signature 2 as well, but its not displaying, why is that? - Attachment (BugSigDB): A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma - BugSigDB > Patient responses to immune checkpoint inhibitors can be influenced by the gastrointestinal microbiome. - Attachment: #591 A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma > A gut-on-a-chip incorporating human faecal samples and peristalsis predicts responses to immune checkpoint inhibitors for melanoma – Mattia Ballerini – Nature Biomedical Engineering
> https://www.nature.com/articles/s41551-024-01318-z

Anushka Paharia (06:25:38) (in thread): > Hello@Shahenda Soliman. Welcome!

Adeshile Oluwatosin (06:26:54) (in thread): > Hello@Anushka Pahariawell done,I will have a look.You could refresh your browser or check out signature 2 this way.https://bugsigdb.org/39939548/Experiment_1/Signature_2 - Attachment (BugSigDB): 39939548/Experiment 1/Signature 2 > Source: figure 6 a. Description: Taxa which were abundant in Responders but not in non-responders Abundance in Group 1: decreased abundance in Non-Responsive Patients…

Adeshile Oluwatosin (06:29:50) (in thread): > Itmight not be reflecting because of network.

Svetlana Ugarcina Perovic (07:57:28) (in thread): > And here is a nice summary thread by<@U1LCB8WEA>https://bsky.app/profile/leviwaldron1.bsky.social/post/3lijpoizsic2b - Attachment (bluesky): Attachment > Excited to share our MicrobiomeBenchmarkData preprint, addressing compositional data analysis for microbiome DA. This Bioconductor package features 3 datasets with biological ground truths. Spoiler: simple methods like LEfSe, Wilcoxon, RNA-seq methods performed well https://www.biorxiv.org/content/10.1101/2025.02.13.638109v1

Svetlana Ugarcina Perovic (08:32:31): > And we are LIVE!@Victoria (Burah) Poromon:sparkles: - File (PNG): Screenshot 2025-02-19 at 14.31.34.png

Svetlana Ugarcina Perovic (08:40:32): > You can join us herehttps://cassyni.com/s/mvif-36

Shahenda Soliman (22:53:16) (in thread): > @Svetlana Ugarcina PerovicNoted, thank you for the clarification:hugging_face::cherry_blossom:

Shahenda Soliman (22:53:51) (in thread): > @Taofeecoh AdesanuThank you:relaxed:

Shahenda Soliman (22:57:04) (in thread): > @Adeshile OluwatosinThnx:hugging_face:

Shahenda Soliman (22:57:46) (in thread): > @Anushka PahariaThnx:relaxed:

2025-02-20

Anushka Paharia (02:23:37) (in thread): > Thankyou! Do you have any feedback?

Adeshile Oluwatosin (02:53:50) (in thread): > Give me some minutes,I’llcomment on GitHub

Svetlana Ugarcina Perovic (03:22:37): > :teapot:Good morningReminder for our weekly team meeting:TODAY at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions!

Svetlana Ugarcina Perovic (03:51:17): > :clap:SHOUT-OUT to@Taofeecoh Adesanuand@Yoko Cfor their ongoing curation:https://github.com/waldronlab/BugSigDBcuration/issues/573 - Attachment: #573 Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status > Subgingival microbiota dysbiosis in systemic lupus erythematosus: association with periodontal status – Jôice Dias Corrêa – Microbiome > https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0252-z

Ndukauba Oluchi (04:04:21) (in thread): > Welcome:hugging_face:@Shahenda Soliman

Mildred Anashie (04:40:51) (in thread): > Hi@Svetlana Ugarcina PerovicI’m encountering the same issue as@Taofeecoh Adesanu

Svetlana Ugarcina Perovic (06:56:00) (in thread): > Let’s check with<@UBNSEMS3S>today at the team meeting.

Ndukauba Oluchi (07:32:59): > Hello everyone:wave:. I need some help here please. > I keep seeing this prompt even after adding a study manually, please what could be the cause? > Cc:@Svetlana Ugarcina Perovic - File (PNG): page prompt.png

Svetlana Ugarcina Perovic (07:36:26) (in thread): > There is a notification under “PMID”:Page Forms permissions test

Svetlana Ugarcina Perovic (07:37:00) (in thread): > Others reported the same issuehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1739959334940549?thread_ts=1739792338.699759&cid=C04RATV9VCY - Attachment: Attachment > Good morning @Svetlana Ugarcina Perovic, is the add study page back together with the main_page? > > From my end, it doesn’t look like it.

Svetlana Ugarcina Perovic (07:37:54) (in thread): > Let’s check with<@UBNSEMS3S>today at the team meeting when the platform will be fully back in function.

USLACKBOT (07:38:47): > svetlana_up made updates to a canvas tab:[canvas content]

Ndukauba Oluchi (07:39:12) (in thread): > Oh:thinking_face:. > Thank you for this clarification.

Svetlana Ugarcina Perovic (07:40:32) (in thread): > Lately some updates were made, for example we now have instead of the study number**** the PMID**. > > Try to open this one to see the change in linkhttps://bugsigdb.org/Study_1281 - Attachment (BugSigDB): Expanding the human gut microbiome atlas of Africa - BugSigDB > Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors.

Ndukauba Oluchi (07:42:15) (in thread): > Alright. > Thank you

U1LCB8WEA (08:04:51) (in thread): > Thanks Svetlana!

Mildred Anashie (09:20:39) (in thread): > Hi@Svetlana Ugarcina PerovicI’vebeen in the waiting room,I’mwondering if the meetinghasn’tstarted yet

Adeshile Oluwatosin (09:24:17) (in thread): > I’vegiven a review on GitHub@Anushka Paharia

Mildred Anashie (09:26:41) (in thread): > Ijust figured it’s my connection

UBNSEMS3S (10:19:53): > Last week’s recording of office hours. I forgot to record today.:woman-facepalming: - File (MPEG 4 Video): bsdb 2025_02_13.mp4

Adeshile Oluwatosin (10:20:38) (in thread): > Thank you:pray:It’sfine, it happens:tulip:

UBNSEMS3S (14:55:30): > Decision trees/xgboost/gradient boosting is now an option for statistical tests.

Shahenda Soliman (17:01:38) (in thread): > @Ndukauba OluchiThanks:hugging_face:

Adeshile Oluwatosin (20:09:29) (in thread): > Noted

2025-02-21

Joy (03:10:36) (in thread): > :dancer::dancer::dancer:that’s good to know. Thank you<@UBNSEMS3S>

Ndukauba Oluchi (03:39:28) (in thread): > Thank you<@UBNSEMS3S>

Anushka Paharia (05:27:59) (in thread): > So can we not curate new studies till this is resolved? (This error still persists)

Akriti (06:45:15) (in thread): > Hello@Svetlana Ugarcina Perovicmam , u assigned me a issue i have completed my task now what should my next step

Akriti (06:45:36) (in thread): > like should i make a pull request

Adeshile Oluwatosin (06:53:25) (in thread): > Hello@AkritiThe next step is todrop a comment on github putting it up for review. > There is no need to make a pull request.

Adeshile Oluwatosin (06:55:02) (in thread): > You can send a link to your article so I send the direct link where you can drop a comment. Tag Svetlana and say Something simple as “This article is ready for review.”

Mildred Anashie (06:55:37) (in thread): > Yea@AkritiJust like@Adeshile Oluwatosinhas said > > You just need to drop a comment on the issue with the link to the study you curated, stating it is ready for a review and you await feedback on the curation

Akriti (06:57:44) (in thread): > thankyou@Adeshile Oluwatosin@Mildred Anashiefor helping me

Akriti (06:57:54) (in thread): > but still i have doubt

Akriti (06:58:38) (in thread): > Do we have a hurdle I just wanna a clearification from someone who have enough knowledge about it

Mildred Anashie (07:00:02) (in thread): > You can also post the link to the curation here on slack and request peer review before asking for a review on GitHubI’mpositive fellow contributors would give it a look and share their thoughts on it

Akriti (08:08:42) (in thread): > yeah ok

Akriti (08:08:48) (in thread): > thank you

Adeshile Oluwatosin (08:59:12) (in thread): > @Akritiis there any other thing bothering you? > You are free to ask questions

Ndukauba Oluchi (09:19:55) (in thread): > Yes@Anushka PahariaI believe so. > But you can review studies and even add studies to the GitHub issues while waiting for the issue to be resolved.

Ndukauba Oluchi (09:20:51) (in thread): > Oops:face_with_peeking_eye:

UBNSEMS3S (09:36:59): > I am continuing to ask our developer to fix the issue where you can’t create studies on BugSigDB. As of right now, I haven’t received a response yet. I will let you all know the moment I hear back from them.

Akriti (11:15:51) (in thread): > yeah actually I have completed it from my side still confused wheather my work is fine or not

Akriti (11:15:53) (in thread): > :slightly_smiling_face:

Adeshile Oluwatosin (11:26:48) (in thread): > You can send a link to your curation here on slack for peer review.

Adeshile Oluwatosin (11:27:15) (in thread): > There’snothing to be worried about

Akriti (11:30:02) (in thread): > https://bugsigdb.org/39813205If there is any mistake or anything missing please let me know - Attachment (BugSigDB): Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study - BugSigDB > Behavioral dysfunctions in dogs represent one of the main social concerns, since they can endanger animals and human-dog relationship.

Adeshile Oluwatosin (11:36:54) (in thread): > Okay, noted

Adeshile Oluwatosin (11:37:41) (in thread): > Send it on the main channel to start a new thread

Adeshile Oluwatosin (11:41:05) (in thread): > @Akriti

Akriti (12:09:15) (in thread): > it is ok?

Akriti (12:09:32) (in thread): > did you see it

Adeshile Oluwatosin (12:13:45) (in thread): > I am writing out the corrections, can you kindly drop the link on the main channel or would you prefer I send the review on github@Akriti

Taofeecoh Adesanu (15:12:37) (in thread): > The issue has been fixed. > A slightly different interface, but it seems to work now. I confirmed some moments ago:slightly_smiling_face:. > > Thank you!

2025-02-22

Svetlana Ugarcina Perovic (02:35:21) (in thread): > Great curation and review@Akriti@Adeshile Oluwatosinteam up to finalize it! Have a nice weekend! - Attachment: #555 Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study > Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study – Luigi Sacchettino – PlosOne
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315374

Akriti (03:31:08) (in thread): > thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (04:28:21) (in thread): > Alright, noted

Akriti (08:14:23) (in thread): > SvetlanaUPassignedTheTosinwhy?

Akriti (08:15:02) (in thread): > I am not getting what is it I was working on it but u assigne it someone else mam

Akriti (08:15:06) (in thread): > why?

Svetlana Ugarcina Perovic (10:55:55) (in thread): > @AkritiI believe you’re refering tohttps://github.com/waldronlab/BugSigDBcuration/issues/555? > > You were assigned as an original curator and@Adeshile Oluwatosinwas assigned as a reviewer because Tosin provided a thorough feedback on your curation.Each curation has at least one original curator and at least one reviewer. Both have the same goal: to finalize a curation, as a team! No worries, ALL your efforts have been recorded herehttps://bugsigdb.org/Special:Contributions/Akritishakya(this is visible for every curator and reviewer) > > Keep up the good work! - Attachment (BugSigDB): Special:Contributions/Akritishakya - Attachment: #555 Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study > Altered microbiome and metabolome profiling in fearful companion dogs: An exploratory study – Luigi Sacchettino – PlosOne
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0315374

Svetlana Ugarcina Perovic (10:57:33) (in thread): > Next step:@Akritidoes corrections based on@Adeshile Oluwatosin’s feedback.

Karima Diafi (17:32:34): > Hello, I hope you’re having a great weekend. I have a quick question:If thep-valuefor thespearman correlationbetween microbiota and disease characteristics isborderline, should I still curate it as part of a potential signature, or should I exclude it? - File (PNG): image.png

2025-02-23

Adeshile Oluwatosin (02:21:49) (in thread): > Hello@Karima DiafiWe do not curate spearman correlation. > We curate significant differential abundance between a case and a control. > In situations where the p value is above the significant threshold for differential abundance, such signature(s) should be excluded.

Karima Diafi (06:28:56) (in thread): > Thank you@Adeshile Oluwatosin! I thought that the correlation provides insights about the abundance. Noted then.@Svetlana Ugarcina Peroviccould you kindly remove experiments 5 to 7? Thank you!

Mildred Anashie (08:41:33) (in thread): > Hi@Adeshile OluwatosinI have seen a few curations with spearman correlation as the statistical test because of what was being contrasted (e.ghttps://bugsigdb.org/36253847/Experiment_16), so I’m thinking@Karima Diaficould share a link to the study or figure/table that’s being referred to - Attachment (BugSigDB): 36253847/Experiment 16 > .

Anushka Paharia (10:53:08): > Hello everyone! I have put a study up for review > study link ->https://bugsigdb.org/38551926github link ->https://github.com/waldronlab/BugSigDBcuration/issues/599 - Attachment (BugSigDB): Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia - BugSigDB > The role of the gut microbiota in energy metabolism of the host has been established, both in overweight/obesity, as well as in undernutrition/stunting.Dysbiosis of the gut microbiota may predispose to stunting. - Attachment: #599 Gut microbiota differences in stunted and normal-lenght children aged 36–45 months in East Nusa Tenggara, Indonesia > Gut microbiota differences in stunted and normal-lenght children aged 36–45 months in East Nusa Tenggara, Indonesia – Ingrid S. Surono – PlosOne
> https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0299349

Anushka Paharia (10:54:04) (in thread): > In this study, there should be one signature for increased abundance only, right?

Karima Diafi (13:47:50) (in thread): > Sure, here is the link to the study:https://doi.org/10.1186/s41983-021-00407-z. I am referring to Table 3 where they perform the correlation between copy number of 5 gut microbiota and Parkinson’s disease characteristics & Table 4 where they study the correlation between the same 5 microbiota and the risk factors. - Attachment (SpringerOpen): Gut microbiota in Parkinson’s disease patients: hospital-based study - The Egyptian Journal of Neurology, Psychiatry and Neurosurgery

Ndukauba Oluchi (15:11:34) (in thread): > Hello@Anushka Pahariayou have done well, will take a look at it.

Yoko C (17:45:45) (in thread): > Hello, I agree with@Mildred Anashiethat Spearman correlations could be curated. I think the tricky part might be the rho value more than marginally significant p values. If the paper doesn’t specify what rho value they consider meaningful, it’s hard to tell if 0.30 is considered weak or moderate strength (or at least I wouldn’t know how to). In this case, I think you can curate the table because the copy number reflects abundance, and for curation purposes don’t worry if p is marginally significant or not, just include bacteria with p < 0.05. Looking forward to others’ input, as I’m not 100% sure.

Mildred Anashie (18:02:10) (in thread): > Hi@Anushka PahariaWell done on your curation,I’lltake a proper look at it but concerning the question on the signature…..We curate both increased and decreased abundance, so you’d curate increased abundance in your Group 1 (The taxa increased in the stunted children) as signature 1 and increased abundance of Group 0 (The taxa increased in the normal children) as signature 2 (This would be your decreased abundance. > > Still looking through but I believeit’sa cross sectional not case control study rather than a case control study, and I see other comparisonsI’mstill trying to figure out. > > PS:@Adeshile Oluwatosintake a look at this, it looks like spearman was used for majority of the contrasts in this study and they appear curatable.

Adeshile Oluwatosin (18:04:31) (in thread): > Okay, let me have a proper look at this study@Mildred Anashie

Adeshile Oluwatosin (18:10:57) (in thread): > Hello@Mildred Anashiein the instance of thestudy shared, there were significant differences hence the curation. I agree

Adeshile Oluwatosin (18:28:58) (in thread): > @Karima DiafiI looked through the study. > * Table 2: There are 4 comparisons, so four different experiments. Kindly curate only taxa within 0.05 thre’shold. You can take a look at the write up specific to Table 2. Mann-Whitney test > see “we used the Mann–Whitney test to compare the two groups with each other”. > * Table 3 (only bifidobacterium) is significant between non-pesticide exposed (Group 0) and pesticide exposed (Group 1) which should be curated as increased abundance of Group 1. No decreased abundance. Spearman correlation. > “There were significant associations between pesticide exposure and Bifidobacterium (P = 0.002) as PD patients who had been exposed to pesticide had a lower level of Bifidobacterium than non-pesticide exposed patients (Table 3)”. > * Table 4 is also curatable, Go through the write up in the article specific to Table 4. Spearman correlation (test) > > * Table 6 (only Akkermansia) is significant between non-constipating (Group 0) and constipating patients (Group 1) which is an increased abundance in constipating patients. No decreased abundance. Mann Whitney test. > “there was a significantly higher copy number of Akkermansia in constipating patients than patients without constipation with no significant diff in other gut Microbiota”. > * Antibiotics exclusion is 3 months : “we excluded patients who had taken antibiotics or probiotic supplements for the 3 months prior to taking samples”. > > * The significant threshold is 0.05, > So to answer your initial question, I suggest using the P values in curating. 0.308 and 0.056 is above the threshold (Hence should not be curated).****“Non-parametric Spearman correlations between the copy number of each microbiome and different clinical scales were performed. A P-value < 0.05 was regarded as statistically significant” > **** > * It is a case control study andmatched on factors is “age and sex” : This case–control study included 46 patients diagnosed as Parkinson’s disease (PD) and 31 healthy volunteers age and sex matched.

2025-02-24

Anushka Paharia (00:41:44) (in thread): > @Mildred Anashieyes, but as u said all comparisons were spearmen correlation and there was nothing about decreased abundance. So I’m not clear what I should do in that case.

Peace Daniel (00:42:14) (in thread): > I agree, it is a cross sectional study@Mildred Anashie@Anushka Pahariaplease read this in your methods > “ > A cross-sectional study was conducted in children aged 3–5 years old with stunting (n = 100) and those without stunting (n = 100), at two locations:” > > Also, am I the only one seeing just one experiment and signature?

Anushka Paharia (00:44:03) (in thread): > Yes, you are right. I don’t know how I missed that. thankyou@Peace Daniel

Peace Daniel (00:48:27) (in thread): > Alpha diversity reports significance for faith and Shannon

Anushka Paharia (00:51:20) (in thread): > @Peace DanielI thought shannon was not statistically strong enough to be conclusive, unless I’m missing something can you clarify?

Peace Daniel (00:57:54) (in thread): > I believe table 3 is curatable@Anushka PahariaWith respect to α-diversity, the Shannon- and Faith’s phylogenetic diversity (PD-)indices were different between stunted children and non-stunted children (q = 0.084 and 0.0072, respectively). Evenness (q = 0.245) and observed_features (q = 0.056; which is called observed_OTUs in QIIME2, but measures ASVs) were not significantly different > > Would also like to know why you read decreased for both

Peace Daniel (00:58:43) (in thread): > Can you quote this part you’re referring to@Anushka Paharia? > > > You might need to check if it was age matched again as Ididn’tsee that

Adeshile Oluwatosin (01:07:53) (in thread): > @Anushka PahariaTo add to what@Mildred Anashiesaid. > > It’s a cross sectional study. Age is not a matched on factor. > THESE ARE THE FIGURES/TABLES TO CURATE: > > Table 3: only Bacteroidetes and Cyanobacteria are significant and should both be curated as increased abundance in stunted children. MHT (no) > See “Of these Bacteroidetes were significantly higher in stunted children (23.9% ± 10.8% vs 20.0% ± 11.1%). Also Cyanobacteria (with overall very low abundance and prevalence) were significantly higher in stunted children (0.32% ± 0.70% vs. 0.17% ± 0.28%)”. EXP 1 > > Figure 4; Kruskal Wallis test, MHT (Yes), Lachnoclostridium, Faecalibacterium and veillonella should first be curated as increased abundance in stunted children in EXP 2. Third experiment with normal length children in Kujang (Group 0) and stunted children in kujang (Group 1), fourth experiment do same but in North Kodi. > > Figure 6A and 6B : Test (spearman correlation), MHT (Yes), 7 experiments with different comparisons here (Height, Weight, BMI, Zlen, ZBMI, Zwei, and ZWFL). Group 0( low body mass Index), Group 1(High Body Mass index) … do the same for the rests. > See “Blue: Positive correlation (increased abundance); red: Negative correlation (decreased abundance)” > > Figure 7A; Test (spearman correlation), MHT (Yes), Green (increased abundance), purple (decreased abundance). 3 experiments asides Type of toilet. > e.g Group 0 (low correlation to waste water disposal facility), Group 1 (High correlation to waste water disposal facility). > > NB: sample size in Exp 1, 2 is a total of kujang/North kodi > Sample size in Exp 3, 4, is specific to Kujang/North kodi. > Also have a look at the taxa with “” as this indicates significance. > > FOR ALPHA DIVERSITY: > Shannon, Faith, evenness (pielou) and observed (Richness) > Curate specific to the comparisons as seen in Table 4. > If the comparison isn’t mentioned, kindly leave blank > The significant values are extremely dark in the Table. > > If you have any questions, feel free to ask

Adeshile Oluwatosin (01:28:20) (in thread): > @Peace Danielif you look at Table 4, the write up for alpha diversity was just specific to the first line of comparison Hence the statement. Evenness and observed are still significant for other comparisons.

Peace Daniel (01:32:25) (in thread): > Yes I know that, I wrote based on what she have curated which I observed@Adeshile Oluwatosin

Peace Daniel (01:33:21) (in thread): > Also, I don’t think fig 5 is curatable and some* of those ones you listed@Adeshile OluwatosinFig 5 is literally a map, they’re comparing two studies which they did…look at it again

Peace Daniel (01:36:21) (in thread): > Figure 5isn’ta heat map

Adeshile Oluwatosin (01:40:00) (in thread): > In figure 5, if you read through the write up you should understand better. Also in the figure, you would see the taxa mentionedexcluding “other” as insignificant.This was also mentioned“Of the 133 taxa in the combined dataset, 87 were signficiantly different between the two regions (q < 0.05). for the three most prevalent taxa in this figure the q-values are Prevotella 9 6.0 * 10−22, Faecalibacterium: 5.8 * 10−4, Escherichia/ Shigella: 3.1 * 10−22”.

Peace Daniel (01:52:24) (in thread): > So, what’s the comparison in fig 5? > > I don’t think fig 7, 8 should be curated either but if there’s something like that pls point to it

Kate Rasheed (04:11:46) (in thread): > Okay. Thank you so much for this.

Svetlana Ugarcina Perovic (05:48:14) (in thread): > @Karima Diafihttps://github.com/waldronlab/BugSigDBcuration/issues/561#issuecomment-2678044194 - Attachment: Comment on #561 Gut microbiota in Parkinson’s disease patients: hospital-based study > Hi @Ka-di1 please when requesting deletion make comments in the corresponding issue. Thanks! > Experiments 5, 6, 7 deleted.

Yoko C (06:08:47) (in thread): > Hello@Anushka Paharia, I think the way you curated table 4 is good, sometimes there isn’t both increasing and decreasing signatures. I would check the transformation, since I don’t see it was mentioned. I would include Shannon, since in the table it’s 0.0082 and in the text mentioned with Faith as different. For the other tables or graphs, table 3 seems to be prevalence, so it’s not curatable. For the Spearman correlations, I have seen curations that include them, and they seem to be curatable. But if I think about it, I’m not sure what the two contrasting groups would be. For example for 6a, for weight, would the groups be “higher weight”, “lower weight”?

Karima Diafi (06:10:58) (in thread): > Hi@Svetlana Ugarcina Perovic, I noticed some discussions here about signature deletion, so I assumed it was allowed. But I understand now, and I’ll report it on the corresponding issue—thank you for the clarification.

Svetlana Ugarcina Perovic (06:12:13) (in thread): > No problem@Karima Diafijust keep the activity records in one issue and this will avoid any confusion.

Karima Diafi (06:12:56) (in thread): > well noted:writing_hand:

Karima Diafi (06:16:07) (in thread): > Thank you for your help@Yoko C@Adeshile Oluwatosin@Mildred Anashie

Anushka Paharia (06:17:25) (in thread): > @Yoko Cso I should not curate the spearmen correlation tables yet right? > My doubt remains with figure 5.

Yoko C (06:29:25) (in thread): > The caption for figure 5 says “for the three most prevalent taxa in this figure theq-values …” so that tells you it’s prevalence, which as far as I understand isn’t curatable.

Yoko C (06:37:32) (in thread): > For Spearman, I am really not sure, but because they don’t specify if they are comparing abundance or have any other info, I think these wouldn’t be curatable.

Adeshile Oluwatosin (06:37:39) (in thread): > @Anushka PahariaYou can exclude Figure 5.Having another look once again…it should be omitted

Karima Diafi (06:40:28) (in thread): > I really appreciate the time you took to take a look on the study@Adeshile Oluwatosin, I curated these information earlier under this study:https://bugsigdb.org/Study_1272, since I previously requested the experiments removal, I need to add them back and curateTable 6that I skipped earlier thinking that its information is redundant with theTable 4. Thanks again! - Attachment (BugSigDB): Gut microbiota in Parkinson’s disease patients: hospital-based study - BugSigDB > Background > > Parkinson’s disease (PD) is one of the most common neurodegenerative diseases.There is accumulating evidence that link gut microbiota to symptomatology and pathophysiology of PD.

Adeshile Oluwatosin (06:46:22) (in thread): > @Yoko CI already suggested the group names. > But you can have a look at this study, it also gave me clarity as well towards the curations of such tables/figures.https://bugsigdb.org/26230509 - Attachment (BugSigDB): Obesity Alters the Microbial Community Profile in Korean Adolescents - BugSigDB > Obesity is an increasing public health concern worldwide.According to the latest Organization for Economic Co-operation and Development (OECD) report (2014), the incidence of child obesity in Korea has exceeded the OECD average.

Yoko C (06:48:00) (in thread): > Oh, and I think that if you want a general review you first post it here, then when you are ready for the “official” review, you request it on Github.

Adeshile Oluwatosin (06:48:02) (in thread): > You are welcome > Yes, please ask for restoration of the experiments@Karima Diafi

Adeshile Oluwatosin (06:54:51) (in thread): > Thanks:thumbsup:@Peace Daniel@Yoko C

Karima Diafi (06:55:19) (in thread): > @Adeshile OluwatosinWow, I’m glad to know that restoring information is possible—Thanks:innocent:

Adeshile Oluwatosin (06:55:59) (in thread): > Kindly tag Svetlana on Github requesting for restoration.

Karima Diafi (06:56:36) (in thread): > Done:+1:

Adeshile Oluwatosin (06:58:08) (in thread): > @Anushka PahariaOnce a study has the “needs review” tag, corrections are not meant to be made anymore till a reviewer drops a comment or corrections.

Yoko C (06:59:01) (in thread): > @Adeshile Oluwatosinthank you, the remaining doubt I have is if these are comparing abundance I don’t see that mentioned? And you mention MHT correction, which I don’t think is applied for Spearman correlations.

Adeshile Oluwatosin (07:04:22) (in thread): > @Yoko CWell, maybe we can confirm from Chloe at the office hour.

Adeshile Oluwatosin (07:06:00) (in thread): > I have a few doubts but there is mention of significant taxa correlated with (q value <0.05). Hence, my initial conclusion

Svetlana Ugarcina Perovic (07:57:03) (in thread): > @Karima Diafiplease be more precise in your GitHub communication. I have to go back here to see and recheck what to restore exactly. Experiments 5, 6, 7 have been undeleted.

Peace Daniel (07:58:30) (in thread): > Why do you say table 3 is prevalence@Yoko CSurely not this I hope bcz it’s literal English to me ? > > “Both Actinobacteria (Actinomycetota) and Verrucomicrobia (Verrucomicrobiota) were present at low prevalence. “

Svetlana Ugarcina Perovic (08:03:12) (in thread): > “I would appreciate it if the information could be restored.” -> “I would appreciate it if theExperiments 5, 6, 7could be restored.”

Svetlana Ugarcina Perovic (08:03:25) (in thread): > Thanks!

Ndukauba Oluchi (09:44:48): > hello everyone, how are we doing? please i have a question > recently bugsigdb add study page has been changed, you have to input a study’s PMID number before you can add the study. > Now here’s my concern, the study i am curating seems to be a recent study and it doesn’t have any PMID assigned to it yet, PLEASE what do i do in this case? > here’s the link to the paper:https://www.mdpi.com/1422-0067/24/11/9533Cc:@Svetlana Ugarcina Perovic - Attachment (MDPI): Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes > T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.

Svetlana Ugarcina Perovic (09:47:37) (in thread): > That can happen, no worries.You can instead enter a DOI or URL to identify the source: note those other identifiers are only needed if there is not a PMID, otherwise PMID alone is enough.

Svetlana Ugarcina Perovic (09:48:22) (in thread): > https://pubmed.ncbi.nlm.nih.gov/37298483/ - Attachment (PubMed): Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes - PubMed > T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial compositio …

Ndukauba Oluchi (09:48:24) (in thread): > Alright! thank you

Svetlana Ugarcina Perovic (09:48:40) (in thread): > @Ndukauba Oluchithere is PMID for your study… see above!

Ndukauba Oluchi (09:49:15) (in thread): > ohhh! thank you so much:hugging_face:

Yoko C (10:18:02) (in thread): > @Peace Daniel, the paragraph is describing what phyla were present in the samples. This part “After filtering for those that were present in at least 20% of the samples, 10 phyla remained (Table 3).” describes table 3. And the table is described as composition rather than differential abundance.

Peace Daniel (10:22:03) (in thread): > Alright, a confirmation is best

Ndukauba Oluchi (12:39:11): > hello everyone. please when curating for alpha diversity, what is equivalent to ACE? because i can’t find it there. > Cc:@Svetlana Ugarcina Perovic

Aleru Divine (12:43:04) (in thread): > Here@Ndukauba Oluchihttps://community-bioc.slack.com/archives/C04RATV9VCY/p1704800731587329?thread_ts=1704795243.428709&channel=C04RATV9VCY&message_ts=1704800731.587329 - Attachment: Attachment > @UBNSEMS3S once mentioned during a meeting that you can curate ACE results as richness

Ndukauba Oluchi (12:43:57) (in thread): > Alright, confirmed. i wanted to be sure > thank you

Karima Diafi (13:24:55) (in thread): > @Svetlana Ugarcina PerovicI’ll be clearer next time, Thanks for your help!

Mildred Anashie (15:19:06): > Hi everyone, I’m currently working on curating thispaperand I have a bit of concern.1. The condition in the paper is Bovine Metritis, I couldn’t find this on Bugsigdb so I went with “Uterine inflammatory disease’. Is this a suitable fit?@Svetlana Ugarcina PerovicI’m also wondering if “Bovine metritis” can be added?:thinking_face:2. There is no clear antibiotic exclusionandthe groups were later stratified based on antimicrobial treatment (MET_Treatment and MET_no Treatment) the no treatment group was recruited based on “Not taking antibiotics within 14 days” can I consider this to beantibioticexclusion?3.I’mcurating Fig6 and Table S3 but I’m in doubt if I shouldcontinuebecause the paper stated that the experiments were done to determine if the genera identified in other studies were also identified in this study.Thank you in anticipation for your responses:blush: - Attachment (PubMed Central (PMC)): Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome > The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine …

Peace Daniel (16:06:08) (in thread): > I think uterine inflammatory disease is fine > I read through in your methods, it says antimicrobial treatment and not specifically antibiotics so I suggest leaving exclusion blank

2025-02-25

Kate Rasheed (02:34:05): > Good morning everyone. Happy Tuesday:sparkles:. > > Thispapersays that Table S5 was computed with Songbird. I would like to find out how to curate Songbird in BugSigDB. > > I would also like to find out if supplementary image 2 of thisarticleis curatable. > > Thank you so much. - Attachment (Frontiers): Frontiers | Altered Actinobacteria and Firmicutes Phylum Associated Epitopes in Patients With Parkinson’s Disease > Recent evidence suggests that inflammation was participated in the pathogenesis of PD, thus, to understand the potential mechanism of gut microbiota in the p…

Kate Rasheed (03:45:19) (in thread): > Good morning@Mildred Anashie. I believe Figure 6 and Table S3 are curatable because there is significant result for it and the experiment was carried out on the samples for this study. > > See this: “To determine whether genera often associated with metritis or uterine health by other studieswere differentially abundant within our sample population, a heat map was created in Fig. 6 to analyze natural LFC in the abundance of MET_No_Treatment and MET_Treatment compared to CT for 31 selected genera. None of the selected genera were significantly changed in natural LFC abundance for Pus when compared to CT.”

Mildred Anashie (05:51:06) (in thread): > Okay then > > Thank you@Peace Daniel@Kate Rasheed:pray:

Svetlana Ugarcina Perovic (08:00:55) (in thread): > Check outhttps://github.com/biocore/songbirdand the paper cited.

Svetlana Ugarcina Perovic (08:04:56) (in thread): > As for Fig S2, I do not see its caption, but also I do not see “significance”. - File (TIFF): Image 2.TIF

Svetlana Ugarcina Perovic (08:05:47) (in thread): > and it’s about bacterial numbers…

Kate Rasheed (08:57:08) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Taofeecoh Adesanu (10:11:57): > Hello everyone. > I’m having trouble curating the taxa in thisstudy’s supplementary file: image below. I’m confused on what column (median diff, mean diff, log 2 median ratio) to use in identifying the up/down abundant taxonomy. > > Thank you so much. - Attachment (BioMed Central): Fecal microbiota transplantation modulates jejunal host-microbiota interface in weanling piglets - Microbiome > Background Weaning-associated enteric diseases are a major concern in the swine industry. This study investigates the effects of fecal microbiota transplantation (FMT) on the jejunum of weanling piglets, a segment of bowel less studied in terms of microbiomic changes despite its primary involvement in major post-weaning enteric diseases, including postweaning diarrhea (PWD). Thirty-two 3-week-old piglets were divided equally into two groups: Control and FMT. The FMT group received fecal microbiota preparation from 3-month-old healthy pigs on the 1st and 3rd day after weaning. Half of each group was inoculated with an enterotoxigenic E. coli (ETEC) isolate 10 days post-FMT. Piglets were euthanized in the third week (14th and 18th days post-FMT) after weaning to collect intestinal tissues and contents for microbiomic, metabolomic, and transcriptomic analyses. Results The jejunal microbiota showed a significant increase in alpha diversity in the third week post-FMT compared with the ileum and colon. FMT significantly enriched the jejunal microbiota composition, while multiple bacterial genera were specifically lacking in control weanling piglets. FMT was strongly associated with the enrichment of the genus Pseudoscardovia of the Bifidobacteriaceae family, which was found lacking in the jejunum of weanling control piglets and inversely associated with the abundance of the genus Bifidobacterium within the same family. Other genera associated with FMT included Solobacterium, Shuttleworthia, and Pseudoraminibacter, whereas bacteria such as Erysipelotrichaceae and Acidaminococcus were identified as most abundant in the control piglets. Metabolomic analysis revealed a significant modulatory effect of FMT on carbohydrate, amino acid, nucleotide, vitamin, and xenobiotic metabolisms, suggesting improved nutrient utilization. Transcriptomic analyses further confirmed the regulatory effects of FMT on gene expression associated with immune, metabolic, barrier, and neuroendocrine functions. Prior FMT treatment in the context of ETEC infection indicated a potential protective role, as evidenced by a significant shift in microbial diversity and metabolomic compositions and decreased diarrhea severity even though no effect on pathogen shedding was evident. Conclusions This study underscores the promise of FMT in enhancing jejunal health. In addition, the results suggest that FMT could be considered a potential strategy to address conditions associated with small intestinal dysbiosis in swine and other monogastric species with similar gut anatomy and physiology, such as humans. Video Abstract - File (PNG): image.png

UBNSEMS3S (10:37:26): > Median diff where positive means increased in cases relative to controls and negative means decreased in cases relative to controls.

Taofeecoh Adesanu (10:47:31): > Thank you so much<@UBNSEMS3S>

Mildred Anashie (15:21:40): > Hi@Svetlana Ugarcina PerovicPlease delete Experiment 5 signature 2 in thisstudy. Thank you:pray:

2025-02-26

Svetlana Ugarcina Perovic (01:50:06) (in thread): > https://bugsigdb.org/37986012/Experiment_5/Signature_2deleted.

Mildred Anashie (07:11:56) (in thread): > Thank you

2025-02-27

Svetlana Ugarcina Perovic (03:49:18): > :teapot:/:coffee:Good morningReminder for our weekly team meeting:TODAY at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions!

Svetlana Ugarcina Perovic (03:51:54): > ****?**** - File (PNG): Screenshot 2025-02-27 at 09.50.30.png

Adeshile Oluwatosin (03:52:27) (in thread): > Tea today:wink:

Svetlana Ugarcina Perovic (03:58:33): > @Kate Rasheedis working ona selection of whole genome metagenomic studies on Parkinson’s disease::white_check_mark:https://github.com/waldronlab/BugSigDBcuration/issues/600assigned to@Kate Rasheedand@Aleru Divine:white_check_mark:https://github.com/waldronlab/BugSigDBcuration/issues/601assigned to@Kate Rasheedand@Aleru Divine:white_check_mark:https://github.com/waldronlab/BugSigDBcuration/issues/602assigned to@Kate Rasheedand@Adeshile Oluwatosin:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/603assigned to@Anushka Paharia/@Kate Rasheedand@Karima Diafi:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/604assigned to@Kate Rasheedand@Adeshile Oluwatosin:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/605assigned to@Kate Rasheedand@Mildred AnashieUNDER REVIEW https://github.com/waldronlab/BugSigDBcuration/issues/606assigned to@Kate Rasheedand@Aleru Divine:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/607assigned to@Joy/@Kate Rasheedand@Karima DiafiFeel free to join!

Taofeecoh Adesanu (04:17:44) (in thread): > Tea but make it Hibiscus:slightly_smiling_face:

Mildred Anashie (04:24:48) (in thread): > Tea

Mildred Anashie (04:26:22) (in thread): > Well done@Kate Rasheedand everyone > > > How do you join in if interested@Svetlana Ugarcina PerovicRequest to review or you can be assigned to curate?

Adeshile Oluwatosin (04:27:48) (in thread): > I believeit’seither of the two@Mildred AnashieJust request on GitHub

Mildred Anashie (04:29:11) (in thread): > Okay@Adeshile OluwatosinI needed to be sure > Thank you

Peace Daniel (05:17:43) (in thread): > Coffee always

Kate Rasheed (06:06:18) (in thread): > Thank you everyone for the review.

USLACKBOT (09:24:02): > svetlana_up made updates to a canvas tab:[canvas content]

UBNSEMS3S (14:59:36): > Meeting recording. Thank you everyone who attended. - File (MPEG 4 Video): bsdb 2025_02_27.mp4

UBNSEMS3S (14:59:37) (in thread): > Tea. I buy my own tea from a small importer in Massachusetts by the kilogram.:tea:

Adeshile Oluwatosin (15:00:06) (in thread): > Thank you for today

Svetlana Ugarcina Perovic (15:01:10) (in thread): > <@UBNSEMS3S>what kind of tea, green tea?

UBNSEMS3S (15:01:48) (in thread): > I do enjoy a green tea on occasion but my favorite is a breakfast blend (English or Scottish).

Kate Rasheed (15:43:38) (in thread): > Thank you for today.

2025-02-28

Svetlana Ugarcina Perovic (01:44:51): > Happy Friday!https://blog.bioconductor.org/posts/2025-02-26-outreachy-mentoring/ - Attachment (Bioconductor community blog): Open Science Mentoring: My Journey with Outreachy Mentees – Bioconductor community blog > A blog for the Bioconductor community!

Svetlana Ugarcina Perovic (08:15:50): > and another good READ for today: > > In her latest Outreachy blog post,@Kate Rasheedchatted with three remarkable individuals who are my regular conversation partners on bioinformatics and microbiome science—people from whom I continually gain valuable knowledge. They provided Kate with several helpful recommendations.<@UBNSEMS3S>:Be flexible and open-minded.Celio:Read widely on Bioinformatics.Vedanth:**** Put yourself out there.****and I could not agree more, > just to add: do not forget toBE KIND!https://katerasheed1.wordpress.com/2025/02/24/true-worth-in-networking/ - Attachment (Kate Rasheed): True worth in Networking > Are you familiar with the popular phrase; “your network is your networth”? We will dive into this in this blog post. Graphic illustration of networking culled from Google Making Connect…

2025-03-03

Victoria (Burah) Poromon (03:00:25): > Hi@Svetlana Ugarcina Perovic. Good morning. > Happy New Month! > > Please, I’d like to delete the following from this study:https://bugsigdb.org/39772703 > 1. Signature 2 of Experiment 1 to 4 > 2. Experiment 5 and its signatures. > Thank you so much! - Attachment (BugSigDB): Strawberry dietary intervention influences diversity and increases abundances of SCFA-producing bacteria in healthy elderly people - BugSigDB > The gut microbiome is amenable to dietary interventions, and polyphenol-rich diets have been shown to enhance abundances of bacteria associated with short-chain fatty acid (SCFA) production.

Svetlana Ugarcina Perovic (03:06:04) (in thread): > Deleted.

Victoria (Burah) Poromon (03:11:48) (in thread): > Thank you!

Svetlana Ugarcina Perovic (03:47:00) (in thread): > Please see UPDATE on curation of**** whole genome metagenomic studies on Parkinson’s disease.****Feel free to join the effort to finalize this preferably today. Thanks and happy Monday!

Svetlana Ugarcina Perovic (05:01:01) (in thread): > @Kate Rasheedplease join@Anushka Pahariaand@Joyin their curations. Thanks!

Kate Rasheed (05:03:41) (in thread): > Okay.

Kate Rasheed (07:07:45): > Good afternoon everyone. Please I would appreciate your thoughts on Fig.S6and Fig.S7of thisarticle. I would like to know if they are curatable as they talk about coverage depth and GRiD score. > > Thank you so much. - Attachment (Nature): Metagenome-assembled microbial genomes from Parkinson’s disease fecal samples > Scientific Reports - Metagenome-assembled microbial genomes from Parkinson’s disease fecal samples

Svetlana Ugarcina Perovic (07:40:49) (in thread): > We are curating differences between two groups inabundance.GRiDhttps://github.com/ohlab/GRiDis a measure of growth rate. > Coverage depth of a genome usually corresponds to the number of bases of all short reads that match a genome divided by the length of this genome. > So, the answer isnot curatable.

Kate Rasheed (07:41:57) (in thread): > Thank you so much@Svetlana Ugarcina Perovic.

Taofeecoh Adesanu (08:01:53): > Hello everyone. > Please I need your opinions on the possibility of curating the figures in thisstudy. > Excerpt from the statistical analysis:“This analysis considered the three body sites and the four time points of the diet interventions. However, since no significant differences were observed…”.Thank you.

Svetlana Ugarcina Perovic (08:20:57) (in thread): > Based on ANCOM-BC results, there is no significant data to record BUTthe regression analysis results (in the text) are curatable.

Taofeecoh Adesanu (08:23:36) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (08:25:27) (in thread): > Sometimes results are not illustrated in the figures but mentioned in the text. Just please check the Supplementary material once again, although I did not spot any curatable results there.

Taofeecoh Adesanu (08:28:36) (in thread): > No, there was no curatable result in the extra material. > Thank you once again, this was absolutely helpful.

Karima Diafi (09:02:52) (in thread): > Hi@Svetlana Ugarcina Perovic, if there is anything else I can help with, please let me know. I would be happy to review; however, as I have only curated two papers so far, I am not sure if I am fully qualified to do so.

Svetlana Ugarcina Perovic (09:03:58) (in thread): > @Karima Diafiyou can do a review ofhttps://github.com/waldronlab/BugSigDBcuration/issues/607 - Attachment: #607 Gut Microbiota in Monozygotic Twins Discordant for Parkinson’s Disease > Gut Microbiota in Monozygotic Twins Discordant for Parkinson’s Disease – Carlotta Bolliri – Annals of Neurology
> https://onlinelibrary.wiley.com/doi/10.1002/ana.26454 > BolliriC_2022.pdf

Anushka Paharia (12:41:20) (in thread): > Hello everyone, really sorry for my inactivity I started the curation but then some personal stuff came up that I had to take care of, I just saw, the paper is curated as well as reviewed, So I’ll start curation on something else. Apologies:sweat:

Yoko C (20:59:07): > Hello everyone, I have a doubt. I have taxa in the following format: G000320405_Clostridium_celatum (source). I looked the up the accession number and got the following results:https://gtdb.ecogenomic.org/genome?gid=GCF_000320405.1, in this case should I go with the ” Species Taxid 36834 ” or the “Taxid 545697” ? Thanks

Adeshile Oluwatosin (23:23:27) (in thread): > Hi@Yoko Cthis is what I found > > The identifier “G000320405” corresponds to the genome assembly accession number for Clostridium celatum strain DSM 1785. This strain is registered under NCBI Taxonomy ID “545697”.

2025-03-04

Svetlana Ugarcina Perovic (05:01:39) (in thread): > @Anushka Pahariano problem at all,we are a team!

Svetlana Ugarcina Perovic (05:09:12): > A big SHOUT-OUT to the PD curation team:Curation ofa selection of whole genome metagenomic studies on Parkinson’s disease::white_check_mark:https://github.com/waldronlab/BugSigDBcuration/issues/600assigned to@Kate Rasheedand@Aleru Divine:white_check_mark:https://github.com/waldronlab/BugSigDBcuration/issues/601assigned to@Kate Rasheedand@Aleru Divine:white_check_mark:https://github.com/waldronlab/BugSigDBcuration/issues/602assigned to@Kate Rasheedand@Adeshile Oluwatosin:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/603assigned to@Anushka Paharia/@Kate Rasheedand@Karima Diafi:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/604assigned to@Kate Rasheedand@Adeshile Oluwatosin:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/605assigned to@Kate Rasheedand@Mildred Anashie:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/606assigned to@Kate Rasheedand@Aleru Divine:white_check_mark:**** ****https://github.com/waldronlab/BugSigDBcuration/issues/607assigned to@Joy/@Kate Rasheedand@Karima Diafi:clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap::clap:Adding to this selection 3 morewhole genome metagenomic studies on Parkinson’s diseasepreviously curated:https://bugsigdb.org/28449715https://bugsigdb.org/32844199https://bugsigdb.org/39443634Take your time to go through them especially their signatures and share below in the comments your observations.

Svetlana Ugarcina Perovic (05:44:12): > Sharing a mentoring secret with you ;) > > By the way, have you noticed or you can guess when/why I sometimes give different flowers emojis?:tulip:welcome!:potted_plant:good job, continue to grow!:bouquet:I’m very proud.

Adeshile Oluwatosin (05:45:16) (in thread): > I didn’t pay so much attention to this:blush::blush::blush:Now I know !

Chioma Onyido (05:46:11) (in thread): > Ooouu okay…What does this mean “:cherry_blossom:“I’veseen you use it before…

Svetlana Ugarcina Perovic (05:47:23) (in thread): > hahahah, it’s like a special THANKS

Kate Rasheed (07:34:29) (in thread): > Wow.:smile:

Ndukauba Oluchi (08:44:45) (in thread): > :rolling_on_the_floor_laughing:

Ndukauba Oluchi (09:55:18): > Hello everyone:wave:, How are you all? > please i need some help. > i need to confirm if Figure 4 and 5 in this paper is curatable > Link:https://journals.asm.org/doi/10.1128/spectrum.02582-24Cc:@Svetlana Ugarcina Perovic

Mildred Anashie (10:18:54) (in thread): > Interesting:blush:

Kate Rasheed (10:19:58) (in thread): > Good afternoon@Ndukauba Oluchi. > > Figure 4A-B is curatable. Figure 5 isn’t curatable (we don’t curate metabolic pathways)

Ndukauba Oluchi (10:25:15) (in thread): > okay. thank you@Kate Rasheed

2025-03-05

Svetlana Ugarcina Perovic (03:22:12): > NEWSGood morning, this week is the last week of@Kate Rasheedand@Aleru Divine’s Outreachy internship, and tomorrow (Thursday) when we usually have our office hoursthe Outreachy organizers are hosting a social hour event for interns, mentors, and coordinators:This event is good for networking, sharing your stories, and appreciating the people who helped you in your internship (mentors, fellow interns, community members). Prepare to attend, engage, connect, and learn from others.The social event will happen on Thursday, March 6, 2025, at 2:00 PM UTC.Venue: Big Blue Button (https://bbb.sfconservancy.org/b/sag-y6y-hcc-sww)We decided to cancel our office hours and instead attend the Outreachy internship social event.AND, we are happy to share that Kate and Divine will stay with us as co-mentors in the supporting team together with @Scholastica Urua**** ****@Chioma Onyido**** ****@Peace Sandy**** ****@Esther Afuape**** ****:sparkles:P.S. Kate and Divine will share with you here the insights from the event. > > cc<@UBNSEMS3S>

Adeshile Oluwatosin (03:24:02) (in thread): > @Aleru Divine@Kate RasheedI’m so proud of you both:heart:will definitely attend

Svetlana Ugarcina Perovic (03:26:13) (in thread): > I am not sure if this is open to the public… that’s why I suggested that Kate and Divine will share with you here the insights from the event.

Adeshile Oluwatosin (03:27:25) (in thread): > That’s fine

Aleru Divine (04:12:47) (in thread): > Thank you@Svetlana Ugarcina PerovicI’mlooking forward to the event:blush:

Kate Rasheed (04:33:34) (in thread): > Thank you so much@Svetlana Ugarcina Perovic@Adeshile Oluwatosin

Kate Rasheed (09:06:02) (in thread): > Good afternoon@Svetlana Ugarcina Perovic. > > My observations from these curated studies: > 1. The participants were matched on age and sex. > 2. WikiWorks is one of the Revision editors

Svetlana Ugarcina Perovic (09:10:20) (in thread): > BugSigDB is maintained by developers from the service called WikiWorks. They are the ones who did recent changes in the platform.

Svetlana Ugarcina Perovic (09:11:14) (in thread): > Any observations on signatures across different studies but on the same disease i.e. PD?

Kate Rasheed (09:22:40) (in thread): > Bifidobacterium and Streptococcus species are more abundant in Parkinson’s disease patients.@Svetlana Ugarcina Perovic:thinking_face:

Mildred Anashie (09:25:01) (in thread): > Hi@Svetlana Ugarcina PerovicFrom my observation, Recurring patterns of microbial presence of certain genera such as, Akkermensia, Faecalibacterium, Bifidobacterium etc are reported to be increasing or decreasing in the studies.

Svetlana Ugarcina Perovic (09:30:04) (in thread): > @Kate Rasheed@Mildred Anashiegood direction, be more precise.

Svetlana Ugarcina Perovic (09:33:19) (in thread): > “BugSigDB also allows for the identification of trends across multiple studies, making it easier to spot consistent patterns in microbial composition that may contribute to health conditions.” > > We should be able to see the trends, right?

Karima Diafi (10:35:27) (in thread): > In 5 out of 7 studies,******Bifidobacterium******was identified as part of the microbial signature in PD.******Bifidobacterium longum******and******Bifidobacterium dentium******were significantlyincreasedin two studies, while in another two studies,******Bifidobacterium bifidum******and******Bifidobacterium catenulatum******and******Bifidobacterium pseudocatenulatum.******

Juliana Kentomahun Mautin (11:21:20) (in thread): > Congratulations@Kate Rasheedand@Aleru Divine:tada::tada:

2025-03-06

Peace Sandy (04:15:32) (in thread): > Congratulations@Kate Rasheedand@Aleru Divine

Svetlana Ugarcina Perovic (04:15:53) (in thread): > IMPORTANT > Outreachy changed the day of social event:We’re moving the internship wrap-up social event to Friday, March 7th2025, at 2:00 PM UTC.

Svetlana Ugarcina Perovic (04:18:19): > :teapot:/:coffee:Good morning, please see update above:arrow_up:WE WILL HAVE our weekly team meeting:TODAY at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions! > > CC<@UBNSEMS3S>

UBNSEMS3S (08:51:09): > I am going to be about 5-10 minutes late to starting the meeting. Apologies for the delay.

Adeshile Oluwatosin (09:24:50): > <@UBNSEMS3S>Please have a look - File (MPEG 4 Video): RPReplay_Final1741089199

Scholastica Urua (09:34:46) (in thread): > Congratulations@Kate Rasheedand@Aleru Divine:tada::clap:

Adeshile Oluwatosin (10:12:00): > Thank you so much for today’s office hour<@UBNSEMS3S>I humbly await a response on curation of “Linear discriminative analysis” as a statistical test. > Thank you

UBNSEMS3S (10:12:34) (in thread): > It has been added.

Adeshile Oluwatosin (10:12:48) (in thread): > Thank you once again

Adeshile Oluwatosin (10:29:42) (in thread): > @Anushka PahariaYou can have a look at today’s office hour towards this article curation. > Table 3, Figure 4, Figure 6A and B, Figure 7A are curatable. > > Ignore Figure 8 and Figure 5.She mentioned something about writing a note on 6B, so you can watch the office hour’s recording to be clear on that.

Anushka Paharia (10:33:48) (in thread): > @Adeshile OluwatosinThankyou so much! I will do that.

Ndukauba Oluchi (10:34:11): > Omg, I totally forgot that today was Thursday, when i saw@Svetlana Ugarcina Perovicmessage on office hours link, i was thinking it would be tomorrow:sob::sob:

Svetlana Ugarcina Perovic (10:35:43) (in thread): > no worries:slightly_smiling_face:<@UBNSEMS3S>will share the recordings

Ndukauba Oluchi (10:37:16) (in thread): > :face_holding_back_tears:

Ouma Ronald (10:37:42) (in thread): > Actually i have also wanted to join but

Ouma Ronald (10:38:15) (in thread): > Maybe I will have to set up my Calendar for this meeting

Anushka Paharia (10:59:31) (in thread): > @Adeshile OluwatosinShould the curation for Figure 6A be separate signatures for weight height and bmi?

Svetlana Ugarcina Perovic (11:30:23): > Right now: ScienceCluster Lecture:Science Communication for Greater Research Impact https://vimeo.com/1061233687 - Attachment (Vimeo): Lecture: Science Communication for Greater Research Impact > Join us for a session in the company of three exciting scientific communicators sharing their thoughts and experiences on communicating science to peers and public.

Aleru Divine (12:14:04) (in thread): > I’mso sorry about that@Ndukauba OluchiThis is a great idea@Ouma Ronald

Aleru Divine (12:15:07) (in thread): > Thank you so much@Adeshile Oluwatosin@Juliana Kentomahun Mautin@Peace Sandy@Scholastica Urua:blush:

Ndukauba Oluchi (12:15:45) (in thread): > Eyyyyyyyyyy:fire::fire::fire::tada:Congratulations@Aleru Divineand@Kate Rasheed

Aleru Divine (12:21:25) (in thread): > Thank you@Ndukauba Oluchi

Adeshile Oluwatosin (15:24:58) (in thread): > @Anushka PahariaYes, they are three seperate experiments. > See previous suggestion:https://community-bioc.slack.com/archives/C04RATV9VCY/p1740377273517519?thread_ts=1740325988.838259&channel=C04RATV9VCY&message_ts=1740377273.517519 - Attachment: Attachment > @Anushka Paharia To add to what @Mildred Anashie said. > > It’s a cross sectional study. Age is not a matched on factor. > THESE ARE THE FIGURES/TABLES TO CURATE: > > Table 3: only Bacteroidetes and Cyanobacteria are significant and should both be curated as increased abundance in stunted children. MHT (no) > See “Of these Bacteroidetes were significantly higher in stunted children (23.9% ± 10.8% vs 20.0% ± 11.1%). Also Cyanobacteria (with overall very low abundance and prevalence) were significantly higher in stunted children (0.32% ± 0.70% vs. 0.17% ± 0.28%)”. EXP 1 > > Figure 4; Kruskal Wallis test, MHT (Yes), Lachnoclostridium, Faecalibacterium and veillonella should first be curated as increased abundance in stunted children in EXP 2. Third experiment with normal length children in Kujang (Group 0) and stunted children in kujang (Group 1), fourth experiment do same but in North Kodi. > > Figure 6A and 6B : Test (spearman correlation), MHT (Yes), 7 experiments with different comparisons here (Height, Weight, BMI, Zlen, ZBMI, Zwei, and ZWFL). Group 0( low body mass Index), Group 1(High Body Mass index) … do the same for the rests. > See “Blue: Positive correlation (increased abundance); red: Negative correlation (decreased abundance)” > > Figure 7A; Test (spearman correlation), MHT (Yes), Green (increased abundance), purple (decreased abundance). 3 experiments asides Type of toilet. > e.g Group 0 (low correlation to waste water disposal facility), Group 1 (High correlation to waste water disposal facility). > > NB: sample size in Exp 1, 2 is a total of kujang/North kodi > Sample size in Exp 3, 4, is specific to Kujang/North kodi. > Also have a look at the taxa with “*” as this indicates significance. > > FOR ALPHA DIVERSITY: > • Shannon, Faith, evenness (pielou) and observed (Richness) > Curate specific to the comparisons as seen in Table 4. > If the comparison isn’t mentioned, kindly leave blank > The significant values are extremely dark in the Table. > > If you have any questions, feel free to ask

2025-03-07

Svetlana Ugarcina Perovic (04:09:55): > Hey hey PD team@Aleru Divine@Kate Rasheed@Adeshile Oluwatosin@Anushka Paharia@Karima Diafi@Mildred Anashie@JoyWe have very well-replicated differential abundance seen in your PD curations, and it would be goodto see how much of that could be explained as a result of the constipation that occurs in PD patients, because it also occurs in non-PD-associated constipation. > > Your next task is**** to look for any studies of constipation that is not PD-related ****and add them to our GitHub issues for curationhttps://github.com/waldronlab/BugSigDBcuration/issuesDo not forget to check if your selected paper: > * has Condition: constipation > * has significant differential abundance results curatable > * has not been already curated > And, please use Create new issue>BugSigDB study curation template.Happy Friday, ALL!

Svetlana Ugarcina Perovic (04:10:51) (in thread): > Seehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1741188927759839?thread_ts=1741082952.880069&cid=C04RATV9VCY - Attachment: Attachment > In 5 out of 7 studies, Bifidobacterium was identified as part of the microbial signature in PD. Bifidobacterium longum and Bifidobacterium dentium were significantly increased in two studies, while in another two studies, Bifidobacterium bifidum and Bifidobacterium catenulatum and Bifidobacterium pseudocatenulatum.

Aleru Divine (04:43:05) (in thread): > Got it, thank you! On to the exploration!:female-technologist:

Joy (04:55:12) (in thread): > Duly noted@Svetlana Ugarcina Perovic. Thanks:blush:

Kate Rasheed (05:06:54) (in thread): > Duly noted with thanks.

Taofeecoh Adesanu (05:16:44) (in thread): > @Svetlana Ugarcina PerovicWill it be too late to join this task now?

Adeshile Oluwatosin (05:18:36) (in thread): > Duly noted@Svetlana Ugarcina PerovicThank you!

Svetlana Ugarcina Perovic (05:39:27) (in thread): > Sure@Taofeecoh Adesanufeel free to join!

Victoria (Burah) Poromon (06:42:21) (in thread): > Hi@Svetlana Ugarcina PerovicI’ll love to add studies too!

Anushka Paharia (08:48:13) (in thread): > Hello@Taofeecoh Adesanucheck this thread out, and let me know!

Taofeecoh Adesanu (09:26:23): > Hello<@UBNSEMS3S>Here is a warm reminder that the office hour recording from yesterday is yet to be dropped. > Thank you.

Adeshile Oluwatosin (10:12:59): > Good afternoon@Svetlana Ugarcina Perovic<@UBNSEMS3S>How would these two taxa “Romboutsia” and “Johnsonella” be curated if both are significant (p>0.05) and doesn’t signify an increase or decrease specific to Wilcoxon test.articleThank you so much - File (JPEG): IMG_3786

Kate Rasheed (11:06:21) (in thread): > @Adeshile OluwatosinSee this from the paper “Among 181 common bacterial genera detected in saliva samples, thehigherrelative abundance of eight genera (i.e., Megasphaera, Anaeroglobus, Dialister, Rothia, Atopobium, Actinomyces, Howardella, andRomboutsia) and thelowerrelative abundance of the genus******Johnsonella******in smokers was observed,”

Adeshile Oluwatosin (11:08:59) (in thread): > Thank you@Kate RasheedBut that was specific to MaAslin2 test since there was adjustment and that text referencedFig. 3A C, and Supplementary Table S2). > > Wicoxon test was used in Table S3 and there were no confounders

Adeshile Oluwatosin (11:10:52) (in thread): > Hence,I didn’twant to assume

Kate Rasheed (11:17:55) (in thread): > Yes I saw it too and noticed reference was made to the taxa in supplementary table 3. > > See “Specifically, the most notable difference in relative abundance between smokers and non-smokers among these features was observed for Megasphaera, with a difference in their median relative abundance of 1.43%. These genera are classified under two phyla, Firmicutes and Actinobacteria, primarily comprising anaerobic bacteria (Supplementary Table S3).”@Adeshile Oluwatosin

Adeshile Oluwatosin (11:24:22) (in thread): > Okay, thank you so much@Kate RasheedI just wanted to be sure

2025-03-08

UBNSEMS3S (10:51:11): > Office Hours Recording. Apologies I thought I had posted it. Thank you@Taofeecoh Adesanufor the reminder. - File (MPEG 4 Video): bsdb 2025_03_06.mp4

Peace Daniel (15:15:35): > Hello everyone, > Can anyone please assist me with the NCBI ID for Peptostreptococcales TissierellalesI couldn’tfind the ID for the order > > Thank you so much:heart_hands:

Adeshile Oluwatosin (15:18:26) (in thread): > Hello@Peace DanielKindly curate as seen

Peace Daniel (15:19:16) (in thread): > Hey,you couldn’tfind it too? > Yup, done that

Adeshile Oluwatosin (15:19:41) (in thread): > Yes, both on NCBI and Uniprot

Peace Daniel (15:21:08) (in thread): > Same, thank you so much tho:heart:

2025-03-09

Anushka Paharia (04:21:42): > Hello everyone, whenever I try to edit on the BugSigDB website, I get a notification that “this page might be slowing down your browser” , and eventually it stops working. > Is this a common occurrence or should I change something?

Taofeecoh Adesanu (05:58:33) (in thread): > Hi@Anushka PahariaI don’t experience this, but if you are using Chrome, you might want to minimize the number of tabs you have opened at once.@Adeshile Oluwatosinis this similar to what you had experienced?

Adeshile Oluwatosin (09:35:18) (in thread): > Hi@Taofeecoh AdesanuI have never gotten this prompt.I use chrome though@Anushka PahariaI also suggest closing some unused tabs, refresh your browser and check your network

Anushka Paharia (09:43:35) (in thread): > I have tried closing tabs, it doens’t help, I use Firefox so I guess I’ll try chrome and see if it persists.

Ouma Ronald (12:07:23) (in thread): > Clearing Cache and Cookies could be my best recommendation.**** C**lear your browser’s cache and cookies. This can resolve conflicts caused by outdated data

2025-03-10

Adeshile Oluwatosin (07:33:23): > Hello, Good afternoon@Svetlana Ugarcina PerovicI hope you had a nice weekend and doing well as well > Please what would you say the data transformation for edgeR is.

Mildred Anashie (08:11:56) (in thread): > Hi@Adeshile Oluwatosin, this is an alreadyreviewed studyand it says Raw counts. Check Experiment 7 - Attachment (BugSigDB): Microbiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study - BugSigDB > BACKGROUND: Gastric cancer is one of the global health concerns.A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases.

Adeshile Oluwatosin (08:12:39) (in thread): > Hi dear@Mildred AnashieI went through some already reviewed studies and “relative abundance” was reported as well

Mildred Anashie (08:15:38) (in thread): > Maybe thosepapersstatedtheir data transformation tobe relative abundance@Adeshile Oluwatosin. See this,https://community-bioc.slack.com/archives/C04RATV9VCY/p1696865038905849?thread_ts=1696864182.317959&cid=C04RATV9VCY - Attachment: Attachment > Unless they say otherwise, usually it will be raw counts or relative abundances. Sometimes you have to infer from the statistical methods, for example, a glm, DESeq2, or edgeR, require raw counts. LEfSe requires relative abundance input.

Svetlana Ugarcina Perovic (08:18:43) (in thread): > See thishttps://academic.oup.com/nar/article/53/2/gkaf018/7973897

Svetlana Ugarcina Perovic (08:19:52) (in thread): > or just to go the documentation:https://bioconductor.org/packages/release/bioc/html/edgeR.html - Attachment (Bioconductor): edgeR > Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce read counts, including ChIP-seq, ATAC-seq, Bisulfite-seq, SAGE and CAGE.

Adeshile Oluwatosin (08:20:39) (in thread): > Thank you so much for responding:pleading_face:@Svetlana Ugarcina PerovicI appreciate@Mildred Anashie

2025-03-12

Svetlana Ugarcina Perovic (05:40:08): > TOMORROW (Thursday)We will have our weekly team meeting:at 9 AM EST athttps://us02web.zoom.us/j/2737200499CC<@UBNSEMS3S>NOTE: it is 1 hour earlier in many time zones, check your local timehttps://www.timeanddate.com/worldclock/converter.html?iso=20250313T130000&p1=179&p2=37&p3=176&p4=3395&p5=125

Svetlana Ugarcina Perovic (05:41:17): > NEXT WEEK: MVIF - Microbiome Virtual International ForumWe are looking forward to welcoming you and our guest speakers bringing theirlatest findings from extreme environments! > > Join us:https://buff.ly/TZQHE9b - File (PNG): mvif 37.png

Aleru Divine (08:00:43) (in thread): > I’m really excited for this one! > “MICROBES IN SPACE”:shocked_face_with_exploding_head::shocked_face_with_exploding_head:I remember suggesting to add talks on microbiomes in extreme environments in a survey shared by MVIF, so it is amazing to see it happening. I think this is a very fascinating aspect of microbiome research and it kind of feels like something out of a sci-fi movie. Can’t wait!

Anushka Paharia (10:46:56): > Hello everyone, I am curating a study. I don’t know if it’s a silly doubt but if the taxa is given as Lachnospiraceae.**, should I include the dots and underscore in the curation or not?

Kate Rasheed (10:47:54) (in thread): > Hello@Anushka Paharia. Please don’t include the dots and underscore.

Anushka Paharia (10:51:20) (in thread): > @Kate Rasheedyes, I didn’t. But as I’m not a microbiology student I googled and it seemed like it has a specific meaning and then in the curation study it states that if we aren’t able to find the exact taxa ncbi id, just include it as it’s written in the study. > For example, I can’t find Clostridales…D_5__Family.XIII.AD3011.group so i curated it without dots and underscore but why is it written like that in the first place?

Adeshile Oluwatosin (10:55:11) (in thread): > Hello@Anushka PahariaYou can curate “Lachnospiraceae” with Taxa ID “186803”excluding the dots and underscore

Kate Rasheed (10:55:49) (in thread): > For this example, you can curate it as Family XIII AD3011.

Adeshile Oluwatosin (10:57:45) (in thread): > Clostridiales has the taxonomic rank “Order” > And Family XIII AD3011 group “genus”Hence curate the lowest rank which in this case is “Family XIII AD3011 group” as kate mentioned

Anushka Paharia (10:58:40) (in thread): > Thankyou@Kate Rasheed@Adeshile Oluwatosin

Anushka Paharia (11:00:50) (in thread): > @Adeshile OluwatosinI have curated figure 6a, can you check it out?https://bugsigdb.org/38551926I’ll make the necessary changes. - Attachment (BugSigDB): Gut microbiota differences in stunted and normal-lenght children aged 36-45 months in East Nusa Tenggara, Indonesia - BugSigDB > The role of the gut microbiota in energy metabolism of the host has been established, both in overweight/obesity, as well as in undernutrition/stunting.Dysbiosis of the gut microbiota may predispose to stunting.

Adeshile Oluwatosin (11:01:34) (in thread): > Okay, I will have a look > Well done:clap:

Svetlana Ugarcina Perovic (11:54:08) (in thread): > NOTE:Family XIII AD3011 group has a genus rank

Svetlana Ugarcina Perovic (11:54:26) (in thread): > the genus is called “Family XIII AD3011 group”

Adeshile Oluwatosin (11:55:13) (in thread): > Noted

Svetlana Ugarcina Perovic (11:59:59) (in thread): > https://www.midasfieldguide.org/guide/fieldguide/genus/family_xiii_ad3011_group

Adeshile Oluwatosin (12:02:40) (in thread): > Thank you so much

2025-03-13

Taofeecoh Adesanu (09:04:16): > Hello everyone! > The office hour is on now

Aleru Divine (09:12:24) (in thread): > Thank you:face_with_peeking_eye:

Adeshile Oluwatosin (09:36:26) (in thread): > <@UBNSEMS3S>Good afternoon, kindly let me in

Taofeecoh Adesanu (09:38:29) (in thread): > Good afternoon@Adeshile Oluwatosin, the meeting ended early due to small audience, it took about 30 minutes.

Adeshile Oluwatosin (09:39:20) (in thread): > I had questions prepared:pleading_face:

Taofeecoh Adesanu (09:39:28) (in thread): > Let’s wait for<@UBNSEMS3S>to drop the recording.

UBNSEMS3S (09:49:12): > Thank you all for attending our small, short office hour this morning! - File (MPEG 4 Video): bugsigdb 2025_03_13.mp4

Kate Rasheed (09:50:27) (in thread): > Thank you<@UBNSEMS3S>. For the indepth explanation on relative abundance.

Ndukauba Oluchi (09:58:10): > what is going on? > office hour ended? > oh no:broken_heart:

UBNSEMS3S (10:00:51): > Yes I think there may have been some confusion. US had daylight savings time last Sunday so we are an hour earlier. I highly recommend using a time and date calculator like the one Svetlana linked:https://www.timeanddate.com/worldclock/converter.html?iso=20250313T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Ndukauba Oluchi (10:02:16) (in thread): > alright:heavy_check_mark:

2025-03-14

Svetlana Ugarcina Perovic (06:44:03): > Daylight time savings in March differ across the globe, that’s why we have in some countries (like in Serbia, Nigeria etc.) an hour earlier weekly meeting. In April, our meeting time will be back as usual. > > You can check your time here:https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=37&p3=176&p4=3395&p5=125If you missed it yesterday, no worries, ask questions here and cc <@UBNSEMS3S>**** and me.*******Happy Friday!*** - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Adeshile Oluwatosin (06:44:54) (in thread): > Okay:pleading_face:Thank you

Juliana Kentomahun Mautin (13:06:40) (in thread): > Thank you so much for the update@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (13:50:08): > @Akritijust asked how to work on the next curation (after closing the GitHub issue that you have been working on). > Go tohttps://github.com/waldronlab/BugSigDBcuration/issuesand comment in the github issue with a study that you want to curate. > Please note that we communicate in Slack channel dedicated to the project. Thanks!

Akriti (14:16:23): > ok thankyou@Svetlana Ugarcina Perovic

Peace Daniel (15:06:21) (in thread): > Way to go@Akriti:dancer:

Ndukauba Oluchi (17:14:20) (in thread): > Okay

Shahenda Soliman (23:12:32): > Good morning. > Sorry if I interrupt. This is my first exposure to open source & science projects, so I feel very dumb. I just wonder if I have permission to contribute, or I have to wait for the initial application results? > Thank you:white_heart:

2025-03-15

Adeshile Oluwatosin (02:13:54) (in thread): > Good morning@Shahenda SolimanNice to have you aroundThere’sno such thing as dumb,there’sa canvas material to get you started and you can always ask questions if stuck. > Regarding contributing, Yes we are always free to contribute > But outreachy officially starts next week

Adeshile Oluwatosin (02:17:25) (in thread): > Please check the pinned message “Welcome material”

Mildred Anashie (08:04:48) (in thread): > Hi@Shahenda Solimanwelcome:hugging_face:Feel free to ask questions and also go through the welcome material like@Adeshile Oluwatosinsuggested, to get familiar with everything

Peace Daniel (08:26:12) (in thread): > Welcome@Shahenda Solimantake a look at thishttps://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Ouma Ronald (11:22:57): > Hi<!channel>,@Svetlana Ugarcina Perovic. I was working on tests for finding out the safety of Bugsigdb API Sandbox and also if it really gives reproducible studies. I was provided with a test study to use and in the zipped files here, I am basically using the test study but The tests can work on all the studies. Below are the files for the APISandbox tests and based on the findings, The API isSAFE AND GIVES REPRODUCIBLE STUDIES.Though, the reason as to why I did it this way is because modifications that are carried on any study onbugsigdb.orgcan modify the wiki thereby changing live data - File (Zip): API-tests.zip

Svetlana Ugarcina Perovic (15:11:23) (in thread): > Thanks for the update!

USLACKBOT (21:44:19): > This message was deleted.

Juliana Kentomahun Mautin (21:46:11): > This is the paper I’m curating .https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02880-3. - Attachment (BioMed Central): Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic - BMC Microbiology > Background Functional constipation (FC) in children affects their growth, development and quality of life. L-pipecolic acid (L-PA) was decreased in FC children based on gut microbiome and serum metabolomic. In this study, loperamide-induced constipation in mice was used to evaluate the effects of L-PA on constipated mice. Method 26 FC and 28 healthy children were recruited. Stool samples and serum samples were subjected to 16S rDNA sequencing and ultra-performance liquid chromatography/quadrupole time of flight (UPLC-Q/TOF-MS) approach, respectively. A loperamide-induced mouse constipation model was developed, and all mice were randomly divided into control (Con), loperamide (Lop) and L-PA (Lop + L-PA) treatment groups (6 mice per group). The mice in the Lop + L-PA group were given L-PA (250 mg/kg, once a day) and loperamide; the Lop group was given loperamide for 1 week, and the Con group was given saline. The fecal parameters and intestinal motility of mice in each group were detected. serum 5-HT levels and colon 5-HT expression were detected by ELISA and immunohistochemistry, respectively; qRT-PCR was used to detect the expression of AQP3 and 5-HT4R mRNA in each group. Results 45 differential metabolites and 18 significantly different microbiota were found in FC children. The α and β diversity of gut microbiota in FC children was significantly reduced. Importantly, serum L-PA was significantly reduced in FC children. The KEGG pathway enrichment were mainly enriched in fatty acid biosynthesis, lysine degradation, and choline metabolism. L-PA was negatively associated with Ochrobactrum, and N6, N6, N6-trimethyl-l-lysine was positively associated with Phascolarcrobacterium. In addition, L-PA improved the fecal water content, intestinal transit rate, and increased the serum 5-HT levels in constipated mice. Moreover, L-PA increased the expression of 5-HT4R, reduced AQP3, and regulated constipation-associated genes. Conclusions Gut microbiota and serum metabolites were significantly altered in children with FC. The abundance of Phascolarctobacterium and Ochrobactrum and serum L-PA content were decreased in FC children. L-PA was found to alleviate the fecal water content, increase intestinal transit rate and the first black stool defecation time. L-PA improved constipation by increasing 5-HT and 5-HT4R expression while down-regulating AQP3 expression.

2025-03-16

Anushka Paharia (02:07:21) (in thread): > Hello@Juliana Kentomahun Mautin, In the paper, I think Figure 1 B and F should be curated. > For the signatures, you identify increased abundance and decreased abundance of the taxa from the figures in the case and the control. > Then, you start with finding the ncbi id of the taxa from the website and add it to your signature. > Let me know what’s troubling you.

Peace Daniel (07:55:19) (in thread): > Hey there, do send me a message so we can schedule a huddle. Well done:clap:

Taofeecoh Adesanu (11:12:20) (in thread): > Hi@Juliana Kentomahun Mautin, how is it going now?

Ndukauba Oluchi (13:48:40) (in thread): > Hello@Juliana Kentomahun Mautin:hugging_face:Do you still have any issues? > I can help.

Ndukauba Oluchi (18:11:43): > Hello everyone, please i need your help. > 1. Regarding this study:https://journals.asm.org/doi/10.1128/spectrum.02582-24 > Figure 4B has both a box plot and a volcano plot, please which do i curate (Signatures) for BV-Positive VS BV-Negative

Ndukauba Oluchi (18:17:11): > 2. we don’t curate for metabolic pathways right? just differential abundance? > 3. Am I to create Experiments for the CST(community state type) samples since their relative abundance is on a heat map(fig 3)

Shahenda Soliman (23:56:23) (in thread): > thank you all:blush:@Adeshile Oluwatosin@Mildred Anashie@Peace DanielI’ve already checked the pinned message as suggested, but I didn’t know if it’s possible to contribute even without being an intern in outreachy, so thank you for clarifying that.:hugging_face:

2025-03-17

Adeshile Oluwatosin (01:47:19) (in thread): > You are allowed and free to contribute > Request for an article to curate and tag a mentor

Adeshile Oluwatosin (01:47:42) (in thread): > Good morning

Adeshile Oluwatosin (01:48:23) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues

Peace Daniel (01:50:31) (in thread): > 2. Yes > 3. Fig 3 doesn’t show differential abundance

Adeshile Oluwatosin (01:50:41) (in thread): > Hello@Ndukauba OluchiCould you kindly post in a single thread. > > As for number 2, yes we don’t curate metabolic pathways

Adeshile Oluwatosin (01:51:09) (in thread): > Fig 3 is not curatable

Adeshile Oluwatosin (01:52:34) (in thread): > Do you mean Figure 4A and 4B?

Peace Daniel (01:54:36) (in thread): > Hello,I don’tthink to include fig 4B bcz it says > > Boxplots comparing the relative abundances of select taxa between BV-POS and BV-NEG samples, with statistical significance indicated to the right

Adeshile Oluwatosin (01:56:14) (in thread): > If yes, both seems curatable > * As Figure 4A shows differential abundance between BV-POS and BV-NEG > * Figure 4B shows relative abundance between same groups indicating statistical significance indicated to the right

Peace Daniel (01:57:18) (in thread): > It seems it contains the same taxa btw both but fig 4A has all and 4B has some that were selected. My thoughts *

Adeshile Oluwatosin (01:59:54) (in thread): > In that case both Fig 4A and 4B should be referenced as a source

Adeshile Oluwatosin (02:10:10) (in thread): > With statistical test: ANCOM-BC, MHT: Yes > “The differential abundance analysis of microbes between BV-POS and BV-NEG samples was performed by using the ANCOM-BC v2.0.3 R package”

Ndukauba Oluchi (03:30:37) (in thread): > How do I do that?@Adeshile Oluwatosin

Ndukauba Oluchi (03:31:41) (in thread): > @Adeshile OluwatosinNoted, will post a single thread moving forward, Thanks a bunch:100:

Ndukauba Oluchi (03:31:59) (in thread): > Thank you@Peace Daniel:relieved:

Svetlana Ugarcina Perovic (03:56:08): > :tulip:**** Welcome to the Outreachy contribution period! ****To get started, please check out our GitHub issue for instructions:https://github.com/waldronlab/BugSigDBcuration/issues/94If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors:<@U1LCB8WEA><@UBNSEMS3S>@Esther Afuape@Chioma Onyido@Peace Sandy@Scholastica Urua@Kate Rasheed@Aleru Divineand@Svetlana Ugarcina PerovicTip: New to contributing? Watch this helpful video on getting started with open source contributions:https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Adeshile Oluwatosin (03:56:34) (in thread): > Thank you so much@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (03:59:09) (in thread): > You can curate the taxa in red as increased abundancein BV-POS, those in blue as decreased abundance. > > Indicate figure 4a and 4B for increased as a source and just 4a as decreased.

Adeshile Oluwatosin (04:00:22) (in thread): > Hello everyone:wave:I’m Adeshile Oluwatosin from Nigeria, and I’m excited to be joining the Outreachy contribution phase once again! Having previously contributed to BugSigDB, I look forward to continue curating, learning from this amazing community, and making even more meaningful contributions. With a background in biochemistry, I’m eager to apply my skills and collaborate with all of you!

Adeshile Oluwatosin (04:12:05) (in thread): > BV-negative: Group 0,BV-positive: Group 1

Adeshile Oluwatosin (04:12:20) (in thread): > @Ndukauba Oluchi

Ndukauba Oluchi (04:19:24) (in thread): > Thank you so much@Svetlana Ugarcina PerovicMy name is Ndukauba Oluchi from Nigeria, I am happy to be contributing to the Bugsigdb project:hugging_face:, I look forward to Collaborate and Network with each and everyone of you. Let’s do this:rocket::rocket:

Ndukauba Oluchi (04:23:42) (in thread): > Noted@Adeshile Oluwatosin

Anushka Paharia (04:38:50) (in thread): > Hello everyone! > > I am Anushka, a cs undergrad from India. I am excited to contribute to BugSigDB for my outreachy application. > > Looking forward to collaborate and grow:smiling_face_with_3_hearts::rocket::rocket:

Ndukauba Oluchi (06:09:29) (in thread): > Hello everyone:hugging_face:Once again I have a question. > The lowercase alphabet before the signature name is it relevant? > For example f_mitochondria, g_lactobacillus > What does the f and g prefix mean? > Cc@Svetlana Ugarcina Perovic - File (JPEG): Screenshot_2025-03-17-11-06-15-076_com.android.chrome.jpg

Svetlana Ugarcina Perovic (06:15:29) (in thread): > Letters before taxa/signatures are actually taxonomy ranks:Domain: BacteriaPhylum: BacillotaClass: BacilliOrder: LactobacillalesFamily: LactobacillaceaeGenus: Lactobacillus > > g_lactobacillus -> genus Lactobacillus -> BugSigDB recordinghttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1578&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Ndukauba Oluchi (06:18:17) (in thread): > Wow, interesting:thinking_face:Thanks for the clarification.

Svetlana Ugarcina Perovic (06:21:48) (in thread): > As for the family Mitochondria please check herehttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Victoria (Burah) Poromon (07:08:18) (in thread): > Thank you!@Svetlana Ugarcina PerovicHello everyone, my name is Victoria Poromon from Nigeria.I’mso excited to be joining the contribution stage again andI’mlooking forward to collaborating and networking with everyone.

Ndukauba Oluchi (07:09:33) (in thread): > @Svetlana Ugarcina Perovicdoes that mean that I should not curate f_mitochondria because it is a cell organelle and not a bacteria? > 2. I couldn’t also find s_DNF00809 > What do I do at this point?

Svetlana Ugarcina Perovic (07:27:30) (in thread): > mitochondria skip > s_DNF00809 stands for species DNF00809:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1588753Coriobacteriales bacterium DNF00809 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Ndukauba Oluchi (07:28:26) (in thread): > Okay@Svetlana Ugarcina Perovicthank you for clarifying:blush:

Juliana Kentomahun Mautin (08:33:32) (in thread): > Hello everyone:slightly_smiling_face::slightly_smiling_face::slightly_smiling_face:My name is Juliana Kentomahun Mautin, and I’m from Lagos Nigeria. I have a background in Health Education with a strong interest in Microbiology, and I’m thrilled to be part of this community. > > This is my third time applying for the Outreachy internship. I’m super excited to work together with everyone and look forward to making meaningful contributions! > > Cheers and good luck to everyone!:sparkling_heart::sparkling_heart::sparkling_heart::sparkling_heart:

Joy (09:29:32) (in thread): > Thank you@Svetlana Ugarcina PerovicHello everyone!:wave:I’m Joy from Nigeria, and I’m excited to be part of the Outreachy contribution phase once again! Having previously contributed to BugSigDB, I’m eager to continue curating, learning from this incredible community, and making even more meaningful contributions. With a background in Mass Communications and experience in software engineering, I’m passionate about bridging the gap between tech and effective communication. Looking forward to collaborating with all of you!

Akriti (09:30:00): > when do we get mail

Kate Rasheed (09:31:22) (in thread): > 4pm UTC > > Check the time here:https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Svetlana Ugarcina Perovic (09:31:45) (in thread): > https://www.outreachy.org/apply/project-selection/ - File (PNG): Screenshot 2025-03-17 at 14.31.11.png

Akriti (09:32:40): > I didn’t get any mail

Svetlana Ugarcina Perovic (09:42:43) (in thread): > Be patient and for any question related to the final results of selection please contact Outreachy. We are responsible for the BugSigDB project, not the initial applicants selection. Good luck!

Juliana Kentomahun Mautin (09:52:08) (in thread): > @AkritiSome people recieved a mail on Friday but the organizer post it on their social media platform that an updated mail would be sent out today at 4pm UTC

Akriti (09:58:19) (in thread): > exactly it’s 7:30 pm , but I didn’t get any mail

Svetlana Ugarcina Perovic (10:01:04) (in thread): > There are 2 more hours left…https://www.timeanddate.com/worldclock/converter.html?iso=20250317T160000&p1=179&p2=37&p3=176&p4=3395&p5=125

Adeshile Oluwatosin (12:08:26): > Hello Everyone:wave:I have completed my initial contribution and would soon request to be assigned a paper. If you need help. > Please feel free to ask!

Ndukauba Oluchi (12:14:16) (in thread): > Well done:rocket:@Adeshile Oluwatosin

Adeshile Oluwatosin (12:17:59): > Helpful tips for the initial contribution: > * The aim is to familiarize ourselves with a microbiome research article and to extract key details about the research to correctly answer the questions. > * Download the pdf titled “Annotated MacCann Article”. Read thoroughly, noting down the annotated (coloured) parts.link > * Head over to the questions in the curation formlinkto have an idea of what’s required. Go back to the article once again to confirm your answer is accurate and then fill the form. > Follow instructions strictly as well. I hope this helps out:tulip:

Svetlana Ugarcina Perovic (12:42:58) (in thread): > TOMORROW join MVIF, see you there!

Mildred Anashie (12:54:36) (in thread): > Thank you@Svetlana Ugarcina PerovicHi everyone!:wave:My name is Mildred Anashie , and I’m from Nigeria. I’m a microbiologistand aPublic Healthenthusiastand I’m excited to be part of this community. > > I’ve previously contributed to BugSigDBand thisis my fourth time applying for the Outreachy internship. I’m eager to work together and look forward toconnecting with everyone andmaking meaningful contributions!Good luck to everyone!:sparkles:

Precious Chijioke (13:02:13): > Hello everyone, my name is Precious Chijioke. I’m excited to be part of this community, and I look forward to making meaningful and amazing contributions!

Adeshile Oluwatosin (13:03:23) (in thread): > Welcome to the community:tulip:@Precious Chijioke

Precious Orakwe (13:03:59) (in thread): > Welcome@Precious Chijioke

Precious Orakwe (13:05:31) (in thread): > Great@Adeshile Oluwatosin

Shade Akinremi (13:05:52) (in thread): > Thank you@Svetlana Ugarcina Perovic. I am Shade from Nigeria, I am an electrical engineer and this is my first time contributing to an open source.

Jesulolufemi Adelanke (13:11:39): > Hello everyone, my name is Jesulolufemi Adelanke. I’m really excited to be here and contribute to this project. > Looking forward to interacting with everyone. Nice to meet y’all!

Adeshile Oluwatosin (13:13:13) (in thread): > Welcome to the community:tulip:@Jesulolufemi Adelanke

Precious Orakwe (13:16:30) (in thread): > Hello everyone!:star2:I’m Precious from Nigeria, with a background in Industrial Chemistry:dna:. I’m thrilled to be back and grateful for being selected to contribute to BugSigDB again:pray:. This is my fifth attempt, and I’m hoping it will be a successful one:crossed_fingers:. > > I’m excited to learn more about reviewing and curating papers, and I’m looking forward to working with the team to achieve great things:rainbow:. A big thank you to our amazing mentors for their guidance and support:raised_hands:. > > Let’s collaborate and make this project a success!:muscle:”

Precious Orakwe (13:17:54) (in thread): > You are so welcome@Jesulolufemi Adelanke

Dorcas Odetayo (13:23:43): > Hello everyone, My name is Dorcas Odetayo, and I’m excited to be part of this community. I’m looking forward to learning, collaborating, and contributing to this project!

Adeshile Oluwatosin (13:28:16) (in thread): > Welcome to the community:tulip:@Dorcas Odetayo

Juliana Kentomahun Mautin (13:28:33) (in thread): > You are welcome@Precious Orakwe. We are glad to have you here:sparkling_heart:

Juliana Kentomahun Mautin (13:29:06) (in thread): > Welcome@Precious Orakwewe are glad to have you here:sparkling_heart:

Juliana Kentomahun Mautin (13:29:45) (in thread): > Welcome@Dorcas Odetayowe are glad to have you here

Eniola Kolawole (13:34:23): > Hi everyone > Good day to all the mentors in the house > I’m Eniola Kolawole > > Good to be here again. A lot happened the last time, from spoilt devices to no power supply. Hope to make this one count by being able to contribute massively, receive much help and as well help others. Thank you

Anne-Marie Sharp (13:35:06): > Hello everyone,my name is Anne-Marie Sharp. Super excited to be part of this community. Looking forward to learning and collaborating.

Adeshile Oluwatosin (13:38:17) (in thread): > Welcome:hugging_face:@Eniola Kolawole

Adeshile Oluwatosin (13:38:57) (in thread): > Welcome:hugging_face:@Anne-Marie Sharp

Mildred Anashie (13:48:53) (in thread): > Hi@Precious ChijiokeWelcome:hugging_face:

Mildred Anashie (13:49:27) (in thread): > Hi@Jesulolufemi AdelankeWelcome:hugging_face:

Mildred Anashie (13:49:58) (in thread): > Hi@Dorcas OdetayoWelcome:hugging_face:

Mildred Anashie (13:51:30) (in thread): > Hi@Anne-Marie SharpWelcome to the community:hugging_face:

Eniola Kolawole (13:51:38) (in thread): > Thanks much@Adeshile Oluwatosin

Mildred Anashie (13:53:10) (in thread): > Hi@Eniola KolawoleGood to have you here again:hugging_face:

Joy (13:55:45) (in thread): > Welcome@Anne-Marie Sharp:sparkles:

Joy (13:56:15) (in thread): > Welcome@Eniola Kolawole:sparkles:

Joy (13:56:49) (in thread): > Welcome@Dorcas Odetayo:sparkles:

Joy (13:57:19) (in thread): > Welcome@Jesulolufemi Adelanke:sparkles:

Eniola Kolawole (13:57:30) (in thread): > Thanks much@Mildred Anashie

Eniola Kolawole (13:57:41) (in thread): > Thanks much@Joy

Joy (13:57:52) (in thread): > Welcome@Precious Chijioke

Anne-Marie Sharp (14:05:51) (in thread): > Hello@Precious Chijiokewelcome

Anne-Marie Sharp (14:06:29) (in thread): > Hello@Jesulolufemi Adelankewelcome

Anne-Marie Sharp (14:07:01) (in thread): > Hello@Dorcas Odetayowelcome

Eseoghene Cynthia Princewill-Ukot (14:07:42): > Hello everyone! My name is Princewill-Ukot Eseoghene Cynthia. Happy to be part of this community.

Anne-Marie Sharp (14:07:42) (in thread): > Hello@Eniola Kolawoleyou’rewelcome

Anne-Marie Sharp (14:08:43) (in thread): > Thank you !:innocent:@Adeshile Oluwatosin@Mildred Anashie@Joy

Anne-Marie Sharp (14:09:52) (in thread): > Hello@Eseoghene Cynthia Princewill-Ukotyou’rewelcome

Eseoghene Cynthia Princewill-Ukot (14:10:50) (in thread): > Thank you@Anne-Marie Sharp

Eniola Kolawole (14:19:44) (in thread): > Thanks much@Anne-Marie Sharp

Eniola Kolawole (14:20:14) (in thread): > Welcome:hugging_face:@Anne-Marie Sharp

Ndukauba Oluchi (14:20:39) (in thread): > you are welcome@Eseoghene Cynthia Princewill-Ukotfeel free to ask any questions if you feel stuck! cheers:tada:

Eniola Kolawole (14:20:42) (in thread): > Welcome:hugging_face:@Eseoghene Cynthia Princewill-Ukot

Adeshile Oluwatosin (14:23:58) (in thread): > Welcome@Eseoghene Cynthia Princewill-Ukot

Mildred Anashie (14:37:17) (in thread): > Welcome@Eseoghene Cynthia Princewill-Ukot

Precious Chijioke (14:39:56) (in thread): > Thank you@Adeshile Oluwatosin

Precious Chijioke (14:41:36) (in thread): > Hello@Anne-Marie Sharpwelcome to the community

Jane Ezeala (Jannyblink’s) (14:44:19): > Hello everyone! my name is Jane Ezeala, and I’m excited to be part of this group. I look forward to learning, collaborating, and sharing insights with you all.

Eniola Adebayo (14:49:13): > Hello everyone! My name isEniolaand Iam glad to be here

Anne-Marie Sharp (14:49:57) (in thread): > Hello@Jane Ezeala (Jannyblink’s)you’rewelcome

Anne-Marie Sharp (14:51:25) (in thread): > Hello@Eniola Adebayowelcome

Ndukauba Oluchi (14:52:10) (in thread): > welcome@Jane Ezeala (Jannyblink’s)

Ndukauba Oluchi (14:52:28) (in thread): > welcome@Eniola Adebayo

Adeshile Oluwatosin (15:05:00) (in thread): > Welcome:tulip:@Jane Ezeala (Jannyblink’s)

Adeshile Oluwatosin (15:05:26) (in thread): > Welcome:tulip:@Eniola Adebayo

Juliana Kentomahun Mautin (15:10:23): > Welcome@Eniola Adebayo. We are excited to have you here. Do not hesitate to sek for clarification when needed.

Eseoghene Cynthia Princewill-Ukot (15:13:19) (in thread): > Thanks everyone

Precious Chijioke (15:18:43) (in thread): > Welcome@Eniola Adebayo

Mildred Anashie (15:19:12) (in thread): > Welcome@Jane Ezeala (Jannyblink’s):hugging_face:

Anne-Marie Sharp (15:39:15) (in thread): > Thank you!:pray:@Eniola Kolawole@Precious Chijioke

Dorcas Odetayo (15:42:47) (in thread): > Welcome@Eseoghene Cynthia Princewill-Ukot

Dorcas Odetayo (15:43:13) (in thread): > Welocme@Jane Ezeala (Jannyblink’s)

Dorcas Odetayo (15:43:39) (in thread): > Welcome@Eniola Adebayo

Dorcas Odetayo (15:44:09) (in thread): > Welcome@Anne-Marie Sharp

Charles Ebong (15:44:39) (in thread): > Hello Everyone, I am Charles Ebong, and I am excited to be a part of this wonderful community. I am eager to learn, collaborate, and contribute to this project.

Igber Nicholas (15:44:52): > Hi Everyone, I’m Nicholas Igber, super excited to be here, cheers!

Charles Ebong (15:45:21): > Hello Everyone, I am Charles Ebong, and I am excited to be a part of this wonderful community. I am eager to learn, collaborate, and contribute to this project.

Anne-Marie Sharp (15:46:22) (in thread): > Hello@Igber Nicholas, welcome

Anne-Marie Sharp (15:47:05) (in thread): > Hello@Charles Ebongyou’rewelcome

Ndukauba Oluchi (15:53:05) (in thread): > You are welcome@Charles Ebong

Precious Chijioke (15:54:24): > @Svetlana Ugarcina PerovicPlease how do we reach out to mentors to mentor us. I have checked if there’s instructions on how to reach out to mentors but can’t trace it in the channel. Should we send direct message via this communication channel or reach out to them through any of handles provided in Outreachy website.

Ndukauba Oluchi (15:56:22) (in thread): > Hi@Precious Chijiokeyou can just tag them here and ask your questions. They are very much available to help you!

Adeshile Oluwatosin (15:56:40) (in thread): > Welcome:tulip:@Igber Nicholas

Adeshile Oluwatosin (15:57:57) (in thread): > Hello@Precious ChijiokeThe main communication channel is slack. Feel free to ask your questions.

Adeshile Oluwatosin (15:58:28) (in thread): > Welcome:tulip:@Charles Ebong

Ndukauba Oluchi (15:58:51): > Hello everyone this is the link to the welcome material :https://community-bioc.slack.com/canvas/C04RATV9VCYIt will guide you while curating your papers, don’t forget to ask your questions when you feel stuck! Thank you. - File (Canvas): Welcome material

Igber Nicholas (16:03:42) (in thread): > Thank you!!

Jesulolufemi Adelanke (16:04:03): > Thank you@Ndukauba Oluchi

Anne-Marie Sharp (16:09:04) (in thread): > Thank you@Dorcas Odetayo:pray:

Adeshile Oluwatosin (16:10:15): > Welcome everyone:tulip:If you are just joining, Read all instructions to get started herelinkIt is stated that you must complete the initial contribution before you move to the second one. > Happy contributing:dizzy:I also think it’s best to reply in threads when needed, my opinion. - Attachment: #94 Welcome Outreachy Applicants! > ### Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > ### BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > ### Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > ### First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > ### Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > ### Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > ### Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > ### Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > ### Contributions > > Remember to record your contributions in Outreachy.

Scholastica Urua (16:16:07) (in thread): > Hi@Precious ChijiokeInstead of sending direct messages to mentors, you can post your question(s) here on the Slack channel. This way, other applicants can also benefit from the discussion. A mentor will respond, and others in the community may also be able to help as well.

Jesulolufemi Adelanke (16:39:46) (in thread): > Hi@Adeshile OluwatosinThank you so much.

Ndukauba Oluchi (16:40:05): > Hello everyone, Please I need help. > Fig 3 in this paper:https://journals.asm.org/doi/10.1128/mbio.02023-24Shows the LDA score and relative abundance > > Am I to curate the relative abundance considering the clusters? And if yes How do I do so?@Scholastica Urua@Aleru Divine@Kate RasheedThank you so much!

Adeshile Oluwatosin (16:45:09) (in thread): > Hello@Ndukauba OluchiFigure 3 is curatable

Adeshile Oluwatosin (16:46:30) (in thread): > I can see that Figure 3A and 3D both have different groups, hence curate as different experiments

Adeshile Oluwatosin (16:49:11) (in thread): > Group 0: POS f0 (3A), Neg-17 (3B) > Group 1: pos f7(3A), Pos-10 (3B)

Ndukauba Oluchi (16:51:01) (in thread): > Thank you@Adeshile OluwatosinIs 3B and 3E (relative abundance) curatable and how do I curate it?

Lois Omonaiye (17:03:01): > Hello everyone! I’m Lois Omonaiye. I’m excited to contribute meaningfully, collaborate with the team, and learn from each of you. Looking forward to this journey together!

Adeshile Oluwatosin (17:04:05) (in thread): > Figure 3B and 3E shows significance tbh > Bacteroidaceae to Bacteroidales is NS in Fig 3B. > > There are three comparisons each : > 1. In fig 3B > Group 0: Neg-F0, Neg-F7, Neg-F30 > Group 1: POS-F0, POS-F7, POS-F30 > > 2. In fig 3E > Group 0: Neg-I0, Neg-I7, Neg-I30 > Group 1: POS-I0, POS-I7, POS-I30

Dorcas Odetayo (17:04:24) (in thread): > Welcome@Lois Omonaiye

Adeshile Oluwatosin (17:04:54) (in thread): > Kindly write in full when curating@Ndukauba Oluchi

Adeshile Oluwatosin (17:06:05) (in thread): > Welcome:tulip:@Lois Omonaiye

Mildred Anashie (17:09:35) (in thread): > Hi Lois > > Welcome:hugging_face:

Shahenda Soliman (17:09:37) (in thread): > Welcome:hugging_face::cherry_blossom:

Richard Akintola (17:19:42) (in thread): > Hello, good day everyone, > > My name is Richard Akintola and I am glad to be here to contribute to BugSigDB. > > I look forward to collaborating, honing my skills, and learning/relearning. > > Thank you for having me.

Juliana Kentomahun Mautin (17:21:46) (in thread): > Welcome@Lois Omonaiye.

Francisca Gundu (17:30:57): > Hello everyone! I’m Francisca. I’m excited to contribute meaningfully, collaborate with the team, and learn from each of you. Looking forward to this journey together:hugging_face:!

Precious Orakwe (17:32:32) (in thread): > Welcome to the community@Francisca Gundu

Francisca Gundu (17:41:07) (in thread): > Thank you@Svetlana Ugarcina Perovic

Anne-Marie Sharp (17:43:29) (in thread): > Hello@Lois Omonaiyewelcome

Anne-Marie Sharp (17:44:03) (in thread): > Welcome@Francisca Gundu

Mildred Anashie (17:51:24) (in thread): > Hi@Adeshile OluwatosinI’m thinking the taxa in 3B and 3E is quite similar to 3A and 3D (more like, exactly the same). It appears to be quite unclear if 3B and 3E should be curated, the comparison isn’t so clear to me:thinking_face:

Adeshile Oluwatosin (17:51:56) (in thread): > The contrast is different,that’swhy

Adeshile Oluwatosin (18:09:36) (in thread): > Following the groups , use the colours to figure which taxa to curate as increased or decreased abundance

Anne-Marie Sharp (18:16:51) (in thread): > Well done@Adeshile Oluwatosin

Juliana Kentomahun Mautin (18:34:20) (in thread): > Welcome@Francisca Gundu. We are excited to have you here

Precious Orakwe (18:36:38): > Good day@Svetlana Ugarcina Perovicthe link to the already curated artical for the mini curation is not opening, what can i do?

Juliana Kentomahun Mautin (18:47:40) (in thread): > Really excited about this:slightly_smiling_face::slightly_smiling_face::smiley::slightly_smiling_face:. Please what time is MVIF starting?

Halima Momoh (18:55:49) (in thread): > If you want to accurately curate the study’s findings, this is what I think you should do > focus on microbial taxa that exhibit significant differences in abundance between the clusters presented in Figure 3, then note the LDA scores associated with these taxa, as they indicate the effect size of each taxon’s differential abundance. > once you’ve been able to this, you can then get the relative abundance values of these taxa within each cluster to provide context to their differential presence. I hope this helps too.

isaac imitini (19:13:45): > Hi Everyone, Isaac here. Excited to be part of the contribution phase and looking forward to working with everyone.

Mildred Anashie (19:40:19) (in thread): > @Adeshile OluwatosinIt doesn’t appear to be pairwise, or am I missing something?

Juliana Kentomahun Mautin (19:44:24) (in thread): > Hello@Precious Orakweit’s opening from my end. I suggest you try again

Mildred Anashie (19:45:52) (in thread): > Hi@Precious OrakweI experienced same but felt it was my connection, What I did was copy the PMID and paste on BugSigdb and I got the study. You can try same, however here’s thelinkto the study - Attachment (BugSigDB): Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users - BugSigDB > INTRODUCTION: Smoked, and especially smokeless, tobacco are major causes of oral cancer globally.Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing.

Juliana Kentomahun Mautin (19:46:51) (in thread): > Hello@isaac imitiniyou are welcome, we are excited to have you here:blush:. > > Kindly check out the message by@Svetlana Ugarcina Perovicto get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out the post which provides insightful tips on how to start your first curation by@Aleru Divine.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY. > > If you need any clarification, please do not hesitate to reach out,we are here to help each other. Welcome again - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Mildred Anashie (19:47:47) (in thread): > Welcome@isaac imitini

isaac imitini (19:48:19) (in thread): > Thank you@Juliana Kentomahun Mautin, currently familiarizing myself with every information before I get started.

isaac imitini (19:48:32) (in thread): > Thank you as well@Mildred Anashie

Anne-Marie Sharp (20:00:13) (in thread): > Welcome@isaac imitini

Mildred Anashie (20:27:22): > Hello Everyone:wave:I just successfully completed my first contribution (You can find link and information about the first contributionhere).Wondering how to get started? Do well to carefully go through the onboarding materials and videos. The instructions on theGithub issueis quite straight forward and this helped me to easily navigate the quiz form.N/B; The annotated article and the instructions on the quiz form has the information you need to finish this task.Also, If you need further assistance/clarity feel free to ask questions.Thank youand all the best:sparkles: - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Anne-Marie Sharp (20:28:19) (in thread): > Same here. I noticed that the linkhttps://bugsigdb.org/34436669on the curation form/quiz page was repeatedly not working on my end. > So I entered BugSigDB main page and searched for the PMID(that is34436669) in the search bar and I could access the article. - Attachment (BugSigDB): Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users - BugSigDB > INTRODUCTION: Smoked, and especially smokeless, tobacco are major causes of oral cancer globally.Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing.

Anne-Marie Sharp (20:36:09): > Hello everyone. Please how can I record my first contribution if I have already closed the link/page where I took the quiz/mini-curation

Jesulolufemi Adelanke (20:46:45) (in thread): > Check if you received a confirmation email or any record of your submission. If not, you might need to retake it or reach out to the BugSigDB team to confirm whether your contribution was recorded. You can also check your account to see if there’s a history of your submissions

Anne-Marie Sharp (20:48:58) (in thread): > Ididn’treceive an email. I only saw a message on the page that it has been recorded or something similar to that when I was done with the quiz and submitted.

Ndukauba Oluchi (20:51:26) (in thread): > Hello@Anne-Marie SharpUse this linkhttps://github.com/waldronlab/BugSigDBcuration/issues/94 - Attachment: #94 Welcome Outreachy Applicants! > ### Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > ### BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > ### Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > ### First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > ### Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > ### Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > ### Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > ### Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > ### Contributions > > Remember to record your contributions in Outreachy.

Ndukauba Oluchi (20:52:18) (in thread): > I would advice that you pin it, so you can always go back to it anytime. > Welldone!

Mildred Anashie (20:53:12) (in thread): > Hi@Anne-Marie SharpTo record your first contribution you enter thelinkto the mini curation form as your contribution URL (You don’t need to worry or take another quizif your responsesdon’tappear when you click the link, as the mentors already have a record of your submission). > > The “merged date” for this would be the date you submitted your contribution.

Ndukauba Oluchi (20:54:40) (in thread): > Hello@Mildred Anashieplease reply inside the thread so the messages can be orderly. > Welldone!

Anne-Marie Sharp (20:56:52) (in thread): > Oh, I see. Thank you@Ndukauba Oluchi@Mildred Anashiefor quickly clarifying.I’lldo that.

Mildred Anashie (21:03:26) (in thread): > Noted@Ndukauba OluchiHowever, I did reply in thread just sent to channel so anyone who might have the same question can easily come across the response

Dorcas Odetayo (21:43:22) (in thread): > I also experiencied this , I saw a message on the page that it has been recorded but i’m still filling the curation form

Jesulolufemi Adelanke (22:17:11): > Hello everyone. I’m yet to get a confirmation email for my request account to BugSigDB. Please, how do I continue?

Dorcas Odetayo (22:18:42): > Hi everyone, what url should i put in the Contribution URL on outreachy

Jesulolufemi Adelanke (22:29:25) (in thread): > Enter the link to the mini curation form as your contribution URL

Dorcas Odetayo (22:32:46) (in thread): > Ohk, Thank you@Jesulolufemi Adelanke

Fik (23:14:58): > Hi everyone, my name is Gideon. I’m excited to contribute to the BugSigDB project as part of Outreachy. I have a background in technical writing and a keen interest in microbiome research. I look forward to learning, collaborating, and improving documentation to make contributions more accessible for others. Excited to connect with you all

Fik (23:28:28) (in thread): > Thank you@Svetlana Ugarcina PerovicHi everyone, my name is Gideon from Nigeria. I’m excited to contribute to the BugSigDB project as part of Outreachy. I have a background in technical writing and a keen interest in microbiome research. I’m looking forward to learning, collaborating, and improving documentation to make contributions more accessible for others. Excited to connect with you all

Adeshile Oluwatosin (23:49:37) (in thread): > Welcome:tulip:@Francisca Gundu

Adeshile Oluwatosin (23:51:21) (in thread): > Welcome:tulip:@isaac imitini

Adeshile Oluwatosin (23:51:56): > How to record your first contribution:After successfully completing the curation form. Ensure you record your contribution as mentors can close out projects once they have gotten enough contributors. > > Concisely, Kindly follow these steps: > 1. Head to outreachy website:https://www.outreachy.org/dashboard/ > 2. Click “My Application”, then click “project lists” > 3. Click “Microbiome Study Curation” > 4. Then click “Record contributions and Apply to this project” > 5. Then Record your contribution. > Merged date is the Date you submit your contribution. > This is the contribution URL;https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw

2025-03-18

Adeshile Oluwatosin (00:02:27) (in thread): > Welcome:tulip:@Fik

Adeshile Oluwatosin (00:13:05): > Here is also a link to Frequently asked questions (FAQ):https://community-bioc.slack.com/archives/C04RATV9VCY/p1696436306217349 - Attachment: Attachment > Hi Everyone :wave: > Welcome, I noticed a lot of people joined us recently and I decided to compile the FAQ for easy access. > > 1. how do i record my contribution in the outreachy website? > Answer > > Once you complete the survey we will have a record of it. You can document in your outreachy contributions that you completed the mini curation/first contribution and just include a link to the survey or the GitHub issue talking about the first contribution. We will have what we need to link your response with your application. > > 2. Do I need to wait for first contribution to approved or reviewed before I start the second contribution > > Answer > > You do not need to wait for us to “approve” or review your first contribution before you ask for assignment for the second contribution. As long as you have completed and submitted the first contribution (the Qualtrics survey), you can then take a look at the papers available for curation which are posted as GitHub issues here: https://github.com/waldronlab/BugSigDBcuration/issues. Svetlana, Levi, or I will assign you to that article. > > 3. How do I know if my first contribution is accepted or merged? > > Answer > Once you complete the survey we will have a record of it. Don’t worry! > > 4. Should I always send a DM to mentors > > Answer > Everyone, please ask questions in this channel rather than by DM, so that everyone can participate in and benefit from the discussion. > > @C. Mirzayi (please do not tag this account) @Levi Waldron and @Svetlana Ugarcina Perovic are our mentors > > If you just joined you can get started here :point_down: > > https://community-bioc.slack.com/archives/C04RATV9VCY/p1696254316863939

Adeshile Oluwatosin (00:14:22) (in thread): > Hi@Jesulolufemi AdelankeCheck your junk/spam folder while you wait. It’s possible your approval went there.

Ouma Ronald (00:38:05) (in thread): > Welcome@Igber Nicholas. Feel at home

Anne-Marie Sharp (01:15:36) (in thread): > @Dorcas Odetayoifyou’vefilled and submitted then youdon’thave to fill it again. I guess that will be multiple submissions

Anne-Marie Sharp (01:17:28) (in thread): > Youare welcome@Fik

Anne-Marie Sharp (01:21:37) (in thread): > @Adeshile Oluwatosinthank you for sharing all the tips:pray:

Anne-Marie Sharp (01:28:20) (in thread): > Thank you for sharing!@Adeshile Oluwatosin

Krisha Jada (01:36:20): > Hi everyone! I’m Krisha, a software development student interested in contributing to the BugSigDB project for the Outreachy June 2025 cohort. I’m new to microbiome research but eager to learn and contribute. Any guidance on how to get started with my first contribution would be greatly appreciated!

Adeshile Oluwatosin (01:37:43) (in thread): > Welcome:tulip:@Krisha JadaHave a look at this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Jesulolufemi Adelanke (01:41:12) (in thread): > Thank you for sharing. To be clear, it means for every task we record our contribution, so we can have multiple contributions on outreachy?@Adeshile Oluwatosin

Adeshile Oluwatosin (01:50:21) (in thread): > Yes@Jesulolufemi AdelankeWhat is compulsory and required is to submit and record the first and second contribution > But if you contribute further, you should record as well

Adeshile Oluwatosin (01:52:23) (in thread): > NB: Do not curate an article not assigned to you yet > You must wait to be assigned > I will drop tips regarding the second contribution as well

Adeshile Oluwatosin (01:53:40): > Next steps after completing the initial contribution and recording.**** > **** > * The next thing to do is to request for a Bugsigdb account (please be patient, and check your spam folder as well for a mail)https://bugsigdb.org/Special:RequestAccount > * Head over to Github to request for a paper with tag “paper to curate” to be assigned to you by tagging a mentor with a simple statement like “I would like to curate this article”. Ensure, it is not already assigned to anyone else.link > * Navigate through theWelcome materialandCuration policyto properly get started. > **** > Good Morning:dizzy: > > ** - Attachment (BugSigDB): Special:RequestAccount - File (Canvas): Welcome material

Anne-Marie Sharp (01:55:50) (in thread): > Welcome@Krisha Jadayou can go through the welcome material at the top centre of thisbugsigdbchat. You can also go through the pins/pinned messages. You will find them helpful

Jesulolufemi Adelanke (01:57:42) (in thread): > Okay, thank you sis

isaac imitini (02:00:37) (in thread): > This has been helpful. Thank you

Adeshile Oluwatosin (02:02:29) (in thread): > You are welcome:hugging_face:

Dorcas Odetayo (02:32:30) (in thread): > @Anne-Marie SharpYes, I realized that and have already completed it

Anne-Marie Sharp (02:33:40) (in thread): > @Dorcas Odetayookay:+1:

Juliana Kentomahun Mautin (02:51:12) (in thread): > Welcome@Krisha Jada. We are super excited to have you here. I look forward to making meaningful contributions with you .

Juliana Kentomahun Mautin (02:57:07) (in thread): > Hello@Fikyou are welcome, we are excited to have you here:blush:. > > Kindly check out the message by at mentor to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out the post which provides insightful tips on how to start your first curation . > > Please do not hesitate to ask your question, we are all here to help you. Cheers to making meaningful contributions with you.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Mildred Anashie (02:57:27) (in thread): > Welcome to the community@Krisha Jada

Agboola Abimbola (03:20:02): > Hi everyone > I am Abimbola, nice to meet you all

Jesulolufemi Adelanke (03:20:46) (in thread): > :hugging_face:Welcome@Agboola Abimbola

Adeshile Oluwatosin (03:23:01) (in thread): > Welcome:tulip:@Agboola AbimbolaSee this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Anne-Marie Sharp (03:27:44) (in thread): > You’rewelcome@Agboola Abimbolado well to go through the link above that@Adeshile Oluwatosinposted so you can start your own contribution.You can also go through previous messages for a little more info.

Juliana Kentomahun Mautin (03:30:36): > Welcome@Agboola Abimbola. we are excited to have you join our community, do well to go through the post made by@Adeshile Oluwatosin. If you have any questions please do not hesitate to share it in this channel, we are all here to help you. I look forward to making impactful contributions with you here.

Mildred Anashie (03:31:36) (in thread): > Hi@Agboola AbimbolaWelcome:hugging_face:

Fik (04:01:41) (in thread): > You’re welcome@Agboola Abimbola

Fik (04:04:23) (in thread): > Thank you everyone, looking forward to working with you all

Adeshile Oluwatosin (04:09:23) (in thread): > My thought process, the description explains that the abundance is between TWO groups and not groups. Hence, why I think it can be curated in the above listed. She can reconfirm in the office hour.One of the instances “cladogram (panel C) before and after FMT in the two groups. It also examines the differences in the small intestinal microbiota (panels D and E) and their cladogram (panel F) between the two groups. “

Dorcas Odetayo (04:09:48) (in thread): > Welcome@Agboola Abimbola

Daberechi Okorie (04:58:22) (in thread): > Hi@Adeshile OluwatosinPlease I’d like to confirm, is it that after our email has been confirmed then we’ll wait for the account creation request to be approved?

isaac imitini (05:04:14) (in thread): > Concerning account creation: When you request for an account, check your spam/ junk folder for the email to confirm your account and another email containing your temporary password. If the confirmation email says the code has expired, go ahead and attempt to login with the temporary password provided. > If you do not receive an email with your temporary password, you can request for an account with a different email and username.@Daberechi Okorie

Anne-Marie Sharp (05:08:26): > Hello everyone, please when recording our contribution on Outreachy page. There’s a section for Description. Does this description have to be very detailed? Do we have to mention every step or change done?PS: I recorded my first contribution butIam not sure if I should edit the description to be more lengthy

Mildred Anashie (05:10:50) (in thread): > Also@Daberechi OkorieYou can go through this for more clarityhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727940469459309?thread_ts=1727940203.037609&channel=C04RATV9VCY&message_ts=1727940469.459309 - Attachment: Attachment > Account Creation Process: > 1. After requesting an account, check your spam folder for two emails: > ◦ A confirmation email > ◦ A temporary password email > 2. If the confirmation code has expired, proceed to log in using the temporary password provided. > 3. If you don’t receive the temporary password email, you may request an account again using a different email address and username.

Adeshile Oluwatosin (05:13:01) (in thread): > It depends on the contributorIt’syour choice > Just a simple description on how you went about the contribution should be fine@Anne-Marie Sharp

isaac imitini (05:13:22) (in thread): > I do believe a short detailed description is just fine.

Juliana Kentomahun Mautin (05:13:52) (in thread): > @Daberechi Okorieyes, it is when your email has been confirmed , them your account creation request would be approved. Check your email for an email confirmation and a temporary password email. If it happens that your code has expired, you can go ahead to login using your temporary password. > > If you still encounter any challenge, please let us know:slightly_smiling_face:

Mildred Anashie (05:16:09) (in thread): > Hi@Anne-Marie SharpI don’t think there’s a limit to what you can write, I know a description is required but your description is also based on preference > > Something brief worked for me, in this case we completed a survey, reviewed an annotated article and answered the questions.

Jesulolufemi Adelanke (05:18:14) (in thread): > Hello everyone, Please is there anything I should be doing while waiting to be assigned paper for my second task?

Anne-Marie Sharp (05:21:25) (in thread): > @Adeshile Oluwatosinnoted, thank you

Anne-Marie Sharp (05:21:41) (in thread): > @isaac imitininoted:innocent:

Anne-Marie Sharp (05:22:37) (in thread): > @Mildred Anashiethat’sinsightful,I thinkI’llstick to brief description for this first one.

Anne-Marie Sharp (05:23:47) (in thread): > @Jesulolufemi AdelankeI am also waiting to be assigned a paper for my second task but I am goingthrough all the guidelines over and over. Especially the YouTube videos. There’s always something new you will notice when you review the guidelines

Adeshile Oluwatosin (05:24:33) (in thread): > You can go through the curation policy and welcome material@Jesulolufemi Adelanke

Adeshile Oluwatosin (05:27:45) (in thread): > @Daberechi OkorieI believe your question has been answered now. > Kindly Let us know ifthere’sany other issue

Taofeecoh Adesanu (05:29:32) (in thread): > @Juliana Kentomahun MautinThere is a link attached to the beginning of this thread, please click on the link to find details of event.

Juliana Kentomahun Mautin (05:30:49) (in thread): > @Taofeecoh AdesanuThank you

Mildred Anashie (05:35:09) (in thread): > @Jesulolufemi AdelankeSince you are done with your first contribution and awaiting to start the second, while you wait, you can familiarize yourself with everything. > 1. View an already curated study to understand what is expected that can be foundhereit takes you to a random study on BugSigdb. > 2. If you haven’t already gone through the curation policy here’s alink > 3. You can also go through theFAQsmost questions you might have could have been answered there already > 4. Also scanning through and reading the welcome material thoroughly would be helpfulhttps://community-bioc.slack.com/canvas/C04RATV9VCY > 5. Finally, if you are the only one who has dropped a comment on the issue on GitHub thenI’mpositive it would be assigned to you. You can start going through the article to get acquainted with it (I personally like to read through and highlight everything I find significant before I start curating. I think this tip is very helpful). > If you have any other questions, feel free to ask:blush: - Attachment (BugSigDB): Curation Policy > .

Halima Momoh (05:38:41) (in thread): > I completely agree with@Mildred Anashie

Mildred Anashie (05:42:30): > Hello everyone:wave:Based on a question asked concerning what to do while you wait for an article to be assigned to you on GitHub, this tips could be helpful. > While you wait, you can familiarize yourself with everything. > 1. View an already curated study to understand what is expected that can be foundhereit takes you to a random study on BugSigdb. > 2. If you haven’t already gone through the curation policy here’s alink > 3. You can also go through theFAQsmost questions you might have could have been answered there already > 4. Also scanning through and reading the welcome material thoroughly would be helpfulhttps://community-bioc.slack.com/canvas/C04RATV9VCY > 5. Finally, if you are the only one who has dropped a comment on the issue on GitHub then I’m positive it would be assigned to you. You can start going through the article to get acquainted with it (I personally like to read through and highlight everything I find significant before I start curating. I think this tip is very helpful). > PS: If you are done with your first contribution and not sure what to do > > I think you can follow the Steps below > 1. Make sure to record your contribution on the outreachy website > 2. You can then go to Github to request one of the studies tagged “Paper to curate”and“outreachyJune2025” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account viahttps://bugsigdb.org/Special:RequestAccount(If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you waitallI’velisted above would surely be helpful > If you have any other questions, feel free to ask:blush: - Attachment (BugSigDB): Special:RequestAccount

Svetlana Ugarcina Perovic (05:43:44) (in thread): > Number 5: do not start with creating a study in the BugSigDB platform**** until being assigned**!

Mildred Anashie (05:45:24) (in thread): > Thank you@Svetlana Ugarcina Perovic:blush:That’svery important

Svetlana Ugarcina Perovic (05:45:33) (in thread): > I would add only one tip: while waiting to be assigned to your task, help others with their task

Star Chukwunyerenwa (Ozi) (05:47:50) (in thread): > Thank you@Mildred Anashie@Svetlana Ugarcina Perovic

Star Chukwunyerenwa (Ozi) (05:50:35): > Hi everyone, My name is Star. Looking forward to making meaningful contributions and collaborating!

Adeshile Oluwatosin (05:50:58) (in thread): > Welcome@Star Chukwunyerenwa (Ozi)

Adeshile Oluwatosin (05:51:31) (in thread): > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Halima Momoh (05:51:45): > I’m available to help if you’re having any difficulty navigating the platform or the task given:hugging_face:. feel free to reach out or ask me any question and I sure will help in the best way I can.

isaac imitini (05:51:47) (in thread): > Welcome Star.

Svetlana Ugarcina Perovic (05:52:25): > :sunny:**** Good morning, all messages checked and accounts approved!****(do not forget to tag me when communicate in the GitHub issue) > > Take your time. > Enjoy your curation. > And, do not hesitate to share here your doubts (ask questions!) and solutions for others’ doubts.

Halima Momoh (05:52:26) (in thread): > Welcome@Star Chukwunyerenwa (Ozi)

Anne-Marie Sharp (05:52:58) (in thread): > @Svetlana Ugarcina Perovicnoted

Star Chukwunyerenwa (Ozi) (05:52:59) (in thread): > Thank you

Dorcas Odetayo (05:53:07) (in thread): > Welcome@Star Chukwunyerenwa (Ozi)read the welcome material:https://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Adeshile Oluwatosin (05:53:35) (in thread): > Thank you@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (05:53:35) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742242567533189?thread_ts=1742241264.479049&cid=C04RATV9VCY - Attachment: Attachment > Hi @Precious Chijioke > Instead of sending direct messages to mentors, you can post your question(s) here on the Slack channel. This way, other applicants can also benefit from the discussion. A mentor will respond, and others in the community may also be able to help as well.

Anne-Marie Sharp (05:53:56) (in thread): > You are welcome@Star Chukwunyerenwa (Ozi)

Daberechi Okorie (05:54:08) (in thread): > Thank you@isaac imitini,@Mildred Anashie,@Juliana Kentomahun Mautin,@Adeshile Oluwatosin, I’ve gotten the temporary password and I’ve logged in!

Anne-Marie Sharp (05:54:23) (in thread): > Thank you@Svetlana Ugarcina Perovic

Halima Momoh (05:54:36) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (05:55:34) (in thread): > Thank you@Svetlana Ugarcina PerovicNoted

Adeshile Oluwatosin (05:56:01): > Hello everyone:hugging_face:I have submitted my second contribution > You can reply in threads or ask questions if stuck > I will definitely help out > > Happy contributing:dizzy:

Dorcas Odetayo (05:56:15) (in thread): > Thank You@Svetlana Ugarcina Perovic

Juliana Kentomahun Mautin (05:57:19) (in thread): > Thank you@Mildred Anashiefor sharing this.@Svetlana Ugarcina PerovicThank you for the No 5 Clarification.

Juliana Kentomahun Mautin (05:59:05) (in thread): > I’m glad you were able to login. Cheers to making impactful contributions@Daberechi Okorie

Juliana Kentomahun Mautin (06:01:54) (in thread): > Thank you@Svetlana Ugarcina Perovic.

Juliana Kentomahun Mautin (06:02:36) (in thread): > This is duly noted@Adeshile Oluwatosin

Eseoghene Cynthia Princewill-Ukot (06:02:53) (in thread): > Thank you:+1:

Anne-Marie Sharp (06:03:43) (in thread): > Well done:+1:@Adeshile Oluwatosinand thank you for assisting

Adeshile Oluwatosin (06:04:11) (in thread): > You are welcome

isaac imitini (06:04:25) (in thread): > Thank you

Daberechi Okorie (06:05:00): > Hi everyone!:wave:I just wrapped up my first contribution and I’m working on my first BugSigDB curation and wanted to thank the team for the helpful resources — they made it much easier to get started. > > If anyone is just starting out or has questions about the first contribution task, feel free to reach out to me. I’d be happy to help however I can. > Excited to be here and learn with you all!

isaac imitini (06:06:07) (in thread): > My Pleasure@Daberechi Okorie

Juliana Kentomahun Mautin (06:07:25) (in thread): > Welldone and congratulations on completing your first contributions@Daberechi Okorie:clap::clap::clap:

Daberechi Okorie (06:08:03) (in thread): > Thank you@Juliana Kentomahun Mautin!

Adeshile Oluwatosin (06:08:30) (in thread): > Well done:+1:@Daberechi Okorie

Mildred Anashie (06:10:19) (in thread): > Well done on completing your first contribution@Daberechi Okorie:clap:

Anne-Marie Sharp (06:14:04) (in thread): > Hello@Daberechi Okorie:raised_hands:well done on completing your first contribution.

Anne-Marie Sharp (06:23:50): > Hello everyone. Please, I noticed that in the tutorial video on adding a studyto bugsigdb, theURI wasn’t inputed. Are we to also leave it blank when curatingour own article?

Adeshile Oluwatosin (06:25:15) (in thread): > Yes you can

Adeshile Oluwatosin (06:25:52) (in thread): > It will auto-update@Anne-Marie Sharp

Mildred Anashie (06:25:54) (in thread): > Hi@Anne-Marie SharpOnce you input the PMID every other field should auto populate

Anne-Marie Sharp (06:42:35) (in thread): > @Adeshile Oluwatosinokay

Anne-Marie Sharp (06:43:44) (in thread): > @Mildred Anashieactually,not every other field auto populated when I put the PMID and put the mode on Auto.That’swhy I am confirming

Eniola Kolawole (06:59:32) (in thread): > Thank you@Svetlana Ugarcina Perovic

Marjorie Bourgoin (07:11:59): > Hello everyone ! I’m Marjorie, an Outreachy applicant excited to contribute to the BugSigDB project. > I have a background in Bioinformatics and transitioned into design and editorial. I’ve recently dived into data analysis and visualization, and this project seems like the perfect opportunity to reunite with science while working on my analytical skills ! > > It’s great to see such an enthusiastic and supportive community here, it’s very reassuring as i take my first step reading the documentation. I’m looking forward to contributing !:hugging_face:

Adeshile Oluwatosin (07:18:33) (in thread): > Welcome:tulip:@Marjorie Bourgoin

Adeshile Oluwatosin (07:19:00) (in thread): > See:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Anne-Marie Sharp (07:21:16) (in thread): > Hello@Marjorie BourgoinI’malready enjoying the community, I bet you will too.You are welcome. I am an aspiring Bioinformatician:innocent:looking forward to collaborating and learning

Dorcas Odetayo (07:31:10) (in thread): > Welocome to the community@Marjorie Bourgoin

Ndukauba Oluchi (07:32:44) (in thread): > Goodday Everyone:wave:I am stuck! Please help. > In a case like this how do I curate this signature considering the clusters? > Cc:@Svetlana Ugarcina Perovic - File (JPEG): IMG_20250318_123049.jpg

Ndukauba Oluchi (07:36:01) (in thread): > In Figure 3C > Link:https://journals.asm.org/doi/10.1128/mbio.02023-24I can see some prefix like Ab, bc just before the taxon e.g > ab:o__Enterobacterales > What does ab mean?

Ndukauba Oluchi (07:44:20) (in thread): > Exactly:100:@Mildred Anashie

Daberechi Okorie (07:55:00): > Hi @Svetlana Ugarcina Perovic****,****I was reviewing a study and it seems like they used more than one statistical test in their analysis. I wanted to ask— > should all the tests be recorded and reported in the curation? > > Here is a link to thepaper.

Ndukauba Oluchi (07:56:53) (in thread): > Hello@Daberechi Okoriecan you share the link to the paper for referencing ?

Ndukauba Oluchi (07:58:27) (in thread): > And for an indepth understanding on this > See:https://community-bioc.slack.com/canvas/C04RATV9VCYThe statistical test used for differential abundant testing is the one to be curated - File (Canvas): Welcome material

Daberechi Okorie (07:59:33) (in thread): > Yeah of course,https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1320567/full - Attachment (Frontiers): Frontiers | The gut microbiome and metabolites are altered and interrelated in patients with functional constipation > IntroductionGut microbiota and metabolites have been identified to contribute to the pathogenesis of functional constipation (FC); however, the underlying me…

Mildred Anashie (08:04:45) (in thread): > I see those prefix on the taxa beside the cladogram and those cladogramsdon’tlook curatable in my opinion > > The paper alsodoesn’treally state what it means@Ndukauba Oluchi

Ndukauba Oluchi (08:05:52) (in thread): > Statistical test is LEfSe > See: figure 1, LEfSe analysis was conducted to further identify the key differential genera between the two groups, and 30 differential genera with LDA value > 3

Mildred Anashie (08:06:00) (in thread): > Hi@Daberechi OkorieYou record only the statistical test used for differential abundance > > Other experiments could have been done in the paper but BugSigdb focus is on Differential abundance

Precious Chijioke (08:06:57): > Good Day Everyone > I’m filing the curation form and finding it a bit difficult to identify theleftmost taxon in the PDF that shows differential abundance results. I have gone through it over and over but can’t trace the differentially abundant. Please how can I navigate through so that I’ll complete the curation form.@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine

Ndukauba Oluchi (08:08:12) (in thread): > @Daberechi Okoriejust read the Bugsigdb welcome material I sent, you would understand these terms in no time! Well Done:+1:

Ndukauba Oluchi (08:09:29) (in thread): > Hi@Precious Chijiokethe leftmost taxon is the the first signature at the left.

Mildred Anashie (08:09:36) (in thread): > Hi@Precious ChijiokeYou can do Ctrl + F and type differential abundance, this can help you find the figures or tables that show differential abundance. > > From what I remember you are to identify the leftmost from the first figure that is showing differential abundance

Precious Chijioke (08:10:45) (in thread): > Thank you@Ndukauba Oluchi@Mildred Anashiefor your assistance. I truly appreciate your help.

Ndukauba Oluchi (08:11:01) (in thread): > Anytime!

Mildred Anashie (08:11:29) (in thread): > Also, pay attention to the annotations on the articleit’sstated somewhere there@Precious ChijiokeAnd you are welcome:hugging_face:

Ndukauba Oluchi (08:12:04) (in thread): > Right?@Mildred AnashieI agree with you. > Thank you.

Ndukauba Oluchi (08:14:07) (in thread): > Yes for example when you see g_lactobacillus > It means genus Lactobacillus > When you see s_ firmicuties > It means Specie Firmicuties > Do you understand?

Svetlana Ugarcina Perovic (08:16:09) (in thread): > p_ firmicutes Firmicutes only can be phylum > here is an example for species: > s_lactobacillus_crispatus

Ndukauba Oluchi (08:17:34) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the clarification > I misspelt firmicutes:joy::joy::joy:

Svetlana Ugarcina Perovic (08:19:21) (in thread): > Please note Firmicutes are not species. Firmicutes is the phylum taxonomy rank.

Precious Chijioke (08:19:55) (in thread): > @Ndukauba Oluchiyes I understood what you said.@Svetlana Ugarcina Perovicthank you for the clarity.

Eseoghene Cynthia Princewill-Ukot (08:20:51): > I just finished with my first contribution and i saw this- ’ We thank you for your time spent taking this survey. your response has been recorded’. Is that right?

Mildred Anashie (08:21:45) (in thread): > That’scorrect@Eseoghene Cynthia Princewill-UkotThe mentors have a record of your submission

Eseoghene Cynthia Princewill-Ukot (08:22:46) (in thread): > Great. So what do i do next?

Mildred Anashie (08:23:38) (in thread): > Please see this > I already outlined what you could do nexthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742290950340199 - Attachment: Attachment > Hello everyone :wave::skin-tone-5: > > Based on a question asked concerning what to do while you wait for an article to be assigned to you on GitHub, this tips could be helpful. > While you wait, you can familiarize yourself with everything. > > 1. View an already curated study to understand what is expected that can be found here it takes you to a random study on BugSigdb. > 2. If you haven’t already gone through the curation policy here’s a link > 3. You can also go through the FAQs most questions you might have could have been answered there already > 4. Also scanning through and reading the welcome material thoroughly would be helpful https://community-bioc.slack.com/canvas/C04RATV9VCY > 5. Finally, if you are the only one who has dropped a comment on the issue on GitHub then I’m positive it would be assigned to you. You can start going through the article to get acquainted with it (I personally like to read through and highlight everything I find significant before I start curating. I think this tip is very helpful). > PS: If you are done with your first contribution and not sure what to do > > I think you can follow the Steps below > 1. Make sure to record your contribution on the outreachy website > 2. You can then go to Github to request one of the studies tagged “Paper to curate” and “outreachy June2025” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait all I’ve listed above would surely be helpful > > If you have any other questions, feel free to ask :blush:

Eseoghene Cynthia Princewill-Ukot (08:24:47) (in thread): > Thanks@Mildred Anashie

Kate Rasheed (08:46:04): > We are live:sparkles:Link to register and join:https://cassyni.com/s/mvif-37https://community-bioc.slack.com/archives/C04RATV9VCY/p1742229778962219?thread_ts=1741772477.052139&cid=C04RATV9VCY - Attachment (Cassyni): MVIF 37 - Special event on Microbiomes in Extreme Environments - Schedule of sessions · Cassyni > Microbiome Virtual International Forum (MVIF) is a recurring bite-sized alternative to multi-day microbiome conferences: Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference. > > Forum n. 37 is a Special Atlantic-first event, with live panel talks starting 18th March 2025, 9:00 am New York time (see what time it is where you are here and add to your calendar here). > > For Pacific time zones, recorded panel talks with live hosting and discussion will start on 20th March at 10 am Tokyo time (see what time and date it is where you are here and add to your calendar here). > > MVIF is a non-profit association registered in Italy > If you’d like to support MVIF, you can donate to our crowdfunding campaign . > > Thanks to our co-organizing non-commercial partners the Seerave Foundation and CUNY Graduate School of Public Health & Health Policy and our Gold Sponsor Roche for their support. > > Matanu! - Attachment: Attachment > TOMORROW join MVIF, see you there!

Eniola Kolawole (09:14:17) (in thread): > Just seeing this > I’m unable to register and join from my end.

Precious Chijioke (09:16:57) (in thread): > @Adeshile OluwatosinThank you for sharing this guide. It’s very helpful.

Anne-Marie Sharp (09:38:45) (in thread): > @Kate Rasheedplease which part of the page/site exactly is the live happening?I’veregistered butit’sunclear to me

Kate Rasheed (09:40:05) (in thread): > Try this@Anne-Marie Sharp:https://streamyard.com/watch/HDQGayRaFMaX - Attachment (StreamYard): MVIF 37 - Special event on Microbiomes in Extreme Environments [ATLANTIC] > You’ve been invited to join this webinar!

Eniola Kolawole (09:40:11): > Good afternoon everyone > > I will like to ask if there’s a need to request for another BugSigDB account if I already have one? > Thanks.

Anne-Marie Sharp (09:41:56) (in thread): > @Kate Rasheedthank you,I’vejoined now.

Svetlana Ugarcina Perovic (09:44:07) (in thread): > No, please do not request more than one account: you need just one active BugSigDB account.

Eniola Kolawole (10:07:41) (in thread): > Thank you@Svetlana Ugarcina Perovic

Taofeecoh Adesanu (10:15:07): > Hello everyone! > Here is a subtle reminder that thecuration policywill always be your best friend as you are acclimatizing yourself to contributing to BugSigDb:slightly_smiling_face:. - Attachment (BugSigDB): Curation Policy > .

Jesulolufemi Adelanke (10:36:19): > Yes, I absolutely agree with you@Taofeecoh Adesanu

Precious Chijioke (10:37:33) (in thread): > Yes, I totally agree with you@Taofeecoh Adesanu

Dorcas Odetayo (10:50:15) (in thread): > Agreed:white_check_mark:

Shade Akinremi (11:03:23): > I accidentally submitted an incorrect mini-curation. After answering the questions on the first page, I kept clicking the “Next” button to check the remaining questions, but this unintentionally submitted the form. I have since submitted a complete and accurate version. What are the implications?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (11:03:54) (in thread): > No worries. Noted. cc<@UBNSEMS3S>

Dorcas Odetayo (11:05:02): > Hi@Svetlana Ugarcina Perovic, When I’ve completed writing a study. What are the next steps?

Svetlana Ugarcina Perovic (11:08:42) (in thread): > This onehttps://github.com/waldronlab/BugSigDBcuration/issues/636?

Svetlana Ugarcina Perovic (11:09:20) (in thread): > Just comment “ready for review” and leave a link to your curation i.e. BugSigDB study. Thanks!

Dorcas Odetayo (11:10:08) (in thread): > :white_check_mark:Ok

Kafayat Azeez-Fashola (11:12:08): > Hi everyone!I am Kafayat Azeez-Fashola, a data analyst and researcher. I am excited to explore the world of Microbiome with you all.Would you kindly guide me on how to get started?Thank you.

Svetlana Ugarcina Perovic (11:12:19) (in thread): > While waiting for the review select another paper to curate AND help others to finalize their curation.

Jesulolufemi Adelanke (11:12:48) (in thread): > Welcome@Kafayat Azeez-FasholaKindly go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169. Don’t hesitate to reach out when you have questions - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Dorcas Odetayo (11:13:25) (in thread): > Welcome@Kafayat Azeez-Fashola

Daberechi Okorie (11:13:35): > Hi@Svetlana Ugarcina Perovic, > > I accidentally duplicated an experiment entry and just realized I can’t delete it because I don’t have admin access. Could you please help me remove it or guide me on what to do? This is the link to theduplicate.. > Thank you! - Attachment (BugSigDB): 38125567/Experiment 2 > .

Adeshile Oluwatosin (11:14:36) (in thread): > Welcome:tulip:@Kafayat Azeez-Fashola

Svetlana Ugarcina Perovic (11:15:34) (in thread): > Please go to your GitHub issue and comment what exactly to delete. Thanks!

Dorcas Odetayo (11:15:42) (in thread): > Okay, I’ll work on another paper and help others.

Jesulolufemi Adelanke (11:16:15) (in thread): > @Kafayat Azeez-Fasholayou should also go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742290950340199?thread_ts=1742290950.340199&cid=C04RATV9VCY. Most of your questions might have been answered already, you can always scroll up. - Attachment: Attachment > Hello everyone :wave::skin-tone-5: > > Based on a question asked concerning what to do while you wait for an article to be assigned to you on GitHub, this tips could be helpful. > While you wait, you can familiarize yourself with everything. > > 1. View an already curated study to understand what is expected that can be found here it takes you to a random study on BugSigdb. > 2. If you haven’t already gone through the curation policy here’s a link > 3. You can also go through the FAQs most questions you might have could have been answered there already > 4. Also scanning through and reading the welcome material thoroughly would be helpful https://community-bioc.slack.com/canvas/C04RATV9VCY > 5. Finally, if you are the only one who has dropped a comment on the issue on GitHub then I’m positive it would be assigned to you. You can start going through the article to get acquainted with it (I personally like to read through and highlight everything I find significant before I start curating. I think this tip is very helpful). > PS: If you are done with your first contribution and not sure what to do > > I think you can follow the Steps below > 1. Make sure to record your contribution on the outreachy website > 2. You can then go to Github to request one of the studies tagged “Paper to curate” and “outreachy June2025” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait all I’ve listed above would surely be helpful > > If you have any other questions, feel free to ask :blush:

Daberechi Okorie (11:16:31) (in thread): > Will do, thank you!

Kafayat Azeez-Fashola (11:17:21) (in thread): > Thanks for the heads up@Jesulolufemi Adelanke

Anne-Marie Sharp (11:21:00) (in thread): > You are welcome@Kafayat Azeez-Fashola

Dorcas Odetayo (11:22:53): > Hi everyone, > I’ve completed my second contribution! & i’m Happy to help anyone who needs assistance.:blush:

Anne-Marie Sharp (11:23:36) (in thread): > Well done@Dorcas Odetayo

Mildred Anashie (11:24:17) (in thread): > Well done@Dorcas Odetayo:clap:

Dorcas Odetayo (11:25:12) (in thread): > Thanks every one:heart:

Jesulolufemi Adelanke (11:28:47) (in thread): > Under experiment, for the condition stated. In my paper, I have constipation listed there, but it’s showing no results and it’s not in the ontology lookup

Dorcas Odetayo (11:31:26) (in thread): > I had the same issue, so I selected Constipation Disorder instead of Functional Constipation since it wasn’t available.

Mildred Anashie (11:32:01) (in thread): > @Jesulolufemi AdelankeConstipation is a condition on Bugsigdb….

Jesulolufemi Adelanke (11:32:32) (in thread): > Thank you.

Jesulolufemi Adelanke (11:35:43) (in thread): > So, I have two condition listed here. And they both have different sample sizes under group 1, how do I include them

Mildred Anashie (11:36:53) (in thread): > You can record as different experiments@Jesulolufemi Adelanke

Precious Chijioke (11:37:09): > Hello Everyone, > I’ve completed my first contribution. If you need any help I will glad to assist you. > One of the tips that helped me is going through the welcome materialhttps://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Anne-Marie Sharp (11:38:28) (in thread): > Well done@Precious Chijioke

Jesulolufemi Adelanke (11:39:05) (in thread): > Okay, can you explain further

Mildred Anashie (11:40:54) (in thread): > Share a link to your paper, It could help me explain better

Precious Chijioke (11:41:42): > Please I clicked on the link in my mail few seconds ago after requesting for BugSigDB account creation and it says confirmation code have expired. Please I need assistance@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine

Svetlana Ugarcina Perovic (11:43:41) (in thread): > It’s approvedhttps://bugsigdb.org/User:PreciousChijioke - Attachment (BugSigDB): User:PreciousChijioke > I am Precious Chijioke, a product Designer skilled in crafting intuitive, engaging, user-friendly, digital experiences that merge aesthetics with functionality….

Jesulolufemi Adelanke (11:44:12) (in thread): > https://www.nature.com/articles/s41598-024-60683-6 - Attachment (Nature): Microbial imbalance in Chinese children with diarrhea or constipation > Scientific Reports - Microbial imbalance in Chinese children with diarrhea or constipation

Precious Chijioke (11:44:22) (in thread): > Alright, thank you for the confirmation@Svetlana Ugarcina Perovic

Mildred Anashie (11:54:52) (in thread): > I somehow missed this:pensive:

Jesulolufemi Adelanke (11:54:54) (in thread): > @Mildred Anashie

Mildred Anashie (12:07:23) (in thread): > You have two conditions in the paper Diarrhea and Constipation. For the experiments with Diarrhea and Healthy controls the condition would be diarrhea and for the experiment between constipation and healthy control the condition would be Constipation@Jesulolufemi Adelanke

Adeshile Oluwatosin (12:16:32) (in thread): > Well done@Dorcas Odetayo

Jesulolufemi Adelanke (12:20:29) (in thread): > In the curation policy, if I have multiple experiments, I should duplicate. How do I do that, to record the different conditions

Adeshile Oluwatosin (12:21:43) (in thread): > Use the “duplicatethisexperiment”button

Adeshile Oluwatosin (12:22:04) (in thread): > Then edit the condition, for the second experiment

Adeshile Oluwatosin (12:22:52) (in thread): > And then click save.

Adeshile Oluwatosin (12:23:48) (in thread): - File (JPEG): IMG_3863

Jesulolufemi Adelanke (12:27:09) (in thread): > Okay, I’ll find this “duplicate this experiment” after I save study?.

Adeshile Oluwatosin (12:29:20) (in thread): > When you create an experiment and save > It saves as Experiment 1 > Then you will see the tabs in the image listed > You can proceed to duplicate

Adeshile Oluwatosin (12:30:03) (in thread): > You don’t necessarily need to duplicate experiments though, you can as well just create another experiment that saves as experiment 2

Karima Diafi (12:30:38) (in thread): > Hi@Svetlana Ugarcina Perovic, should I proceed with the curation, or do more articles need to be added?

Jesulolufemi Adelanke (12:30:39) (in thread): > Okay, thank you so much for clarifying.

Adeshile Oluwatosin (12:33:28) (in thread): > I think either ways is a part of contributing@Karima DiafiSimply request to be assigned a paper on github. Wait for a response from a mentor before curating.

Krisha Jada (12:50:10) (in thread): > I have been facing the same issue. I would really appreciate some help.@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine

Adeshile Oluwatosin (13:20:37) (in thread): > Well done@Precious Chijioke

Ndukauba Oluchi (13:41:06) (in thread): > Hi@Krisha JadaBe patient, I believe it is been looked into. Cheers:tada:

Muraina Boluwatife (13:59:05): > Hi everyone. > > My name is Muraina Boluwatife, an outreachy intern candidate, It is my pleasure to be part of this community and I am looking forward to collaborate with community members and mentors to learn and have a wide range of experience in this field. > > Thank you all

Munachi Elekwa (14:02:36): > Hi everyone, Please I’m trying to complete my first contribution and I’m at the stage where you are required to view a study created by a past intern, I clicked on the link but it’s not working, it seems the link is broken. Did anyone else have this problem?

Adeshile Oluwatosin (14:02:57) (in thread): > Welcome:tulip:@Muraina Boluwatife

Adeshile Oluwatosin (14:03:34) (in thread): > See:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Munachi Elekwa (14:03:44) (in thread): > Thank you , Tosin

Adeshile Oluwatosin (14:06:16) (in thread): > Ohh yes the link is broken

Munachi Elekwa (14:06:23) (in thread): > I figured this out already, thanks

Adeshile Oluwatosin (14:07:03) (in thread): > I personally changed a part of the url to “https://“ > Or you can type out the article topic, paste on bugsigdb

Munachi Elekwa (14:07:04) (in thread): > yes, I just search the study id on the site@Adeshile Oluwatosin

Adeshile Oluwatosin (14:07:16) (in thread): > Great:+1:

Precious Chijioke (14:10:53) (in thread): > @Adeshile Oluwatosinhow do I know that a paper have been assigned to someone to curate?

Adeshile Oluwatosin (14:14:49) (in thread): > @Precious Chijiokeyou will see the tag “assigned”Which means someone else is already curating that article > You can then search for another paper without the “assigned” tag, and then request to curate

Adeshile Oluwatosin (14:15:32) (in thread): > E.g - File (JPEG): IMG_3864

Precious Chijioke (14:18:15) (in thread): > @Adeshile Oluwatosinthank you for the clarity

Precious Chijioke (14:21:49) (in thread): > @Krisha Jadacheck your inbox for the second mail with your password. Try logging in if it’ve been approved you’ll be able to login and change your password.

Juliana Kentomahun Mautin (14:47:18) (in thread): > Hello@Muraina Boluwatife, you are welcome to this amazing community. Kindly go through the post@Adeshile Oluwatosinjust sent. If you need any clarification, please do not hesitate to reach out. We are all here to up out, looking forward to your impactful contributions.

Anne-Marie Sharp (14:47:38) (in thread): > Welcome@Muraina Boluwatife

Juliana Kentomahun Mautin (14:49:21) (in thread): > You can also go through this post for clarity on how to make your first contribution.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY. - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Mildred Anashie (15:41:59): > Hello everyone > > Hi@Aleru Divine@Kate Rasheed@Svetlana Ugarcina PerovicI’m currently working on curating this paper and I’m unsure what the statistical test is…. > > The study mentions use of LEfSe under Beta diversity Analysis and but captures it as a between group analysis and also mentions T test and Mann Whitney U. See excerpt “A normality test was performed for continuous data. If all groups met normality and the variance between the two groups was uniform, a t-test was used for comparisons between groups. If the above conditions were not met, the non-parametric Mann-Whitney U test was used”. > > I have identified experiments in Fig 2 (I) and Fig 2 (G,H, J and K). Also, Fig 4 (F) and Fig 4 (G- M). > > My concern is what would the statistical test be for the experiments, it isn’t so clear to me. > > Thank you:pray::skin-tone-5:* > **Link to article: *https://pmc.ncbi.nlm.nih.gov/articles/PMC11704160/ - Attachment (PubMed Central (PMC)): The Role of Gut Microbiota in Male Erectile Dysfunction of Rats > Erectile dysfunction (ED) is a common male sexual dysfunction. Gut microbiota plays an important role in various diseases. To investigate the effects and mechanisms of intestinal flora dysregulation induced by high-fat diet (HFD) on erectile …

Precious Orakwe (15:46:15): > Alrigh, Thank you@Mildred Anashie

Kate Rasheed (15:46:16) (in thread): > Hello@Mildred Anashie. Please attach the link to the paper.

Mildred Anashie (15:47:45) (in thread): > Apologies@Kate RasheedI omitted it:pray:Thank you

Precious Orakwe (16:01:24): > @Mildred AnashieCan you please resend the link to that study.

Mildred Anashie (16:06:38) (in thread): > https://pmc.ncbi.nlm.nih.gov/articles/PMC11704160/

Precious Orakwe (16:19:10) (in thread): > Thank you

Precious Chijioke (16:19:35): > @Kate Rasheed@Peace Sandy@Svetlana Ugarcina Perovicplease when one applies to curate a paper how long does it take to be assigned? > > Also can I apply to curate another paper if the one I applied to takes longer time to be assigned?

Anne-Marie Sharp (16:22:11) (in thread): > @Precious Chijiokefrom what I read,you’reto apply/request for just one and wait tillit’sassigned to you. > Just be patient. I was reviewing the video tutorials, other curated papers and the curation policy while waiting.

Taofeecoh Adesanu (16:24:10) (in thread): > Hello@Precious Chijiokeit depends on the time of the day that you requested.@Svetlana Ugarcina Perovicwill typically respond to your request within 24 hours. So far you tagged her, be rest assured you’d be assigned.

Precious Chijioke (16:24:18) (in thread): > @Anne-Marie Sharpthank you for the heads up

Anne-Marie Sharp (16:26:19) (in thread): > @Precious Chijiokeyou’rewelcome.

Utibe Ita (17:14:36): > Hello Everyone, I am Miracle Ita , thrilled to be here and I am eager to dive in and help out.

Ndukauba Oluchi (17:19:13) (in thread): > Welcome@Utibe Ita:tada::clap:

Ndukauba Oluchi (17:20:08) (in thread): > See this :https://github.com/waldronlab/BugSigDBcuration/issues/94To get started:rocket: - Attachment: #94 Welcome Outreachy Applicants! > ### Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > ### BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > ### Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > ### First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > ### Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > ### Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > ### Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > ### Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > ### Contributions > > Remember to record your contributions in Outreachy.

Anne-Marie Sharp (17:20:41) (in thread): > You are welcome@Utibe Ita. Read through this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169You can also go through the welcome material at the top section of this chat and go through the previous messages for a little more info - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Utibe Ita (17:22:16) (in thread): > Thank you@Anne-Marie Sharp@Ndukauba Oluchi

Semango Nicholas (17:25:25): > Hello everyone am Nicholas and and am here to collaborate and learn

Adeshile Oluwatosin (17:30:27) (in thread): > @Mildred AnashieFigure 4F: LeFSe > 4G-M: Kruskal Wallis > > If you see Fig 4E, beta diversity was performed > If you look further: it was stated that “In LeFSe analysis, non-parametric Kruskal Wallis test was used to conduct simultaneous difference analysis for all classification level” > > For Fig 2 G-K :Kruskal WallisAll test mentioned in the statistical analysis part was not referenced to differential abundance. > My thoughts.

Adeshile Oluwatosin (17:31:14) (in thread): > Welcome:tulip:@Semango Nicholas

Adeshile Oluwatosin (17:31:42) (in thread): > Welcome:tulip:@Utibe Ita

Adeshile Oluwatosin (17:31:43) (in thread): > Welcome:tulip:@Utibe Ita

Svetlana Ugarcina Perovic (17:33:39) (in thread): > What about Fig 2 (I) identified by@Mildred Anashie,@Adeshile Oluwatosin?

Mildred Anashie (17:34:00) (in thread): > Welcome to the community@Utibe Ita:hugging_face:

Juliana Kentomahun Mautin (17:34:33) (in thread): > Welcome@Utibe Ita. Check out the post by@Ndukauba Oluchi. If you need any clarification, please do not hesitate to reach out. We are here for you. I wish you afun filled contribution:smiley:

Mildred Anashie (17:34:39) (in thread): > Hi@Semango NicholasWelcome:hugging_face:

Adeshile Oluwatosin (17:35:35) (in thread): > 2I is also Kruskal Wallis > Since the caption states this “ Heat map of the abundance of the top 20 intestinal microbiota at the genus level of the two groups of rats.”

Juliana Kentomahun Mautin (17:36:39) (in thread): > Hello@Semango Nicholasyou are welcome, we are excited to have you here:blush:. > > Kindly check out this message to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out this post which provides insightful tips on how to start your first curation .https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Svetlana Ugarcina Perovic (17:37:00) (in thread): > @Adeshile Oluwatosinhow do you know here in Fig2I what’s significant and even differential abundance result?

Juliana Kentomahun Mautin (17:37:23) (in thread): > If you need any clarification, please do not hesitate to reach out, we are here to help you:smiley:. Enjoy your contribution

Adeshile Oluwatosin (17:40:00) (in thread): > True, Figure 2I should be omittedand not curatedAs there’s no indication of which taxa is significant or not

Svetlana Ugarcina Perovic (17:41:01) (in thread): > Good night:slightly_smiling_face:

Adeshile Oluwatosin (17:41:27) (in thread): > Thank you mentor

Adeshile Oluwatosin (17:41:46): > @Svetlana Ugarcina Perovic@Kate Rasheed@Esther AfuapeGood evening > How is “Good coverage” alpha diversity curated. > Looking through slack discussion, it was omitted > Thank you so much

Yoko C (17:52:32) (in thread): > I think Good’s coverage is like a rarefaction curve, so you don’t need to curate it.

Svetlana Ugarcina Perovic (17:53:00) (in thread): > Based on this discussion herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710872789028329?thread_ts=1710868377.174839&cid=C04RATV9VCYand how@Scholastica Uruacurated it in the end:https://bugsigdb.org/37800955you can find the solution to your question. - Attachment: Attachment > I’m not sure how Goods coverage is curated > > My interpretation of the Alpha diversity from S1 is that > Sobs=increased in case > Chao=increased in case > Good coverage= unchanged > Simpson= not so sure, but I think unchanged > Shannon = increased in health > PD=increased in case > > The mentors opinions will help better - Attachment (BugSigDB): Salivary microbiome profiles for different clinical phenotypes of pituitary adenomas by single-molecular long-read sequencing - BugSigDB > The gut and salivary microbiomes have been widely reported to be significantly associated with a number of neurological disorders.

Adeshile Oluwatosin (18:00:28) (in thread): > Thank you so much

Mildred Anashie (18:14:40) (in thread): > I interpretedFig 2I to be significant since there is a clear group at the top and the color code at the sides seems to show only what is increased in both groups > > But if itisn’tcuratable thenI’llomit it > > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (18:18:06) (in thread): > @Adeshile OluwatosinLEfSe was mentioned as part of Beta diversity analysis hence my confusion as 4f plot looks somewhat like LEfSe whereas the statistical analysis sectiondoesn’tmention it > > It also clearly says T test was used for comparisons between groups (that involves two groups):thinking_face:

Adeshile Oluwatosin (18:23:04) (in thread): > Normally there’s a star or write up in the article itself indicating significance for 2I, I omitted that initially@Mildred AnashieThe reason why I didn’t consider T-test as the test used here is because of the mention of a normality test performed for continuous data previously. Also, an LDA score is shown in the image of 4F and that’s how a LeFSe result is represented. > > If you also check, 2E and 4E beta diversity results were presented first before the mention of the statistically significant resultswhich correlates with the supplementary information. You can always reconfirm at the office hour or await other responses

Anne-Marie Sharp (18:33:02): > Hello@Svetlana Ugarcina Perovic@Kate Rasheed@Esther Afuape@Aleru Divine@C. Mirzayi (please do not tag this account)@Chioma OnyidoI am curating a paper for my second contribution and I mistakenly created the same experiment twice. Please can the second experiment be deleted for me. This is the link for it:https://bugsigdb.org/25073603/Experiment_2 - Attachment (BugSigDB): 25073603/Experiment 2 > .

Mildred Anashie (18:52:46) (in thread): > I see it now@Svetlana Ugarcina PerovicFig 2I isn’t curatable. Thank you again:blush:

Mildred Anashie (18:55:08) (in thread): > @Adeshile OluwatosinThank you:hugging_face:, hopefully I can get one more response to be sure. I really want to be sure I am doing the right thing and not assuming

Juliana Kentomahun Mautin (20:08:48) (in thread): > @Anne-Marie Sharpclick on delete to remove one of the experiment

Adeshile Oluwatosin (20:35:18) (in thread): > It is not possible for a contributor to delete an experiment, only a mentor can approve that@Juliana Kentomahun Mautin

Krisha Jada (23:00:23) (in thread): > Hello, Thankyou so much. My issue has been resolved.@Ndukauba Oluchi@Precious Chijioke

2025-03-19

Daberechi Okorie (01:31:26) (in thread): > I think you should comment what you want deleted under the Github issue@Anne-Marie Sharp

Adeshile Oluwatosin (01:32:55) (in thread): > She would definitely get a response here butthat’sa great idea too@Daberechi Okorie

Anne-Marie Sharp (01:57:39) (in thread): > @Juliana Kentomahun Mautinthat doesn’t work, I tried it@Daberechi OkorieI have done that now, thank you

Daberechi Okorie (03:01:26) (in thread): > You’re welcome@Anne-Marie Sharp

Juliana Kentomahun Mautin (03:18:04) (in thread): > Oh… Thank you for the clarification@Adeshile Oluwatosin

Mariam Omiteru (03:18:51): > Hello everyone, I’m Mariam. Excited to collaborate, learn and contribute

Mildred Anashie (03:20:22) (in thread): > Welcome to the community@Mariam Omiteru:blush:Kindly go through this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Marvellous Jayesimi (03:20:34): > Hello everyone, I am Marvellous Jayesimi, excited to join this community! I am looking forward to learn from community members and mentors. Thank you all

Mildred Anashie (03:21:50) (in thread): > Welcome@Marvellous JayesimiKindly go through this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Juliana Kentomahun Mautin (03:22:37) (in thread): > Please do not hesitate to ask for clarification when needed, we are all here for each other

Juliana Kentomahun Mautin (03:25:54) (in thread): > Hello@Mariam Omiteruyou are welcome to this amazing community. Please kindly go through what@Mildred Anashiesent. If you need any clarification please do not hesitate to reach out, we are here to help out. Have a fun filled contribution:smiley:

Juliana Kentomahun Mautin (03:27:13) (in thread): > You can also check this welcome material .https://community-bioc.slack.com/archives/C04RATV9VCY/p1742241531724199 - Attachment: Attachment > Hello everyone this is the link to the welcome material : https://community-bioc.slack.com/canvas/C04RATV9VCY > > It will guide you while curating your papers, don’t forget to ask your questions when you feel stuck! Thank you.

isaac imitini (03:28:21) (in thread): > Welcome Marvelous.

isaac imitini (03:28:47) (in thread): > Welcome Mariam.

Juliana Kentomahun Mautin (03:34:46) (in thread): > You can also check out this welcome material.https://community-bioc.slack.com/archives/C04RATV9VCY/p1742241531724199

Adeshile Oluwatosin (03:37:32) (in thread): > Welcome:tulip:@Mariam Omiteru

Adeshile Oluwatosin (03:37:48) (in thread): > Welcome:tulip:@Marvellous Jayesimi

Adeshile Oluwatosin (03:51:36): > Good morning > A few things for everyone to know > Thought to drop this here. > 1. Once you request for an article to be assigned to you on GitHub. Be patient, and await the tag “assigned” before commencing curation. > 2. Once you’ve submitted on GitHub simply by tagging a mentor “SvetlanaUp” and mentioning that you are done curatingattached with a link to the study. The “needs review” tag will be added. Ensure, you make no corrections to the study till after review by a mentor. > > 3. Request for one article at a time. Complete a curation before you request for another article to be assigned to you. > > 4. You cannot request for an article with the “assigned” tag. This means someone else is already curating the article. You can only ask to assist. > > 5. Lastly, only request to be assigned to an article with the “outreachy june25” and “paper to curate” tag.

Dorcas Odetayo (04:06:53) (in thread): > Welcome@Marvellous Jayesimi

Svetlana Ugarcina Perovic (04:14:53) (in thread): > Thanks for the summary of the GitHub steps!

Adeshile Oluwatosin (04:16:23) (in thread): > My pleasure:pray:

Svetlana Ugarcina Perovic (04:17:25) (in thread): > If you need to delete something already recorded, please comment what you want to be deleted under the Github issue with your curation and tag SvetlanaUP.

Joy (04:29:14) (in thread): > Welcome@Muraina Boluwatifeto the community

Joy (04:31:14) (in thread): > Welcome to the community@Mariam Omiteru

Joy (04:31:56) (in thread): > Good job@Adeshile Oluwatosin!

Anne-Marie Sharp (04:36:01) (in thread): > @Adeshile Oluwatosinthanks for sharing@Svetlana Ugarcina Perovicnoted

Lois Omonaiye (04:39:23) (in thread): > Thank you for sharing

Mariam Omiteru (04:41:21) (in thread): > Thank you everyone, I’ll go through them

Eseoghene Cynthia Princewill-Ukot (04:48:50) (in thread): > @Adeshile Oluwatosin, pls how can i request for an article?

Joy (04:51:07) (in thread): > @Eseoghene Cynthia Princewill-Ukotyou will request for an article on github

Joy (04:51:44) (in thread): > Ensure you tag@Svetlana Ugarcina Perovicto assign one to you.

Adeshile Oluwatosin (04:51:46) (in thread): > @Eseoghene Cynthia Princewill-UkotHead over togithub issues > * Pick a paper with “outreachy june25” and “paper to curate” tag which is not yet assigned > * Click on the issue, then tag “SvetlanaUp” saying something like “I want to curate this”

Eseoghene Cynthia Princewill-Ukot (04:53:42) (in thread): > in the comments?

Joy (04:54:45) (in thread): > Yes

Eseoghene Cynthia Princewill-Ukot (04:58:00) (in thread): > Thanks@Adeshile Oluwatosin@Joy

Precious Chijioke (05:02:41) (in thread): > You are welcome@Mariam Omiteru

Precious Chijioke (05:06:40) (in thread): > Thanks for the summary@Adeshile OluwatosinYou captured all the steps for curating an article

Mildred Anashie (05:09:11) (in thread): > Thank you@Adeshile Oluwatosin:blush:

Victoria (Burah) Poromon (05:25:34): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742370696122539Just to add to this… > > Please don’t be in a hurry to submit your second contribution. You can ask for peer reviews and give 1 or 2 personssometime to send a review under your GitHub issue. > > Thank you for the clear summary!@Adeshile Oluwatosin - Attachment: Attachment > Good morning > A few things for everyone to know > Thought to drop this here. > 1. Once you request for an article to be assigned to you on GitHub. Be patient, and await the tag “assigned” before commencing curation. > 2. Once you’ve submitted on GitHub simply by tagging a mentor “SvetlanaUp” and mentioning that you are done curating attached with a link to the study. The “needs review” tag will be added. Ensure, you make no corrections to the study till after review by a mentor. > > 3. Request for one article at a time. Complete a curation before you request for another article to be assigned to you. > > 4. You cannot request for an article with the “assigned” tag. This means someone else is already curating the article. You can only ask to assist. > > 5. Lastly, only request to be assigned to an article with the “outreachy june25” and “paper to curate” tag.

Adeshile Oluwatosin (05:26:22) (in thread): > You are welcome:tulip:@Victoria (Burah) Poromon

Joy (05:29:53) (in thread): > Thank you@Victoria (Burah) Poromonand@Adeshile Oluwatosinfor this piece of information.

Anne-Marie Sharp (05:44:44): > Hello@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru DivineI am curating a paper and I noticed this “Our data showed a trend of increased abundance of Firmicutes in the gut of the constipated patients, but no statistical significance was achieved with the small sample size in this pilot study (Table 2, Fig. 3A)” In this case, am I still to report them as it was stated that no statistical significance was achieved in this study

Adeshile Oluwatosin (05:45:20) (in thread): > Kindly share a link to the paper

Svetlana Ugarcina Perovic (05:45:27) (in thread): > Please leave the link to the GitHub issue

Star Chukwunyerenwa (Ozi) (05:46:15): > Hello does anyone have an Idea on how to get the PMID or DOI of an article? I used Pubmed and I got it, just need other ideas . Thanks

Mildred Anashie (05:47:08) (in thread): > Hi@Star Chukwunyerenwa (Ozi)Typically a pubmed search does the trick, you are on track

Star Chukwunyerenwa (Ozi) (05:47:40) (in thread): > Thank you@Mildred Anashie

Adeshile Oluwatosin (05:47:54) (in thread): > Hello@Star Chukwunyerenwa (Ozi)Head topubmedThen copy the paper title, paste on pubmed > Click “cite” > Then copy out only PMIDIt should contain only numbers

Svetlana Ugarcina Perovic (05:48:24) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/637 - Attachment: #637 [Study]: Structural changes in the gut microbiome of constipated patients > ### Study Title > > Structural changes in the gut microbiome of constipated patients > > ### Pubmed ID > > 25073603 > > ### The Digital Object Identifier (DOI) > > https://doi.org/10.1152/physiolgenomics.00082.2014 > > ### First Author > > Zhu L. > > ### Journal > > Physiological Genomics > > ### Year > > 2014 > > ### Study Source > > https://journals.physiology.org/doi/full/10.1152/physiolgenomics.00082.2014 > > ### Code of Conduct Agreement > > • I agree to follow this project’s Code of Conduct

Anne-Marie Sharp (05:51:07) (in thread): > @Svetlana Ugarcina Perovicthank you, yes that is the link, was checking for it.@Adeshile Oluwatosinthat’s the link above

Star Chukwunyerenwa (Ozi) (05:56:56): > As a new contributor, it’s easy to feel overwhelmed, especially when learning a new tool. Remember to take a breather, and don’t hesitate to ask questions, fellow contributors are always here to help! > Wishing you the best:blush:You can easily find your PMID for your articles here:https://pubmed.ncbi.nlm.nih.gov/ - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 38 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Adeshile Oluwatosin (06:00:20) (in thread): > @Anne-Marie SharpDon’t curate Firmicutes, Actinobacteria and Proteobacteria as there is no significance. > From figure 3, only curate Bacteroidetes > > See: “the abundances of Bacteroidetes were significantly decreased in the gut of the constipated patients compared with the control groups”

Adeshile Oluwatosin (06:06:29) (in thread): > Table 2, Fig 3, Fig 4, Fig 5 and Table 3. > > The significance threshold is 0.05 > Hence, Curate only taxa within 0.05 > Use the (control/constiption %) to determine which would be increased or decreased abundance > You can check the text in the article as well.Table 3 has the significant taxa mentioned but check across the mentioned tables and figures

Joy (06:10:01) (in thread): > @Anne-Marie SharpSince the study explicitly states that there was no statistical significance, should not report the increase in Firmicutes as a significant finding in BugSigDB. > > In BugSigDB, findings without statistical significance should not be curated following the curation policy. > Good job@Adeshile Oluwatosin

Precious Orakwe (06:14:10): > good day@Svetlana Ugarcina Perovic@Aleru Divine@Kate Rasheedplease how do I curate this paper, which one will be the decrease and which one will be the increase - File (PNG): Screenshot (162).png

Anne-Marie Sharp (06:14:57) (in thread): > @Adeshile OluwatosinYes, I believe I am to compile the figures and tables in my source. Thank you for clarifying, it was really confusing.@Joythank you, yes. although some taxa are within/under Firmicutes, I will report them on their own. I won’t report Firmicutes as a phylum.

Mildred Anashie (06:16:09) (in thread): > Hi@Precious OrakweFrom what I see it looks like a one against all LEfSe plot. You would have just increase signatures from this > > A link to the article will help me confirm this, thank you

Precious Orakwe (06:16:25): > The red one is the control group while the green and blue one are the exposed group. Should I put in the two exposed groups together? please help me, thank you

Precious Orakwe (06:16:46) (in thread): > ok

Adeshile Oluwatosin (06:16:53) (in thread): > @Precious OrakweThis LeFSe results definitely reflects an increased abundance for one against all analysis. > Looks like three separate experiments already with just increased abundance of group 1.

Precious Orakwe (06:17:43) (in thread): > Please i dont understand@Adeshile Oluwatosinplease break down your english

Precious Orakwe (06:18:06) (in thread): > this is a link to the paperhttps://www.sciencedirect.com/science/article/pii/S2090123224000766?via%3Dihub#s0010

Adeshile Oluwatosin (06:18:13) (in thread): > Please share the link to the paper > So I can help out with listing the experiments to curate

Precious Orakwe (06:18:41) (in thread): > I have done that already

Joy (06:19:32) (in thread): > Look at the Relative Abundance Bar Charts: > > The bar charts for Allivibrio and Butyricimonas show how their abundance changes across the different conditions. > > If a taxon has a higher abundance in the experimental condition compared to control, it’s an increase. > > If a taxon has a lower abundance in the experimental condition compared to control, it’s a decrease.

Joy (06:19:59) (in thread): > Yes, please share a link to the study

Adeshile Oluwatosin (06:22:29) (in thread): > Exp 1: Grp 0( combination of con + HS), Grp 1 (Hs + Mel) > Exp 2; Grp 0( combination of con + Hs + Mel), Grp 1(Hs) > Exp 3: Grp 0(combination of Hs + Hs + Mel), Grp 1(con) > > They all have only increased abundance@Precious OrakweHence curate Red colour in Exp 3, Green bar in Exp 2 and Blue bar inExp 1

Mildred Anashie (06:23:49) (in thread): > I agree with@Adeshile Oluwatosin

Precious Orakwe (06:24:32) (in thread): > Alrigt, thanks@Mildred Anashie@Adeshile Oluwatosinfor you assistance

USLACKBOT (06:31:08): > This message was deleted.

Adeshile Oluwatosin (06:31:40) (in thread): > Okay, let me have a look

Aiysha shahid (06:32:27) (in thread): > Sure.

Mildred Anashie (06:33:54) (in thread): > I’llhave a look too

Joy (06:34:14) (in thread): > Thank you@Aiysha shahidfor this curation

Adeshile Oluwatosin (06:35:58) (in thread): > Figure 7;Mann-Whitney (Wilcoxon) testFigure 8: Mann-Whitney(Wilcoxon) test > Figure 9: LeFSe

Adeshile Oluwatosin (06:36:31) (in thread): > See: The Mann-Whitney test was used to analyze the differences in the relative abundance of species at the phylum and genus levels between two groups.

Adeshile Oluwatosin (06:37:23) (in thread): > So you have just 2 experiments > Figure 7 and 8; Exp 1 > Figure 9: Exp 2

Mildred Anashie (06:37:34) (in thread): > I see2experiments within the body of the paper > > Fig 7 and 8 used Wilcoxon and fig 9 used LEfSe > > It’s written within the figure@Aiysha shahidFig @7 and 8 would be curated as one experiment because 7 shows phylum and 8 shows genus for the same group. > > Fig 9 would be curated separately since it is a different statistical test

Joy (06:39:22) (in thread): > You are correct in your understanding of the statistical methods and experimental design employed in the study > > 1. Statistical Method – Mann-Whitney Test: The Mann-Whitney U test, also known as the Wilcoxon rank-sum test. > > > 2. Significance Threshold of 0.05: A significance threshold (alpha level) of 0.05 is commonly used in statistical analyses. > > > 3. Experimental Design: The study involved a case-control design where 29 children with functional constipation (FCG) were randomly selected, and 26 healthy children, matched for age, sex, and area, served as the control group (CG). > > > 4. Figures 7 & 8: figures labeled 7 and 8 in such studies typically present key findings related to the differences in microbiota composition or diversity between the FCG and CG. These figures are likely curatable, meaning they can be extracted and used for further analysis or presentation,@Aiysha shahid

Aiysha shahid (06:46:22) (in thread): > Yes that was a confusion that there was Leffse and Wilcoxon. So should I include 2experiment’s with FCG AND CG,with twoStatistical test in one it’s Mann-Whitney and in 2nd Leffse? As in the paper it’s written for Statistical analysis:Statistical analysis of data was performed using SPSS 29.0 software. For continuous variables with normal distribution, data were expressed as mean ± standard deviation and compared using the t-test. For non-normally distributed data, the median (interquartile range) was used and compared using the Mann-Whitney test. Categorical variables were presented numerically, with proportions expressed as percentages, and comparisons between groups were made using the χ2 test. And for it also mentioned: Further LEfSe multi-level species difference discriminant analysis was conducted from phylum to genus level, with an LDA threshold of 4.

Adeshile Oluwatosin (06:48:27) (in thread): > One statistical test means one experiment > An experiment should have one statistical test except in extremely rare case@Aiysha shahidIn this case include the statistical test seperately > As I initially listed

Aiysha shahid (06:51:59) (in thread): > Yes,let me brief it up: So there would 2experiment. 1st Experiment would include: theStatistical test as: Wilcoxon. And then there would be another experiment with Statistical test as: LEfSe. Right?

Mildred Anashie (06:53:11) (in thread): > Yes@Aiysha shahidThat’scorrect:white_check_mark:On BugSigdbyou’dchoose Mann Whitney (Wilcoxon) sincethat’show it appears

Aiysha shahid (06:54:34) (in thread): > Yeah, Thanks!:heart::raised_hands:

Juliana Kentomahun Mautin (08:39:47) (in thread): > Thank you@Adeshile Oluwatosinfor this detailed information.

Mildred Anashie (08:50:42): > Hi@Svetlana Ugarcina PerovicPlease I’ll like to delete experiment 2 in this studyhttps://bugsigdb.org/38772541 - Attachment (BugSigDB): The Role of Gut Microbiota in Male Erectile Dysfunction of Rats - BugSigDB > PURPOSE: Erectile dysfunction (ED) is a common male sexual dysfunction.Gut microbiota plays an important role in various diseases.To investigate the effects and mechanisms of intestinal flora dysregulation induced by high-fat diet (HFD) on erectile function.

Anne-Marie Sharp (08:53:01) (in thread): > @Mildred Anashiemake a comment on the GitHub site/link and tag her

Svetlana Ugarcina Perovic (09:01:24) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/646

Mildred Anashie (09:02:21) (in thread): > Okay > > Noted@Anne-Marie Sharp

Mildred Anashie (09:02:33) (in thread): > Thank you@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (09:11:49) (in thread): > TIP: try to find a paper already curated with a similar figure type and see how has been curated, in this case:https://bugsigdb.org/38378622 - Attachment (BugSigDB): Gut dysbiosis induces the development of depression-like behavior through abnormal synapse pruning in microglia-mediated by complement C3 - BugSigDB > BACKGROUND: Remodeling eubiosis of the gut microenvironment may contribute to preventing the occurrence and development of depression.

Jesulolufemi Adelanke (09:55:32): > Hello everyone > I’m working on curating this paper and I’m unsure what the statistical test is… > > The study mentions multiple tests used for the differential abundance testing, LEfSe, MaAsLin2, Kruskal-Wallis test. > and PERMANOVA used for the beta diversityhttps://www.nature.com/articles/s41598-024-60683-6 - Attachment (Nature): Microbial imbalance in Chinese children with diarrhea or constipation > Scientific Reports - Microbial imbalance in Chinese children with diarrhea or constipation

Adeshile Oluwatosin (09:55:54) (in thread): > Well done, I will have a look

Adeshile Oluwatosin (10:04:52) (in thread): > Figure 2: LeFSe “Identification of potential biomarkers using LEfSe.” > Table S3: Maaslin2 between constipation and Healthy control > Fig S3: LeFSe, description says a “cladogram used by LeFse demonstrates different bacterial genera between constipation and heathy control” > Fig S4. LeFSe, description says a “cladogram used by LeFse demonstrates different bacterial genera between diarrhea and heathy control” > Table S5/Figure 3:spearman correlation(unsure)

Jesulolufemi Adelanke (10:06:39) (in thread): > So LEfSe is the statistical test

Adeshile Oluwatosin (10:07:40) (in thread): > All the figures and tables listed should be curated

Jesulolufemi Adelanke (10:08:18) (in thread): > Thank you

Adeshile Oluwatosin (10:09:22) (in thread): > Remember different statistical test = different experiments

Adeshile Oluwatosin (10:11:54) (in thread): > I also figured that there are two different contrasts > * One between healthy controls and constipation group > * Second between healthy controls and diarrhea group

Jesulolufemi Adelanke (10:13:11) (in thread): > Yes, I duplicated the experiment to report both

Jesulolufemi Adelanke (10:14:47) (in thread): > I’m still trying to be clear on what I’m recording for the statistical test under statistical analysis. > Both LEfSe and MaAsLin2

Adeshile Oluwatosin (10:16:02) (in thread): > As said earlier > Record LEFse for one experiment > Record MaAslin2 for another experiment

Adeshile Oluwatosin (10:16:25) (in thread): > Then curate signatures with the tables or figures listed above

Anne-Marie Sharp (10:22:15): > Hello@Svetlana Ugarcina Perovic@Kate Rasheed@Esther AfuapeI added a signature to experiment 1 in the article I am curating and saved the page, but its not reflecting on the experiment 1 page where it is supposed to behttps://bugsigdb.org/25073603/Experiment_1. I checked recent changes in Bugsigdb page and saw that I added the signature, but its still not reflecting. Please what do I do? Should I record it all over again? - Attachment (BugSigDB): 25073603/Experiment 1 > .

Mildred Anashie (10:23:12) (in thread): > I agree with@Adeshile Oluwatosinon the statistical test listed. However I noticed Fig S3 and S4 is showing Family, phylum, class and not genus while Table S7 and S8 is showing the genus. Confirm this in File S1. Also, I don’t think Figure 3 and Table 5 is showing differential abundance

Adeshile Oluwatosin (10:24:39) (in thread): > In this casehttps://bugsigdb.org/25073603/Experiment_1/Signature_1 - Attachment (BugSigDB): 25073603/Experiment 1/Signature 1 > Source: Table 2, Table 3, Figure 3, Figure 4, Figure 5 Description: Abundant taxa in the gut microbiome of the constipated patients and controls Abundance in Group…

Adeshile Oluwatosin (10:24:51) (in thread): > There’sno need to record all over again@Anne-Marie Sharp

Adeshile Oluwatosin (10:25:53) (in thread): > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Mildred Anashie (10:27:32) (in thread): > You can try refreshing the study page and if it stilldoesn’twork, you can search the experiment or signature > Check to see how to search herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&channel=C04RATV9VCY&message_ts=1727957860.907319 - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Anne-Marie Sharp (10:31:41) (in thread): > @Adeshile Oluwatosin@Mildred AnashieThank you so much:pray:Noted.I’vetried both and they worked.

Francisca Gundu (10:49:47): > Hi@Svetlana Ugarcina Perovicthe condition in my paper is “stool**** consistency (EFO:0007709)****”, however, I can not find it in the BugSigDB. What should I do?https://gut.bmj.com/content/65/1/57 - Attachment (Gut): Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates > Objective The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time. > > Design Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women, we evaluated associations between microbiome richness, Bacteroidetes:Firmicutes ratio, enterotypes, and genus abundance with self-reported, Bristol Stool Scale-based stool consistency. Each sample’s microbiota growth potential was calculated to test whether transit time acts as a selective force on gut bacterial growth rates. > > Results Stool consistency strongly correlates with all known major microbiome markers. It is negatively correlated with species richness, positively associated to the Bacteroidetes:Firmicutes ratio, and linked to Akkermansia and Methanobrevibacter abundance. Enterotypes are distinctly distributed over the BSS-scores. Based on the correlations between microbiota growth potential and stool consistency scores within both enterotypes, we hypothesise that accelerated transit contributes to colon ecosystem differentiation. While shorter transit times can be linked to increased abundance of fast growing species in Ruminococcaceae- Bacteroides samples, hinting to a washout avoidance strategy of faster replication, this trend is absent in Prevotella -enterotyped individuals. Within this enterotype adherence to host tissue therefore appears to be a more likely bacterial strategy to cope with washout. > > Conclusions The strength of the associations between stool consistency and species richness, enterotypes and community composition emphasises the crucial importance of stool consistency assessment in gut metagenome-wide association studies.

Jesulolufemi Adelanke (10:49:57) (in thread): > Since I have two different experiments (based on two different conditions) and now, I’m told I’m recording two different experiments for the two statistical tests. > > Am I adding one of the statistical tests in each of the conditions or it’s a total different experiment

Adeshile Oluwatosin (10:52:31) (in thread): > E.g: if you are comparing Healthy controls and constipation > One figure has LeFSe as test, another figure/table has MaAslin2. For same comparison > That’s two different experiments > > Likewise between healthy controls and diarrhea

Jesulolufemi Adelanke (10:54:05) (in thread): > That’s two experiment under constipation

Jesulolufemi Adelanke (10:54:39) (in thread): > So, that’s four different experiments in total?

Mildred Anashie (10:54:53) (in thread): > You definitely have more than 2 experiments@Jesulolufemi Adelanke

Mildred Anashie (10:57:50) (in thread): > In textdoesn’tcite S7 and S8 as well as Fig S3 and S4 but I thinking the experiments might be more than 4I’lllook through again to confirm ifthere’s aconnection between Fig 2 and the onesI’vementioned above, sinceit’sthe same group name and statistical test

Mildred Anashie (11:08:25) (in thread): > Hi@Francisca GunduI actually do not see Stool consistency on Bugsigdb, the closest term I see is ’Abnormal stool composition’ and I think this can work. Usually if you don’t find the exact term you can work with the closest term.

Svetlana Ugarcina Perovic (11:10:10) (in thread): > Indeed closest but more general term.

Aiysha shahid (11:15:02) (in thread): > Also one more help needed@Mildred Anashie@Adeshile Oluwatosin,As this paper does not mention any changes in Alpha Diversity for Lefse test, should I mark it as unchanged or leave it blank? What would be the better approach? I think so leaving blank would be ok.

Amaka (11:15:43): > Hello everyone. My name is Amaka, am happy to join this community. Am looking forward to learning and contributing.

Mildred Anashie (11:17:29) (in thread): > It’s best to leave it blank if it doesn’t report alpha diversity for a particular contrast@Aiysha shahid

Adeshile Oluwatosin (11:18:54) (in thread): > Kindly leave blank > We record as unchanged only when the alpha diversity is mentioned but it shows no statistical significance

Adeshile Oluwatosin (11:19:00) (in thread): > @Aiysha shahid

Aiysha shahid (11:19:30) (in thread): > Hello, Welcome@Amaka. Kindly go through this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Adeshile Oluwatosin (11:20:19) (in thread): > Welcome:tulip:@Amaka

Mildred Anashie (11:20:49) (in thread): > Hi@AmakaWelcome to the community. Kindly go through what@Aiysha shahidshared to get started, the pinned messages and the welcome material would help too. Here’s a linkhttps://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Munachi Elekwa (11:21:04) (in thread): > Welcome, Amaka:tada:@Amaka, it’s nice to have you here

Aiysha shahid (11:22:38) (in thread): > Okay Thank’s@Adeshile Oluwatosin@Mildred Anashie

Francisca Gundu (11:24:32) (in thread): > Thank you@Svetlana Ugarcina Perovicand@Mildred Anashie

Jesulolufemi Adelanke (11:27:53) (in thread): > Welcome@Amaka, good to have you here

Marvellous Jayesimi (11:31:46) (in thread): > You are welcome@Amaka:hugging_face:

Anne-Marie Sharp (11:34:11) (in thread): > You’rewelcome@Amaka

Preethi grace Manthena (11:39:52) (in thread): > Hello everyone, and thank you@Svetlana Ugarcina PerovicI’m Preethi grace, and I’m curious to contribute to BugSigDB and work on microbiome research, I joined last year but due to academic commitments I haven’t contributed much, Now I am very confident to give my 100% effort to contribute, collaborate and learn. Very happy to be here :)

Anne-Marie Sharp (12:08:33): > Hello everyone. Please is it just on my end or is the NCBI site down? I’ve been trying to access it for a while now with different browsers to no availhttps://www.ncbi.nlm.nih.gov/ - Attachment (ncbi.nlm.nih.gov): National Center for Biotechnology Information

Adeshile Oluwatosin (12:09:11) (in thread): > Someone just complained of this. Just keep trying > Try another network as well

Mildred Anashie (12:10:41) (in thread): > Hi@Anne-Marie SharpI’m experiencing the same issue currently > You can tryhttps://www.uniprot.org/if you are looking for taxas - Attachment (uniprot.org): UniProt > UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.

Anne-Marie Sharp (12:11:32) (in thread): > @Adeshile Oluwatosin@Mildred Anashiethank you, maybeit’sfrom the site then. Hopefully it won’t be for long

Anne-Marie Sharp (12:12:35) (in thread): > @Mildred Anashiethank you.I’llcheck that out, although whatI’mtrying to confirm is particularly on NCBI

Ndukauba Oluchi (12:16:06) (in thread): > You are welcome:hugging_face:@Preethi grace Manthena

UBNSEMS3S (12:16:49) (in thread): > It’s up for me right now but it’s not unheard of for NIH services such as the taxonomy browser to be down for small amounts of time.

Anne-Marie Sharp (12:19:33) (in thread): > @C. Mirzayi (please do not tag this account)okay,I’llkeep that in mind, thank you

Svetlana Ugarcina Perovic (12:25:03): > Given the recent and ongoing service interruptions in PubMed, National Library of Medicine, NIH Reporter, etc., Sean Davis created a status page covering some key resources and some NIH institute pages:https://stats.uptimerobot.com/Zrqh8AhvKncc<@UBNSEMS3S>

Adeshile Oluwatosin (12:26:08) (in thread): > Thank you@Svetlana Ugarcina Perovic

Ndukauba Oluchi (12:29:19) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (12:33:10) (in thread): > Thank you@Svetlana Ugarcina Perovic

Anne-Marie Sharp (12:35:40) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic

Kafayat Azeez-Fashola (12:36:49) (in thread): > Thank you@Svetlana Ugarcina Perovic

Precious Chijioke (12:48:56): > Hello Everyone, I am working on curating this paper and need clarity in some areas. I see that there are two experiments in this paper, and I think Fig 2 & 6 are curatable. The statistical method used is Tukey’s test or Wilcoxon rank-sum test, with a sequencing platform as Metagenomics Sequencing. There’s no diversity in this paper and I understand that not all paper contain diversity. Also how can I identify the NCBI. Please I need help to know if I am correct or not.@Svetlana Ugarcina Perovic@Kate Rasheed@Peace Sandy@Scholastica UruaLink to paper:https://www.dovepress.com/therapeutic-mechanism-of-zhuyang-tongbian-decoction-in-treating-functi-peer-reviewed-fulltext-article-IJGM#f0002 - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB

Oriade Adeola (12:49:27) (in thread): > Hello everyone, Thank you@Svetlana Ugarcina PerovicMy name is Adeola Oriade from Lagos Nigeria. I’m excited to be joining the Outreachy contribution stage with BugSigDB, I look forward to collaborating, contributing and learning from this amazing community!

Adeshile Oluwatosin (12:52:11) (in thread): > Hello@Precious ChijiokeI will have a look

Adeshile Oluwatosin (12:53:00) (in thread): > First of, this is NCBI link:https://www.ncbi.nlm.nih.gov/taxonomy

Mildred Anashie (12:55:26) (in thread): > Hi@Precious ChijiokeI’lltake a look as well

Eseoghene Cynthia Princewill-Ukot (12:55:52) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (12:56:48) (in thread): > Good job@Precious Chijiokeon this curation, we will take a look at this paper.

Joy (13:01:35) (in thread): > @Precious Chijioke, Upon reviewing the paper does not include analyses of microbial diversity, such as alpha or beta diversity metrics. The research focuses on the composition of the gut microbiota and its metabolic functions, as well as the levels of fecal short-chain fatty acids (SCFAs) and serum concentrations of inflammatory markers like TLR4, NF-κB, TNF-α, and IL-6 in patients with functional constipation.

Eseoghene Cynthia Princewill-Ukot (13:02:58) (in thread): > @Adeshile Oluwatosinare you free to help?

Adeshile Oluwatosin (13:03:47) (in thread): > Figure 2C, Figure 3a, Figure 3c, Figure 4seems curatable

Adeshile Oluwatosin (13:06:30) (in thread): > Kindly state out the issues you are facing on here@Eseoghene Cynthia Princewill-Ukotso others can learn as well.I’m readilyavailable to answer all questions

Mildred Anashie (13:07:16) (in thread): > From what I see there’s alpha diversity in Fig 1c > > PD is for Faiths phylogenetic diversity

Eseoghene Cynthia Princewill-Ukot (13:07:57) (in thread): > Just got assigned to curate an article. Is the curating done on GitHub or bugsigdb?

Eseoghene Cynthia Princewill-Ukot (13:08:18) (in thread): > I’m lost

Mildred Anashie (13:08:37) (in thread): > I agree with@Adeshile Oluwatosinon the curatable figures

Joy (13:09:42) (in thread): > How are you lost@Eseoghene Cynthia Princewill-Ukot?

Anne-Marie Sharp (13:10:34) (in thread): > @Eseoghene Cynthia Princewill-Ukotcurating is done on bugsigdb. Please watch the YouTube videos explaining it herehttps://www.youtube.com/playlist?list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIqAnd read through the curation policy, you will understand what to do at each step of your curationhttps://bugsigdb.org/Curation_Policy - Attachment (YouTube): BugSigDB HOWTO videos > Videos describing the functionality and purpose of BugSigDB.org - Attachment (BugSigDB): Curation Policy > .

Mildred Anashie (13:11:14) (in thread): > Statistical test is LEfSe for Figure 4@Precious ChijiokeSee image below

Eseoghene Cynthia Princewill-Ukot (13:11:42) (in thread): > Thanks@Anne-Marie Sharp

Adeshile Oluwatosin (13:13:27) (in thread): > First thing to do when assigned an article is to: > * Copy out the project title, paste onhttps://pubmed.ncbi.nlm.nih.gov/ > * Click “cite” > * copy out the “PMID” which contains only numbers > * Head tohttps://bugsigdb.org/Main_Page > * click “Add a study” > * Input just the PMID digits, everything else auto populates > * Click save and start curating:dizzy:

Mildred Anashie (13:13:55) (in thread): - File (PNG): IMG_5902

Anne-Marie Sharp (13:14:14) (in thread): > @Eseoghene Cynthia Princewill-Ukotyou’rewelcome. Watch the videos properly. Then also go through the details in this link properlyhttps://github.com/waldronlab/BugSigDBcuration/issues/94It will guide you on what to do step by step. - Attachment: #94 Welcome Outreachy Applicants! > ### Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > ### BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > ### Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > ### First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > ### Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > ### Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > ### Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > ### Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > ### Contributions > > Remember to record your contributions in Outreachy.

Joy (13:14:42): > Yes@Eseoghene Cynthia Princewill-Ukot, follow the steps given here:point_up_2:

Precious Chijioke (13:22:46) (in thread): > @Mildred Anashie@Adeshile Oluwatosin@JoyThank for for your assistance

Precious Chijioke (13:27:17) (in thread): > I agree with@Adeshile Oluwatosinthe steps she outlined is a tip that makes curating easy and saves time.

Taofeecoh Adesanu (14:13:24) (in thread): > @Eseoghene Cynthia Princewill-UkotIt’s very normal to feel lost and overwhelmed when just starting to curate. All you need to do is take it one at a time, carefully and if you have questions, don’t hesitate to reach out here for help. > Happy BugSigDb!

Eseoghene Cynthia Princewill-Ukot (15:15:25) (in thread): > Thanks@Taofeecoh Adesanu

UBNSEMS3S (17:38:05): > Hi everyone, > > Just a reminder that we have our office hour is at 9 AM EDT tomorrow athttps://us02web.zoom.us/j/2737200499. Looking forward to seeing you there. > > Please use this application to find the time in your local time zone so you don’t miss it:https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Adeshile Oluwatosin (17:38:45) (in thread): > Thank you so much<@UBNSEMS3S>

Anne-Marie Sharp (17:40:14) (in thread): > Thanks for the reminder

Precious Chijioke (17:54:20) (in thread): > @Adeshile Oluwatosinany idea on the number of experiment? I think it have 2 experiment and fig 6 captures the result of experiment 2

isaac imitini (18:28:38) (in thread): > Thank you.

Munachi Elekwa (20:18:05) (in thread): > Thank you<@UBNSEMS3S>

Jesulolufemi Adelanke (21:18:53) (in thread): > Thank you for the remember@C. Mirzayi (please do not tag this account)

2025-03-20

Dorcas Odetayo (00:50:55) (in thread): > Thank You

Dorcas Odetayo (01:28:09): > Good morning@Svetlana Ugarcina PerovicCould you please delete the following :https://bugsigdb.org/37049619/Experiment_1/Signature_2https://bugsigdb.org/37049619/Experiment_1/Signature_3https://bugsigdb.org/37049619/Experiment_1/Signature_4https://bugsigdb.org/37049619/Experiment_1/Signature_5

Mildred Anashie (01:40:15) (in thread): > Thank you<@UBNSEMS3S>

Ifunanya Benita Obiaku (01:43:44) (in thread): > Thank you.

Ifunanya Benita Obiaku (01:46:32) (in thread): > This is super helpful, thank you so much.

Joy (02:13:24) (in thread): > Thank you<@UBNSEMS3S>

Precious Chijioke (02:56:55) (in thread): > <@UBNSEMS3S>Thank you for the reminder

Juliana Kentomahun Mautin (03:15:09) (in thread): > Thank you<@UBNSEMS3S>. I look forward to the office hour.

Anne-Marie Sharp (03:28:35) (in thread): > Hello@Dorcas Odetayo,@Svetlana Ugarcina Perovicmentioned earlier that ifyou need to delete something already recorded,you shouldcomment what you want to be deleted under the Github issue with your curation(that is the GitHub link that has your curation)and tagher.

isaac imitini (03:36:33) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742372245212109?thread_ts=1742370696.122539&cid=C04RATV9VCYYou should tag Svetlana under the github issue. - Attachment: Attachment > If you need to delete something already recorded, please comment what you want to be deleted under the Github issue with your curation and tag SvetlanaUP.

Dorcas Odetayo (03:37:53) (in thread): > Thank you@Anne-Marie Sharp@isaac imitinii’ll do that now

Anne-Marie Sharp (03:40:03) (in thread): > @isaac imitini:face_with_peeking_eye:please how do you all get link for an exact message like this? I wanted to share, couldn’t see where to copy the link@Dorcas Odetayookay:thumbsup:well done

isaac imitini (03:45:46): > Hi everyone, just to confirm as I am already curating. On this study in the first experiment. Fecal samples were collected from both groups of neonatal rats for 16S rRNA sequencing and To explore the potential microbiota-gut-brain axis mechanisms underlying long-term cognitive impairments after HI insult, the colonic tissues, serum, and hippocampal tissues were collected. > > My question here is for the first experiment where we input the “Body Site” I have added Colonic Mucosa, Blood serum , CA1 field of hippocampus , Feces. But I then begin to think Feces shouldn’t be added being that the fecal samples were collected for the 16S rRNA sequencing. Is this correct? I’d appreciate some assistance here. Thank you. > > Here is the link to the study:Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia - PMC@Svetlana Ugarcina Perovic@Aleru Divine@Esther Afuape - Attachment (PubMed Central (PMC)): Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia > Neonatal hypoxic-ischemic brain damage (HIBD) is considered as a major cause of long-term cognitive impairments in newborns. It has been demonstrated that gut microbiota is closely associated with the prognosis of various neurological disorders. …

isaac imitini (03:47:46) (in thread): > You can click here@Anne-Marie Sharp - File (PNG): image.png

isaac imitini (03:48:20) (in thread): > Then you will find “Copy Link”

Anne-Marie Sharp (03:51:45) (in thread): > @Dorcas Odetayo@isaac imitinithank you.I’musing the app, so it shows as a menu, but Ididn’tknow that the menu was longer and I could scroll:smile::woman-facepalming:so I never saw it at the bottom of the menu. But I have now, thank you:pray:

isaac imitini (03:52:31) (in thread): > My Pleasure@Anne-Marie Sharp

Victoria (Burah) Poromon (04:13:23) (in thread): > Hi@isaac imitiniSo typically an experiment should have 1 body site, which is the site that was analysed for microbial samples. > > If you look at the second paragraph under materials and methods, you’ll see this “To explore the potential microbiota-gut-brain axis mechanisms underlying long-term cognitive impairments after HI insult, the colonic tissues, serum, and hippocampal tissues were collected on the 3rd day post-HI insult” > > And if you go to the second paragraph under Oral DEX improved intestinal and long-term cognitive function in the neonatal HIBD rats by partially dependent on gut microbiota. > You will see this “To determine whether oral DEX influenced the gut microbiota in the neonatal HIBD rats, the qPCR was used to quantify two specific bacteria, f_Enterobacteriaceae and f_Akkermansiaceae, in the feces of the Sham group, HI group, and HI+DEX group rats on the 3rd day following HI insult.” > > That means feces is the body site that should be included.

isaac imitini (04:17:12) (in thread): > Alright:smiley:. Thank you very much that confused me.@Victoria (Burah) Poromon

Adeshile Oluwatosin (04:19:46) (in thread): > Hello@isaac imitiniI believe feces was used in this case. > > Figure 2G, I, k-oThe description states the body site as feces

Adeshile Oluwatosin (04:20:49) (in thread): > 2I : “Linear discriminant analysis effect size (LEfSe) was used to identified bacterial species exhibiting significant differences at all taxonomic levels of the gut microbiota of two group’s FECAL sample”

isaac imitini (04:20:50) (in thread): > Thank you, to think what I had doubts about was in fact the body site.

Adeshile Oluwatosin (04:21:19) (in thread): > 2j : “Indicator species analysis was used to identified bacterial species exhibiting significant differences at family levels of the gut microbiota of two group’s FECAL samples.”

Svetlana Ugarcina Perovic (05:10:19) (in thread): > TODAY! Bring all your questions ;)

Victoria (Burah) Poromon (06:53:56): > Hi@Ayomide Olugbenga OjoHere’sthe welcome materialhttps://community-bioc.slack.com/canvas/C04RATV9VCY - File (Canvas): Welcome material

Victoria (Burah) Poromon (07:02:30) (in thread): > After reviewing the material, you can go to the GitHub page and follow the instructions to make your first contribution.https://github.com/waldronlab/BugSigDBcuration/issues/94And you can always ask your questions here if/whenever you feel stuck. - Attachment: #94 Welcome Outreachy Applicants! > ### Welcome Outreachy Applicants! > > Note: This task can be completed by multiple Outreachy applicants. > > ### BugSigDB Project > > BugSigDB is a wiki built to capture standardized microbial signatures of health outcomes and enables the systematic comparison and synthesis of published human microbiome studies, https://bugsigdb.org/Main_Page. As context, the human microbiome is the collection of microorganisms colonizing the human body. It performs essential functions such as producing vitamins and important nutrients, metabolizing food and drugs and toxins, regulating epithelial development, and influencing innate immunity. It is modified by diet, medical treatment, and host-to-host transmission, and can be a mediator between environment and health. The main result of most published human microbiome studies are lists or “signatures” of differentially abundant microbial taxa in different groups, which are often classified by health condition, behavior or risk factor. A microbial signature is a list of bacteria, viruses, and/or archaea reported to be differentially abundant with respect to health outcomes (e.g., cancer, diabetes, obesity) or with respect to sociodemographic characteristics (e.g., age, smoking, income, or place of residence). These signatures are often reported in heterogeneous ways with different taxonomic nomenclature databases and do not allow direct comparison of methods or results in different studies. BugSigDB contributors aim to create a comprehensive coverage of the human microbiome literature that allows for (1) comparisons between new research findings and previously published results in any area of the health literature and (2) identification of common patterns of differentially abundant microbes across otherwise disparate health outcomes. > > ### Prep Work > > To make a contribution to the BugSigDB project, applicants should first review the onboarding materials:
> BugSigDB project information, estimated time: 15 minutes (link)
> Reading materials on the human microbiome, estimated time: 2 hours (link)
> Step-by-step guidance on how to document a signature in BugSigDB (link)
> View examples of completed BugSigDB curations, estimated time: 15 minutes (link)
> Video trainings on BugSigDB curation (link) > > ### First Contribution Task > > 1. Go to the first curation form > 2. Review the article on the human microbiome that has been heavily annotated by BugSigDB project leaders (e.g., explaining the section(s) of the article that convey study design and the specific characteristics that determine study design) > 3. Complete a mini-curation, akin to BugSigDB curations, on Qualtrics XM. > > Link to curation form: https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw > > Please submit a fully completed mini-curation via the form above before continuing to the second contribution task. > > ### Second Contribution Task (Optional) > > As an optional, higher-difficulty-level task, you may claim an article on the human microbiome from the BugSigDBcuration GitHub issues tagged “paper to curate” and work on a full curation. > > To claim an article for curation, post a response to the issue with your name and we will mark it as claimed. Please only claim one article for curation until you have completed this curation and it has been graded. > > To curate the article you select, first create a BugSigDB account (https://bugsigdb.org/Special:RequestAccount) and follow the website prompts to complete the curation. > > ### Assessment & Grading > > Your first contribution will be scored for accuracy. Your second contribution will be scored with the following rubric: > > 1. All elements marked “Needs review” (none “Incomplete”) (1 point): > 2. Correct study design (1 point): > 3. Entered all relevant experiments and no irrelevant experiments (1 point): > 4. Body site correctly identified (i.e. does not include multiple sites) (1 point): > 5. Condition entered according to contrast (correct EFO ontology) (1 point): > 6. Contrast groups correctly identified (1 point): > 7. Groups correctly labeled as 1 and 0 (1=cases, 0=controls) (1 point): > 8. Antibiotic exclusion correctly identified (1 point): > 9. Correctly identified sequencing details (1 point for sequencing type and variable region, 1 point for sequencing platform) (2 points): > 10. Identified correct statistical test (1 point): > 11. Identified MHT correction (1 point): > 12. Correctly recorded matched on variables (1 point): > 13. Entered correct number of statistical tests per experiment (1 point): > 14. All diversity measures identified (1 point): > 15. Diversity results correctly entered as increased/ decreased/ unchanged (1 point): > 16. All signature sources correctly identified (-1 for each error) (2 points): > 17. Abundance direction correctly selected (1 point): > 18. Members of signatures identified correctly (1 point for single small error, 0 points for anything more. Incorrect means missing or extraneous taxon) (2 points): > 19. Correct use of NCBI taxonomy (don’t deduct if can’t easily find correct taxon in NCBI taxonomy database. 1 for one error, 0 for multiple errors) (2 points): > > Total (maximum 23 points): > > Please note it may take us several days to score your second contribution, depending on how many contributions we receive. Once scored, you will have the opportunity to revise your curation to remedy any identified errors; however, we will record both your original and revised score when evaluating your second contribution. We strongly recommend you ask questions on our Slack channel, compare your curation to completed curations on BugSigDB, and attend office hours prior to submitting your second contribution for grading. > > ### Questions > > Communication regarding specific tasks should be done on a task’s GitHub issue or on the Bioconductor Slack channel #bugsigdb, which is monitored by mentors and other project participants who can help you. Sign up for an account at https://slack.bioconductor.org/. After you log in, join the channel #bugsigdb. > > To reduce duplicate questions, please do not directly message or email the BugSigDB mentors. > > ### Office Hours > > Office hours will be held at 9 AM EDT (eastern daylight time) every Thursday. Attendance by all applicants is highly encouraged. More details here #95 > > ### Contributions > > Remember to record your contributions in Outreachy.

Aiysha shahid (07:07:19) (in thread): > Hi,@Mildred Anashie@Adeshile OluwatosinI again have some confusion in this paper. So I have searched on NCBI Taxonomy,Oscillospiralesso it’s comingEubacteriales, but there’s no evidence of Oscillospirales as homotypic and heterotypic synonym. Same is for Escherichia-Shigella,NCBI BLAST name: enterobacteria.So I just wanted to know if I can use them or not. Also in this paper for Leffse, there’s no direct mentioned of significant threshold but overall it’s 0.05. So in this we would consider or not. I am little confuse. I would highly appreciateyour help:pray:

Ayomide Olugbenga Ojo (07:11:10) (in thread): > Thank you Victoria.

Mildred Anashie (07:12:55) (in thread): > Hi@Aiysha shahidFor the threshold you can use 0.05. Check this to confirm Eubacteriales is another name for Oscillospiraleshttps://www.uniprot.org/taxonomy/186802. I usually do a gogle search and search Uniprot to come to a conclusion most times. Still trying to find Escherichia-Shigella. - Attachment (uniprot.org): UniProt > UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.

Adeshile Oluwatosin (07:19:19) (in thread): > @Aiysha shahidEscherichia-Shigella for species can be curated asthis. They are closely related. > Eubacteriales is another name for Oscillospirales.Most times the significant threshold is 0.05 > But check the paper very well - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Juliana Kentomahun Mautin (08:02:43) (in thread): > Welcome@Ayomide Olugbenga Ojo. You are welcome to this amazing community:slightly_smiling_face:. Go through all the post by@Victoria (Burah) Poromon. Please don’t hesitate to ask your questions on this channel whenever you any clarification. We are all here you help you:blush:. Have a fun filled contribution:smiley:

Svetlana Ugarcina Perovic (08:34:22): > Hello everyone, all messages replied. (please do not forget to tag me to not skip your request or comment) > > See you in 30 min - Attachment: Attachment > Hi everyone, > > Just a reminder that we have our office hour is at 9 AM EDT tomorrow at https://us02web.zoom.us/j/2737200499. Looking forward to seeing you there. > > Please use this application to find the time in your local time zone so you don’t miss it: https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=37&p3=176&p4=3395&p5=125

Ndukauba Oluchi (09:00:50): > Hello everyone:hugging_face:Office hours is On now > Kindly join in:rocket:

Juliana Kentomahun Mautin (09:01:18) (in thread): > Thank you:relaxed:@Ndukauba Oluchi

Eseoghene Cynthia Princewill-Ukot (09:04:16) (in thread): > Thank you

Precious Chijioke (09:06:01) (in thread): > I’ve been trying to join and keeps getting kicked out

Svetlana Ugarcina Perovic (09:12:48): > TODAY’s tips:<@UBNSEMS3S>: “Our goal here is not speed,our goal is qualityi.e. accuracy in curation”@Svetlana Ugarcina Perovic: “When curating always check**** the supplementary/additional/supporting material ****usually located in the end of paper”

Svetlana Ugarcina Perovic (09:26:56): > A thread on closely related taxa and how we curate them:https://community-bioc.slack.com/archives/C04RATV9VCY/p1734620491588179 - Attachment: Attachment > @Kate Rasheed asked: When taxa has slashes, do we curate them individually or together as stated in the paper. For example: Eggetherlla lenta/Clostridiodes difficile, Bacteroides ovatus/vulgatus. > > We curate them together as they represent closely related species.

Svetlana Ugarcina Perovic (09:29:27) (in thread): > Another example: theBurkholderia-Caballeronia-Paraburkholderia(BCP) group > > “The BCP group is composed of the three independent generaBurkholderia,Caballeronia, andParaburkholderia. The V3 +V4 segment of the 16 S rRNA selected in this sequencingcould not separate the specific genera due to their close genetic relationship (Luo et al., 2021).” > > In this case, we do not curate 3 genera separately, we curate them together as BCP group.

Adeshile Oluwatosin (09:32:16) (in thread): > Thank you@Svetlana Ugarcina Perovic,in this case:eubacterium coprostanoligens(g, f), Escherichia_Shigella (g), Lachnospiraceae NK4A136 (g), Incertae Sedis (g)… > > Are all represented as Eubacterium/cpprostanoligens, Escherichia/Shigella, Incertae/Sedis, Lachnospiraceae NK4A136 > Exactly as seen…Thank you so much

Adeshile Oluwatosin (09:33:33) (in thread): > I was confused as already reviewed articles states otherwise > Thank you for clarifying

Svetlana Ugarcina Perovic (09:33:46) (in thread): > first one is specieshttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=290054 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (09:34:58) (in thread): > Yes, the confusion here is in the paper they were stated as generaand family. Hence why I was unsure on if it should be curated as species

Adeshile Oluwatosin (09:39:35) (in thread): > @Svetlana Ugarcina PerovicFor instance: Escherichia_Shigella has taxa IDlinkas species. > Lachnospiraceae NK4A136 group Taxa IDlinkas species > > Sincethey were represented as genus in the paper > To reconfirm should I curate as species since there is a taxa ID - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Svetlana Ugarcina Perovic (09:41:21) (in thread): > Follow NCBI IDs.

Svetlana Ugarcina Perovic (09:42:09) (in thread): > Second link correction:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=877420 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Ndukauba Oluchi (09:42:09) (in thread): > You’re welcome

Adeshile Oluwatosin (09:42:30) (in thread): > Noted. Thank you so much

Eseoghene Cynthia Princewill-Ukot (09:43:47) (in thread): > Noted@Svetlana Ugarcina Perovic

Joy (09:53:36) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (10:01:54): > Thank you so much for today’s office hour.@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Kate Rasheed@Esther Afuape@Aleru DivineThese are the remaining questions I’d appreciate a clarification/confirmation on: > 1. if figure5should be curated > https://pmc.ncbi.nlm.nih.gov/articles/PMC10808787/#F22.https://pmc.ncbi.nlm.nih.gov/articles/PMC11776479/https://bugsigdb.org/39834317 > * If figure 6 is curatable > * If yes, would fatty acid measurement work as a condition > * Colostrum, milk and feces were reported, unsure if feces should not be curated here > * Data Transformation for linear regression, spearman correlation and Welch t test here. “Raw ASV data counts were transformed into relative abundance.” Should relative abundance be curated for all tests. > 3. In this meta-analysis.https://www.nature.com/articles/s41564-024-01870-zhttps://bugsigdb.org/39762435 > * Curation of Supplementary Table 10-12, 13 as the signatures appears more than once and have different Q values. Also, alpha diversity results (1b). > Thank you once again

Victoria (Burah) Poromon (10:02:46): > Hi everyone, I just finished my second contribution and I’m putting it up for peer review. > > Please leave your GitHub username so I can tag you on it. Thank you so much! > > Also, leaving mine if someone wants a review too. @Buraah > > Study link:https://bugsigdb.org/39856736 - Attachment (BugSigDB): No rumen fermentation profiles and associated microbial diversities difference were found between Hu sheep and Karakul sheep fed a cottonseed hull diet - BugSigDB > BACKGROUND: This research aimed to investigate differences in rumen fermentation characteristics between Karakul sheep and Hu sheep reared under identical conditions.

Mildred Anashie (10:03:17): > Thank you so much for the office hour@Svetlana Ugarcina Perovic<@UBNSEMS3S>:blush:

Francisca Gundu (10:03:47): > Thank you@Svetlana Ugarcina Perovicand<@UBNSEMS3S>for the office hour!

Mildred Anashie (10:04:18): > Hello Everyone,Just like@Victoria (Burah) PoromonI’m done with my second contribution and I’ll appreciate a peer review on this.I’ll share a link to the study here and on GitHub, If you’ll like to review it you can drop your GitHub user in the comment and I’ll tag you to it.Thank you:blush:This is my GitHub User if you’ll like a peer review as well@MyleeeAhttps://bugsigdb.org/38772541 - Attachment (BugSigDB): The Role of Gut Microbiota in Male Erectile Dysfunction of Rats - BugSigDB > PURPOSE: Erectile dysfunction (ED) is a common male sexual dysfunction.Gut microbiota plays an important role in various diseases.To investigate the effects and mechanisms of intestinal flora dysregulation induced by high-fat diet (HFD) on erectile function.

Utibe Ita (10:04:35): > Thank you so much for the office hour@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)

Mildred Anashie (10:04:51) (in thread): > Hi@Victoria (Burah) PoromonI’dlove to > > My username is @MyleeeA

Adeshile Oluwatosin (10:05:02) (in thread): > Duly noted > Well done on your curation:clap:@Mildred Anashie

Adeshile Oluwatosin (10:05:18) (in thread): > Well done@Victoria (Burah) Poromon:clap::clap::clap:

Anne-Marie Sharp (10:05:27): > Thank you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)for the office hour today

Victoria (Burah) Poromon (10:09:02) (in thread): > Well done@Mildred AnashiePlease tag me on it. > > Username: Buraah

Adeshile Oluwatosin (10:09:46): > Hello everyone:wave:Well done on curating > If you would like a peer review on your curation.Kindly post on the channelI will be happy to assist

Svetlana Ugarcina Perovic (10:11:41): > A peer review should be done here in Slack, transparently, so the others can learn too. Thanks! > Feel free to do a peer review but not after submitting your curation for an official review.

Victoria (Burah) Poromon (10:12:50) (in thread): > Okay thank you@Svetlana Ugarcina PerovicWill do.

Mildred Anashie (10:13:09) (in thread): > Duly noted@Svetlana Ugarcina PerovicThank you

Adeshile Oluwatosin (10:13:44) (in thread): > Noted, thank you@Svetlana Ugarcina Perovic

Mildred Anashie (10:14:42) (in thread): > @Adeshile Oluwatosin@Victoria (Burah) Poromonhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742479901947439Thank you in anticipation:blush: - Attachment: Attachment > A peer review should be done here in Slack, transparently, so the others can learn too. Thanks! > Feel free to do a peer review but not after submitting your curation for an official review.

Joy (10:31:38) (in thread): > Good job@Victoria (Burah) Poromon:sparkles:

Joy (10:32:51) (in thread): > Duly noted@Svetlana Ugarcina Perovic

Kate Rasheed (10:41:32) (in thread): > Good afternoon@Adeshile Oluwatosin. Thanks for your question. > 1. Figure 6 is about the differential abundance in KEGG pathway. We don’t curate KEGG pathway. > 2 i. Figure 6 is not curatable because it shows therelationshipbetween fatty acids and the relationship between infant gut bacteria. > ii. Relative abundance should be curated as the data transformation for the listed tests. > iii. Milk samples was used for analysis > > 3. I’m unclear on your third question.

Adeshile Oluwatosin (10:43:05) (in thread): > Thank you so much for your response@Kate RasheedI meant how to curate supplementary Table 10-12

Adeshile Oluwatosin (10:43:20) (in thread): > And alpha diversity (1b)

Oriade Adeola (10:43:35) (in thread): > Thank you<@UBNSEMS3S>

Adeshile Oluwatosin (10:54:04) (in thread): > Sorry, for number 1. I meant figure 5@Kate Rasheed

UBNSEMS3S (10:54:26) (in thread): > Yeah looks like Kate has this covered. Good answers.

UBNSEMS3S (10:55:44): > Office Hours recording. Thank you everyone who attended and I’m sorry I couldn’t answer all your questions. See you next week! - File (MPEG 4 Video): bsdb 2025_03_20.mp4

Adeshile Oluwatosin (10:56:09) (in thread): > Thank you<@UBNSEMS3S>

Anne-Marie Sharp (10:56:26) (in thread): > Thank you@C. Mirzayi (please do not tag this account)see you next week

Mariam Omiteru (10:57:47) (in thread): > thank you, helpful for those of us that couldn’t make it

Mariam Omiteru (10:58:04) (in thread): > Looking forward to joining next week

Adeshile Oluwatosin (10:59:30) (in thread): > I also wanted to ask this: e.g in the case of number 2 > * How am I sure on if a figure is to be curated with statistical test: spearman correlation or if a table/figure explains strictly correlation and should be ignored > Checking through already reviewed studies,it’sstill unclear

Victoria (Burah) Poromon (11:00:50) (in thread): > Hi@Mildred AnashieMy only suggestion is that we expand the group names completely for the last 2 experiments (3 & 4). > > Well done again!

D-coder111 (11:04:24): > Hey can anyone help me in requesting a bugsigdb account?

Juliana Kentomahun Mautin (11:05:17) (in thread): > Thank you@Svetlana Ugarcina Perovic

Precious Chijioke (11:05:18) (in thread): > Thank you<@UBNSEMS3S>

Juliana Kentomahun Mautin (11:05:55) (in thread): > Thank you<@UBNSEMS3S>. I look forward to next week.

Mildred Anashie (11:07:56) (in thread): > Hi@D-coder111You canUse this linkto request for an accounthttps://bugsigdb.org/Special:RequestAccount - Attachment (BugSigDB): Special:RequestAccount

D-coder111 (11:09:59) (in thread): > ok thanks

Mildred Anashie (11:12:06) (in thread): > You are welcome

Precious Chijioke (11:44:58): > Please can anyone help me with curation policy link or where I can see. I’ve been going through the welcome material and other documents trying to trace where I saw it. Please I need help@Kate Rasheed@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Peace Sandy

Mildred Anashie (11:45:51) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742290950340199 - Attachment: Attachment > Hello everyone :wave::skin-tone-5: > > Based on a question asked concerning what to do while you wait for an article to be assigned to you on GitHub, this tips could be helpful. > While you wait, you can familiarize yourself with everything. > > 1. View an already curated study to understand what is expected that can be found here it takes you to a random study on BugSigdb. > 2. If you haven’t already gone through the curation policy here’s a link > 3. You can also go through the FAQs most questions you might have could have been answered there already > 4. Also scanning through and reading the welcome material thoroughly would be helpful https://community-bioc.slack.com/canvas/C04RATV9VCY > 5. Finally, if you are the only one who has dropped a comment on the issue on GitHub then I’m positive it would be assigned to you. You can start going through the article to get acquainted with it (I personally like to read through and highlight everything I find significant before I start curating. I think this tip is very helpful). > PS: If you are done with your first contribution and not sure what to do > > I think you can follow the Steps below > 1. Make sure to record your contribution on the outreachy website > 2. You can then go to Github to request one of the studies tagged “Paper to curate” and “outreachy June2025” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait all I’ve listed above would surely be helpful > > If you have any other questions, feel free to ask :blush:

Mildred Anashie (11:46:28) (in thread): > https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > .

Halima Momoh (11:50:40): > Hi@Svetlana Ugarcina Perovic@Kate Rasheed, > I hope you’re doing well. I’m almost done with my curationhttps://link.springer.com/article/10.1007/s10620-024-08334-8, but I have a few things I need your help with before submitting. > 1. The paper I’m curating was behind a paywall, and I had to reach out to a friend in the U.S. to help me access the full text. Are there any platforms or sites you recommend for accessing subscription-based papers more easily in the future? > 2. Regarding confounders, the experiment controlled forbody weight, food intake, and gut motility measurements, but I can only findbody weightandfoodas options on the BugSigDB platform. Should I proceed with just those two, or is there another way to account forgut motility measurements? > 3. Lastly, I’m still struggling to fully understand thesignature aspect of the curation, even after watching the tutorial video. Could you please clarify this further or provide additional guidance? > These are the last things holding me back from submitting. I’d really appreciate your help! > Looking forward to your response. > Best, > Halima - Attachment (SpringerLink): Gastrointestinal Characteristics of Constipation from the Perspectives of Microbiome and Metabolome > Digestive Diseases and Sciences - Constipation is one of the most common gastrointestinal complaints. Yet, the underlying mechanisms of constipation remain to be explored deeply. Integration of…

Precious Chijioke (11:54:21) (in thread): > Thank you@Mildred Anashie

Svetlana Ugarcina Perovic (11:54:27) (in thread): > 1. pdf addedhttps://github.com/waldronlab/BugSigDBcuration/issues/656 > Next time we recommend to contact us.

Precious Orakwe (11:56:23) (in thread): > Thanks@C. Mirzayi (please do not tag this account)

Precious Orakwe (11:57:21) (in thread): > Noted, thank you for the update@Svetlana Ugarcina Perovic

Mildred Anashie (11:58:10) (in thread): > Okay > > Thank you@Victoria (Burah) Poromon:blush:Rounding up your review soon

Adeshile Oluwatosin (11:59:18) (in thread): > Hello@Halima MomohI will have a look

Halima Momoh (11:59:25) (in thread): > Thank you.

Svetlana Ugarcina Perovic (11:59:30) (in thread): > 2. add all confounders

Adeshile Oluwatosin (11:59:55) (in thread): > @Precious Chijiokehttps://bugsigdb.org/w/index.php?title=Curation_Policy&veaction=edit§ion=9 - Attachment (BugSigDB): Curation Policy > .

Svetlana Ugarcina Perovic (11:59:56) (in thread): > 3.@Adeshile Oluwatosincan explain our signature concept

Mildred Anashie (12:00:32) (in thread): > Hi@Halima MomohI’ll take a look at this

Svetlana Ugarcina Perovic (12:01:47) (in thread): > @Adeshile Oluwatosinwill explain it (3), there is no need for a double work@Mildred Anashie

Mildred Anashie (12:03:48) (in thread): > Got it@Svetlana Ugarcina Perovic

Halima Momoh (12:06:50) (in thread): > Thank you@Svetlana Ugarcina Perovic, I’ve taken note of that I’ll reach out next time.

Ndukauba Oluchi (12:07:18): > Hello<@UBNSEMS3S>thank you for today’s Office hours. Please don’t forget to take a look at this paper > Link:https://journals.asm.org/doi/10.1128/mbio.02023-24The questions are: > 1. How do I curate Figures 3B,3C, 3E, 3F and Figures 4. > Thank you so much.

Svetlana Ugarcina Perovic (12:07:48) (in thread): > @Mildred Anashieyou can help here:wink:

Precious Orakwe (12:09:18): > Good day everyone@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Aleru Divine@Adeshile Oluwatosinplease i am still confuse on how to curate this paper, which one to use as the control group and exposed group. From the paper, Con = 8 is the control group and HS = 9, HS+Mel = 10 are the exposed group, I am thinking of adding the two exposed groups together and also their size. > I can see any sequencing platform for this study. > > Also wnt to know if the study has more than one experiment, I am confused with the image of the taxa in fig 4E. > > This is the link to the study:https://www.sciencedirect.com/science/article/pii/S2090123224000766?via%3Dihub#s0010Thank you for your assistance. - File (PNG): Screenshot (162).png

Mildred Anashie (12:09:24) (in thread): > On it:saluting_face:Thanks@Svetlana Ugarcina Perovic

Precious Chijioke (12:10:43) (in thread): > Thank you@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (12:12:43) (in thread): > @Precious ChijiokeI added it to the Welcome material. Thanks!

Ndukauba Oluchi (12:13:38): > @Adeshile Oluwatosinneed some help hereThe pregnant mice were divided into control (Con, n = 8), HS (n = 9), and HS supplemented with Mel (HS + Mel, n = 10) groups. Mice in the Con group were maintained under 25 ± 2 °C.Which is the control?

Adeshile Oluwatosin (12:14:24) (in thread): > I will have a look

Adeshile Oluwatosin (12:15:11) (in thread): > Can I see a link to the paper? > It depends on if pairwise analysis or one against all analysis was done

Adeshile Oluwatosin (12:16:02) (in thread): > But def Con should be the control : group 0 > HS: group 1if pairwise

Ndukauba Oluchi (12:17:58): > @Precious Orakwefor the statistical test, > I seeThe bacterial taxa that were significantly different among groups were identified using linear discriminant analysis (LDA) effect size (LEfSe) analysis (LDA > 2.5, P < 0.05) > So it should be Lefse

Adeshile Oluwatosin (12:19:39) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742379749248589?thread_ts=1742379250.242249&channel=C04RATV9VCY&message_ts=1742379749.248589 - Attachment: Attachment > Exp 1: Grp 0( combination of con + HS), Grp 1 (Hs + Mel) > Exp 2; Grp 0( combination of con + Hs + Mel), Grp 1(Hs) > Exp 3: Grp 0(combination of Hs + Hs + Mel), Grp 1(con) > > They all have only increased abundance @Precious Orakwe > Hence curate Red colour in Exp 3, Green bar in Exp 2 and Blue bar in Exp 1

Svetlana Ugarcina Perovic (12:19:45) (in thread): > Please stick to the corresponding thread. This discussion is hard to follow.

Oriade Adeola (12:20:00): > Hello everyone:wave:i just finished my first task. please can someone guide me on what to do next. Thank you.

Precious Orakwe (12:20:15) (in thread): > I am not talking about this, I am talking about the sequencing platform

Svetlana Ugarcina Perovic (12:20:48) (in thread): > Oh my:smile:I do not know where are your main questions…

Precious Orakwe (12:21:25) (in thread): > Well-done on completing your first task,

Oriade Adeola (12:21:57) (in thread): > Thank you.

Ndukauba Oluchi (12:22:38) (in thread): > Oh my apologies, I thought I answered this in a thread

Adeshile Oluwatosin (12:23:19) (in thread): > Well done@Oriade AdeolaKindly ask your questions

Ndukauba Oluchi (12:23:40) (in thread): > @Svetlana Ugarcina Perovicthis is the main thread

Oriade Adeola (12:24:09) (in thread): > Thank you. I don’t know what next to do. please can you put me through?

Halima Momoh (12:25:25) (in thread): > @Oriade Adeola**** Next steps after completing the initial contribution and recording.**** > * The next thing to do is to request for a Bugsigdb account (please be patient, and check your spam folder as well for a mail)https://bugsigdb.org/Special:RequestAccount > * Head over to Github to request for a paper with tag “paper to curate” to be assigned to you by tagging a mentor with a simple statement like “I would like to curate this article”. Ensure, it is not already assigned to anyone else.link > Navigate through theWelcome materialandCuration policyto properly get started. - Attachment (BugSigDB): Special:RequestAccount - Attachment (BugSigDB): Curation Policy > . - File (Canvas): Welcome material

Precious Orakwe (12:26:07) (in thread): > From the message you go the link to your first curation, go to the click on paper to curate it will tke you to the GitHub issue, select a paper and tag@Svetlana Ugarcina Perovicto assign the paper to you with your name, before that, make sure to create a BugSigDB account.

Aleru Divine (12:26:48) (in thread): > Hi@Precious OrakweIt seems like your concern is related to Figure 3E. This figure represents a one-vs-all comparison. > > In this approach, you compare one group against the other two, repeating this process until all groups have been compared. There are a total of three experiments from this figure. Be sure to add sample sizes where appropriate. Group 1 should be the reference group for comparison against the other two (group 0).

Adeshile Oluwatosin (12:27:00) (in thread): > @Oriade Adeolahttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742269916896359 - Attachment: Attachment > How to record your first contribution: > > After successfully completing the curation form. Ensure you record your contribution as mentors can close out projects once they have gotten enough contributors. > > Concisely, Kindly follow these steps: > > 1. Head to outreachy website: https://www.outreachy.org/dashboard/ > 2. Click “My Application”, then click “project lists” > 3. Click “Microbiome Study Curation” > 4. Then click “Record contributions and Apply to this project” > 5. Then Record your contribution. > Merged date is the Date you submit your contribution. > This is the contribution URL; > https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw

Adeshile Oluwatosin (12:28:16) (in thread): > Once you have recorded, then do this@Oriade Adeolahttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742277220157329 - Attachment: Attachment > Next steps after completing the initial contribution and recording. > > • The next thing to do is to request for a Bugsigdb account (please be patient, and check your spam folder as well for a mail) https://bugsigdb.org/Special:RequestAccount > • Head over to Github to request for a paper with tag “paper to curate” to be assigned to you by tagging a mentor with a simple statement like “I would like to curate this article”. Ensure, it is not already assigned to anyone else. link > • Navigate through the Welcome material and Curation policy to properly get started. > Good Morning:dizzy:

Svetlana Ugarcina Perovic (12:28:30) (in thread): > @Aleru Divinediscussed herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742389909909229?thread_ts=1742379250.242249&cid=C04RATV9VCYalready - Attachment: Attachment > TIP: try to find a paper already curated with a similar figure type and see how has been curated, in this case: https://bugsigdb.org/38378622

Precious Orakwe (12:28:32) (in thread): > Am still not understanding@Aleru Divinecan you give an example please.

Ndukauba Oluchi (12:31:27) (in thread): > @Svetlana Ugarcina PerovicI couldn’t also find a sequencing platform > But I have a question: when we see 16sRna V3-V4 do we assume the sequencing platform is Ilumina or else it is stated?

Svetlana Ugarcina Perovic (12:36:26) (in thread): > @Ndukauba OluchiDo not assume, it’s ok to leave field blank: sometimes paper does not provide all the info clearly.

Aleru Divine (12:36:28) (in thread): > @Precious Orakwelook at the suggestions in this thread. Andsee the study shared by@Svetlana Ugarcina Perovic, that should give you a better understanding.

Joy (12:49:35) (in thread): > Well done on completing your first task.

Joy (12:51:36) (in thread): > You can go through the pinned messages above and guide your self on the next steps.

Oriade Adeola (12:53:33) (in thread): > Thank so much everyone. I already created an account, and i have asked@Svetlana Ugarcina Perovicto assign a task to me. thank you so much for your assistance and guidiance

Adeshile Oluwatosin (12:54:16) (in thread): > Hello@Halima MomohI will use the curatable Figure 2D to explain in details the signature aspect of curation:Which is a LeFSe result between two groups: Negative control (NC) and constipation group (CG) > * The first thing required is to identify an experiment and create one, in this case Fig 2D. > * Remember one statistical test = one experiment in most cases. > * Colour comparisons helps us determine which is an increased abundance or decreased abundance of group 1 (group 1 here means the case group) > * Since we know this, firstly, figure out the case which is the exposed group, in this case CG is group 1. > hint: in most cases: Grp 0 are people without a disease/Negative, Grp 1 are people with the disease/Positive > * Now, that we know CG is the case group, head to the article. Blue (CG) and Red (NC). > NB: since there are two colours, it means the other colour is a decrease of the case. Hence we will have two signatures (one for increase of group 1 and the other for decrease of group 1). > * We curate increased abundance of group 1 first. So curate all taxa with blue colour in front here. (Lachnospiraceae, Veillonellaceae, Phascolarctobacterium, Bilophila) > * Then curate decreased abundance of group 1 (CG) secondly. So curate all taxa with red colour in front of it (24 taxa). > So specific to Figure 2D: we have just one experiment with 2 signatures

Precious Chijioke (12:57:29): > Hello@Svetlana Ugarcina Perovic, I shared the link to the paper I am working on curating during the office hour because I needed clarity on the number of experiments in the paper and curatable figs. While it was reviewed, it was stated that there are 5 experiments in the paper as seen in Fig. 5 (https://www.dovepress.com/article/fulltext_file/509592/aW1n/IJGM_A_509592_O_F0004g.jpg), and the curatable figs were been traced a few minutes before the closure of the meeting. Please how many experiments am I supposed to site and how do I trace them. Also can you explain more on the curatable Figs, I’m still a bit confused. Fig 2 (https://www.dovepress.com/article/fulltext_file/509592/aW1n/IJGM_A_509592_O_F0002g.jpg) and Fig 3 (https://www.dovepress.com/article/fulltext_file/509592/aW1n/IJGM_A_509592_O_F0003g.jpg) > > Please I need help@Kate Rasheed<@UBNSEMS3S>@Peace SandyLink to paper:https://www.dovepress.com/therapeutic-mechanism-of-zhuyang-tongbian-decoction-in-treating-functi-peer-reviewed-fulltext-article-IJGM - Attachment: Attachment - Attachment: Attachment - Attachment: Attachment - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB

Adeshile Oluwatosin (12:59:59) (in thread): > Other curatable figure: 2B > So reference 2B and 2D as a source > And curate from both figures > Since the paper states that it is same test (LeFSe analysis) and we have same comparison.There is no curatable information in the supplementary material

Adeshile Oluwatosin (13:10:50) (in thread): > I humbly await a response@Kate Rasheed<@UBNSEMS3S>

Joy (13:15:26) (in thread): > Well done@Precious Chijiokeon this curation, from your paper, I can see Fig. 2A, B, and C are curatable even from the in-line text.

Joy (13:17:07) (in thread): > Figure 3A, B and C are also curatable.

Joy (13:22:19) (in thread): > **Figure 4 is also curatable, take a look at this: To further characterise the significant changes in the intestinal microorganisms of FC patients after administration of ZTD, we performed a linear discriminant analysis effect size (LEfSe) and plotted histograms of LDA distributions based on taxonomic information. This identified statistically significant differences in bacterial populations at different taxonomic levels (Figure 4). O__Oscillospirales, F__Oscillospiraceae, P__Desulfobacterota and its subordinate C__Desulfovibrionia, O__Desulfovibrionales, etc. were significantly enriched in the FC_PreZY group, but after treatment with ZTD, the significantly enriched flora became c__Bacilli, f__Streptococcaceae, o__Lactobacillales, o__Clostridia_UCG_014 and its subordinate f__Clostridia_UCG_014 and g__Clostridia_UCG_014.**

Precious Chijioke (13:29:05) (in thread): > Thank you@Joyfor your assistance

Precious Chijioke (13:30:19) (in thread): > @Svetlana Ugarcina Perovic@Kate Rasheed@Peace Sandy<@UBNSEMS3S>please I want to know how many experiments I am supposed to site since there are 5 experiments in the paper.

Mildred Anashie (13:37:06) (in thread): > Hi@Precious ChijiokeI’ll take a look at this again to properly outline the experiments but I remember the curatable figures here areFigure 2C, Figure 3a, Figure 3candFigure 4

D-coder111 (13:41:23): > Can anyone help me for adding signature to the experiment? for exp 1, i am adding signature, it’s not getting updated?

Mildred Anashie (13:46:08) (in thread): > Hi@Ndukauba OluchiI have had a second look at this (Looked at this a few days back). > I’m of the opinion that Fig4 is relative abundance, see part of the text describing that figure “At the genus level, the abundance of Veillonella in the SIBO group (13.90%) was higher than that in the non-SIBO group (11.30%), while the abundances of Escherichia-Shigella and Acinetobacter were lower than those in the non-SIBO group. The abundance of Escherichia-Shigella was 6.10% in the non-SIBO group and 1.17% in the SIBO group, and the abundance of Acinetobacter was 3.41% in the non-SIBO group and 0.26% in the SIBO group (Fig. 4G and H)”. > > For Fig 3c and 3f I really can’t see the comparisons done there. > > For Fig 3b and 3E(I’mabout to speculate)despite it beingsomewhatgrouped,I zoomed in and identified a pattern, if you look closelyfollowing the color code,for the significant taxas it appears the box plots for Neg F0 and POS F0 are not far apart and this is same for NegF7 vs Pos F7, Neg F30 vs Pos F30, Neg I0 vs Pos I0, Neg I7 vs Pos I7 and Neg I30 vs Pos I30. > SoI’mof the opinion that if this pattern is acceptable thenyou’llhave 6 experiments from here. Other than this, I really do not see any other way we can curate this. > > Like I said,I’mnot sure this is right:blush:so let’s wait for a final say from Chloe.

Anne-Marie Sharp (13:46:37) (in thread): > @Precious Chijiokeyou can use these tips to know if a table or figure is curatable: 1. if it contains microbial signatures then it is curatable 2. if it contains relevant statistical comparisons then it is curatable 3. if it reports alpha or beta diversity then it is curatable 4. if the table/figure only describes methods, demographics or general scope/trends without having actual comparative data then it is not curatable. Keep in mind the purpose of curating, its for having a record of significant microbial signatures, so for example, you can’t curate a figure talking just about study population Also@C. Mirzayi (please do not tag this account)mentioned during office hours, that for your article, you can curate 5experiments but if you curate 3(that is, excluding the metagenomic analysis that doesn’t contain actual microbial signatures) then it will still be accepted. PS: I stand to be corrected

Joy (13:47:11) (in thread): > @D-coder111, well done on your curation. Kindly refresh the page using the three dots on the top of the page.

Mildred Anashie (13:48:01) (in thread): > Hi@D-coder111See thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Ndukauba Oluchi (13:49:04) (in thread): > Thank you@Mildred Anashieit is really a tough one. > Let’s wait for<@UBNSEMS3S>contribution

Joy (13:49:17) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1727957860907319?thread_ts=1727956855.063979&cid=C04RATV9VCY - Attachment: Attachment > If your experiment or signature doesn’t appear after creation, you can manually enter the link using this format: > > https://bugsigdb.org/Study_[StudyNumber]/Experiment_[ExperimentNumber]/Signature_[SignatureNumber] > > Replace [StudyNumber], [ExperimentNumber], and [SignatureNumber] with the appropriate values.

Mildred Anashie (13:49:34) (in thread): > For your question on deleting an experiment see this@D-coder111https://community-bioc.slack.com/archives/C04RATV9VCY/p1742372245212109?thread_ts=1742370696.122539&cid=C04RATV9VCY - Attachment: Attachment > If you need to delete something already recorded, please comment what you want to be deleted under the Github issue with your curation and tag SvetlanaUP.

D-coder111 (13:51:08) (in thread): > ok thanks@Joy@Mildred Anashie:blush:, I am trying the solution.

Joy (13:53:00) (in thread): > :bioc:Nice one@Anne-Marie Sharp!

Halima Momoh (13:56:02) (in thread): > Thank you@Adeshile Oluwatosinthis is super helpful. I’m grateful for your contribution. Thank you again@Svetlana Ugarcina Perovicfor your prompt response.

Precious Chijioke (14:06:25): > Please@Svetlana Ugarcina Perovic@Kate Rasheedis PMID editable, I made a mistake while adding a study and the BSDB can’t import automatically. If it’s not editable can the study be deleted so that I’ll start afresh. > Please Note: I tried using the edit button over and over but the PMID section wasn’t visible to be edited. > > Link to BugSigDB:https://bugsigdb.org/Special:FormEdit/Study/Https://pubmed.ncbi.nlm.nih.gov/40026814/?reload=1&returnto=Https%26%2358%3B%2F%2Fpubmed.ncbi.nlm.nih.gov%2F40026814%2F - Attachment (BugSigDB): Special:FormEdit/Study/Https://pubmed.ncbi.nlm.nih.gov/40026814/

Anne-Marie Sharp (14:08:44) (in thread): > Thank you@Joyand@Precious Chijiokealso, in BugSigDB, figures or tables containing only biochemical, metabolite information or basically non-microbial information are not curated, the focus is on microbial signatures; thats why the other figures or tables in your article besides those mentioned above by@Mildred Anashieand@Joyare not curatable.

Mildred Anashie (14:09:54) (in thread): > In Fig 2c I see 2 experiments > 1. Group 0:Nc vsGroup 1:FCprezy > 2. Group 0: FCprezy vs Group 1: Prozy > Fig 4 has 3 experiments with only increased signatures > 1. Group 0:Nc vs Group 1: FCprezy and Prozy > 2. Group 1: FCprezy vsGroup 0:Nc and Prozy > 3. Group 1: Prozy vsGroup 0:Nc and FCprezy > Still figuring Fig 3 out but Fig 5 isn’t curatable@Precious Chijioke

Victoria (Burah) Poromon (14:10:42) (in thread): > Hi@Precious ChijiokeThis study has five experiments. > NC vs. FC_PreZY > NC vs. FC_PreCG > FC_PreZY vs. ProZYProZY vs. ProCG > FC_PreCG vs. ProCG > > And I believe you’ll end up with 8 experiments. Because fig 4 used a different statistical test (LEfSe). It’s also going to be curated as one against all. > > FC_PreZY and ProZY vs. NC (Record red bars as increased in NC) > NC and FC_PreZY vs. ProZY (Record blue bars as increased in ProZY) and. > NC and ProZY vs. FC_PreZY (Record green bars as increased in FC_PreZY)

Mildred Anashie (14:14:53) (in thread): > @Victoria (Burah) Poromonhas listed the experiments in Fig 3 already

Precious Chijioke (14:17:40) (in thread): > @Victoria (Burah) Poromonthank you for your assistance

Victoria (Burah) Poromon (14:18:07) (in thread): > @Mildred AnashieI agree, fig 5 is not curatable, itdoesn’tshow differential abundance.

Precious Chijioke (14:19:55) (in thread): > Thank you@Anne-Marie Sharpfor the tips

Precious Chijioke (14:22:25) (in thread): > Thank you@Mildred Anashiefor your assistance

Adeshile Oluwatosin (14:24:37) (in thread): > @Precious Chijiokeclick edit since you have created the experiment

Precious Chijioke (14:28:15) (in thread): > @Adeshile OluwatosinI have not added any experiment. I only added a study. I have editing over time and it didn’t go through that’s why I brought it here

Anne-Marie Sharp (14:35:18) (in thread): > @Precious Chijiokeyou’re welcome

Halima Momoh (14:39:39) (in thread): > @Precious ChijiokeIt looks like thePMIDfield inBugsigDBmay not be directly editable once a study has been added. Since the BSDB can’t import automatically due to the mistake, your best option would be to delete the study and re-add it with the correct PMID.@Svetlana Ugarcina Perovicshould be able to give you more clarity on how to go about it.

Svetlana Ugarcina Perovic (14:41:35) (in thread): > https://bugsigdb.org/Https://pubmed.ncbi.nlm.nih.gov/40026814/deleted.

Precious Chijioke (14:44:18) (in thread): > Thank you@Svetlana Ugarcina Perovicfor deleting the study

Juliana Kentomahun Mautin (16:36:18) (in thread): > Welldone@Adeshile Oluwatosin. This is helpful:grinning::+1:

UBNSEMS3S (16:37:02) (in thread): > Figures 3B, 3C, 3E, and 3F: Not curatable or at the very least not easily curatable. > Figure 4 is not curatable.

UBNSEMS3S (16:41:37) (in thread): > 1. I wouldn’t curate Figure 5. I don’t see a useful contrast here. > 2. Figure 6 is not curatable. > 3. When a meta-analysis reports individual study results, it’s better to curate the original research reports as studies (as in look up the paper, enter the PMID, and curate it as a new study). For a meta-analysis, we want to curate the pooled/combined results.

Adeshile Oluwatosin (16:50:36) (in thread): > Thank you so much<@UBNSEMS3S>I’mgrateful

Ndukauba Oluchi (17:02:49) (in thread): > Okay Noted! > Thank you so much.

Mildred Anashie (17:05:22) (in thread): > Hi@Victoria (Burah) PoromonThis looks perfect, Well done. I was trying to access the Second supplementary zip file to see if we could get any other other info from it but it appears to be in XML format, I doubt there’s anything there. Do you have access to it?

Victoria (Burah) Poromon (17:18:48) (in thread): > Yes, I searched it.Couldn’tfind anything either

Mildred Anashie (17:21:03) (in thread): > Then I believe you are good to go

Victoria (Burah) Poromon (17:39:12) (in thread): > Thank you!

Precious Orakwe (19:38:26): > @Svetlana Ugarcina Perovicplease i can’t see all the signatures i have been curating in my study, what can i do?

Precious Orakwe (19:46:46): > https://bugsigdb.org/38382594@Svetlana Ugarcina Perovicplease delete signature 2 in experiment 1. Thank you. - Attachment (BugSigDB): Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice - BugSigDB > INTRODUCTION: Global warming augments the risk of adverse pregnancy outcomes in vulnerable expectant mothers.

Jesulolufemi Adelanke (22:30:22): > Hello everyone, I just finished my second contribution and I’d like a peer review. > > Please leave your GitHub username I can tag you on it. > Thank you.bugsigdb.org/38866797

Adeshile Oluwatosin (23:34:28) (in thread): > Hello > Reviews are done here on slack@Jesulolufemi Adelanke

2025-03-21

Mildred Anashie (00:32:47) (in thread): > Hi@Precious Orakwehave you tried this?https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Joy (01:09:03) (in thread): > Well done@Jesulolufemi Adelankeon your curation. It will be reviewed

Mildred Anashie (02:20:16) (in thread): > Hi@Jesulolufemi AdelankeI’lltake a look at this > Well done:thumbsup:

Joy (03:35:12): > Hello everyone,@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine<@UBNSEMS3S>@Victoria (Burah) PoromonI am curating this study and the study design is****“single-arm, single-blinded intervention design” Iwant to know if“single-arm, single-blinded intervention design” is considered the same as a” cross-sectional observational, not case-control study”**or do they differ in terms of study methodology and data collection appraoch?https://gut.bmj.com/content/70/9/1665#DC2 - Attachment (Gut): Blue poo: impact of gut transit time on the gut microbiome using a novel marker

Joy (03:58:16) (in thread): > Once again, well done@Jesulolufemi AdelankeAfter reviewing the study, the taxa should be checked in the NCBI browser for updated names. For example,******Actinobacteriota********** is now **********Actinomycetota********** (ID: 201174), and **********Actinomycetia********** is now **********Actinomycetes********** (ID: 1760)****. Use this:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Victoria (Burah) Poromon (04:27:03) (in thread): > Hi@JoyI’mnot too sure what a “single-arm, single-blinded intervention design” really is. > > But this study is experimental, from the materials and methods section, researchers had the participants follow a standardised diet and lifestyle instructions prior to the clinic visit. And when they arrived the clinic they were given “blue” muffins within a time period and chocolate beverage. > > And they were asked to record the time they first see a blue stool. > > I’m not too sure but from the method, it closely resembles a Randomized controlled trial.

Joy (04:29:49) (in thread): > Duly noted@Victoria (Burah) Poromon. Thanks

Mildred Anashie (04:40:23) (in thread): > Hi@JoyThis seems to be a randomized controlled trial but I’ll check again to see ifthere’sanything that confirms this

iniobong simeon (04:40:41) (in thread): > Good day all, please what’s the first task

Francisca Gundu (04:48:46): > Hello everyone,@Svetlana Ugarcina Perovic@Victoria (Burah) PoromonI am curating this study, I want to be sure of the statistical test used in the study for differential abundance. There is Wilcoxon and Spearman’s rank order correlationhttps://gut.bmj.com/content/65/1/57 - Attachment (Gut): Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates > Objective The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers. Here, we investigate the link between gut microbiota variation and stool consistency using Bristol Stool Scale classification, which reflects faecal water content and activity, and is considered a proxy for intestinal colon transit time. > > Design Through 16S rDNA Illumina profiling of faecal samples of 53 healthy women, we evaluated associations between microbiome richness, Bacteroidetes:Firmicutes ratio, enterotypes, and genus abundance with self-reported, Bristol Stool Scale-based stool consistency. Each sample’s microbiota growth potential was calculated to test whether transit time acts as a selective force on gut bacterial growth rates. > > Results Stool consistency strongly correlates with all known major microbiome markers. It is negatively correlated with species richness, positively associated to the Bacteroidetes:Firmicutes ratio, and linked to Akkermansia and Methanobrevibacter abundance. Enterotypes are distinctly distributed over the BSS-scores. Based on the correlations between microbiota growth potential and stool consistency scores within both enterotypes, we hypothesise that accelerated transit contributes to colon ecosystem differentiation. While shorter transit times can be linked to increased abundance of fast growing species in Ruminococcaceae- Bacteroides samples, hinting to a washout avoidance strategy of faster replication, this trend is absent in Prevotella -enterotyped individuals. Within this enterotype adherence to host tissue therefore appears to be a more likely bacterial strategy to cope with washout. > > Conclusions The strength of the associations between stool consistency and species richness, enterotypes and community composition emphasises the crucial importance of stool consistency assessment in gut metagenome-wide association studies.

Precious Orakwe (04:49:01) (in thread): > Yes

Joy (04:53:08) (in thread): > Sure@Mildred Anashie

Precious Orakwe (04:58:58): > @Aleru Divine, this is from your curation, I went through your study I didn’t see the size of group 0 and group 1, please how did you come up with the number you used - File (PNG): Screenshot_20250320-180045.png

Victoria (Burah) Poromon (04:59:20) (in thread): > Hi@Francisca GunduThe statistical test used for differential abundance is Wilcoxon. > > Here’s an excerptfrom the statistical analysis section: “Significance of differences in microbiota growth potential between enterotypes was assessed by Wilcoxon signed rank test”

Aleru Divine (05:07:03) (in thread): > @Precious Orakwe, this study had sample sizes stated in figure captions.

Francisca Gundu (05:08:25) (in thread): > Thank you@Victoria (Burah) Poromon

Juliana Kentomahun Mautin (05:12:08): > Hello@Ayomide Olugbenga Ojoyou are welcome, we are excited to have you here:blush:. > > Kindly check out the message to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out the post which provides insightful tips on how to start your first curation .https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Juliana Kentomahun Mautin (05:16:13) (in thread): > @Ayomide Olugbenga Ojocheck out this welcome material :https://community-bioc.slack.com/canvas/C04RATV9VCYIt will guide you while curating your papers, don’t forget to ask your questions when you feel stuck! Thank you:blush: - File (Canvas): Welcome material

Oriade Adeola (05:19:48) (in thread): > @iniobong simeonHello, the first thing you need to do is to complete the initial applicationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742228279769089Helpful tips for the initial contribution: > * The aim is to familiarize ourselves with a microbiome research article and to extract key details about the research to correctly answer the questions. > * Download the pdf titled “Annotated MacCann Article”. Read thoroughly, noting down the annotated (coloured) parts.link > * Head over to the questions in the curation formlinkto have an idea of what’s required. Go back to the article once again to confirm your answer is accurate and then fill the form. > Follow instructions strictly as well. I hope this helps out:tulip:cunysph.az1.qualtrics.comBugSigDB Outreachy First TaskBugSigDB Outreachy First Task - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy First Task > BugSigDB Outreachy First Task

Ndukauba Oluchi (06:26:00) (in thread): > Hmm this is a technical one:thinking_face:@Joy

Precious Orakwe (06:42:04): > https://bugsigdb.org/38382594Good day,@Aleru Divine@Kate Rasheed@Adeshile Oluwatosin@Mildred Anashie, I am done with my second contribution, please I would really appreciate a peer review for corrections before I can finally submit it. Thank you.@Svetlana Ugarcina Perovicplease delete signature 2 in experiment 1, Thank you. - Attachment (BugSigDB): Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice - BugSigDB > INTRODUCTION: Global warming augments the risk of adverse pregnancy outcomes in vulnerable expectant mothers.

Joy (06:59:54) (in thread): > Well done@Precious Orakweon your curation. Kindly submit a link to your second contribution.

Oriade Adeola (07:01:48): > Good day,@Aleru Divine@Kate Rasheed@Mildred Anashiei have been assigned my second task. please i’d appreciate your guidance on how to go about it. Thank you.

Adeshile Oluwatosin (07:25:59) (in thread): > Kindly drop a link to your study > Well done:clap:@Precious Orakwe

Mildred Anashie (07:27:55) (in thread): > Hi@Precious OrakweI’llbe happy to once you drop a link

Mildred Anashie (07:28:51) (in thread): > Hi@Oriade AdeolaHave you gone through the onboarding materials > > That’s a good place to startAlso, see this the links here can help you starthttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742290950340199If you have more questions,I’llbe happy to help:blush: - Attachment: Attachment > Hello everyone :wave::skin-tone-5: > > Based on a question asked concerning what to do while you wait for an article to be assigned to you on GitHub, this tips could be helpful. > While you wait, you can familiarize yourself with everything. > > 1. View an already curated study to understand what is expected that can be found here it takes you to a random study on BugSigdb. > 2. If you haven’t already gone through the curation policy here’s a link > 3. You can also go through the FAQs most questions you might have could have been answered there already > 4. Also scanning through and reading the welcome material thoroughly would be helpful https://community-bioc.slack.com/canvas/C04RATV9VCY > 5. Finally, if you are the only one who has dropped a comment on the issue on GitHub then I’m positive it would be assigned to you. You can start going through the article to get acquainted with it (I personally like to read through and highlight everything I find significant before I start curating. I think this tip is very helpful). > PS: If you are done with your first contribution and not sure what to do > > I think you can follow the Steps below > 1. Make sure to record your contribution on the outreachy website > 2. You can then go to Github to request one of the studies tagged “Paper to curate” and “outreachy June2025” to be assigned to you. Make sure it isn’t already assigned to someone and no one else has requested for it to be assigned to them. > 3. Also request for a Bugsigdb account via https://bugsigdb.org/Special:RequestAccount (If you request for an account and you don’t receive a mail with your temporary password please check your spam folder, also be patient, you’ll surely receive the mail. > 4. While you wait all I’ve listed above would surely be helpful > > If you have any other questions, feel free to ask :blush:

Halima Momoh (07:36:14) (in thread): > @Oriade AdeolaTo add to what@Mildred Anashieshared > * Visit BugSigDB and explore an already curated study. This will give you an idea of the expected format and data extraction process. > * You can usethis linkto view a random curated study. > * Go through the BugSigDB curation guidelines to understand the rules and best practices. > * Pay attention to details such as data interpretation, formatting, and metadata extraction. > * Look at previously completed BugSigDB curations to familiarize yourself with the process and expectations. > * Go through any video tutorials on BugSigDB curation to get a hands-on understanding of how to curate articles correctly. > * Lastly, if you need further assistance, feel free to ask here on the platform. - Attachment (BugSigDB): Main Page > .

Precious Orakwe (07:55:03) (in thread): > To add to the answer, have you requested for an BugSigDB account, if yes. > > Go through the paper that have been assigned to you, read through the paper thoroughly. > > Then go to you BugSigDb account and create a study and start curating.

Precious Orakwe (08:01:43) (in thread): > So sorry team, I thought I dropped the link before, but I have updated it now, I have dropped the link. Thanks for your support.

Utibe Ita (08:05:12) (in thread): > @Oriade AdeolaHave you opened a BugSigDB account?

Precious Orakwe (08:06:23) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742404407009359?thread_ts=1742291761.479479&cid=C04RATV9VCYFollow this steps - Attachment: Attachment > First thing to do when assigned an article is to: > • Copy out the project title, paste on https://pubmed.ncbi.nlm.nih.gov/ > • Click “cite” > • copy out the “PMID” which contains only numbers > • Head to https://bugsigdb.org/Main_Page > • click “Add a study” > • Input just the PMID digits, everything else auto populates > • Click save and start curating :dizzy:

Oriade Adeola (08:09:07) (in thread): > @Utibe Itayes ihave

Oriade Adeola (08:09:57) (in thread): > @Mildred AnashieYes i have

Oriade Adeola (08:10:28) (in thread): > @Precious OrakweO. Thank you

Oriade Adeola (08:10:35) (in thread): > thank you very one

Utibe Ita (08:11:17) (in thread): > Follow the steps in the link@Precious Orakwejust highlighted from@Adeshile Oluwatosinit was very helpful, if you need any help you can reach out

Oriade Adeola (08:12:11) (in thread): > @Utibe ItaI will. Thank you very much

Joy (08:12:30) (in thread): > Well done@Precious Orakwe. You should verify you taxa via the NCBI browser.The taxon Amulumruptor has the current: Candidatus amulumruptor with the ID: 2510710 while the taxon Firmenecus has the current name: Candidatus firmenecus with the ID: 2840564.Kindly use the taxonomy browser to correct your taxa.https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2840564&lvl=3&lin=f&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Joy (08:48:13): > Hi everyone, I’ve completed my second curation for the study PMID: 33722860****. I would really appreciate a peer review. Let me know if you have any feedback. Thanks (****https://bugsigdb.org/33722860) - Attachment (BugSigDB): Blue poo: impact of gut transit time on the gut microbiome using a novel marker - BugSigDB > BACKGROUND AND AIMS: Gut transit time is a key modulator of host-microbiome interactions, yet this is often overlooked, partly because reliable methods are typically expensive or burdensome.

Adeshile Oluwatosin (09:04:16) (in thread): > @Precious OrakweYou have a number of taxa that can be found on NCBI.https://www.ncbi.nlm.nih.gov/taxonomyHelicobacter: 209 > Luxibacter:2813348Ruminococcus: 1263 > Eubacterium: 1730 > Merdisoma:2840622etcSo please check for taxa with missing ID In your curation

Precious Orakwe (09:18:08) (in thread): > Alright, thank you, how about the statistical analysis, group sizes, names and definitions

Ayomide Olugbenga Ojo (09:19:34): > @Ayomide Olugbenga Ojo has left the channel

Precious Chijioke (09:22:35): > Hello Everyone, I am creating my first experiment on the paper I’m curating and finding it difficult to identify the condition. I have checked for the ontology through theEFObut haven’t seen the one whose explanation is close to the content in the paper in relation to the treatment of Functional constipation with Traditional Chinese Medicine. Please I need assistance@Svetlana Ugarcina Perovic@Kate Rasheed@Peace Sandy<@UBNSEMS3S>and anyone that can help me. > > Link to paper:https://www.dovepress.com/therapeutic-mechanism-of-zhuyang-tongbian-decoction-in-treating-functi-peer-reviewed-fulltext-article-IJGM#f0002 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB

Adeshile Oluwatosin (09:23:45) (in thread): > I will check that:pleading_face:

isaac imitini (09:31:51) (in thread): > You can select the closest to “Functional Constipation” Which is “Irritable Bowel Movement (IBS)” > > IBS is a functional bowel disorder characterized by chronic abdominal pain, bloating, and altered bowel habits, which can include constipation. It shares overlapping symptoms with functional constipation, making it a relevant match.https://www.ebi.ac.uk/ols4/ontologies/efo/classes/http%253A%252F%252Fwww.ebi.ac.uk%252Fefo%252FEFO_0000555 - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Precious Chijioke (09:36:10) (in thread): > @isaac imitiniThank you for your assistance

isaac imitini (09:36:41) (in thread): > You are welcome@Precious Chijioke

Adeshile Oluwatosin (09:42:44) (in thread): > @Precious Chijiokethe condition is “Chronic constipation” > As that is another name for functional constipation

Precious Chijioke (09:46:09) (in thread): > @Adeshile Oluwatosin@isaac imitini@Kate Rasheedthank you for your assistance. I needed something that is very close to Functional constipation and your assistance resolved it. Since Functional Constipation is substituted with Chronic Constipation, should I also substitute my group naming with CC where FC e.g Patients with CC instead of Patients with FC or I should use the group names the way it is.

Precious Orakwe (09:57:18) (in thread): > No, if FC is in the study, use the FC, the chronic constipation is just a condition

Precious Chijioke (09:57:51) (in thread): > @Precious Orakwethank you for your assistance

Precious Orakwe (09:58:08) (in thread): > You are welcome

Precious Orakwe (10:00:22): > When one is done with the second contribution, what is the next thing to do.@Aleru Divine@Svetlana Ugarcina Perovic@Mildred Anashie@Adeshile Oluwatosin@Kate Rasheed

Svetlana Ugarcina Perovic (10:03:19) (in thread): > Helping others to finalize their curations.

Svetlana Ugarcina Perovic (10:04:17) (in thread): > @Precious Orakweassigned:wink:to provide feedback here in Slack.

Svetlana Ugarcina Perovic (10:05:00) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742561293329909 - Attachment: Attachment > Hi everyone, I’ve completed my second curation for the study PMID: 33722860. I would really appreciate a peer review. Let me know if you have any feedback. Thanks (https://bugsigdb.org/33722860)

Precious Orakwe (10:05:07) (in thread): > Thanks@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (10:07:01) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/647#issuecomment-2743478436 - Attachment: Comment on #647 [Study]: Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice > Signature 2 in experiment 1 deleted.

Adeshile Oluwatosin (10:07:34) (in thread): > @Precious ChijiokeDo not substitute the group names

Utibe Ita (10:18:49): > Hello everyone > how is the contribution phase progressing? > > I hope this answers a lot of recurring questions as earlier shared by@Scholastica UruaPlease feel free to add other questions and answers under this thread. I hope this helps someone! > > Q1. I couldn’t find how to record my first contribution. > A: Steps for recording your first contribution: > - Go to the Outreachy website. > - Click on the ‘Microbiome Study Curation’ project. > - Click on ‘Record Contributions and Apply to This Project’. > - Then proceed to record your contribution. > > Q2. When recording the first contribution, what is the ‘merged date’? > A: The merged date refers to the date you submitted your contribution. > > Q3. What URL are we submitting for the first contribution? > A: The link to the curation form:https://cunysph.az1.qualtrics.com/CP/File.php?F=F_6tUXvlDsehCQr7Uwill serve as your Contribution URL. > > Q4. After I submit my first contribution, can I go back to edit it if I notice I made a mistake, or if I didn’t add something somewhere? > A: Unfortunately, you cannot edit a submitted contribution but you can make another submission from scratch. > > Q5. Are we making 2 contributions? > A: While you can make as many contributions as possible, the first contribution is compulsory. After completing the first contribution, you may proceed to the second. Although the second contribution is not mandatory, it is advisable to complete it. Once your second contribution has been graded, you can claim another article for curation. While waiting for grading, some other ways you can contribute to BugSigDB are; > - Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice here in slack. > - Try to figure out some of the taxa with missing NCBI ids:https://bugsigdb.org/Category:Pages_with_missing_NCBI_ID- See other possible ways to help on the help page:https://bugsigdb.org/Help:ContentsQ6. For the second contribution, after Adding a Study in BugSigDB, does it need to be reviewed by a Mentor on BugSigDB before being able to Add a new experiment for the study? > A: You do not need to wait for mentors to review. You can click on the ‘Add Experiment’ button to add an experiment. > > Q7. I want to know how many times I can use the record my contribution option on the Outreachy website. > A: You can use the ‘Record My Contribution’ option as many times as needed, depending on how many contributions you make. > > Q8. How to I get assigned a paper for my second curation? > A: Find an unassigned paper you’ll like to curate viahttps://github.com/waldronlab/BugSigDBcuration/issues, then ask for it to be assigned to you by commenting on itand tag SvetlanaUP@Svetlana Ugarcina Perovic**** .****Mentors will assign it to you if you are the first to request for it.

Precious Orakwe (10:19:09) (in thread): > Thanks@Svetlana Ugarcina Perovic

Precious Orakwe (10:20:54) (in thread): > I can’t see the signatures for the study

Anne-Marie Sharp (10:21:20): > Hello everyone, I’m done with my second contribution andwill gladly help with peer-reviews or if you need any assistance.

Adeshile Oluwatosin (10:23:16): > Good Afternoon > Please remember that you cannot request for a peer review once you’ve submittedWell done everyone:clap::clap::clap:

Adeshile Oluwatosin (10:24:42) (in thread): > You can leave a link to the study@Anne-Marie SharpWell done

Anne-Marie Sharp (10:26:15) (in thread): > @Adeshile Oluwatosinthank you. I meant I am done. And willing to help anyone that needs a peer review or assistance

Adeshile Oluwatosin (10:26:44) (in thread): > Ohhh great:heart:

Precious Chijioke (10:30:57) (in thread): > I added my first experiment and saved but can’t see the button to add signature and the first experiment I added is invisible. The interface I’m seeing is same as when I added only a study. I reloaded the page and it’s showing same thing. Please I need assistance on how to navigate through.@Kate Rasheed@Svetlana Ugarcina Perovic@Peace Sandy - File (PNG): Screenshot (675).png

isaac imitini (10:31:36) (in thread): > Reload your page it would show.

Precious Chijioke (10:32:19) (in thread): > @isaac imitiniI have reloaded the page and it’s same thing

isaac imitini (10:33:22) (in thread): > You can refer to this for a solution.https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Adeshile Oluwatosin (10:34:00) (in thread): > https://bugsigdb.org/40026814/Experiment_1 - Attachment (BugSigDB): 40026814/Experiment 1 > .

Anne-Marie Sharp (10:36:20) (in thread): > @Utibe ItaPlease I’m confused on Q5, you mentioned after the second contribution has been graded you can claim another article for curation. But@Svetlana Ugarcina Perovicjust mentioned that we should assist others to finish theirs by reviewing their article. So are we to doone or both? Can we do both?

Precious Chijioke (10:37:01) (in thread): > Thank you for your asssistance@isaac imitini@Adeshile Oluwatosin

Svetlana Ugarcina Perovic (10:58:51) (in thread): > You can do both, but team work is preferable.

Anne-Marie Sharp (11:00:50) (in thread): > @Svetlana Ugarcina Perovicokay, noted. Thanks for clarifying.

Utibe Ita (11:01:45) (in thread): > @Anne-Marie Sharphelping others with their article curation broadens your understanding and experience level

Anne-Marie Sharp (11:03:12) (in thread): > @Utibe Itatrue, I get. Thank you for the tips.

Joy (11:16:08) (in thread): > Hi@Precious Orakwe, the signatures are there, they’ll eventually populate.

Precious Chijioke (11:42:29): > Hello Everyone, for the past 1 hour I have been trying to add signature to my first experiment as it takes longer time for each NCBI I input to load. I entered all the NCBI, clicked on complete and saved and it loaded but did not reflect. I refreshed the page following the solutionhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439and yet the experiment have not reflected. Please I need help so that I will continue with the second second signature entry and other experiments@Kate Rasheed@Svetlana Ugarcina Perovic@Peace Sandy<@UBNSEMS3S> - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Kate Rasheed (11:57:21) (in thread): > @Precious Chijioke. Edit your experiment by changing it from Complete to Incomplete

Precious Chijioke (12:01:37) (in thread): > @Kate Rasheedthank you for your assistance. It’s visible now.

Precious Chijioke (12:18:08) (in thread): > Please@Kate Rasheedshould I change it from incomplete to complete after entering the second signature?

Kate Rasheed (12:26:50) (in thread): > Yes yes@Precious Chijioke

Precious Chijioke (12:30:54) (in thread): > Thank you@Kate Rasheed@Peace Sandy@Svetlana Ugarcina PerovicPlease one more question on the addition of a signature. While adding the NCBI of the second signature (for decreased abundance) how do I identify the taxon not mentioned in the paper using theNCBI taxon identifier by searching here. I’m a bit confused on how to go about it. Also, can I edit a signature if I made a mistake while entering the signature? - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Svetlana Ugarcina Perovic (12:40:48): > Reminder:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742565799989129?thread_ts=1742565622.843429&cid=C04RATV9VCYPlus note: corrections should be done SOLELY by the original curator based on our official feedback provided by one of the mentors. - Attachment: Attachment > Helping others to finalize their curations.

Oriade Adeola (12:42:08) (in thread): > Thank you@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (12:42:10) (in thread): > Alright, noted@Svetlana Ugarcina Perovic

Anne-Marie Sharp (12:54:40) (in thread): > Hello@Precious ChijiokeIf you mean to identify a taxon on NCBI, go to the NCBI Taxonomy page (https://www.ncbi.nlm.nih.gov/taxonomy). In the search bar at the top, type the name of the organism (eg. E. coli) and you will see the results, check for the closest match and ensure it is the same taxon (if the signature you are searching for is a phylum then the match should be a phylum as well, not species, genus or others). According to the curation policy, If a taxon is reported as something like this Prevotella KQ959344_s, and you cannot find this in the NCBI taxonomy browser, report it exactly the way it’s reported in the paper since it could be referring to a certain strain of Prevotella. And you can edit a signature by yourself if you made a mistake, as far as you have not submitted your article for review.

Precious Chijioke (12:59:46) (in thread): > @Anne-Marie SharpThank you for your assistance though my concern is not totally resolved. > In a situation I have g_Fusicatenibacter, g_Faecalibacterium, etc in the paper as decreased abundance, how do I identify the other one apart from the ones mentioned?

Anne-Marie Sharp (13:04:16) (in thread): > @Svetlana Ugarcina Perovicnoted:white_check_mark:

Anne-Marie Sharp (13:04:18) (in thread): > @Precious ChijiokeOkay, you’re welcome. Perhaps there is a supplemental material. Kindly share your article here so I can take a look for you.

Precious Chijioke (13:12:37) (in thread): > @Anne-Marie Sharpplease check Fig 2b:https://www.dovepress.com/article/fulltext_file/509592/aW1n/IJGM_A_509592_O_F0002g.jpgin the paper few taxon were mentioned as increase and decrease abundance respectively while in the supplemental material as seen in the link there’s a broader list of taxon. How can I classify those with increase and decrease abundance which is not mentioned in the paper. > > Article link:https://www.dovepress.com/therapeutic-mechanism-of-zhuyang-tongbian-decoction-in-treating-functi-peer-reviewed-fulltext-article-IJGM#f0002 - Attachment: Attachment - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB

Jesulolufemi Adelanke (13:13:22) (in thread): > Noted. Thank you

Anne-Marie Sharp (13:41:34) (in thread): > @Precious ChijiokeI’ve seen what you’re referring to. g_Fusicatenibacter, g_Faecalibacterium, etc were stated as significantly decreased. For those in the ‘etc category’ you can get them from the article itself first, before confirming on NCBI. You can do this by checking the figures/tables if there is any other additional significant taxon mentioned (If a taxon is not explicitly mentioned as significant in the text/tables/figures, do not curate it). I will still go through the article meticulously to check for the signatures in the ‘etc category’ then we can compare our findings.

Utibe Ita (13:41:36) (in thread): > Noted@Svetlana Ugarcina Perovic

Precious Chijioke (13:45:07) (in thread): > @Anne-Marie Sharpwhere I am having difficulty is my inability to identify the “etc” not captured in the paper from the table for both increased and decreased abundance.

Anne-Marie Sharp (13:52:19) (in thread): > @Precious ChijiokeI understand you, sorry about that. You can identify the ‘etc category’ by checking the figures/tables one by one if there is any other additional significant taxon mentioned. I am also checking through each one and will give you my findings.

Precious Chijioke (13:53:10) (in thread): > @Anne-Marie SharpThank you for your assistance

Mildred Anashie (14:25:39) (in thread): > Noted@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (14:40:56) (in thread): > Corrections: > * Provide peer review of other Outreachy applicant curations by reviewing their work and posting any issues you notice~on the GitHub issue for that curation.~here in Slack > > * Find an unassigned paper you’ll like to curate viahttps://github.com/waldronlab/BugSigDBcuration/issues, then ask for it to be assigned to you by commenting on itand tag SvetlanaUP.Mentors will assign it to you if you are the first to request for it. > @Utibe Itaplease edit your post and thanks for this helpful FAQ!

Adeshile Oluwatosin (14:47:45) (in thread): > @Precious Chijiokeinstances of g_Fusicatenibacter. G means genus, so ensure you check > Search only for fusicatenibacter usingNCBI LinkIn this caseyou should see the rank as genus > > Do the same for the remaining taxa - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (14:49:19) (in thread): > Your other questions are unclear

Svetlana Ugarcina Perovic (14:53:18): > Letters before taxa/signaturesdpcofgsare first letters of taxonomy ranks. > > Example:Domain: BacteriaPhylum: BacillotaClass: BacilliOrder: LactobacillalesFamily: LactobacillaceaeGenus: LactobacillusSpecies: Lactobacillus iners > > g_lactobacillus -> genus Lactobacillus -> BugSigDB recordinghttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1578&lvl=3&lin=f&keep=1&srchmode=1&unlockNOTE: we do not record “g_”

Utibe Ita (14:54:49) (in thread): > Thank you@Svetlana Ugarcina Perovic

Precious Chijioke (14:57:32) (in thread): > Thank you@Svetlana Ugarcina Perovic

Anne-Marie Sharp (14:59:54) (in thread): > You’re welcome@Precious Chijioke. These are my findings: The comparison here is FC_PreZY vs. NC****. ****Figure 2C is the best figure for identifying significantly increased or decreased taxa in the FC_PreZY group as its a heatmap that displays the relative abundance of specific genera (which includes your ‘etc category’), blue is for decreased and orange/yellow is for increased but I think the red box beside confirms statistically and significantly increased and the blue box beside confirms statistically and significantly decreased . > Significantly Increased in FC_PreZY (before treatment): g__Collinsella, g__Romboutsia, g__Desulfovibrio, g__UCG-002, g__Ruminococcus, g__NK4A214_group. > Significantly Decreased in FC_PreZY (before treatment): g__Faecalibacterium, g__Fusicatenibacter, g__Subdoligranulum, g__Agathobacter, g__Christensenellaceae_R-7_group

Precious Chijioke (15:04:58): > Hello@Svetlana Ugarcina Perovic@Kate RasheedI added signature 1 to my second experiment and refreshed the page using the update experiment guide. I left the experiment as incomplete since I’m working on it but signature is not visible.https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Anne-Marie Sharp (15:07:11) (in thread): > @Precious Chijiokeso you can now confirm them on NCBIif itdoesn’tautocomplete while you are entering them on BugSigDB. As@Adeshile Oluwatosinmentioned, the g represents genus, so search for just the name after the slash _

Anne-Marie Sharp (15:08:47) (in thread): > @Svetlana Ugarcina PerovicThank you for sharing

Svetlana Ugarcina Perovic (15:09:09) (in thread): > There is a duplicate to this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742571749896569 - Attachment: Attachment > Hello Everyone, for the past 1 hour I have been trying to add signature to my first experiment as it takes longer time for each NCBI I input to load. I entered all the NCBI, clicked on complete and saved and it loaded but did not reflect. I refreshed the page following the solution https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 and yet the experiment have not reflected. Please I need help so that I will continue with the second second signature entry and other experiments @Kate Rasheed @Svetlana Ugarcina Perovic @Peace Sandy @UBNSEMS3S

Svetlana Ugarcina Perovic (15:09:56) (in thread): > and a solution in the thread is provided.

Precious Chijioke (15:19:10) (in thread): > Thank you@Anne-Marie Sharpfor your assistance

Precious Chijioke (15:21:14) (in thread): > Thank you@Adeshile OluwatosinI already search the rank usinghttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1407607&lvl=3&lin=f&keep=1&srchmode=1&unlockbefore bringing the concern here.@Anne-Marie Sharphave helped to resolving my concern. Thank you all.

Precious Chijioke (15:25:34) (in thread): > @Svetlana Ugarcina PerovicI’m sorry for the duplicate. I’ll write my second concern regarding this in the existing thread.

Anne-Marie Sharp (15:32:55) (in thread): > @Precious Chijiokeyou’rewelcome:pray:

Jesulolufemi Adelanke (15:44:39) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing

Ndukauba Oluchi (15:45:34): > Hello everyone Please I have a question: > 1. The condition of my study is Fecal Microbiota transplantation, but I don’t seem to see that in Bugsigbd so I used the Ontology search to find the EFO, I found it but I can’t paste it in Bugsigbd, what do I do please. > I’ve looked for similar names but didn’t find any in Bugsigbd too

Oriade Adeola (15:48:22) (in thread): > https://www.youtube.com/watch?v=yfpnwxefLFc&list=PLIUETfW6tVu2OGgZcIxqI7DbUBReHVdIq&index=4i think you should what this video. it might be of assistance to you - Attachment (YouTube): Adding a study to bugsigdb.org

Halima Momoh (15:49:53) (in thread): > hello@Svetlana Ugarcina PerovicI don’t really understand. could you please elaborate more? Thank you.

Ndukauba Oluchi (15:52:26) (in thread): > Thank you@Oriade Adeolabut in that video, the Condition was found in the Bugsigdb website, but in my study case, the condition isn’t there, when I click the drop down I would get a “No results found” output. > Do you understand now?

Oriade Adeola (15:57:31) (in thread): > Did you log into the bugsigdb website first?

Precious Chijioke (15:57:59) (in thread): > @Ndukauba OluchiI had similar experience look for the close word to Microbiota transplantation. I’ll also look at it and get back to you.

Ndukauba Oluchi (15:58:05) (in thread): > Yes I did@Oriade Adeola

Ndukauba Oluchi (15:58:31) (in thread): > Alright please do@Precious ChijiokeThank you

Oriade Adeola (15:59:49) (in thread): > @Nanlop Blessing Dafwati think you should try thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742583898433959 - Attachment: Attachment > Hello @Svetlana Ugarcina Perovic @Kate Rasheed I added signature 1 to my second experiment and refreshed the page using the update experiment guide. I left the experiment as incomplete since I’m working on it but signature is not visible. > https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439

Oriade Adeola (16:00:28) (in thread): > check@Svetlana Ugarcina Perovicreply and try thaatif it would work

Precious Chijioke (16:01:44) (in thread): > @Ndukauba Oluchianother word for Microbiota transplantation is “Stool transplant”.

Ndukauba Oluchi (16:02:24) (in thread): > Stool transplant is still not there

Ndukauba Oluchi (16:02:44) (in thread): > I also tried Bacteriotherapy, but I didn’t find it

Precious Chijioke (16:04:50) (in thread): > @Svetlana Ugarcina Perovic@Kate Rasheed<@UBNSEMS3S>please check and reply

Precious Chijioke (16:11:37) (in thread): > Hello@Svetlana Ugarcina Perovic@Kate Rasheed<@UBNSEMS3S>@Peace Sandyadded signature 1 to my second experiment and refreshed the page using the update experiment guide. I left the experiment as incomplete since I’m working on it but signature is not visible. > > Please Note: the earlier concern stated on addition of signature is for experiment 1 and I followed the guide provided by@Kate Rasheedby leaving experiment 2 as incomplete before entering the signature but the signature is invisible. - File (JPEG): Screenshot_20250321-210707_1.jpg

Victoria (Burah) Poromon (16:12:41) (in thread): > Hi@Ndukauba Oluchi, can you share a link to your study please?

Mildred Anashie (16:14:14) (in thread): > Hi@Precious ChijiokeTry to complete the signature and refresh, I think it will come up

Ndukauba Oluchi (16:14:50) (in thread): > Sure! Here it ishttps://bugsigdb.org/39194187 - Attachment (BugSigDB): The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation - BugSigDB > UNLABELLED: To investigate the impact of Small Intestinal Bacterial Overgrowth (SIBO) on the efficacy of Fecal Microbiota Transplantation (FMT) in patients with chronic constipation, our research team included 218 patients with chronic constipation treated with FMT.

Victoria (Burah) Poromon (16:15:46) (in thread): > Also you can click edit on experiment 2, delete something, save. Then go and put it back. > > This works for me most times

Adeshile Oluwatosin (16:16:46) (in thread): > Change browser too if you can or check your network@Precious Chijioke

Ndukauba Oluchi (16:17:01) (in thread): > Hey, kindly go to “Recent changes” click on it you’d find your experiment there

Ndukauba Oluchi (16:17:27) (in thread): > Due to network sometimes it takes time to reflect

Ndukauba Oluchi (16:19:05) (in thread): > Or you can also go to your browser add signature_1 to the link, it takes you straight to the page > > Like thishttps://bugsigdb.org/“study number/Experiment_1/ signature_1 > > Do you understand?

Precious Chijioke (16:20:31) (in thread): > @Mildred AnashieI completed the signature and followed the guide provided by@Kate Rasheedwhen I had similar concern where working on experiment 1. I refreshed the page over and over using the update:https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439But the signature didn’t reflect. - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Victoria (Burah) Poromon (16:20:37) (in thread): > Okay, the condition for this study is “Chronic Constipation”@Ndukauba OluchiPatients with chronic constipation were treated with FMT.

Precious Chijioke (16:21:41) (in thread): > @Victoria (Burah) PoromonI also tried editing the experiment, saved changes and it didn’t work

Precious Chijioke (16:23:40) (in thread): > @Ndukauba Oluchithe screenshot I shared is from my experiment 1 which I opened in browser but the signature haven’t reflected.

Mildred Anashie (16:26:34) (in thread): > From the screenshot it looks like experiment 1 has reflected@Precious Chijiokeand I asked you complete experiment 2let’ssee if it works

Ndukauba Oluchi (16:26:44) (in thread): > Hmm! Good Job@Victoria (Burah) Poromonbut if you study the welcome materialhttps://community-bioc.slack.com/docs/T35G93A5T/F05URJ0P021The Condition is what is being contrasted in the experiment, not something shared by both groups. > Don’t* you think *chronic constipation is shared by both groups?

Precious Chijioke (16:26:56) (in thread): > @Svetlana Ugarcina Perovic<@UBNSEMS3S>@Kate Rasheed@Peace Sandyplease I need help.

Ndukauba Oluchi (16:29:19) (in thread): > @Victoria (Burah) PoromonAlso refer to this material from my study > Link:https://clinicaltrials.gov/study/NCT06208930?term=NCT06208930&viewType=Table&rank=1The condition was given to be “Fecal Microbiota transplantation”

Ndukauba Oluchi (16:31:41) (in thread): > Just try to click on “recent changes” and follow the steps I highlighted first, it will work like magic:ok_hand:

Precious Chijioke (16:34:09) (in thread): > @Ndukauba OluchiI already tried the “recent changes” but it didn’t resolve the problem.

Ndukauba Oluchi (16:34:54) (in thread): > Oops, try the second step

Ndukauba Oluchi (16:35:32) (in thread): > Like thishttps://bugsigdb.org/“study number”/“Experiment_1”/ “signature_1”

Precious Chijioke (16:38:11) (in thread): > @Ndukauba OluchiI stated earlier that I’ve tried the “study number”/“Experiment_1”/“signature 1”. The options you suggested have been tried before I brought the concern here.

Anne-Marie Sharp (16:42:07) (in thread): > @Ndukauba OluchiI think you should see thishttps://github.com/EBISPOT/efo/issues/2125this FMT condition seems to have been an issue for a while - Attachment: #2125 New term request for “fecal microbiota transplantation” > This term is in several other ontologies (https://www.ebi.ac.uk/ols4/search?q=fecal+microbiota+transplantation) and could be imported e.g. from MAXO:0000748 or NCIT:C118643. Only NCIT also has a subclass autologous fecal microbiota transplantation, which could be useful, but it looks like it imports from CTRP, which if I understand correctly is not in OLS). > > ## Preferred term label > > fecal microbiota transplantation > > ## Synonyms > > Union of NCIT:C118643 and MAXO:0000748 (although either one would be fine) > > fecal material transplantation
> fecal microbiota transplantation
> fecal transplantation
> FMT
> poo transplant
> poop transplant
> stool transplant
> stool transplantation > > ## Textual definition > > The transplantation of fecal bacteria, via enema, colonoscopy, or other method, from a healthy individual to a recipient. > > (copied from MAXO:748 or NCIT:C118643) > > ## Suggested parent term > > medical procedure

Precious Chijioke (16:42:08) (in thread): > This is the first experiment url.https://bugsigdb.org/40026814/Experiment_1 - Attachment (BugSigDB): 40026814/Experiment 1 > .

Mildred Anashie (16:43:19) (in thread): > @Precious ChijiokeHave you confirmed ifit’sappearing among thecontributions you’vemade? > > If No, see image on where to check. > If itisappearing there then I think it might be your connection,you’llhave to be patient till tomorrow to try again - File (JPEG): c072fc2b-30f0-4a98-9d6b-951847d8b25e

Ndukauba Oluchi (16:43:51) (in thread): > Wow! great Job@Anne-Marie Sharpthank you for pointing that out:+1:

Anne-Marie Sharp (16:46:31) (in thread): > @Ndukauba Oluchiyou’rewelcome.

Anne-Marie Sharp (16:52:03) (in thread): > @Precious ChijiokeI think you should try what@Mildred Anashiesuggested. > Click on Edit experiment 2 and put Experiment 2 as complete.Then in Experiment 2, click on add signature and enter the signature for experiment 2. It should show.That’show I worked on mine though.

Precious Chijioke (16:53:56) (in thread): > @Anne-Marie SharpI’ll retry it

Victoria (Burah) Poromon (17:07:55) (in thread): > Yes, you’re right@Ndukauba Oluchi.The condition is what is being contrasted in the experiment. The condition is also the disease that is being studied. > > The contrast groups are constipated patients with SIBO and constipated patients without SIBO. > > Take this study for example:https://bugsigdb.org/37119437Comparisons were made betweenCovid19 patients with comorbidities and Covid 19 patients without comorbidities. And the condition is Covid 19. Becauseit’sthe disease that is being studied. - Attachment (BugSigDB): Oral Fungal Alterations in Patients with COVID-19 and Recovered Patients - BugSigDB > The oral bacteriome, gut bacteriome, and gut mycobiome are associated with coronavirus disease 2019 (COVID-19).However, the oral fungal microbiota in COVID-19 remains unclear.This article aims to characterize the oral mycobiome in COVID-19 and recovered patients.

Svetlana Ugarcina Perovic (17:16:16) (in thread): > @Halima Momohsee for example this figure for curation:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742206169575949?thread_ts=1742163431.736449&cid=C04RATV9VCY - Attachment: Attachment > Hello everyone :hugging_face: > Once again I have a question. > The lowercase alphabet before the signature name is it relevant? > For example f_mitochondria, g_lactobacillus > What does the f and g prefix mean? > Cc @Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (17:17:46) (in thread): > Often taxa are reported in the papers with taxonomic rank next to their name: g_lactobacillus > > In this case g stands for genus and we do not curate this taxon with “g_” in the beginning

Ndukauba Oluchi (17:29:45) (in thread): > Okay@Victoria (Burah) Poromon

Ndukauba Oluchi (17:49:25): > Hello everyone:hugging_face:I have just completed my second curation for the study: (https://bugsigdb.org/39194187) > I would appreciate a peer review, please let me know if you have any feedback. Thank you:pray: - Attachment (BugSigDB): The impact of small intestinal bacterial overgrowth on the efficacy of fecal microbiota transplantation in patients with chronic constipation - BugSigDB > UNLABELLED: To investigate the impact of Small Intestinal Bacterial Overgrowth (SIBO) on the efficacy of Fecal Microbiota Transplantation (FMT) in patients with chronic constipation, our research team included 218 patients with chronic constipation treated with FMT.

Anne-Marie Sharp (17:52:36) (in thread): > Hello@Ndukauba Oluchiwell done:raised_hands:I’llreview it and give feedback

Adeshile Oluwatosin (18:05:54) (in thread): > No data transformation in experiment 3 > You curated taxa meant to be recorded for decreased abundance as increasefor Experiment 1

Adeshile Oluwatosin (18:06:43) (in thread): > Body site is feces

Svetlana Ugarcina Perovic (18:10:31): > :potted_plant:**** You had an excellent first week of contribution. Take a good rest and I’ll see you on Monday.****

Adeshile Oluwatosin (18:11:02) (in thread): > Thank you so much@Svetlana Ugarcina PerovicAnd you too

Anne-Marie Sharp (18:39:14) (in thread): > @Ndukauba OluchiI think MHT correction shouldn’t be added

Anne-Marie Sharp (18:46:46) (in thread): > Thank you@Svetlana Ugarcina Perovicsee you on Monday

Adeshile Oluwatosin (18:47:59) (in thread): > MHT: noas there are no adjusted values

Anne-Marie Sharp (19:02:18) (in thread): > @Adeshile Oluwatosinyes@Ndukauba Oluchi1)MHT correction wasn’t done so it should be: No not Yes2)You omitted some taxa in Experiment 1, like Bacteroides and Escherichia-Shigella3)In Experiment 3, signature 1 should be increased & signature 2 should be decreased, not the other way around.

Mildred Anashie (19:16:37) (in thread): > Thank you@Svetlana Ugarcina Perovic:hugging_face:

Jesulolufemi Adelanke (23:15:37) (in thread): > Thank you:blush:. Have a great weekend.

Jesulolufemi Adelanke (23:19:25) (in thread): > Hi@Ndukauba Oluchi, well-done:+1:. I just reviewed it. The MHT correction should indicate NO.

Jesulolufemi Adelanke (23:20:13) (in thread): > @Mildred Anashie@Adeshile Oluwatosinany other comments. It will be much appreciated.

2025-03-22

Gonza Gertrude (00:32:07): > Hello everyone! I am Gonza Gertrude Agatha. I am happy to be there and work with you.

Adeshile Oluwatosin (01:55:08) (in thread): > Welcome:tulip:@Gonza Gertrude

Dorcas Odetayo (02:00:25) (in thread): > Thank you so much for sharing this@Svetlana Ugarcina Perovic

Dorcas Odetayo (02:05:26) (in thread): > Welocme@Gonza Gertrude, Kindly go through this to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Anne-Marie Sharp (02:40:16) (in thread): > Hello@Gonza Gertrudeyou’rewelcome

chiamaka Uche (02:47:36): > Hello everyone, I’m Chiamaka Uche. I’m excited to get started. I will appreciate if anyone could help with guide on how to make my first contribution.

Anne-Marie Sharp (02:48:44) (in thread): > @chiamaka UcheYou are welcome. Read through this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Anne-Marie Sharp (02:52:02) (in thread): > @chiamaka UcheGo through the prep work in the link I shared, watch the videos to understand how to make a curation. Then go to ‘first curation form’ for your first contribution task. > The entire guide to all you will do is in the link, just carefully follow it line by line. And ask more questions if it’s still unclear.

chiamaka Uche (02:57:22) (in thread): > Okay, I will read through. Thank you

Anne-Marie Sharp (03:24:46) (in thread): > You’rewelcome

Aiysha shahid (03:54:10) (in thread): > Welcome@chiamaka Uche:tulip:

Eseoghene Cynthia Princewill-Ukot (03:55:47) (in thread): > Thank you@Svetlana Ugarcina Perovic.

Eseoghene Cynthia Princewill-Ukot (03:58:09) (in thread): > Welcome@Gonza Gertrude. Happy curating:kissing_heart:

Mildred Anashie (04:20:01) (in thread): > Welcome@chiamaka Uche:hugging_face:

Precious Orakwe (04:41:57) (in thread): > Thank you so much@Svetlana Ugarcina Perovic, have a blissful weekend.

Dorcas Odetayo (04:49:51) (in thread): > Welcome@chiamaka Uche:tulip:

Gonza Gertrude (05:15:27) (in thread): > Thank you all.

Aiysha shahid (05:33:21) (in thread): > Thank you@Svetlana Ugarcina Perovic:tulip:

Mildred Anashie (05:43:56) (in thread): > Hi@Jesulolufemi AdelankeWell done on your curation:clap::skin-tone-5:I’ve gone through the study and I have a few observations. > 1. Alpha Diversity: I see you recorded Richness but I do not see Richness being reported s a diversity index within the article. What I see is just Choa1, Shannon and Gini-Simpson (which I believe to be same as Simpson because the paper seems to mention it interchangeably). Please remove Richness from the curation and correct the other Alpha diversity indices, > For CC vs HC > Chao1 is Increased > Shannon is Increased > Simpson is Increased > while CD vs HC > Chao1 is Decreased > Shannon is Unchanged > Simpson is Unchanged. > > Asides the visualization done, the Figure caption For Fig 1, also explains it. > > 2. Antibiotic Exclusion: Please change it to month instead of 30 days. > > 3. Group name and Definition: Just my opinion, You can Include (CC group) to Children with Constipation and (CD group) to Children with Diarrhea. Although the paper says under 3, it also mentions 1-3years and not 0-3years for the age groups. > > 4. Signatures: You have to look at your signatures again, the curation doesn’t seem totally accurate and you left some out. You curate the lowest taxonomical level reported, From Table S7 and S8 you are to curate the taxa listed under constipation as Increased in Constipation and those reported under Healthy as Increased in healthy as this would be Decreased for that experiment. Also, for e.g in Figure S3 you curate using the color code and this means those with red beside them would be recorded as Increased in Diarrhea and the green would be increased in Healthy control and that is decreased in Diarrhea. This applies to FigS4 and Fig 2 ( By the way I noticed you didn’t curate taxa from Fig 2).5: Study Design: Also, this looks like a case-control study and not a cross sectional observational not case control.These are my observations so far, If you have more questions feel free to ask. > Well done again:blush:

Joy (06:17:37) (in thread): > Welcome@Gonza Gertrude:sparkles:

Joy (06:19:03) (in thread): > Welcome to the community@chiamaka Uche:sparkles:kindly go through the link above.

Svetlana Ugarcina Perovic (07:33:34): > Hello, Vanisha is stuck in joining our Slack communication. Could someone please help to join our Slack channel? To see where is the problem etc. > > Error message is:“The email address must match one of the domains listed below. Please try another email.”https://github.com/waldronlab/BugSigDBcuration/issues/666

Anne-Marie Sharp (07:41:15) (in thread): > Hello@Svetlana Ugarcina Perovicshe can try using a gmail account if she’s using another type of email.Or she can be manually added to the group ifit’llwork.

Adeshile Oluwatosin (07:43:57) (in thread): > These are the responses I saw online: > 1. Check the allowed domains: > • Ask a Slack admin to go to Slack Settings → Authentication & Security and check the list of allowed domains.2. Use an approved email: > • If Vanisha is using a different email (e.g., a Gmail or Yahoo email), she should try using an email that matches the approved domain.3. Request an admin invite: > • If the workspace requires an invite, a Slack admin can manually send an invitation to Vanisha’s email.4. Temporarily allow her domain (if appropriate): > • If she’s a contributor and needs access, an admin can consider adding her email domain to the approved list.

Svetlana Ugarcina Perovic (07:51:56) (in thread): > Thanks for your suggestions. Sorry, I was not precise, I already looked for solutions and shared with Vanisha. Now I am asking if someone could approach to Vanisha and together solve the problem.

Svetlana Ugarcina Perovic (07:53:27) (in thread): > See:https://github.com/waldronlab/BugSigDBcuration/issues/666#issuecomment-2745233221 - Attachment: Comment on #666 [Study]: Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time > @SvetlanaUP Okay Before asking for official review I will ask help from peers , But yes the problem is I am unable to join slack properly , I am working on that issue but still not able to figure out what is going wrong

Anne-Marie Sharp (07:54:29) (in thread): > Okay, noted. we will help her out however we can.

Svetlana Ugarcina Perovic (07:55:46) (in thread): > I sent again the invitation. Thanks!

Svetlana Ugarcina Perovic (07:56:59): > Please welcome@Vanisha Garg:tulip:Feel free to introduce yourself and do not hesitate to ask questions. Happy curating! > > A PEER REVIEW NEEDED:https://github.com/waldronlab/BugSigDBcuration/issues/666 - Attachment: #666 [Study]: Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time > ### Study Title > > Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time > > ### Pubmed ID > > 37926855 > > ### The Digital Object Identifier (DOI) > > https://doi.org/10.1186/s40168-023-01691-y > > ### First Author > > Minnebo Y > > ### Journal > > Microbiome > > ### Year > > 2023 > > ### Study Source > > https://doi.org/10.1186/s40168-023-01691-y > > ### Code of Conduct Agreement > > • I agree to follow this project’s Code of Conduct

Anne-Marie Sharp (07:57:00) (in thread): > Okay, let’s see if it will work this time

Svetlana Ugarcina Perovic (07:57:07) (in thread): > Sorted!

Adeshile Oluwatosin (07:57:35) (in thread): > Finally, welcome:tulip:@Vanisha Garg

Svetlana Ugarcina Perovic (07:57:54) (in thread): > Thanks@Anne-Marie Sharp@Adeshile Oluwatosinfor your support!

Vanisha Garg (07:58:04): > Hello everyone! > Thanks a lot@Svetlana Ugarcina Perovicfor helping me throughout the process. I am eager to grow , learn and connect with you all!

Adeshile Oluwatosin (07:58:22) (in thread): > Refer to this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169Also have a look at the welcome materials pinned, feel free to ask your questions - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Adeshile Oluwatosin (07:58:41) (in thread): > You are welcome:hugging_face:@Svetlana Ugarcina Perovic

Anne-Marie Sharp (08:00:40) (in thread): > Hello@Vanisha Gargglad to have you here. I noticed you are done with your contribution,you can share the link for your article here for a peer review and we all would chip in our observations and corrections if we find any.

Anne-Marie Sharp (08:01:40) (in thread): > You are welcome:pray:@Svetlana Ugarcina Perovic

Vanisha Garg (08:02:49): > okay@Anne-Marie SharpI will do so! > By the link of the article it means where i have curated it right?

Svetlana Ugarcina Perovic (08:03:06) (in thread): > Already shared above!

Vanisha Garg (08:03:18): > Okay@Svetlana Ugarcina Perovic

Anne-Marie Sharp (08:04:26) (in thread): > @Vanisha Gargyes,I’ve seen it.@Svetlana Ugarcina Perovichas helped you share it already:raised_hands:

Anne-Marie Sharp (08:07:21) (in thread): > @Vanisha Gargyou’rewelcome. Will review and give feedback on your paper.

Vanisha Garg (08:08:11): > Hello everyone I have a question > If we come up with something that is not present in the drop down menu , then we can add that by just adding it simply? > If someone could help me in this , It would be a great help! > Thank you

Adeshile Oluwatosin (08:08:45) (in thread): > Could you be more specific on what exactly?

Adeshile Oluwatosin (08:09:03) (in thread): > Also, kindly reply under a thread

Vanisha Garg (08:12:04) (in thread): > I am asking there are places where we are required to answer from the drop down menu like condition section , what if we don’t find an appropriate option from the drop down menu ?

Adeshile Oluwatosin (08:17:11) (in thread): > In cases like that we use the closest term to the exact condition fromhttps://www.ebi.ac.uk/ols4/ontologies/efoSpecific to condition - Attachment (ebi.ac.uk): Ontology Lookup Service (OLS) > OLS is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions

Adeshile Oluwatosin (08:19:33) (in thread): > * For signatures: you checkhttps://www.ncbi.nlm.nih.gov/taxonomyfr the taxa ID , then paste on BugsigDB > * If no taxa ID, curate as seen > * For confounders: examples like BMI (it is curatable as body mass Index), so check for the full name. If not available curate as seen

Vanisha Garg (08:19:35) (in thread): > Okay@Adeshile OluwatosinI was unable to join this channel for a long time and hence couldn’t get the proper guidance regarding this . > Thank you so much for the guidance and I will make sure to do this.

Adeshile Oluwatosin (08:19:51) (in thread): > I shared a few tips on curation

Adeshile Oluwatosin (08:20:04) (in thread): > You can scroll up to read some of them

Vanisha Garg (08:20:06) (in thread): > Okay I will keep them in mind

Anne-Marie Sharp (08:35:21) (in thread): > Hello@Vanisha Gargthere should be no ‘matched on’ in your curation. It’s well explained in the curation policyhttps://bugsigdb.org/Curation_Policy. Use the curation policy as a guide. - Attachment (BugSigDB): Curation Policy > .

Vanisha Garg (08:42:34) (in thread): > Okay@Anne-Marie Sharpwill keep it in mind

Vanisha Garg (08:44:17) (in thread): > Also there was no section of adding a signature when i was curating the article

Anne-Marie Sharp (08:46:59) (in thread): > @Vanisha Gargyou’re welcome, I’ll add any other correction I see. There is a section to add signatures, for example, In BugSigDB where you have Experiment 1 on your page, just beneath that line on the right there is an option ‘Add a new signature’. You can add and edit on your own.

Adeshile Oluwatosin (08:47:36) (in thread): > See this - File (JPEG): IMG_3899

Vanisha Garg (08:47:39) (in thread): > Okay@Anne-Marie SharpI will try that

Vanisha Garg (08:54:50) (in thread): > Since I have directly asked for the official review before asking peer view . > Will it make any difference as at that point of time I was not on slack.

Vanisha Garg (08:55:06) (in thread): > So i curated the article and directly asked for official review

Joy (08:58:01) (in thread): > Welcome@Vanisha Gargto the community!:sparkles:

Anne-Marie Sharp (09:01:16) (in thread): > @Vanisha Gargin my opinion, our mentors are aware of the issue you had,and the needs review tag has not yet been added to your git issue so I think you can still finish with getting peer reviews here then you finally ask for an official review, then it will be labeled with a ‘needs review’ label

Vanisha Garg (09:02:24) (in thread): > Okay@Anne-Marie SharpI was concerned about this issue , thankyou for clearing it!

Anne-Marie Sharp (09:02:57) (in thread): > @Vanisha Gargyou’rewelcome

Francisca Gundu (09:03:28): > Hello everyone, I am done with my second curation, I would appreciate a peer review to the study thanks:https://bugsigdb.org/26069274 - Attachment (BugSigDB): Stool consistency is strongly associated with gut microbiota richness and composition, enterotypes and bacterial growth rates - BugSigDB > OBJECTIVE: The assessment of potentially confounding factors affecting colon microbiota composition is essential to the identification of robust microbiome based disease markers.

Francisca Gundu (09:04:04) (in thread): > Welcome@Vanisha Garg

Anne-Marie Sharp (09:06:39) (in thread): > Hello@Francisca Gunduwell done with your second curation:raised_hands:I’llreview and make any observation if I have

Francisca Gundu (09:08:54) (in thread): > Noted@Anne-Marie Sharp, thanks

Mildred Anashie (09:22:23) (in thread): > Hi@Francisca GunduWell done:clap:, I’ll take a look also.

Francisca Gundu (09:25:18) (in thread): > Thank you@Mildred Anashie

Adeshile Oluwatosin (09:42:46) (in thread): > Well done@Francisca Gundu

Joy (09:51:50) (in thread): > Well done@Francisca Gunduon your curation. We will have a look at it.

Anne-Marie Sharp (10:03:04) (in thread): > @Vanisha Gargthere were no confounders controlled for in the study. Confounders are factors that can confuse the results of a study by making it look like one thing is causing another thing when it might not be even causing it. For example, if a study is about how exercise affects weight loss, but it doesn’t account for diet, diet could “confound/confuse/affect” the result, so diet will be a confounder to be controlled for. But this study is researching transit time effects, so transit time effects is not a confounder(or confuser as I call it:smile:)

Juliana Kentomahun Mautin (10:04:52) (in thread): > Welcome@Gonza Gertrude. We are super excited to have you here. Please do not hesitate to ask your questions, we are all here to help out

Juliana Kentomahun Mautin (10:06:13) (in thread): > Hello@chiamaka Uche. You are welcome:relaxed:.

Adeshile Oluwatosin (10:08:50) (in thread): > Experiment 1 comparison should be between RB enterotype and P enterotype > Table 1 caption says Spearman’s rank order correlation with Benjamini-Hochberg false discovery rate correction. > > Supplementary Table 3 and 4 seems curatable > I’m also wondering where you got “0.1” as the significance threshold

Juliana Kentomahun Mautin (10:08:57) (in thread): > @chiamaka Uche. You can check out this insightful tips on how to make your first Contribution.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Dorcas Odetayo (10:09:22) (in thread): > Weldone@Francisca Gundu

Juliana Kentomahun Mautin (10:10:06) (in thread): > @Gonza Gertrudeyou check out this insightful tips on how to do your first curation.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609 - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Juliana Kentomahun Mautin (10:11:26) (in thread): > Welcome@Vanisha Garg.

Francisca Gundu (10:28:27) (in thread): > I truly appreciate@Adeshile Oluwatosinet al. I’ll make the necessary corrections and submit it for review on github. As for Supplemtary Table 3 and 4<@UBNSEMS3S>said they were not curatable.

Adeshile Oluwatosin (10:30:01) (in thread): > Alright, noted > I asked about the significant threshold though

Francisca Gundu (10:31:17) (in thread): > Ok, what is the significance threshold suppose to be, I didn’t quite catch that in the paper.

Adeshile Oluwatosin (10:37:25) (in thread): > It was not mentioned > Chloe has once mentioned curating as 0.05 in cases like this > ButI’munsure

Francisca Gundu (10:37:55) (in thread): > Ok, thanks a bunch

Anne-Marie Sharp (10:39:53) (in thread): > @Vanisha GargYou put some alpha diversities as increased/unchanged but I didn’t observe any alpha diversity measure used in the article and in the supplementary material. So you can leave all the sections in alpha diversity blank. For the statistical tests, I observed only Kruskal-Wallis.

Precious Chijioke (10:42:52) (in thread): > Thank you@Mildred Anashiefor your assistance your suggestion helped me to navigate through after some trials and refreshing of the page.

Precious Chijioke (10:43:54) (in thread): > Thank you@Svetlana Ugarcina PerovicHave a great weekend

Precious Chijioke (10:44:17) (in thread): > Welcome@Gonza Gertrude

Francisca Gundu (10:57:43) (in thread): > @Adeshile OluwatosinWhat is the data transformation for Spearman’s rank order correlation?

Jesulolufemi Adelanke (11:25:55) (in thread): > Well-done@Francisca Gundu. We’ll have a look at it

Adeshile Oluwatosin (11:26:29) (in thread): > In this case, think relative abundance

Francisca Gundu (11:28:05) (in thread): > I appreciate.

Jesulolufemi Adelanke (11:29:07) (in thread): > @Vanisha Garg, like@Anne-Marie Sharpsaid. You can also do a search for confounders and matched. If the search results turn up nothing, then it means it’s not in the study.

Jesulolufemi Adelanke (11:29:41) (in thread): > Welcome@chiamaka Uche

Jesulolufemi Adelanke (11:31:31) (in thread): > Welcome@Gonza Gertrudegood to have you join us:hugging_face:

Gonza Gertrude (11:38:57): > Hey everyone. I am trying to access this linkhttp://https//bugsigdb.org/34436669

Gonza Gertrude (11:39:50): > I can’t access that link, its part of the curation form. Did anyone face such an issue?

Anne-Marie Sharp (11:41:31) (in thread): > Hello@Gonza Gertrudeyes most of us did. So I entered BugSigDB main page and searched for the PMID(that is34436669) in the search bar and I could access the article, you can try that

Anne-Marie Sharp (11:43:12) (in thread): > Hello@Gonza Gertrudeyes most of us did. So I entered BugSigDB main page and searched for the PMID(that is34436669) in the search bar and I could access the article, you can try that.

Mildred Anashie (11:43:30) (in thread): > Yes@Gonza Gertrude@Anne-Marie Sharpalready replied with a solution in your previous message

Gonza Gertrude (11:44:15) (in thread): > thanks

Utibe Ita (11:44:45) (in thread): > I have made the necessary corrections. Thank you for pointing them out@Svetlana Ugarcina Perovic

Utibe Ita (11:45:36) (in thread): > Have you been able to access it?@Gonza Gertrudeusing the tip from@Anne-Marie Sharp

Anne-Marie Sharp (11:55:53) (in thread): > @Gonza Gertrudeyou’re welcome

Mildred Anashie (12:13:07) (in thread): > I’m glad it was helpful@Precious Chijioke

Joy (12:46:24) (in thread): > Welcome to the Community@Gonza Gertrude:sparkles:

Vanisha Garg (13:29:51) (in thread): > Thankyou@Jesulolufemi Adelanke@Anne-Marie Sharpfor the reviewing my curation. > I wanted to ask how to make these changes like how to edit my original curation or do I have to start again from adding a study

Vanisha Garg (13:34:52): > Can we curate other articles or do we have to wait for our one article to be completely reviewed officially?

Vanisha Garg (13:38:26): > I am unable to edit my previous responses . Is someone also facing the same issue?

Anne-Marie Sharp (13:40:13) (in thread): > @Vanisha GargYou have to wait for your article to be completely reviewed officially, before you curate another one. While you wait you can also help others with any assistance they might need like a peer review. Afterit’sreviewed officially, you can still go ahead assisting others asyou’lllearn faster that way.

Vanisha Garg (13:41:01) (in thread): > Okay@Anne-Marie SharpThank you so much for clarifying

Vanisha Garg (13:41:23) (in thread): > Could you please tell me how to edit my previous responses too?

Vanisha Garg (13:41:57) (in thread): > As wanted to make modifications on what mentors told me

Anne-Marie Sharp (13:42:50) (in thread): > @Vanisha Gargyou’rewelcome. Youdon’thave to start again.There’sa screenshot above that@Adeshile Oluwatosinshared. On the bugsigdb page where your curation is, click on edit to edit experiment. Andthere’salso an option to edit signature

Anne-Marie Sharp (13:43:52) (in thread): > @Vanisha Gargyou’rewelcome. Okay. I have left a comment in the thread where you first asked.It’seasier to track messages/responses through the main thread

Adeshile Oluwatosin (13:44:30) (in thread): > Create a study then you can click edit - File (JPEG): IMG_3901

Anne-Marie Sharp (13:47:49) (in thread): > @Vanisha Gargcheck these out, I put arrows to indicate. Then when you add a signature.You’llalso see an option to edit the signature. - File (JPEG): IMG_0013 - File (JPEG): IMG_0014

Ndukauba Oluchi (14:02:49) (in thread): > :thinking_face:I thought the taxas with negative values are for decreased and the ones with positive values are for increased?@Adeshile Oluwatosin

Adeshile Oluwatosin (14:04:12) (in thread): > Focus on the colors and the namesinstead

Ndukauba Oluchi (14:06:19) (in thread): > Yes@Anne-Marie SharpI didn’t because they were Genus, and we don’t record that.@Svetlana Ugarcina Perovicsaid it here :https://community-bioc.slack.com/archives/C04RATV9VCY/p1742583198329849?thread_ts=1742583198.329849&cid=C04RATV9VCY - Attachment: Attachment > Letters before taxa/signatures > > d > p > c > o > f > g > s > > are first letters of taxonomy ranks. > > Example: > > Domain: Bacteria > Phylum: Bacillota > Class: Bacilli > Order: Lactobacillales > Family: Lactobacillaceae > Genus: Lactobacillus > Species: Lactobacillus iners > > g_lactobacillus -> genus Lactobacillus -> BugSigDB recording https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1578&lvl=3&lin=f&keep=1&srchmode=1&unlock > > NOTE: we do not record “g_”

Adeshile Oluwatosin (14:07:39) (in thread): > We record all@Ndukauba Oluchi

Ndukauba Oluchi (14:09:18) (in thread): > @Adeshile Oluwatosinwe also had two body sites in the paper > Feces and small intestine fluid.

Ndukauba Oluchi (14:09:54) (in thread): > Even genus ?@Adeshile Oluwatosin

Adeshile Oluwatosin (14:10:51) (in thread): > Only feces was used for analysis

Ndukauba Oluchi (14:16:14) (in thread): > Hmm:thinking_face:This study has certain limitations. Firstly, the examination of patients’ fecal and small intestine fluid samples was conducted using the 16S rRNA sequencing method, and our current functionality is based on 16S rRNA sequencing with KEGG prediction. As a next step, we plan to conduct metagenomic and metabolomics sequencing on the samples. > I read this from the discussion part of the paper > What do you think@Adeshile Oluwatosin?

Anne-Marie Sharp (14:19:04) (in thread): > @Ndukauba Oluchiwe record genus, we record all taxa. What@Svetlana Ugarcina Perovicmeant is that wedon’trecord the g__ (g and slash) the g just indicates genus. The organism itself has to be recorded

Ndukauba Oluchi (14:20:01) (in thread): > Oh! Noted@Anne-Marie Sharp

Anne-Marie Sharp (14:30:14) (in thread): > @Ndukauba OluchiI see what you’re talking about with the body sites, indeed there are two body sites or samples according to the paper; because feces is really not same as intestinal fluid. its to find the best match for the second now. Going through previous messages, there are few articles that have had two body sites curated.

Jesulolufemi Adelanke (14:30:32) (in thread): > Thank you for your detailed review@Mildred AnashieI have 2 experiments for CC and likewise for CD, are the signatures going to be the same for both experiments under CC?

Ndukauba Oluchi (14:31:32) (in thread): > Yes that was why I used intestine secretion, is that okay? Or do I find another match?@Anne-Marie Sharp

Adeshile Oluwatosin (14:33:51) (in thread): > Curate the signatures depending on the source recorded@Jesulolufemi Adelanke

Anne-Marie Sharp (14:38:46) (in thread): > @Ndukauba Oluchiokay, I get you now. that seems to be the best match. And the description given for intestine secretion also seems to match what small intestinal fluid actually is:thumbsup: - File (JPEG): IMG_0015

Ndukauba Oluchi (14:39:41) (in thread): > Great! Welldone@Anne-Marie Sharpand Thank you!

Vanisha Garg (14:40:09) (in thread): > Okay@Anne-Marie Sharp

Anne-Marie Sharp (14:44:41) (in thread): > @Ndukauba OluchiYou’re welcome. I noticed experiment 3 doesn’t have much details under Subjects like body site, groupdefinitionetc. that has me confused, can you please explain:pray:

Ndukauba Oluchi (14:45:34) (in thread): > It’s there, you can check again

Ndukauba Oluchi (14:45:53) (in thread): > Here:https://bugsigdb.org/39194187/Experiment_3 - Attachment (BugSigDB): 39194187/Experiment 3 > .

Anne-Marie Sharp (14:49:19) (in thread): > @Ndukauba Oluchiwait please

Anne-Marie Sharp (14:50:52) (in thread): > @Ndukauba Oluchiin one of the messages above, I mentioned that in Experiment 3, signature 1 should be increased and signature 2 should be decreased, not the other way around. You havent updated that

Ndukauba Oluchi (14:51:29) (in thread): > Oops missed that

Anne-Marie Sharp (14:53:20) (in thread): > @Ndukauba Oluchioh okay. have you already submitted?

Ndukauba Oluchi (14:53:44) (in thread): > Nope not yet

Anne-Marie Sharp (14:54:46) (in thread): > :smile::partying_face:Yay! okay, good. that’s the only one I noticed but still check through. If only there’s a way to swap the signatures, But that means you’ll have to remove all the organisms you put in signature 1 and re-enter the correct ones and same for signature 2.

Svetlana Ugarcina Perovic (14:57:32) (in thread): > Make sure that you are logged in.

Vanisha Garg (14:57:47) (in thread): > It shows this that I don’t have the permission to edit - File (PNG): Screenshot 2025-03-23 at 12.24.25 AM.png

Anne-Marie Sharp (14:59:59) (in thread): > @Vanisha Gargokay.@Svetlana Ugarcina Perovicmentioned that you should ensure you are logged into your bugsigdb account.

Adeshile Oluwatosin (15:01:19): > Good evening@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Aleru Divine@Scholastica UruaIn thisstudyno p values were recorded (significance threshold) > I would have curated as 0.05 but the text within article reports some taxa to be significant which are a little above 0.05 from supplementary table S2-4 > Hence, should I curate with q value 0.1 > I would really appreciate a response > Thank you

Vanisha Garg (15:03:05) (in thread): > Ohh soryy I didn’t notice that. Thankyou

Adeshile Oluwatosin (15:03:40) (in thread): > @Vanisha Gargit could be network > Also try another browser > I get that prompt sometimes, once I reloadI’mable to edit

Vanisha Garg (15:07:25) (in thread): > okayy@Adeshile Oluwatosin

Anne-Marie Sharp (15:13:18) (in thread): > Yes@Adeshile Oluwatosinit could also be network.@Vanisha Gargifyouconfirm thatyou’relogged in and that issue is still coming up then try another browser or check your network as she said.

Precious Orakwe (20:55:15): > good day@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Aleru Divine@Kate Rasheed,i can’t find Ruminococcus_G on NCBI, where else can i search. Thank you

Adeshile Oluwatosin (23:56:07) (in thread): > @Precious OrakweclicklinkRuminococcus has taxa ID: “1263” - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (23:58:51) (in thread): > https://bugsigdb.org/34436669@Gonza Gertrude

2025-03-23

Vanisha Garg (01:23:49) (in thread): > Okay@Anne-Marie SharpThankyou for the help, it was the log in issue only’

Anne-Marie Sharp (01:28:41) (in thread): > @Vanisha Garggreat:+1:you’rewelcome

Vanisha Garg (01:30:50) (in thread): > @Anne-Marie Sharp@Adeshile OluwatosinCan I now ask for official review in github?

Vanisha Garg (01:31:17) (in thread): > I have made all the required changes you all suggested me.

Anne-Marie Sharp (01:32:24) (in thread): > @Vanisha Gargokay, yes but let’s just look at it one more time.Can you reshare the link here please

Vanisha Garg (01:33:48) (in thread): > Yes also I noticed I forgot to add signature . I will add the signature first and then should I reshare the link?

Anne-Marie Sharp (01:36:34) (in thread): > Okay. You can add it and go through it before resharing the link. Let us give it a final look for you .

Vanisha Garg (01:38:57) (in thread): > Okay@Anne-Marie SharpThank you so much!

Adeshile Oluwatosin (01:40:49) (in thread): > @Vanisha Gargyou need to add the signature first > Take your time

Vanisha Garg (01:43:00) (in thread): > Okay@Adeshile Oluwatosin

Vanisha Garg (01:47:09) (in thread): > https://bugsigdb.org/37926855Here is the shared link of my curation. Please review it ? - Attachment (BugSigDB): Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time - BugSigDB > BACKGROUND: Transit time is an important modulator of the human gut microbiome.The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research.

Vanisha Garg (01:49:11) (in thread): > Thank you@Svetlana Ugarcina Perovic

Vanisha Garg (01:51:57) (in thread): > @Svetlana Ugarcina PerovicYou assigned me 2 articles to be curated , But then you assigned my one article@Aleru Divine, but I didn’t get it reviewed from peers. > Could you please explain me what I have to do in that case. > Should I ask for peers review for that article or@Aleru Divinewill review it? > Thank you

Anne-Marie Sharp (01:52:06) (in thread): > @Vanisha Gargin the link you just sent Ican’tsee the signature you added and youhaven’tmade some of the corrections I previously mentioned like thematched on and statistical test, orit’snot reflecting,I’mnot sure which

Vanisha Garg (01:52:57) (in thread): > ohh okay let me check it once more thankyou for letting me know

Vanisha Garg (01:58:33) (in thread): > https://bugsigdb.org/37926855Please review it once more

Anne-Marie Sharp (02:09:29) (in thread): > @Vanisha Gargthe attached picture is a screenshot of the curation policy explaining how to add signatures. I noticed in Signature 1, your source is : journal Microbiome, it should be a figure or table instead.And usually ifthere’sdecreased abundance then there will be signature 2. I’m still going through it though.You can also use the curation policy and any other curated article on bugsigdb to be cross checking your work on your end also. - File (JPEG): IMG_0017

Vanisha Garg (02:13:27) (in thread): > Okay@Anne-Marie Sharp

Adeshile Oluwatosin (02:22:05) (in thread): > Click add a signature from your experiment 1@Vanisha Garg

Adeshile Oluwatosin (02:22:51) (in thread): - File (JPEG): IMG_3907

Vanisha Garg (02:32:01) (in thread): > okay@Adeshile Oluwatosin

Adeshile Oluwatosin (02:36:16) (in thread): > “There was a statistically significant increase in the abundance of Actinobacteria, Firmicutes, and Verrucomicrobia and a statistically significant decrease in the abundance of Bacteroidetes, Euryarchaeota, Fusobacteria, and Synergistetes in the gut of patients with STC compared with the healthy control group.” > > Fusobacteria : q value of “0.0632898277603598” > Synergistestes: q value of “0.0632898277603598”

Vanisha Garg (02:51:59) (in thread): > https://bugsigdb.org/37926855Done! made added 2 signatures for increased and decrease part > Thank you so much everyone for helping me out so much!:heart: - Attachment (BugSigDB): Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time - BugSigDB > BACKGROUND: Transit time is an important modulator of the human gut microbiome.The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research.

Anne-Marie Sharp (02:55:05) (in thread): > @Vanisha GargI can’tsee the second signature you added

Vanisha Garg (02:57:49) (in thread): > I did add signature 2

Vanisha Garg (02:58:06) (in thread): > even for the second time but i don’t know why is it now showing

Vanisha Garg (02:58:35) (in thread): > I have to click on add new signature? right?

Anne-Marie Sharp (03:00:24) (in thread): > Yes, from experiment 1 on the page, click on add a new signature. Then record the details for signature 2 which will be decreased abundance

Vanisha Garg (03:00:40) (in thread): > yess I did the same thing

Vanisha Garg (03:01:03) (in thread): > But only 1 signature is getting shown on the site.

Anne-Marie Sharp (03:03:00) (in thread): > Okay. When you fill in the details for signature 2. Try marking it as complete then save it. Then refresh the main page and check if it refelects

Vanisha Garg (03:03:37) (in thread): > @Anne-Marie SharpI did it exactly the way you told me to , let me try it one more time

Adeshile Oluwatosin (03:04:36) (in thread): > https://bugsigdb.org/37926855/Experiment_1/Signature_2 - Attachment (BugSigDB): 37926855/Experiment 1/Signature 2 > Source: Fig 4 Description: Displaying the absolute and proportional abundance of the most dominant genera in response to different transit times. Abundance in Group…

Vanisha Garg (03:05:41) (in thread): > Yes@Adeshile Oluwatosinthis was my second signature. Could you please help me how is it not getting diplayed at the site?

Anne-Marie Sharp (03:17:10) (in thread): > @Vanisha GargI am using the link@Adeshile Oluwatosinsent. I noticed the article has a supplementary material with more figures. Did you take note of that and include details from there also?

Adeshile Oluwatosin (03:18:24) (in thread): > It would eventually reflect on the main page when you reload@Vanisha Gargsometimes it takes time

Vanisha Garg (03:18:51) (in thread): > Okay@Adeshile Oluwatosinthank you

Vanisha Garg (03:21:25) (in thread): > @Anne-Marie SharpI have included details from Figures 3 and 4 in the main paper for my curation. I haven’t incorporated supplementary figures. > Is it necesaary to add supplementary figures?

Anne-Marie Sharp (03:24:03) (in thread): > @Vanisha Gargyes, it’s very necessary to include any curatable data from the supplementary material. What you’re curating is the main paper + supplementary material. I noticed a figure s10 or so in the supplementary material might be curatable. I would suggest we all take extra time to look at both before you submit.@Adeshile Oluwatosin@Mildred Anashie@Jesulolufemi Adelankeet al,please your help is needed.Can you also look through@Vanisha Gargmain article + supplementary material?It’sa lot of info there

Vanisha Garg (03:27:35) (in thread): > Okay@Anne-Marie SharpI really appreciate this and thank you once again for reviewing it and suggesting me the required changes

Vanisha Garg (03:28:28) (in thread): > Did you find any changes to be made in the study part ? where i have curated the article?

Anne-Marie Sharp (03:30:20) (in thread): > @Vanisha Gargyou’rewelcome. I have to take more time to look at it carefully,Iwon’twant to rush through it. But whileI’mdoing that, others will also help out once they are online.

Vanisha Garg (03:30:39) (in thread): > okay@Anne-Marie Sharp

Vanisha Garg (03:31:54) (in thread): > For every source , I have to create a new signature?

Vanisha Garg (03:32:52) (in thread): > or do I have to mention all sources at once in both increased and decreased Abundance in Group 1??

Mildred Anashie (03:42:11) (in thread): > Hi@Anne-Marie SharpI’ll take a look at this…..Well done everyone:clap:

Mildred Anashie (03:46:06) (in thread): > @Vanisha GargYou need to have either increased signatures or decreased signatures or both from a source. Your decreased abundance in group 1 is usually the taxa reported to be increased in Group 0. You can go through an already curated paper to help understand what should be done, here’s a link to the random study section on bugsigdbhttps://bugsigdb.org/Special:RandomInCategory/Studies - Attachment (BugSigDB): Shifts in the Fecal Microbiota Associated with Adenomatous Polyps - BugSigDB > BACKGROUND: Adenomatous polyps are the most common precursor to colorectal cancer, the second leading cause of cancer-related death in the United States.We sought to learn more about early events of carcinogenesis by investigating shifts in the gut microbiota of patients with adenomas.

Anne-Marie Sharp (03:50:20) (in thread): > @Vanisha Garg, to add to what@Mildred Anashiesaid, you don’t have to create a signature for every source. Let me explain it this way: For example, if signature 1(increased abundance) has info/data in figure 1, figure 2 and table 1, then your source will be figure 1, figure 2 and table 1.Thank you:pray:@Mildred Anashie

Adeshile Oluwatosin (03:57:50) (in thread): > * Data transformation; relative abundance > * Record V4 once (leave the second space blank) > * Test is Mann-Whitney (Wilcoxon): Statistically significant differences between SHIME transit times are indicated by the letters a, b and c (unpaired two-sided Wilcoxon signed rank tests with Holm correction > * Figure 3 shows results from distal and proximal region > * Check out Figure S10, Table S5 > * Condition is incorrect

Vanisha Garg (03:57:52) (in thread): > thankyou so much@Anne-Marie Sharpand@Mildred Anashie. I will make the required changes

Anne-Marie Sharp (04:10:40) (in thread): > @Adeshile Oluwatosinplease can you confirm the statistical test, this is what I saw in the article “Kruskal–Wallis tests were performed to determine statistically signifcant diferences between SCFA concentrations, total and intact microbial cell concentrations > > and quantitative and proportional taxon abundances > > between SHIME transit times and colon compartments > > (stats_3.6.3) [32”

Vanisha Garg (04:11:35) (in thread): > @Adeshile OluwatosinThankyou for the changes , I appreciate it , Wanted to ask that shouldn’t be the bodysite be feces?

Adeshile Oluwatosin (04:12:01) (in thread): > The statistical test is reflected within the figures. > And this statement does not explain the test was used for statistical differences amongst the two groups compared

Adeshile Oluwatosin (04:15:41) (in thread): > Feces is correct:thumbsup:“Six parallel SHIME systems were inoculated with six non-pooled faecal inocula”

Vanisha Garg (04:16:21) (in thread): > To determine significant differences in SCFA concentrations, microbial cell concentrations, and taxon abundances -> For this the test should be Kruskal–Wallis tests ?

Vanisha Garg (04:18:38) (in thread): > Should the condition be gastrointestinal disease along withgut microbiota composition?

Anne-Marie Sharp (04:22:07) (in thread): > @Adeshile OluwatosinI feel it explains that and on a second thought I’m wondering if Wilcoxon test should be added alsoas it was used for post hoc pairwise comparisons.perhaps a third eye review would be helpful to confirm the statistical tests.

Vanisha Garg (04:25:06) (in thread): > Made the changes in the signature as well as in the main curated article? > Someone please review it

Adeshile Oluwatosin (04:33:46) (in thread): > * Please remove Kruskal Wallis as a test, gut microbiome measurement as a condition, figure 4 and S11 as a source

Adeshile Oluwatosin (04:37:52) (in thread): > I’m also thinking results for distal regions should be curated seperately > Also results for proximal regions should be curated seperately > Each with comparison among:short vs medium, medium vs long and short vs long

Vanisha Garg (04:40:44) (in thread): > So should I curate that part separately in a new study?

Adeshile Oluwatosin (04:42:39) (in thread): > @Anne-Marie SharpKruskal-Wallis explains statistical differences between quantitative and proportional taxon abundances which corresponds with TableS5 and notFigure 3

Adeshile Oluwatosin (04:43:02) (in thread): > No, new experiments@Vanisha Garg

Mildred Anashie (04:50:55) (in thread): > So from what I see Fig 3 and S10 seems like it should be curated together. > You’d curate Proximal colon separate from Distal colon and the comparisons might be up to 3 experiments for each site. > i.e short vs Med, Med vs long and Long vs short. Please pay attention to the letters (a,b,c) in the figure and the (*) so you curate only the significant results. > Also read the part of the results that explains he figure and the figure caption, you’d have an idea how to curate it. The statistical test is Wilcoxon. > Table S5 looks curatable as well with 2 experiments which would be, > proximal vs distal colon in Quantitative Microbial community and > proximal vs distal colon in Proportional microbial community. > The statistical test here is Kruskal wallis. > Well done so far@Vanisha Garg,@Adeshile Oluwatosinalready pointed out the rest

Vanisha Garg (05:42:43) (in thread): > Thankyou so much@Mildred AnashieI will keep all these points in mind.

Mildred Anashie (06:37:26) (in thread): > Hi@Adeshile OluwatosinI’ve gone through this study as well and I also do not see a clear significant threshold. And if you curate with 0.1 some taxas would still be omitted. Also, from this text under the statistical methods, I’m thinking some part of it was omitted* “For categorical metadata and enterotype comparisons, samples were pooled into bins and significant features were identified using the Fisher’s exact test with multiple testing correction of p-values”. ** > Here for the response too :blush: *

Adeshile Oluwatosin (06:38:57) (in thread): > Thank you@Mildred Anashieyes, if I curate with a value 0.1 > Some Taxa will be omitted

Adeshile Oluwatosin (06:39:10) (in thread): > But it justwasn’tstated in the paper to be 0.1

Precious Chijioke (07:48:13): > Good Day everyone,@Svetlana Ugarcina Perovic@Kate Rasheed<@UBNSEMS3S>@Peace SandyI have finished my second contribution, I would appreciate a peer review for corrections before I can finally submit it. Thank you. > > Link to study:https://bugsigdb.org/40026814 - Attachment (BugSigDB): Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics - BugSigDB > .

Adeshile Oluwatosin (07:55:48) (in thread): > Okay, I will have a look > Well done:clap:

Joy (08:09:37) (in thread): > Well done@Precious Chijiokeon your curation.:clap:We will have a look at it.

Adeshile Oluwatosin (08:13:08) (in thread): > * Figure 2b not curatable > * All details in Experiment 2 are missing: kindly fill it in (location, host species, body site, condition…) > * Increased abundance comes first for figure 2c (Exp 2) > * Exp 2( group is between NC and FC_PreZY) > * NC is group 0, FC_PreZY is group 1 > * second is between FC_PreZY and ProZY > * figure 4 has three different LeFSe experiments all with only increased abundance (NC vs FC_PreZY, NC vs ProZy and FC_PreZy vs ProZy) > * figure 3a and c are curatable > Use this in correcting your curation@Precious Chijioke

Ndukauba Oluchi (08:21:39) (in thread): > How about 0.01@Adeshile Oluwatosin?

Adeshile Oluwatosin (08:22:17) (in thread): > Itcan’tbe 0.01 > As almost all taxa will be insignificant which is untrue

Joy (08:26:54) (in thread): > Good job@Adeshile Oluwatosin

Joy (08:31:15) (in thread): > @Precious ChijiokeThe taxon Eubacterium_coprosstanoligenes_group has the current name:Eubacterium coprostanoligenes with the:id:****(290054) ****check:point_right:here - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Precious Chijioke (08:38:20) (in thread): > Thank you@Adeshile Oluwatosin@JoyI’ll effect the changes accordingly

Joy (08:47:41): > Hello@Svetlana Ugarcina Perovickindly delete Experiment 2, signatures 1 & 2. Thank youhttps://bugsigdb.org/39856212 - Attachment (BugSigDB): Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder - BugSigDB > Attention-deficit/hyperactivity disorder (ADHD), a common neurodevelopmental disorder in children, is associated with alterations in gut microbiota and short-chain fatty acids (SCFAs), which are metabolites influencing the gut-brain axis.

Svetlana Ugarcina Perovic (08:51:00) (in thread): > @Vanisha Garghttps://github.com/waldronlab/BugSigDBcuration/issues/669is assigned to our mentor@Aleru Divineafter you submitted for review: “I have curated the article . Could you please review it?” > > Divine is reviewing your curation and will provide the feedback based on which you will make corrections. Thank you for your patience!

Svetlana Ugarcina Perovic (08:53:33) (in thread): > This should be communicated in the corresponding gh issue:https://github.com/waldronlab/BugSigDBcuration/issues/671#issuecomment-2746196847 - Attachment: Comment on #671 [Study]: Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder > Experiment 2/Signature 1
> Experiment 2/Signature 2
> deleted.

Joy (08:54:40) (in thread): > Duly noted. Thank you@Svetlana Ugarcina Perovic

Aiysha shahid (10:44:15): > Hi@Svetlana Ugarcina PerovicI was going through the Incomplete Pages. And I want to share you some findings which are as follows:For marking as reviewed: https://bugsigdb.org/30738924https://bugsigdb.org/30231060https://bugsigdb.org/37501202In these, above mentioned studies all the experiment’s and signatures have been marked as reviewed, but the main study is marked as****“Incomplete”****. But I have noticed that if we mark the study as****“Complete”****. It will automatically get marked as****“Reviewed”.****I have done for some. Should I go with other studies as well?Duplicate’s:Duplicate:https://bugsigdb.org/Study_783Github:https://github.com/waldronlab/BugSigDBcuration/issues/247Original Study:https://bugsigdb.org/36625596Duplicate-https://bugsigdb.org/Study_1123Github-https://github.com/waldronlab/BugSigDBcuration/issues/481Original-https://bugsigdb.org/36518275Duplicate-https://bugsigdb.org/Study_1135Github-https://github.com/waldronlab/BugSigDBcuration/issues/494Original-https://bugsigdb.org/38424099Duplicate-https://bugsigdb.org/Study_1147Duplicate-https://bugsigdb.org/Study_1150Original-https://bugsigdb.org/39320101Duplicate-https://bugsigdb.org/Study_1275Github-https://github.com/waldronlab/BugSigDBcuration/issues/537Original-https://bugsigdb.org/36563663So, Can you kindly delete these studies:https://bugsigdb.org/Study_783https://bugsigdb.org/Study_1123https://bugsigdb.org/Study_1135https://bugsigdb.org/Study_1147https://bugsigdb.org/Study_1150https://bugsigdb.org/Study_1275 - Attachment: #247 Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus > Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus – Li et al. – Microbiology Spectrum
> https://journals.asm.org/doi/10.1128/spectrum.03796-22 - Attachment (BugSigDB): Ascaris suum infection was associated with a worm-independent reduction in microbial diversity and altered metabolic potential in the porcine gut microbiome - BugSigDB > The effect of infection of pigs with Ascaris suum on the microbial composition in the proximal colon and fecal matter was investigated using 16S rRNA gene sequencing. - Attachment (BugSigDB): Subgingival microbiome of rheumatoid arthritis patients in relation to their disease status and periodontal health - BugSigDB > OBJECTIVE: Rheumatoid arthritis (RA) and periodontitis are chronic inflammatory diseases that share common risk factors.However, the bidirectional relationship between RA and periodontal disease is not fully understood. - Attachment (BugSigDB): The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels - BugSigDB > BACKGROUND: During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. - Attachment (BugSigDB): - BugSigDB > .

Precious Orakwe (13:16:47) (in thread): > Weldone@Precious Chijioke, you can replace Christensenlla in experiment 2 signature 1 with 990721. > > In experiment 4 replace Oscillospiraceae with 216572, Thermodesulfobacteriota with 200940, Lactobacillaceae with 33958 and Christensenellaceae with 990719. Well done, you can get the correct taxon ID from NCBI with the link shared by@Joy

Anne-Marie Sharp (13:17:10) (in thread): > @Adeshile Oluwatosinnoted, thank you for pointing that out, it got me really confused as I was viewing the wrong page.@Mildred Anashie’s recent explanation further clarified that for me, that Kruskal-Wallis shouldn’t be for experiment 1. Thank you also@Mildred Anashie

Precious Chijioke (13:44:17) (in thread): > @Precious Orakwethank you

Svetlana Ugarcina Perovic (14:06:19) (in thread): > @Aiysha shahidgreat catch, thanks! > Duplicates deleted.<@UBNSEMS3S>please see a list of “incomplete” but “reviewed” curations, thanks!

Precious Chijioke (14:28:48) (in thread): > @Adeshile OluwatosinExp 2( group is between NC and FC_PreZY), you said NC is group 0, FC_PreZY is group 1 but in Fig 2c :https://www.dovepress.com/article/fulltext_file/509592/aW1n/IJGM_A_509592_O_F0002g.jpgthere is decrease in FC_PreZY group and increase in NC group. If NC is named group 0, and FC_PreZY is group 1. The signature will show increase and decrease in only FC_PreZY is group 1. Please can you clarify on the grouping name you mentioned earlier. Thank you - Attachment: Attachment

Adeshile Oluwatosin (14:39:28) (in thread): > When we curate, we take note of the group names first > And curate group 1 of the case first for increased abundance > From the study NC group are the healthy volunteers in comparison withtreatment group )FC_preZY. Hence, NC is group 0

Precious Chijioke (14:42:17) (in thread): > Okay Thank you for clarity@Adeshile Oluwatosin

Vanisha Garg (14:50:36) (in thread): > Thankyou@Svetlana Ugarcina Perovicfor clearing my doubt!

Precious Chijioke (17:08:59): > Hello@Svetlana Ugarcina Perovicplease kindly delete signature 2 in Experiment 3https://bugsigdb.org/40026814 - Attachment (BugSigDB): Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics - BugSigDB > .

Svetlana Ugarcina Perovic (17:13:11) (in thread): > This should be communicated in the corresponding gh issue:https://github.com/waldronlab/BugSigDBcuration/issues/643 - Attachment: #643 [Study]: Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics > ### Study Title > > Therapeutic Mechanism of Zhuyang Tongbian Decoction in Treating Functional Constipation: Insights from a Pilot Study Utilizing 16S rRNA Sequencing, Metagenomics, and Metabolomics > > ### Pubmed ID > > 40026814 > > ### The Digital Object Identifier (DOI) > > https://doi.org/10.2147/ijgm.s509592 > > ### First Author > > Zhang X. > > ### Journal > > International Journal of General Medicine > > ### Year > > 2025 > > ### Study Source > > https://pubmed.ncbi.nlm.nih.gov/40026814/ > > ### Code of Conduct Agreement > > • I agree to follow this project’s Code of Conduct

Precious Chijioke (17:17:17) (in thread): > Duly noted > Thank you@Svetlana Ugarcina Perovic

Shade Akinremi (18:33:23): > Hello everyone. My experiment has 4 different differential expression analysis for experiment Figure 4E and no differential expression analysis were mentioned for Figure 4A,B,C,D.https://www.mdpi.com/2072-6694/14/11/2573. Please how do I represent their Significance threshold in my curation. - Attachment (MDPI): High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis > Obesity, metabolic changes, and intestinal microbiota disruption significantly affect tumorigenesis and metastasis in colorectal cancer (CRC). However, the relationships among these factors remain poorly understood. In this study, we found that a high-fat diet (HFD) promoted gut barrier dysfunction and inflammation in the colorectum and liver. We further investigated gut microbiota changes through 16S rRNA sequencing of faecal samples from HFD-fed rats and CRC hepatic metastasis patients and found an abundance of Desulfovibrio (DSV). DSV could also induce barrier dysfunction in the colorectum and inflammation in the colorectum and liver, suggesting that it contributes to the formation of a microenvironment conducive to CRC tumorigenesis and metastasis. These findings highlight that HFD-induced microbiota dysbiosis, especially DSV abundance, could promote CRC initiation and metastasis.

Joy (19:23:48) (in thread): > Hi@Shade Akinremi, we will have a look at this.

Mildred Anashie (19:39:45) (in thread): > Hi@Shade AkinremiI do not fully understand your question but looking at Figure 4 in the article you shared, Fig 4c, D and E looks curatable.For the significant threshold, from what I understand <0.05 is the commonly accepted threshold for statistical significance. Using <0.0001 implies a much stringent threshold and might lead to rejecting meaningful results that are still statistically valid.I believe others (**** p < 0.01; ***** p < 0.001; ******** p <0.0001) were mentioned to inform how statistical significance was achieved and tell which of the taxa was significant.So in this case you’d use 0.05.Hope this answers your question.

Joy (19:54:01) (in thread): > Hi@Shade AkinremiI am guessing you should use theDefault to p < 0.05 > * This is the standard threshold for statistical significance in most biological studies. > * If a single threshold is required,p < 0.05is the safest and most widely accepted choice. We might have to clarify with<@UBNSEMS3S>and@Svetlana Ugarcina Perovic

Precious Orakwe (20:07:16) (in thread): > @Svetlana Ugarcina Perovic@JoyStill can’t see your signatures from my end. - File (PNG): Screenshot (167).png

Joy (20:11:47) (in thread): > Yes@Precious Orakwe. Still battling with that. I am yet to figure it out. I guess, I’ll have to notify<@UBNSEMS3S>on this.

Precious Orakwe (20:34:53) (in thread): > @Shade Akinremii think you can go with@Mildred Anashieidea because, If the paper doesn’t provide explicit information on the significance threshold, you may use standard thresholds commonly used p-value < 0.05,

Precious Orakwe (22:51:16) (in thread): > The study design is:Case Control or Observational Cohort Study (The study is observational, not randomized, because participants weren’t assigned to controlled interventions)Condition: EFO:0007874Group 0 name: Fast transit time (C1).Group 1 name: Slow transit time (C4).Group 1 definition: Participants with a mean gut transit time of approximately 4.21 days.Group 0 sample size: 79 participants.Group 1 sample size: 174 participants.Sequencing type: Shotgun metagenomic sequencing.16S variable region: NoneSequencing platform: NoneData transformation: Relative AbundanceStatistical test: Mann-Whitney U testSignificance threshold: 0.01 > > Curate Fig 3A

Joy (23:06:56) (in thread): > Hi@Precious OrakweThe signatures have populated now. :bugsigdb.org/33722860

Precious Orakwe (23:07:08): > Blissful morning to you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Aleru Divine@Kate RasheedI trust we had a wonderful weekend rest, wish everyone a successful and stress-free new week. I am done with my study corrections and I am waiting for a peer review from my team members, I have also noted down my observations from the review that was assigned to me by@Svetlana Ugarcina Perovic. can I go ahead with NCBI Cleaning? Thank you. > > Wishing my team members the wisdom, knowledge and understanding that is applicable to our contribution journey. Let’s all have a great new week.

2025-03-24

Anne-Marie Sharp (02:26:56) (in thread): > Hello@Precious Orakwe1) I noticed that the experiments don’t have signature 2. > 2) And the condition should be Fetal Growth Restriction not Pregnancy induced alloimmunization. > 3) For the Sample sizes, in the article Con = 8, HS = 9, HS + Mel = 10. In experiment 1, you put Group 0 name as Con + HS but you put the sample size as 9, I feel you should add the sizes (8 + 9) to get the sample size as 17.

Utibe Ita (02:45:26) (in thread): > Good morning@Precious OrakweWish you a successful week too

Anne-Marie Sharp (02:57:57) (in thread): > Good morning@Precious Orakwethank you:pray:wish you same . > PS: We are still helping you to review your paper. Check the main thread where you shared the link to the paper.https://community-bioc.slack.com/archives/C04RATV9VCY/p1742553724826039 - Attachment: Attachment > https://bugsigdb.org/38382594 > > Good day, @Aleru Divine @Kate Rasheed @Adeshile Oluwatosin @Mildred Anashie, I am done with my second contribution, please I would really appreciate a peer review for corrections before I can finally submit it. Thank you. > > @Svetlana Ugarcina Perovic please delete signature 2 in experiment 1, Thank you.

Svetlana Ugarcina Perovic (02:58:19): > :tulip:Good morning, everyone! > > Take time to thoroughly review your paper. Seek peer feedback before finalizing your curation. Offer support to others completing their work.******We strongly encourage you to aim for quality over quantity.******Enjoy BugSigDB-ing!

Adeshile Oluwatosin (02:58:56) (in thread): > Good morning > Thank you so much:tulip:@Svetlana Ugarcina Perovic

Mildred Anashie (03:00:33) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you for the reminder, Happy BugSigdb-ing everyone:blush:

Anne-Marie Sharp (03:01:28) (in thread): > Good morning@Svetlana Ugarcina PerovicNoted:pencil:and thank you:innocent:enjoying the BugSigDB-ing already.

Mildred Anashie (03:19:11) (in thread): > Yes@Anne-Marie SharpThe experiments were curated from Fig 3E and it is just increased signatures that are to be recorded from that.@Precious OrakweWell done, I also noticed you didn’t curate Fig 3f and Fig S3, is there something I missed as to why?Also for the sample size, for eg Exp 1 Group 0, is Con + Hs vs Group 1 H+Mel > > You can add,Con sample size and HS sample size as given by the article to get the sample size for that group. The group definition is okay but just Expansiate a little on the Group 1 definition for Experiment 2.

Anne-Marie Sharp (03:23:39) (in thread): > @Precious Orakwesame goes for experiment 2. You didn’t put the sample size for group 0 but you can calculate it same way.@Mildred Anashieokay, I see. I thought we must curate 2 signatures for an experiment, that is showing comparison

Eniola Kolawole (03:25:59): > Good morning everyone > > Just starting out with my second contribution. I will appreciate every help I can receive. > > Thank you in advance.

Adeshile Oluwatosin (03:28:01) (in thread): > Alright, well done

Mildred Anashie (03:28:16) (in thread): > Good morning@Eniola KolawoleWell done:thumbsup:Feel free to ask your questions if you encounter any blockers

Aiysha shahid (03:33:09) (in thread): > Thanks@Svetlana Ugarcina Perovic:tulip:

Victoria (Burah) Poromon (03:34:33): > Hi everyone,@Adeshile Oluwatosinand I are working on this study and we’ll like to get some more clarification.https://www.nature.com/articles/s41564-024-01870-zhttps://bugsigdb.org/39762435Please take a look at Supplementary Table 10, 11, 12, 13. Should they be curated? Some signatures appear multiple times and have different Q values. > > We are also not very sure what this study design is. > > Then from figure 1b, the alpha diversity analysis result. We’re unsure how to curate it also. > > Ps: Figure 3b, 3h and 4b have already been curated. > > Thank you so much! Looking forward to your feedback.<@UBNSEMS3S>@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes. - Attachment (BugSigDB): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals - BugSigDB > As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing.However, little is known about diet-pattern-specific metagenomic profiles across populations.

Anne-Marie Sharp (03:41:28) (in thread): > Good morning@Eniola Kolawolewell done:raised_hands:feel free to ask questions,we’rehere to help.You’rewelcome in advance:smiley:

Precious Orakwe (03:44:26) (in thread): > Yes, I understand, I asked the question initially to@Svetlana Ugarcina Perovic@Aleru Divine, but I didn’t get any answer to the question, that was why I left it empty. I asked if I could sum the group 0 sizes together, but no response. I think I should do that.

Adeshile Oluwatosin (03:46:05) (in thread): > Yes, sum up the sample sizes in this case@Precious Orakwe

Ndukauba Oluchi (03:52:36) (in thread): > Hi@Victoria (Burah) PoromonLooking at the study name“Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals” I think the study design should beProspective cohort because the researchers recruited a group of people based on a common characteristic and follow them up over time. > > see the information on the abstract:Here we considered 21,561 individuals spanning 5 independent, multinational, human cohorts to map how differences in diet pattern (omnivore, vegetarian and vegan) are reflected in gut microbiomes.

Mildred Anashie (03:53:22) (in thread): > @Anne-Marie SharpMost experiments would have just one signature either increased or decreased especially for experiments where the contrast is not Pairwise, just like in this studyIt’sa one against the rest kind of plot so in this casewe’dcompare one group against the others and curate the taxa increased in that group for Signature one and repeat the same. > > Idon’tknow if this is clear enough.

Adeshile Oluwatosin (03:53:37) (in thread): > Thank you so much for replying@Ndukauba OluchiThere was report of meta analyzed results from the study

Precious Orakwe (03:56:09) (in thread): > Okay, let me see

Precious Orakwe (04:01:44) (in thread): > I have gone through the signatures, your experiment 1 has not signatures, and you use the same signatures for experiment 2 and 3. > > You can use the corrections i made previously, from my observation, the study has only one experiment with the signatures in Fig 3A.

Precious Chijioke (04:01:55) (in thread): > Good Morning@Svetlana Ugarcina PerovicNoted

isaac imitini (04:02:32) (in thread): > I do agree with@Ndukauba Oluchi, following the Curation policy. “Prospective cohorts” should be the study design.

Precious Chijioke (04:03:23) (in thread): > Alright, well done@Eniola KolawoleFeel free to ask questions anytime

Ndukauba Oluchi (04:03:47) (in thread): > @Adeshile Oluwatosinif that is so, then useMeta Analysis for the study design because they combine results from several different studies in a systematic review - literature review selected on like 20 published studies, took all their results, pooled them, and then did a meta analysis. Such studies usually state specifically that it’s a meta analysis. > > see the methods section:This study encompassed two published, publicly available datasets (Tarallo et al. (2022)12* with 118 individuals and De Filippis et al. (2019)13 with 97 individuals) along with three ZOE PREDICT datasets.*you can refer to the Welcome material for this information :https://community-bioc.slack.com/docs/T35G93A5T/F05URJ0P021

Precious Orakwe (04:04:10) (in thread): > Good morning@Svetlana Ugarcina Perovicnoted with thanks. > > Have a great new week.

Precious Orakwe (04:06:04) (in thread): > Well done@Eniola Kolawoleon completing your first contribution and starting your second contribution, feel free to ask your questions, we are open for collaboration.

Joy (04:07:40): > Hi everyone! I’m analyzing this studyhttps://www.nature.com/articles/s41598-025-87546-y#Fig1and came across****‘Observed Feature’ ****as an alpha diversity metric in the study on ADHD gut microbiota****(see Fig. A in the attached image)****. Could someone clarify what****‘Observed Feature’****represents in this context? Is it synonymous with species richness, or does it include other microbial taxa levels?@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Scholastica Urua@Kate Rasheed@Aleru Divine@Chioma Onyido@Peace Sandy@Esther Afuape - Attachment (Nature): Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder > Scientific Reports - Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder - File (PNG): image.png

Victoria (Burah) Poromon (04:07:52) (in thread): > Thank you@Ndukauba OluchiWe think it’s meta-analysis. > > But we just want to be really sure.

Ndukauba Oluchi (04:08:44) (in thread): > you are welcome@Victoria (Burah) Poromon

Jesulolufemi Adelanke (04:10:38) (in thread): > Good morning@JoyThe link you uploaded is unable to open.

Jesulolufemi Adelanke (04:13:15) (in thread): > Good morning@Eniola KolawolePlease feel free to ask questions. > > You might also want to note thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742583198329849?thread_ts=1742583198.329849&cid=C04RATV9VCY - Attachment: Attachment > Letters before taxa/signatures > > d > p > c > o > f > g > s > > are first letters of taxonomy ranks. > > Example: > > Domain: Bacteria > Phylum: Bacillota > Class: Bacilli > Order: Lactobacillales > Family: Lactobacillaceae > Genus: Lactobacillus > Species: Lactobacillus iners > > g_lactobacillus -> genus Lactobacillus -> BugSigDB recording https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1578&lvl=3&lin=f&keep=1&srchmode=1&unlock > > NOTE: we do not record “g_”

Anne-Marie Sharp (04:13:27) (in thread): > @Mildred Anashiethank you for clarifying:raised_hands:. I also saw this comment from our mentor@Levi Waldronthat further confirms ithttps://community-bioc.slack.com/archives/C04RATV9VCY/p1678694270049059?thread_ts=1678228354.154879&cid=C04RATV9VCY - Attachment: Attachment > Responding to another question from @Barakat Dindi but putting it here to organize in the same thread. Some experiments can have only a signature of increase, or some might not have any significant increases or decreases! But it is still worth recording the experiment to record the negative result and any alpha diversity comparisons they made.

Joy (04:13:47) (in thread): > Thank you@Jesulolufemi Adelanke, there it is.

Jesulolufemi Adelanke (04:13:52) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you

Mildred Anashie (04:14:32) (in thread): > Hi@JoyObserved species is usually curated as Richness (Species richness) and I believe this applies to observed features. > > You could wait for a clarification on this

Adeshile Oluwatosin (04:15:24) (in thread): > @Joyyou can curate it as richness

Jesulolufemi Adelanke (04:20:59) (in thread): > @JoyObserved Features counts the different types of bacteria found in a sample, just like species richness does. Since Observed Species is usually recorded as Richness, it makes sense to record Observed Features the same way.

Precious Orakwe (04:22:32) (in thread): > @JoyObserved Feature in the study serves as a measure of richness

Kate Rasheed (04:29:31) (in thread): > Good morning@Adeshile Oluwatosin@Victoria (Burah) Poromon. Welldone on this curation. > > For the question on the supplementary table, Chloe answered this last week in this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742503297939339?thread_ts=1742479314.184139&cid=C04RATV9VCY() - Attachment: Attachment > 1. I wouldn’t curate Figure 5. I don’t see a useful contrast here. > 2. Figure 6 is not curatable. > 3. When a meta-analysis reports individual study results, it’s better to curate the original research reports as studies (as in look up the paper, enter the PMID, and curate it as a new study). For a meta-analysis, we want to curate the pooled/combined results.

Eniola Kolawole (04:35:48) (in thread): > Thanks much everyone > > I can’t seems to find more details about the control samples in the literature I’m curating please.

Joy (04:36:11) (in thread): > Duly noted. Thank you all.

Mildred Anashie (04:39:54) (in thread): > You can share a link to your article@Eniola Kolawole

Eniola Kolawole (04:41:02): > I have difficulty getting more details on the control sample in the paper I’m curating. Will appreciate every help that comes my way. Thanks.https://pubmed.ncbi.nlm.nih.gov/40032727/@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine<@UBNSEMS3S>@Peace Sandy - Attachment (PubMed): Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids - PubMed > Viral infections, particularly human norovirus (NoV), are a leading cause of diarrheal diseases globally. To better understand NoV susceptibility, it is crucial to investigate both host glycobiology and the influence of the microbiota. Histo-blood group antigens (HBGA) displayed on surfaces of host …

Victoria (Burah) Poromon (04:41:17) (in thread): > Oh thank you so much@Kate RasheedDoes this mean we are not curating thesupplementary’s? Since we’ll have to find the other papers and curate them?

Adeshile Oluwatosin (04:42:13) (in thread): > Alright, I will have a look > Well done

Joy (04:42:21) (in thread): > Thank@Precious Orakwe. Yes Experiment 1 et al. does not have signatures because those were alpha diversities and alpha diversities do not have signatures.

Eniola Kolawole (04:43:50) (in thread): > Thank you

Mildred Anashie (04:57:54) (in thread): > I’ll take a look at this too@Eniola KolawoleDo you mean the sample size?

Eniola Kolawole (05:01:57) (in thread): > Related. I want to know what the controls are here.@Mildred Anashie

Eniola Kolawole (05:02:58) (in thread): > I will check it out now@Aiysha shahid. Thank you.

Eniola Kolawole (05:06:12) (in thread): > I don’t seems to get you. I’m not looking for full article@Aiysha shahid. I already have that. I’m asking about how to get my control sample details from the literature. Thanks

Eseoghene Cynthia Princewill-Ukot (05:09:14): > Good morning all! I’m currently working on this but not sure of the tool used for statistical analysis and I’m also having a hard time figuring out the Alpha diversity. Can anyone help me?@Kate Rasheed@Aleru Divine@Svetlana Ugarcina Perovichttps://www.mdpi.com/1422-0067/20/2/433 - Attachment (MDPI): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls > Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised. We performed two randomised, placebo-controlled, double-blinded trials comparing 7 days of psyllium with a placebo (maltodextrin) in 8 healthy volunteers and 16 constipated patients respectively. We measured the patients’ gastrointestnal (GI) transit, faecal water content, short-chain fatty acid (SCFA) and the stool microbiota composition. While psyllium supplement had a small but significant effect on the microbial composition of healthy adults (increasing Veillonella and decreasing Subdoligranulum), in constipated subjects there were greater effects on the microbial composition (increased Lachnospira, Faecalibacterium, Phascolarctobacterium, Veillonella and Sutterella and decreased uncultured Coriobacteria and Christensenella) and alterations in the levels of acetate and propionate. We found several taxa to be associated with altered GI transit, SCFAs and faecal water content in these patients. Significant increases in three genera known to produce butyrate, Lachnospira, Roseburia and Faecalibacterium, correlated with increased faecal water. In summary, psyllium supplementation increased stool water and this was associated with significant changes in microbiota, most marked in constipated patients.

Aiysha shahid (05:14:12) (in thread): > Oh got it@Eniola Kolawole, let me go through the paper.

Mildred Anashie (05:17:55) (in thread): > I’ve had a brief look at the study and there’s information on the groups in Materials and methods under the Isolation of microbiota from feaces section. > > See attached image, also the figures that look curatable so far are Fig 1 and maybe Fig 5 (not sure yet). I’ll try to look through again.Alsothere’sno clear sample size though, you might have to leave it blank for now - File (JPEG): IMG_6105

Eniola Kolawole (05:20:28) (in thread): > @Mildred Anashieare you saying those ones are the control samples?

Eniola Kolawole (05:21:15) (in thread): > Alright then. Thanks you.@Mildred Anashie

Mildred Anashie (05:22:10) (in thread): > Those are the groups in your study, the control would be determined by the contrast done

Eniola Kolawole (05:23:41) (in thread): > Hmm > > I find it difficult to get your explanation. I will go back and read again. Thank you

Adeshile Oluwatosin (05:26:27) (in thread): > From figure 1A, Kruskal Wallis with MHT(yes) was done. > Light and dark blue (decreased abundance), orange and red (increased abundance) > In this: I’m thinking do pairwise analysis between N, NOV, T and C > E.g rhodococcus reads as Grp 0(N), Grp 1(NOV)increase

Joy (05:27:29) (in thread): > Well done on your curation@Eseoghene Cynthia Princewill-Ukot, we will have a look

Anne-Marie Sharp (05:28:07) (in thread): > Good morning@Eseoghene Cynthia Princewill-Ukotthis is what I saw relating to your question: The baseline differences in SCFA, stool water content, qPCR results and transit times between the patient groups were calculated either with t-test (parametric data) or Wilcox test (nonparametric data). For microbial diversity, we used the inverse Simpson’s diversity index. Correlations between these data was analysed by using Spearman correlation.

Adeshile Oluwatosin (05:28:41) (in thread): > Okay, I will have a look

Eseoghene Cynthia Princewill-Ukot (05:30:57) (in thread): > Thanks@Anne-Marie Sharp

Eniola Kolawole (05:31:55) (in thread): > Thanks much@Adeshile Oluwatosin. I think this was what@Mildred Anashiemeant as well. > > I will do just that and get back to you guys.

Mildred Anashie (05:35:22) (in thread): > Hi @ese > > For the statistical test, see image below > > You are to record the statistical test used for differential abundance, see this for more information on differential abundancehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549 - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups - File (JPEG): IMG_6106

Adeshile Oluwatosin (05:36:56) (in thread): > The statistical test is linear regression@Eseoghene Cynthia Princewill-Ukotas we curate linear models as linear regression in bugsigdb

Amaka (05:37:50): > Hello Svetlana, Please I really need your assistance on how to go about my first contribution. Is my contribution on the topic that has been assigned to me? What exactly is expected from me. I have not been well last week but am okay now, I just need someone to give me a little clarification, thank you.

Eseoghene Cynthia Princewill-Ukot (05:39:11) (in thread): > Thanks for your help@Mildred Anashie@Adeshile Oluwatosin

Joy (05:39:30) (in thread): > @Eseoghene Cynthia Princewill-UkotThe alpha diversity is**** “inverse Simpson’s diversity index” ******4.4. Statistical AnalysisThe effect of psyllium was calculated for both trials separately, since there were notable demographic differences between trial populations. Comparisons between subjects from the two trials were only undertaken at baseline to elucidate differences between the groups. The baseline differences in SCFA, stool water content, qPCR results and transit times between the patient groups were calculated either with t-test (parametric data) or Wilcox test (nonparametric data).For microbial diversity, we used the inverse Simpson’s diversity index. **Correlations between these data was analysed by using Spearman correlation.

isaac imitini (05:40:46) (in thread): > Hi Amaka good morning. > > Here is a well detailed thread on how to go about your first contribution.https://community-bioc.slack.com/archives/C04RATV9VCY/p1742269916896359 - Attachment: Attachment > How to record your first contribution: > > After successfully completing the curation form. Ensure you record your contribution as mentors can close out projects once they have gotten enough contributors. > > Concisely, Kindly follow these steps: > > 1. Head to outreachy website: https://www.outreachy.org/dashboard/ > 2. Click “My Application”, then click “project lists” > 3. Click “Microbiome Study Curation” > 4. Then click “Record contributions and Apply to this project” > 5. Then Record your contribution. > Merged date is the Date you submit your contribution. > This is the contribution URL; > https://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw

Joy (05:42:04) (in thread): > Welcome@Amakato the community

isaac imitini (05:42:26) (in thread): > If you are yet to complete the curation form, this is the link :BugSigDB Outreachy First Task - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy First Task > BugSigDB Outreachy First Task

Anne-Marie Sharp (05:42:38) (in thread): > Hello@Amakasorry about your health, welcome back

Amaka (05:42:54) (in thread): > Thanks a lot isaac

Mildred Anashie (05:43:09) (in thread): > @JoyThe inverse simpson is mentioned here but there don’t seem to be more information on it.

isaac imitini (05:43:56) (in thread): > You are welcome. Do take care as you are just recovering as well.

Joy (05:44:58) (in thread): > Duly noted.@Mildred Anashie

Adeshile Oluwatosin (05:48:27) (in thread): > Welcome:tulip:@Amaka

Adeshile Oluwatosin (05:49:56) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742242215699699 - Attachment: Attachment > Welcome everyone :tulip: > If you are just joining, Read all instructions to get started here link > It is stated that you must complete the initial contribution before you move to the second one. > Happy contributing :dizzy: > I also think it’s best to reply in threads when needed, my opinion.

Adeshile Oluwatosin (05:51:34) (in thread): > I also saw this@JoyThere was no further details to predict if it was unchanged, increased or decreased

Mildred Anashie (05:54:51): > Hello everyone, > Happy Monday:blush:Hi@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine@Esther Afuape@Chioma Onyido@Scholastica Urua@Peace Sandy:hugging_face:I’m currently working on curating thisstudyand I need some help with curating some of the taxa’s reported this way ‘U. m. of Ruminococcaceae family’, ‘U. m. of Clostridiales vadinBB60 group family’ etc.I did some search and found out U. m could mean (Unidentified member of…or Unclassified member of…).With this information I was wondering if it would be Okay to curate, for e.g U. m. of Ruminococcaceae family asunclassified Ruminococcaceae (but this has no rank on NCBI) or to curate as reported.Wishing us all a very productive week ahead. Thank you:pray:

Eseoghene Cynthia Princewill-Ukot (05:54:56) (in thread): > Now you see why i am so confused?@Joy@Mildred Anashie@Adeshile Oluwatosin

Mildred Anashie (05:56:29) (in thread): > It’sokay to leave it blank@Eseoghene Cynthia Princewill-UkotNot everything would be clear or explicitly stated and wecan’tassume

Eseoghene Cynthia Princewill-Ukot (05:57:29) (in thread): > Noted@Mildred Anashie

Adeshile Oluwatosin (05:57:56) (in thread): > Kindly leave blank@Eseoghene Cynthia Princewill-UkotUnless a figure/Table or text states blatantly between the group comparisons, leave it blank

Adeshile Oluwatosin (06:01:52) (in thread): > Hello@Mildred Anashiewell done

Adeshile Oluwatosin (06:05:29) (in thread): > In this case, my opinion is to curate U.m of Ruminococcaceae as unclassified Ruminococcaceaewith NCBI ID: 473772

Adeshile Oluwatosin (06:07:29) (in thread): > Do the same for the rest

Precious Chijioke (06:09:36): > Happy New Week Everyone > > Please I’ll like to know how to identify increased and decreased signatures in a study and how to know that a Fig. that is curatable. > > Also in the screenshot attached I’m finding it difficult to identify increased and decreased signatures and learning how to identify increased and decreased signatures will help me navigate through when I’m curating a paper. - File (JPEG): IMG-20250324-WA0012.jpg

Adeshile Oluwatosin (06:13:39) (in thread): > Hi@Precious Chijioke

Adeshile Oluwatosin (06:14:17) (in thread): > For A. That explains alpha diversity

Anne-Marie Sharp (06:15:49) (in thread): > hello@Precious ChijiokeFor how to identify increased and decreased signatures in a study. 1. Try to identify where differential abundance is reported in the article, you can just search with Ctrl + F or check sections like results, statistical analysis, figures and tables. 2. Also check for statistical evidence and p-values, normally, only statistically significant differences should be recorded. 3. Review figures and tables, like if its a heatmap analyze the colors to check which indicates low or high abundance.

Adeshile Oluwatosin (06:16:57) (in thread): > If your group comparison is between Micronutrients and placebo then first thing to do is we also curate alpha diversity according to the case(group 1). Which I think is micronutrients here. > Hence, Shannon will be increased > Inverse Simpson: increased > Pielou which is evenness: increased > > NB: you must check within text and figure caption if it was significant. Ifit’snot significant and you can vividly see the alpha diversity comparison is between the groups you have curated. Then it’s unchanged

Adeshile Oluwatosin (06:17:16) (in thread): > My responses is only from this figure I can see

Anne-Marie Sharp (06:17:26) (in thread): > for how to know a curatable figure/table. i posted this earlierhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742492797326549?thread_ts=1742489849.904199&channel=C04RATV9VCY&message_ts=1742492797.326549 - Attachment: Attachment > @Precious Chijioke you can use these tips to know if a table or figure is curatable: 1. if it contains microbial signatures then it is curatable 2. if it contains relevant statistical comparisons then it is curatable 3. if it reports alpha or beta diversity then it is curatable 4. if the table/figure only describes methods, demographics or general scope/trends without having actual comparative data then it is not curatable. Keep in mind the purpose of curating, its for having a record of significant microbial signatures, so for example, you can’t curate a figure talking just about study population Also @C. Mirzayi (please do not tag this account) mentioned during office hours, that for your article, you can curate 5experiments but if you curate 3(that is, excluding the metagenomic analysis that doesn’t contain actual microbial signatures) then it will still be accepted. PS: I stand to be corrected

Anne-Marie Sharp (06:22:39) (in thread): > As@Adeshile Oluwatosinsaid. In the screenshot you shared, figure A, is about alpha diversity not microbial abundance so you won’t curate it as in, you won’t add it in Source as a figure when inputing the signature

Eseoghene Cynthia Princewill-Ukot (06:29:40): > Hello everyone! i would like a peer review to my second contribution@Mildred Anashie@Adeshile Oluwatosin@Joy@Anne-Marie Sharphttps://bugsigdb.org/30669509 - Attachment (BugSigDB): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls - BugSigDB > Psyllium is a widely used treatment for constipation.It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment.We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised.

Mildred Anashie (06:30:49) (in thread): > Hi@Precious ChijiokeFor the image you shared, thats a box plot showing taxa abundance in two groups (pairwise comparison).To identify the increase and decrease here, the line above the groups (Micronutrients and Placebo) tells you what contrast was made i.e if it is between A vs B, p value above the plot showing if its significant or not, and the median line inside the box (black line) helps you know if one group is increased or decreased compared to the other.With this we take the first plot in B which is showing us abundance of the genusFaecalibacteriuminMicronutrients and Placebo. If the significant threshold in the study is 0.05 and the P value is for this plot is 0.014 we can tell that is significant and can be curated we then look at the median line and we can observe that placebo is raised here and that means it is increased compared to Micronutrients so we can infer thatFaecalibacteriumisincreasedin Placebo which means it is decreased in Micronutrients.This applies to the rest and it also applies to the A part of this (Alpha diversity) since it was presented the same way.I hope this helps. This is somehow specific to this visualization though

Adeshile Oluwatosin (06:31:49) (in thread): > Noted

Adeshile Oluwatosin (06:32:28) (in thread): > First of all, ensure you mark as complete when done@Eseoghene Cynthia Princewill-Ukot

Eseoghene Cynthia Princewill-Ukot (06:33:54) (in thread): > If I mark complete, can I still edit?

Anne-Marie Sharp (06:34:39) (in thread): > Okay@Eseoghene Cynthia Princewill-Ukotwe will take a look.

Eniola Adebayo (06:35:05): > The supplementary file of the paper I am curating does not contain some of the results referenced in the study. What should I do?

Mildred Anashie (06:35:06) (in thread): > Okay@Eseoghene Cynthia Princewill-UkotI’ll take a look > > Yes you can still edit, as far as youhaven’tsubmitted to the mentors for a review yet

Eseoghene Cynthia Princewill-Ukot (06:35:35) (in thread): > Oh okay!

Adeshile Oluwatosin (06:35:54) (in thread): > Table 2 is curatable: with results all increased in constipated subjectslooking at the percentage. Kindly curate only the bold taxa

Mildred Anashie (06:36:06) (in thread): > Okay > > Thank you@Adeshile Oluwatosin

Adeshile Oluwatosin (06:36:50) (in thread): > Hello@Eniola AdebayoKindly share a link to your study

Eniola Adebayo (06:38:53) (in thread): > https://doi.org/10.1186/s12967-024-05832-1Also, can I curate figure 5?A - Attachment (BioMed Central): Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn’s disease: a prospective trial - Journal of Translational Medicine

Adeshile Oluwatosin (06:43:30) (in thread): > Table 3 seems curatable > For section 2.2: unsure. Also, in case of next time curate the figure/Table number as the source. > Except you curated taxa specific to a text within that section

Adeshile Oluwatosin (06:45:11) (in thread): > Ican’tsee where Age and sex were mentioned as matched on factors or confounders

Eseoghene Cynthia Princewill-Ukot (06:46:45) (in thread): > Noted@Adeshile Oluwatosin

Adeshile Oluwatosin (06:46:54) (in thread): > Also please specify the details missing in the supplementary file

Eseoghene Cynthia Princewill-Ukot (06:48:13) (in thread): > Thanks for your review

Eniola Adebayo (06:48:46) (in thread): > Supplementary Table 8 and 9

Mildred Anashie (06:49:12) (in thread): > Hi@Victoria (Burah) Poromon@Adeshile Oluwatosinwell done on this. I agree that the study design here is meta analysis and it looks like they had five cohorts with different sample sizes for vegan, vegetarian, meat, diary, omnivore etc. The alpha diversity in 1b seems to be specific to Diet (vegan, vegetarian and omnivore) in the five cohorts. In PI the contrasts is between omnivore vs vegetarian and P3 UK22A is between Omnivore vs Vegetarian and Omnivore vs Vegan this applies to P3US22A.

Adeshile Oluwatosin (06:50:01) (in thread): > Thank you:tulip:@Mildred Anashie

Anne-Marie Sharp (06:51:08) (in thread): > @Mildred Anashiewhat a detailed explanation. To be sure, does that mean in Fig b. in the 2nd/middle plot: Bifidobacterium is increased in Placebo and decreased in Micronutrients. Same for Bifidobacteriaceae in the last/3rd plot and Actinobacteria in Fig c

Anne-Marie Sharp (06:53:04) (in thread): > @Mildred Anashieand also for the very last boxplot Will you also report Verrucomicrobiota as increased in Micronutrients and decreased in placebo?

Adeshile Oluwatosin (06:53:25) (in thread): > Yes, it does@Anne-Marie Sharp

Mildred Anashie (06:54:11) (in thread): > That’s right@Anne-Marie Sharp

Anne-Marie Sharp (06:56:43) (in thread): > Okay@Adeshile Oluwatosinnoted, thank you.@Mildred Anashieokay, thanks for your detailed explanation. Hopefully you can explain more plots like this,there’sa particular type of plot that used to be really confusing to read.I’llcheck and share it

Adeshile Oluwatosin (06:57:32) (in thread): > The supplementary tables link is not in the paper I agree > Just for supplementary figures

Precious Chijioke (06:59:04) (in thread): > @Anne-Marie Sharpthank you@Mildred Anashie@Adeshile OluwatosinThank you for the detailed explanation

Eniola Adebayo (06:59:19) (in thread): > What about fig 5A, can it be curated? And Supplementary Fig 2

Precious Orakwe (07:04:04) (in thread): > @Eseoghene Cynthia Princewill-Ukotyour study is still showing incomplete, could you please mark as complete.

Precious Orakwe (07:06:41) (in thread): > @Eniola AdebayoI think they are not curatable

Precious Orakwe (07:07:28) (in thread): > and for the supplementary table you request that from@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (07:07:59) (in thread): > I can’t seem to figure out how to identify significance. Hence not curatable

Shade Akinremi (07:11:29) (in thread): > Okay, thank you.

Juliana Kentomahun Mautin (07:22:46) (in thread): > Good afternoon@Svetlana Ugarcina Perovic. Happy new week. Thank you:blush:

Anne-Marie Sharp (07:27:25) (in thread): > @Precious Chijiokeyou’re welcome.@Mildred Anashiethe figure attached is from an article we all helped review this morning. I understand that herethe colors represent the groups but I read somewhere that in lda score bar the colours represent significant abundance. My questions are: 1. Does it represent group/abundance or both? 2. How would you get the abundance for each microbe in this figure? - File (PNG): IMG_0023

Eseoghene Cynthia Princewill-Ukot (07:29:06) (in thread): > How do I submit my work to the mentors for review?

Anne-Marie Sharp (07:30:22) (in thread): > You can comment in the GitHub issue where you asked that you want to curate the article. Comment that your article is ready for review

Eseoghene Cynthia Princewill-Ukot (07:30:42) (in thread): > That’s all?

Anne-Marie Sharp (07:31:12) (in thread): > @Eseoghene Cynthia Princewill-UkotYesthat’sall. Tag@Svetlana Ugarcina Perovictelling her thatyour article is ready for review

Eseoghene Cynthia Princewill-Ukot (07:31:33) (in thread): > Okay,:pray:

Anne-Marie Sharp (07:31:39) (in thread): > @Eseoghene Cynthia Princewill-Ukotbut ifyou’renot in a hurry you can still give us some time to go over it.

Adeshile Oluwatosin (07:32:52) (in thread): > LDA score and significance threshold are completely different

Adeshile Oluwatosin (07:33:06) (in thread): > Idon’tget the main questions

Eseoghene Cynthia Princewill-Ukot (07:34:21) (in thread): > It’s okay@Anne-Marie Sharp. Thanks alot! You’ve been very helpful.

Svetlana Ugarcina Perovic (07:35:17): > :question:Quiz time:thinking_face:just to warm your curation uphttps://www.amnh.org/explore/ology/microbiology/what-do-you-know-about-the-human-microbiome

Anne-Marie Sharp (07:36:22) (in thread): > @Adeshile OluwatosinI understand that they are completely different.I mentioned that I read somewhere that in LDA score bar or figure like this one, that the colours represent whether the microbe is highly increased/decreased. But now in this figure the colours represent groups, contrary to what I read. SoI’masking, can it represent both? Does it just depend on the article?

Anne-Marie Sharp (07:37:57) (in thread): > @Adeshile Oluwatosinperhaps I should just ask how this figure will be curated, in terms of signatures

Ndukauba Oluchi (07:39:41) (in thread): > ahh! i got 5 out of 10 for the first trial:face_with_spiral_eyes:

Eseoghene Cynthia Princewill-Ukot (07:40:08) (in thread): > In the meantime, what will I be doing?

Anne-Marie Sharp (07:41:14) (in thread): > Okay,@Eseoghene Cynthia Princewill-Ukotyou’rewelcome. In the meantime you can be assisting others by also reviewing their articles and giving directions where necessary.

Adeshile Oluwatosin (07:41:45) (in thread): > LEFse results are generally represented this way > Sometimes in a single LEFse result, we can have increased/decreased abundance of signatures > But specific to the image attached: the three groups have only increased abundances as a one against all analysis. > Meaning group 0(red + green name), group 1(just blue) > Hence, curate just signatures with colour blue as a single experiment > And do the same for the other two groups

Ndukauba Oluchi (07:42:31): > Hello everyone. please I have a question > concerning this Paper :https://www.frontiersin.org/journals/oncology/articles/10.3389/fonc.2022.955313/fullit has 3 experiments > 1. PD VS PR > 2. Bevacizumab PD vs Bevacizumab PR > 3. Cetuximab PD vs Cetuximab PR > My question is looking at Figure 4 we have the Progressive disease (PD) to the negative side and the Partial response (PR) to the positive side. how do i curate for the increased and decreased abundances in this case? - Attachment (Frontiers): Frontiers | Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer > Studies have reported the effects of the gut microbiota on colorectal cancer (CRC) chemotherapy, but few studies have investigated the association between gu…

Adeshile Oluwatosin (07:42:39) (in thread): > And yes the colors actually represent ifit’sincreased/decreased > And we use the colors to also identify the groups.It’salways stated in the figure

Adeshile Oluwatosin (07:43:08) (in thread): > Well done@Ndukauba Oluchi

Mildred Anashie (07:45:43) (in thread): > @Anne-Marie SharpThis is a LefSe plot and It mostly depends on the article (researchers) and how they choose to present their results. The color code always helps to tell increase and decrease and shows us the groups as well. In this one the colors is showing increase pair group with no decrease shown, so we could tell its one against the rest. If it was a pairwise comparison you’d see the contrast would be between two groups with a clear increase and decrease (increase in the control group).

Francisca Gundu (07:49:57) (in thread): > Thank you@Svetlana Ugarcina Perovicfor creating such an interesting and informative quiz! It was a great way to learn more about microbes and their role in our health. it engaging and educational. I got 7 out of 10. Looking forward to more quizzes in the future!

Anne-Marie Sharp (07:51:19) (in thread): > :smiley:thank you@Svetlana Ugarcina Perovicenjoyed this

Precious Chijioke (07:53:38) (in thread): > Got 8 out of 10 on first attempt - File (PNG): Screenshot (685).png

Mildred Anashie (07:56:21) (in thread): > Hi@Ndukauba OluchiWell done. From the figure caption in Figure 4 I think they switched how they choose to present their results and I’ve come across this before, where the increase in the case group is presented as negative and the increase in the control group is presented as positive. See part of the text beside the figure, It somehow explains how you’d curate it.****“Figure 4; Results of the log2 fold change in the disease progression and partial response groups and subgroups of bevacizumab and cetuximab. Each dot indicates a specific bacteria species with a significant difference (P < 0.05) indicated on the y-axis. Positive values on the x-axis indicate that the bacterial species was significantly more abundant in the PR than in the PD group and subgroups. Negative values indicate the opposite. The zero point indicates the equal fold of abundance in both the groups (20). Only log2 fold change values >|2| are shown. (A) Bacterial expression was compared between the PD and PR groups. Fusobacterium nucleatum in the PD group was located at approximately the −5 point (log2 fold change = −5.13, Padj = 3.37e-6), indicating that the expression of F. nucleatum was higher in the PD group than in the PR group by approximately 32 (25) times. Prevotella copri in the PR group was located at approximately 3 point (log2 fold change = 2.90, Padj = 0.043), indicating that the expression of P. copri was higher in the PR group than in the PD group by approximately 8 (23) times.”****

Mildred Anashie (08:02:04) (in thread): > Thank you@Svetlana Ugarcina PerovicI somehow always miss the question on where microbes live in our body:woman-facepalming:….

Adeshile Oluwatosin (08:06:56): > Hello everyone, kindly give a peer review to this curation:https://bugsigdb.org/39656003https://pmc.ncbi.nlm.nih.gov/articles/PMC11705824/#SuF1I look forward to your opinion

Adeshile Oluwatosin (08:07:03) (in thread): > * Concerns: curation of “Fusobacteria” as “Fusobacteriota” in Exp2/Sig 2 > * The mention of N= 47 as sample size as a matched pair. Hence sample size as 47 for both groups instead of 47 and 53. > * No specific days/weeks/months recorded for antibiotics exclusion > * Location: “Russia” curated as Russian federation > * Confounders: mentioned just in “reviewer’s comments”

Adeshile Oluwatosin (08:08:11) (in thread): > * Nomatched on factors; just for a second eye

Ndukauba Oluchi (08:08:23) (in thread): > i understand@Mildred Anashieso do you mean the increased group is the PR(control) and decreased is PD(case group)?

Adeshile Oluwatosin (08:09:05) (in thread): > Also please ignore Experiment 1/signature 3 > It would be deleted

Adeshile Oluwatosin (08:12:30) (in thread): > Group 0(PR) > Group 1(PD) > > Increased abundance of PD (curate all taxa represented with negative values), do the opposite for PR as decreased abundance

Ndukauba Oluchi (08:15:04) (in thread): > Ahh! thank you@Adeshile Oluwatosin

Precious Orakwe (08:15:14) (in thread): > Thanks@Svetlana Ugarcina Perovicthe quiz was fun and educative. > > I now understand what cause allergies in the human system.

Mildred Anashie (08:16:17) (in thread): > Yes@Ndukauba Oluchi

Precious Orakwe (08:18:36): > i am done with the correction on my study, i would appreciate a final review before submission@Mildred Anashie@Adeshile Oluwatosinand everyone in the team, Thank you all for your assistance, I appreciate it.https://bugsigdb.org/38382594 - Attachment (BugSigDB): Melatonin alleviates high temperature exposure induced fetal growth restriction via the gut-placenta-fetus axis in pregnant mice - BugSigDB > INTRODUCTION: Global warming augments the risk of adverse pregnancy outcomes in vulnerable expectant mothers.

Shade Akinremi (08:19:22) (in thread): > Should the review be done under this thread?

Adeshile Oluwatosin (08:19:47) (in thread): > Yes please

Shade Akinremi (08:25:12) (in thread): > I got 8/10 in my first attempt too. Thank you for the quiz,@Svetlana Ugarcina Perovic.

Eseoghene Cynthia Princewill-Ukot (08:26:36) (in thread): > 5/10 first attempt

Joy (08:29:31) (in thread): > Thank you@Svetlana Ugarcina Perovicit’s a sure fun way to get off the steam. I got 9/10.

Shade Akinremi (08:30:32) (in thread): > Your experiment 2 is not showing Subject description.

Adeshile Oluwatosin (08:32:30) (in thread): > It’sa duplicate experiment with just the differences reflecting

Anne-Marie Sharp (08:32:40) (in thread): > Okay@Adeshile Oluwatosinfusobacteriota is also fusobacteria sothat’scorrect

Adeshile Oluwatosin (08:33:24) (in thread): > I have to be sure of the rank > In this case it was stated as species represented with LEFSE > Hence the confusion

Adeshile Oluwatosin (08:34:22) (in thread): > Fusobacteriia was also mentioned“class” in this case, in same figure

Anne-Marie Sharp (08:35:32) (in thread): > Fusobacteriia is a class within the phylum fusobacteriota/fusobacteria. But for that one stated as species,I’llconfirm

Precious Orakwe (08:36:05) (in thread): > The healthy control is 47 while the Psoriasis which is group 1 is 53,

Adeshile Oluwatosin (08:37:03) (in thread): > What I mean isFigure S6 caption (states a representation of species only) > Hence, why I’m skeptical of the curation of fuspbacteria > Although class, order and other ranks were represented in this figure@Anne-Marie Sharpdo you get?

Adeshile Oluwatosin (08:38:20) (in thread): > @Precious Orakweyes dear, I saw that > > But figure 2caption states N as 47 and explains thatit’sa matched pair. Hence I’m unsure if both groups have same sample size because of this statement

Halima Momoh (08:40:34) (in thread): > What an interesting quiz@Svetlana Ugarcina Perovic, thanks for sharing:tulip:. I got 7 in my first attempt, although there were some questions i was sure of the answer but to my surprise i was wrong. especially question 4, i thoughtforehead would be the correct answer because it isa sebaceous (oily) area, which provides a stable and nutrient-rich environment for many different microbial species. Thearmpit on the other hand has high microbial density but is dominated by fewer types of bacteria due to moisture and sweat gland activity. Thekneeis drier and less diverse compared to the forehead which informed my answer:grin:but i was wrong!. I have learnt something new today.

Anne-Marie Sharp (08:41:53) (in thread): > @Adeshile OluwatosinI understand.Figure S6 description in the article is contradictory then. Because it states species but the figure goes ahead to mention genus, class, order etc. Perhaps a mentor could clarify.

Ndukauba Oluchi (08:45:35) (in thread): > The differential abundance analysis was performed using DESeq2 package v.1.30.1 (35). Our hypothesis was tested using the Wald test, and P values were adjusted using the Benjamini– Hochberg method.In this case what should be the statistical test? > DEseq2 or Wald test?@Anne-Marie Sharp@Adeshile Oluwatosin@Victoria (Burah) Poromon@Mildred Anashie

Adeshile Oluwatosin (08:47:49) (in thread): > Yes dear, it is

Mildred Anashie (08:49:08) (in thread): > The test used for differential abundance@Ndukauba Oluchi

Ndukauba Oluchi (08:49:43) (in thread): > so Wald test?

Mildred Anashie (08:50:19) (in thread): > DESeq2 from what you shared

Ndukauba Oluchi (08:50:47) (in thread): > okay

Shade Akinremi (08:52:21) (in thread): > “53 psoriasis patients and 47 healthy donors”, your group 1 should be 53.

Adeshile Oluwatosin (08:52:48) (in thread): > Data transformation:raw counts

Ndukauba Oluchi (08:54:26) (in thread): > Ah yes! you are correct@Adeshile Oluwatosin

Victoria (Burah) Poromon (08:56:50) (in thread): > Hi@Precious OrakweWell done on your curation. > > Please expand the group names in experiment 2 and 3.

Anne-Marie Sharp (09:03:23) (in thread): > @Adeshile Oluwatosinthere was actually a match on sex, they tried to match on age but didn’t succeed. And yes, Russia is same as Russian federation, that’s just an official name

Precious Orakwe (09:11:30) (in thread): > If no timeframe was provided in the study, we recommend adding a note acknowledging this limitation > > If there were indeed 47 and 53 samples in two different groups, it is essential to maintain this distinction. > > I think since the confounders are in the review section, you can exclude them.

Anne-Marie Sharp (09:14:45) (in thread): > @Adeshile Oluwatosinit’s a bit tricky though but it states “In this case-control study, we recruited 47 healthy adult donors and 53 psoriatic patients, balanced by sex (Table 1).” that balanced should mean matched, because the percentage of females in Table 1 was 51%, hence males would be 49% so that seems like a match to me.

Adeshile Oluwatosin (09:18:04) (in thread): > Thank you guys > I also saw this in the abstract: Unlike previous studies, we first identified matched pairs for each patient with healthy donors to adjust for microbiome variability and increase power.

Precious Orakwe (09:19:21) (in thread): > Done thank you

Anne-Marie Sharp (09:27:51) (in thread): > @Precious OrakweI agree with you on the confounders.@Adeshile Oluwatosinyou’reon point:thumbsup:the review section extensively talked about the confounders but they were not controlled for. So you can exclude that.

Adeshile Oluwatosin (09:32:35) (in thread): > Ohhh yes, sex is a matched on factors > Thank you

Precious Orakwe (09:33:49): > @Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Aleru Divine@Kate RasheedI am done with my second contribution and I have submitted it for review while waiting for my paper to be reviewed. Can I contribute to the NCBI Cleaning while waiting for my study to be reviewed? Thank you.

Adeshile Oluwatosin (09:35:40) (in thread): > Yes, cosI’venever seen confounders stated as that > Thanks once again@Anne-Marie Sharp

Anne-Marie Sharp (09:41:01) (in thread): > @Ndukauba OluchiI agree with@Mildred Anashieit should be Deseq2, wald is part of Deseq2

Adeshile Oluwatosin (09:41:10) (in thread): > Just to round this up, what’s your opinion on figure 4 > Ican’t findany statistical significance

Victoria (Burah) Poromon (09:43:07) (in thread): > @Adeshile OluwatosinI think they did some tests to control for confounders after the review. So maybe it should be curated?

Adeshile Oluwatosin (09:47:35) (in thread): > I saw this though: “With this effect size estimate, we performed power analysis at a significance level of 0.05 for a range of sample sizes from 10 to 400 (Fig. S1). It is clear that to detect group-wise differences between cases and controls, one needs over 200 donors to achieve a reasonable power of 0.8 (Fig. S1), while 100 samples would be underpowered. “

Victoria (Burah) Poromon (09:49:29) (in thread): > Figure 4doesn’tseem curatable.

Mildred Anashie (09:52:26) (in thread): > @Victoria (Burah) Poromonthe only thing I see pointing to confounders is in the abstract and it says they adjusted for increased power and microbiome variability:thinking_face:

Anne-Marie Sharp (09:54:21) (in thread): > @Adeshile Oluwatosinyou’re welcome. I also can’t find any statistical significance in figure 4. The excerpt you shared is just talking about power analysis, like it says, thetestneedsa bigger sample size to properly detect differences.

Shade Akinremi (09:55:24) (in thread): > Please can someone explain the concept of confounder and how to look out for it.

Anne-Marie Sharp (09:57:19) (in thread): > @Shade Akinremihave a look at this brief explanationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742652184450169?thread_ts=1742645291.695329&channel=C04RATV9VCY&message_ts=1742652184.450169So you can use keywords to search for confounders, key words like ‘confounders’ ‘controlled’ ‘age’ ‘sex’ ‘race’ - Attachment: Attachment > @Vanisha Garg there were no confounders controlled for in the study. Confounders are factors that can confuse the results of a study by making it look like one thing is causing another thing when it might not be even causing it. For example, if a study is about how exercise affects weight loss, but it doesn’t account for diet, diet could “confound/confuse/affect” the result, so diet will be a confounder to be controlled for. But this study is researching transit time effects, so transit time effects is not a confounder(or confuser as I call it:smile:)

Victoria (Burah) Poromon (09:57:49) (in thread): > Right@Mildred AnashieSo I’m looking at the reviewers comment about how they address the confounders. (Age and BMI) and in response to that, they added tests to see whether age and BMI correlate with microbial variation in their dataset. > > That’s why I’m thinking it might mean that they controlled for them.:thinking_face:

Anne-Marie Sharp (10:02:02) (in thread): > @Shade Akinremithe curation policy further explains ‘Confounders controlled for’ - File (JPEG): IMG_0025

Mildred Anashie (10:02:16) (in thread): > @Victoria (Burah) Poromonas part of the papers weaknesses in the reviewers comment they mentioned this “Potential Confounding Factors: Differences in age and BMI between patients and healthy controls may confound the results, and the study’s adjustments for these variables could be more robust.” So I’m thinking if they eventually controlled for it then it wouldn’t be a weakness

Victoria (Burah) Poromon (10:06:30) (in thread): > Hi@Precious Orakwe@Svetlana Ugarcina Perovicmentioned somewhere that after your second contribution you can help others finalised theirs.

Victoria (Burah) Poromon (10:08:34) (in thread): > Ah yeah, I agree.@Mildred AnashieIt’sa little confusing whenthere’sbits of information everywhere:sweat_smile:

Mildred Anashie (10:11:59) (in thread): > Yeah > > The paper is loaded with scattered information:satisfied:

Adeshile Oluwatosin (10:12:05) (in thread): > Thank you everyone:heart::heart::heart:

Anne-Marie Sharp (10:20:34) (in thread): > @Mildred Anashie@Adeshile OluwatosinI see, it makes more sense now.I’vetaken notes, thank you for explaining.

Ndukauba Oluchi (10:24:44): > Hello everyone:hugging_face:I have just completed my curation for this study: (https://bugsigdb.org/36212420) > I would appreciate a peer review, please let me know if you have any feedback. Thank you:pray: - Attachment (BugSigDB): Gut microbiota composition in chemotherapy and targeted therapy of patients with metastatic colorectal cancer - BugSigDB > Studies have reported the effects of the gut microbiota on colorectal cancer (CRC) chemotherapy, but few studies have investigated the association between gut microbiota and targeted therapy.

Anne-Marie Sharp (10:24:59) (in thread): > @Mildred Anashie:smile:the paper is really loaded with scattered information, it requires extra care in curating,though that review section was quite interesting:blush:You’rewelcome@Adeshile Oluwatosinandwell done on the work done.

Shade Akinremi (10:27:57): > I am done with my second contribution. Please help me review it, @everyone.https://bugsigdb.org/35681554,https://bugsigdb.org/35681554/Experiment_2/Signature_1,https://bugsigdb.org/35681554/Experiment_2/Signature_2.https://www.mdpi.com/2072-6694/14/11/2573Thanks - Attachment (BugSigDB): High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis - BugSigDB > Obesity, metabolic changes, and intestinal microbiota disruption significantly affect tumorigenesis and metastasis in colorectal cancer (CRC).However, the relationships among these factors remain poorly understood. - Attachment (BugSigDB): 35681554/Experiment 2/Signature 1 > Source: Figure 5A, 5B, 5C Description: Comparison of fecal bacterial composition at the phylum and genus levels between colorectal cancer patients with and without… - Attachment (BugSigDB): 35681554/Experiment 2/Signature 2 > Source: Figure 5A, 5B, 5C Description: Comparison of fecal bacterial composition at the phylum and genus levels between colorectal cancer patients with and without… - Attachment (MDPI): High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis > Obesity, metabolic changes, and intestinal microbiota disruption significantly affect tumorigenesis and metastasis in colorectal cancer (CRC). However, the relationships among these factors remain poorly understood. In this study, we found that a high-fat diet (HFD) promoted gut barrier dysfunction and inflammation in the colorectum and liver. We further investigated gut microbiota changes through 16S rRNA sequencing of faecal samples from HFD-fed rats and CRC hepatic metastasis patients and found an abundance of Desulfovibrio (DSV). DSV could also induce barrier dysfunction in the colorectum and inflammation in the colorectum and liver, suggesting that it contributes to the formation of a microenvironment conducive to CRC tumorigenesis and metastasis. These findings highlight that HFD-induced microbiota dysbiosis, especially DSV abundance, could promote CRC initiation and metastasis.

Anne-Marie Sharp (10:28:25) (in thread): > Hello@Precious Orakwelike@Victoria (Burah) Poromonsaid, you can assist others to review theirs and help anyone that needs help.@Ndukauba Oluchialso needs a peer review:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742826284124629 - Attachment: Attachment > Hello everyone :hugging_face: I have just completed my curation for this study: (https://bugsigdb.org/36212420) > I would appreciate a peer review, please let me know if you have any feedback. Thank you:pray::skin-tone-2:

Anne-Marie Sharp (10:31:26) (in thread): > Hello@Ndukauba Oluchiwell done:raised_hands:we’ll look through it for you.

Mildred Anashie (10:35:38) (in thread): > Well done@Ndukauba OluchiI’lltake a look at it

Aiysha shahid (10:43:45): > Hi Everyone, I am curating a study-https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312606, And my observation is that- This study has 2exp, with the statistical test as- Wilcoxon and Lefse, with fig S1-S7 curatable for wilcoxon and fig 5for lefse. Also alpha diversity is for “Wilcoxon Test”,no significant results for Lefse test. If someone could look into this and clarify, that I am on the right track or not? Or this something else to be added. - Attachment (journals.plos.org): The gut microbiota-SCFA-inflammation axis in patients with AECOPD > Objectives The aim of the study was to explore the alteration of microbiota and SCFA in gut and inflammation in acute exacerbation chronic obstructive pulmonary disease (AECOPD) patients, and to test the hypothesis that a disorder of gut microbiota will lead to the alteration of SCFA, which will aggravate inflammation in AECOPD patients. Methods and results 24 patients with AECOPD and 18 healthy volunteers were included in the study. Gut microbiota were analyzed by 16S rDNA and serum was used to detect levels of inflammatory factors by ELISA. Fatty acid concentrations were determined in lumen via gas chromatography-mass spectrometry. The richness and diversity of gut microbiota were decreased in AECOPD patients. β-diversity analysis revealed differences between AECOPD patients and healthy controls. p_Bacteroidetes, g_Paraprevotella, g_Ruminococcus2, g_Parasutterella, o_Rhodospirillales, and g_Romboutsia in the healthy controls and p_Firmicutes, o_Actinomycetales, f_Actinomycetadeae, g_Actinomyces, g_Mogibacterium, f_Veillonellaceae, f_Enterococcaceae, and g_Enterococcus in AECOPD patients were the most abundant microbiota. SCFA levels were decreased in patients with AECOPD. In addition, the results demonstrated that except for a reduction in IL-6, there was no change in inflammatory markers in AECOPD patients. Conclusion In AECOPD patients, the gut microbiota-SCFA-inflammation axis is augmented, with decreased diversity and abundance of gut microbiota, leading to a reduction in SCFA and an imbalance of inflammation.

Victoria (Burah) Poromon (10:45:11) (in thread): > @Shade AkinremiWell done!

Svetlana Ugarcina Perovic (10:46:03): > Could you please give more examples of when and why we do not curate first letters of taxonomic levels when recoding signatures:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742583198329849 - Attachment: Attachment > Letters before taxa/signatures > > d > p > c > o > f > g > s > > are first letters of taxonomy ranks. > > Example: > > Domain: Bacteria > Phylum: Bacillota > Class: Bacilli > Order: Lactobacillales > Family: Lactobacillaceae > Genus: Lactobacillus > Species: Lactobacillus iners > > g_lactobacillus -> genus Lactobacillus -> BugSigDB recording https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1578&lvl=3&lin=f&keep=1&srchmode=1&unlock > > NOTE: we do not record “g_”

Adeshile Oluwatosin (10:47:19) (in thread): > Hello@Aiysha shahidI would have a look

Adeshile Oluwatosin (10:47:48) (in thread): > Well done@Ndukauba OluchiI would check

Svetlana Ugarcina Perovic (10:49:14) (in thread): > Here is an example of the supplementary material. How do we read the 2nd row and what we eventually curate here? - File (PNG): Screenshot 2025-03-24 at 15.48.14.png

Anne-Marie Sharp (10:55:05) (in thread): > @Svetlana Ugarcina Perovicthe second row would be read as Archaea, Euryarchaeota, Methanobacteria, Methanobacteriales, Methanobacteriaceae andMethanobrevibacter

Anne-Marie Sharp (10:56:08) (in thread): > I think we will curate all since all taxa should be curated

Adeshile Oluwatosin (10:57:00) (in thread): > We curate the taxa lowest in rank. From the second row > Since the taxonomical rank goes Kingdom - Phylum- Class- Order- Family - Genus - Species. > The letter in front g represent genus. Hence Only Methanobrevibacter should be curated > In this case genus “Methanobrevibacter” with taxa ID: 2172

Adeshile Oluwatosin (10:57:35) (in thread): > As genus is the lowest in rank compared to other taxa mentioned just in the second row

Victoria (Burah) Poromon (10:59:01) (in thread): > In experiment 1 signature 1 > ChangeProteobacteriatoPseudomonadota(ID: 1224) > Bacteroidetes to Bacteroidota (ID: 976) > > Also there are other increased taxa. > From figure 4E, if you look closely at the figure, you’ll see the asterisks (, , *****, *******). They indicate significance.

Mildred Anashie (10:59:18) (in thread): > We do not curate the first letter because they serve as prefixes to indicate the taxonomic rank. > > From the second row, the prefix before each taxa shows the taxonomic rank from Kingdom up to Genus and we curate the lowest taxonomic rank in cases like this which is the Genus: Methanobrevibacter

Victoria (Burah) Poromon (11:01:07) (in thread): > Figure 5a & b are not curatable. 5c is curatable,it’sthe only one showing differential abundance.

Svetlana Ugarcina Perovic (11:01:25) (in thread): > @Anne-Marie Sharpwe read the 2nd row like this: > the genus Methanobrevibacter belongs to the family Methanobacteriaceae which belongs to the order Methanobacteriales which belongs to the class Methanobacteria which belongs to the phylum Euryarchaeota which belongs to the Archaea kingdom. > > We curate the genus Methanobrevibacter as a signature, the rest are its higher taxonomical ranks as description of its classification. > > Hope it’s now more clear.

Aiysha shahid (11:01:26) (in thread): > Okay Thanks, Also an addition that the Body site isFeces and there’s no matched on and co-founder’s. And no significant LDA score is mentioned for LefSe test

Svetlana Ugarcina Perovic (11:02:58) (in thread): > See here:https://www.ncbi.nlm.nih.gov/datasets/taxonomy/2172/ - Attachment (NCBI): Methanobrevibacter > Methanobrevibacter is a genus of euryarchaeote in the family Methanobacteriaceae.

Svetlana Ugarcina Perovic (11:04:10) (in thread): > NOTE: Different ranks we curate as signatures when they are NOT descriptive part of taxa. Can someone give an example from the paper?

Anne-Marie Sharp (11:04:20) (in thread): > @Svetlana Ugarcina Perovicthank you for clarifying. I assumed that as the curation policy says ‘Curate all taxa no matter of their taxonomic levels’ then we should indeed mention all:face_with_peeking_eye:

Svetlana Ugarcina Perovic (11:05:23) (in thread): > @Anne-Marie Sharpyes, you are right. See my NOTE above.

Svetlana Ugarcina Perovic (11:08:12) (in thread): > See for example this Figure. How many different taxonomical ranks you see? - File (PNG): Screenshot 2025-03-24 at 16.07.23.png

Anne-Marie Sharp (11:09:25) (in thread): > @Svetlana Ugarcina Perovicokay, I see 4 different taxonomical ranks

Victoria (Burah) Poromon (11:09:47) (in thread): > There are no matched on factors for this study and the study design is “Laboratory experiment” it used animals. > You can take a look at the curation policyhttps://bugsigdb.org/Curation_Policy#Study_Design - Attachment (BugSigDB): Curation Policy > .

Svetlana Ugarcina Perovic (11:10:18) (in thread): > order Clostridiales and class Clostridia, which one you will record?

Joy (11:11:11) (in thread): > In BugSigDB curation, we typically do not curate the first letters of taxonomic levels when recoding signatures because they do not add meaningful taxonomic information and can be redundant or misleading. First Letters Represent Redundant Taxonomic Levels > > Example: > > g__Bacteroides > > Taxonomic Level: Genus (g) > > Why we do not curate g? > > The prefix (g__) already indicates the taxonomic rank in the raw database but does not add value in the curated signature.

Svetlana Ugarcina Perovic (11:11:43) (in thread): > Please leave@Anne-Marie Sharpto say

Adeshile Oluwatosin (11:11:53) (in thread): > Okay, noted

Svetlana Ugarcina Perovic (11:11:57) (in thread): > @Joywe clarified that above

Anne-Marie Sharp (11:12:39) (in thread): > @Svetlana Ugarcina PerovicI will enter both because they are stated as two different organisms with their own abundance in the figure

Svetlana Ugarcina Perovic (11:12:54) (in thread): > wooohooo

Svetlana Ugarcina Perovic (11:13:13) (in thread): > I do hope now it’s clear! Thank you ALL for this discussion.

Anne-Marie Sharp (11:13:54) (in thread): > @Svetlana Ugarcina Perovic:blush:yes it is, thank you so much for explaining.

Svetlana Ugarcina Perovic (11:14:27) (in thread): > @Halima Momohplease see this discussion from the very beginning:potted_plant:

Halima Momoh (11:16:37) (in thread): > Yes@Svetlana Ugarcina Perovici’ve been following. Thank you to everyone that contributed:tulip:.

Adeshile Oluwatosin (11:30:50) (in thread): > Figure 5is a LEFse result curatable (curate LDA score as 2)

Adeshile Oluwatosin (11:32:49) (in thread): > “t-test was used to analyze the differences among two groups.”

Adeshile Oluwatosin (11:33:57) (in thread): > Youdon’tneed to record “Wilcoxon test” for alpha diversity

Adeshile Oluwatosin (11:39:15) (in thread): > S1-7 seems curatable. Also, the comparison is saw across family, phylum, class, order, genus, species so just one experiment here and LeFSe as second > Go through the text within the article regarding this

Adeshile Oluwatosin (11:40:20) (in thread): > There should be no LDA score

Aiysha shahid (11:49:48) (in thread): > Okay,so in brief exp-1,t test,with s1-7 as curatable with no results for alpha diversity.Right?, And exp-2 is lefse,with fig5,and same with no results for alpha diversity.

Adeshile Oluwatosin (11:55:09) (in thread): > Richness, chao1, Shannon and Simpson should be curated for both experiments as they have same comparisons

Anne-Marie Sharp (12:05:29) (in thread): > @Ndukauba OluchiI think there’s a mistake in experiment 2, the source for signature 1 is Figure 3b while the source for signature 2 is figure 4b

Anne-Marie Sharp (12:07:15) (in thread): > But figure 4b should be the actual source for both

Anne-Marie Sharp (12:35:16) (in thread): > That’s all I observed, you did a neat work I must say

Anne-Marie Sharp (12:37:51) (in thread): > Well done@Shade Akinremiwe’ll look through it for you

Precious Chijioke (13:22:05) (in thread): > I agree with@Anne-Marie Sharp@Ndukauba Oluchirecheck the source for the signatures and effect changes

Jesulolufemi Adelanke (13:22:52) (in thread): > @Svetlana Ugarcina PerovicThank you for clarifying this.

Precious Chijioke (13:28:16) (in thread): > @Svetlana Ugarcina Perovicthank for the clarity > Thank you everyone for your contributions. I learnt something.

Anne-Marie Sharp (14:06:20) (in thread): > @Victoria (Burah) Poromon@Shade Akinremifigure 5G is also curatable, Desulfovibrio is increased in HFD

Victoria (Burah) Poromon (14:09:31) (in thread): > Yes 5g is curatable. > Thank you@Anne-Marie Sharp

Anne-Marie Sharp (14:34:10) (in thread): > @Shade AkinremiI noticed an error in the article unclassified_desulfovibrionales in figure 4E was written as Desulfibrionales in the text. In NCBI, unclassified_desulfovibrionales has a taxon ID: 271093, although it has no rank, it is the closest match and you can try it in Bugsigdb.

Anne-Marie Sharp (14:46:37) (in thread): > Also in experiment 1, Clostridium XIVb is one name, its not separate(That is another error in the text), so you can enter it whole in BugSigDB.

Anne-Marie Sharp (14:50:52) (in thread): > Still in experiment 1, Oscillibacter and unclassified firmicutes are also two separate words(that is another error in the text) . so you can also enter Oscillibacter in BugSigDB, then I saw unclassified firmicutes as unclassified bacillota on Uniprot with a taxon ID:84086, although it has no rank you can still try entering it on BugSigDB - Attachment (uniprot.org): UniProt > UniProt is the world’s leading high-quality, comprehensive and freely accessible resource of protein sequence and functional information.

Anne-Marie Sharp (16:25:30) (in thread): > 1)Experiment1 has 2 host species: Rattus norvegicus and Mus musculus. 2) In Experiment1, signature 1 should have increased abundance and signature 2 should be decreased abundance.

isaac imitini (21:03:20): > Hello Everyone, to confirm please. > > It appears that there may be more than 1 experiments to be curated in my study.Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia - PMCI wanted to be sure, I’d appreciate the extra eyes. If you check the supplementary document you will find a table with 6 experimental objectives. Currently curating the first experiment and I am also trying to figure out if there is an LDA score. - Attachment (PubMed Central (PMC)): Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia > Neonatal hypoxic-ischemic brain damage (HIBD) is considered as a major cause of long-term cognitive impairments in newborns. It has been demonstrated that gut microbiota is closely associated with the prognosis of various neurological disorders. …

Adeshile Oluwatosin (21:41:20) (in thread): > Figure 2G, I (LeFSe), j, K-O > Student t-testused for pairwise analysis (check “statistical analysis”)LDA Score is 2 if not in the paper > Could not access the supplementary material

2025-03-25

Anne-Marie Sharp (02:19:52) (in thread): > Hello@isaac imitinigive us some time to check through properly.@Adeshile Oluwatosinyou can try this link to access the supplementary materialhttps://www.tandfonline.com/action/downloadSupplement?doi=10.1080%2F19490976.2025.2471015&file=kgmi_a_2471015_sm7223.docx

Joy (02:45:12): > Hello everyone, I trust we are all good, I would appreciate a peer review to this study I have curated. Thanks.https://bugsigdb.org/39856212 - Attachment (BugSigDB): Impact of psychostimulants on microbiota and short-chain fatty acids alterations in children with attention-deficit/hyperactivity disorder - BugSigDB > Attention-deficit/hyperactivity disorder (ADHD), a common neurodevelopmental disorder in children, is associated with alterations in gut microbiota and short-chain fatty acids (SCFAs), which are metabolites influencing the gut-brain axis.

Adeshile Oluwatosin (03:10:07) (in thread): > Alright, well done

Victoria (Burah) Poromon (03:18:39) (in thread): > Hi@isaac imitiniYes there are more than 1 experiments > Sham vs. HI > HI vs. HI+DEX@Adeshile Oluwatosinalready listed curatable figures. > > For HI vs. HI+DEX, you can refer to Figure S3a & b from the supplemental material or the text. “The results showed that the content of f_Enterobacteriaceae in the HI+DEX group was significantly lower than that in the HI group. Conversely, the content of f_Akkermansiaceae in the HI+DEX groups was significantly higher than that in the HI groups (Figure s3a, b).”

Victoria (Burah) Poromon (03:22:43) (in thread): > Icouldn’tfind a table 6 from the supplement material.There’sa figure S6, andit’snot curatable becauseit’snot showing differential abundance.

Eseoghene Cynthia Princewill-Ukot (03:57:00): > Good morning everyone! While curating, The condition ‘nutritional supplement exposure measurement’ is not found. I searched and tried using this -EFO:0600066 but wasn’t accepted. Is there another way I can go about this?@Svetlana Ugarcina Perovic

Mildred Anashie (04:07:51) (in thread): > Hi@isaac imitiniWell done:clap:I’velooked through and I agree with the experiments pointed out by@Adeshile Oluwatosinand@Victoria (Burah) Poromon

Victoria (Burah) Poromon (04:07:55) (in thread): > Hi@Eseoghene Cynthia Princewill-UkotCan you share the link to your paper?

Adeshile Oluwatosin (04:08:00) (in thread): > You can send in a link to your study so everyone can contribute

Eseoghene Cynthia Princewill-Ukot (04:09:30) (in thread): > https://pubmed.ncbi.nlm.nih.gov/30669509/ - Attachment (PubMed): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls - PubMed > Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised. We …

Anne-Marie Sharp (04:09:36) (in thread): > Good morning@Eseoghene Cynthia Princewill-Ukotyes, nutritional supplement exposure measurement is actually not on BugSigDB, the closest to it is Environmental exposure measurement, butthat’sa way broader condition:thinking_face:. You can share a link as well,let’sconfirm the condition

Mildred Anashie (04:11:26) (in thread): > Hi@Eseoghene Cynthia Princewill-UkotI’vechecked too and the Nutritional Supplement exposure measurementisn’tavailable. > > Most times youwouldn’tfind the exact term butit’sokay to use a closely related term. > > As suggested above, a link to your article would help us figure out a closely related term for the condition.

Adeshile Oluwatosin (04:12:44) (in thread): > @JoyExperiment 1,2 and 3 has nosignatures

Eseoghene Cynthia Princewill-Ukot (04:13:40) (in thread): > my work has been reviewed and was suggested i changed the condition from ‘constipation’ to ‘nutritional supplement exposure measurement’https://bugsigdb.org/30669509 - Attachment (BugSigDB): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls - BugSigDB > Psyllium is a widely used treatment for constipation.It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment.We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised.

Anne-Marie Sharp (04:15:30) (in thread): > @Eseoghene Cynthia Princewill-Ukotoh, okay I see. You can still confirm from our mentors if you can use the closest term available on Bugsigdb

Adeshile Oluwatosin (04:20:31): > Good morning everyone,random question: > Would you consider TM7a to be unclassified candidatus saccharibacteria.

Esther Afuape (04:20:39) (in thread): > What’sthe closest term available on BugsigDB?

Anne-Marie Sharp (04:22:10) (in thread): > @Esther Afuapethe closest term to it on BugSigDB is Environmental exposure measurement

Mildred Anashie (04:23:53) (in thread): > I also see vitamin supplement exposure measurement@Esther Afuape:thinking_face:

Adeshile Oluwatosin (04:24:03) (in thread): > There’svitamin supplement exposure measurement

Anne-Marie Sharp (04:25:02) (in thread): > Yes there is but psyllium husk is not a vitamin:thinking_face:

Esther Afuape (04:25:15) (in thread): > That’s not so accurate either:smiling_face_with_tear:

Eseoghene Cynthia Princewill-Ukot (04:25:26) (in thread): > ‘Environmental’ too broad, ‘Vitamin’ not accurate

Anne-Marie Sharp (04:25:50) (in thread): > I know right:smile::smile:sorry@Eseoghene Cynthia Princewill-Ukot

Eseoghene Cynthia Princewill-Ukot (04:27:08) (in thread): > :disappointed_relieved:

Anne-Marie Sharp (04:28:49) (in thread): > Don’tworryit’llbe sorted out:wink:

Esther Afuape (04:28:52) (in thread): > @Eseoghene Cynthia Princewill-Ukotuse“response to diet” for now

Joy (04:29:47) (in thread): > @Adeshile Oluwatosinthey are alpha diversities. Alpha diversities do not have signatures.

Eseoghene Cynthia Princewill-Ukot (04:30:41) (in thread): > Thanks everyone

Victoria (Burah) Poromon (04:31:32) (in thread): > Uhmm, I just saw online that TM7 is now known as Saccharibacteria. > Here:https://en.wikipedia.org/wiki/Saccharibacteria - Attachment: Saccharibacteria > Saccharibacteria, formerly known as TM7, > is a major bacterial lineage. It was discovered through 16S rRNA sequencing .
> TM7x from the human oral cavity was cultivated and revealed that TM7x is an extremely small coccus (200-300 nm) and has a distinctive lifestyle not previously observed in human-associated microbes. It is an obligate epibiont of various hosts, including Actinomyces odontolyticus strain (XH001) yet also has a parasitic phase thereby killing its host. The full genome sequence revealed a highly reduced genome (705kB) and a complete lack of amino acid biosynthetic capacity. An axenic culture of TM7 from the oral cavity was reported in 2014 but no sequence or culture was made available. > Along with Candidate Phylum TM6, it was named after sequences obtained in 1994 in an environmental study of a soil sample of peat bog in Germany where 262 PCR amplified 16S rDNA fragments were cloned into a plasmid vector, named TM clones for Torf, Mittlere Schicht (lit. peat, middle layer). > It has been found in several environments since such as from activated sludges, water treatment plant sludge rainforest soil, human saliva, in association with sponges, cockroaches, gold mines, acetate-amended aquifer sediment, and other environments (bar thermophilic), making it an abundant and widespread phylum. Recently, TM7 rDNA and whole-cells were detected in activated sludge with >99.7% identity to a human skin TM7 and 98.6% identity to the human oral TM7a, suggesting metabolically active TM7 isolates in environmental sites may serve as model organisms to investigate the role TM7 species play in human health.

Adeshile Oluwatosin (04:33:44) (in thread): > Thank you Victoria > Yes google says that for TM7@Victoria (Burah) PoromonI was asking about TM7a as I saw it reported as “Unclassified candidatus saccharibacteria” in bugSIgDB NCBI missing ID

Esther Afuape (04:33:56) (in thread): > Also, include a discussion page explaining that the closest EFO term for the conditions in experiments 1 and 2 (nutritional supplement exposure, EFO:0600066) is not available in bugSigDB. Therefore, “response to diet” is used as an alternative.

Precious Chijioke (04:34:21) (in thread): > Well done@Joy

Anne-Marie Sharp (04:36:32) (in thread): > Good morning@Adeshile Oluwatosinyes I would also consider it to be unclassified Candidatus saccharibacteria, its a subgroup within Candidatus saccharibacteria, but if it is not classified beyond this level then yes, I’ll consider it unclassified

Adeshile Oluwatosin (04:37:47) (in thread): > TM7a is said to begenusand not unclassified

Adeshile Oluwatosin (04:38:35) (in thread): > Seelink

Adeshile Oluwatosin (04:40:04) (in thread): > @Victoria (Burah) Poromon@Anne-Marie Sharp

Esther Afuape (04:41:51) (in thread): > Hi@Eseoghene Cynthia Princewill-UkotSorry for the back and forth > “Treatment outcome measurement” is an even better fit. Please use this instead. No need for a discussion page too. > Thank you!

Victoria (Burah) Poromon (04:43:28) (in thread): > Yeah, okay.

Victoria (Burah) Poromon (04:43:30) (in thread): > Give me a minute

Anne-Marie Sharp (04:51:39) (in thread): > In the link you shared it is said to be a genus but Uniprot refers to it as an isolate within Candidatus saccharibacteria phylum rather than a genus. An in NCBI whats also there iscandidate division TM7 single-cell isolate TM7a but the rank is species. So…I’m really not sure. I would still go with unclassified. But then whats the taxon in the paper?

Precious Chijioke (04:53:49) (in thread): > Good Morning@Adeshile Oluwatosinyes I would consider TM7 as candidatus saccharibacteria not unclassified candidatus saccharibacteria.https://pmc.ncbi.nlm.nih.gov/articles/PMC6481004/ - Attachment (PubMed Central (PMC)): Saccharibacteria (TM7) in the Human Oral Microbiome > Bacteria from the Saccharibacteria phylum (formerly known as TM7) are ubiquitous members of the human oral microbiome and are part of the Candidate Phyla Radiation. Recent studies have revealed remarkable 16S rRNA diversity in environmental and …

Adeshile Oluwatosin (04:55:21) (in thread): > TM7a and not TM7

Anne-Marie Sharp (04:56:31) (in thread): > @Adeshile OluwatosinI also saw this online: ‘TM7ais an isolate within theCandidatus Saccharibacteriaphylum, but it has not been officially classified as a genus’ so perhaps you should go with NCBI and Uniprot ie. unclassified

Adeshile Oluwatosin (05:02:16) (in thread): > Thank you, this makes more sense to me now

Adeshile Oluwatosin (05:02:49) (in thread): > Unclassified Candidatus Saccharibacteria it is then

Victoria (Burah) Poromon (05:02:58) (in thread): > I think unclassified candidatus saccharibacteria works, since it has no rank.

Mildred Anashie (05:04:27): > Hello Everyone:wave::skin-tone-5:I’m working on curating thisarticleand I’ll really appreciate other set of eyes to help take a look. > > I’ve gone back and forth and I can’t seem to find information on the sequencing platform or the variable region as the article mentions using 16s rRNA. > > Thank you so much:blush:

Mildred Anashie (05:06:17) (in thread): > Hi@JoyWell doneI’lltake a look

Precious Chijioke (05:06:47) (in thread): > I agree with you@Anne-Marie Sharp@Victoria (Burah) Poromon@Adeshile Oluwatosin

Adeshile Oluwatosin (05:08:37) (in thread): > Well done > I saw this: “ To further explore the role of neohesperidin, we assessed the gut microbial composition of mice by 16S sequencing”

Adeshile Oluwatosin (05:13:34) (in thread): > Could not find the variable regionas well

Precious Orakwe (05:16:40) (in thread): > I thought we only curate experiments with differential abundance@Adeshile Oluwatosin@Mildred Anashie

Mildred Anashie (05:18:06) (in thread): > Yea@Precious OrakweAlpha diversity with no signature,it’sadvisable to leave it out

Adeshile Oluwatosin (05:19:06): > @Svetlana Ugarcina Perovic@Esther Afuape@Kate Rasheed@Aleru DivineGood morning mentors, > Could you kindly confirm not curating experiments with no signatures? Irrespective of ifthere’san alpha diversity results > It was mentioned to leave it out previously

Mildred Anashie (05:20:56) (in thread): > Okay@Adeshile OluwatosinThank you > > What about Sequencing platform?

Juliana Kentomahun Mautin (05:23:12) (in thread): > So much clarity in this . Thank you@Svetlana Ugarcina Perovicfor the discussion.

Kate Rasheed (05:24:17) (in thread): > Good morning@Adeshile Oluwatosin. > > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1697369622005969?thread_ts=1697280916.975139&cid=C04RATV9VCY - Attachment: Attachment > This experiment does name at least two differentially abundant taxa (although not in figure 1). In an experiment with only non-significant results you could still report alpha diversity unchanged and no signatures under the experiment.

Anne-Marie Sharp (05:24:31) (in thread): > @isaac imitiniI also agree with the others as they explained above. The LDA score was actually not mentioned, you can double-check with our mentors if you should just use 2 as a default or omit it. I noticed the table you mentioned in the supplemental material, I think you can use it as a guide and just focus on those experimental objectives listed where differential abundance analysis on microbial taxa was conducted.

Adeshile Oluwatosin (05:27:11) (in thread): > Noted, thank you so much

Adeshile Oluwatosin (05:27:39) (in thread): > Kate confirmed that it can be curated

Joy (05:39:15) (in thread): > Yes@Adeshile Oluwatosinand<@UBNSEMS3S>once said alpha diversities can be curated.

Kate Rasheed (05:44:50) (in thread): > Take note of “in an experiment with insignificant taxa”.

Precious Orakwe (05:46:55) (in thread): > Ok@Kate RasheedThank you

Semango Nicholas (05:47:14): > hello@SvetlanaI need help on curating this article .https://doi.org/10.1007/s00535-018-1488-5titled Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects. Note the erratum which corrects figures and text. Focus on stool consistency component, could skip age and sex analyses.Am failing to find the experiments and I see its gender and age based

Adeshile Oluwatosin (05:47:23) (in thread): > I’m still a littleunclear to be honest

Precious Orakwe (05:48:48) (in thread): > @Kate Rasheedcan you please give us an example, if that is possible

Semango Nicholas (05:49:06): > hello@Svetlana_up ,@Esther AfuapeAfupe I need help on curating this article .https://doi.org/10.1007/s00535-018-1488-5titled Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects. Note the erratum which corrects figures and text. Focus on stool consistency component, could skip age and sex analyses.Am failing to find the experiments and I see its gender and age based

Anne-Marie Sharp (05:49:38) (in thread): > Hello@Mildred Anashiethe variable region and sequencing platform are not mentioned, I think you can leave those blank.

Adeshile Oluwatosin (05:59:08) (in thread): > Curate 16S leaving the variable region blank if it’s possible to do that. Also, no sequencing platform was mentioned (so leave blank as well.

Victoria (Burah) Poromon (06:24:43) (in thread): > I think this means that if differential abundance was done but there was no significant taxa, then we can still curate those experiments. But without signatures

Eseoghene Cynthia Princewill-Ukot (06:34:36): > I’m here again!:grinning:while curating the Statistical analysis for Table 2, I chose relative abundance as data transformation with a significance of 0.05 (is that right?) but statistical test wasn’t stated.https://pubmed.ncbi.nlm.nih.gov/30669509/ - Attachment (PubMed): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls - PubMed > Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised. We …

Eseoghene Cynthia Princewill-Ukot (06:35:54): > I need an extra pair of eyes pls???

Mildred Anashie (06:40:05) (in thread): > Thank you all > > I really needed to be sure itwasn’tmentioned

Anne-Marie Sharp (06:42:22) (in thread): > @Mildred Anashieokay,you’rewelcome

Mildred Anashie (06:44:04) (in thread): > Please share a link to your curation as well@Eseoghene Cynthia Princewill-Ukot

Adeshile Oluwatosin (06:45:17) (in thread): > “. The baseline differences in SCFA, stool water content, qPCR results and transit times between the patient groups were calculated either with t-test (parametric data) or Wilcox test (nonparametric data).”

Victoria (Burah) Poromon (06:45:45) (in thread): > Hi@Semango NicholasI’ll take a look at your study

Vanisha Garg (06:45:49): > Hello everyone ! > I am curating this study . Please review it oncehttps://bugsigdb.org/34081625Also I am in doubt about the cofounders and matched factors, Please if someone gets that help mee! - Attachment (BugSigDB): The effects of psyllium husk on gut microbiota composition and function in chronically constipated women of reproductive age using 16S rRNA gene sequencing analysis - BugSigDB > Chronic constipation is a common gastrointestinal disorder that occurs in the elderly and in women.Psyllium husk is widely used to treat this condition.

Anne-Marie Sharp (06:46:01) (in thread): > okay@Eseoghene Cynthia Princewill-Ukotlets have a view of your curation

Adeshile Oluwatosin (06:46:21) (in thread): > Well done, I’ll have a look

Vanisha Garg (06:46:34) (in thread): > Thankyou@Adeshile Oluwatosin

Eseoghene Cynthia Princewill-Ukot (06:49:02) (in thread): > https://bugsigdb.org/30669509 - Attachment (BugSigDB): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls - BugSigDB > Psyllium is a widely used treatment for constipation.It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment.We aimed to assess the impact of psyllium on faecal microbiota, whose key role in gut physiology is being increasingly recognised.

Adeshile Oluwatosin (06:49:26) (in thread): > I would check it out

Victoria (Burah) Poromon (06:49:43) (in thread): > I’munable to access the full article.@Svetlana Ugarcina Perovicplease can you help?

Vanisha Garg (06:50:45) (in thread): > @Svetlana Ugarcina PerovicI wanted to know that everytime we are updating out curated articles , we have to make a contribution in this page . I am working on articles regularly but didn’t updated it here. > Also what do we have to add into the description , and if I make 3 4 times in a single day in my article , I have to show that in this page . > Please guide me in this . > Thankyou for your guidance - File (PNG): Screenshot 2025-03-25 at 4.19.28 PM.png

Eseoghene Cynthia Princewill-Ukot (06:51:31) (in thread): > @Svetlana Ugarcina Perovic@Esther AfuapeCould you please help delete Experiment 4? Thank you

Adeshile Oluwatosin (06:51:33) (in thread): > Descriptiondoesn’tneed to be anything complex > Explain in simple terms how you went about contributing

Vanisha Garg (06:52:42) (in thread): > Okay thankyou so much and everytime I am editing it I have to make contribution here?

Adeshile Oluwatosin (06:52:59) (in thread): > I don’t thinkthere’sany changes to make > As long asyou’vefilled in > Date contribution was started: date it got assigned to you to start or date you actually started > Date contribution was accepted or merged: date a mentor adds the “needs review” tag

Vanisha Garg (06:53:05) (in thread): > I worked on a study previous week too , so had to add that also?

Adeshile Oluwatosin (06:53:30) (in thread): > Add as a seperate record > It should have a different contribution URL

Adeshile Oluwatosin (06:54:10) (in thread): > Details of your contribution is different because of the date, hence you can’t record in just one place. My opinion

Svetlana Ugarcina Perovic (06:54:19) (in thread): > @Eseoghene Cynthia Princewill-Ukotthis it for GitHub communication in the issue where is your paper and curation changes recorded:https://github.com/waldronlab/BugSigDBcuration/issues/631#issuecomment-2750862366

Vanisha Garg (06:54:55) (in thread): > But if I am working on a single project and updating that constantly , then I don’t have to make any changes right? > Just add that article link and till The time I am not assigned another article I should’t be doing anything in this add contribution page??@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (06:56:28) (in thread): > If you are working on a single article (second contribution) > You can always edit and make your changes by clicking save

Svetlana Ugarcina Perovic (06:56:41) (in thread): > @Victoria (Burah) Poromonhttps://github.com/waldronlab/BugSigDBcuration/issues/667#issuecomment-2750871372 - Attachment: Comment on #667 [Study]: Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects > Full paper: s00535-018-1488-5.pdf > > Electronic supplementary material: > > 535_2018_1488_MOESM1_ESM.xlsx
> 535_2018_1488_MOESM2_ESM.pptx

Vanisha Garg (06:57:16) (in thread): > Yes that’s what I meant , no new contributions just editing the previous untill I start working on some other article?

Adeshile Oluwatosin (06:57:23) (in thread): > If you are not assigned another articleThere’snothing else for you to record > > Except you contribute in other ways.

Victoria (Burah) Poromon (06:57:31) (in thread): > Thank you so much!

Adeshile Oluwatosin (06:57:47) (in thread): > It’sokay to edit your previous contributions

Mildred Anashie (06:58:00) (in thread): > I’m leaning towards Wilcoxonor we record both T test and WilcoxonSee this@Eseoghene Cynthia Princewill-UkotThe baseline differences in SCFA, stool water content, qPCR results and transit times between the patient groups were calculated either with t-test (parametric data) or Wilcox test (nonparametric data).

Vanisha Garg (06:58:19) (in thread): > okay , Can i get to know what are other way contributions

Svetlana Ugarcina Perovic (06:59:06) (in thread): > We are creating an experiment based on differential abundance results. Additional information is alpha diversity if reported by the authors.

Vanisha Garg (06:59:13) (in thread): > And If it is okay could be send me a sample of how the description should look like , I just wanted to know what all I have to include in that

Svetlana Ugarcina Perovic (07:00:17) (in thread): > That said, we are creating an experiment when we want to add significant taxa from differential abundance results.

Eseoghene Cynthia Princewill-Ukot (07:00:59) (in thread): > Noted@Svetlana Ugarcina Perovic:pray:

Svetlana Ugarcina Perovic (07:01:12) (in thread): > Still, if there are no significant results, we can create an experiment with alpha diversity reported. This is up to you. Our primary goal is to record significant results from differential abundance results.

Adeshile Oluwatosin (07:02:43) (in thread): > Can we choose to focus on creating experiments only with differential abundance as that the main aim

Adeshile Oluwatosin (07:03:53) (in thread): > Else for instance, this experiment would have records of several experiments with just record of alpha diversity and a statistical test - File (JPEG): IMG_3917

Adeshile Oluwatosin (07:04:22) (in thread): > Thank you@Svetlana Ugarcina PerovicI would curate only experimentswith differential analysis results

Svetlana Ugarcina Perovic (07:04:33) (in thread): > I think I answered here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742900472594739?thread_ts=1742894346.713009&cid=C04RATV9VCY - Attachment: Attachment > Still, if there are no significant results, we can create an experiment with alpha diversity reported. This is up to you. Our primary goal is to record significant results from differential abundance results.

Adeshile Oluwatosin (07:04:50) (in thread): > Thank you

Anne-Marie Sharp (07:05:38) (in thread): > @Eseoghene Cynthia Princewill-UkotI’ll also go with relative abundance as the data transformation

Adeshile Oluwatosin (07:09:36) (in thread): > So update guys;it’syour choice to curate or not.

Montana-D (07:09:48): > Hello everyone, I am new to this project and I look forward to working with you all in contributing to the project.:raised_hands:

Adeshile Oluwatosin (07:10:03) (in thread): > Welcome:tulip:@Montana-D

Adeshile Oluwatosin (07:10:23) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169 - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w

Vanisha Garg (07:10:32) (in thread): > Welcome@Montana-D!!

Anne-Marie Sharp (07:12:24) (in thread): > You are welcome@Montana-Dlooking forward to working with you too. Kindly go through the link@Adeshile Oluwatosinshared above. And feel free to ask questions if you need help.

Vanisha Garg (07:13:11) (in thread): > Please could anyone guide me over this

Montana-D (07:13:50) (in thread): > Thank you@Vanisha Gargand@Anne-Marie SharpI have already > Thank you

USLACKBOT (07:14:06): > Svetlana Ugarcina Perovic made updates to a canvas tab:[canvas content]

Montana-D (07:14:46) (in thread): > Thank you@Adeshile OluwatosinThe information you provided is very helpful:pray:

Adeshile Oluwatosin (07:15:18) (in thread): > Svetlana mentioned assisting others

Adeshile Oluwatosin (07:15:34) (in thread): > Or curate another article

Adeshile Oluwatosin (07:15:55) (in thread): > From your curation: we record only one statistical testper experiment

Adeshile Oluwatosin (07:16:29) (in thread): > Figure 3 is not curatable

Vanisha Garg (07:18:41) (in thread): > Okay ig I wrote 3 instead of 4 then! > Because i saw that fig 4 was curatable

Vanisha Garg (07:18:49) (in thread): > Thankyou for letting me know

Adeshile Oluwatosin (07:19:09) (in thread): > Figure 4 is curatable with a LEFse result

Victoria (Burah) Poromon (07:19:09) (in thread): > Hi@Semango NicholasSo these are the comparisons that were made in the study. > 1. Male vs. Female(gender) Alphadiversityresultin figure 2 a,b,c. Curatable result in figure 4 > 2. Hard vs.Intermediate (Stool consistency) > 3. Hard vs. Loose > 4. Intermediate vs. Loose. > Alpha diversity results in figure 7. Curatable results in figure 8. > > Please note that for stool consistency,you’recurating separate experiments for male and female. All the results are in the same figure.

Anne-Marie Sharp (07:20:04) (in thread): > Okay@Montana-Dyou’rewelcome

Victoria (Burah) Poromon (07:20:19) (in thread): > Please let’s know if you need any further clarification or assistance.:tulip:@Semango Nicholas

Adeshile Oluwatosin (07:20:29) (in thread): > Note that our major aim is to curate differentia abundance analysis

Vanisha Garg (07:21:09) (in thread): > Yes, but the signature info other than sources is correct ?

Adeshile Oluwatosin (07:21:11) (in thread): > Record the source specific to the figure/table you are curating from

Adeshile Oluwatosin (07:21:28) (in thread): > It does not meanit’sdifferential analaysis

Adeshile Oluwatosin (07:21:47) (in thread): > You needtofirst figure out which figure or table is curatable or not

Vanisha Garg (07:21:48) (in thread): > Okay I will keep this in mind . Thankyou so much@Adeshile Oluwatosinfor guiding me

Eseoghene Cynthia Princewill-Ukot (07:22:15) (in thread): > You are welcome@Montana-D. Feel free to ask questions whenever you are stuck. Happy Curating!

Adeshile Oluwatosin (07:22:52) (in thread): > Ihaven’tgone through the supplementary info

Adeshile Oluwatosin (07:27:31) (in thread): > The two treatment groups were commonly matched by age, body mass index (BMI), straining, <3 bowel movements (BMs) / week, hard stool, pain with BMs, feeling of incomplete defecation, digital maneuvering, and feeling of blockage (Table 1)

Adeshile Oluwatosin (07:27:42) (in thread): > Record all of them@Vanisha Garg

Montana-D (07:27:54) (in thread): > Thank you so much, I look forward to

Adeshile Oluwatosin (07:28:02) (in thread): > Find similar terms,If not curate as seen

Adeshile Oluwatosin (07:29:01) (in thread): > If this article has been reviewed by a mentor > Follow strictly what you were told to correct

Adeshile Oluwatosin (07:29:06) (in thread): > Well done

Mildred Anashie (07:35:58) (in thread): > Welcome@Montana-D

Montana-D (07:36:47) (in thread): > Thank you@Mildred Anashie

Adeshile Oluwatosin (07:39:06) (in thread): > Someone pointed this out “For analysing the effect of health status on the overall microbiota composition, we used a MANOVA test”

Victoria (Burah) Poromon (07:41:26): > Hi Everyone. > I’m putting my study up for peer review. > Thank you for your feedback in advance! > > Study link:https://bugsigdb.org/40013792Article link:https://journals.asm.org/doi/10.1128/msystems.00805-24 - Attachment (BugSigDB): Multi-omics analysis reveals associations between gut microbiota and host transcriptome in colon cancer patients - BugSigDB > UNLABELLED: Colon cancer (CC) is one of the most common cancers globally, which is associated with the gut microbiota intimately.In current research, exploring the complex interaction between microbiomes and CC is a hotspot.

Adeshile Oluwatosin (07:42:01) (in thread): > Alright, I would have a look

Adeshile Oluwatosin (07:42:08) (in thread): > Well done:clap:

Adeshile Oluwatosin (07:43:06): > Hello everyone > Please give a peer review > Thankshttps://bugsigdb.org/39707461https://pmc.ncbi.nlm.nih.gov/articles/PMC11662449/

Eseoghene Cynthia Princewill-Ukot (07:43:13) (in thread): > I’m not sure i have seen that@Adeshile OluwatosinAny reference?

Adeshile Oluwatosin (07:43:48) (in thread): > You can use “ctrl F” > Still within statistical analysis

Anne-Marie Sharp (07:44:41) (in thread): > @Adeshile Oluwatosin@Eseoghene Cynthia Princewill-Ukottake a look at this: Differences in bacterial abundances and associations between bacterial taxa and SCFAs, stool water content and transit times within each study were estimated with generalized linear mixed models from all available data points. In both models, the obtained read counts were modelled as a function of time point, using subject ID as a random factor and the total number of reads per sample as an offset, assuming negative binomial distribution. The resultantp-values were corrected for multiple comparisons with false discovery rate (FDR), and subsequentq-values bellow 0.1 were considered to be significant [40]. Doesn’t this relate to the statistical test being negative binomial regression and the data transformation being raw counts instead of relative abundance? - Attachment (PubMed Central (PMC)): The Effect of Psyllium Husk on Intestinal Microbiota in Constipated Patients and Healthy Controls > Psyllium is a widely used treatment for constipation. It traps water in the intestine increasing stool water, easing defaecation and altering the colonic environment. We aimed to assess the impact of psyllium on faecal microbiota, whose key role in …

Adeshile Oluwatosin (07:45:52) (in thread): > Yes, thank you > I saw that I stated that someone pointed the other reference out, incase it makes sense to anyone else

Mildred Anashie (07:47:13) (in thread): > @Adeshile OluwatosinThis is the description for Table 2 “Relative abundance of bacterial taxa showing a statisticaldifference between healthy and constipated patients at baseline.Fc—fold change of taxa in constipated versus healthy subjects.”:thinking_face:

Mildred Anashie (07:48:39) (in thread): > Well done@Victoria (Burah) PoromonI’ll take a look

Adeshile Oluwatosin (07:48:54) (in thread): > I guess we should stick to our initial opinion then

Mildred Anashie (07:49:20) (in thread): > Well done@Adeshile OluwatosinI’ll take a look shortly

Adeshile Oluwatosin (07:49:35) (in thread): > Thank you

Adeshile Oluwatosin (07:51:25) (in thread): > https://bugsigdb.org/39707461/Experiment_4/Signature_1Only experiment not reflecting signatures yet

Oriade Adeola (07:54:16): > Hello everyone. please i think i have made a mistake can someone help me check it out so i know if i’m on the right track. my network as been lagging and i think i have added one signature twice. please help me check please:pray:https://bugsigdb.org/36875281 - Attachment (BugSigDB): Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status - BugSigDB > BACKGROUND: Patients with chronic constipation (CC) show altered gut microbial composition.OBJECTIVES: To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.DESIGN: This is a prospective cohort study.

Adeshile Oluwatosin (07:55:18) (in thread): > @Victoria (Burah) Poromoncheck out figure 4

Anne-Marie Sharp (07:56:21) (in thread): > Hello@Oriade AdeolaI can’tsee any signature on my end. You can give it a while and reload to check again.

Adeshile Oluwatosin (07:56:39) (in thread): > @Victoria (Burah) Poromon

Oriade Adeola (07:56:45): > ok thank you

Adeshile Oluwatosin (07:57:25) (in thread): > Can you kindly chat under a thread?

Joy (07:57:44) (in thread): > Welcome on board@Montana-Dto this wonderful community:sparkles:

Victoria (Burah) Poromon (07:58:03) (in thread): > Okay

Adeshile Oluwatosin (07:59:36) (in thread): > Differentially abundant species between tumors with and without TP53 (A), APC (B), KRAS (C), SMAD4 (D) alterations, respectively:thinking_face:

Mildred Anashie (08:01:05) (in thread): > @Oriade Adeolathere’s a signature 3 that seem to be same as Signature 1 in Experiment 1.https://bugsigdb.org/36875281/Experiment_1/Signature_3You signatures are not showing yet from my end, try to refresh the study - Attachment (BugSigDB): 36875281/Experiment 1/Signature 3 > Source: Figure 3a Description: Statistic analysis of bacterium in the phylum level in STC, NTC, and HC groups. Abundance in Group 1: increased abundance in Chronic…

Victoria (Burah) Poromon (08:03:19) (in thread): > There’s no indication of differential abundance in fig 4:eyes:

Montana-D (08:03:28) (in thread): > Thank you@Joy

Anne-Marie Sharp (08:03:34) (in thread): > @Mildred Anashieyes that’s the description but regarding estimation of differential abundance, generalized linear mixed models and negative binomial distribution were mentioned, its confusing.@Adeshile OluwatosinI saw the MANOVA test mentioned but it wasn’t used for differential abundance. The curation policy says we should use the Statistical test or computational tool used for differential abundance testing. That’s why I think it should be Negative Binomial Regression. We will need a mentor to double-check

Adeshile Oluwatosin (08:04:48) (in thread): > It is not negative binomial regression > Ididn’tsee that anywhere

Mildred Anashie (08:05:55) (in thread): > @Anne-Marie SharpNegative Binomial regression is not mentioned to be used for differential abundance here

Adeshile Oluwatosin (08:06:06) (in thread): > See:“Based on the taxonomic profiles and functional pathway abundance, we used LEfSe to assess microbial difference between subjects with or without specific somatic mutated genes. The significance was determined by LDA scores with a threshold of 2.0. Furthermore, the correlations between differentially abundant species and deregulated genes were estimated using spearman’s rank test. Associations with P values < 0.01 were considered statistically significant.”

Adeshile Oluwatosin (08:06:23) (in thread): > Also, figure 2C is curatable

Oriade Adeola (08:06:41): > @Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divineplease can you help delete signature 3? - Attachment (BugSigDB): 36875281/Experiment 1/Signature 3 > Source: Figure 3a Description: Statistic analysis of bacterium in the phylum level in STC, NTC, and HC groups. Abundance in Group 1: increased abundance in Chronic…

Adeshile Oluwatosin (08:07:08) (in thread): > You indicated 2F as a source “Ican’t find that”

Oriade Adeola (08:07:10) (in thread): > ok thank you

Oriade Adeola (08:07:57) (in thread): > https://bugsigdb.org/36875281please help me check it out. i think i’ve made a lot of mistakes - Attachment (BugSigDB): Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status - BugSigDB > BACKGROUND: Patients with chronic constipation (CC) show altered gut microbial composition.OBJECTIVES: To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.DESIGN: This is a prospective cohort study.

Anne-Marie Sharp (08:08:07) (in thread): > Hello@Oriade Adeola, you can ask for the deletion in the GitHub issue that has your curation.

Mildred Anashie (08:08:11) (in thread): > Check again@Adeshile Oluwatosin2C isn’t curatable It’s 2F

Victoria (Burah) Poromon (08:08:33) (in thread): > Are we looking at the same article?@Adeshile Oluwatosin:weary:2C is not curatable on my end.

Oriade Adeola (08:08:40) (in thread): > ok thanks. will do that now

Anne-Marie Sharp (08:09:04) (in thread): > Okay, I thought negative binomial regression is same as negative binomial distribution

Adeshile Oluwatosin (08:09:14) (in thread): > I opened a different article > Sorry, let me check again

Adeshile Oluwatosin (08:09:45) (in thread): > Apologies

Victoria (Burah) Poromon (08:09:45) (in thread): > https://journals.asm.org/doi/10.1128/msystems.00805-24#F2

Anne-Marie Sharp (08:09:51) (in thread): > Okay,you’rewelcome

Mildred Anashie (08:13:22) (in thread): > Check this outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&cid=C04RATV9VCY@Anne-Marie Sharpfor more on Differential Abundance, that’s why I’m leaning more towards T test and Wilcoxon - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Adeshile Oluwatosin (08:13:55) (in thread): > Alright dear

Adeshile Oluwatosin (08:14:13) (in thread): > It seems accurate

Adeshile Oluwatosin (08:15:36) (in thread): > There’sno record of body site, condition

Mildred Anashie (08:15:36) (in thread): > I also think you’ve done a good job@Victoria (Burah) Poromon

Adeshile Oluwatosin (08:15:52) (in thread): > Data transformation is not correct

Adeshile Oluwatosin (08:16:09) (in thread): > We records 4 weeks as 1 month for antibiotics exclusion

Victoria (Burah) Poromon (08:16:30) (in thread): > Thank you!@Mildred Anashie@Adeshile Oluwatosin

Anne-Marie Sharp (08:22:25) (in thread): > @Mildred Anashiethanks for sharing. Okay, I understand the explanation and at first I saw t-test and wilcoxon and thought they were the statistical tests used. but in the article clip I shared above, it says ‘Differences in bacterial abundances and associations between bacterial taxa…..were estimated with generalized linear mixed models’ so that part got me wondering.

Mildred Anashie (08:23:43) (in thread): > If you go through@Eseoghene Cynthia Princewill-Ukotcuration the experiments with Generalized Linear Model is already recorded

Adeshile Oluwatosin (08:24:12) (in thread): > Hi dear@Anne-Marie Sharpthat excerpt is for table 3

isaac imitini (08:27:02) (in thread): > Thank you very much everyone this was very helpful. Apologies for replying late.

Oriade Adeola (08:27:06) (in thread): > ahh

Oriade Adeola (08:27:31) (in thread): > i added everything. or so i thought

Oriade Adeola (08:27:42) (in thread): > can i start allover again?

Oriade Adeola (08:27:52) (in thread): > r what do i do please?

Anne-Marie Sharp (08:28:24) (in thread): > Okay, but why I ruled out t-test and wilcox test is that there’s no mentioned of them being used for estimating differential abundance. The article states ‘The baseline differences in SCFA, stool water content, qPCR results and transit times between the patient groups were calculated either with t-test (parametric data) or Wilcox test (nonparametric data)’ but I’m like differences in scfa, stool water…, pcr results, transit times, but where is the differential abundance

isaac imitini (08:29:46) (in thread): > I was thinking the same@Anne-Marie Sharpfor the table, I will use that as a guide.

Adeshile Oluwatosin (08:29:51) (in thread): > Inexperiment1

Adeshile Oluwatosin (08:30:19) (in thread): > It’sshowing for the rest

Svetlana Ugarcina Perovic (08:33:14) (in thread): > @Oriade Adeolahttps://github.com/waldronlab/BugSigDBcuration/issues/668#issuecomment-2751101993

Peace Sandy (08:34:00) (in thread): > I think it has been deleted already

Anne-Marie Sharp (08:40:38) (in thread): > @isaac imitiniokay,you’rewelcome

Mildred Anashie (08:48:35) (in thread): > I Understand you@Anne-Marie Sharpbut it is definitely not Negative binomial regression in my opinion

Anne-Marie Sharp (08:50:22) (in thread): > Okay, yes@Mildred Anashieyour explanation above cleared that binomial distribution/binomial regression bit part.

Montana-D (08:56:02): > Patterning to the paper I’m required to curate, adding it to a study requires a PMID, after thorough study and search of the article, I couldn’t find the PMID, how do I go about it. Has anyone experienced this, or has it been answered to someone before?

Mildred Anashie (08:58:10) (in thread): > Search the article name onPubmedyou’d getthe PMID - Attachment (pubmed.ncbi.nlm.nih.gov): PubMed > PubMed® comprises more than 38 million citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full text content from PubMed Central and publisher web sites.

Adeshile Oluwatosin (09:11:24) (in thread): > * Paste the article title here > * Click cite > * Copy out the PMID : containing only numbers > * Then paste on bugsigdb

Montana-D (09:16:38) (in thread): > Thank you both so much

Mildred Anashie (09:27:05) (in thread): > Experiment 9 is also not reflecting signatures yet but I’ve been able to see it. Everything seems right@Adeshile Oluwatosinmy only concern is if the alpha diversity that weren’t pointed to show comparison or significance for the last 5 experiments should have been left blank or curated as unchanged like you did.:thinking_face:

Adeshile Oluwatosin (09:27:50) (in thread): > Thank you so much for your review

Mildred Anashie (09:32:52) (in thread): > @Peace Sandy@Esther Afuape@Svetlana Ugarcina Perovic@Aleru Divine@Kate Rasheed<@UBNSEMS3S>Please a little help here. I am currently curating a paper with the same concern and I’d appreciate more insights on how to go about it. Thank you:pray:

Svetlana Ugarcina Perovic (09:34:20) (in thread): > @Mildred Anashiebe patient:slightly_smiling_face:

Mildred Anashie (09:36:06) (in thread): > Thank you@Svetlana Ugarcina Perovic:pray:

Oriade Adeola (09:48:06) (in thread): > Hello@Adeshile Oluwatosinplease can you help me check again?

Precious Chijioke (11:30:32): > Good Day@Kate Rasheedfrom the correction given in my study, for experiment 3-5 you said Figure 4 is a one-against-the-rest analysis. If I want to curate for NC, It should be recorded as Group 0: FC_PreZY + ProZY while Group 1 would be NC. In the experiment, I would curate the taxa with blue bars alone as increased in NC. Please I am a bit confused, in Fig 4 NC is represented with red bars, FC_PreZY = green bars while ProZY = blue bars.

Kate Rasheed (11:38:03) (in thread): > Please make this comment on the GitHub issue.

Precious Chijioke (11:39:52) (in thread): > @Kate RasheedThank you > Thought as much but wasn’t too sure of where to make the comment.

Vanisha Garg (12:03:43) (in thread): > @Adeshile OluwatosinThankyou so much for reviewing , I really appreciate it .

Vanisha Garg (12:18:37) (in thread): > @Adeshile OluwatosinI tried searching for similar words as they were not present in drop down menu , But was unable to find the closest. > Could you please help me in this

Adeshile Oluwatosin (12:20:32) (in thread): > If you can’t find it, write exactly what you can see in the paper

Vanisha Garg (12:20:52) (in thread): > Even if it is not there in the drop down

Vanisha Garg (12:20:55) (in thread): > ?

Adeshile Oluwatosin (12:24:26) (in thread): > Yes for matched on factors

Vanisha Garg (12:24:43) (in thread): > okay thanks@Adeshile Oluwatosin

Vanisha Garg (12:25:31) (in thread): > @Adeshile OluwatosinShould I present this to mentor . Do you find this ready?

Vanisha Garg (12:27:49) (in thread): > Are there any cofounders for this ? > I couldn’t find them . Please someone help me in this

Adeshile Oluwatosin (12:39:44) (in thread): > Remove all tests recorded, leave only lefse

Adeshile Oluwatosin (12:40:08) (in thread): > Have you submitted previously?

Adeshile Oluwatosin (12:41:05) (in thread): > Can’tfind any confounders > Didn’t check the supplemtary article

Vanisha Garg (12:58:38) (in thread): > Yes initially I didn’t knew that we have to get it reviewed by peers first.

Svetlana Ugarcina Perovic (12:58:42): > :question:I found ONLINE COMMUNICATION challenging, you? Effective online communication requires clarity and thoughtfulness. We should write our ideas concisely and precisely, keeping a balance between brevity and comprehensiveness. Overly lengthy or extremely brief messages can slow down our online communication and produce misunderstandings. Above all, maintaining a spirit of kindness and respect in our interactions is a must. > > For example, this message I rewrote 5 times: > 1. I put all my thoughts > 2. I reread and deleted “noise” in my message > 3. I reread and deleted “noise” in my sentences > 4. I rewrote some sentences to be more clear > 5. I read it one last time :)

Adeshile Oluwatosin (13:00:29) (in thread): > Please follow all instructions given by the mentor > Thank you

Adeshile Oluwatosin (13:01:10) (in thread): > Thank you so much for these notes

Vanisha Garg (13:01:53) (in thread): > Thank you for the help@Adeshile Oluwatosin:heart:

isaac imitini (13:02:13) (in thread): > Thank you for communicating this.

Adeshile Oluwatosin (13:02:19) (in thread): > Personally for me, I’ve been working on being concise and precise in my responses. I incorporate the habit of reading all over. Hence the need to edit my messages sometimes.

Anne-Marie Sharp (13:02:31) (in thread): > @Svetlana Ugarcina Perovicit’schallenging sometimes especially whenit’sjust texting as misunderstandings occur more often. But those are goodpoints I’llalso keep in mind. Thank you for sharing.

Vanisha Garg (13:03:45) (in thread): > @Svetlana Ugarcina PerovicThese points will be very helpful. Thank you for sharing.

Svetlana Ugarcina Perovic (13:10:47): > A BIG shout-out to the Outreachy co-mentors::star:@Chioma Onyido:star:@Esther Afuape:star:@Scholastica Urua:star:@Peace Sandy:star:@Aleru Divine:star:@Kate Rasheedwho are working hard to provide you with concise and precise review feedback!

Svetlana Ugarcina Perovic (13:11:15): > Thank you for your patience!

Adeshile Oluwatosin (13:11:22) (in thread): > Thank you mentors:heart:

Mildred Anashie (13:11:41) (in thread): > Thank you for the tips@Svetlana Ugarcina Perovic

Vanisha Garg (13:11:56) (in thread): > Thankyou so much mentors for constantly guiding us and helping us:heart:

Anne-Marie Sharp (13:13:39) (in thread): > Well done and thank you to our mentors:pray:

Joy (13:15:15) (in thread): > A big thank you to our co-mentors. We appreciate your hard work:sparkles:

Adeshile Oluwatosin (13:17:06): > @Svetlana Ugarcina PerovicI would like to point this out. > I have figured over 22 articles with the antibiotics exclusion issue. Can I proceed with correcting this! And is there a need to list them out. Thank you so much

Joy (13:19:02) (in thread): > Thank you@Svetlana Ugarcina Perovicfor this piece of information. We will strive to improve on our Online Communication keeping it concise and brief while enhancing comprehension.:sparkles:

Eseoghene Cynthia Princewill-Ukot (13:41:51) (in thread): > Thank you so much for all you do:kissing_heart:

Svetlana Ugarcina Perovic (13:51:55) (in thread): > This message is incomplete:wink:What type of issue you spotted in antibiotics exclusion recordings?

Adeshile Oluwatosin (13:53:42) (in thread): > Antibiotics exclusion curated as > * N/A or n/a instead of being blank > * four/4 weeks instead of “1 month”, > * eight/8 weeks instead of “2 months”, > * twelve/12 weeks instead of “3 months” > * No antibiotics instead of being blank > * 12 months instead of “1 year”

Utibe Ita (13:56:16) (in thread): > Thank you for the tips@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (14:00:57) (in thread): > @Samuel Nnannais responsible for this task. Let’s see how he prefers this to be organized. Ok?

Svetlana Ugarcina Perovic (14:01:37) (in thread): > Feel free to write to@Samuel Nnannadirectly.

Adeshile Oluwatosin (14:01:50) (in thread): > Alright then,that’sfine > I would contact him. Thank you so much

Utibe Ita (14:08:30): > Good day@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)Help delete experiment 3https://bugsigdb.org/37593638/Experiment_3 - Attachment (BugSigDB): 37593638/Experiment 3 > .

Anne-Marie Sharp (14:11:11) (in thread): > Hello@Utibe Ita, you can ask for the deletion in the GitHub issue that has your curation.

Utibe Ita (14:13:26) (in thread): > @Anne-Marie Sharpthank you

Anne-Marie Sharp (14:13:55) (in thread): > You’rewelcome

Aiysha shahid (14:34:18) (in thread): > Thank you so much for the sharing these tips:tulip:@Svetlana Ugarcina Perovic

Oriade Adeola (15:10:08) (in thread): > Thank you very much for tips.

Oriade Adeola (15:14:11): > Hello everyone, i would like a peer review to my study:pray:https://bugsigdb.org/36875281 - Attachment (BugSigDB): Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status - BugSigDB > BACKGROUND: Patients with chronic constipation (CC) show altered gut microbial composition.OBJECTIVES: To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.DESIGN: This is a prospective cohort study.

Oriade Adeola (15:16:25) (in thread): > it has been rectified. Thank yoou

Anne-Marie Sharp (15:16:39) (in thread): > Hello@Oriade Adeola, we will look through it

Oriade Adeola (15:17:36) (in thread): > Thank you@Anne-Marie Sharpi’ll appreciate that

Joy (15:20:39) (in thread): > Well done@Oriade Adeolaon your curation, you have all these statistical tests for differential abundance in one place?:thinking_face:We will take a look at it.

Utibe Ita (15:48:15): > Hello Everyone > I will like a peer review on my studyhttps://bugsigdb.org/37593638I need as much eyes as I can get - Attachment (BugSigDB): Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study - BugSigDB > We conducted a feasibility cohort study which aimed to recruit and retain adults from the community to collect saliva (oral) and stool (gut) samples at three time points, at the start of the study (baseline), during a respiratory tract infection (RTI) and post-RTI.

Mildred Anashie (16:15:30) (in thread): > Well done@Oriade AdeolaI’llalso take a look

Aiysha shahid (16:49:02) (in thread): > Hello@Oriade Adeola, I’ll would also go through it.

Anne-Marie Sharp (16:55:27) (in thread): > @Oriade Adeola1) There were no confounders controlled for in the article. 2) There were no factors matched on. 3) No sequencing platform was mentioned. 4) Data transformation should be relative abundance. 5) Statistical test is Mann-Whitney U-test. 6. Your experiments/signatures need to be modified to includeallthe subtypes compared. 7. The taxonID for Christensenellaceae is 990719, you can select that in BugSigDB drop-down menu when curating.

Joy (17:05:47) (in thread): > Well done@Utibe Itaon your curation, we will have a look 1. Sequencing type isIllumina. :point_right:A library of 16S amplicons were barcoded,sequenced on Illumina NovaSeq 6000 **** *******2***. Figure. 3 (Prevalence) & 4 are curatable

Joy (17:34:09) (in thread): > 1. The study used theMann–Whitney U-testfor differential abundance analysis of fecal microbiota between constipation subtypes and the control group. Additionally, theBenjamini–Hochberg methodwas applied to control for the false discovery rate, with adjusted p-values <0.05 considered statistically significant. > 2. Furthermore, alpha diversity analysis (e.g.observed species (richness), Shannon index, Chao1 index, and Simpson index) was conducted on the OUT data using the QIIME software (Version, 1.7.0). > 3. No matched on 4. Figure. 2B is also curatable. Let’s hear from others as well@Oriade Adeola

Precious Orakwe (18:15:52) (in thread): > Thanks to the co-mentors for your hard work.

Precious Orakwe (18:18:33) (in thread): > Thank you@Svetlana Ugarcina Perovicgreat idea, when discussions are concised, they are easy to understand

Anne-Marie Sharp (19:05:25) (in thread): > Hello@Utibe Itawe have our eyes on it:raised_hands:

Mildred Anashie (19:25:28) (in thread): > Hi@Oriade AdeolaWell done on your curation > I have a few observations, > 1. Maintain 1 month for the antibiotic exclusion. > 2. I can’t find Illumina or ion torrent as sequencing platform. Although they said this “The protocol for the bioinformatics methods has beenpreviously published.” I followed the link and found the mention of Miseq which is based on illumina. Unsure if you should use that though. > 3. No matched on and confounders as mentioned above. > 4. Alpha diversity in table 1 you didn’t record Richness which is unchanged in CC vs HC. > 5. Your experiments are to come from Fig 2b and d which is showing CC vs HC with Mann Whitney as statistical test. Please focus only on the ones showing significance. > Fig 3a and b seems to show 2 experiments as well which I believe to be STC vs NTC and NTC vs NC. > Fig 3c and d also has two experiments which I believe to be DD vs non-DD and non-DD vs HC > (Read the results text to confirm this please). The test is also Mann Whitney for Fig 3. > 6. Table 2 and 3 also has a number of comparisons. From what I understand r stands for relative abundance and p stands for p value. You’d curate only the r values that have * besides them those are the only significant ones (thepvalues confirm that).I’ll look closely to see how the groups can be compared. > Thestatisticaltest used is spearman correlation > > N/B: Data transformation for Mann Whitney is relative abundance. > > Well done again - Attachment (PubMed): Modulation of Gut Microbiome Composition and Function in Experimental Colitis Treated with Sulfasalazine - PubMed > Inflammatory bowel disease (IBD) results from alterations in intestinal flora and the immune system. Sulfasalazine (SASP) is a sulfa antimicrobial used to treat IBD in clinic for years. However, how SASP affects gut microbes and its potential functions remains unclear. To investigate the relationshi …

Mildred Anashie (19:27:35) (in thread): > Well done@Utibe ItaI’ll give it a look as well

Juliana Kentomahun Mautin (19:39:21): > Hello everyone, I am pleased to announce that I have completed my second contribution. In order to ensure the quality and accuracy of my work, I would greatly appreciate it if you could provide a peer review of this study. Thank you:blush:https://bugsigdb.org/39963956. - Attachment (BugSigDB): Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study - BugSigDB > Micronutrients have demonstrated promise in managing inattention and emotional dysregulation in children with attention-deficit/hyperactivity disorder (ADHD).One plausible pathway by which micronutrients improve symptoms is the gut microbiome.

Juliana Kentomahun Mautin (19:40:24) (in thread): > Welldone@Utibe Ita, I would check it out.

Juliana Kentomahun Mautin (19:45:14) (in thread): > Thank you so much my amazing mentors for your relentless effort towards providing a concise and precise review feedback.

Juliana Kentomahun Mautin (19:59:41) (in thread): > Thank you so much@Svetlana Ugarcina Perovic. Overly lengthy message can be overwhelming and can slow down our online communication. Moving on I would try to break my messages into concise paragraphs or bullet points for enhance readability and to facilitate faster understanding.

Mildred Anashie (20:00:03) (in thread): > Hi@Utibe ItaWell done:+1:I have just a few observations, > 1. I am unsure if Table 2 is curatable or how it should be curated, I’ll take a second look. But it appears that is the table they used RT-qPCR as the sequencing platform. Whereas the paper generally used illumina as@Joypointed out. > 2. You already curated Fig 5 and that’s showing baseline comparison for RTI and non RTI in oral and fecal samples while Fig S3a and b is showing same comparison but at end of study. You should curate Fig S3a and b as well. > 3. Fig S1b shows results for RTI symptoms (RTI - blue) compared to those who remained healthy (no-RTI – coral) at baseline done with the different sample subtypes (A, B and C). But I’m unclear on how to interpret the figure. > 4. The LDA score is 2, you used 1.4 for the second experiment. > 5. The study design seems to be more of a longitudinal/time-series study than prospective cohort. > Well done again:clap:

Mildred Anashie (20:06:53) (in thread): > Thank you to our co-mentors > We appreciate your efforts:pray:

Mildred Anashie (20:20:24) (in thread): > Hi@Juliana Kentomahun MautinWell done:clap:

Mildred Anashie (20:25:46) (in thread): > I have a few observations for now, TableS5, S6, Fig S1, Table 2 and Fig5, Table 4 and Figure 7, Fig 6 should be curated separately from Table 2Those are the curatable figures and tablesbut I’ll look through again to confirm how they should be curated.

Adeshile Oluwatosin (20:45:04) (in thread): > Well done@Juliana Kentomahun Mautin

Anne-Marie Sharp (21:05:47) (in thread): > Well done with your curation@Utibe ItaAs stated above, > 1) The sequencing platform is Illumina. > 2) Figures S3a & S3b can be added to a second experiment(for the end of the study) while Experiment1 can be for baseline. > 3) The study design is Time series/Longitudinal. > 4) Synergistia is in BugSigDB, you can also try the TaxonID: 1294150 > 5) In Experiment 2, signature1 should be increased abundance & signature 2 should be decreased abundance (although you may still edit the whole experiment)@Mildred Anashie, Table 2 & Fig. S1b are not curatable

Juliana Kentomahun Mautin (21:19:17) (in thread): > Thank you@Adeshile Oluwatosinand@Mildred Anashie. I look forward to your response on how to go about curating them.

Anne-Marie Sharp (22:01:08) (in thread): > Hello@Juliana Kentomahun Mautin, well done with your curation, I have some observations > 1.The condition should be Attention deficit hyperactivity disorder not ADHD symptom measurement. > 2.There was no characteristic matched on.

Anne-Marie Sharp (22:19:35) (in thread): > 3.Actinobacteriota is Actinomycetota. > 4.Oscillospiraceae is Oscillospiraceae(216572) > 5.Firmicutes is Bacillota

2025-03-26

Juliana Kentomahun Mautin (01:41:11) (in thread): > @Anne-Marie SharpThere’s no ADHD on bugsidDB just ADHD measurements. > > Please could you please explain what you meant by there’s no characteristics it was matched on?

Anne-Marie Sharp (02:36:39) (in thread): > @Juliana Kentomahun Mautinthere is, but you have to type out the full name not the abbreviation

Anne-Marie Sharp (02:37:18) (in thread): > Type out Attention Deficit Hyperactivity Disorder,you will see it on BugSigDB

Mildred Anashie (02:55:08): > Hi everyone,
> It’s Wednesday and we are halfway through the second week of our contribution phase already:pleading_face:I just concluded the curation of this study and I’ll appreciate peer review. > Any help with the missing NCBI would be appreciated andI need another pair of eyes to confirmANOVA is the right statistical test for the first 2 experiment. > Thank you:pray::skin-tone-5:Link to study:https://bugsigdb.org/38226659 - Attachment (BugSigDB): Orally administered neohesperidin attenuates MPTP-induced neurodegeneration by inhibiting inflammatory responses and regulating intestinal flora in mice - BugSigDB > Parkinson’s disease (PD), a neurodegenerative disease, is the leading cause of movement disorders.Neuroinflammation plays a critical role in PD pathogenesis.Neohesperidin (Neo), a natural flavonoid extracted from citric fruits exhibits anti-inflammatory effects.

Adeshile Oluwatosin (02:55:49) (in thread): > Hello dear > Good morning > I will have a look

Adeshile Oluwatosin (03:00:53) (in thread): > Saw this for the statistical test > “The differences among multiple groups were analyzed using one-way analysis of variance (ANOVA) combined with multiple comparisons and followed by Tukey’s post hoc test. A p-value < 0.05 was considered statistically significant.”

Mildred Anashie (03:04:56) (in thread): > Thank you@Adeshile Oluwatosin:pray:That’swhat I used to curate as ANOVA but I needed other pair of eyes to look through > > Not everything is clearly stated in the article

Francisca Gundu (03:05:23) (in thread): > Well done@Mildred Anashieon your curation, I’ll also give it a shot.

Juliana Kentomahun Mautin (03:11:05) (in thread): > Okay thank you will make the correction for the condition.@Anne-Marie Sharp, please what do you mean by there was no characteristics matched on, please kindly explain better and how to go about identifying the characteristics. Thank you:blush:.

Juliana Kentomahun Mautin (03:12:11) (in thread): > Welldone@Mildred Anashie.

Francisca Gundu (03:13:24) (in thread): > @Mildred Anashie1. The taxonChloracidobacteriais**** ****Chloracidobacteriumwith the ID: 458032 (Expt. 4 Sig.1) > > 2. The taxon Gemellales is******Gemella******with the ID: 1378 (Expt. 3 Sig. 1) - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (03:20:51) (in thread): > Hi dear@Francisca GunduI believe the rank is different hence she has to curate as it is

Francisca Gundu (03:22:16) (in thread): > Oh, Ok.

Mildred Anashie (03:22:22) (in thread): > Yes@Francisca Gundu@Adeshile Oluwatosinis right > The rank is different

Mildred Anashie (03:24:05) (in thread): > Also if it isn’t a lot of stress, I feel like I missed out on one taxa in Experiment 3. Anyone willing to help me check > Ps: you need to really zoom in to see what’s reported in fig5a

Mildred Anashie (03:28:02) (in thread): > @Juliana Kentomahun MautinMatched on wasn’t reported in the article so you shouldn’t record it, what was mentioned was just the demographic characteristics of the participants and itdoesn’timply they were matched on those

Anne-Marie Sharp (03:31:10) (in thread): > You’re welcome@Juliana Kentomahun MautinI mean there was no matched on in the article eg the patients were not matched on age, race etc.(Theydon’tall have similar age, race etc) . The attached screenshot of the curation policy explains how to identify them. - File (JPEG): IMG_0039

Juliana Kentomahun Mautin (03:39:53) (in thread): > Oh Thank you so much@Mildred Anashieand@Anne-Marie Sharpfor the clarification. I would implement your feedback

Anne-Marie Sharp (03:41:32) (in thread): > You’rewelcome@Juliana Kentomahun Mautin:raised_hands:

chiamaka Uche (03:51:35): > Hey everyone!:wave:I just finished curating this study and would appreciate a second pair of eyes on the signature section, especially the NCBI taxon identifiers and overall accuracy. If you’re free please look through it, I’d love your feedback! > > Thanks in advance!:blush:Link to study:https://bugsigdb.org/39642873 - Attachment (BugSigDB): The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children - BugSigDB > Respiratory syncytial virus (RSV) is the leading cause of infant respiratory infections and hospitalizations.

Joy (03:52:57) (in thread): > Well done@chiamaka Ucheon your curation. We will have a look.

Anne-Marie Sharp (03:58:57) (in thread): > Hello@Mildred Anashie, nice one. 1)I also checked and confirmed, those taxa with missing NCBI are actually missing.

Mildred Anashie (04:02:54) (in thread): > Please look through again@Anne-Marie SharpIt wassignificant for Saline andnot MPTP

Mildred Anashie (04:03:17) (in thread): > I see you changed it:blush:

Anne-Marie Sharp (04:03:54) (in thread): > @Mildred AnashieYes:smile:I quickly observed, the figure count is 39 and yours is 38. Still cross checking

Aiysha shahid (04:05:16) (in thread): > Hi@chiamaka Uche, Well Done. I’ll also go through it.

Aiysha shahid (04:06:14): > Hi everyone, I have a question that if in our research paper, the LDA score in not directly mentioned, so I can use 2 as the score or just leave it blank? paper link-https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0312606 - Attachment (journals.plos.org): The gut microbiota-SCFA-inflammation axis in patients with AECOPD > Objectives The aim of the study was to explore the alteration of microbiota and SCFA in gut and inflammation in acute exacerbation chronic obstructive pulmonary disease (AECOPD) patients, and to test the hypothesis that a disorder of gut microbiota will lead to the alteration of SCFA, which will aggravate inflammation in AECOPD patients. Methods and results 24 patients with AECOPD and 18 healthy volunteers were included in the study. Gut microbiota were analyzed by 16S rDNA and serum was used to detect levels of inflammatory factors by ELISA. Fatty acid concentrations were determined in lumen via gas chromatography-mass spectrometry. The richness and diversity of gut microbiota were decreased in AECOPD patients. β-diversity analysis revealed differences between AECOPD patients and healthy controls. p_Bacteroidetes, g_Paraprevotella, g_Ruminococcus2, g_Parasutterella, o_Rhodospirillales, and g_Romboutsia in the healthy controls and p_Firmicutes, o_Actinomycetales, f_Actinomycetadeae, g_Actinomyces, g_Mogibacterium, f_Veillonellaceae, f_Enterococcaceae, and g_Enterococcus in AECOPD patients were the most abundant microbiota. SCFA levels were decreased in patients with AECOPD. In addition, the results demonstrated that except for a reduction in IL-6, there was no change in inflammatory markers in AECOPD patients. Conclusion In AECOPD patients, the gut microbiota-SCFA-inflammation axis is augmented, with decreased diversity and abundance of gut microbiota, leading to a reduction in SCFA and an imbalance of inflammation.

Anne-Marie Sharp (04:09:47) (in thread): > Check Desulfovibrionaceae

Victoria (Burah) Poromon (04:10:22) (in thread): > Hi@Aiysha shahidYes, if the score is not mentioned in the paper, you can use 2.

Mildred Anashie (04:11:41) (in thread): > That is it…..Thank you:dancer:

Aiysha shahid (04:18:45) (in thread): > Okay,Thanks@Victoria (Burah) Poromon

Adeshile Oluwatosin (04:31:17) (in thread): > I could not find any matched on factors as well > I agree with everything said here > Well done

Adeshile Oluwatosin (04:31:46) (in thread): > Back to this, let me look at this

Anne-Marie Sharp (04:33:08) (in thread): > @Mildred AnashieAnd for the statistical test in the first 2experiments, yesit’sANOVA

Adeshile Oluwatosin (04:35:42) (in thread): > Experiment 5: MHT should be no

Adeshile Oluwatosin (04:36:02) (in thread): > @Mildred Anashiealso point me to where there was record of MHT for the experiments

Adeshile Oluwatosin (04:36:31) (in thread): > Yes, default LDA score if not in the paper is 2

Adeshile Oluwatosin (04:37:11) (in thread): > Well done@chiamaka Uche

Adeshile Oluwatosin (04:37:22) (in thread): > We record only one statistical test per experiment

Mildred Anashie (04:43:55) (in thread): > Thank you@Adeshile Oluwatosin…..The post-hoc test:thinking_face:

Adeshile Oluwatosin (04:44:18) (in thread): > Alright, I will have a look

Adeshile Oluwatosin (04:46:23) (in thread): > * For figure 2E-F: see this “(E and F) Log2 fold change (FC) of features (genera [E]/ASVs [F]) based on MaAsLin2 (linear mixed-effects model) with RSV severity (compared to healthy controls) as variable of interest, adjusted for age, gender (fixed effects), and study site (random effect)” > Hence, confounders from thisspecificexperimentare age, gender and study site. Test: MaAsLin2 > * I can only see Shannon diversity in the paper, leave every other one blank and accurately for Shannon. Figure 3A. > NB; NS means not significant hence curate as unchanged.

Adeshile Oluwatosin (04:47:52) (in thread): > Figure 3E and F seems curatable

Adeshile Oluwatosin (04:48:27) (in thread): > 16S variable region, remove V4 from the second button

Adeshile Oluwatosin (04:48:56) (in thread): > Figure 4A andB

Utibe Ita (04:57:28) (in thread): > @Aiysha shahidThe default LDA score is 2 while the default p value is 0.05 where the values are not given

Adeshile Oluwatosin (05:07:38) (in thread): > Idon’tthink that means MHT is yes

Precious Chijioke (05:16:51) (in thread): > Thank you for the tips@Svetlana Ugarcina Perovic

Precious Chijioke (05:19:18) (in thread): > A big thank you to our co-mentors for your guidance and feedbacks

Utibe Ita (05:35:56) (in thread): > Thank you for the corrections@Joy. Can you assist with how i can go about curating Figure. 3 (Prevalence) & 4

Kate Rasheed (05:36:48) (in thread): > @JoyPlease see this thread.

Utibe Ita (05:40:39) (in thread): > Thank you@Mildred Anashie. I need assistance with how to go about curating figure 3a and b. I have made other necessary corrections that you highlighted.

Mildred Anashie (05:42:36) (in thread): > It’sFigS3 a and bIt’sin the supplemental file

Juliana Kentomahun Mautin (05:46:14) (in thread): > Thank you@Adeshile Oluwatosin.@Mildred Anashieplease I’m still looking forward to your response regarding the table curation.

Juliana Kentomahun Mautin (05:47:07) (in thread): > @Adeshile Oluwatosinplease do you have any suggestions regarding the signatures and Experiment for this study.

Utibe Ita (05:57:42) (in thread): > Thank you for the corrections@Anne-Marie Sharphowever, this TaxonID: 1294150 showed uncultured Synergistia bacterium

Utibe Ita (05:57:52) (in thread): > Thank you@Mildred Anashie

Adeshile Oluwatosin (06:01:24) (in thread): > Can you wait for a while as I’mintransit:pleading_face::pleading_face::pleading_face:

Anne-Marie Sharp (06:13:25) (in thread): > You’rewelcome@Utibe Itathat’sthe closest match I saw, I believeit’salso a specie

Joy (06:15:08) (in thread): > Sure@Utibe ItaFor Fig. 3 1.Comparisons: > * Oral microbiota: RTI-S (left) vs. No-RTI (right). > * Gut microbiota: RTI-S (left) vs. No-RTI (right). > 2. Suggested colors: > * :red_circle:Red (low prevalence) > * :large_yellow_circle:Yellow (moderate prevalence) > :large_blue_circle:Blue (high prevalence) Let’s leave Fig. 4 out of it.

Anne-Marie Sharp (06:22:49) (in thread): > @Mildred AnashieMHT is different from post-hoc.@Adeshile Oluwatosinis right, there was no MHT done.

Mildred Anashie (06:28:47) (in thread): > Okay > > I’ll just try to confirm this, I already submitted for review though. > But I got it from the fact that Bonferroni is also a type of post hoc testingjust as Tukey’s test.

Victoria (Burah) Poromon (06:30:38): > Hi everyone,@Adeshile Oluwatosinand I curated this study and we are putting it up for peer review. > > Thank you so much for your feedback in advance. > > Study link:https://bugsigdb.org/39762435Article link:https://www.nature.com/articles/s41564-024-01870-z - Attachment (BugSigDB): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals - BugSigDB > As plant-based diets gain traction, interest in their impacts on the gut microbiome is growing.However, little is known about diet-pattern-specific metagenomic profiles across populations. - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.

Anne-Marie Sharp (06:33:26) (in thread): > Hello@Victoria (Burah) Poromonwe will look through it. I want to clarify, are we also to pair up for curations as part of our contributions?

Victoria (Burah) Poromon (06:37:31) (in thread): > Uhmm, not really as part of the contribution, It’s not a criteria. But yes, you can absolutelyworkon a curation withsomeone else.We’re supposed to collaborate with each other.

Juliana Kentomahun Mautin (06:41:00) (in thread): > Okay…I can wait@Adeshile Oluwatosin

Precious Chijioke (06:50:52): > Hello Everyone, please I need clarity in some areas: > 1. While curating a study if the signature for an experiment is not found in the Taxonomy database should it be reported as it appears in the study. > 2. Please how do I identify the increased and decreased signatures in Fig 3a and 3c:https://www.dovepress.com/article/fulltext_file/509592/aW1n/IJGM_A_509592_O_F0003g.jpg > Study link:https://www.dovepress.com/therapeutic-mechanism-of-zhuyang-tongbian-decoction-in-treating-functi-peer-reviewed-fulltext-article-IJGM - Attachment: Attachment - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB

Victoria (Burah) Poromon (06:51:39) (in thread): > Yes, it should be reported as seen in the study.

Precious Chijioke (06:55:10) (in thread): > Thank you@Victoria (Burah) Poromonplease any idea on question 2

Victoria (Burah) Poromon (06:58:38) (in thread): > Does the description explain thedifference between the signs? (# and *)

Precious Chijioke (07:04:21) (in thread): > In contrast, the ProZY group exhibited a marked improvement in the relative abundance of these genera (Figure 2C). In addition, we further analysed the changes in the abundance of Bifidobacterium spp. and Lactobacillus spp. before and after the treatment of the patients, and the relative abundance of Bifidobacterium spp. and Lactobacillus spp. was significantly lower in the FC_PreZY group compared with the NC group, whereas the relative abundance of the two spp. in the ProZY group was significantly increased compared with that of the FC_PreZY group, and was closer to the level of the NC group (Figure 3A). At the species level, the relative abundance of s__Faecalibacterium_prausnitzii, s__Bifidobacterium_longum, s__Bifidobacterium_adolescentis and s__Bifidobacterium_pseudocatenulatum under the genus Bifidobacterium was significantly lower in the FC_PreZY group, whereas the relative abundance of these beneficial bacterial species in the ProZY group increased significantly and tended to favour the NC group (Figure 3BandC).Difference between the signs (# and ):****Figure 3Comparison of relative abundance of specific flora.(A)*Comparison of the abundance of Bifidobacterium spp. and Lactobacillus spp. in each group, P<0.05, P<0.01, P<0.001, ns: No significant difference;(B)Comparison of the relative abundance of each group of flora at species level;(C)Comparison of significantly different flora before and after treatment with ZTD at the species level, P<0.05, P<0.01, **P<0.001vs.NC, #P<0.05, ##P<0.01, ###P<0.001 vs. FC_PreZY. - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB - Attachment (dovepress.com): Therapeutic mechanism of Zhuyang Tongbian Decoction in Treating Functi | IJGM > In this study, we employed a comprehensive range of analytical techniques to investigate the correlation between intestinal flora, SCFAs and TLR4/NF-κB

Juliana Kentomahun Mautin (07:05:15) (in thread): > Does this LDA score being 2 by default applies to all studies with any statistical test or just LEFSe Analysis?

Aiysha shahid (07:10:14) (in thread): > Hi@Juliana Kentomahun Mautin, the LDA score is usually recorded for the LeFse Analysis, so if there’s no mention of the LDA score in the research paper,we can record the score as 2.

Victoria (Burah) Poromon (07:20:03) (in thread): > Okay, so according to this text, the 4 signatures in the red box will be curated as decreased in fc_PreZY and increased in ProZY group.

Victoria (Burah) Poromon (07:20:59) (in thread): > This is what I understand from the text

Utibe Ita (07:22:32) (in thread): > @Joyokay, thank you

Aiysha shahid (07:29:07): > Hi Everyone, I have just complete my curation, and I would like a peer review of this study. Study link-https://bugsigdb.org/39787116, Research Paper Link-http://dx.doi.org/10.1371/journal.pone.0312606 - Attachment (BugSigDB): The gut microbiota-SCFA-inflammation axis in patients with AECOPD - BugSigDB > .

Adeshile Oluwatosin (07:31:19) (in thread): > Well done > I will have a look

Precious Chijioke (07:32:08) (in thread): > @Victoria (Burah) Poromonthank you > I believe your response is in respect to 3c

Adeshile Oluwatosin (07:34:32) (in thread): > It applies only to lefse result with no LDA score stated in the paper@Juliana Kentomahun Mautin

Adeshile Oluwatosin (07:36:31) (in thread): > 1. If you cannot find the signature, search onNCBIfirst > If you still can’t find it, check Google orpages with NCBI missing ID

Victoria (Burah) Poromon (07:36:57) (in thread): > Yes, 3c@Precious Chijioke

Precious Chijioke (07:38:23) (in thread): > @Svetlana Ugarcina Perovic@Kate Rasheed@Peace Sandyplease I need assistance

Adeshile Oluwatosin (07:42:59) (in thread): > Experiment 1: S1-S7 test is metastat

Kate Rasheed (07:45:01) (in thread): > @Precious ChijiokeFor Fig. 3c, * represents significant taxa between NC vs FC_PreZy; # represent significant taxa between FC_PreZy vs ProZy.

Adeshile Oluwatosin (07:45:59) (in thread): > Also recheck the curation of the taxa for S1-S7. > The bigger circle has a more increased abundance in that specific group

Precious Chijioke (07:51:36) (in thread): > Thank you@Kate Rasheed@Adeshile Oluwatosin@Victoria (Burah) Poromonfor your assistance > > Please one more thing, is 3a curatable?

Victoria (Burah) Poromon (07:54:05) (in thread): > Yes, 3a is curatable. > The asterisks (*) indicate significance.

Aiysha shahid (08:01:04) (in thread): > Yes, It’s written S2-S7 is metastat,but in S1,it’s not mentioned what type of statistical test it is. I have considered wilcoxon as the statistical test and recorded it’s alpha diversity. As according to the google,Wilcoxon rank-sum test is used in Metastat analysis to compare differential microbial abundance between groups. These both are inter-connected. That’s why I have used Wilcoxon,would that works?

Kate Rasheed (08:06:16) (in thread): > @Precious ChijiokeAre you clear on the decreased/increased signatures?

Aiysha shahid (08:06:43) (in thread): > And for Fig S1-S7, I have already cross-checked, but most of them look similar,as in I mean both the circles look’s same in size. Is there some taxa that I have missed out?

Mildred Anashie (08:16:26) (in thread): > @Precious ChijiokeDid you see the responsehereon how to identify increase and decrease? It applies to 3a - Attachment: Attachment > Hi @Precious Chijioke > For the image you shared, thats a box plot showing taxa abundance in two groups (pairwise comparison). > > To identify the increase and decrease here, the line above the groups (Micronutrients and Placebo) tells you what contrast was made i.e if it is between A vs B, p value above the plot showing if its significant or not, and the median line inside the box (black line) helps you know if one group is increased or decreased compared to the other. > > With this we take the first plot in B which is showing us abundance of the genus Faecalibacterium in Micronutrients and Placebo. If the significant threshold in the study is 0.05 and the P value is for this plot is 0.014 we can tell that is significant and can be curated we then look at the median line and we can observe that placebo is raised here and that means it is increased compared to Micronutrients so we can infer that Faecalibacterium is increased in Placebo which means it is decreased in Micronutrients. > > This applies to the rest and it also applies to the A part of this (Alpha diversity) since it was presented the same way. > > I hope this helps. This is somehow specific to this visualization though

Precious Chijioke (08:18:52) (in thread): > Thank you@Mildred Anashie

Mildred Anashie (08:23:52) (in thread): > Hi@Aiysha shahidI’ll take a look at this also

Mildred Anashie (08:26:06) (in thread): > Hi@Victoria (Burah) PoromonI’ll give this a look. Just to confirm, 3 experiments only right?

Victoria (Burah) Poromon (08:27:09) (in thread): > Yes 3 experiments. We are not curating the supplementary materials because we already found the related studies. And we’ll be curating each one separately,

Mildred Anashie (08:29:31) (in thread): > Hello@Juliana Kentomahun MautinI’ll get to this soon

Mildred Anashie (08:30:49) (in thread): > Okay then:nerd_face:

Mildred Anashie (08:46:10) (in thread): > Hi@JoyFig 3 is prevalence and not differential abundance > Itisn’tcuratable

Precious Chijioke (08:53:22) (in thread): > @Kate RasheedI’m not really cleared. Going through the tips shared so far to understand more.

Joy (08:53:26) (in thread): > <@UBNSEMS3S>once said prevalence = differential abundance@Mildred Anashie

Mildred Anashie (08:56:42) (in thread): > Really?:astonished:I haven’t heard that before…I know of relative abundance between groups=Differential abundance. Since<@UBNSEMS3S>is tagged to this, I’ll wait for a response . We learn everyday:blush:

Oriade Adeola (09:00:02) (in thread): > Thank you everyone i’ll work on these errors.

Adeshile Oluwatosin (09:24:50) (in thread): > Thank you

Oriade Adeola (09:37:26) (in thread): > @Mildred AnashieI used 1 month. the sequencing was done at GNOME, and gnome is not in the drop down i used illumina because of the bioinformation referenced in the study mentiond MiSeq which is an illumina based platform and thats what is on the dropdown. is that ok or i should remove it completely?

Joy (09:59:10) (in thread): > Duly noted, thanks@Kate Rasheed

Svetlana Ugarcina Perovic (10:15:39): > Here is a list of ongoing 2nd curations:https://github.com/waldronlab/BugSigDBcuration/issues/667https://github.com/waldronlab/BugSigDBcuration/issues/659https://github.com/waldronlab/BugSigDBcuration/issues/658https://github.com/waldronlab/BugSigDBcuration/issues/657https://github.com/waldronlab/BugSigDBcuration/issues/648https://github.com/waldronlab/BugSigDBcuration/issues/644https://github.com/waldronlab/BugSigDBcuration/issues/642https://github.com/waldronlab/BugSigDBcuration/issues/640https://github.com/waldronlab/BugSigDBcuration/issues/626https://github.com/waldronlab/BugSigDBcuration/issues/609https://github.com/waldronlab/BugSigDBcuration/issues/577https://github.com/waldronlab/BugSigDBcuration/issues/547https://github.com/waldronlab/BugSigDBcuration/issues/364https://github.com/waldronlab/BugSigDBcuration/issues/668https://github.com/waldronlab/BugSigDBcuration/issues/673https://github.com/waldronlab/BugSigDBcuration/issues/653https://github.com/waldronlab/BugSigDBcuration/issues/677https://github.com/waldronlab/BugSigDBcuration/issues/680https://github.com/waldronlab/BugSigDBcuration/issues/674You could reach out to the original curator and offer your support. - File (JPEG): team building hands.jpg

Adeshile Oluwatosin (10:15:58) (in thread): > Noted, Thank you so much

Svetlana Ugarcina Perovic (10:17:36): > Reminder for our weekly team meeting:tomorrow at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your questions! > > cc<@UBNSEMS3S>NOTE: You can check your time here:https://www.timeanddate.com/worldclock/converter.html?iso=20250327T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Anne-Marie Sharp (10:18:24) (in thread): > Noted, will do

Mildred Anashie (10:21:50) (in thread): > Okay@Svetlana Ugarcina Perovic:blush:

Aiysha shahid (10:22:11) (in thread): > Dully Noted!:raised_hands:

Joy (10:29:28) (in thread): > Team work is unbeatable! Thanks@Svetlana Ugarcina Perovicfor putting this out here.:sparkles:

Aiysha shahid (10:53:28) (in thread): > Sure@Mildred Anashie, Thanks:raised_hands:

Mildred Anashie (11:01:35) (in thread): > Hi@Svetlana Ugarcina PerovicI’d like to know if it’s okay to reach out to more than one person at a time

Adeshile Oluwatosin (11:15:51) (in thread): > From what I read this morning, I guess I saw wilcoxon asthetest for alpha diversity not for differentiation abundance@Aiysha shahid

UBNSEMS3S (11:16:43) (in thread): > Hi–just to clarify prevalencecan mean abundance and if they compare different prevalences of bacteria across groups then that is a differential abundance analysis. The figure in this case, figure 3, does not present results from a statistical test to detect differential abundances between groups. They are presenting relative abundances with no statistical testing.

UBNSEMS3S (11:18:03) (in thread): > It’s an RCT.

Mildred Anashie (11:18:17) (in thread): > Great….Thank you<@UBNSEMS3S>for the clarification

UBNSEMS3S (11:20:08) (in thread): > If they said fusobacteria was sig. with a q of 0.06 then they almost certainly used a threshold of 0.1.

Adeshile Oluwatosin (11:21:08) (in thread): > Thank you so much for clarifying@C. Mirzayi (please do not tag this account)The study was curated with a threshold of 0.1. > I would submit for review now > I appreciate

Aiysha shahid (11:28:50) (in thread): > Yes, there is not a direct mention of the Wilcoxon for being used for differentital abudance,but that’s what I’m saying. In Fig-S1, it’s isn’t mentioned that what’s the statistical test has been used, From Fig-S2, Meta-stat was used,to identify the differentital abudance between the ranks. But when I searched on google- It’s say that “Wilcoxon Test are usually used to derive the results for Meta-stat”, extact text I have mentioned in my pervious message.@Adeshile Oluwatosin

Eseoghene Cynthia Princewill-Ukot (11:30:06) (in thread): > Okay@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (11:35:49) (in thread): > Please curate exactly what you seewhich is “Metastats”As metastats is curatable on bugsigdbas a statistical testfor Figure S1-S7

Joy (11:46:57) (in thread): > Thank you<@UBNSEMS3S>for this explanation!

Kate Rasheed (11:47:06) (in thread): > Thanks for clarifying this<@UBNSEMS3S>. I actually thought it was a Cross-sectional study design.

Aiysha shahid (12:09:34) (in thread): > Okay, I will edit the statistical test as “Metastats”, and also as this paper does not mention any changes in Alpha Diversity for Metastat, should I mark it as unchanged or leave it blank? I think so, leaving it blank,would works. What do you think@Adeshile Oluwatosin?

Adeshile Oluwatosin (12:15:42) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1742989158928969?thread_ts=1742988547.841519&channel=C04RATV9VCY&message_ts=1742989158.928969 - Attachment: Attachment > All alpha diversity in the article should be unchanged as there is no significant differences

Svetlana Ugarcina Perovic (13:07:18) (in thread): > @Mildred Anashieyes, it’s ok, if nobody already approached to the curator.

Juliana Kentomahun Mautin (13:10:09) (in thread): > Okay@Mildred Anashie. I look forward to your response:relaxed:

Svetlana Ugarcina Perovic (13:12:28) (in thread): > @Eseoghene Cynthia Princewill-Ukotok, I see that you found our suggestions for the next steps:wink:

Mildred Anashie (13:13:49) (in thread): > Noted@Svetlana Ugarcina PerovicThank you

Joy (13:14:23) (in thread): > Thank you<@UBNSEMS3S>and@Kate Rasheed.

nithya (13:24:24): > Hello members. I am nithya mathivanan > I am m.tech bioinformatics graduate. I worked as an assistant professor in the department of bioinformatics with 5+ years experience in India. I have lectured subjects like biostatistics, machine learning and gene expression analysis. I have used R and python for my data analysis research. I am very happy to be a part of BugSigDB and very eager to learn from my mentors.

Ameenat Oloko (13:29:20): > Hello, everyone.I’m Ameenat Oloko, from Nigeria.I am a new member of this community,and I look forward to contributing immensely to our projects. I am excited to learn from you all.

Juliana Kentomahun Mautin (13:30:34) (in thread): > Okay, I’m cleared on this. Thank you@Adeshile Oluwatosinand@Aiysha shahid

Juliana Kentomahun Mautin (13:33:13) (in thread): > Hello@nithyayou are welcome, we are excited to have you here:blush:. > > Kindly check out this message on to get startedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out the post which provides insightful tips on how to start your first curationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Juliana Kentomahun Mautin (13:35:02) (in thread): > Hello@Ameenat Olokoare welcome, we are excited to have you here:blush:. > > Kindly check out this message to help you get started.https://community-bioc.slack.com/archives/C04RATV9VCY/p1742198168683169?thread_ts=1742198168.683169&cid=C04RATV9VCY. > > You can also check out the post which provides insightful tips on how to start your first curation .https://community-bioc.slack.com/archives/C04RATV9VCY/p1727830699572609?thread_ts=1727830699.572609&cid=C04RATV9VCY - Attachment: Attachment > :tulip: Welcome to the Outreachy contribution period! > To get started, please check out our GitHub issue for instructions: https://github.com/waldronlab/BugSigDBcuration/issues/94 > > If you have any questions, feel free to post them in this channel. This way, all applicants can benefit from the discussion. > Feel free to introduce yourself in the comment below and thank you for joining this project. > > We’re looking forward to working with you! > Your mentors: @U1LCB8WEA @UBNSEMS3S @Esther Afuape @Chioma Onyido @Peace Sandy @Scholastica Urua @Kate Rasheed @Aleru Divine and @Svetlana Ugarcina Perovic > > Tip: New to contributing? Watch this helpful video on getting started with open source contributions: https://www.linkedin.com/posts/xlindata_opensourcecontribution-internship-paidinternship-ugcPost-7246192197857857536-VI-w - Attachment: Attachment > Quick Tip for the First Contribution: > > Here’s how I approached my first contribution, which you might find helpful: > > 1. Understand the Goal: Please read the instructions carefully. The aim of this task is to familiarize yourself with a microbiome research paper and extract key details to answer the questions. > 2. Review the Questions: I started by going through the questions on the form (quiz) to get an idea of what to expect. > 3. Read the Paper Thoroughly: Then I carefully read the entire paper, noting the annotated parts, as they are very important. > 4. Return to the Quiz Form: Once I was familiar with the content, I went back to the quiz form (now very familiar with the terms I had earlier seen) > This approach made it easier for me to find the relevant information for each question. > I hope this helps somebody!:sparkles: > > If/when you’re stuck, don’t hesitate to ask questions. You can try to figure it out on your own but this is open source, and the community is here to support you. > > Cheers!:clinking_glasses:

Juliana Kentomahun Mautin (13:39:16) (in thread): > If you need further clarification, please do not hesitate to reach out, we are all here to collaborate with you and help out. Cheers an impactful contributions@Ameenat Oloko

Juliana Kentomahun Mautin (13:41:09) (in thread): > If you need further clarification, please do not hesitate to reach out, we are all here to collaborate with you and help you. Cheers an impactful contributions@nithya

nithya (13:41:28) (in thread): > Definitely

Anne-Marie Sharp (13:43:13) (in thread): > Hello@nithyayou are welcome

Anne-Marie Sharp (13:44:11) (in thread): > Hello@Ameenat Olokoyou are welcome, looking forward to collaborating

Mildred Anashie (13:49:41) (in thread): > Hi@Adeshile OluwatosinThe alpha diversity isn’t unchanged from what I see

Mildred Anashie (13:50:28) (in thread): > Check Fig 3

Adeshile Oluwatosin (13:52:22) (in thread): > True, I just saw this > > “The Wilcoxon rank sum test suggested that the values of Chao, Observed, ACE, and Shannon in the healthy group were significantly increased compared to the AECOPD patients (all P<0.05). However, the Simpson’s diversity index and coverage values were increased in patients with AECOPD. The results indicated that the richness and diversity of gut microbiota decrease during acute episodes of COPD (Fig 3)”

Mildred Anashie (13:52:49) (in thread): > @Aiysha shahidThe statistical test should be Metastats as@Adeshile Oluwatosinhas pointed out

Adeshile Oluwatosin (13:52:58) (in thread): > Welcome@Ameenat Oloko

Adeshile Oluwatosin (13:53:13) (in thread): > Welcome@nithya

Oriade Adeola (14:01:14): > Welcome@Ameenat Oloko

Mildred Anashie (14:03:04) (in thread): > Hi@Juliana Kentomahun MautinI’ve looked through this and I think we should bring it up during office hours tomorrow:pensive:

Adeshile Oluwatosin (14:03:37) (in thread): > @Aiysha shahidPlease curatechao1, observedand aceis richness,Shannon as decreased.

Adeshile Oluwatosin (14:04:16) (in thread): > And Simpson increased.Please ignorethe initialstatemenr

Joy (14:06:56) (in thread): > Well come to the community@nithya:sparkles:

Ameenat Oloko (14:07:17) (in thread): > Thank you. I’d check them out.

Joy (14:07:58) (in thread): > Welcome to the community@Ameenat Oloko:sparkles:

Eseoghene Cynthia Princewill-Ukot (14:10:37) (in thread): > Welcome@nithya

Eseoghene Cynthia Princewill-Ukot (14:11:47) (in thread): > Welcome@Ameenat Oloko. Happy curating!

Mildred Anashie (15:06:35) (in thread): > Welcome@Ameenat Oloko:blush:Happy BugSigdb-ing

Mildred Anashie (15:07:20) (in thread): > Hi@nithyaWelcome to the community:blush:

Joy (15:28:14): > Is it just me, I have been unable to access the Taxonomy browser for some hours now. Any body experiencing this as well?

Francisca Gundu (15:47:16) (in thread): > Yes, I can’t access it at my end too.

Anne-Marie Sharp (15:48:04) (in thread): > Hello@JoyIt normally would come up soon. You can try other alternatives like Uniprot

Anne-Marie Sharp (15:48:37) (in thread): > That’sifit’sNCBI you are referring to

Joy (16:00:54) (in thread): > Yes@Anne-Marie Sharpit’s NCBI I am referring to. I’ll try Uniprot then. Thanks

Anne-Marie Sharp (16:21:26) (in thread): > Hello@Victoria (Burah) Poromon@Adeshile Oluwatosinwell done with your curation. In Experiment1, you added Philippines as a location but I didn’t see it mentioned in the article. Kindly confirm.

Mildred Anashie (16:37:00) (in thread): > You can also change your browser@JoyI experienced it earlier in the day but switched devices and browsers and it worked

Anne-Marie Sharp (16:40:22) (in thread): > I observed that in Experiment2, Group 0 sample size wasn’t included and in Experiment3 Group1 name & sample size were not included. I’m not sure, is this the norm when they have been mentioned previously?

Mildred Anashie (16:44:57) (in thread): > Hi@Anne-Marie SharpThe sample sizes are recorded. And yesit’sa norm in BugSigdb to show just differences from previous experiments in subsequent experiments

Victoria (Burah) Poromon (16:45:06) (in thread): > Hi@Anne-Marie SharpThank you so much. Experiment 2 and 3 are duplicates. That’s why they appear like that, only the differences are showing. > > The sample sizes and group 1 names are all included.Filipinos are mentioned in the study.That’swhy we have Philippines

Anne-Marie Sharp (16:47:39) (in thread): > @Mildred Anashie@Victoria (Burah) PoromonOkay duly noted, thanks for clarifying.

Anne-Marie Sharp (16:48:11) (in thread): > @Victoria (Burah) PoromonWhat I saw was ‘De Filippis et al’ not filipinos

Victoria (Burah) Poromon (16:49:35) (in thread): > Okay, we’ll take a look at it again > Thanks for pointing it out@Anne-Marie Sharp

Mildred Anashie (16:54:11) (in thread): > Exactly@Anne-Marie SharpI also do not see Fillipino’s being mentioned. See this, “To do so, we capitalized onthree cohorts from the ZOE PREDICT programme from the United Kingdom(P1n= 1,062 individuals10,11, P3 UK22An= 12,353)and from the United States (P3 US22An= 7,931; Methods). Wefurther included two additional, publicly available cohorts comprising Italian participants(Tarallo et al. (2022)12n= 118 individuals and De Filippis et al. (2019)13n= 97 individuals; Fig.1a)”. No mention of Fillipino’s, Just De Fillippis. - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes. - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes. - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes. - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes. - Attachment (Nature): Gut microbiome signatures of vegan, vegetarian and omnivore diets and associated health outcomes across 21,561 individuals > Nature Microbiology - Using 21,561 individuals, the authors present a cross-sectional study of how gut microbiome signatures are associated with dietary intake patterns and with host health outcomes.

Juliana Kentomahun Mautin (16:55:11) (in thread): > Ok… Thank you

Anne-Marie Sharp (16:57:15) (in thread): > Yes:thumbsup:@Mildred Anashieit’san intext citation, mistook for a location

Joy (17:00:11) (in thread): > Ok, thanks@Mildred AnashieI’ll give that a try

Mildred Anashie (17:37:50) (in thread): > The significant threshold for Exp 3 should 0.1 not 0.01@Victoria (Burah) Poromon@Adeshile Oluwatosin…..I’m still looking through

isaac imitini (21:02:15) (in thread): > Welcome to the community@nithya:tulip:

isaac imitini (23:24:24): > Hello everyone I have just completed my curation for this studyGut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia - BugSigDBI would appreciate a peer review. Thank you:pray: - Attachment (BugSigDB): Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia - BugSigDB > Neonatal hypoxic-ischemic brain damage (HIBD) is considered as a major cause of long-term cognitive impairments in newborns.It has been demonstrated that gut microbiota is closely associated with the prognosis of various neurological disorders.

isaac imitini (23:28:16) (in thread): > Please I would also appreciate if anyone can check if you can see signature 2 for the first experiment. I have refreshed and I can’t seem to see it. At first I thought I forgot to add it and did it again.

Precious Orakwe (23:42:31) (in thread): > Welcome@nithya

Precious Orakwe (23:52:07): > Good day@Svetlana Ugarcina Perovic@Aleru Divine@Kate Rasheed<@UBNSEMS3S>@Adeshile Oluwatosin@Mildred Anashieplease i have been trying to curate thiß study, i can’t really figure out our many experiment are in the study, I was thinking it’s 4 but the differential abundance link is sending to Table S7, which i dont understand what it is all about, and Fig 7F, is it curatable and fig 5, if yes, i can’t find the names of taxa on uniprot. > > Please help me thank you.Https://pubmed.ncbi.nlm.nih.gov/35987213/ - Attachment (PubMed): Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance - PubMed > Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses. We causally assessed NNS impacts in humans and their microbiomes in a randomized-controlled trial en …

2025-03-27

Anne-Marie Sharp (01:48:47) (in thread): > Hello@isaac imitiniwell done with your curation. We’ll review it:+1:I alsocan’tsee Signature2 for Experiment1

Anne-Marie Sharp (01:52:29) (in thread): > I searched manually and saw it. Butit’snot yet reflecting normally. - File (JPEG): IMG_0052

Anne-Marie Sharp (02:29:35) (in thread): > 1) I have a suggestion, In Experiment1, you can use the actual group names used in the article which are Sham & HI > 2) I think figure 2g is also curatable > 3) In Experiment1, Signature2, you can as well specify the source as you did in Signature1, which are Fig.2n & 2o > 4) There was no antibiotics exclusion; they were in fact, included.5) In Experiment 2, Signature1 should be increased abundance & Signature2 should be decreased abundance

Mildred Anashie (02:34:07) (in thread): > Hi@isaac imitiniWell done….I’ll have a look

Adeshile Oluwatosin (03:27:03) (in thread): > Well done:tulip:I’llhave a look

Adeshile Oluwatosin (03:28:04) (in thread): > Good morning@Precious OrakweI’llhave a look

Mildred Anashie (03:28:07) (in thread): > Hi@Precious OrakweI’m looking through, there’s differential abundance in Table S7 and I see two experiments there’s a sheet that saysBottom vs Top Bacteria Day 21andBottom vs Top Bacteria Baseline. Those sheets are curatable and you’d focus on the p-value less than 0.05 and the Log fold change would tell you increase and decrease. > See this for group definition“In total, we transplanted microbiomes from 42 individuals, the four individuals in each group that had the most potent response (“top responders”), and the three that had the lowest response (“bottom responders”) in their respective groups”. > > I’m looking through to see the other four experiments you mentioned, but I doubt Figure S5 is curatable. Figure S3 E, F, G and HI’mthinking is curatable but not sure how it would be

Mildred Anashie (03:40:57) (in thread): > I think every other thing looks okay. I can’t pinpoint anything else, Well done@Adeshile Oluwatosinand@Victoria (Burah) Poromon

Mildred Anashie (03:51:01) (in thread): > Hi@isaac imitiniYou’d have to request this is deleted, I’m still looking throughhttps://bugsigdb.org/40008452/Experiment_1/Signature_3 - Attachment (BugSigDB): 40008452/Experiment 1/Signature 3 > .

Victoria (Burah) Poromon (04:19:56) (in thread): > Thank you so much!@Mildred Anashie

Aiysha shahid (04:21:44) (in thread): > Welcome@nithya:tulip:

Mildred Anashie (04:25:18) (in thread): > 1. You would curate fig 2i and j separately, it’s LEfSe > 2. The statistical test for Fig 2G, K, L, M and O shouldn’t be lefse, I believe it’s t-test. > 3. The MHT for Lefse should be No, It wasn’t stated that MHT was done for LEfSe. > 4. I agree, No Antibiotic exclusion and group name should be changed too > 5. You should have two experiments from Figure S3a and b and the sample size is 8 per group not 13. Still trying to find more info on the figurebased on statistics and sequencing

isaac imitini (04:32:01) (in thread): > Yes for signature 2@Anne-Marie SharpI was trying to do that and I couldn’t seem to see signature 2 for experiment one. Thank you for all feedbacks I’ll implement that. Also please how are you able to search manually? Still unable to see signature 2

Aiysha shahid (04:32:06) (in thread): > Hi@Adeshile OluwatosinThat’s what I have earlier,curated but as per your review, I had removed it and gave it for the offical review.:smiling_face_with_tear:

isaac imitini (04:32:28) (in thread): > Thank you@Mildred Anashie@Adeshile Oluwatosin

Mildred Anashie (04:43:50) (in thread): > @isaac imitiniuse this formathttps://bugsigdb.org/40008452/Experiment_1/Signature_3You can replace 3 with 2 if you want to see signature 2 and replace 1 to 3 if you want to see let’s say experiment 3 signature 2

isaac imitini (04:47:26) (in thread): > @Mildred Anashiefor figure S3a and b are you referring to curating FMT as the second experiment?

Eseoghene Cynthia Princewill-Ukot (04:47:44) (in thread): > Hi@Precious OrakweHow about using NCBI Taxonomy to check for the names of taxa

Anne-Marie Sharp (04:48:42) (in thread): > Okay@isaac imitinito search manually, > 1) I copied and pasted your curation link:https://bugsigdb.org/400084522)then I first added /Experiment_1 to the end:point_right:https://bugsigdb.org/40008452/Experiment_13)next I added the signature I wanted to see which is /Signature_2:point_right:https://bugsigdb.org/40008452/Experiment_1/Signature_2And it opened - Attachment (BugSigDB): Gut microbial dysbiosis exacerbates long-term cognitive impairments by promoting intestinal dysfunction and neuroinflammation following neonatal hypoxia-ischemia - BugSigDB > Neonatal hypoxic-ischemic brain damage (HIBD) is considered as a major cause of long-term cognitive impairments in newborns.It has been demonstrated that gut microbiota is closely associated with the prognosis of various neurological disorders. - Attachment (BugSigDB): 40008452/Experiment 1 > . - Attachment (BugSigDB): 40008452/Experiment 1/Signature 2 > Source: Figure 2 Description: Taxonomic differences in gut microbiota between rats without hypoxic-ischemic (HI) insult and those post-HI insult. Abundance in Group…

Mildred Anashie (04:49:31) (in thread): > NoThere’ssham vs HI and HI vs HI+DEX@isaac imitini

isaac imitini (04:54:12) (in thread): > Okay thank you@Mildred Anashie@Anne-Marie SharpI will wait for any other feedbacks and implement all at the same time.

Mildred Anashie (04:55:41) (in thread): > Yeathat’sa good idea@isaac imitiniHopefully someone can find info on the statistical test and others

isaac imitini (04:56:05) (in thread): > Thank you

Anne-Marie Sharp (05:10:21) (in thread): > Hello@Precious Orakwewell done with your curation. We will look through with you:+1:

Anne-Marie Sharp (05:11:08) (in thread): > 1)Figure 7f is not curatable. It doesn’t contain microbesbut pathways

Adeshile Oluwatosin (05:33:34) (in thread): > Figure 5 is not curatable > Figure 7F is not curatable > I don’t see Table S3 curatable as they all don’t show me significantly different taxa between groups. > In Figure S3F -H,:thinking_face:Table S7 seems curatable

Adeshile Oluwatosin (05:34:41) (in thread): > The text reflected the significance > Apologies for the confusion

Oriade Adeola (05:42:21): > Good morning@Kate Rasheed@Aleru Divineplease what do i do next after i have made correction given in my peer review? thank you.

Aiysha shahid (05:50:11) (in thread): > Hi@Oriade Adeola, once you have applied the changes to your curation based on the peer review, please submit it for the official review by attaching the link to your study on GitHub and tag Svetlana.

Precious Orakwe (06:27:52) (in thread): > Thank you everyone for your kind assistance, i will go with@Mildred Anashieidea because I have seen the supplementary material for Table S7, i was looking for it initially, but I can see it now. Thanks

Precious Orakwe (08:22:36): > @Mildred Anashie@Adeshile Oluwatosinthe file to table S7 - File (PDF): mmc7 (2).pdf

UBNSEMS3S (08:44:23) (in thread): > It’s up for me now but yeah it can go down at times unfortunately.

Mildred Anashie (08:55:24) (in thread): > Hi@Precious OrakweDo you have a specific question on this?

Adeshile Oluwatosin (08:56:30) (in thread): > Hello@Precious Orakwe

Precious Orakwe (08:57:11) (in thread): > yes, the sheet to curate as my signatures, there are more than 9 sheets that has taxas on it, so i dont know which one to use

Kate Rasheed (09:02:26): > Office hour is onhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742998656752499 - Attachment: Attachment > Reminder for our weekly team meeting: tomorrow at 9 AM EST at https://us02web.zoom.us/j/2737200499 > > Bring your questions! > > cc @UBNSEMS3S > > NOTE: You can check your time here: https://www.timeanddate.com/worldclock/converter.html?iso=20250327T130000&p1=179&p2=37&p3=176&p4=3395&p5=125

Adeshile Oluwatosin (09:04:07) (in thread): > Can I kindly look at this after the meeting:pleading_face:

Adeshile Oluwatosin (09:04:15) (in thread): > Thank you mentor

Oriade Adeola (09:06:11) (in thread): > please its asking me to launch meeting

Ndukauba Oluchi (09:07:11): > i’m not in yet

Kate Rasheed (09:08:31) (in thread): > Yes, launch meeting@Oriade Adeola

Mildred Anashie (09:08:56) (in thread): > Please open with Excel so you can clearly see the spreadsheet

Oriade Adeola (09:10:31) (in thread): > its still not going

Oriade Adeola (09:18:05): > As the meeting started? i cant join

Mildred Anashie (09:19:17) (in thread): > Yes it has

Oriade Adeola (09:19:18) (in thread): > ok thank you so much

Oriade Adeola (09:20:15) (in thread): > please can you send me the link?

Mildred Anashie (09:21:04) (in thread): > https://us02web.zoom.us/j/2737200499

Oriade Adeola (09:23:08) (in thread): > its still not going

Oriade Adeola (09:30:59) (in thread): > see what its showing - File (PNG): Screenshot 2025-03-27 at 2.29.35 PM.png

Mildred Anashie (09:35:15) (in thread): > Okay > > You are in the waiting roomI’vebeen logged out too > > In the waiting room too@Kate Rasheedcould you please inform Chloe about it > Thank you

Mildred Anashie (09:38:14) (in thread): > Are you in now@Oriade AdeolaI’mback in

Oriade Adeola (09:38:43) (in thread): > yes i’m in. thank you

Montana-D (09:45:51) (in thread): > Please I’m not

Anne-Marie Sharp (09:46:49) (in thread): > Please@Kate RasheedI’m also waiting to be let in.Thank you:pray:in now

Mildred Anashie (10:08:13): > Thank you<@UBNSEMS3S>for todays office hour

Adeshile Oluwatosin (10:08:43): > @C. Mirzayi (please do not tag this account)you are amazing, thank you for today

Juliana Kentomahun Mautin (10:09:47): > Thank you so much<@UBNSEMS3S>for today’s office hour and taking out time to answer my question. I look forward to the next office hour:grinning:.

Utibe Ita (10:10:30): > Thank you so much for today’s office hour@C. Mirzayi (please do not tag this account)

Ameenat Oloko (10:12:18): > Thank you fortoday’soffice hour,@C. Mirzayi (please do not tag this account).

Precious Orakwe (10:13:27): > Thank you@C. Mirzayi (please do not tag this account)for the help today and for the office hour.

Anne-Marie Sharp (10:18:14): > Thank you for your guidance@C. Mirzayi (please do not tag this account),today’soffice hour was helpful.

UBNSEMS3S (10:58:58): > Office hours recording. Thank you everyone who joined. You certainly asked some tough questions today. - File (MPEG 4 Video): bsdb_2025_03_27.mp4

Juliana Kentomahun Mautin (11:11:29) (in thread): > Thank you<@UBNSEMS3S>

UBNSEMS3S (11:32:31): > Just noting here that I wrote the authors of this paper:https://www.mdpi.com/2072-6643/17/3/458“Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition” asking them to clarify their analyses. Reaching out to authors is something we should only do as a last resort–the research report should ideally stand on its own–and when I do so I’m always exceedingly polite. I do not accuse the authors of poor writing, or even imply that they did, I phrase my questions as an engaged scholar interested in learning more. Writing papers can be very difficult especially on complex subjects like the microbiome and it’s easy for ambiguities and mistakes to slip in and we don’t want them to feel like we’re attacking their writing quality.

Kate Rasheed (11:36:13) (in thread): > Thanks for this<@UBNSEMS3S>. I’ll be looking forward to their response > > Cc@Taofeecoh Adesanu

Mildred Anashie (11:41:37) (in thread): > Thank you:blush:<@UBNSEMS3S>

Adeshile Oluwatosin (13:57:54) (in thread): > Thank you<@UBNSEMS3S>

Taofeecoh Adesanu (14:54:53) (in thread): > Thank you<@UBNSEMS3S>and@Kate Rasheed

Halima Momoh (16:45:29): > Hello everyone, > I’m currently working on curatingthis paperand would really appreciate any assistance. If anyone has experience with similar curations, your insights would be invaluable . > Additionally, I have made some corrections tothis paperand would love a second pair of eyes before final submission. If you have a moment to review and provide feedback, it would be greatly appreciated. > Thank you in advance for your support:pray::hugging_face: - Attachment (PubMed): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features - PubMed > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. To explore how these structural differences impact constipation intervention, a 14-day study was conducted on loperamide-induced constipated mice using five dietary fibers: soluble dietary … - Attachment (BugSigDB): Gastrointestinal Characteristics of Constipation from the Perspectives of Microbiome and Metabolome - BugSigDB > BACKGROUND: Constipation is one of the most common gastrointestinal complaints.Yet, the underlying mechanisms of constipation remain to be explored deeply.Integration of microbiome and metabolome is powerful and promising to demonstrate characteristics of constipation.

Mildred Anashie (18:45:41) (in thread): > Hi@Aiysha shahidTwo links were dropped with two questions

Mildred Anashie (18:45:57) (in thread): > I’ll take a look at this@Halima Momoh

Aiysha shahid (18:50:32) (in thread): > Yeah, got it!, it got little bit mixed up.:sweat_smile:

Aiysha shahid (19:02:20) (in thread): > Hi@Halima Momoh, > I’ll also go through it. > Meanwhile, just from an oversight of your sheet, here are my observations: > 1. ForOscillospira, you can enter the Taxonomy ID as119852. > 2. Actinobacteriacan be curated asActinomycetota, Taxonomy ID:201174.

nithya (22:48:41): > hi i requested to create an account in bugsigdb. i have not recieved any reply yet.

2025-03-28

Eseoghene Cynthia Princewill-Ukot (00:50:32) (in thread): > Hi@nithya. You can tag@Svetlana Ugarcina Perovicto this post.

Anne-Marie Sharp (01:52:00) (in thread): > Hello@nithyacheck your spam/junk folder, the email may be there. Ifit’snot thenyou’llsurely get it soon.

Anne-Marie Sharp (01:56:49) (in thread): > Hello@Halima Momohwell done with your curations. A quick observation: > 1) In the 2nd link you posted, the Group1 definition can be more concise and shorter eg Male rats diagnosed with constipation based on certain criteria2) It will help if you can share the link for the full article in that 2nd link.

Adeshile Oluwatosin (01:59:37) (in thread): > Hi@Halima MomohI see just figure 4 curatable for the first study. > > Second study; In signature 2 > Oscillospira: Add taxa ID 119852 > Add Lachnospiraceae: 186703 > Add Veillonellaceae : 31977 > > Signature 1: > Actinobacteria: 201174 > TM7 is saccharibacteria: 95818 > CW040 : 163601 > Add peptstreptococcacea clostridium > > Remove Veillonellaceae and Lachnospiraceae from signature 1. Well done

Precious Orakwe (02:03:31): > Good day@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)after curating my study, my signatures are not coming up, I have tried to refresh the site and I have also logged out and logged in again, but it’s still the same, please can you do something about this. Thank you.

Anne-Marie Sharp (02:11:57) (in thread): > Hello@Precious Orakwesorry about that. Since you’ve already refreshed. Try entering the signature manually:https://community-bioc.slack.com/archives/C04RATV9VCY/p1743065322243339?thread_ts=1743045864.439119&channel=C04RATV9VCY&message_ts=1743065322.243339 - Attachment: Attachment > Okay @isaac imitini to search manually, > 1) I copied and pasted your curation link: https://bugsigdb.org/40008452 > 2)then I first added /Experiment_1 to the end :point_right::skin-tone-5: https://bugsigdb.org/40008452/Experiment_1 > 3)next I added the signature I wanted to see which is /Signature_2 :point_right::skin-tone-5: https://bugsigdb.org/40008452/Experiment_1/Signature_2 > And it opened

Mildred Anashie (02:23:15) (in thread): > Hi@Precious OrakweThere’sa trick I noticed that usually work. Try to edit each experiment by changing complete to incomplete and back to complete, they usually populate from my end once I do that > > You can trylet’ssee if it works

Svetlana Ugarcina Perovic (02:44:42) (in thread): > @Precious Orakwedid the “trick” worked for you? How did you sorted out your issue? Hope all is good now.

Svetlana Ugarcina Perovic (02:45:52) (in thread): > @nithyaI do not see any pending requests. Have you managed to get your access? If yes, what was the issue and how did you sort it out?

Svetlana Ugarcina Perovic (02:57:57): > Good morning, how are you today?:coffee:OR:teapot:?What did you grasp from the first two weeks of BugSigDB-ing during Outreachy contribution?

Adeshile Oluwatosin (03:00:21) (in thread): > Good morning mentor > > From the first two weeks > I’m learning to be more patient, basically read, re-read and read again. The importance of collaborating with others as this enforces learning from each other andI’vehad the opportunity to learn from the articles I’ve curated.

Anne-Marie Sharp (03:05:04) (in thread): > Good morning@Svetlana Ugarcina Perovic,I’mgood, hope you are. Definitely tea:blush:.I’velearned to communicate better.Ive learned that effective team work really makes the dream workI’velearned that I learn faster from helping others.I’velearned to be patient with others & especially with myself as I navigate this new endeavor.

Joy (03:07:23) (in thread): > Good morning@Svetlana Ugarcina Perovicfor the two weeks of BugSigDB-ing during Outreachy contribution, I grasped thatTeam workis Key!

Ndukauba Oluchi (03:07:32) (in thread): > Goodmorning@Svetlana Ugarcina Perovici’ve learnt to be patient and kind in communication. > i’ve learnt that Attention to detail is a great skill and not having it can cost you alot.

Mildred Anashie (03:33:45) (in thread): > Good morning@Svetlana Ugarcina Perovic:coffee:today > > The first two weeks of contributions have been truly rewarding. > During this time, I’ve learnt the importance of asking questions,the need to collaborate and seek opinions from others,most importantlylearning, unlearning and relearning and the ability to accept positive feedbackis a key part of growth. > > Thank you to our mentors, co-mentors and fellow contributors for the experience so far:heart_hands:

iniobong simeon (03:44:39) (in thread): > Good morning@Svetlana Ugarcina Perovicfor the two weeks of BugSigDB-ing during Outreachy contribution I have learnt that; > Balancing clarity with brevity in communication—sometimes over-explaining ideas to ensure understanding, while other times struggling to simplify complex thoughts. > Navigating differing work styles in teamwork. Adapting to others’ approaches . > Self-criticism during setbacks. When mistakes happened, I had to remind myself that patience with others starts with patience toward myself. > > These hurdles taught me that growth often lives in the tension between effort and self-compassion.

Eseoghene Cynthia Princewill-Ukot (04:32:26) (in thread): > Good morning@Svetlana Ugarcina PerovicI’m doing well, thank you. Definitely:coffee:! > From the first two weeks of BugSigDB-ing during my Outreachy contribution > 1. I learned how BugSigDB is organized and why it’s useful for keeping track of how microbes and diseases are connected. > 2. I got to see how data is carefully taken from research papers and made ready for the database. > 3. I understood why using standard terms is important so everyone understands the data the same way. > 4. I saw how everyone works together on the project and how important it is to talk clearly.

Montana-D (05:36:14) (in thread): > Good morning Mentor. I’m doing okay. Hope you too?:teapot:The past two weeks at BugSigDB, - Tho I’m barely a week in, have been incredibly insightful, marked by both mind tiring challenges and significant learning. > > I came to understand the critical role of patience in data curation, a lesson learned through my initial tendency to rush with the intent of catching up with the others, which ultimately hindered accuracy and understanding. This experience highlighted the importance of careful, methodical reading. > > I also gained confidence in seeking help and collaborating with my colleagues; the only way I could move ahead:sweat_smile:, fostering a supportive and productive environment/experience. > I’ve found the curation work itself to be genuinely engaging, as it allows me to explore the nuances of various diseases in a way that transcends my prior clinical knowledge. This experience has been both educational and enjoyable, reinforcing the value of kindness and thoroughness in data analysis not forgetting collaboration.

Precious Orakwe (06:12:50) (in thread): > Good morning@Svetlana Ugarcina Perovicthe first two weeks of BugSigDB-ing have been amazing, I have learnt that, I can’t always do it alone, collaboration and patience is a key to successfully achieving your goal. > > When I was curating my studies, I always got stucked, and i realised that when ever I bring my case to the group, solution always comes up. > > I’m grateful to be here and for the opportunity to meet amazing people here, our mentors and my teammates. > > Thank you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Chioma Onyido@Kate Rasheed@Aleru Divine@Scholastica Urua@Adeshile Oluwatosin@Mildred Anashieand @Everyone for your kind assistance and patience.

Joy (06:28:21): > Good morning <@UBNSEMS3S>****, ****@Svetlana Ugarcina Perovic****, ****I would like to confirm the curatable nature ofFig. 1C and Fig. 2Ain this study? Let me know what you think. Thankshttps://journals.asm.org/doi/10.1128/spectrum.02559-24

Precious Orakwe (06:31:38) (in thread): > Yes@Svetlana Ugarcina Perovicit worked, thanks@Mildred Anashiefor this awesome idea.

Adeshile Oluwatosin (06:45:19) (in thread): > Hi@JoyI think Chloe explained curation of figures similar yesterday at the office hour

Adeshile Oluwatosin (06:45:26) (in thread): > You can rewatch the video

nithya (06:46:55) (in thread): > Hi@Svetlanamam. I request to create an account. I did not get any mail. I’ll do it again.

Joy (06:52:27) (in thread): > Sure@Adeshile Oluwatosin

Mildred Anashie (06:54:18) (in thread): > That’sgreat@Precious Orakwe:blush:

Adeshile Oluwatosin (07:39:06): > Hello everyone > Kindly give a review to this > Thank youhttps://bugsigdb.org/39694919https://pmc.ncbi.nlm.nih.gov/articles/PMC11660412/

nithya (08:01:30) (in thread): > Thank you Cynthia! Yes it’s in my spam folder.

Anne-Marie Sharp (08:03:19) (in thread): > Hello@Adeshile Oluwatosinwe’lldo that:raised_hands:

Svetlana Ugarcina Perovic (08:04:21) (in thread): > Thanks for your kind words! We are happy that you have been enjoying BugSigDB-ing. > > Feel free to share you experience on your preferable social media. You can share link here. Thanks!

nithya (08:06:14) (in thread): > Thanks anne

Precious Orakwe (08:07:05) (in thread): > Well done@Adeshile Oluwatosin

Anne-Marie Sharp (08:07:08) (in thread): > Hello@JoyI believe they are curatable. As@Adeshile Oluwatosinsuggested,you can rewatch the video to guide you better.

Adeshile Oluwatosin (08:07:54) (in thread): > Thank you

Anne-Marie Sharp (08:08:12) (in thread): > @nithyagreat!You’rewelcome

Svetlana Ugarcina Perovic (08:10:45) (in thread): > By the way, which social media platform you have been using? > I am active on X, Bluesky and LinkedIn.

Precious Orakwe (08:11:17) (in thread): > @Adeshile OluwatosinExp. 3 fig 8C and D, replace Hyphopichia with 507510, Exp. 4 has no signature.

Ndukauba Oluchi (08:11:40) (in thread): > @Svetlana Ugarcina PerovicI am very active on X and Linkedin

Adeshile Oluwatosin (08:12:03) (in thread): > I am active on LinkedIn, Twitter, Instagram, Facebook and Snapchat. Very active on LinkedIn and Instagram

Svetlana Ugarcina Perovic (08:14:04) (in thread): > Ok ok, I will follow you immediately:eyes:if not already connected there.

Anne-Marie Sharp (08:14:16) (in thread): > Iam moderately active on LinkedIn

Eseoghene Cynthia Princewill-Ukot (08:15:06) (in thread): > @Svetlana Ugarcina PerovicI’m active on LinkedIn and X

Mildred Anashie (08:15:40) (in thread): > I’vebeen trying to navigate LinkedIn and slowly becoming active there@Svetlana Ugarcina Perovic

Mildred Anashie (08:16:18) (in thread): > Hi@Adeshile OluwatosinI’lltake a look at this?

Precious Orakwe (08:16:53) (in thread): > I am a little bit active on LinkedIn and X, I am not a social media person. I don’t post, I just go there to see what is happening around the world. > > In summary, I will say I am an introvert.

Adeshile Oluwatosin (08:17:07) (in thread): > @Precious Orakwegracias! It justdidn’tpop up on my end. > Also, here you gohttps://bugsigdb.org/39694919/Experiment_4/Signature_1 - Attachment (BugSigDB): 39694919/Experiment 4/Signature 1 > Source: Figure 8e Description: The significance analysis of the fungi in the RA and RC groups of HMA-T2D mice Abundance in Group 1: decreased abundance in CC treatment…

Adeshile Oluwatosin (08:17:17) (in thread): > Thank you@Mildred Anashie

Ndukauba Oluchi (08:32:20): > Hello everyone, i have a question please. > when curating a paper and the study is trying to compare and confirm an analysis that was carried out with an animal model to humans, what could be the study design of such paper?

Adeshile Oluwatosin (08:33:21) (in thread): > Chloe confirmed as randomized controlled trial yesterday for a similar study

Ndukauba Oluchi (08:33:53) (in thread): > hmm, I thought so.

Mildred Anashie (08:41:41) (in thread): > The question is not so clear@Ndukauba OluchiAnd most things could be specific to an article based on what they did. > > For context maybe you should share a link to the study

Ndukauba Oluchi (08:42:41) (in thread): > okay@Mildred Anashiehttps://www.tandfonline.com/doi/full/10.1080/19490976.2025.2465896#d1e1465

Adeshile Oluwatosin (08:42:53) (in thread): > I was about to say it was specific to the article

Ndukauba Oluchi (08:44:41) (in thread): > Okay here is an example > > a study is trying to analyse the effect of high protein diet on the gut microbiota. now they carry out the experiment using mice and got their results. > Afterwards, they want to confirm if what they experimented using mice will give them the same results when human are used (clinical trial) > > my question is , what should be the study design?

Anne-Marie Sharp (08:48:23) (in thread): > @Ndukauba Oluchiit should still be RCT

Mildred Anashie (08:57:31) (in thread): > From their methods here it looks like an RCT, I agree with@Adeshile Oluwatosinand@Anne-Marie SharpThe differential abundance results was mainly from the human model experiment

Utibe Ita (09:03:59) (in thread): > Good day@Svetlana Ugarcina PerovicThese two weeks have been an eye opener for me and I have been privileged to; > * Learn how to handle micro biome data > * Learn how to pay close attention to details because the articles involve reading in-between the lines and re-reading all over again to make sure the important data have been extracted. > * I have also been able to learn the basic principles of data curation > * I have learnt from your constant reminder about quality over quantity when it comes to curations. > * I have also learnt the power of Collaboration because strong communication skills is essential.

Victoria (Burah) Poromon (09:34:31) (in thread): > Hi@Svetlana Ugarcina PerovicDefinitely tea!:teapot:As with everything that is being nurtured intentionally,I’llsay my communication has gotten better. My tone is more confident. > > From the first two weeks,I’munderstanding more how important effective communication is, and thatit’sokay to take your time.

Ndukauba Oluchi (09:35:20) (in thread): > Alright, Thank you all

Utibe Ita (09:57:48): > Hello everyone > > Can you help me go through my studyhttps://bugsigdb.org/37593638I noticed that the experiment 3 and 4 that I created using figure 3a and b is not showing on my study > However it is showing under my contributions that it had been created as seen below - Attachment (BugSigDB): Oral and gut microbial biomarkers of susceptibility to respiratory tract infection in adults: A feasibility study - BugSigDB > We conducted a feasibility cohort study which aimed to recruit and retain adults from the community to collect saliva (oral) and stool (gut) samples at three time points, at the start of the study (baseline), during a respiratory tract infection (RTI) and post-RTI. - File (JPEG): IMG_8984

Anne-Marie Sharp (10:03:50) (in thread): > Hello@Utibe Itayou can try@Mildred Anashie’s trick:wink::point_right:https://community-bioc.slack.com/archives/C04RATV9VCY/p1743142995545179?thread_ts=1743141811.916219&channel=C04RATV9VCY&message_ts=1743142995.545179 - Attachment: Attachment > Hi @Precious Orakwe > There’s a trick I noticed that usually work. Try to edit each experiment by changing complete to incomplete and back to complete, they usually populate from my end once I do that > > You can try let’s see if it works

Joy (10:09:42) (in thread): > @Svetlana Ugarcina PerovicI am active LinkedIn, X and Facebook.

Anne-Marie Sharp (10:10:37) (in thread): > Synergistia sp.is on NCBI with Taxonomy ID: 1294150

Utibe Ita (10:12:01) (in thread): > Thank you@Anne-Marie Sharplet me try this out now

Utibe Ita (10:28:19) (in thread): > It worked perfectly well@Anne-Marie SharpThank you

Anne-Marie Sharp (10:36:03) (in thread): > @Utibe Itagreat.you’rewelcome

Ndukauba Oluchi (10:49:50): > Hey BugSigDBians:face_with_peeking_eye:please do we curate metabolomic data?

Adeshile Oluwatosin (10:52:21) (in thread): > We curate only significant differential abundance between two/ more groups or relative abundance between two or more groups

Ndukauba Oluchi (10:53:48) (in thread): > Okay. thank you@Adeshile Oluwatosin

Anne-Marie Sharp (10:53:49) (in thread): > Hello@Ndukauba Oluchifrom whatI’veobserved,no wedon’t

Precious Orakwe (10:54:56) (in thread): > No,BugSigDB does not curate metabolomic datadirectly. It focuses on microbiome signatures, which are associations between microbes and conditions.

Ndukauba Oluchi (11:04:25) (in thread): > please i need some help.

Ndukauba Oluchi (11:05:43) (in thread): > this study has 2 experiment, one for the animal model and one for the human model. > i cant seem to find the group 0 and group 1 sample size. > please have a look at this > link :https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2465896#d1e1465

Precious Orakwe (11:05:59): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovichttps://www.cell.com/cell/fulltext/S0092-8674(22)00919-9?_returnURL=https%3A%2F%2Fl[…]vier.com%2Fretrieve%2Fpii%2FS0092867422009199%3Fshowall%3DtrueI still don’t understand how to curate the signatures of this study, as the differential abundance is in Table S7, i don’t know the sheet to use for the signature. > > from this; > To further exemplify such personalized microbiome differences, we compared the fecal microbiome configurations of GF mouse groups transplanted with microbiomes of top (n = 3) and bottom (n = 3) human sucralose responders (n = 3,Figure 7A), in which each of the top human donors and none of the bottom donors exhibited a significant difference in glycemic response between baseline and day 21 of the clinical trial (Figure S5). GF mouse recipients of microbiomes from top sucralose human responders on day 21 featured a distinct microbiome configuration compared with GF mouse recipients of microbiome from bottom sucralose human responders on day 21 (Rcpt: D21, PERMANOVA with donor as random effect PC3 p = 0.008,Figure 7B), in line with the differential glycemic responses noted in the human donors at day 21 time point (Figure S5). Total 22 species and 19 pathways were differentially abundant between mouse recipients of microbiomes from top and bottom human sucralose responders on day 21, of which only two were also different at baseline (pyrimidine biosynthesis and tRNA charging,Table S7). The putrescine biosynthetic pathway was overrepresented in mice conventionalized with top responders’ day 21 samples (p < 0.0001); elevated plasma levels of putrescine were previously associated with type-2 diabetes (Fernandez-Garcia et al., 2019) and gestational diabetes (Liu et al., 2021). > > Notably, transplantation of baseline microbiomes of top and bottom sucralose responders into GF mice resulted in comparable glucose tolerance in recipient mice (Rcpt: BL,Figure 7C). Nonetheless, microbiome configurations of mice receiving baseline pre-exposure microbiomes from human top sucralose responders were already significantly different from those of recipients of baseline microbiomes from human bottom sucralose responders. Microbiome composition of mouse recipients of baseline samples of top and bottom human responders was significantly separated on PC3 (PERMANOVA with donor as random effect p = 0.008,Figure 7D), and function was separated on PC5 (p = 0.008,Figure 7E). The microbial features that potentially mediate these differences included 25 species and 27 pathways that are significantly (FDR-corrected linear-mixed model p < 0.05) differentially abundant between the two subsets (Table S7). Pathways related to menaquinol biosynthesis, previously associated with type 1 (Roth-Schulze et al., 2021) and type 2 diabetes (Balvers et al., 2021;Dash and Bataineh, 2021;Wu et al., 2020), were the most overrepresented features in mouse recipients of baseline microbiomes from top responders (p = 0.0006,Figure 7F). > > I chose these options from the sheet to be my signatures for the two experiments, but i don’t know how to go about curating the Bottom vs. top day 21 pathwayBottom vs. top day 21 pathwayBottom vs. top day 21 bacteria@Aleru Divine**** ****@Kate Rasheed**** ****@Mildred Anashie**** ****@Adeshile Oluwatosin**** ****@Anne-Marie Sharp**** can you please give me a hand here, Thank you.**** - File (Excel Spreadsheet): mmc7 (2).xlsx

Adeshile Oluwatosin (11:06:06) (in thread): > I’mstill waiting for a feedback guys:blush:

Ndukauba Oluchi (11:13:43) (in thread): > @Precious Orakweplease drop the link to this study

Precious Orakwe (11:15:50) (in thread): > updated@Ndukauba Oluchi

Mildred Anashie (11:17:34) (in thread): > Please curate only the sheets withBottom vs Top Day 21 bacteria and Bottom vs Top Baseline Bacteria. Don’t curate the pathway sheets > > The first experiment would beGroup 0 : Bottom responders at baseline and Group 1 : Top responders at baseline > > The second experiment would beGroup 0: Bottom Responders at Day 21 and Group 1: Top responders at day 21@Precious Orakwe

Precious Orakwe (11:20:15) (in thread): > ok, how do i go about the groups, like the group 0 and the group 1

Mildred Anashie (11:21:04) (in thread): > I mentioned it above@Precious Orakwe

Precious Orakwe (11:23:01) (in thread): > Yesterday during the weekly meet,@C. Mirzayi (please do not tag this account)said i should use the Top as the control and the Bottom as the Exposed

Adeshile Oluwatosin (11:24:11) (in thread): > Group 0 is the control > Group 1 is the case@Precious Orakwe

Mildred Anashie (11:24:16) (in thread): > Let me watch the office hours and get back to you…

Ndukauba Oluchi (11:26:01) (in thread): > @Precious Orakwesince it was mentioned yesterday, i think you should look for the recorded session, watch it again so you could get some inspiration on how to curate it

Adeshile Oluwatosin (11:36:09) (in thread): > I would also check the video again to give a better insight on this study’s curation

Anne-Marie Sharp (11:38:06) (in thread): > @Adeshile Oluwatosinwell done with your curation.It looks good to go:+1:

Adeshile Oluwatosin (11:41:37) (in thread): > I intentionally didn’t addIllumina and Antibiotics exclusioninExperiment 3 and 4.

Adeshile Oluwatosin (11:43:40) (in thread): > Did you see figure 8 alpha diversity?

Adeshile Oluwatosin (11:44:30) (in thread): > @Anne-Marie Sharp

Precious Orakwe (11:49:02) (in thread): > Alright thank you all

Precious Orakwe (11:51:12) (in thread): > @Adeshile Oluwatosinyea I saw experiment 8 I asked earlier why you didn’t put the signatures.

Mildred Anashie (11:58:14) (in thread): > Hi@Precious OrakweI’ve watched and yes Chloe said it should be curated as top = group 0 and bottom =group 1. > > But I’ve been going through the article and I saw this, “To further exemplify such personalized microbiome differences, we compared the fecal microbiome configurations of GF mouse groups transplanted with microbiomes of top (n = 3) and bottom (n = 3) human sucralose responders (n = 3, Figure 7A), in which******each of the top human donors and none of the bottom donors exhibited a significant difference in glycemic response between baseline and day 21 of the clinical trial (Figure S5)”.******I’m not sure if it meansanything but you have your group sample size from it. Please curate as<@UBNSEMS3S>advised

Adeshile Oluwatosin (11:59:47) (in thread): > There’sno experiment 8 in this study though

Precious Orakwe (12:00:33) (in thread): > Another thing, the signatures in the Bottom vs Top day 21 mice, should i curate everything there, because it’s too long ooo

Mildred Anashie (12:03:34) (in thread): > P values less than 0.05 onlyand I believe the first 22 only…. It’s also mentioned in the office hours recording@Precious Orakwe

Adeshile Oluwatosin (12:04:20) (in thread): > @Mildred Anashie:eyes:

Ndukauba Oluchi (12:25:20) (in thread): > Has anyone been able to check this out?

Anne-Marie Sharp (12:51:42) (in thread): > @Ndukauba OluchiI didn’tsee anywhere sample sizes were mentioned for the human model > And the sample sizes for the animal model were not explicitly mentioned

Anne-Marie Sharp (12:56:19) (in thread): > Hello@Precious Orakwesorry for the late response.I agree with@Mildred Anashie’s explanation,if its not clear to you, please still ask

Ndukauba Oluchi (13:06:18) (in thread): > I think for the animal models, they were 120 in total.@Taofeecoh Adesanuplease could you have a look at this?

Anne-Marie Sharp (13:06:50) (in thread): > @Ndukauba OluchiOn a 2nd thought, it can be calculated. Assuming your control isno antibiotics and your case is with antibiotics,it should be 60 each

Ndukauba Oluchi (13:07:30) (in thread): > is it for the human model or for the animal model?

Adeshile Oluwatosin (13:08:22) (in thread): > Ifit’snot stated in the paper, leave it blank > Don’t calculate

Anne-Marie Sharp (13:08:32) (in thread): > @Ndukauba OluchiFor the animal model

Ndukauba Oluchi (13:09:44) (in thread): > really? group 0 and group 1 Sample sizes?@Adeshile Oluwatosin

Adeshile Oluwatosin (13:13:25) (in thread): > Except in meta-analysis probably

Adeshile Oluwatosin (13:13:52) (in thread): > I just looked through the study, no mention of sample size

Anne-Marie Sharp (13:16:16) (in thread): > @Ndukauba Oluchiit wasn’t explicitly stated but it was explained in the methods. > The total sample size was stated as 120mice. > There are 3diet groups, each diet group has 20mice given Antibiotics/20 mice given No antibiotics > That’s 60mice with antibiotics for each of the 3diets > And 60mice without antibiotics for each of the 3diets. > But if we really are not to calculate, then you can omit it

Adeshile Oluwatosin (13:23:41) (in thread): > It could mean this though

Ndukauba Oluchi (13:24:48) (in thread): > I am talking about the Human model.

Ndukauba Oluchi (13:25:13) (in thread): > I have curated for the Mice model. And you are correct@Anne-Marie Sharp

Ndukauba Oluchi (13:26:12) (in thread): > Generally that paper is not really explicit:face_holding_back_tears::smiling_face_with_tear::face_exhaling:

Adeshile Oluwatosin (13:27:48) (in thread): > Don’tget me wrong@Anne-Marie Sharpwe can in some cases,it’sjust that we just need to be careful to avoid assumptions. > > This analysis might be correct

Anne-Marie Sharp (13:31:02) (in thread): > @Ndukauba Oluchiokay,Yh it’snot really explicit, butyou’rehandling it well, you already curated for the mice model:raised_hands:@Adeshile Oluwatosinokay, yes I understand

Anne-Marie Sharp (13:31:37) (in thread): > @Ndukauba Oluchi@Adeshile Oluwatosincheck this out:thinking_face: - File (PNG): IMG_0066

Anne-Marie Sharp (13:39:16) (in thread): > @Ndukauba Oluchi@Adeshile Oluwatosinsothere’sa sample size of 20 for the human model,butI don’tknow ifthere’scontrol/case

Ndukauba Oluchi (13:43:59) (in thread): > It is 19

Ndukauba Oluchi (13:44:11) (in thread): > 11 females and 8 males

Ndukauba Oluchi (13:44:49) (in thread): > Saw that too. > So what could be the Group 0 and Group 1?:thinking_face::thinking_face::thinking_face:

Ndukauba Oluchi (13:44:57) (in thread): > That is where I feel stuck.

Adeshile Oluwatosin (13:45:57) (in thread): > Can you send a link to your study curation?

Mildred Anashie (13:46:07) (in thread): > Hi@Ndukauba Oluchiare you curating the experiment for humans from Fig 10?

Ndukauba Oluchi (13:46:47) (in thread): > Yeahh Fig 10d specifically

Ndukauba Oluchi (13:47:15) (in thread): > @Adeshile Oluwatosinhttps://www.tandfonline.com/doi/full/10.1080/19490976.2025.2465896#d1e1465

Mildred Anashie (13:47:54) (in thread): > Then I believe Baseline should be Group 0 and Group 1 should be End of study@Ndukauba Oluchi. It makes a lot of sense to me as the study is an RCT

Adeshile Oluwatosin (13:48:55) (in thread): > I was about to say we can determine that based on the comparison in the curatable figure/Table which has been stated out. Well done

Ndukauba Oluchi (13:49:00) (in thread): > Baseline of What?@Mildred Anashie

Anne-Marie Sharp (13:49:05) (in thread): > @Mildred Anashiethat’sright.It’s abefore and after clinical trial. So the same participants were used.:woman-shrugging:

Anne-Marie Sharp (13:51:33) (in thread): > @Ndukauba Oluchibaseline of same 19 and control of same 19

Ndukauba Oluchi (13:52:03) (in thread): > Hmm:thinking_face::thinking_face:

Mildred Anashie (14:00:00) (in thread): > @Ndukauba OluchiIn my opinion Baseline Participants vs End of Study Participants could work. And you define the group 1, also the human study was to access the effect of High fat diet in the humans used for the study. Also, see this to help with a better understanding of the group definition and condition. “A before-and-after clinical trial was conducted to evaluate the effect of a high-protein diet. Participants were recruited between August and September 2023. Participants who met all eligibility criteria were selected ad enrolled. Inclusion criteria were as follows: age over 18 years, with a body mass index (BMI) below 30 kg/m2 . Exclusion criteria were subjects diagnosed with ay chronic disease, taking ay medication or antibiotics 3 moths prior to the study, subjects with creatinine >1.3 mg/dL for me ad >1 mg/dL for women, and urea nitrogen >20 mg/dL, and smokers. The study consisted of a 14-day intervention divided into two phases. The first phase of 1 week (0 - 7 days) was a diet with total energy intake based o their total energy expenditure measured by indirect calorimetry, which included a macronutrient distribution of 50% carbohydrate, 30% fat ad 20% protein”.

Ndukauba Oluchi (14:08:49) (in thread): > great job@Mildred Anashiethank you

Mildred Anashie (14:11:38): > Hello Everyone, I just finished curating thisarticleand I’ll appreciate peer review…. Thank you in anticipation:pray: - Attachment (BugSigDB): Gut microbiota-derived propionate mediates the neuroprotective effect of osteocalcin in a mouse model of Parkinson’s disease - BugSigDB > BACKGROUND: Parkinson’s disease (PD) is a neurodegenerative disorder with no absolute cure.The evidence of the involvement of gut microbiota in PD pathogenesis suggests the need to identify certain molecule(s) derived from the gut microbiota, which has the potential to manage PD.

Adeshile Oluwatosin (14:12:54) (in thread): > Well done,I’llcheck it

Mildred Anashie (14:14:53) (in thread): > Thank you@Adeshile OluwatosinPlease confirm the condition and sequencing platform.

Mildred Anashie (14:16:29) (in thread): > You are welcome@Ndukauba Oluchi

Victoria (Burah) Poromon (14:31:39) (in thread): > Hi@Adeshile OluwatosinFor experiment 3 the signature source should be 8B & C instead of 8C & D

Adeshile Oluwatosin (14:35:42) (in thread): > Thank you > > Can you kindly check exp 3/4 alpha diversity curation > Figure 8 wasn’t explicit enough@Victoria (Burah) Poromon

Victoria (Burah) Poromon (14:47:31) (in thread): > Okay

Mildred Anashie (14:59:11) (in thread): > Hi@Adeshile OluwatosinI agree Fig 8 isn’t so clear, but I’d curate the alpha diversity how you curated for Ace but since Shannon isn’t clear on what those letters denote (could be significance though) so I am not sure how it should be curated.

Adeshile Oluwatosin (15:00:11) (in thread): > Exactly:pleading_face:the text within the article aswellisn’t defined well enough too

Mildred Anashie (15:05:10) (in thread): > Also,@Adeshile OluwatosinI’m thinking the sample size for Exp 3 should be 5 for each group and not 8. I understand within text says 8 but the figure caption says 5. See this,“Analysis of the gut fungal community in the HMA-T2D mice. (a) The alpha diversity analysis of the gut fungal community in the HMA-T2D mice. (b-c) analysis of the gut fungal community abundance differences between the RA and RC groups of HMA-T2D mice (LEfSe analysis). (d) The bar charts of the gut fungal distribution comparison among the different treatment groups of HMA-T2D mice. (e) The significance analysis of the fungi in the RA and RC groups of HMA-T2D mice. (f) The effect of COS on the mRNA expression in the colon midgut barrier-related genes in the HT2D mice (n = 5)”.

Victoria (Burah) Poromon (15:05:33) (in thread): > Hi@Mildred AnashieWell done! > > I think the sequencing platform is correct. I did a little search and found that the primers mentioned in the study are designed to target the V3-V4 region and are sequenced on illumina. > > For the condition, i think “protein treatment” would have worked better, butIt’snot available.

Adeshile Oluwatosin (15:06:41) (in thread): > @Mildred AnashieI saw that and considered it > But looking at F where it was mentioned they stated it’s the sample size for HT2D mice and not the treatment group of HMA-T2D mice. Hence, why I left it as it is

Adeshile Oluwatosin (15:13:44) (in thread): > Or do you think the abbreviation means same@Mildred Anashie@Victoria (Burah) Poromon

Mildred Anashie (15:21:44) (in thread): > Thank you@Victoria (Burah) PoromonI’m considering “treatment outcome measurement” what do you think?

Mildred Anashie (15:24:02) (in thread): > The paper is truly not clear, but I felt it meant for the figure:thinking_face:

Victoria (Burah) Poromon (15:39:46) (in thread): > Uhmm, that might work too.I thinkit’sbetter than just “treatment”

Victoria (Burah) Poromon (15:51:55) (in thread): > So the alpha diversity in experiment 3/4 seems accurate to me.

Anne-Marie Sharp (16:24:44) (in thread): > @Adeshile Oluwatosinno,I didn’tsee it also, the data givenisn’t clear

Anne-Marie Sharp (16:39:27) (in thread): > Well done@Mildred AnashieFor Unclassified S24-7 try Taxonomy ID: 2005473 (Muribaculaceae)

Mildred Anashie (19:02:16) (in thread): > Itdoesn’trepresent the unclassified@Anne-Marie SharpI already curated the S24-7 family which is Muribaculaceae

Anne-Marie Sharp (19:18:29) (in thread): > @Mildred Anashienoted. I saw only S24-7 in the text and figure, please which unclassified S24-7 are you referring to?

Mildred Anashie (19:23:40) (in thread): > It’scurated from the supplementals

Anne-Marie Sharp (19:25:32) (in thread): > Oh, I thinkthere’sa mixup somewhere

Anne-Marie Sharp (19:25:52) (in thread): > I kept searching for it in s3 butit’sin s5, your curation says s3

Anne-Marie Sharp (19:32:44) (in thread): > For the unclassified S24-7, unclassified Muribaculaceae is the closest match

Mildred Anashie (19:40:38) (in thread): > Thank you for pointing that out > > Just noticed it too

Anne-Marie Sharp (19:42:46) (in thread): > You’rewelcome

Adeshile Oluwatosin (21:22:49) (in thread): > I also think treatment outcome measurement seems better

Adeshile Oluwatosin (21:30:43) (in thread): > Good morning

2025-03-29

Eniola Adebayo (03:33:40): > Hello@Svetlana Ugarcina PerovicThe signatures are not showing, after adding them.

Montana-D (03:35:53): > Hi@Eniola AdebayoThere’s a trick which was provided the other day which works. > Edit the experiment and keep as incomplete, save and edit again and make it complete. It should appear immediately to make it incomplete

Anne-Marie Sharp (03:36:59) (in thread): > Hello@Eniola Adebayoyou can also try refreshing the page using the refresh option at the top right corner - File (JPEG): IMG_0076

Adeshile Oluwatosin (03:41:24) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1728399751459439 - Attachment: Attachment > UPDATE when your experiment or signature not showing up > > Temporary solution from our team: It is possible that some Studies, especially new ones, will not show all data. You should be able to fix that by clicking “…” and then “Refresh”. Here is a screenshot:

Adeshile Oluwatosin (03:43:06) (in thread): > Guys I saw “transplantoutcome measurement” instead of “response to transplant” for first experiment > > There’s no definition to that though:thinking_face:

Montana-D (03:45:52): > Hi@Svetlana Ugarcina Perovicand@C. Mirzayi (please do not tag this account)Please could you delete the 2 signatures below. They appeared as duplicates after edithttps://bugsigdb.org/Special:FormEdit/Signature/40108637/Experiment_2/Signature_1?reload=1&returnto=40108637https://bugsigdb.org/Special:FormEdit/Signature/40108637/Experiment_2/Signature_2?reload=1&returnto=40108637Thank you

Anne-Marie Sharp (03:46:36) (in thread): > @Montana-Dthe comment for deletion is to be made in the GitHub issue

Montana-D (03:52:47) (in thread): > Okay thank you@Anne-Marie Sharp:hugging_face:

Anne-Marie Sharp (03:56:11) (in thread): > You’rewelcome:innocent:

Montana-D (04:17:20): > Hello everyone. > Please do need clarifications on certain questions and we’ll greatly appreciate your contribution/clarifications patterning to the curation below.https://bugsigdb.org/40108637 > 1. The sequencing type and platform: According to the article, it makes mention of Limma & Wilcoxon testing which isn’t in the database of BugSigDB. > 2. Please cross-check the statistical analyses if correct > 3. Is the study actually cross sectional or Longitudinal > @Svetlana Ugarcina PerovicArticle:https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1Thank you all - Attachment (BugSigDB): Exploring the female genital tract mycobiome in young South African women using metaproteomics - BugSigDB > BACKGROUND: Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. - Attachment (BioMed Central): Exploring the female genital tract mycobiome in young South African women using metaproteomics - Microbiome > Background Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. Results We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. Conclusions The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract

Adeshile Oluwatosin (04:46:56) (in thread): > Hello everyone, I made a post on LinkedIn > You can engage as well > Here is thelink:hugging_face::hugging_face::hugging_face:@Svetlana Ugarcina Perovic

Francisca Gundu (05:13:43) (in thread): > Hi@Montana-DWilcoxon is in the BugSigDB data base under statiscal test. > 1. I am not sure of the sequencing type, I think it’s eitherITS or Shotgun but the sequencing platform ismass spectrometry > **** ****3. Yes your study design is cross-sectional

Adeshile Oluwatosin (05:45:30) (in thread): > * Figure 2A and 2B is not curatable. > * specific to Table 1: statistical test is t-test with MHT as yes > See” The false discovery rate (FDR) corrected p-values were obtained based on the log2-transformed intensity-based absolute quantification (iBAQ) values of each protein by applying the moderated t-test (limma R package). Proteins with FDR-adjusted p-values < 0.05 were considered as differentially abundant proteins”

Anne-Marie Sharp (05:55:26) (in thread): > Okay@Adeshile Oluwatosinwill do:raised_hands:

Adeshile Oluwatosin (06:01:07) (in thread): > “Seventy-four of these women provided another sample at a second-time point 9 weeks later.”So it’snot cross sectional according to the curation policy.

Montana-D (06:17:40) (in thread): > Thank you all for your detailed corrections

Montana-D (06:18:52) (in thread): > @Francisca Gundu, i checked based on my sequencing type and I couldn’t find. What would be the sequencing type of the article then? > Cuz for WMS, Wilcoxon isn’t found

Montana-D (06:19:26) (in thread): > @Adeshile OluwatosinAre you saying it is a longitudinal study then?

Montana-D (06:22:54) (in thread): > With reference to the article, specifically in the first paragraph of the abstract, it was stated otherwise and I quote: “To reduce this knowledge deficit, we present a cross-sectional study of the FGT mycobiome….”

Adeshile Oluwatosin (06:27:34) (in thread): > In the abstract, cross sectional study was not mentioned.“To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women.” > > Yes, I suggest longitudinal

Francisca Gundu (06:32:30) (in thread): > @Montana-DIn the statistical test:Mann-Whitney (Wilcoxon) It is not in the sequencing type. > I think you can leave the sequencing type asWMS (Shotgun), We will allow others and the mentors to have a look and confirm.

Adeshile Oluwatosin (06:34:57) (in thread): > See this:From methods > “Swab eluants were analyzed by PCR to identify women with STIs”

Anne-Marie Sharp (06:37:58) (in thread): > @Francisca Gundu@Adeshile OluwatosinPCR was only used to screen for Sexually Transmitted Infections. So do we still record PCR as a sequencing type?

Precious Orakwe (06:38:33) (in thread): > can i curate the bacteria that has 0.8 as well, because the ones that are within the range of 0.05 is not up to 22@Mildred Anashie - File (PNG): Screenshot (173).png

Adeshile Oluwatosin (06:38:41) (in thread): > I read it again, no it should not

Adeshile Oluwatosin (06:39:57) (in thread): > There’sno explicit details on sequencing itself used specific to the study

Anne-Marie Sharp (06:41:41) (in thread): > Okay, that’s the issue, I also didn’tseeany explicit details on sequencing because even Mass spectrometry was not used for sequencing itself. > I agree that figure 2a is not curatable. > But figure 2b actually presents relative abundance data, statistical tests, and it quantifies taxa differences. > So what do you suggest?

Adeshile Oluwatosin (06:42:06) (in thread): > No, don’t curate > The significant threshold is 0.05@Precious Orakwe

Adeshile Oluwatosin (06:42:37) (in thread): > Leave sequencing details blank

Precious Orakwe (06:43:04) (in thread): > so, i cant curate 0.08 or 0.3

Montana-D (06:46:30) (in thread): > @Adeshile Oluwatosin, I agree with you on the study design. Longitudinal it is

Mildred Anashie (06:47:03) (in thread): > No youcan’tthose are above 0.05

Anne-Marie Sharp (06:49:36) (in thread): > @Precious Orakwefocus on those with pvalue less than 0.05 > That is the threshold/mark you are to look at to guide your curation

Montana-D (06:50:20) (in thread): > Voilà !, so I thought. > So Cross sectional study stays, yes?

Mildred Anashie (06:53:26) (in thread): > @Precious Orakwefor Day 21 I can seeup to 21 actually

Precious Orakwe (06:54:43) (in thread): > Thank you guys, I understand now, I can see them now, I was looking else where. Thank you so much for your guidance.

Adeshile Oluwatosin (06:57:47) (in thread): > Please, leave as longitudinal:sweat_smile:I got the details I needed from the supplementary information. > Seems like there was a visit 2

Adeshile Oluwatosin (06:57:56) (in thread): > @Montana-D

Montana-D (06:58:57) (in thread): > Yes, there was visit 2 alright, samples from same patients, but the study didn’t tract the disease in question over time, did it?

Anne-Marie Sharp (06:58:59) (in thread): > Yes@Adeshile Oluwatosinthere was actually a visit 2. The supplement materials contain info on it. > The paper looks longitudinal with a touch of cross sectional:melting_face:

Adeshile Oluwatosin (06:59:17) (in thread): > The back and forth:sweat_smile:

Adeshile Oluwatosin (07:00:56) (in thread): > From additional file 2: At visit 1, 57 patients were BV positive, 47 were BV negative and 7 were BV intermediate. At visit 2, 37 patients were BV positive, 38 were BV negative, and 5 were BV intermediate. From left to right, BV negative, BV intermediate to BV positive

Montana-D (07:01:01) (in thread): > Cuz from what I understand from the definition of longitudinal, ; This involves repeated observations of the same variables over a period of time to detect changes or developments.. > But our study didn’t observe developmental changes

Montana-D (07:02:27) (in thread): > It also says not all participants took part in the study again, some didn’t show up

Montana-D (07:03:04) (in thread): > Also it didn’t state nor comment on the change in numbers so much as it wasn’t the goal of the study I think

Montana-D (07:06:28) (in thread): > For the sequencing type, I do agree greatly with@Anne-Marie SharpPCR was used to rule out STIs only

Adeshile Oluwatosin (07:07:19) (in thread): > Your analysis is correct > The thing is the study comprises of both of them > Wejustneed to figure out and follow which was the main aim of the study and not a subset

Montana-D (07:09:50) (in thread): > @Francisca GunduYou made mention ITS (internal transcribed spacer). Article made mentioned of this method in the background of study as it was used in a similar study for Estonian women. It also made mention of the fact that ITS was kinda limited due to variability among different fungal species

Montana-D (07:16:42) (in thread): > @Adeshile Oluwatosin,@Francisca Gundu, please did you check for the definition of WMS (whole metagenome Shotgun) sequencing?

Adeshile Oluwatosin (07:21:50) (in thread): > It does not seem like they usedit for sequencing in the study.

Anne-Marie Sharp (07:29:29) (in thread): > @Adeshile Oluwatosinplease can you also confirm that figure 2b, it looks curatable to me

Adeshile Oluwatosin (07:33:33) (in thread): > I cannottell which is significant or not > Also when I see a diagram represented like that > I kind of know it’s not curatable.

Montana-D (07:40:55) (in thread): > @Adeshile Oluwatosin@Anne-Marie Sharp, I found something on the web. > WMS(Whole Metagenome Shotgun Sequencing is a cutting-edge technique that enables detailed exploration of microbial diversity and functionality in various environments, making it a valuable tool in microbiome research and environmental studies.) > LC- MS/MS (Liquid chromatography -tandem mass spectrometry) analyzes peptide mixtures allowing for the identification and quantification of proteins in proteomics studies. > > Now looking at the methods in the article, the only place where there was analysis which had to do with proteins, proteomics or metagenome was under mass spectrometry > > Could you both check it out and give insights?:palms_up_together:

Precious Orakwe (08:42:44): > Hello team good afternoon, I am done with my curation and would appreciate a review for any corrections. Thank You.https://bugsigdb.org/35987213 - Attachment (BugSigDB): Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance - BugSigDB > Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses.

Anne-Marie Sharp (09:28:46) (in thread): > Hello@Precious Orakwewell done with your curation. There was no matched on in the study

Anne-Marie Sharp (09:29:50) (in thread): > In experiment 2, signature 2 should be decreased abundance in Top

USLACKBOT (09:31:05): > This message was deleted.

Precious Orakwe (09:32:15) (in thread): > ok, Thank you, it was a mistake, I didn’t see that.

Anne-Marie Sharp (09:33:32) (in thread): > Hello@Precious Chijiokeplease go through thishttps://community-bioc.slack.com/archives/C04RATV9VCY/p1742479901947439 - Attachment: Attachment > A peer review should be done here in Slack, transparently, so the others can learn too. Thanks! > Feel free to do a peer review but not after submitting your curation for an official review.

Montana-D (09:45:07): > Hello@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Aleru Divine@Kate Rasheed@Chioma Onyidoplease could you help me in identify the study design in this article. It is somewhat confusing. > The study design seems to be a mixture of cross sectional and longitudinal, please can you help to confirm?https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1Thank you - Attachment (BioMed Central): Exploring the female genital tract mycobiome in young South African women using metaproteomics - Microbiome > Background Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. Results We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. Conclusions The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract

Precious Chijioke (09:48:31) (in thread): > Duly noted

Precious Chijioke (09:53:55) (in thread): > Hello@Precious Orakwewell done with your curation. I’ll take a look.

Francisca Gundu (10:02:51): > Hello team, a beautiful afternoon, I would appreciate a peer review on this paper I collaborated on with@JoyThank you.https://bugsigdb.org/40013780https://journals.asm.org/doi/10.1128/spectrum.00852-24 - Attachment (BugSigDB): Exploring oral microbiome in oral squamous cell carcinoma across environment-associated sample types - BugSigDB > The relationship between the oral microbiome and oral squamous cell carcinoma (OSCC) has been extensively investigated.Nonetheless, most previous studies were single-center, resulting in the absence of systematic evaluations.

Precious Chijioke (10:23:31) (in thread): > @Precious Orakwecan you share link to your study, the DOI from BugSigDB is not opening

Precious Orakwe (10:28:49) (in thread): > https://www.cell.com/cell/fulltext/S0092-8674(22)00919-9?_returnURL=https%3A%2F%2Fl[…]vier.com%2Fretrieve%2Fpii%2FS0092867422009199%3Fshowall%3Dtrue

Anne-Marie Sharp (11:11:52) (in thread): > Hello@Francisca Gundu@Joy, well done on your curation. We will go through it:+1:

Anne-Marie Sharp (11:16:21) (in thread): > 1. In Experiment 1, the group 0 name - NAT (normal tissue adjacent to the tumor) that was used in the paper gives more detail. 2.Experiment1 Signature1 should be increased abundance 3. There are duplicates of Experiment1 Signature2, that shouldn’t be there

Mildred Anashie (11:56:27) (in thread): > Well done@Precious OrakweI’ll look through

Mildred Anashie (11:58:01) (in thread): > Well done on this curation@Joyand@Francisca GunduI’ll look through it

Francisca Gundu (12:23:35) (in thread): > Thank you@Anne-Marie Sharp, Experiment 1 signature 1 (all decreased) is curated based on instructions from the last office hours. I have requested that signatures 2, 3 & 4 be deleted.

Ndukauba Oluchi (14:46:57): > Hello BugSigDBians:wave:I just finished curating a very interesting paper Link :https://bugsigdb.org/39980327I would appreciate a peer review, please let me know if you have any feedback. Thank you:pray:Happy weekend Everyone:hugging_face: - Attachment (BugSigDB): Increased dietary protein stimulates amino acid catabolism via the gut microbiota and secondary bile acid production - BugSigDB > Excess amino acids from a protein-rich diet are mainly catabolized in the liver.However, it is still unclear to what extent the gut microbiota may be involved in the mechanisms governing this catabolism.

Adeshile Oluwatosin (14:59:59) (in thread): > Well done@Ndukauba Oluchi > * From your curation: remove LDA score as 2 in experiment 1 and 2, we record that only for Lefse results. > * Figure 4D seems curatable

Anne-Marie Sharp (15:02:03) (in thread): > Hello@Ndukauba OluchiHappy weekend. We’ll review for you:+1:

Ndukauba Oluchi (15:03:03) (in thread): > Done@Adeshile Oluwatosin. I don’t think 4D is curatable. but let’s see what others have to say

Mildred Anashie (15:16:19) (in thread): > Hi everyone > > I shared my experience on LinkedInHere’salinkto the post - Attachment (linkedin.com): #bugsigdb #bugsigdb #outreachy #bugsigdb | Anashie Mildred > My first ever post on LinkedIn was last year and it reflected on my journey with #BugSigDB and the incredible community it is. > > I embarked on this journey with the #BugSigDB community through #Outreachy over a year ago. Through continuous and consistent contributions, I have grown to love the community and the work we do. > . > > . > > . > > BugSigDB is an editable database of manually curated studies that provides information on published signatures of differentially abundant microbes associated with a wide range of health outcomess. It is built on the technology of Wikipedia to allow community contributions, revisions, and review for quality control. > . > > . > > . > My experience with the community has taught me a lot of lessons and impacted skills that I had to continuously build on. Over the past months and recently I’ve been reminded of a few things; > > :sparkles: Embracing Continuous Learning: By not dwelling on the duration of time spent within the community but rather be open to learning, unlearning and relearning. > > :sparkles: Building Connections: Through this community and collaborative work I have connected with people who are passionate about building relationships and connecting. > > :sparkles: Constructive Feedback: Accepting feedback in a positive light is an important part of growth. > > :sparkles:The Power of Mentorship: This right here has always stood out as the most important part of being in this community as guidance from mentors has been pivotal in navigating challenges. > > Looking Ahead: > > As I continue this journey, I’m excited to contribute further and explore innovative projects within the #BugSigDB community. > > The experience has not only enhanced my technical skills but also deepened my appreciation for collaborative efforts. > Special thank you to my mentors Svetlana Ugarcina Perovic Levi Waldron Chloe Mirzayi and my co mentors Peace Sandy Chioma Onyido Esther Afuape Scholastica Urua Aleru Divine Kate Rasheed > > Want to know more about this project? Visit: BugSigDB Project Page > > You can share your experiences with open source projects or how community involvement has impacted your professional growth. Let’s inspire and learn from each other! :dizzy:

Adeshile Oluwatosin (15:16:42) (in thread): > Experiment 1 has no antibiotics exclusion

Anne-Marie Sharp (15:16:59) (in thread): > @Francisca Gundu@Joyyou can rephrase your group1 definition in the different experiments with this clip from your article -
> First, Bios samples were divided into three groups: FEP (Fibroepithelial polyp), NAT (normal tissue adjacent to the tumor), and Cancer. Specifically, the FEP group acts as a control setting for supplementary histological examination, mainly applicable when biopsies cannot be obtained from normal tissues (26). For Bios samples from OSCC patients, the NAT group represents normal tissues adjacent to the tumor, the most common control setting in prior studies, whereas the Cancer group represents cancerous tissues.

Ndukauba Oluchi (15:27:05) (in thread): > @Adeshile OluwatosinTo investigate the influence of antibiotics on gut microbiota and amino acid catabolism, we conducted a parallel study in which mice were exposed to different levels of dietary protein (6%, 20% or 50%) in the presence of antibiotics. Notably, antibiotic treatment effectively abolished the differential weight gain that would typically occur with varying levels of dietary protein, resulting in almost no net weight gain over the 10-day periodi saw this that was why i added antibiotics exclusion

Anne-Marie Sharp (15:29:55) (in thread): > @Ndukauba OluchiI agree with@Adeshile Oluwatosinthe antibiotics were included not excluded

Ndukauba Oluchi (15:30:00) (in thread): > Hello Everyone, I just shared a post on Linkedin, please do well to check it out and ENGAGE. Here’s theLink)to the Post

Ndukauba Oluchi (15:33:02) (in thread): > Okay, for experiment 1 right?

Anne-Marie Sharp (15:33:22) (in thread): > Yes, I thinkit’sto leave it blank if there was no exclusion

Ndukauba Oluchi (15:33:36) (in thread): > okay Done!

Anne-Marie Sharp (15:37:20) (in thread): > Figure 4c & 4d look curatable.Please confirm

Ndukauba Oluchi (15:38:00) (in thread): > Please how do i curate it?

Adeshile Oluwatosin (15:40:51) (in thread): > 4C is not curatableas I cannot tell which is significant

Anne-Marie Sharp (16:05:27) (in thread): > @Adeshile Oluwatosin@Adeshile OluwatosinOn a second thought, the figures lack explicit p/qvalues, effect sizes etc for individual taxa. > So, not curatable

Svetlana Ugarcina Perovic (16:27:40) (in thread): > First, this is not metagenomic study, this ismetaproteomic study: fungal species identification is based on taxonomic assignment of the peptide sequences obtained from the mass spectrometry analysis ->Sequencing platform: Mass spectrometry > > Table 1 and Table S2 are curatable with two tests done for differential abundance analysis results: Wilcoxon rank sum and Limma adjusted test (Linear Models for Microarray and RNA-Seq Data) > > The study does havea longitudinal component: it involvedtwo time pointsfor participant data collection, specifically referred to as “visit 1” and “visit 2,”

Svetlana Ugarcina Perovic (16:31:41) (in thread): > Answered here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1743280060845509?thread_ts=1743236240.755029&cid=C04RATV9VCY - Attachment: Attachment > First, this is not metagenomic study, this is metaproteomic study: fungal species identification is based on taxonomic assignment of the peptide sequences obtained from the mass spectrometry analysis -> Sequencing platform: Mass spectrometry > > Table 1 and Table S2 are curatable with two tests done for differential abundance analysis results: Wilcoxon rank sum and Limma adjusted test (Linear Models for Microarray and RNA-Seq Data) > > The study does have a longitudinal component: it involved two time points for participant data collection, specifically referred to as “visit 1” and “visit 2,”

Anne-Marie Sharp (16:33:25) (in thread): > @Svetlana Ugarcina Perovicthank you for clarifying:pray:Sincelimma’st-testisn’ton BugSigDB can we curate it as T-test?

Adeshile Oluwatosin (16:39:17) (in thread): > She mentioned curating Limma’s adjusted test as linear models which is curatableas linear regression@Anne-Marie Sharp

Anne-Marie Sharp (16:42:46) (in thread): > @Adeshile Oluwatosinnoted, thank you:pray:

Svetlana Ugarcina Perovic (16:44:10) (in thread): > Limma adjusted test (Linear Models for Microarray and RNA-Seq Data) ->Linear Regression

Anne-Marie Sharp (16:45:02) (in thread): > @Svetlana Ugarcina Perovicthank you for clarifying:pray:

Svetlana Ugarcina Perovic (16:45:11) (in thread): > This was a trick “paper to curate” I have to admit:wink:

Svetlana Ugarcina Perovic (16:45:17) (in thread): > Well done, all!

Svetlana Ugarcina Perovic (16:47:28) (in thread): > Unintentionally I added it to the list of papers to curate and it turned out with some tricky points…

Anne-Marie Sharp (16:52:54) (in thread): > @Svetlana Ugarcina PerovicThank you so much:innocent:

Mildred Anashie (17:06:07) (in thread): > Hi@Francisca Gundu@JoyWell done again > The signatures in Experiment 1 should all be decreased with no increase ( I see you said you have requested 2,3 and 4 to be deleted, I agree on that). > > Fig 2f seems curatable from text and the supplemental material, I’m thinking it would be a one against all experiment per all five sample types (The statistical test is LEfSe and I see only increased signatures). But let’s wait for other opinions to confirm the comparison although I’m positive it’s curatable. > > The Alpha diversity from Fig 3b should be all increased for experiment 3.That’sall for now, I’ll look through again

Mildred Anashie (17:11:30) (in thread): > Hi@Ndukauba OluchiWell done, just go confirm does this have only one experiment?

Montana-D (17:12:38) (in thread): > @Svetlana Ugarcina Perovic@Adeshile Oluwatosin@Anne-Marie SharpThank you so much for clarifications:pray:

Adeshile Oluwatosin (17:15:45) (in thread): > 2@Mildred Anashie

Montana-D (17:18:31) (in thread): > Please I am also curious to know how the curation is to be done as@Ndukauba Oluchirequested

Montana-D (17:22:37) (in thread): > Thank you so much mentor@Svetlana Ugarcina PerovicI greatly appreciate your contribution:pray:

Mildred Anashie (17:35:52) (in thread): > In my opinion 4d is curatable, the test is ANOVA and it’s used to compare means of three or more groups. ANOVA doesn’t tell us where there’s a difference, so posthoc is usually done to tell us the specific group that differ from each other. > > From research I see that it assigns letters (a, b, c) to indicate significant differences: > • Groups with the same letter are not significantly different. > • Groups with different letters are significantly different. > > Also see an excerpt from figure caption “Statistical analyses were performed by two-way ANOVA followed by Tukey’s post hoc test (for A and D). Multiple comparisons are indicated by lowercase letters (a > b > c); n=8-10. Data are expressed as mean ± SEM”. > Going by that I’m of the opinion this is a Pairwise comparison with two or three experiments (HP vs NP, HP vs LP and maybe LP vs NP). > Since all the letters are different in all the plots I believe all the taxas are significant. And I’d possibly interpret it as Lactobacillus, SMB53, Allobaculum, Sutterella to be increased in HP compared to LP and NP and Rikenella, Oscillospira, Coprococcus, AF12 to be decreased in HP compared to others. > > I hope this makes sense:thinking_face:This is my opinion though

Mildred Anashie (17:36:29) (in thread): > I’mseeing just one@Adeshile OluwatosinLet me try to refresh

Mildred Anashie (17:41:56) (in thread): > Thank you@Adeshile OluwatosinI see it now. > > The statistical test for Experiment 1 should be LEfSe with data transformation as relative abundance and not Deseq2 with raw counts@Ndukauba Oluchi

Mildred Anashie (18:15:56) (in thread): > Hi@Precious OrakweI believe your curation (group names) should have been Top responders at Baseline vs Bottom responders at Baseline (1 experiment) and Top responders at Day 21 vs Bottom responders at Day 21 (another experiment). > > But it doesn’t look like that’s what was done. > Also from the supplementals they said they used Linear Mixed models so I am of the opinion the statistical test should be linear regression or mixed effect regression:thinking_face:For matched on and LDA score I think it should have been left blank I don’t see either mentioned for the experiments you curated > > Lastly, pleasecurate only less than 0.05 anduse the Log fold change column to tell which taxas are increased or decreased (Positive values are increased and negative values are decreased) I see you curated some taxas you shouldn’t have curated. > > Well done again:raised_hands:

Adeshile Oluwatosin (18:50:11) (in thread): > I agree > * Experiment 1 statistical test is Lefse, MHT: no, LDA score: 2. See “linear discriminant analysis (LDA) shows significant differences in the relative abundance of bacterial species in mice fed different protein concentrations” > * For 4D, from the excerpt Mildred dropped, kindly do a pairwise analysis amongst the three stated groups. > The stated taxa are all decreased in NP and HP when comparing with LP, also decreased in HP when comparing with LP and NP4D: ANOVA with MHT: yes

Adeshile Oluwatosin (20:08:20) (in thread): > Well done > * No group 0 sample size > * Group names should be written in full > * Figure 2F is curatable and it’s a lefse result with only increased signatures. That is five experiments already. > The caption states pairwise comparison test to be wilcoxon which isn’t the case here.curate from here “Specifically, Pseudomonadales, Fusobacteriaceae, and Fusobacterium are enriched in Bios samples; Pasteurellales, Porphyromonadaceae, and Porphyromonas are enriched in Swab samples; Bacillota, Veillonellaceae, and Veillonella are enriched in Salv samples; Bacteroidia, Prevotellaceae, and Prevotella are enriched in Rins samples; while Pseudomonadota, Fusobacteriales, and Fusobacteria are enriched in Plaq samples.”

2025-03-30

Adeshile Oluwatosin (02:07:07): > Good morning > Kindly give a peer review: > Thank youhttps://bugsigdb.org/30551387https://www.sciencedirect.com/science/article/pii/S0753332218371774

Adeshile Oluwatosin (02:08:00) (in thread): > Experiments not reflecting at the moment:https://bugsigdb.org/30551387/Experiment_2/Signature_1https://bugsigdb.org/30551387/Experiment_3/Signature_1https://bugsigdb.org/30551387/Experiment_5/Signature_1https://bugsigdb.org/30551387/Experiment_5/Signature_2 - Attachment (BugSigDB): 30551387/Experiment 5/Signature 2 > Source: Figure 5 Description: Comparison of relative abundance at the phylum, family and genus levels among the three groups Abundance in Group 1: decreased abundance…

Francisca Gundu (04:25:55) (in thread): > Thank you all@Anne-Marie Sharp,@Mildred Anashieand@Adeshile Oluwatosinfor the reviews. I have noted your corrections. I’ll update the study.

Montana-D (05:07:04) (in thread): > Greetings@Adeshile OluwatosinDid you try the golden trick yet?

Montana-D (05:49:22) (in thread): > Hi@Adeshile OluwatosinGreat job on your curation > I’ve taken a look, have some questions > 1. The article made mention of the Shannon alpha index diversity. You did get to find out its state? > 2. I noticed the article made mention of the use of Mann-Whitney U test for taxon differentiation > 3. Why did you combine controls and recovery? Please help me understand

Adeshile Oluwatosin (06:08:42) (in thread): > Hi dear@Montana-DYes I have refreshed > It should work in few minutes > 1. Shannon is curated in Exp 4 and 5 as decreased and increased according to the contrast > 2. Cladogram represents a Lefse results hence the curation of exp 1-3 > Mann-Whitney (Wilcoxon) test was curated for Exp 4 and 5. > 3. They were combined as it’s a one against all analysis hence the three seperate experiments would have just increased signatures with no decreased signatures. Curation is according to the color stated for each group.

Montana-D (06:23:12) (in thread): > @Adeshile OluwatosinThank you > You should try the trick of changing your experiments to incomplete and back to complete that makes them appear soonest. > > Your explanation is understood. Last question > How did you go about curating?, like what was the criteria for increased or decreased?

Eniola Kolawole (06:29:49): > Hi @shulamite from GitHub > I’m Eniola-C > > I don’t know your slack name. Kindly signify here as well please. Thanks.

Adeshile Oluwatosin (06:33:35) (in thread): > @Montana-DA one against all analysis for LeFse has only increased signatures if all colours are moving towards the positive sign only. > > A pairwise comparison e.g control vs patients with a disease > > Might have both decreased and increased signatures > Or just decreased or just increased > > Depending on the result displayed in the table/Figure. > Always curate the increased signature of the case as “signature 1”except result states only signatures as decreased p/q value.

Adeshile Oluwatosin (06:35:07) (in thread): > Sometimes we use the mean to curate.

Montana-D (06:38:28) (in thread): > This part was understood, looking at your experiment 5@Adeshile Oluwatosinfor example, how did you differentiate? Cuz I see them all moving towards the positive only aswell

Adeshile Oluwatosin (06:40:58) (in thread): > I was about saying that explanation was specific tofigure 4.

Adeshile Oluwatosin (06:42:08) (in thread): > For figure 5: “: Compare with control group, P < 0.05;#: Compare with recovery group, P < 0.05)” > > Look at or # in front of each colours to determine if a taxa increases or decreases when compared against the other

Adeshile Oluwatosin (06:45:27) (in thread): > Any taxa without either signsisinsignificant

Montana-D (06:51:13) (in thread): > Thank you so much:pray:

Montana-D (06:51:33) (in thread): > Did the trick I mentioned earlier work?

Precious Orakwe (06:51:37) (in thread): > How about the body site, host specie

Adeshile Oluwatosin (06:58:23) (in thread): > No:pleading_face:Thank you by the way

Montana-D (06:59:54) (in thread): > So you edit the experiment to incomplete and save > Edit again to complete and save

Mildred Anashie (07:00:22) (in thread): > Hello@Adeshile OluwatosinWell done on your curation,I’lllook at it

Adeshile Oluwatosin (07:01:05) (in thread): > Thank you

Precious Orakwe (07:08:38): > Hi@Eniola KolawoleI’m here.

Precious Orakwe (07:10:49) (in thread): > @Eniola KolawoleI’m here

Eniola Kolawole (08:01:51) (in thread): > Alright sis. I will chat you up in the evening when I get back from my place of worship. Thanks

Anne-Marie Sharp (08:15:02) (in thread): > @Precious Orakwethe body site is correct. For the host specie I think you should confirm, because tests were also carried out on mice

Anne-Marie Sharp (08:59:03) (in thread): > @Adeshile Oluwatosinwell done with your curation. 1)I think your group1 definition should be Aged constipated rats not Age constipated rats

Adeshile Oluwatosin (09:03:12) (in thread): > Thanks for catching that@Anne-Marie Sharp

Anne-Marie Sharp (09:15:30) (in thread): > You’re welcome. I observed in Experiment5 Signature1, the phylum Proteobacteria was not included

Adeshile Oluwatosin (09:19:31) (in thread): > It has no significance

Anne-Marie Sharp (09:35:20) (in thread): > Okay, noted

Anne-Marie Sharp (09:48:11): > Hello everyone. Please do we curate a figure that has correlation between fungal taxa & clinical variables, like the figure below. - File (PNG): IMG_0097

Ndukauba Oluchi (10:05:15) (in thread): > @Adeshile Oluwatosin@Mildred Anashieso i’d have like 6 experiments?

Mildred Anashie (10:06:35) (in thread): > For the figure shared I don’t see how this can be curated@Anne-Marie SharpSo I’d say No

Anne-Marie Sharp (10:27:35) (in thread): > @Mildred Anashieokay, noted. To confirm, the correlation we curate is between fungal taxa, right? > Like in the figure below - File (PNG): IMG_0096

Eniola Kolawole (10:45:06) (in thread): > @Precious Orakwe

Adeshile Oluwatosin (11:30:52) (in thread): > Uhmm in this case, nodon’tcurate@Anne-Marie Sharp

Anne-Marie Sharp (11:33:10) (in thread): > @Adeshile Oluwatosinin which case? The first figure or the second figure?

Adeshile Oluwatosin (11:41:11) (in thread): > Figure S1 right?

Anne-Marie Sharp (11:41:58) (in thread): > Figure S4 and Figure S1, I am asking if they are both curatable

Adeshile Oluwatosin (11:42:04) (in thread): > We actually do curate some figures/tables similar, with spearman correlation as the statistical test

Adeshile Oluwatosin (11:44:12) (in thread): > For both figures,I’munable to identify which is significant > And curating this will be a whole lot > Hence why I saiddon’tcurate

Anne-Marie Sharp (12:16:21) (in thread): > Okay. We’re putting upthe curation that contains itfor a peer review so you can have another look:pray:

Montana-D (12:18:20): > Hello Everyone > My Co:@Anne-Marie Sharpand I just finished curating an interesting study and would appreciate another peer review. Thank you for your feedback > > Here’s theLink to ArticleLink toCuration in BugSigDB - Attachment (BioMed Central): Exploring the female genital tract mycobiome in young South African women using metaproteomics - Microbiome > Background Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. Results We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. Conclusions The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract - Attachment (BugSigDB): Exploring the female genital tract mycobiome in young South African women using metaproteomics - BugSigDB > BACKGROUND: Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk.

Adeshile Oluwatosin (13:21:42) (in thread): > Well done:hugging_face:I will look through

Adeshile Oluwatosin (14:24:28) (in thread): > * Experiment 1: Test is Mann-U Whitney (Wilcoxon) > specify the group names to be BV negative and positive at Visit 1. > NB: curate one statistical test per experiment according to the curation policy except in extremely rare cases. > * Curate a seperate experiment for linear regression, signatures are in additional sheet 3 since Not all taxa in Wilcoxon was displayed with linear regression. > > * I can’t see vaginal PH as confounder, please specify the excerpt > * Experiment 2 between negative and intermediate : we have only increased signatures (Table 1, sheet 3). Curate two seperate experiments for Wilcoxon and linear regression too. > * Experiment 3 test is just linear regression, please delete signature 2

Adeshile Oluwatosin (14:26:44) (in thread): > Couldn’t access additional file2

Anne-Marie Sharp (14:29:27) (in thread): > @Adeshile Oluwatosinokay. This is the link for ithttps://static-content.springer.com/esm/art%3A10.1186%2Fs40168-025-02066-1/MediaObjects/40168_2025_2066_MOESM2_ESM.docx

Adeshile Oluwatosin (14:30:52) (in thread): > But from Table S1, sheet 3 > BV positive vs BV negative has two experiments : one with wilcoxon as a test (only increased signature) and linear regression as the other (both increased and decreased). > > BV positive Vs BV intermediate > Linear regression: only increased signatureMake all corrections following strictly this guideline > Well done:clap:

Adeshile Oluwatosin (14:31:34) (in thread): > Specify the group names for visit 2 when curating for visit 2

Adeshile Oluwatosin (15:03:37) (in thread): > @Anne-Marie Sharp@Montana-D

Adeshile Oluwatosin (15:05:45) (in thread): > Figure 4E, 10D, 3 seperate experiments from 4D@Ndukauba Oluchi

Mildred Anashie (15:08:50) (in thread): > You have 2 already, that’s additional 3 experiments@Ndukauba Oluchi

Anne-Marie Sharp (16:00:04) (in thread): > Thank you so much@Adeshile Oluwatosinwe will effect the changes

Montana-D (16:21:08) (in thread): > Thank you a bunch@Adeshile Oluwatosin:pray:

Ifunanya Benita Obiaku (16:26:19): > @Svetlana Ugarcina Perovicplease delete experiment 2https://bugsigdb.org/39976263 - Attachment (BugSigDB): Roseburia hominis improves host metabolism in diet-induced obesity - BugSigDB > Next-generation live biotherapeutics are promising to aid the treatment of obesity and metabolic diseases.

Anne-Marie Sharp (16:59:19) (in thread): > Hello@Ifunanya Benita Obiaku, for experiment deletion, you can leave a comment like this in the GitHub issue that has your curation.

Ifunanya Benita Obiaku (16:59:46) (in thread): > Alright. Thank you.

Anne-Marie Sharp (17:00:21) (in thread): > You’rewelcome

Montana-D (17:22:17) (in thread): > @Adeshile OluwatosinAn ANOVA test demonstrated that pro-inflammatory cytokines (p-value = 1.78e − 12) and vaginal pH (p-value = 1.04e − 08) were significantly associated with BV status. Therefore, differential expression analyses using limma were also adjusted for these variables (Additional file 3). > This is the reason we used Vaginal pH as a confounding factor

Juliana Kentomahun Mautin (22:11:46): > Hello everyone:blush::smile::blush::smile:. Happy new week to y’all. It’s being an amazing two weeks of contributing to BugsigDB, I welcome y’all to another great week of contribution. Please I would appreciate a peer review on this stud. > > Firstly, while curating I couldn’t find any antibiotics exclusion please kindly help me check if you would see it. Please help me cross-check that the signatures are properly curated. > > Secondly I discovered that this study has signatures for significant within-group and signatures for significant between-group. My question is would I curate signatures for both within-group and between-group or just signature between-group. Please I need clarification on that. Thank you:blush:.https://bugsigdb.org/39963956 - Attachment (BugSigDB): Gut microbiome changes with micronutrient supplementation in children with attention-deficit/hyperactivity disorder: the MADDY study - BugSigDB > Micronutrients have demonstrated promise in managing inattention and emotional dysregulation in children with attention-deficit/hyperactivity disorder (ADHD).One plausible pathway by which micronutrients improve symptoms is the gut microbiome.

Juliana Kentomahun Mautin (22:22:19) (in thread): > Good morning@Svetlana Ugarcina Perovic, Joining this amazing community is one of my highlights for the month of March. The first two weeks of contributing to BugSigDB during the Outreachy program have been an eye-opening journey of learning, collaboration, and growth. Stepping into this project has deepened my understanding of microbiome signature curation while also reinforcing essential skills that extend beyond technical expertise. > > One of the key lessons I have grasped is the power of collaboration. Engaging with the community, seeking feedback, and working alongside others have shown me that scientific research and database curation thrive on collective effort. Effective communication plays a vital role in this process, as articulating challenges, sharing insights, and asking for guidance have been crucial to making progress. > > Additionally, I have learned the importance of perseverance and patience. The process of curating microbial signatures is meticulous, requiring careful attention to detail and the ability to navigate complex datasets. At times, it has been challenging, but each hurdle has strengthened my problem-solving skills. > > As I move forward in this journey, I am excited to build upon these lessons, deepen my contributions, and continue developing skills that will serve me in both scientific and technical domains. Outreachy has already proven to be a transformative experience, and I look forward to what the coming weeks will bring.

Anne-Marie Sharp (22:29:33) (in thread): > Hello@Juliana Kentomahun MautinHappy new week and well done with your curation. 1)For the antibiotics exclusion - ‘Additional exclusion criteria included: ……. (iii) usage of antibiotics or antifungals within three months prior to participation;’ 2) there was no matched on

Juliana Kentomahun Mautin (22:29:42) (in thread): > I’m active onXandLinkedIn. I already sent you connect request on LinkedIn@Svetlana Ugarcina Perovic:smile: - Attachment (X (formerly Twitter)): Mautin:princess: (@Julianakent57) on X > Product manager :female-technologist: ll Driving Innovation, Strategy & User-Centric Solutions ll Women Techster fellow Class of 2024 ll GOD’S FAV:sparkling_heart::sparkling_heart: ll Exploring Web3 :globe_with_meridians: - Attachment (ng.linkedin.com): Juliana Kentomahun - Rexversity | LinkedIn > I'm a result- driven product manager with a proven track record in driving product innovation, delivering exceptional user experiences and transforming ideas into successful user centered product. I am deeply committed to understanding user needs and behaviors, dedicated to leveraging market insights, user feedback and cross-functional collaboration to drive sustainable product growth and success in the marketplace. · Experience: Rexversity · Education: Tech4Dev · Location: Ikeja · 500+ connections on LinkedIn. View Juliana Kentomahun’s profile on LinkedIn, a professional community of 1 billion members.

Juliana Kentomahun Mautin (22:31:40) (in thread): > Please where did you find it because I checked and checked, I didn’t see it@Anne-Marie Sharp

Juliana Kentomahun Mautin (22:38:09) (in thread): > Yes the participants weren’t matched on anything

Juliana Kentomahun Mautin (22:42:26) (in thread): > Okay…I would refresh. For the antibiotics exclusion part, do you mind sending a screenshot? > I can’t still find it in the part you asked me to check

Juliana Kentomahun Mautin (22:45:03) (in thread): > The matched on isn’t showing from my end, please help me confirm from your end

Anne-Marie Sharp (22:49:04) (in thread): > @Juliana Kentomahun Mautinmy sincere aplogies, I was in a wrong link. But for the antibiotics exclusion this is what I saw in your article ‘Antibiotic history was recorded with no restrictions on participation for recent antibiotic use.’ There was no exclusion

Anne-Marie Sharp (22:49:34) (in thread): > The matched on isnt showing:+1:

nithya (23:26:01): > hi! im interested to curate the paper titled “Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis #701” can i start curating it?

Adeshile Oluwatosin (23:29:26) (in thread): > Hello@nithyaNo you cannot > You have to wait to be assigned that paper by a mentor

Adeshile Oluwatosin (23:29:40) (in thread): > Also, have you finished the first contribution

nithya (23:36:05) (in thread): > Yes I have finished my first contribution

Juliana Kentomahun Mautin (23:36:45) (in thread): > @nithyayou need to request for it on GitHub via the comments section under the issues then wait for at@Svetlana Ugarcina Perovicto assign the study to you.

nithya (23:37:01) (in thread): > After my first contribution I have not recieved any further instructions though

Adeshile Oluwatosin (23:37:10) (in thread): > Wait to be personally assigned to the article

nithya (23:37:20) (in thread): > Ok

Juliana Kentomahun Mautin (23:38:50) (in thread): > Yes…I saw that part too that was I why I decided to ask here to be sure. Thank you very much@Anne-Marie Sharp.

nithya (23:43:18) (in thread): > i have sumbitted the first contribution. should i inform it to the mentors?

Juliana Kentomahun Mautin (23:44:40) (in thread): > Just request for the paper on GitHub, then wait for our Mentor’s approval on GitHub

Juliana Kentomahun Mautin (23:46:09) (in thread): > This should help@nithyaOnce you request for an article to be assigned to you on GitHub. Be patient, and await the tag “assigned” before commencing curation. > > 2. Once you’ve submitted on GitHub simply by tagging a mentor “SvetlanaUp” and mentioning that you are done curating attached with a link to the study. The “needs review” tag will be added. Ensure, you make no corrections to the study till after review by a mentor. > > 3. Request for one article at a time. Complete a curation before you request for another article to be assigned to you. > > 4. You cannot request for an article with the “assigned” tag. This means someone else is already curating the article. You can only ask to assist. > > 5. Lastly, only request to be assigned to an article with the “outreachy june25” and “paper to curate” tag.

Juliana Kentomahun Mautin (23:48:29): > Hello everyone, I shared my two weeks experience with BugsigDB on X please kindly engage and feel free to drop yours too. Thank you:blush:.X

nithya (23:48:29) (in thread): > yes! the paper i selected has both label as mentioned in point 5.

2025-03-31

Adeshile Oluwatosin (00:06:40) (in thread): > I can see that you have informed Svetlana > Just be patient > She’s probably asleep at the moment

Precious Orakwe (01:31:23): > Good Morning, , > Wishing everyone a great week of BugSigDB-ing. > To the mentors@C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Chioma Onyido@Aleru Divine@Kate Rasheedand to my Teammates, I wish all of us a great week.

Anne-Marie Sharp (02:02:02) (in thread): > Okay. You are correct about it.You’rewelcome@Juliana Kentomahun Mautin

Aiysha shahid (03:22:53) (in thread): > Hi@nithya, you can tag Svetlana on that GitHub issue and let her know that you’d like to curate that paper. Once it’s been assigned to you, you can go ahead and start working on it.

Mildred Anashie (03:24:20) (in thread): > Hi@Juliana Kentomahun MautinWell done, this is a tricky one butI’mthinking between group:thinking_face:

Juliana Kentomahun Mautin (03:33:58) (in thread): > Hmmm:thinking_face::thinking_face::thinking_face::thinking_face:

Juliana Kentomahun Mautin (03:36:32) (in thread): > Please@Svetlana Ugarcina Perovic@Kate Rasheed<@UBNSEMS3S>@Aleru Divine@Scholastica Urua@Peace Sandy. Please kindly help me with this question. Will I be curation signatures for both within-group and between-group or just between-group.https://www.tandfonline.com/doi/full/10.1080/19490976.2025.2463570#abstract

Anne-Marie Sharp (03:36:49) (in thread): > @Juliana Kentomahun Mautinfor the signatures, I would curate for both groups in different experiments, the supplemental material also contains more curatable data

Juliana Kentomahun Mautin (03:40:03) (in thread): > Yes@Anne-Marie Sharp. I’m aware that the supplemental material has more data. I just want to be sure the group to curate for. So when you say both groups are you referring to within-groups and between-group signatures?

Juliana Kentomahun Mautin (03:40:39) (in thread): > The supplemental material contains signature for both within-group and between-group.

Anne-Marie Sharp (03:46:19) (in thread): > @Juliana Kentomahun MautinOkay:+1:.Yes I am referring to curating both within-groups and between-group signatures. > We can still wait for a confirmation from our mentors

Mildred Anashie (04:00:38) (in thread): > I think transplant outcome measurement should work@Adeshile Oluwatosinbecause it looks like the study is checking the effect of COS on Islet cell transplantation. But if it isn’t on BugSigdb then you can stick with Response to transplant.

Adeshile Oluwatosin (04:01:23) (in thread): > Transplant outcome measurement is on bugsigdb > Butthere’sno definition to it > Thank you@Mildred Anashie

Svetlana Ugarcina Perovic (04:05:23): > Good morning, everyone!@nithyapicked a meta-analysis study to curate (https://github.com/waldronlab/BugSigDBcuration/issues/701) > It’s a study of studies and in this case we curate the pooled/combined results of selected original research reports. > > I would like to recommend you all to watch one of our team meetings when@cmirzayiexplained**** how to curate a meta-analysis paper**https://community-bioc.slack.com/archives/C04RATV9VCY/p1734621926221229Nithya, feel free to ask questions during your curation. - Attachment: Attachment > Today’s recording. Thank you everyone who atttended.

USLACKBOT (04:07:02): > Svetlana Ugarcina Perovic made updates to a canvas tab:[canvas content]

Montana-D (04:07:15) (in thread): > Good morning and Thank you so much

Adeshile Oluwatosin (04:08:10) (in thread): > Good morning:tulip:

Mildred Anashie (04:09:11) (in thread): > Good Morning@Svetlana Ugarcina Perovic

Mildred Anashie (04:09:49) (in thread): > All good to me@Adeshile OluwatosinWell done:+1:

Adeshile Oluwatosin (04:10:14) (in thread): > Thank you:heart:@Mildred AnashieGood morning

Anne-Marie Sharp (04:12:19) (in thread): > Good morning@Svetlana Ugarcina Perovicthank you for sharing

Svetlana Ugarcina Perovic (04:20:52) (in thread): > Recently@Kate Rasheedcurated a meta-analysis study, see as an examplehttps://bugsigdb.org/38773112 - Attachment (BugSigDB): Meta-analysis of shotgun sequencing of gut microbiota in Parkinson’s disease - BugSigDB > We aimed to identify gut microbial features in Parkinson’s disease (PD) across countries by meta-analyzing our fecal shotgun sequencing dataset of 94 PD patients and 73 controls in Japan with five previously reported datasets from USA, Germany, China1, China2, and Taiwan.

Juliana Kentomahun Mautin (04:22:02) (in thread): > Good morning@Svetlana Ugarcina Perovic:blush::blush:. Happy new week.

Svetlana Ugarcina Perovic (04:44:05): > We don’t curate the Firmicutes/Bacteroidetes (F/B) ratio.This ratio is one of the common myths and misconceptions in the human microbiome field:**** ****https://www.nature.com/articles/s41564-023-01426-7.epdf?sharing_token=zQcEAK8DkvIZ39[…]f9Mbti7HkP2JyQ-1lsMDs2aXl754ynqTyA-2rlHeQC5jTEtfEGnZPI8EiU%3D - Attachment (nature.com): Human microbiome myths and misconceptions > Nature Microbiology - Walker and Hoyles highlight selected myths and misconceptions in the human microbiota literature.

Adeshile Oluwatosin (04:44:51) (in thread): > Thank you for stating this out mentor.

Juliana Kentomahun Mautin (04:51:57) (in thread): > Thank you for the update:relaxed:

Mildred Anashie (04:55:57) (in thread): > Great resource > > Thank you@Svetlana Ugarcina Perovic

isaac imitini (04:59:59) (in thread): > Thank you for this update@Svetlana Ugarcina Perovic

Anne-Marie Sharp (05:02:33) (in thread): > Noted, and this is an insightful article, thank you for sharing.

nithya (06:37:10) (in thread): > Sure mam.

nithya (06:37:58) (in thread): > Sure mam.

Precious Orakwe (06:43:10): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovic@Aleru Divine@Kate RasheedI am trying to log into BugSigDb, but this is what I see. - File (PNG): Screenshot (174).png

Precious Orakwe (06:44:39) (in thread): > @Svetlana Ugarcina PerovicThanks for the update. noted

Precious Orakwe (06:45:56) (in thread): > Good morning@Svetlana Ugarcina Perovic

Anne-Marie Sharp (06:49:12) (in thread): > @Precious Orakwesorry about that, mine is normal. Confirm your login details. And you can tag our mentors for assistance

Mildred Anashie (07:08:55) (in thread): > Is it still that way?@Precious Orakwe

Precious Orakwe (07:09:22) (in thread): > Yes,

Mildred Anashie (07:09:58) (in thread): > I think you should refresh your browser or change browsers

Adeshile Oluwatosin (07:54:03) (in thread): > Yes, try that@Precious Orakwe

Montana-D (08:05:35) (in thread): > Or clear cache and cookies

Montana-D (08:28:16): > Hello Everyone > My Co:@Anne-Marie Sharpand I just finished effecting all the corrections which were suggested yesterday and would appreciate another peer review. Thank you for your feedback > > Here’s theLink to ArticleLink to Curation inBugSigDB - Attachment (BioMed Central): Exploring the female genital tract mycobiome in young South African women using metaproteomics - Microbiome > Background Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. Results We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. Conclusions The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract - Attachment (BugSigDB): Exploring the female genital tract mycobiome in young South African women using metaproteomics - BugSigDB > BACKGROUND: Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk.

Precious Orakwe (08:36:33) (in thread): > I have done that and I am still seeing the same result

Mildred Anashie (08:37:07) (in thread): > Well done on your curation@Anne-Marie Sharpand@Montana-D:clap:I’lltake a look at this soon

Montana-D (08:56:32) (in thread): > Hi@Adeshile Oluwatosin, good day > Please what is your final verdict on the confounding factor, should I maintain or take it out?:palms_up_together:

Adeshile Oluwatosin (08:59:36) (in thread): > Hello@Montana-Dgenuinely can’tsee this from here - File (JPEG): IMG_4101

Montana-D (09:00:57) (in thread): > Let me get it for you

Montana-D (09:01:22) (in thread): > Screenshots will do?

Juliana Kentomahun Mautin (10:37:39) (in thread): > @Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine<@UBNSEMS3S>@Aleru Divine@Scholastica Urua@Peace Sandy. Please I need clarifications on my question, please kindly help out.

Precious Chijioke (11:19:03) (in thread): > Well done@Adeshile OluwatosinI have taken a look at it and they’re all good to me

Adeshile Oluwatosin (11:42:22) (in thread): > Yes, any

Mildred Anashie (13:30:36) (in thread): > Hi@Montana-Dand@Anne-Marie SharpWell done again > I see data transformation for the first experiment is recorded as Log transformation, Linear regression uses Relative abundance which is same as Wilcoxon in the last experiment.

Mildred Anashie (13:34:50) (in thread): > Also, looking at Supplementary File 3, I don’t think You should have curated another experiment with Wilcoxon because it doesn’t show where they were increased or decreased, rather the Limma does and I think curating just one experiment per comparison in that file with Table 1 and Table S1 as source would have been okay. Also, see this to confirm what I mean******“Differentially abundant proteins, fungal taxa, and biological processes between bacterial vaginosis (BV) states using a non-parametic Wilcoxon rank sum test and adjusted limma test at visit 1” ****same thing was said about Visit 2 and the file presents a Log FC for just Limma.

Mildred Anashie (13:40:01) (in thread): > I’m of the opinion that the tests (limma and wilcoxon)were donetogether.After Wilcoxon they performed Limma and I think those confounders were adjusted for but not sure how you’d record “pro-inflammatory cytokines”

Montana-D (13:50:07) (in thread): > Thank you so much@Mildred Anashiefor your detailed corrections.

Montana-D (13:51:58) (in thread): > Please@Adeshile Oluwatosindo you see eye to eye to what@Mildred Anashiesays, or what have you to contribute:palms_up_together:, I would like all of your opinions so I could do a final edit > > Thank you all for your prompt reviews and corrections:pray:

Montana-D (13:54:49) (in thread): > Visit 1 - File (PNG): Screenshot_20250331-141110.png - File (PNG): Screenshot_20250331-141122.png - File (PNG): Screenshot_20250331-141130.png

Adeshile Oluwatosin (14:21:35) (in thread): > @Mildred Anashiesee my suggestion here > We had a prior discussion with Svetlana > > Where she stated Limma curated as linear regression

nithya (14:22:59): > hi i need help finding URI fo my paper

Mildred Anashie (14:24:53) (in thread): > Hi@nithyaAre you trying to add a study to BugSigdb? > Do you mean PMID?

nithya (14:26:41) (in thread): > hi no. under citation. there is URI after DOI

Montana-D (14:27:04) (in thread): > Hi@nithyaYou need not add the URI > Just put in the PMID, ensure to click on auto and save, every other info will appear

Mildred Anashie (14:27:47) (in thread): > Yea > I’m not disputing Limma being curated as Linear Regression, I’ve seen that. But I’m saying that Wilcoxon shows significance but not if it was significantly increased or decreased. From the table only Limma (linear regression) is showing that@Adeshile OluwatosinPlease look through the table again, you could also point me to where the increase or decrease is, I might have missed it.

nithya (14:28:11) (in thread): > ok under form data i should click incomplete right?since i didnt enter URI

Montana-D (14:28:42) (in thread): > But if you want to do it manually > The URI should be the link to the article you want to curate

Mildred Anashie (14:28:58) (in thread): > Once you add the PMID, click on Auto and then complete. Every other field will automatically populate@nithya

Montana-D (14:29:59) (in thread): > Just as@Mildred Anashiehas said > If you put in the PMID, without the URI. select complete and save

Mildred Anashie (14:30:16) (in thread): > If itdoesn’tit’sokay, as far as you added the right PMID and the study is created successfully (With the abstract being visible)@nithya

nithya (14:30:29) (in thread): > yes i see abstract

Adeshile Oluwatosin (14:30:48) (in thread): > All details are automatically uploaded > Youdon’tneed to fill it in yourself

Adeshile Oluwatosin (14:31:10) (in thread): > Once you input the PMID > Just input the study design, click complete > And begin curating by adding an experiment

nithya (14:31:38) (in thread): > okay

Montana-D (14:36:55) (in thread): > @nithyaEverything good?

nithya (14:37:24) (in thread): > hi yes just started with experiment 1

Montana-D (14:39:31) (in thread): > Awesome:white_check_mark:Good luck

Mildred Anashie (14:40:39) (in thread): > I’m wondering if it’s okay to curate as increase when the article doesn’t in any way point towards that@Adeshile Oluwatosinwhat I am seeing is that both Wilcoxon and Limma was done but Wilcoxon was adjusted with Limma > > Or do we assume since there is significance it should be increased for that test? > > I think we need mentors opinion on this, hopefully I’m wrong@Kate Rasheed@Svetlana Ugarcina Perovic@Aleru Divine<@UBNSEMS3S>a little help please in understandingsupplementary File 3 in this study.Thank you:pray::skin-tone-5:

Adeshile Oluwatosin (14:54:56) (in thread): > I saw the mention of logFC for Limma test to be used for the direction on if it’s a increased or decreased signatureabsent or Wilcoxon resultsI get your point now

Adeshile Oluwatosin (14:56:50) (in thread): > But I don’t think Wilcoxon should be ignored as there is an adjusted p value specifically for Wilcoxontest

nithya (15:00:53) (in thread): > in data collection if it is “no history of antibiotic medication usage”. so, should i leave the antibiotics exclusion “blank”?

Montana-D (15:02:35) (in thread): > Yes, you should

Mildred Anashie (15:11:18) (in thread): > Truth is, I also understand your point

Anne-Marie Sharp (15:14:11) (in thread): > @Mildred Anashie@Adeshile Oluwatosinthank you for thinking it through with us:pray:that’swhy we actually curated both tests together from the beginning but we had to change it later on

Anne-Marie Sharp (15:23:32) (in thread): > Well done with your curation@nithya:raised_hands:Cross checkingwiththe curation policy at each step during my curationhelped mea lotin my second contribution.You can try that too, this is the link:https://bugsigdb.org/Curation_Policy - Attachment (BugSigDB): Curation Policy > .

Montana-D (15:31:22) (in thread): > Thank you@Adeshile Oluwatosin@Mildred Anashiefor your reviews, thoughts and comments. They were truly enlightening and educative > Also we can’t rule out the fact that@Adeshile Oluwatosinhas a point as to why the two tests had different p-values and all, as we noticed that too during our curation but knew not what to do with it. > > We’ll plead for a mentor’s comment so we might know what to conclude on@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)@Kate Rasheed@Chioma Onyido:pray::palms_up_together:

Anne-Marie Sharp (15:35:12) (in thread): > Thank you for your observations@Mildred AnashieAt first, the tests were curated together and in the first peer review we were advised to curate them separately which wedid.

Precious Orakwe (16:28:14): > Hello team is this curatable. - File (PNG): Screenshot_20250331-212002.png

Utibe Ita (16:32:57) (in thread): > i think it is curatable but sending the link to the study will make it easier to confirm that the figure is curatable.

Mildred Anashie (16:43:04) (in thread): > From the image I believe B can be curated butcan’ttell if A is@Precious Orakwe

Precious Orakwe (18:04:15): > Hello team, please i would appreciate a team review on this study;https://bugsigdb.org/35987213Thank you. - Attachment (BugSigDB): Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance - BugSigDB > Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses.

Adeshile Oluwatosin (19:01:07) (in thread): > Hi precious, seems like both is curatable

Victoria (Burah) Poromon (19:39:04) (in thread): > Hi@Precious OrakweWell done! > > Here’s my suggestion: > 1. From the description of Table S7, ithinkWMS is the sequencing type. > 2. Host species should be Mice, because that’s where the results came from. > 3. Body site is just “Feces” > 4. For statistical test, I found this in the study “Statistical tests were employed using repeated measures one way ANOVA for testing of three time points, and by paired t-test for the two time point analysis (for the sucralose and control groups), FDR-BH correction was applied”:thinking_face:

Mildred Anashie (19:40:43) (in thread): > Well done@Precious OrakweI’ll take a look as well

Precious Orakwe (19:59:02) (in thread): > How can i curate the fig b, and how many experiment are in the study, because i am guessing that it is one experiment, what do you think guys.

Adeshile Oluwatosin (19:59:29) (in thread): > Well done@Precious Orakwe

Adeshile Oluwatosin (20:00:11) (in thread): > Seems like Pairwise comparison

Mildred Anashie (20:04:55) (in thread): > 3 experiments from B > > Nov vs C > Nov vs T > Nov vs N > > Is what I’m seeing@Precious OrakweNov was compared to the rest and it looks like Rhodococcus would be increased in all 3

Precious Orakwe (20:58:20) (in thread): > do all the experiment have the same signature

Precious Orakwe (20:58:58) (in thread): > This is the link too the curation;http://bugsigdb.org/40032727 - Attachment (BugSigDB): Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids - BugSigDB > Viral infections, particularly human norovirus (NoV), are a leading cause of diarrheal diseases globally.To better understand NoV susceptibility, it is crucial to investigate both host glycobiology and the influence of the microbiota.

Eniola Kolawole (22:20:28): > Hello everyone > > I need peer review on what@Precious Orakweand I worked on please > Below is the linkhttp://bugsigdb.org/40032727Thank you. - Attachment (BugSigDB): Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids - BugSigDB > Viral infections, particularly human norovirus (NoV), are a leading cause of diarrheal diseases globally.To better understand NoV susceptibility, it is crucial to investigate both host glycobiology and the influence of the microbiota.

nithya (22:47:10) (in thread): > hi in the paper in statistical analysis : F-test is performed.

nithya (22:47:30) (in thread): > by definition F-test is used to compare variances of two or more groups and assess if they are significantly different

nithya (22:48:16) (in thread): > i dont see f-test in the drop down menu. should i choose ANOVA?

nithya (22:51:03): > hi in the paper in statistical analysis : F-test is performed. > by definition F-test is used to compare variances of two or more groups and assess if they are significantly different > i dont see f-test in the drop down menu. should i choose ANOVA?

isaac imitini (23:36:47) (in thread): > Hi Nithya, kindly share the link to the study so we can have a look as well. Thank you.

nithya (23:42:03) (in thread): > sure.https://www.mdpi.com/2076-2607/9/10/2149 - Attachment (MDPI): Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis > (1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we aimed to construct a classification model based on fecal bacterial and identify the potential gut microbes’ biomarkers. (2) Methods: We collected 3056 fecal amplicon sequence data from five research cohorts. The data were subjected to a series of analyses, including alpha- and beta-diversity analyses, phylogenetic profiling analyses, and systematic machine learning to obtain a comprehensive understanding of the association between constipation and the gut microbiome. (3) Results: The alpha diversity of the bacterial community composition was higher in patients with constipation. Beta diversity analysis evidenced significant partitions between the two groups on the base of gut microbiota composition. Further, machine learning based on feature selection was performed to evaluate the utility of the gut microbiome as the potential biomarker for constipation. The Gradient Boosted Regression Trees after chi2 feature selection was the best model, exhibiting a validation performance of 70.7%. (4) Conclusions: We constructed an accurate constipation discriminant model and identified 15 key genera, including Serratia, Dorea, and Aeromonas, as possible biomarkers for constipation.

2025-04-01

isaac imitini (00:08:03) (in thread): > From “2.3. Gut Microbiome Diversity AnalysisTo explore the differences in α-diversity between healthy and constipation samples, the Wilcoxon rank-sum test was performed using the “wilcox.test()” function in the basic package of R-3.4.4, with thep-value adjusted based on the FDR using the “p.adjust()” function in the basic package of R.” > > It appears Mann-Whitney (Wilcoxon) is the statistical test that was used. Our co-curators could also help confirm as well.

Adeshile Oluwatosin (01:04:50) (in thread): > Kindly send a link to the paper

Anne-Marie Sharp (01:49:15) (in thread): > Well done with your curation@Precious Orakwe

Adeshile Oluwatosin (02:03:27) (in thread): > Hi@isaac imitinithat excerpt describes the test used for alpha diversity and not differential analysis

Anne-Marie Sharp (02:07:52) (in thread): > Well done@Eniola Kolawole@Precious OrakweQuick observation:For Candidatus Tremblaya try Taxonomy ID: 189384

Adeshile Oluwatosin (02:10:29) (in thread): > Well done@Eniola KolawoleI will have a look

isaac imitini (02:25:51) (in thread): > Oh, thank you for correcting me,@Adeshile Oluwatosinthen is it possible it was not stated as they used over 9 different test in the study?

Anne-Marie Sharp (02:45:02): > Hello everyone. Please I need some guidance:pray:-Wilcoxon rank-sum test was used in figures 2d to 2f-LEfSe was used in figure 2g > -The result in 2g(LEfSe) is same with the result in 2f(Wilcoxon) > -Should I curate both statistical tests in 1experiment? Or in separate experiments? - File (JPEG): IMG_0116

Adeshile Oluwatosin (02:48:56) (in thread): > There was no explicit state of the statistical testused for differential analysis in the curatble figures I can see,but I saw this: > “To identify key OTUs, the relative abundances were compared using the balances algorithm. The cross-validation in balances selection demonstrated that a total of 19 genera were identified as key lineages associated with constipation, including Lachnospiraceae, Agathobacter, Dorea, and Ruminococcaceae (Figure 4D)”

Adeshile Oluwatosin (02:52:00) (in thread): > Good morning@Anne-Marie Sharp

Adeshile Oluwatosin (02:52:56) (in thread): > Curate as seperate experiments > > They are two different statistical tests and theydon’thave exactly same taxa > 2F shows significance for some other taxa not reflected in lefse, from what I can see

Adeshile Oluwatosin (02:53:26) (in thread): > So 2d - 2F as an experiment (Wilcoxon) > 2F as another experiment (Lefse)

Adeshile Oluwatosin (02:54:08) (in thread): > I would check out the study one more time

Adeshile Oluwatosin (02:55:03) (in thread): > Good morning@Montana-DI suggest curating the experiments with linear regression first as an experiment > > During the office hour you can reconfirm the curation of Wilcoxon

Adeshile Oluwatosin (02:55:23) (in thread): > I would still go over the paper again ifthere’sany thing else I can see towards that

Anne-Marie Sharp (02:56:11) (in thread): > Good morning@Adeshile OluwatosinI mean that, the taxon(the species) in the Lefse plot (2g) are all included in 2f (which is also for species but through Wilcoxon)

Anne-Marie Sharp (02:56:49) (in thread): > It’slike an overlap,that’swhyI’mconfirming

Adeshile Oluwatosin (02:58:07) (in thread): > I know, but unless fully overlap you have to curate seperately. > > Only if other taxa reflected to be significant with wilcoxon is insignificant then you can curate as just one experiment

Anne-Marie Sharp (02:59:30) (in thread): > Okay, thank you for clarifying

Mildred Anashie (02:59:31) (in thread): > Hi > Share figure caption@Anne-Marie SharpOr article

Anne-Marie Sharp (03:00:31) (in thread): > Hello@Mildred Anashieokay

Anne-Marie Sharp (03:00:35) (in thread): > Fig. 2. Overview of the studied community architecture and recognition of the bacterial species connected to psoriasis. (a–b) Alpha diversity based on richness indices and Shannon indices revealed no substantial alterations in the fecal microbiota between psoriasis and healthy controls. (c) Comparison of the intestinal microbiota’s beta diversity between people with psoriasis and healthy controls (ANOSIM R = 0.018, P = 0.279). Each point represents a distinct sample. Each axis’ percentage of variation reflects the proportion of the overall variance that might be explained via projection. (d–f) Boxplot showing the difference of the relative abundance at the phylum, genus and species level between psoriatic and healthy control samples. Only the top 5 phyla and top 10 genera and species are listed. *P < 0.05. (g) Plot from LEfSe examination revealing enriched bacterial genera related to either psoriasis individuals (green) or healthy controls (red). The length of the bar column denotes the LDA score. (h) Bubble graph representing the top 10 KEGG pathways with greatest difference between psoriatic and healthy control samples. The horizontal axis represents enrichment factors and the vertical axis represents paths. Different colors represent different p-values. From blue to red, the enrichment degree of P-values becomes more and more significant. The size of the circle represents the number of genes enriched into this pathway. The negative number indicates an upregulated KEGG pathway and the positive number indicates a downregulated KEGG pathway.

Adeshile Oluwatosin (03:01:29) (in thread): > @Anne-Marie Sharphttps://community-bioc.slack.com/archives/C04RATV9VCY/p1735290056211099?thread_ts=1735228665.854329&channel=C04RATV9VCY&message_ts=1735290056.211099 - Attachment: Attachment > @UBNSEMS3S we should revise this. I would say: If signatures are reported using two different statistical tests and they are FULLY overlapping, use the test that reports a larger number of signatures. record one experiment and note about two tests performed. Curate as two different experiments when results are very different different (not fully overlapping) between the tests.

Anne-Marie Sharp (03:04:02) (in thread): > @Adeshile Oluwatosinthank you!:smiley:this clears it all up!:raised_hands:

Mildred Anashie (03:11:54) (in thread): > Hi@Precious OrakweYou have not fully effected the corrections statedhereAlso the host species should be mice > Well done again - Attachment: Attachment > Hi @Precious Orakwe > > I believe your curation (group names) should have been Top responders at Baseline vs Bottom responders at Baseline (1 experiment) and Top responders at Day 21 vs Bottom responders at Day 21 (another experiment). > > But it doesn’t look like that’s what was done. > Also from the supplementals they said they used Linear Mixed models so I am of the opinion the statistical test should be linear regression or mixed effect regression :thinking_face: > > For matched on and LDA score I think it should have been left blank I don’t see either mentioned for the experiments you curated > > Lastly, please curate only less than 0.05 and use the Log fold change column to tell which taxas are increased or decreased (Positive values are increased and negative values are decreased) I see you curated some taxas you shouldn’t have curated. > > Well done again :raised_hands::skin-tone-5:

Adeshile Oluwatosin (03:12:50) (in thread): > Mice is mus musculus@Precious Orakwe

Mildred Anashie (03:15:14) (in thread): > All sorted then@Anne-Marie Sharp

Anne-Marie Sharp (03:16:05) (in thread): > @Mildred Anashieyes, thank you:blush:

Adeshile Oluwatosin (03:33:36) (in thread): > Please confirm only one experiment was curated.

Mildred Anashie (04:21:58) (in thread): > Well done@Eniola Kolawoleand@Precious OrakweI’ll look through this

Eniola Kolawole (04:43:58) (in thread): > Yes please@Adeshile Oluwatosin

Eniola Kolawole (04:44:15) (in thread): > Thank you@Anne-Marie Sharp

Victoria (Burah) Poromon (04:54:29): > Hi everyone, I just finished curating this study and I’ll appreciate your thoughts on it. > > Thank you so much in advance. > Study link:https://bugsigdb.org/39868783Article link:https://journals.asm.org/doi/10.1128/spectrum.01255-24 - Attachment (BugSigDB): Effects of vaginal microbiota on in vitro fertilization outcomes in women with different infertility causes - BugSigDB > UNLABELLED: Backed by advancements in technologies like microbial sequencing, many studies indicate that the vaginal microbiome is a key marker of female reproductive health.

Precious Orakwe (05:03:31) (in thread): > Thank you everyone for the assistance, we will be waiting for your reviews.

Adeshile Oluwatosin (05:06:28): > Good MorningeveryoneI’d appreciate a peer review on this:https://bugsigdb.org/32079430https://www.tandfonline.com/doi/full/10.2217/fmb-2019-0283Thanks

Mildred Anashie (05:19:24) (in thread): > Well done on your curation@Victoria (Burah) PoromonI’ll look through

Victoria (Burah) Poromon (05:26:51) (in thread): > Thank you!

Anne-Marie Sharp (05:27:01) (in thread): > Nice work@Victoria (Burah) PoromonThe closest match withButyricimonas lubricus seems to beTaxonomy ID: 1969738

Victoria (Burah) Poromon (05:27:55) (in thread): > Okay@Anne-Marie SharpThank you!

Mildred Anashie (05:28:33) (in thread): > Well done on your curation@Adeshile Oluwatosin…..Looking through everything looks good

Adeshile Oluwatosin (05:29:22) (in thread): > Well done@Victoria (Burah) PoromonI’lllook through

Precious Orakwe (05:30:18) (in thread): > @Mildred AnashieI can’t see more taxa that are below 0.05 in the sheet, so, i replace them

Mildred Anashie (05:31:49) (in thread): > Also someone should please look keenly for the matched on. I see it mentioned just in abstract and no where else within the study

Chioma Onyido (05:40:15) (in thread): > @Juliana Kentomahun MautinIn bugsigdb, an experiment corresponds to contrast between groups. Additionally, If there are subgroups within a specific group and the contrast isunique (that is, signatures reported are not duplicates of existing experiments), then it can be curated.

Mildred Anashie (05:43:21) (in thread): > It’s okay if you can’t see but remove the ones that didn’t meet statistical significance. That’s 0.05@Precious Orakwe

Aiysha shahid (05:45:55): > Hi everyone, > Can anyone check how many experiments are included in this paper?Link: https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852. > According to me, there are three experiments: > 1. First experiment– Based on samples fromTable 1, with statistical analysis usingANCOM-BC.Curtable Fig. 2, Supplementary Fig. 1 & 2. > 2. Second experiment– Based onTable 2, withCurtable Fig. 3, Supplementary Fig. 5. > 3. Third experiment– Based onTable 3, with statistical analysis usingANCOM-BC.Curtable Fig. 4, Supplementary Fig. 6. > However, I’m not sure how differential abundance is derived from the heatmap. Any insights would be appreciated!

Anne-Marie Sharp (05:48:46) (in thread): > Well done with your curation@Adeshile Oluwatosin:raised_hands:it seems to be good to go@Mildred Anashiethey were matched on age, table 1 in the article confirms it

Adeshile Oluwatosin (05:55:27) (in thread): > Thank you so much:heart:@Mildred Anashie

Adeshile Oluwatosin (05:56:49) (in thread): > Thank you@Anne-Marie Sharp

Adeshile Oluwatosin (05:57:13) (in thread): > Hello@Aiysha shahidAlright, will do

Mildred Anashie (06:04:48) (in thread): > Hi@Victoria (Burah) PoromonI see 2 experiments in 4H based on history of pregnancy. Also I think ‘Butyricimonas lubricus’ should be left that way. If 4e is curatable then I think you’d have an additional 6 experiments

Mildred Anashie (06:09:02) (in thread): > I just confirmed it is, its like stratification based on weight (BMI) and pregnancy history. Read within text and see this excerpt “Our findings (Fig. 4D****) indicate a noticeable variation in the composition of vaginal bacteria between the PCOS and TFI groups when categorized by BMI, with this disparity being particularly pronounced in the PCOS group. Compared with overweight women, the abundance of **********Lactobacillus********** was relatively higher in obese PCOS women (85.13% vs 47.88%, **********P**********=0.027) (****Fig. 4E****). The abundance of **********Prevotella********** increased in the overweight women, but no significant difference was found (**********P********** > 0.05). The abundance of **********Streptococcus********** was significantly lower in normal women than in the overweight women (0.32% vs 13.40%, **********P********** = 0.042). In the TFI group, the abundance of **********Prevotella********** significantly increased in underweight women compared with the normal and overweight women (13.76% vs 2.46%, 0.57%) (**********P********** = 0.025, 0.020).****”

Joy (06:14:51) (in thread): > Hi@Aiysha shahidwell done on your curation, we will take a look

Victoria (Burah) Poromon (06:22:49) (in thread): > Hi@Mildred AnashieThank you so much! > > Iwasn’treally sure about curating 4E, since the significance is > 0.05 but they’re all below that threshold

Mildred Anashie (06:25:36) (in thread): > The significant threshold is 0.05 and the p values for the significant results are actually below 0.05:thinking_face:

Victoria (Burah) Poromon (06:26:44) (in thread): > Right, the significant threshold is above 0.05, butthey’reall below the threshold

Mildred Anashie (06:28:55) (in thread): > Could it be because of this? The abundance ofPrevotellaincreased in the overweight women, but no significant difference was found (P> 0.05). Or the paper generally used >0.05

Vanisha Garg (06:37:56): > hello everyone ! > Could someone tell me how to add an alpha diversity while curating the article?

Victoria (Burah) Poromon (06:38:03) (in thread): > Yes, because of that, it also already said the differencewasn’tsignificant.That’swhy I left that particular figure out. > > ButI’mjust seeing that 4Hdidn’tshow any p value, so I might to curate that one

nithya (06:39:47) (in thread): - File (JPEG): 1743503980448.jpeg

Mildred Anashie (06:40:00) (in thread): > In my opinion, that was specific to the Prevotella box plot showing comparisons for overweight women. > > Idon’tthink you should leave out the other comparisons showing significance in text and figure

nithya (06:40:43) (in thread): > The f-test is applied in feature selection method. That should be mentioned in statistical analysis while curating right?

Adeshile Oluwatosin (06:41:29) (in thread): > Hello > > There is always a figure/table for alpha diversity in papers. > We curate it increased/decreased depending on the case in the comparison

Adeshile Oluwatosin (06:42:08) (in thread): > We have chao1, ace and observed which is richness, pielou is evenness, Shannon, Simpson …Curate as increased when there is an increase in the case (group 1), same as decreased. > There is usually a star (*) indicating significance from where to where. If there is no significance curate as unchanged > You can also check the text for extra details > Leave as blank when the comparison is totally different from group 0 and 1

Mildred Anashie (06:43:19) (in thread): > Hi@Vanisha GargYou search for alpha diversity within the article you are curating (it’susually stated in text or figure)they’dmention most of the alpha diversity indices on BugSigdb (or just one).You’dcurate as increased/decreased or unchanged if it states that there was no significance. > > If itisn’tmentioned,it’sokay to leave it blank

Adeshile Oluwatosin (06:43:21) (in thread): > Hi nithya, it was stated alongside with 8 other tests and was mentioned to beforfeature selection methods not for differential analysis

nithya (06:46:17) (in thread): > Aiysha here the heat map is applied to find the correlation between two variables. They have applied linkage analysis for finding it.

Victoria (Burah) Poromon (06:46:49) (in thread): > Uhmmm, but if the significant threshold for Prevotella is >0.05, should it not be the same significant threshold for the other taxa’s in the same figure?:thinking_face:

Vanisha Garg (06:47:01) (in thread): > * Add the third alpha diversity metric, ACE, which can be curated as Richness. > I got this review from my mentor , please help me in this , I am unable to find out how to add another alpha diversity

Mildred Anashie (06:50:15) (in thread): > You can wait for other opinions in this butI’mof the opinion that the text implies Prevotella p value for that comparison was above 0.05 hence, it being not significant. Not the threshold for the whole 4E

Victoria (Burah) Poromon (06:55:02) (in thread): > Right, thank you. I’ll hold on and clarify more during the office hour.

Adeshile Oluwatosin (07:01:49) (in thread): > Idon’tget your question

Adeshile Oluwatosin (07:02:12) (in thread): > There is a drop down richness > Click on it to add whether increased or decreased

Mildred Anashie (07:04:08) (in thread): > It simply means you should curate for richness (Ace) based onwhat’sstated in the article@Vanisha Garg

Adeshile Oluwatosin (07:17:17) (in thread): > Butyricimonas lubricus should be left as it is. > 4H is curatable. > I’m also of the opinion of curating Figure4Eas well > > This is just based on the discussion here

Mildred Anashie (07:18:29) (in thread): > It’s4E@Adeshile OluwatosinYou can please go through the article, thanks

Adeshile Oluwatosin (07:19:03) (in thread): > 4E I mean:sweat_smile:

Oriade Adeola (07:25:20): > Hello everyone happy new month. Please i have been working on my study, and i can seem to find the new signatures i added, i don’t know what to do, can someone help me out?https://bugsigdb.org/36875281there should be a signature 1 and 2 in the second experiment, but its not reflecting here:pray: - Attachment (BugSigDB): Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status - BugSigDB > BACKGROUND: Patients with chronic constipation (CC) show altered gut microbial composition.OBJECTIVES: To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.DESIGN: This is a prospective cohort study.

Victoria (Burah) Poromon (07:30:42) (in thread): > Thank you@Adeshile OluwatosinI can go ahead and curate butI’lljust wait and ask soI’mnot confused next time.

Victoria (Burah) Poromon (07:32:04) (in thread): > Hi@Oriade AdeolaPlease edit the experiment. You can just change it to “incomplete” and revert back.

Oriade Adeola (07:33:11) (in thread): > i’m sorry i dont understand

Montana-D (07:34:27) (in thread): > Hi@Oriade AdeolaTap on edit experiment, change it to incomplete and save > Afterwards edit again and change to complete and save > Give it a few seconds, it should appear

Oriade Adeola (07:36:17) (in thread): > @Victoria (Burah) Poromon@Montana-Dthank you very much it worked.

Joy (07:38:07) (in thread): > Hi@Aiysha shahid, Fig. 2, 3, and 4 are curatable as well as supplementary Fig. 1 & 2, supplementary Fig. 5, and Supplementary Fig. 6.

Anne-Marie Sharp (07:44:50) (in thread): > @Vanisha Gargfrom your mentor’s review, it seems you had curated 2alpha diversity metrics > Simply add Richness as the third one:Example, 1)in experiment 1, click on Edit & an edit page will open > 2)Scroll down to Alpha Diversity > 3) You will see Richness > 4)select from the menu: decreased,increased or unchanged, depending on what is in your article

Anne-Marie Sharp (07:46:20) (in thread): - File (JPEG): IMG_0132

Precious Chijioke (07:55:09) (in thread): > Thank you@Adeshile Oluwatosinfor the reference

Joy (08:01:18): > Hi everyone, I’d appreciate a peer review of this study, which I just curated. Thankshttps://bugsigdb.org/39898646This is the link to the study:study paper - Attachment (BugSigDB): Gut microbiome features associate with immune checkpoint inhibitor response in individuals with non-melanoma skin cancers: an exploratory study - BugSigDB > Immune checkpoint inhibitor (ICI) therapy has yielded revolutionary outcomes among some individuals with skin cancer, but a large percentage of individuals do not benefit from these treatments.The gut microbiota is hypothesized to impact ICI therapy outcomes.

Oriade Adeola (08:11:17): > @Aiysha shahidHello Aiysha.

Aiysha shahid (08:11:48) (in thread): > Hi!!:raised_hands:

Oriade Adeola (08:13:55) (in thread): > hello aiysha, so how do we go about the collaboration

Montana-D (08:22:48) (in thread): > Okay > Thank you so much@Adeshile OluwatosinI appreciate

Aiysha shahid (08:23:46) (in thread): > Yes@nithyaand@Joy,but I was asking—according to this image, how do we find out which taxa have increased or decreased? - File (PNG): m_jiaf043f3.png

Aiysha shahid (08:26:21) (in thread): > Let me go through your study and research paper and share the finding’s and you can also share your finding’s with me regarding the research paper. And Then we can start curating the study. Hope that work’s for you?

Oriade Adeola (08:28:25) (in thread): > ok that works. i have already started curating the paper though. you can check it out to know what can be added or adjusted

Adeshile Oluwatosin (08:29:55) (in thread): > That’sfine, well done:clap:

Joy (08:35:00) (in thread): > Hi@Aiysha shahidthe mentors@Svetlana Ugarcina Perovicand<@UBNSEMS3S>would be in a better position to explain this.

Aiysha shahid (08:42:32) (in thread): > Okay,can you share the study link to me here as well.

Oriade Adeola (08:43:02) (in thread): > https://bugsigdb.org/36875281Here it is - Attachment (BugSigDB): Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status - BugSigDB > BACKGROUND: Patients with chronic constipation (CC) show altered gut microbial composition.OBJECTIVES: To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.DESIGN: This is a prospective cohort study.

Svetlana Ugarcina Perovic (08:44:26) (in thread): > @Aiysha shahid > 1. this is a correct link to share an imagehttps://academic.oup.com/view-large/figure/502884084/jiaf043f3.jpg(attached one is impossible to read) > 2. the colorkey of heatmap (in the left upper corner) indicates decrease/increase -> blue/red > 3. you can check that out by reading text associated with the figure, for example: “…higher intake of saturated and trans-unsaturated fatty acids was associated with an enrichment ofRuminococcus bromii, a SCFA producer, and depletion of key gut commensals such asPyramidobacter piscolensandBacteroidesspp (Figure 3).”

Adeshile Oluwatosin (08:45:17) (in thread): > * Rothia: 32207 > * I’m thinking curate the test as lefse for fig 1a, with MHT: yes > Then write a note on the mention of Kruskal Wallis too > * data transformation: relative abundance > > * This is fig 1a description : “LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of the 15 taxa with significant differences (p < 0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented. “ > * Figure 1b is curatable with just three experiments listed: > a.T vs Nov, Nov vs C, Nov vs N

nithya (08:48:39) (in thread): > Abundance is explained wrt color where blue indicates highly positively correlated meaning when one variable increases other also increases and red is negatively correlated when one increases other decreases. Say for example transfat and rumi have red which means negatively correlated and transfats and pyra indicated in blue are positively correlated

Adeshile Oluwatosin (08:49:30) (in thread): > Group names for figure 1a is wrongtoo

Aiysha shahid (08:51:38) (in thread): > Noted! Thank you so much@Svetlana Ugarcina Perovicand@nithya:tulip:

Aiysha shahid (08:54:25) (in thread): > Ohk,will do the needful!:raised_hands:

Oriade Adeola (08:54:45) (in thread): > Tghank you

Victoria (Burah) Poromon (09:21:04) (in thread): > @Adeshile OluwatosinWell done! Everything looks good, I think the matched-on factor is correct too.

Adeshile Oluwatosin (09:21:42) (in thread): > Thank you@Victoria (Burah) Poromon

Aiysha shahid (09:38:20) (in thread): > I have added more taxa to sig 1&2 according to fig2b&2d, also corrected them using NCBI taxonomy, so it’s final now. You can cross-check if you want. Now we have work for exp 2.

Victoria (Burah) Poromon (09:50:52) (in thread): > Hi@JoyWell done! This looks well put together. > > I suggest changing the LDA score to “2” instead of “2.0”. Also, the study says that alpha diversity was not significant. So let’s leave them as unchanged.

Joy (09:53:28) (in thread): > I appreciate@Victoria (Burah) Poromon, I ’ll apply the changes.

Victoria (Burah) Poromon (10:02:40) (in thread): > The study design seems more like a Time series / longitudinal observational because samples were collected from the same participants at different time points. See here: “In this study, we performed an exploratory analysis using 16S rRNA amplicon sequencing and untargeted metabolomics data from 68 samples collected from 21 individuals with NMSC before, during, and after ICI treatment.”

nithya (10:36:38) (in thread): > So no need to mention those test in curation correct?

Adeshile Oluwatosin (11:00:13) (in thread): > This is another excerpt “To identify the significant differences in genera between the two groups, the balances algorithm provided by the selbal package of R was used to analyze whether balances of particular gut microbial genera could discern constipation phenotype.” > > Leave statistical test blank for now and ask during the office hour on howbalance’s algorithmby selbal package can be curated in bugsigDB

Oriade Adeola (11:34:38) (in thread): > Thank you very much. I have already started working on experiment 2,3 and 4 in respect to the review i got from our mentor. so you can check them out as well and feel free to add and adjust them.

Shade Akinremi (12:02:01) (in thread): > Thank you@Victoria (Burah) Poromonand@Anne-Marie Sharp. The review was quite detailed. I really appreciate it.

Shade Akinremi (12:03:05) (in thread): > @Anne-Marie Sharp, the host species section only allows me to enter one host.

Shade Akinremi (12:05:32): > @Svetlana Ugarcina Perovic, hello. What should we do if our experiment has more than one host specie. For example, the experiment I am curating used both Rattus norvegicus and Mus musculus.https://www.mdpi.com/2072-6694/14/11/2573 - Attachment (MDPI): High-Fat Diet Enhances the Liver Metastasis Potential of Colorectal Cancer through Microbiota Dysbiosis > Obesity, metabolic changes, and intestinal microbiota disruption significantly affect tumorigenesis and metastasis in colorectal cancer (CRC). However, the relationships among these factors remain poorly understood. In this study, we found that a high-fat diet (HFD) promoted gut barrier dysfunction and inflammation in the colorectum and liver. We further investigated gut microbiota changes through 16S rRNA sequencing of faecal samples from HFD-fed rats and CRC hepatic metastasis patients and found an abundance of Desulfovibrio (DSV). DSV could also induce barrier dysfunction in the colorectum and inflammation in the colorectum and liver, suggesting that it contributes to the formation of a microenvironment conducive to CRC tumorigenesis and metastasis. These findings highlight that HFD-induced microbiota dysbiosis, especially DSV abundance, could promote CRC initiation and metastasis.

Mildred Anashie (12:07:59) (in thread): > Hi@JoyI’lltake a look at this

Anne-Marie Sharp (12:10:05) (in thread): > @Shade Akinremiyou’rewelcome. Okay, I observed it now thatyou’vementioned it. Perhaps a mentor will clarify

Mildred Anashie (12:11:07) (in thread): > Hi@Shade AkinremiI think going through this thread would give you an idea on how to go about it, pending when you get a definite response.https://community-bioc.slack.com/archives/C04RATV9VCY/p1727442139045629 - Attachment: Attachment > Good day everyone, Happy Friday :smiley: > > Please I have a concern regarding the study I am currently reviewing. In some experiments, the host species involved were both seabirds, specifically Cory’s shearwaters (C. borealis) and northern fulmars (F. glacialis). However, BugSigDB allows for the curation of only one host species at a time. > > In this case, how should I proceed? > > Also, they are referred to as “Procellariiformes” collectively. > > Thank you so much! > > @Svetlana Ugarcina Perovic @UBNSEMS3S @Levi Waldron @Scholastica Urua

Shade Akinremi (12:22:44) (in thread): > Thank you@Mildred Anashie

Precious Orakwe (12:37:20) (in thread): > how about the group sizes for these experiments, we can’t find any in the study, or should we use the same group sizes for all the experiments.

Precious Orakwe (12:51:51) (in thread): > @Mildred Anashiein the study, the first experiment has 22 signatures and the second experiment has 25 signatures, but in the supplementary material, that is the sheets with the taxa, the taxa below. are not up to 22 and 25. That is why i did it like that.

Svetlana Ugarcina Perovic (13:18:21) (in thread): > You can check it out from the thread above how eventually the study was curatedhttps://bugsigdb.org/36973353 - Attachment (BugSigDB): Current levels of microplastic pollution impact wild seabird gut microbiomes - BugSigDB > Microplastics contaminate environments worldwide and are ingested by numerous species, whose health is affected in multiple ways.A key dimension of health that may be affected is the gut microbiome, but these effects are relatively unexplored.

Svetlana Ugarcina Perovic (13:18:47) (in thread): > @Shade Akinremirecord one host species and make a note about the other.

Precious Orakwe (13:39:01) (in thread): > @Adeshile Oluwatosinfor the group names what should it be, and for the 3 remaining experiments, where can I get the signatures, please help me.

Ndukauba Oluchi (13:45:33) (in thread): > Hi@Adeshile Oluwatosinif the 8 taxa’s are all decreased in HP, what then should be the increased?

Ndukauba Oluchi (13:47:30) (in thread): > and i just want to confirm, i have 3 experiments to curate from fig 4D HP (0)VS NP(1), HP(0) VS LP(1), NP(0) VS LP(1) > i don’t know if this is correct, still having a bit of confusion

Adeshile Oluwatosin (13:55:32) (in thread): > There are increased and decreased signatures in 4D > And yes you have three seperate experiments from it > LP(0) vs NP (1), LP (0) vs HP (1),NP (0) vs HP (1)

Adeshile Oluwatosin (13:56:52) (in thread): > Please use the colors to determine which will be increased or decreased of the group 1

Adeshile Oluwatosin (13:57:01) (in thread): > Hello

Ndukauba Oluchi (13:58:39) (in thread): > From 4d, colors weren’t specified

Adeshile Oluwatosin (14:00:06) (in thread): > First of ensure you write the group names in full > See: “T, total bacteria present in stools before experiment; C, bacteria recognized by the IgG isotype control antibody; N, bacteria not recognized by the isotype control antibody nor the specific antibody; NoV, bacteria recognized by the anti-NoV GII.4 Sydney 2012 antibody.”

Adeshile Oluwatosin (14:01:34) (in thread): > For the three seperate experiments@Precious Orakwethe taxa is reflected infigure 1b

Adeshile Oluwatosin (14:03:02) (in thread): > T vs Nov: Rhodococcus is increased in Nov > T vs C: Rhodococcus is increased in C > Nov vs N: Rhodococcus isincreased in N

Adeshile Oluwatosin (14:04:28) (in thread): > Leave sizes blank ifit’snot in the paper

Adeshile Oluwatosin (14:06:17) (in thread): > Orange is LP > Grey is NPBlue is HP > > Thank you so much

Eniola Kolawole (14:16:43) (in thread): > Thanks much@Adeshile Oluwatosin. Now I get it well enough.

nithya (14:25:42): > https://www.mdpi.com/2076-2607/9/10/2149. Can figure 4D considered to create signature? - Attachment (MDPI): Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis > (1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we aimed to construct a classification model based on fecal bacterial and identify the potential gut microbes’ biomarkers. (2) Methods: We collected 3056 fecal amplicon sequence data from five research cohorts. The data were subjected to a series of analyses, including alpha- and beta-diversity analyses, phylogenetic profiling analyses, and systematic machine learning to obtain a comprehensive understanding of the association between constipation and the gut microbiome. (3) Results: The alpha diversity of the bacterial community composition was higher in patients with constipation. Beta diversity analysis evidenced significant partitions between the two groups on the base of gut microbiota composition. Further, machine learning based on feature selection was performed to evaluate the utility of the gut microbiome as the potential biomarker for constipation. The Gradient Boosted Regression Trees after chi2 feature selection was the best model, exhibiting a validation performance of 70.7%. (4) Conclusions: We constructed an accurate constipation discriminant model and identified 15 key genera, including Serratia, Dorea, and Aeromonas, as possible biomarkers for constipation.

Juliana Kentomahun Mautin (14:41:04) (in thread): > Thank you@Chioma Onyido

Anne-Marie Sharp (14:48:28) (in thread): > Hello@nithyano it can’t be considered.

Anne-Marie Sharp (14:51:26) (in thread): > It does not contain relevant statistical comparisons

Mildred Anashie (15:01:26) (in thread): > If I’m looking at the right article then Figure 4d does have significant results@nithya

Mildred Anashie (15:03:23) (in thread): > Its a comparison between DEN(Bars in orange) and NUM(Bars in Green). Can you confirm this is your article@nithya

nithya (15:09:31) (in thread): > Yes it is.@Mildred Anashie

Mildred Anashie (15:17:46) (in thread): > Okay@nithyaThat figure can definitely be curated > > But I do not see the statistical test used for it yet

nithya (16:16:27) (in thread): > Yes. It states significant genera were identified by balance selected. No statistical analysis.

Mildred Anashie (16:16:59): > Hi everyone > I am working on curating this article and I need another pair of eyes in concluding on a few things. > 1. The sequencing type wasn’t mentioned explicitly but they mentioned 2bRAD-M sequencing somewhere in Supplemental material that contains Legends. I saw metagenomics somewhere in text and recorded it, did a second reading and realized it wasn’t WMS. Not sure if it should be left blank or what 2bRAD-M means. > 2. I curated Experiment 6 from Figure S3 but I am having second thoughts on if it should be curated in the first place and if my interpretation of the comparisons is right. > 3. Was there antibiotic exclusion? There’s a mention of Antibiotics but I don’t see the exclusion criteria. > 4. Lastly, is the sample size and Grouping in Experiment 3 (curated from Table S1) wrongly recorded?. > Thank you in anticipation for your responses. > Link to article:https://bugsigdb.org/39387592 - Attachment (BugSigDB): Integrated analysis of microbiome and metabolome reveals signatures in PDAC tumorigenesis and prognosis - BugSigDB > UNLABELLED: Pancreatic cancer, predominantly pancreatic ductal adenocarcinoma (PDAC), is one of the most malignant tumors of the digestive system.Emerging evidence suggests the involvement of the microbiome and metabolic substances in the development of PDAC, yet the results remain contradictory.

Mildred Anashie (16:20:27) (in thread): > I am trying to do a bit of research and it appears Sebal Balances is a type of statistical method used in microbiome research to identify microbial signatures that distinguish between different conditions or phenotypes. I think we need mentors help on if it is curatable in BugSigdb and how you should go about it@nithya

nithya (16:21:31) (in thread): > Ok ill ask the mentors during office hours tomorrow

nithya (22:09:41) (in thread): > for the second point the fig.3 is Kaplan-Meier curve which is for tumor samples. here we donot study any differential analysis but how the pariticular microbe changes with respect to time.

nithya (22:16:27) (in thread): > point 3: antibiotics is used by 10 patients out of 105 patients as you can see in the bracket (9.5 %).

nithya (22:27:03) (in thread): > point 4: as you can see in table 1 in N Stage the sample size was 3 for M stage

Vanisha Garg (22:32:49) (in thread): > Okay Thank you so much for helping me out

2025-04-02

Adeshile Oluwatosin (02:08:26) (in thread): > Hello@Mildred AnashieI will have a look

Anne-Marie Sharp (02:32:53) (in thread): > Hello@Mildred AnashieI did some search and 2bRAD-M is most similar to DNA sequencing than the other types in the drop-down menu.The mention of antibiotics indicates that some patients took it, soI’ll say there was no antibiotic exclusion.

Anne-Marie Sharp (02:33:47) (in thread): > Our mentors can confirm also

Adeshile Oluwatosin (02:49:40) (in thread): > 1. “ The code and raw sequencing data for this study is available upon request from corresponding author Lei You,florayo@163.com.” This is what I saw, so maybe they didn’t intentionally give in much details on sequencing. > 2. There’s no further details from the image telling me if either of the taxa is significant or not. I can only see a mention of if they were enriched or depleted. > > Also, within text I saw this “According to the PERMANOVA results (Fig. 1C), we conducted an analysis of bacterial changes associated with the M stage. The pathogens Pseudomonas fulva, Dietzia maris, Massilia timonae, and Brevundimonas diminuta were positively associated with the M1 stage, whereas Pseudomonas_E sp900187635 was depleted in the M1 stage (Fig. S3). “ > > Hence, I doubt its curation. > > 3. There was no antibiotics exclusion reported in the study. > > 4. Table S1 is showing me the “STORMS checklist” couldn’t see anything on differential analysis:thinking_face:

Adeshile Oluwatosin (02:49:48) (in thread): > @Mildred Anashie

Anne-Marie Sharp (03:00:09) (in thread): > @Mildred Anashielike@Adeshile Oluwatosinsaid,there’snot enough info to use in Figure S3 > Kindly confirm the Table S1 you are referring to or share the direct link here

Adeshile Oluwatosin (03:27:46): > Good morning mentors and everyone@Svetlana Ugarcina Perovic@Kate Rasheed@Esther Afuape@Scholastica Urua@C. Mirzayi (please do not tag this account)How would you interpret table 2A and 2B. > > Taking 0.05 as the significant threshold. > AllTaxa withadjusted p values are insignificant. > Looking at the values recorded for control and psoriasis individually some taxa likeAlistipesreported to be significant within text is insignificant. > > Even 0.1 doesn’t work in this case. > I would appreciate a responsehttps://pmc.ncbi.nlm.nih.gov/articles/PMC8047475/

Adeshile Oluwatosin (03:28:45) (in thread): > See “There was a significant decrease in the phylum Euryarchaeota in the psoriasis group (0.031 vs 0.003, P < 0.05). Decreases in the families Oxalobacteraceae, Porphyromonadaceae, Pasteurellaceae, Rikenellaceae, Sphingobacteriaceae and Comamonadaceae were observed in the psoriasis patients ( Table 2A ). Nine genera, Butyricimonas, Oxalobacter, Actinobacillus, Odoribacter, Anaerotruncus, Alistipes, Pseudoflavonifractor, Pedobacter, and Comamonas, were significantly more abundant in the healthy control individuals than in the psoriasis patients ( Table 2B ).”

Mildred Anashie (03:38:07) (in thread): > You can find the table S1I’mreferring to here@Anne-Marie Sharp@Adeshile Oluwatosinhttps://journals.asm.org/doi/suppl/10.1128/spectrum.00962-24/suppl_file/spectrum.00962-24-s0009.docx

Precious Chijioke (03:49:48): > Good Morning Everyone > According to the curation videos it’s stated that signature 1 is generally recorded as increased. In a situation where signatures are recorded as decreased in a study will I record them as both increased and decreased in signatures 1 & 2 or record them as only decreased in signature 1@Svetlana Ugarcina Perovic@Kate Rasheed@Peace Sandyplease I need assistance

Adeshile Oluwatosin (03:53:25) (in thread): > Good morning > If you have only decreased signatures > The experiment has only one signature as decreased > And it can be recorded as signature 1 in this case@Precious Chijioke

Adeshile Oluwatosin (03:54:27) (in thread): > Hence, record as only decreased in signature 1

Precious Chijioke (03:57:22) (in thread): > Alright > Thank you@Adeshile Oluwatosin

Anne-Marie Sharp (04:03:29) (in thread): > Good morning@Precious ChijiokeLike@Adeshile Oluwatosinsaid, youshould record as only decreased in signature 1 > You can still share your curation link later for us to confirmyou’reon the right track

Precious Chijioke (04:10:15) (in thread): > Alright@Anne-Marie Sharp

Svetlana Ugarcina Perovic (04:18:59): > :question:I was wondering is there anymicrobiome myththat surprised you from this article?https://community-bioc.slack.com/archives/C04RATV9VCY/p1743410645789549 - Attachment: Attachment > We don’t curate the Firmicutes/Bacteroidetes (F/B) ratio. > > This ratio is one of the common myths and misconceptions in the human microbiome field: https://www.nature.com/articles/s41564-023-01426-7.epdf?sharing_token=zQcEAK8DkvIZ39[…]f9Mbti7HkP2JyQ-1lsMDs2aXl754ynqTyA-2rlHeQC5jTEtfEGnZPI8EiU%3D - File (JPEG): microbiome-myths.jpg

Mildred Anashie (04:43:24) (in thread): > Hi@Svetlana Ugarcina PerovicGood morning:sunny:A few points surprised me, but the one that stood out the most was the claim that “Most of the human microbiota is ’unculturable.’” > > I didn’t realize this was such a widely accepted idea, especially considering the thousands of microbes that have been identified. It made me think about how this narrative may have shaped microbiome research over the years.

Scholastica Urua (04:46:15) (in thread): > Hi@Adeshile Oluwatosin, > The adjusted p-value should be prioritized over the initial p-value when interpreting statistical significance (that’s for studies with adjusted p-value). Only taxa with adjusted p-values within the significance threshold should be considered significant. If all taxa have adjusted p-values above this threshold, they are therefore insignificant and not curatable.

Anne-Marie Sharp (04:53:36) (in thread): > @Mildred AnashieAccording to Table1 the sample size for M1 is indeed 3. M1 patients are exclusively Stage IV(3/2.9%). But your grouping/group name/contrast in that Experiment3 seem off. We would need extra eyes on this

Adeshile Oluwatosin (04:54:09) (in thread): > Good morning@Svetlana Ugarcina Perovic“The human microbiota weighs 1-2kg”:thinking_face:I keep wondering how that got spread out in the first place. >
> Also the mention ofmicrobiome research being a new field

Adeshile Oluwatosin (04:55:05) (in thread): > Thank you so much for your response and confirming this > I really appreciate@Scholastica Urua

Adeshile Oluwatosin (04:57:02) (in thread): > I would request to delete the created experiment

Anne-Marie Sharp (05:04:04) (in thread): > Hello@Svetlana Ugarcina Perovic, the 3rd myth ‘There are 10^12 bacterial cells per gram of human faeces’ surprised me because thats what I was taught in school. And I have carried that knowledge/myth

Precious Orakwe (05:13:02) (in thread): > I was thinking this is what should be curated instead of the fig 1b, this is the from the supplementary materials.@Adeshile Oluwatosin@Mildred Anashie - File (PNG): Screenshot_20250402-012833.png

Precious Orakwe (05:14:03): > @C. Mirzayi (please do not tag this account)@Svetlana Ugarcina Perovicis this curatable? - File (PNG): Screenshot_20250402-012833.png

Eseoghene Cynthia Princewill-Ukot (05:15:36) (in thread): > Hi@Svetlana Ugarcina PerovicI can’t open this link from my end…. I don’t know why

Adeshile Oluwatosin (05:15:59) (in thread): > This still shows significance as well > If they have same comparison, then you can add both figures as a source. > You should get more clarity on thispaper’scuration attomorrow’soffice hour

Precious Orakwe (05:18:11) (in thread): > ok, i will leave it till then

Ndukauba Oluchi (05:19:51) (in thread): > @Precious OrakweI strongly doubt

Ameenat Oloko (05:24:02) (in thread): > Good morning,@Svetlana Ugarcina Perovic. The myth that surprised methe mostfrom this article has got to be that “the microbiota is inherited from the mother at birth”. I was taught in school that babies are born without any microbes, but their bodies become rapidly colonised by microbes from the birth canal of their mothersduring birth.

Ndukauba Oluchi (05:26:02) (in thread): > Wow! “*The microbiota is inherited from the mother **at birth” *is really new to me. does the gut microbiota have any link with the mitochondria?:thinking_face:

Ndukauba Oluchi (05:26:42) (in thread): > @Eseoghene Cynthia Princewill-UkotTry to open it with a different browser let’s see

Anne-Marie Sharp (05:26:58) (in thread): > @Eseoghene Cynthia Princewill-Ukotcheck your network and try different browsers

Eseoghene Cynthia Princewill-Ukot (05:29:53) (in thread): > It has opened@Ndukauba Oluchi@Anne-Marie Sharp:pray:

Eseoghene Cynthia Princewill-Ukot (05:38:03) (in thread): > Yes@Svetlana Ugarcina Perovic. The myth that the microbiota outnumbers human cells by a 10:1 ratio . Recent studies have challenged this claim, suggesting that the ratio is closer to 1:1, with approximately 30 trillion human cells and 38 trillion bacteria in the average adult human body. This ratio can vary significantly among individuals, influenced by factors such as body size and gut content. The persistence of this myth highlights the need for more understanding and comprehensive research across diverse populations and life stages.

Eseoghene Cynthia Princewill-Ukot (05:40:57): > Hello@SvetlanaUPThis is to provide an update on the collaboration with@Mautin. We are done and currently awaiting review. > In the meantime, I’m eager to continue contributing and was wondering if I can be reassigned to other articles available for curation. I understand the importance of focusing on the current review process, but I’m keen to utilize this time productively. > Thank you for your guidance and consideration.

Mildred Anashie (05:44:46) (in thread): > Hi@Precious OrakweThe imagedoesn’tappear organized and it’s hard to tell but I see significance in the second plot in the B part but the groups are not clear > > Maybe a link to the article would provide more context

Mildred Anashie (05:45:04) (in thread): > I agree with@Adeshile Oluwatosin

Adeshile Oluwatosin (05:46:30) (in thread): > Hi@Eseoghene Cynthia Princewill-Ukotyou can pick another article and request to be assigned to it, tag Svetlana GitHub > Well done

Precious Orakwe (06:25:25) (in thread): > This is the link tp the supplementary material - File (PDF): DOC-20250331-WA0048.pdf

Victoria (Burah) Poromon (06:30:50) (in thread): > Ah > Definitely@Svetlana Ugarcina PerovicThe myth that “Microbiome research is a new field” > I’m surprised that it’s a popular misconception, I always thought thisideology was limited. > > And “The human microbiota weighs 1 to 2 kg”:sweat_smile:Like who weighed it? Why was it weighed? How was it even weighed? I have so many questions.

Francisca Gundu (06:59:42) (in thread): > Good morning@Svetlana Ugarcina PerovicAnother surprising myth in microbiome research is the belief that**** “the human microbiota weighs 1 to 2 kg.” ****This misconception has been debunked, with studies suggesting that the human microbiota is more likely to weigh less than 500 grams.

Joy (07:03:41) (in thread): > Waoh!!@Svetlana Ugarcina PerovicRecognizing and understanding such myths is essential for advancing our comprehension of the microbiome’s role in health and disease. > > Another prevalent myth in microbiome research is the belief that****“most diseases are caused by an altered microbiota or ‘dysbiosis.’”****While changes in the microbiome have been associated with various health conditions, establishing direct causation is complex. The relationship between the microbiota and disease is influenced by numerous factors, including genetics, environment, and lifestyle.

Mildred Anashie (07:33:21) (in thread): > @Anne-Marie Sharpit’s not stated any where that M1 is same as stage IV.Could it be because they share same values (3/2.9%)?

Anne-Marie Sharp (08:08:56) (in thread): > @Mildred AnashieI believe so

Anne-Marie Sharp (08:22:12) (in thread): > @Precious Orakweit should be curatable but the diagrams are not clear, organized and complete, so I also doubt.

Anne-Marie Sharp (08:25:54) (in thread): > @Mildred Anashie@Precious Orakwe@Ndukauba Oluchilet us analyze it with this document, it appears that the first document was not properly downloaded - File (Word Document): kgmi_a_2469716_sm9834.docx

Anne-Marie Sharp (08:31:47) (in thread): > @Precious OrakweI observed that viewing the document in different document readers changes the format. > It appears clear now on my end. > > So share the direct link for the article for each person to download. Or we can use this - File (JPEG): IMG_0145

Mildred Anashie (08:55:50) (in thread): > Thank you for the clearer version@Anne-Marie Sharp@Precious Orakweit looks like the same comparisons were done as the other, so you should curate both

Halima Momoh (09:01:24) (in thread): > Thank you@Adeshile Oluwatosin@Anne-Marie Sharp@Aiysha shahidfor your help and my Apologies for the late response.

Dorcas Odetayo (09:52:52): > Hi everyone, > I’m currently curating this article and would appreciate any help in reviewing it. Thanks in advance:tulip:This is thestudy paper,https://bugsigdb.org/39873191 - Attachment (BugSigDB): Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet - BugSigDB > Hyperoxaluria, including primary and secondary hyperoxaluria, is a disorder characterized by increased urinary oxalate excretion and could lead to recurrent calcium oxalate kidney stones, nephrocalcinosis and eventually end stage renal disease.

Anne-Marie Sharp (09:56:00) (in thread): > @Mildred Anashieyou’re welcome.@Precious OrakweI believe with this it is curatable, take note of the significant taxa when curating.

Adeshile Oluwatosin (09:56:34) (in thread): > Well done:+1:

Victoria (Burah) Poromon (10:03:20) (in thread): > Well done! > I’ll take a look.

Precious Orakwe (10:08:24) (in thread): > well done:+1::+1:

Adeshile Oluwatosin (10:13:27) (in thread): > * Comparison for figure 1e, f, g and h are totally different > Hence they are separate experiments. > * Eubacterium coprostaligenes group, 290054 > * RB41: Taxa ID 2609296 > * Figure 4A, 4B and 4C : Welch’s t-test > see: “Welch’s t-testswere used for the relative abundance of differential bacteria.

Juliana Kentomahun Mautin (10:18:13): > Hi everyone and Happy New month:tada:Just a reminder that our office hour is at 9 AM EDT tomorrow. Looking forward to seeing you there. > > Please use this application to find the time in your local time zone so you don’t miss it:https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=37&p3=176&p4=3395&p5=125For office hour reminder - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Dorcas Odetayo (10:25:21) (in thread): > Thank you@Adeshile Oluwatosin, > Does this mean the study includes more than four experiments due to the differences between Figures 1E, 1F, 1G, and 1H?

Adeshile Oluwatosin (10:26:06) (in thread): > Yes, just figure 1 has four experiments > Group 0 and 1 seems to be different for the specified figures

Adeshile Oluwatosin (10:26:46) (in thread): > Also you left a wholelotof details emptye.g statistical analysis details and the likes.Not all alpha diversity is to be curatedtoo

Adeshile Oluwatosin (10:27:43) (in thread): > Read the conversations here@Dorcas Odetayohttps://community-bioc.slack.com/archives/C04RATV9VCY/p1743503876971139 - Attachment: Attachment > hello everyone ! > Could someone tell me how to add an alpha diversity while curating the article?

Dorcas Odetayo (10:35:09) (in thread): > Thanks for the clarification@Adeshile Oluwatosin, I’ll fill in the missing details

Victoria (Burah) Poromon (10:44:56): > Hi everyone, as per our last discussion here….https://community-bioc.slack.com/archives/C04RATV9VCY/p1743497669274239What do you think is the statistical test for figure 4E & H??? > > T-test or Mann-Whitney? - Attachment: Attachment > Hi everyone, I just finished curating this study and I’ll appreciate your thoughts on it. > > Thank you so much in advance. > Study link: https://bugsigdb.org/39868783 > > Article link: https://journals.asm.org/doi/10.1128/spectrum.01255-24

Anne-Marie Sharp (11:15:10) (in thread): > Hello@Dorcas Odetayowell done with your curation. I agree with@Adeshile Oluwatosin, key details were omitted in the curation. > There are many experiments to curate. > You could ask questions as you curate step by step, that would help.

Dorcas Odetayo (11:22:10) (in thread): > Thanks for the feedback@Anne-Marie Sharp, > I’ll also ask questions as I go.

Anne-Marie Sharp (11:27:27) (in thread): > You’rewelcome@Dorcas Odetayo

Victoria (Burah) Poromon (11:47:16) (in thread): > Hi@Dorcas OdetayoSo to make it easier, there are 4 experiments in figure 1: > 1. 5%K2Ox-0day vs. 5%K2Ox-45day (1e) > 2. 5%Hyp-0day vs. 5%Hyp-45day (1f) > 3. Normal-45day vs. 5%K2Ox-45day (1g) > 4. Normal-45day vs. 5%Hyp-45day (1h) > Figure 4 has a lot of experiments too, fromthe first figure(box) in4a; > 1. Normal-45day vs. 5%K2Ox-45day > 2. Normal-45day vs. 5%K2Ox-45day-fmt > 3. 5%K2Ox-45dayvs.5%K2Ox-45day-fmt > From the second figure in 4a. > 1. Normal-45day vs. 5%Hyp-45day > 2. 5%Hyp-45dayvs.5%Hyp-45day-fmt > Normal-45day vs. 5%Hyp-45day-fmt had no significance, so youwon’tbe curating this. > > Figure 4b and 4c are also curatable.That’s9 experiments that I can count. > Well done

Joy (11:59:14) (in thread): > Well done@Victoria (Burah) Poromonon your curation. I thinkMann-Whitney is the statistical test for figures 4E & 4H, because the data are not normally distributed and the sample sizes are small. In 4H, the group 1 size is 2 and in 4E the group 1 is unknown.

Dorcas Odetayo (12:00:19) (in thread): > Thanks for breaking it down@Victoria (Burah) PoromonI’ll go through these and ensure they’re properly curated. Appreciate the guidance:pray:

Victoria (Burah) Poromon (12:04:26) (in thread): > Thank you so much!@Joy

Adeshile Oluwatosin (12:12:40) (in thread): > Uhmmmm > > The non-parametric Mann–Whitney test was performed to compare differences in ordinal variables between the groups.”:thinking_face:When I googled what ordinal variables means, I saw that the meaning somewhat matched with the comparison

Victoria (Burah) Poromon (12:28:08) (in thread): > The study just said they used t-test (normally distributed) or Mann-Whitney to compare the groups for continuous variables. > > I’malsothinkingmann-Whitney since BMI is not a normally distributed data.

Anne-Marie Sharp (14:01:35) (in thread): > Based on the info in the article, it should be Mann-Whitney. You could curate with Mann-Whitney and confirm it tomorrow

Aiysha shahid (14:31:39) (in thread): > Hi@Oriade Adeola, I have gone through the study and there are lot of things to be adjusted, it will take sometime,will adjust it soon and get back to you. Hope that work’s for you?

Oriade Adeola (14:34:23) (in thread): > Ok. Thank you.

Mildred Anashie (15:00:11) (in thread): > Hi@Adeshile Oluwatosinplease where did you see this?. “ The code and raw sequencing data for this study is available upon request from corresponding author Lei You,florayo@163.com.”

Mildred Anashie (15:01:37) (in thread): > Thank you@nithya@Anne-Marie Sharp@Adeshile OluwatosinI’ll try to confirm the other questions tomorrow

nithya (22:59:06): > good morning members! I and@Anne-Marie Sharphave curated a paperhttps://bugsigdb.org/34683469. we would like to have a peer review before submitting. thanks in advance. - Attachment (BugSigDB): Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis - BugSigDB > (1) Background: Constipation is a common condition that affects the health and the quality of life of patients.Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort.

nithya (22:59:57) (in thread): > since the paper is meta analysis few details are taken from reference papers.

nithya (23:00:54) (in thread): > Location: Reference paperAmerican Gut: an Open Platform for Citizen Science Microbiome Research - PubMedFull article: Limited prolonged effects of rifaximin treatment on irritable bowel syndrome-related differences in the fecal microbiome and metabolomeFrontiers | Lactobacillus casei Strain Shirota Alleviates Constipation in Adults by Increasing the Pipecolinic Acid Level in the Gut(ILLUMINA)Differential Effects of Lactobacillus casei Strain Shirota on Patients With Constipation Regarding Stool Consistency in China(ILLUMINA) > Sequencing type and 16s variable region:American Gut: an Open Platform for Citizen Science Microbiome Research - PubMedAlpha diversity: Refer fig 2 - Attachment (PubMed): American Gut: an Open Platform for Citizen Science Microbiome Research - PubMed > Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiom … - Attachment (Frontiers): Frontiers | Lactobacillus casei Strain Shirota Alleviates Constipation in Adults by Increasing the Pipecolinic Acid Level in the Gut > The benefits of probiotics for constipation are widely accepted, but the mechanisms involving gut metabolites are unclear. In this study, we investigated the…

nithya (23:02:28) (in thread): > the data is collected from 5 different sources so for location and sequencing type the other articles were referred.

2025-04-03

Mildred Anashie (02:28:57) (in thread): > Hi@nithyaand@Anne-Marie SharpWell done on your curation

Precious Chijioke (03:02:55) (in thread): > Hello@nithyaand@Anne-Marie Sharpwell done on your curation > I’ll take a look at it

Mildred Anashie (03:22:03) (in thread): > Just to mention there’s an incomplete experiment and the first experiment has three signatures

Montana-D (03:54:29) (in thread): > Hi@nithyaand@Anne-Marie Sharp, well done on your curation

Shade Akinremi (05:20:16) (in thread): > Thank you@Svetlana Ugarcina Perovic

Anne-Marie Sharp (05:20:59) (in thread): > Thank you all so much.@Mildred Anashieexperiment2 will be deleted soon. Signature3 has same statistical tests as the others. But is there a better way we should curate it?

Mildred Anashie (05:22:44) (in thread): > Is it the same comparison, location, body site and sample size?@Anne-Marie SharpIf itisn’tthen curate as a different experiment, but if it is curate as one experiment but include it in the Signatures 1 and 2 based on increase and decrease and be sure to include the source

Precious Orakwe (05:58:28): > good day@Svetlana Ugarcina Perovicplease delete experiment 5 in this study,https://bugsigdb.org/40032727Thank you. - Attachment (BugSigDB): Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids - BugSigDB > Viral infections, particularly human norovirus (NoV), are a leading cause of diarrheal diseases globally.To better understand NoV susceptibility, it is crucial to investigate both host glycobiology and the influence of the microbiota.

Svetlana Ugarcina Perovic (06:00:55) (in thread): > Please note for this matter we communicate in the corresponding gh issue:https://github.com/waldronlab/BugSigDBcuration/issues/653#issuecomment-2775159980 - Attachment: Comment on #653 [Study]: Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids > 40032727/Experiment 5 deleted.

Precious Orakwe (06:02:11) (in thread): > alright, thanks@Svetlana Ugarcina Perovicfor the update, noted.

Precious Chijioke (06:29:52) (in thread): > @Anne-Marie Sharplike@Mildred Anashiesaid curate as different experiment if the comparison is different and curate as one experiment if it’s same comparison ensuring you include the signatures as increased and decreased respectively

Shade Akinremi (06:40:04): > @Svetlana Ugarcina Perovic, while waiting for my 2nd curation to be reviewed, can I pick another study?

Svetlana Ugarcina Perovic (06:41:19) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1743586857629429 - Attachment: Attachment > Hello @SvetlanaUP > This is to provide an update on the collaboration with @Mautin. We are done and currently awaiting review. > In the meantime, I’m eager to continue contributing and was wondering if I can be reassigned to other articles available for curation. I understand the importance of focusing on the current review process, but I’m keen to utilize this time productively. > Thank you for your guidance and consideration.

Shade Akinremi (06:43:02) (in thread): > Alright.

Svetlana Ugarcina Perovic (07:09:16) (in thread): > Please note this is the correct time converter for today’s meeting:https://www.timeanddate.com/worldclock/converter.html?iso=20250403T130000&p1=179&p2=37&p3=176&p4=3395&p5=125See you soon! - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Juliana Kentomahun Mautin (07:41:54) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the update

Adeshile Oluwatosin (08:41:18) (in thread): > Pleasewhere’sthe meeting link?@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (08:42:39) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/95 - Attachment: #95 Office Hours > Welcome, Outreachy applicants! > > My name is Chloe, pronouns she/her. We’re excited for the contribution period to begin and to meet you all. I have been working with Svetlana (pronouns: she/her) on the BugSigDB project and am available to answer questions you have about BugSigDB contribution tasks. > > In case it’s useful - here is the link to guidance for the first contribution task and the second (optional) contribution task on our GitHub repo: #94 > > Also, during the Outreachy contribution month, we will be offering weekly office hours for you to log in and ask questions during our normal team meetings. If you are interested in learning more about the BugSigDB project, we strongly recommend attending one of these BugSigDB team meetings. You are welcome to come participate or observe these meetings as well as ask questions. > > These meetings are scheduled for: > > Thursday March 20, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499)
> Thursday March 27, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499)
> Thursday April 3, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499)
> Thursday April 10, 9-10 AM ET* (https://us02web.zoom.us/j/2737200499) > > **Find out the time in your local time zone here: https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=3395
> We are happy to meet with you on a different day or time upon request. Thank you!

Adeshile Oluwatosin (08:44:12) (in thread): > Got it, thank you

nithya (09:01:17): > Meeting link

Mildred Anashie (09:02:04) (in thread): > https://us02web.zoom.us/j/2737200499

Ameenat Oloko (09:02:28): > The meeting has started, everyone.Kindly joinhttps://us02web.zoom.us/j/2737200499

Ndukauba Oluchi (09:02:28): > Office hours is ON guyss

nithya (09:11:17) (in thread): > @Mildred Anashiesignature 3 is output of same experiment. correlation of taxa and constipation

Svetlana Ugarcina Perovic (09:36:15): > <@UBNSEMS3S>2b-RAD added to the Sequencing platform options

nithya (09:50:50): > do we curate the biomarkers(gut microbata) obtained by different feature selection method?

Adeshile Oluwatosin (10:00:35): > Thank you so much<@UBNSEMS3S>@Svetlana Ugarcina Perovicfor today’s office hour:pleading_face:

Ameenat Oloko (10:01:47): > Thank you for the office hour,@C. Mirzayi (please do not tag this account)and@Svetlana Ugarcina Perovic. It was an insightful one.

Mildred Anashie (10:03:14) (in thread): > Thank you<@UBNSEMS3S>@Svetlana Ugarcina PerovicFor the office hours:blush:

Mildred Anashie (10:04:54) (in thread): > Thank you for adding it@Svetlana Ugarcina Perovic:tada:

Francisca Gundu (10:10:22): > Thank you@Svetlana Ugarcina Perovicand<@UBNSEMS3S>for the office hour today!

Svetlana Ugarcina Perovic (10:34:23) (in thread): > Please provide an example, more specific.

nithya (10:50:56) (in thread): > http://dx.doi.org/https://doi.org/10.3390/microorganisms9102149In this article supplementary shows the biomarkers of the microbata of different feature selection methods. Increase or decrease of the microbata with respect to disease was not provided in the supplementary. Around 700 microbata are provided in the supplement table through feature selection methods. - Attachment (MDPI): Predicting the Role of the Human Gut Microbiome in Constipation Using Machine-Learning Methods: A Meta-Analysis > (1) Background: Constipation is a common condition that affects the health and the quality of life of patients. Recent studies have suggested that the gut microbiome is associated with constipation, but these studies were mainly focused on a single research cohort. Thus, we aimed to construct a classification model based on fecal bacterial and identify the potential gut microbes’ biomarkers. (2) Methods: We collected 3056 fecal amplicon sequence data from five research cohorts. The data were subjected to a series of analyses, including alpha- and beta-diversity analyses, phylogenetic profiling analyses, and systematic machine learning to obtain a comprehensive understanding of the association between constipation and the gut microbiome. (3) Results: The alpha diversity of the bacterial community composition was higher in patients with constipation. Beta diversity analysis evidenced significant partitions between the two groups on the base of gut microbiota composition. Further, machine learning based on feature selection was performed to evaluate the utility of the gut microbiome as the potential biomarker for constipation. The Gradient Boosted Regression Trees after chi2 feature selection was the best model, exhibiting a validation performance of 70.7%. (4) Conclusions: We constructed an accurate constipation discriminant model and identified 15 key genera, including Serratia, Dorea, and Aeromonas, as possible biomarkers for constipation.

Anne-Marie Sharp (10:51:04): > Thank you@Svetlana Ugarcina Perovic@C. Mirzayi (please do not tag this account)fortoday’soffice hour:pray:

Svetlana Ugarcina Perovic (10:58:12) (in thread): > Table S1: Biomarkers of gut microbiota associated with constipation obtained by different feature selection methods. > There is no differential abundance results nor significance reported.

nithya (10:58:37) (in thread): > Yes mam

UBNSEMS3S (11:20:28): > Office hours recording. Thank you who attended. I know I have an outstanding question to answer about this paper:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#supplementary-materialand what is the difference between Table S1 and Figure S2 which I am looking into presently. - File (MPEG 4 Video): bsdb_2025_04_03.mp4

Juliana Kentomahun Mautin (11:43:49) (in thread): > Thank you@Svetlana Ugarcina Perovicand<@UBNSEMS3S>for today’s office hour.

Anne-Marie Sharp (12:15:20) (in thread): > @Svetlana Ugarcina PerovicThank you for clarifying:pray:

Precious Orakwe (12:26:24) (in thread): > Thank you@C. Mirzayi (please do not tag this account)for today’s session, i will be waiting for your update concerning my study.

Anne-Marie Sharp (12:44:56): > Hello everyone. Please I would like a peer review on this curationhttps://bugsigdb.org/36621696Thank you in advance:pray:

Adeshile Oluwatosin (12:45:17) (in thread): > Well done:thumbsup:

Anne-Marie Sharp (12:53:45) (in thread): > Thank you@Adeshile Oluwatosin

Mildred Anashie (12:58:13) (in thread): > Okay@Anne-Marie SharpI’ll take a look at this

Adeshile Oluwatosin (13:06:27) (in thread): > Experiment 3 : source should be 3f only

Anne-Marie Sharp (13:08:55) (in thread): > Okay, I thought that since the three boxplots(d to f) are all curatable, then I am supposed to include them, even though only f has increase/decrease

Adeshile Oluwatosin (13:09:34) (in thread): > Include only the figure you curated from

Anne-Marie Sharp (13:15:51) (in thread): > Noted, I will correct all like that. thank you!

Adeshile Oluwatosin (13:42:11): > Hello > Kindly give a review of this curationhttps://bugsigdb.org/33869074Thanks

nithya (13:42:42): > https://doi.org/10.1128/msystems.00043-25In this article there are 6 groups (group 1-4 cancer, 5 healthy and 6 polyps). in the experiment we have 2 groups (0 and 1). Group 0 healthy, group 1: cancer. Now, polyps group should be added in cancer or healthy?

Mildred Anashie (14:01:15) (in thread): > I believe your curation is on point@Anne-Marie Sharponce you effect the changes Tosin talked about

Mildred Anashie (14:01:43) (in thread): > Well done@Adeshile Oluwatosin

Mildred Anashie (14:15:04) (in thread): > Hi@nithyaSo I don’t think you should include Polyps in either cancer or healthy. Each group was grouped individually and your group 0 and 1 would be based on the contrast you are curating. For context, this are the individual groups “All volunteers were divided into six groups: C1 (35 samples), C2 (101 samples), C3 (110 samples), and C4 (15 samples) groups corresponded to CRC stages I, II, III, and IV, respectively. The H group (120 samples) were healthy volunteers, and the P group (92 samples) were patients with polyps”.

UBNSEMS3S (14:51:29): > I spent some more time with this article:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2023.1094800/full#supplementary-material“Reducing bias in microbiome research: Comparing methods from sample collection to sequencing” and I still don’t know how or why Table S1 and Figure S2 differ since they seem to be the same comparisons. Table S1 appears to apply an additional filter of an MHT-corrected p-value that Figure S2 does not have, but the LDA scores in Table S1 do not seem to match those in Figure S2 (which only displayed LDA scores above 4.0). In light of these difficulties, I would curate Figure S2 since it is more expansive and call it good enough from there. - Attachment (Frontiers): Frontiers | Reducing bias in microbiome research: Comparing methods from sample collection to sequencing > BackgroundMicrobiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results. To investigate and…

Victoria (Burah) Poromon (14:54:43) (in thread): > Will do! > Well done@Adeshile Oluwatosin

nithya (15:09:35) (in thread): > Thanks@Mildred AnashieIf we skip polyps here then in sample size it will be skipped and in analysis also it will be skipped. Right?

Mildred Anashie (15:10:54) (in thread): > For the experiments that involve polypsyou’dnot skip it but if itdoesn’tthenthere’sno need including it as a group > > Just curate based on the comparisons done

nithya (15:12:14) (in thread): > Ok

Anne-Marie Sharp (15:35:13) (in thread): > Okay@Mildred Anashiethank you too

Victoria (Burah) Poromon (15:47:26) (in thread): > Hi@Adeshile OluwatosinAre you curating based on the main p values or the adjusted one for experiment 2? > > The table is showing adjusted p values. And the taxa in table 2a are all above 0.05

Adeshile Oluwatosin (15:48:01) (in thread): > Hi Victoria > Chloe mentioned ignoring the adjusted p values

Adeshile Oluwatosin (15:48:09) (in thread): > In this case

Victoria (Burah) Poromon (15:49:34) (in thread): > Yeah, okay > That means you have to make a note in the discussion page then,that’sall.

Victoria (Burah) Poromon (15:49:49) (in thread): > Everything else looks okay to me

Adeshile Oluwatosin (15:59:47) (in thread): > Thank you so much > What do you think about the taxa with missing ID? > Have not been able to find those taxa left as such in reviewed studies

Adeshile Oluwatosin (15:59:54) (in thread): > @Victoria (Burah) Poromon

Victoria (Burah) Poromon (16:00:30) (in thread): > I tried to find them too,I’llcheck again

Aiysha shahid (16:04:54): > Hi everyone! :tulip:Can someone check this paper -https://bugsigdb.org/39854172and let me know if I am on the right track? > In Exp-1, I didn’t use S1 in the signature as it was highly contradictory to the text and Fig-2. Specifically, the text and Fig-2 show that**** **********Odoribacter splanchnicus******is decreased in HIV+ people, but S1 indicates an increase. For Fig-4 & S6, the data is curatable, but I am unsure about the sample size. Should I use the sample size from Exp-1? > Also, an addition that the NCBI taxonomy hasn’t been updated yet—I’ll do that soon. Before that, I just want to confirm if everything else I’ve done is correct.:page_facing_up:Link to the paper:https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056Thanks!:blush: - Attachment (BugSigDB): Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV - BugSigDB > BACKGROUND: Inflammation and innate immune activation are associated with chronic HIV infection, despite effective treatment.Although gut microbiota alterations are linked to systemic inflammation, the relationships between the gut microbiome, inflammation and HIV remain unclear.

Adeshile Oluwatosin (16:07:21) (in thread): > Thanks

Anne-Marie Sharp (16:10:08) (in thread): > Nice work. well done with your curation@Adeshile Oluwatosin.

Anne-Marie Sharp (16:10:26) (in thread): > I also couldn’t find the taxa with missing ID

Adeshile Oluwatosin (16:16:29) (in thread): > Thank you@Anne-Marie Sharp

Anne-Marie Sharp (16:17:05) (in thread): > Well done with your curation@Aiysha shahid1)Most of the missing taxa (in red) are available on NCBI, try searching for them there. 2)I believe your sample sizes should remain same as Exp1

Adeshile Oluwatosin (16:17:19) (in thread): > Well done, I will check

nithya (16:24:49) (in thread): > Nice aiysha. I am curious to know how the fig.3 was curated

Aiysha shahid (16:42:24) (in thread): > Hi@Anne-Marie Sharpthanks! Yes, I know, as I already mentioned, that I haven’t updated the NCBI taxonomy. I’ll update that soon. Apart from that, does everything else look good to you?

Aiysha shahid (16:42:57) (in thread): > Hi@nithya, > For Figure 3, we can see thatBacteroidessp.,Alistipessp., and a few other taxa are marked in blue, and the same applies to the red ones. Additionally, the text provides clarity:“For example, higher intake of saturated and trans-unsaturated fatty acids was associated with an enrichment of Ruminococcus bromii, a SCFA producer, and depletion of key gut commensals such as Pyramidobacter piscolens and Bacteroides spp (Figure 3). Additionally, higher intake of sugars and calories correlated with depletion of SCFA-producing Bacteroides spp and Alistipes spp.

nithya (16:44:16) (in thread): > Did u check today morning meeting video. In that heatmap curation was mentioned.

nithya (16:46:19) (in thread): > From the meeting what i learnt was each row (HFD) should be considered as separate experiment.

Anne-Marie Sharp (17:03:51) (in thread): > @Aiysha shahidmy apologies,I missed that in the text. I will look through the curation/article more and give feedback

Aiysha shahid (17:06:28) (in thread): > Yes, I also noticed the same and was thinking along the same lines. That’s why I wanted to discuss it here before proceeding. Similarly,Figure 4and some in the Supplementary section would also need to be curated.

Eniola Kolawole (19:04:33): > Good morning everyone > > Please I need peer review on what@Precious Orakweand I worked on. Any corrections or additions will be highly welcomed. Thank you.http://bugsigdb.org/40032727 - Attachment (BugSigDB): Rhodococcus spp. interacts with human norovirus in clinical samples and impairs its replication on human intestinal enteroids - BugSigDB > Viral infections, particularly human norovirus (NoV), are a leading cause of diarrheal diseases globally.To better understand NoV susceptibility, it is crucial to investigate both host glycobiology and the influence of the microbiota.

Montana-D (19:09:24) (in thread): > Hi@Eniola Kolawole@Precious Orakwewell done on your curation > I’ll have a look

Montana-D (20:22:20) (in thread): > 1. I think you should make your sources of experiments 2 and 3 more defined; (supplementary Figure S2B. > 2. You could replace Rothia with the NCIB: 508215 > > 3. Does your experiment 4 have any signatures?

Precious Orakwe (20:44:45) (in thread): > Thank you<@UBNSEMS3S>for this assistant

Precious Chijioke (22:46:56): > Good Morning Everyone > Please@Kate RasheedI sent you a message on GitHub issue.

2025-04-04

Mildred Anashie (00:02:00) (in thread): > @Aiysha shahidNithya is right, thenyou’duse the asterisk per column to know whichtaxas were increased or decreased per experiment.I’lllook through to give a more detailed feedback, well done:pray:

Mildred Anashie (00:17:00) (in thread): > Good morning@Precious ChijiokeJust to mention thatI’mpositive our mentors would get to our messages once they see it, we are advised to be patient > Well done:blush:

Anne-Marie Sharp (02:23:29) (in thread): > Good morning@Precious Chijiokeyou can check your GitHub issue again if youhaven’t

Anne-Marie Sharp (02:25:19) (in thread): > Well done with your curation@Eniola Kolawole@Precious Orakwewe’ll have a look

Adeshile Oluwatosin (02:29:13) (in thread): > Good morning > Kindly be patient as she will get back to you@Precious Chijioke

Adeshile Oluwatosin (02:33:27) (in thread): > This is okay for figure 1a description > “LDA of bacterial genera quantified from clinical samples with NoV. The LDA score of the 15 taxa with significant differences (p < 0.05 in Kruskal-Wallis test, adjusted by FDR) in a LEfse analysis is presented.”

Joy (03:08:26): > Good morning everyone,@Montana-Dand I would appreciate your reviews on this study we curated. Thanks.https://bugsigdb.org/35071858 - Attachment (BugSigDB): Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking - BugSigDB > Introduction: Smoking affects the occurrence and development of many diseases.We attempt to study the structure of intestinal flora in the middle-aged and elderly population as well as how smoking affects the intestinal flora.

Adeshile Oluwatosin (03:20:47) (in thread): > Well done

Adeshile Oluwatosin (03:34:00) (in thread): > Figure 7 was not interpreted well, if curatableLow TBIL vs High TBIL : Bifidobacterium is increased > Low UA vs High UA: Bifidobacterium and shigella is increased > Low GGT vs High GGT: burkholderia is increased > Low BMI vs High BMI: paraprevotella is decreased > Low cr vs High cr: Sutterella is decreased > Low FBG vs High FBG: Bifidobacterium is decreased, shigella and sutterrela isincreased

Joy (03:36:05) (in thread): > Duly noted@Adeshile Oluwatosin

Montana-D (03:43:22) (in thread): > Thank you so much@Adeshile Oluwatosin

Aiysha shahid (04:13:03) (in thread): > Hi@nithya@Mildred Anashie, can you kindly look through the fig-4 and I think so S3-S4 is not curatable for per experiment’s, S5 and S6 can be curated as single experiment’s. Can you kindly confirm if I am correct or not. And what would be the Group 0 and Group 1

Oriade Adeola (04:37:22) (in thread): > Hello@Aiysha shahidHow are you doing? I had to hold on for a while to allow you adjust what You feel is necessary so we don’t contradict each other on the curation. so i just want to know how its going from your end.

Mildred Anashie (04:39:33) (in thread): > Thumbs up@Adeshile OluwatosinIn my opinion all good

Anne-Marie Sharp (04:46:16) (in thread): > @Precious Orakwe@Eniola Kolawole1)I agree with the above reviews > I have these to clarify as I am confused > 2)Your group names & definition in Exp1, I thought they should be IgG isotype control pAb (C) & anti-NoV GII.4 Sydney 2012 pAb (NoV)? > 3)In Exp1, Sig1&2, if you are curating for NoV, shouldn’t you use the colour code for NoV only and the LDA threshold? > 4)Did you later confirm if Fig S2b is curatable?

Precious Orakwe (04:49:04) (in thread): > @Anne-Marie SharpI don’t get your question

Anne-Marie Sharp (04:50:14) (in thread): > Sorry:pray:please which one, let me ask more clearly

Adeshile Oluwatosin (04:55:25) (in thread): > Thank you@Mildred Anashie

Adeshile Oluwatosin (04:55:50) (in thread): > Please write those acronyms in full

Aiysha shahid (04:58:43) (in thread): > Hi, I have made some adjustments and am working on it. As I mentioned earlier, there are a lot of things to be fixed, so it will take some time. Meanwhile, please continue working on the signatures derived from Figure 3. I noticed that only a few have been added so far—more need to be included. Also, we have to include signatures only for the two specified groups.

Oriade Adeola (04:59:54) (in thread): > Ok thank you.

Mildred Anashie (05:08:46) (in thread): > Hi@Joy@Montana-DI noticed yo included matched on and confounders but I do not see that mentioned in the article. For the LefSe I think you can include A and B as the source. I also do not see where Shannon and Chao1 were said to be decreased, they were mentioned but with no mention on significance, asides this ’We detected no significant difference between smokers and nonsmokers with respect to α-diversity evaluated in terms of species richness and diversity indices’.

Montana-D (05:19:45) (in thread): > Thank you@Mildred Anashie, we noticed that and took out the match ons > We shall hence go ahead to take out the alpha diversities > Thank you again

Eniola Kolawole (05:19:54) (in thread): > Ok. Thank you@Montana-D.

Mildred Anashie (05:23:49) (in thread): > I still see it in the first experiment, for the alpha diversity you should record Richness as unchanged and hopefully someone can make an input on if the other diversity measures mentioned in the article should also be recorded as unchanged or left blank.@Montana-D

Montana-D (05:24:40) (in thread): > Okay, noted:+1:@Mildred Anashie

Eniola Kolawole (05:25:36) (in thread): > @Anne-Marie Sharpyou meant, the acronym isn’t right for the group 1 right?

Anne-Marie Sharp (05:31:02) (in thread): > @Eniola KolawoleYes, from what I saw in the paper it should be Group 0 name: IgG isotype control pAb (C) Group1name: anti-NoV GII.4 Sydney 2012 pAb (NoV) Group1 definition: bacteria captured by the anti-NoV GII.4 Sydney 2012 pAb

Anne-Marie Sharp (05:31:13) (in thread): > Please confirm

Precious Orakwe (05:32:05) (in thread): > Yes, that is what we did for the group names

Eniola Kolawole (05:32:48) (in thread): > That was exactly what was there@Anne-Marie Sharp. I think it’s the + sign that’s confusing.

Anne-Marie Sharp (05:34:50) (in thread): > Please crosscheck what is in your curation with what I typed above, they are not exactly the same.

Eniola Kolawole (05:48:26) (in thread): > Kindly check back@Anne-Marie Sharpto see if it correlates with what you meant. Thanks.

Adeshile Oluwatosin (05:49:56) (in thread): > Which figure describes the alpha diversity, let me check

Mildred Anashie (05:52:01) (in thread): > No figure@Adeshile OluwatosinIt’sjust within text

Mildred Anashie (05:53:29) (in thread): > Just to note@Montana-DYou’drecord unchanged, Only if you have an experiment as smokers vs non smokers

Montana-D (05:54:04) (in thread): > Hence only for experiment 1 I guess?@Mildred Anashie

Adeshile Oluwatosin (05:54:12) (in thread): > Richness is unchanged for Experimemt 1only > Leave the rest blank

Mildred Anashie (05:54:38) (in thread): > That’scorrect@Montana-D

Montana-D (05:54:39) (in thread): > We took it out for all other experiments except 1 already

Montana-D (05:55:22) (in thread): > Okay, just richness@Adeshile Oluwatosin?

Montana-D (06:00:48) (in thread): > What about your exp.4@Eniola KolawoleAny signatures?

Eniola Kolawole (06:01:18) (in thread): > @Montana-DI don’t get your second correction please. Replacing Rothia with NCIB:508215!!!

Joy (06:01:52) (in thread): > Thank you all!

Eniola Kolawole (06:02:08) (in thread): > No please@Montana-Dcan’t find any. Any idea?

Anne-Marie Sharp (06:02:37) (in thread): > Yes, it’s okay now. In the article, the words ‘recognized & captured’ were both used in describing the groups. To make it uniform, use one through out the curation.

Anne-Marie Sharp (06:04:47) (in thread): > @Eniola Kolawole@Precious Orakwein our previous group chats here, we were deliberating on if Fig S2b is curatable, since it is normalized counts. which is why I asked if you confirmed(during office hours/from any mentor) that it is curatable

Adeshile Oluwatosin (06:06:41) (in thread): > Shannon and chao1 statements were not specific enough to any of the comparisons we have curated. Henceignore them

Montana-D (06:08:18) (in thread): > @Eniola KolawoleIn your curation, the signature you put in Rothia, has an x marked to it, meaning you didn’t pick from the dropdown menu, so to save you the harsel I provided the taxonomic ID so it takes away the “X” > > I haven’t checked properly, may be someone could help with that, but I’ll check again. Else it is needless creating an experiment with you significant taxa to curate

Eniola Kolawole (06:09:10) (in thread): > Okay@Montana-DI just did that but it’s still the same

Anne-Marie Sharp (06:10:21) (in thread): > Well done with your curation@Joy@Montana-D

Anne-Marie Sharp (06:11:46) (in thread): > @Eniola Kolawoletype just the number, do not include the NCBI that comes before the number

Eniola Kolawole (06:12:12) (in thread): > Thank you@Anne-Marie Sharp

Eniola Kolawole (06:15:28) (in thread): > Thanks@Montana-Dand@Anne-Marie SharpIt’s showing now.

Eniola Kolawole (06:19:10) (in thread): > @Anne-Marie Sharpshe said it’s curatable

Montana-D (06:32:37) (in thread): > @Adeshile Oluwatosin@Mildred AnashieWe have effected all your suggestions and corrections, could you please do us the honors by checking for any lapses? > We would greatly appreciate:pray:

Adeshile Oluwatosin (07:12:37) (in thread): > Alright, well done

Adeshile Oluwatosin (07:17:06) (in thread): > Exp7/Sig 2 should be deleted (it’s a repitition) > Condition for experiment 2-7 should be specific to the comparison > I think Chloe gave an hint yesterday

Adeshile Oluwatosin (07:17:23) (in thread): > @Montana-D

Montana-D (07:18:33) (in thread): > Exp.7/sig2, deletion has been requested

Montana-D (07:18:59) (in thread): > Please do you have a suggestion to the condition?

Precious Orakwe (07:53:18): > Good afternoon everyone, Please I would appreciate your reviews on this study.https://bugsigdb.org/37065158Thank you. - Attachment (BugSigDB): Reducing bias in microbiome research: Comparing methods from sample collection to sequencing - BugSigDB > BACKGROUND: Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results.

Joy (08:30:30) (in thread): > Well done@Precious Orakweon your curation, we will have a look.

Mildred Anashie (08:37:56) (in thread): > Well done on your curation@Precious Orakwe:clap:I’llhave a look

Mildred Anashie (08:39:16) (in thread): > Well done again@Montana-Dand@Joy

Montana-D (08:49:44) (in thread): > Thank you@Mildred Anashie,@Adeshile Oluwatosin@Anne-Marie Sharpfor your appreciation, guidance and corrections@Joyand I are super grateful:pray:

Adeshile Oluwatosin (08:53:10) (in thread): > Something like@Montana-Dcheck the definition if it matches or ifthere’sa more specific/suitable conditionExperiment 2: fasting blood glucose measurement > Exp 3: creatinine measurement > Exp 4: Body mass index > Exp 6: uric acid measurement > Exp 7: bilirubin measurement

nithya (09:29:49) (in thread): > ok aiysha let me have a look at it

Precious Orakwe (09:32:45) (in thread): > Thank you teammates

nithya (09:36:26) (in thread): > 1. Fig 4 is a heatmap of correlation matrix of microbata and biomarkers. while creating signature we report it with respect to disease (HIV) increase or decrease. This heat map doesnot give information of the HIV or non HIV patients so i think this heatmap is tough to curate

Bola (09:45:52): > Good afternoon everyone, I have issue on signature creationdate.itdoesn’t load…it brings ” This page is not responding”. please what can i do to resolve this

Joy (09:50:47) (in thread): > Hi@Precious OrakweIn your signature 1, Experiment 1, The taxon: Escherichia_Shigella is written like this:point_right:Escherichia/Shigella sp. with the ID: 1940338. > Check here:NCBI. > > 2. Actinobacteriota isActinomycetota with the ID: 201174 - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (09:53:34) (in thread): > I’lltake a look at this soon@Aiysha shahid

Precious Orakwe (09:54:29) (in thread): > @Bolaplease what do you mean by signature creation date.

Victoria (Burah) Poromon (09:54:52) (in thread): > Hello@BolaIt’sa network issue, just try it again

nithya (09:55:16) (in thread): > 2. S3 is a very clear explanation enriched and depleted species. but all these heatmaps are overall representation of the species abundance in HIV patients. so it cannot be curated as far as i know.

Precious Orakwe (09:55:43) (in thread): > Have you tried refreshing the page, if yes, then wait for a while it will come up, it’s network, I experienced the same thing.

Precious Orakwe (09:57:49) (in thread): > Yes, I saw it, I didn’t want to change it, because@Kate Rasheedsaid if I don’t see a taxon the way it is I should leave it the way it is in the paper, i left is because of thespin front of it

Joy (09:58:20) (in thread): > Hi@BolaKindly watch the video here:point_right:Create signature - Attachment (BugSigDB): Project:About > .

Joy (09:59:10) (in thread): > It’s ok.

Bola (10:00:51) (in thread): > @Victoria (Burah) Poromonokay, will do just that. Thank You

Kate Rasheed (10:01:04) (in thread): > @Precious OrakweThis example is different from the previous one you worked on.

Bola (10:02:05) (in thread): > @Joyokay …Thanks

Anne-Marie Sharp (10:02:07) (in thread): > @Eniola Kolawoleyou’re welcome. Okay. If its curatable then I think you should curate the significant ones (*) with p<0.05. Eg if experiment 2 is T vs NoV, Signature1 should haveLigilactobacillus murinus and Ligilactobacillus animalis as increased in NoV

Bola (10:03:48) (in thread): > @Precious OrakweThank you so much

Joy (10:05:48) (in thread): > @Precious OrakweChange your V4 to the lower region and remove the negative infront of it. > > This is From the curation policy:point_right:Sequencing type[**edit* | *edit source**] > * Two main types: 16S and WMS (Whole Metagenome Sequencing) > * 16S variable regions (lower and upper) e.g. V3-V4 (V3 will be lower bound and V4 will be upper bound). > * If there is only one variable region given e.g V4, use only lower bound. > Rarely, the paper may be missing the sequencing variable region for 16S. If so, leave the variable region blank. - Attachment (BugSigDB): Curation Policy > . - Attachment (BugSigDB): Curation Policy > .

nithya (10:16:50) (in thread): > As i told you before a heatmap is a representation of the expression of the two variables (biomarkers vs microbata). for eg: Fig 4 IL16 in the heatmap its expression is high in few microbata and low in few microbata (color change ). We are curating our results with respect to the disease state (HIV) so in this heatmap if the linkage analysis is performed using the sample as a varibale then that can be curated. or if the heatmap is generated only with the diseased sample then that also can be curated. Figure 4 can be curated if that is the heatmap of the disease state alone. if thats the case you need create a seperate experiment for each biomarker say for example IL16 then you can create signature as increase/ decrease wrt the pvalue (star) in the heatmap. Aiysha i have explained you what i understand about heatmaps. please take assistance of the mentors/co mentors too.

Anne-Marie Sharp (10:18:14) (in thread): > Well done with your curation@Precious Orakwe1)In antibiotics exclusion, put just ‘3 months’ 2)The location should include Netherlands and the Caribbean islands Bonaire, St. Eustatius, and Saba

Precious Orakwe (10:25:20) (in thread): > @Anne-Marie Sharpin the study, it didn’t say that it was excluded, that is why I recorded it like that.

Anne-Marie Sharp (10:27:03) (in thread): > @Precious Orakwe’None of the participants of both studies had undergone antibiotic treatment 3 months prior to collection’, this means that the antibiotics exclusion was 3months

Precious Orakwe (10:27:05) (in thread): > I thought we should curate 1 country only?

Anne-Marie Sharp (10:27:46) (in thread): > The curation policy says it can be multiple countries in some studies.

Precious Orakwe (10:28:09) (in thread): > Okay@Kate Rasheedthank@Joy

Precious Orakwe (10:28:31) (in thread): > Alright@Anne-Marie Sharp

Anne-Marie Sharp (10:33:18) (in thread): > In Experiment4 Signature1 Bacteroides_vulgatus should bePhocaeicola vulgatus - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (10:44:49) (in thread): > @Anne-Marie SharpFrom a bit of researchCaribbean IslandsBonaire, St. Eustatius, and Saba are part of kingdoms in Netherlands, So Netherlands only is fine

Anne-Marie Sharp (10:47:48) (in thread): > @Mildred Anashiethanks for checking that out.@Precious Orakweyour location is still on point:+1:

Mildred Anashie (10:50:15) (in thread): > Well done@Precious OrakweI see some significant results at the Phylum level in Figure 3b that you haven’t curated yet. > You can use the P values to curate, See this “We further investigated the microbial composition at the phylum level (Figure 3B, Supplementary Figure 1B ). Sample storage at RT without buffer (RT-ZYCON) influences the microbiome with a higher proportion of Proteobacteria (p= 0.000488) and Verrucomicrobiota (p= 0.0143) and a lower abundance of Firmicutes (p= 0.000488). Samples in the stabilization buffer showed an overrepresentation of Bacteroidota (RT-ZYBUFp= 0.000488, RT-OMBUFp= 2.32E-09), Proteobacteria (RT-ZYBUFp= 0.00342, RT-OMBUFp= 2.91E-06), and underrepresentation of Actinobacteriota (RT-ZYBUFp= 0.000488, RT-OMBUFp= 7.87E-05) compared to standard stored samples. Furthermore, a lower proportion of Firmicutes was observed in samples collected using the OMNIgene·GUT collection tubes (p= 0.0025) when compared to the standard frozen condition”.

Precious Orakwe (10:53:56) (in thread): > Yes@Anne-Marie Sharp, I have already checked that, they are all in Netherlands

Anne-Marie Sharp (10:59:41) (in thread): > @Precious Orakwegreat!, The description for Figure S2a should be about just Figure S2a.(it should not include what is not in Figure S2a such as RT-OMBUF, -80-OMCON etc.) Or you simply use ‘LEfSe analysis showing the significantly distinguishing taxa between the different storage methods based on an LDA score >4.0.’

Anne-Marie Sharp (11:03:11) (in thread): > This should apply to the Source description in all the experiments also

Anne-Marie Sharp (11:10:23) (in thread): > Check anywhere in your curation you have ‘Ominigine’ eg ‘Ominigine buffer’ in Exp4 group1 name and correct the spelling to Omnigene

Mildred Anashie (11:18:06) (in thread): > I see three experiments there, done with Wilcoxon; -80-ZYCON vs RT-ZYCON, -80-ZYCON vs RT-ZYBUF and -80-OMCON vs RT-OMBUF. Also, Fig 8 has a few as well that you haven’t recorded yet you can find the alpha diversity in Supp Fig 4

Anne-Marie Sharp (11:21:12) (in thread): > @Precious OrakweIn Experiment4, signature2, Firmicutes is Bacillota not Bacillati. Go through your curation and change any Bacillati to Bacillota

Precious Orakwe (13:40:52) (in thread): > I checked Bacillati is the synonym for Firmicutes

Precious Orakwe (13:42:29) (in thread): > @Mildred AnashieI asked Chloe yesterday, she said I should curate just supplemtary fig 2

Mildred Anashie (13:44:10) (in thread): > I was at the meeting and I think what Chloe implied was regarding supplementary fig 2 and the table below it…I’llwatch the recordings to be sure butI don’tthink you should ignore those experiments and the significant signatures@Precious Orakwe

Anne-Marie Sharp (13:46:45) (in thread): > @Precious OrakweOkay. Yes it shows as a synonym but the NCBI blast name for firmicutes is Bacillota. It can be confusing. Bacillati is kingdom, Bacillota is phylum, I believe what is in the article is phylum. So you should use Bacillota

Aiysha shahid (15:29:59) (in thread): > Yes,I am also confuse in fig-4,for fig-3,we can curate single experiments, and derive data from table-3,but not sure about fig-4,will ask our mentor. Thanks!

Aiysha shahid (15:30:53): > Hi @Svetlana Ugarcina Perovic****,****Could you kindly check and confirm whether I should create separate experiments for each row inFigure 3andFigure 4of this paper:https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056****? ******** Thank you!****

iniobong simeon (15:43:21): > Hello, please i need review on this curation, please.https://community-bioc.slack.com/archives/D08JGHE242X/p1743347596662219 - Attachment (BugSigDB): 34690948/Experiment 2 > .

Aiysha shahid (15:50:36) (in thread): > Hi,Well done! Could you kindly share the link to your research paper? > Meanwhile, inExperiment 2, Signature 1,Clostridialescan be curated asEubacterialeswith theID-186802.@iniobong simeon

Anne-Marie Sharp (15:53:42) (in thread): > Nice one@iniobong simeonwe’ll review. Are you deleting experiment1? Or should we review the full curation with the link below?

Anne-Marie Sharp (15:55:25) (in thread): > @Aiysha shahidtry this for the full curation:https://bugsigdb.org/34690948and this for the paper:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.700718/full - Attachment (BugSigDB): Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation - BugSigDB > Intestinal dysmotility is common in many diseases and is correlated with gut microbiota dysbiosis and systemic inflammation.Functional constipation (FC) is the most typical manifestation of intestinal hypomotility and reduces patients’ quality of life. - Attachment (Frontiers): Frontiers | Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation > Intestinal dysmotility is common in many diseases and is correlated with gut microbiota dysbiosis and systemic inflammation. Functional constipation (FC) is …

Aiysha shahid (16:08:44) (in thread): > Thanks@Anne-Marie Sharp

Aiysha shahid (16:10:32) (in thread): > Also@iniobong simeon, As Functional Constipation is not available you can use the Condition as-“chronic constipation” . As according to the google, Functional Constipation is also known as Chronic Constipation. Text for your reference- “Functional constipation is also known as chronic idiopathic constipation, and may be defined as constipation that does not have an anatomical or physiological cause and occurs at least two days a week for at least three months, but does not have sufficient criteria for IBS.”

Aiysha shahid (16:12:19) (in thread): > And kindly confirm ,I can’t seen any signature’s for Experiment-1.@iniobong simeon

Precious Orakwe (16:49:12) (in thread): > @Aiysha shahidin my opinion I would say yes

Adeshile Oluwatosin (17:05:29) (in thread): > The correct condition is “chronic constipation” > I have not opened the curation yet

Mildred Anashie (17:06:24) (in thread): > Hi@Aiysha shahidI think it should be curated, each column seems to show an experiment and you’d use the green asterisk to know which was significant per experiment. That’s what I believe is in Fig3 as wellYou can use the caption to understand better, see an excerpt***** “Heatmap showing the correlation of the differentially abundant (DA) species with the inflammatory cytokines and T-cell surface markers for people with human immunodeficiency virus (HIV) and those without HIV. DA was assessed by analysis of compositions of microbiomes with bias correction (ANCOM-BC) while adjusting for the covariates based on filtered species abundance (present in at least 10% of samples and with maximum reads ≥10). False discovery”*****

Mildred Anashie (17:06:55) (in thread): > Hi@Aiysha shahidI think it should be curated, each column seems to show an experiment and you’d use the green asterisk to know which was significant per experiment. That’s what I believe is in Fig3 as wellYou can use the caption to understand better, see an excerpt***** “Heatmap showing the correlation of the differentially abundant (DA) species with the inflammatory cytokines and T-cell surface markers for people with human immunodeficiency virus (HIV) and those without HIV. DA was assessed by analysis of compositions of microbiomes with bias correction (ANCOM-BC) while adjusting for the covariates based on filtered species abundance (present in at least 10% of samples and with maximum reads ≥10). False discovery”*****

Aiysha shahid (17:18:34) (in thread): > Yes, I was editing that when got your text@Adeshile Oluwatosin:sweat_smile:

Aiysha shahid (17:21:40) (in thread): > Hi@Mildred Anashie, any idea about the Group-0 and Group-1 in this?

Aiysha shahid (17:46:58) (in thread): > Hi@iniobong simeon, I noticed that you’ve already submitted your study for official review. Just a quick heads-up—as per the instructions, we can have a peer review before submitting it for official review. You can refer to this thread for more details:Slack Thread - Attachment: Attachment > A peer review should be done here in Slack, transparently, so the others can learn too. Thanks! > Feel free to do a peer review but not after submitting your curation for an official review.

2025-04-05

Adeshile Oluwatosin (05:08:42) (in thread): > Would you rather curate unclassified lactobacillus ruminis as it is or as “unclassified ligilactobacillus ruminis” > > And unclassified Enterobacteraerogenes as it is or as “unclassified klebsiella aerogenes”@Mildred Anashie@Victoria (Burah) Poromon

Anne-Marie Sharp (05:42:35) (in thread): > Hello@Adeshile Oluwatosinconsidering that their names have both been updated on NCBI, I feel they should be curated with their new names but we’re also told to curate as it appears in the paper. So it’ll be better a mentor confirms this.

Adeshile Oluwatosin (05:43:41) (in thread): > I curated as the latter for now in this case. Thanks

Anne-Marie Sharp (05:45:13) (in thread): > Okay, you’re welcome

Victoria (Burah) Poromon (05:49:35) (in thread): > Hi@Adeshile OluwatosinI’d curateas “unclassified ligilactobacillus ruminis”and “unclassified klebsiellaaerogenes”

Adeshile Oluwatosin (05:50:01) (in thread): > That’swhat I did:relaxed:Gracias

Precious Orakwe (06:09:28) (in thread): > Thanks@Mildred Anashiefor explaining better

Mildred Anashie (06:19:05) (in thread): > I’ddo what you did too@Adeshile Oluwatosin:blush:

Precious Chijioke (06:25:07) (in thread): > Well done@iniobong simeon

Precious Chijioke (07:43:14): > Good Day and Happy Weekend Everyone > Please in identifying the correct group 1 definition of an experiment from a study how can I search for it if it’s not capture in the figure the experiment was curated from?

Anne-Marie Sharp (07:52:41) (in thread): > Happy weekend@Precious ChijiokeThe group1 definition explains what group1 is and it is gotten from the text/article. Eg. in this curationhttps://bugsigdb.org/40108637/Experiment_5Group 1 name: BV- Positive (BV: Bacterial Vaginosis) at Visit 2Group 1 definition: women classified as having bacterial vaginosis based on the Nugent score - Attachment (BugSigDB): 40108637/Experiment 5 > .

Anne-Marie Sharp (07:54:00) (in thread): > Look carefully through the article for where that group1 was mentioned, you will see how they described/defined it.

Anne-Marie Sharp (07:58:28) (in thread): > E.g In the articlehttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-025-02066-1for the curation above, these are the lines where the Group1 definition above was gotten: 1)As previously described in [59], one lateral vaginal wall swab was rolled onto a glass slide and Gram-stained for microscopy to evaluate BV status using Nugent score. & 2)As previously reported, STI and BV prevalence were high in this cohort, with 42.5% of the women having at least one STI and 50.4% of the women being BV positive by Nugent scoring at visit.. - Attachment (BioMed Central): Exploring the female genital tract mycobiome in young South African women using metaproteomics - Microbiome > Background Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. Results We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. Conclusions The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract - Attachment (BioMed Central): Exploring the female genital tract mycobiome in young South African women using metaproteomics - Microbiome > Background Female genital tract (FGT) diseases such as bacterial vaginosis (BV) and sexually transmitted infections are prevalent in South Africa, with young women being at an increased risk. Since imbalances in the FGT microbiome are associated with FGT diseases, it is vital to investigate the factors that influence FGT health. The mycobiome plays an important role in regulating mucosal health, especially when the bacterial component is disturbed. However, we have a limited understanding of the FGT mycobiome since many studies have focused on bacterial communities and have neglected low-abundance taxonomic groups, such as fungi. To reduce this knowledge deficit, we present the first large-scale metaproteomic study to define the taxonomic composition and potential functional processes of the FGT mycobiome in South African reproductive-age women. Results We examined FGT fungal communities present in 123 women by collecting lateral vaginal wall swabs for liquid chromatography-tandem mass spectrometry. From this, 39 different fungal genera were identified, with Candida dominating the mycobiome (53.2% relative abundance). We observed changes in relative abundance at the protein, genus, and functional (gene ontology biological processes) level between BV states. In women with BV, Malassezia and Conidiobolus proteins were more abundant, while Candida proteins were less abundant compared to BV-negative women. Correspondingly, Nugent scores were negatively associated with total fungal protein abundance. The clinical variables, Nugent score, pro-inflammatory cytokines, chemokines, vaginal pH, Chlamydia trachomatis, and the presence of clue cells were associated with fungal community composition. Conclusions The results of this study revealed the diversity of FGT fungal communities, setting the groundwork for understanding the FGT mycobiome. Video Abstract

Precious Chijioke (07:58:29) (in thread): > Thank you@Anne-Marie SharpI’ll check it out

Anne-Marie Sharp (08:07:00) (in thread): > You’re welcome:pray:@Precious Chijioke

Mildred Anashie (11:24:01) (in thread): > So like the first column, they were checking IL2 (I believe that stands for interleukin 2, just check the paper to confirm). The group 0 would be something like Low-IL2 or IL 2 (decreased) and group 1 would be High-IL2 or IL2 (Increased). > > You’d then curate the taxa with green asterisk in that column only, the enriched species (Increased abundance) are those with the positive values highlighted in purple and depleted species (decreased abundance) are those with the negative values highlighted in green. > > You can also go through this curation to understand better and also get an idea based on conditionshttps://bugsigdb.org/35071858But on a second thought this looks like a lot of work and I don’t know if this inflammatory cytokines and T-cell surface markers should be curatedas that figure alone would amount to almost 15 experiments. - Attachment (BugSigDB): Characteristics of the Intestinal Microorganisms in Middle-Aged and Elderly Patients: Effects of Smoking - BugSigDB > Introduction: Smoking affects the occurrence and development of many diseases.We attempt to study the structure of intestinal flora in the middle-aged and elderly population as well as how smoking affects the intestinal flora.

Aiysha shahid (12:22:01) (in thread): > Thanks@Mildred Anashie:raised_hands:

Mildred Anashie (12:41:09) (in thread): > You are welcome:heart:

Juliana Kentomahun Mautin (14:48:39): > Hello everyone:blush:, hope everyone’s weekend is giving exactly what it needs to give . Chill vibes, good food, and zero stress! If not, hit pause, grab your favorite snack, and treat yourself. You deserve it:smiling_face_with_3_hearts::smiling_face_with_3_hearts::smiling_face_with_3_hearts:. See Y’all next week:hugging_face::hugging_face::hugging_face:.

Mildred Anashie (14:50:23) (in thread): > Hi@Juliana Kentomahun MautinNot exactly:disappointed:I’mstill in work mode > Thank you though:heart:See you next week:blush:

Anne-Marie Sharp (15:53:48) (in thread): > Hello@Juliana Kentomahun Mautinthanks, enjoy your weekend too:raised_hands:

Aiysha shahid (17:28:38) (in thread): > Yes, that’s what I found confusing. Figure 3 clearly appears to be based on a single experiment. However, for Figure 4, there is no mention of the sample size. It states:**“********Building on the links between diet, microbiota, and cardiovascular outcomes,******* we explored associations between microbial taxa and 38 inflammatory biomarkers. Previous work within this cohort identified a distinct inflammatory phenotype defined by elevated circulating levels of I-FABP, T-cell stimulation, and systemic inflammation markers that were associated with subclinical CAD and prevalent CVD [17].”*This clearly suggests that the outcomes presented in Figure 4 are built upon the findings of previous experiments.

Aiysha shahid (17:42:09) (in thread): > Thanks, But what I found confusing is that Figure 3 clearly appears to be based on a single experiment. However, for Figure 4, there is no mention of the sample size. It states: “Building on the links between diet, microbiota, and cardiovascular outcomes, we explored associations between microbial taxa and 38 inflammatory biomarkers. Previous work within this cohort identified a distinct inflammatory phenotype defined by elevated circulating levels of I-FABP, T-cell stimulation, and systemic inflammation markers that were associated with subclinical CAD and prevalent CVD [17].” This clearly suggests that the outcomes presented in Figure 4 are built upon findings from previous experiments. Also do we curate single experiments based on “inflammatory cytokines and T-cell surface markers”?

2025-04-06

Precious Chijioke (05:19:46) (in thread): > Hello@Juliana Kentomahun Mautinthe weekend is not really giving. Work mode is on. > Happy New Week in advance

Adeshile Oluwatosin (09:32:25): > Happy weekend everyone > > Kindly give a review if online, thank you so muchhttps://pmc.ncbi.nlm.nih.gov/articles/PMC10648458/https://bugsigdb.org/37960154 - Attachment (PubMed Central (PMC)): Rifaximin Ameliorates Loperamide-Induced Constipation in Rats through the Regulation of Gut Microbiota and Serum Metabolites > Structural changes in the gut microbiota are closely related to the development of functional constipation, and regulating the gut microbiota can improve constipation. Rifaximin is a poorly absorbed antibiotic beneficial for regulating gut …

Adeshile Oluwatosin (09:32:38) (in thread): > * Is A2, bacterium A2 : 166648 > Or Lachnospiraceae bacterium A2 or left as it is. > * Should Gut metagenome be curated > * Is Actinobacteria (class) acidimicrobiia

Adeshile Oluwatosin (09:34:01) (in thread): > * “s_Clostridium_leptum_g_norank” > unclassified clostridium leptum or just clostridium leptum > > Gracias - File (JPEG): IMG_4144

Adeshile Oluwatosin (09:37:30) (in thread): - File (JPEG): IMG_4145

Adeshile Oluwatosin (09:37:45) (in thread): > Lastly, all of this curated as just unculturedbacterium - File (JPEG): IMG_4146

Adeshile Oluwatosin (09:41:51) (in thread): > Hi@Juliana Kentomahun MautinThank you:relieved:

Juliana Kentomahun Mautin (09:52:01) (in thread): > Hi@Mildred Anashieand@Precious Chijioke. > > I can relate . sometimes the hustle just doesn’t pause. I hope you still get a moment to breathe and reset. Rooting for you always:smiling_face_with_3_hearts::smiling_face_with_3_hearts::smiling_face_with_3_hearts:You’ve got this:muscle::muscle::muscle::muscle:.

Precious Orakwe (10:22:45) (in thread): > Hi@Adeshile Oluwatosinwell done, here are my little suggestions; > > A2 or bacterium A2 : 166648 curate as Lachnospiraceae bacterium A2 > > s_Clostridium_leptum_g_no rank curate as Clostridium leptum

Precious Orakwe (10:24:38) (in thread): > from my little research “If the strain is associated with the Lachnospiraceae family and the A2 is a strain or isolate designation, then”Lachnospiraceae bacterium A2” is more informative and taxonomically meaningful”

Adeshile Oluwatosin (10:26:26) (in thread): > Thank you so much for your opinion

Precious Orakwe (11:00:23): > Good afternoon team, happy new week. Please I’d appreciate a review of this study and every correction is much appreciated. Thank you.https://bugsigdb.org/37065158 - Attachment (BugSigDB): Reducing bias in microbiome research: Comparing methods from sample collection to sequencing - BugSigDB > BACKGROUND: Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results.

Anne-Marie Sharp (11:41:28) (in thread): > Well done@Adeshile Oluwatosin& happy weekend. 1) I think A2 should be curated as it is, its stated as a genus in the article, but the alternatives you mentioned are species. 2) I believe gut metagenome should be curated, its a specie and appears valid even on NCBI. 3)In Experiment4, signature2 the source should be just for that signature & you should adjust the description for the source also. Please can you explain the other questions?

Anne-Marie Sharp (11:59:52): > Hello everyone, please I need some guidance. In this article I am curating,https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1453989/full1)figures 5,6 & 7 in the main article & some figures in the supplementary material show statistical comparison of absolute > abundances between 2groups, each comparison has a p-value but I could not find a specific p-value stated with the statistical test, that was used as a threshold for all and I am unsure how and if it can be curated. 2)Table S1 also seems curatable but has same pvalue issue. - Attachment (Frontiers): Frontiers | Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan > IntroductionTreatment of rodents with the AT1 blocker (ARB) telmisartan (TEL) has an anti-adipose effect. Among other mechanisms, we also have attributed the…

Anne-Marie Sharp (12:05:40) (in thread): > Hello@Precious Orakwewell done with your curation. We’ll review:+1:

Adeshile Oluwatosin (12:08:50) (in thread): > Well done@Precious Orakwe

Precious Chijioke (12:22:56) (in thread): > @Adeshile Oluwatosinwell done on your curation. > > A2 should be curated the way it is in the article as already stated by@Anne-Marie Sharpit’s a genus in the article while the alternatives you mentioned are species > > gut metagenome should be curated, it’s a valid species in NCBI > Yes, Actinobacteria (class) is acidimicrobiia. In NCBI, the BLAST name of Acidimicrobiia is Actinobacteria with Rank: class

Precious Chijioke (12:24:38) (in thread): > Can you paraphrase other questions, it’s not clear

Precious Chijioke (12:26:50): > Good Afternoon Everyone > I’m curating a paper with@chiamaka Ucheand will like to confirm if Figure 3b and 5b is curatable > Fig. 3b:https://www.cell.com/cms/10.1016/j.xcrm.2024.101836/asset/46499d60-3108-4340-9199-6a0d5f3e6f0d/main.assets/gr3_lrg.jpg5b:https://www.cell.com/cms/10.1016/j.xcrm.2024.101836/asset/647baf9e-43a2-407c-a36f-3eaa2343ef5c/main.assets/gr5_lrg.jpgStudy Link:https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(24)00607-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2666379124006074%3Fshowall%3Dtrue#fig3

Precious Chijioke (12:27:51) (in thread): > Well done@Precious OrakweI’ll look at it

Adeshile Oluwatosin (12:31:24) (in thread): > Well done@Anne-Marie Sharp > * I see figure 5B curatable > Chloe as explained previously to use the direction of the red (bigger part) in this case as increased or decreased. (BL/6>f). > Verrucomicrobiota is decreased. See this too “At the phylum level, we identified a decreased abundance of Actinobacteriota, Desulfobacterota, and Firmicutes in the BL/6>fTEL mice.” > > Same for 6B and 7B. > The direction of the bigger part of the red determines if increased or not.We’vealso always mentioned using 0.05 if not stated in the paper

Adeshile Oluwatosin (12:32:51) (in thread): > There aresimilar cases where they are curated in a way explained by@Precious OrakweExtreme cases like curating RF39 as “Enterococcaceae bacterium RF39”

Adeshile Oluwatosin (12:33:21) (in thread): > I meant are you also of the opinion of curating all of the taxa stated in the image as “uncultured bacterium”

Adeshile Oluwatosin (12:33:37) (in thread): > Thank you so much for your response@Anne-Marie Sharp@Precious Chijioke

Precious Chijioke (12:37:44) (in thread): > @Anne-Marie SharpI agree with what@Adeshile Oluwatosinsaid

Precious Chijioke (12:47:31) (in thread): > @Adeshile Oluwatosinnow I got it > I think you should curate all taxa with “uncultured bacterium” as uncultured bacterium. I tried checking some on NCBI and couldn’t find it so curate as seen in the image.

Anne-Marie Sharp (13:28:26) (in thread): > @Adeshile Oluwatosinokay, that’s interesting to note, but then how do we confirm that the A2 mentioned is associated with Lachnospiraceae family?

Adeshile Oluwatosin (13:30:56) (in thread): > I’m notcertain as well hence why I asked > But when I searched google > I was referred to Lachnospiraceae bacterium A2

Anne-Marie Sharp (13:45:48) (in thread): > @Adeshile OluwatosinOkay, I saw this in the curation policy ‘Sometimes papers report an unclassified species, but provide classification up to the genus level. Such unclassified species should be excluded from the curation as opposed to curating the taxon up to the genus level.’ > These uncultured bacteria in your article, are they what is referred to above as unclassified species? If yes, I feel they should be excluded.If no,I’mfollowing this thread to know how this is sorted out:raised_hands:

Anne-Marie Sharp (14:05:12) (in thread): > Thank you@Precious Chijioke@Adeshile Oluwatosinthank you for clarifying the p-value.

Anne-Marie Sharp (14:07:33) (in thread): > @Adeshile Oluwatosinplease if I understood you well, in Figure5B, Verrucomicrobiota is decreased in BL/6>fTEL, because the big red part is pointing towards the right?

Anne-Marie Sharp (14:09:05) (in thread): > And if I’m using p-value: 0.05 for all, then I’m not to curate Verrucomicrobiota as it is >0.05, right?

Adeshile Oluwatosin (14:09:13) (in thread): > They should not be excluded in this case as they are stated to be significant in the article I curated > If you check Table S1 and S2 > Just uncultured bacterium, uncultured rumen bacterium and uncultured bacteria were stated to be species for over 20 taxa. I just stated this in the discussion page the reason for my curation. > I should get

Anne-Marie Sharp (14:31:04) (in thread): > @Precious Orakwe1)In Exp3 Sig1, change bacillati to bacillota.2)In Exp4 Sig2, Actinobacteriota should be Actinomycetota.3)I don’t think Figure S1b is curatablesince the relative abundances are presented with no statistical testing

Anne-Marie Sharp (16:30:38) (in thread): > Hello@Precious Chijioke@chiamaka UcheFor figure 3b, it’s not curatable, as we don’t curate Principal coordinate analysis (PCoA)

Anne-Marie Sharp (16:33:11) (in thread): > Same applies to figure 5B

Aiysha shahid (16:55:10) (in thread): > Hi@Oriade Adeola, this study is all-most done, only NCBI taxonomy and cross-checking everything is left, would giving it for peer review by tuesday, hope that work for you?

Mildred Anashie (16:58:14) (in thread): > Hi@Anne-Marie SharpTab S1 is curatable as well….all p values are significant at P<0.05, so you’ll use the Log fold change to tell the direction of significance. > See this found under Data evaluation and Statistics “Differences were considered statistically significant if the calculatedp-value was less than 5%”. This implies the threshold was <0.05

Anne-Marie Sharp (17:17:32) (in thread): > Thanks@Mildred Anashienoted for Table S1 & the pvalues. I saw that sentence but I thought it was referring to the change in glucose in the ITT(Insulin Tolerance Test) which is in Figure3. My confusion was where they said ‘The differences in the abundance of the various phyla, families, and genera were described with the tool ANCOMBC..’ Please can you explain how to read the plot in figures 5b,6b,7b?

Precious Chijioke (17:19:55) (in thread): > @Anne-Marie Sharpokay > Thank you

Mildred Anashie (17:40:43) (in thread): > Hi@Adeshile OluwatosinWell done:clap:So I’m thinking you should curate the genus level for those taxa where the Genus were mentioned and for those with no rank you can curate Uncultured bacterium and leave a note like you have done. > > For the A2 taxa, it’s a bit confusing because I also saw this (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id=1934250) so unless we are sure this particular genus is from the family Lachnospiraceae, It might be curating as stated or curating as bacterium A2. > Yes you are correct aboutAcidimicrobiia. I’ll look through the curation, Well done again. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (18:05:57) (in thread): > Its just as@Adeshile Oluwatosinexplained already. > > Look closely at the plot (focusing on the red will be better since it’s more visible). From 5B I see three significant taxa and they are all decreased (Actinobacteriota, Desulfobacterota, and Firmicutes). > Let’s take Deulfobacterota for example, the red bally part is a little more towards the back compared to the white and the P value is less than 0.05 so this is significant and decreased in BL/6>fTEL. I hope it’s clearer, that’s how you identify increase and decrease in all (pay close attention, you’ll be able to tell).

Mildred Anashie (18:17:32) (in thread): > Hi@Precious OrakweWell done, I agree with@Anne-Marie SharpFigure S1 doesn’t appear curatable but S3 is though > > I’ll look through the rest of the curation

Mildred Anashie (18:23:12) (in thread): > I agree with@Anne-Marie SharpThe figures aren’t curatable

Anne-Marie Sharp (18:28:02) (in thread): > Thank you so much@Mildred Anashieyes its much clearer now:dancer::pray:

Precious Orakwe (20:05:30) (in thread): > @Mildred AnashieYou said Fig S1 is curatable, when I told you that@C. Mirzayi (please do not tag this account)said I should curate only Fig S2

Precious Orakwe (20:08:18) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1743778215141999?thread_ts=1743767598.132069&cid=C04RATV9VCY - Attachment: Attachment > Well done @Precious Orakwe I see some significant results at the Phylum level in Figure 3b that you haven’t curated yet. You can use the P values to curate, See this “We further investigated the microbial composition at the phylum level (Figure 3B, Supplementary Figure 1B ). Sample storage at RT without buffer (RT-ZYCON) influences the microbiome with a higher proportion of Proteobacteria (p = 0.000488) and Verrucomicrobiota (p = 0.0143) and a lower abundance of Firmicutes (p = 0.000488). Samples in the stabilization buffer showed an overrepresentation of Bacteroidota (RT-ZYBUF p = 0.000488, RT-OMBUF p = 2.32E-09), Proteobacteria (RT-ZYBUF p = 0.00342, RT-OMBUF p = 2.91E-06), and underrepresentation of Actinobacteriota (RT-ZYBUF p = 0.000488, RT-OMBUF p = 7.87E-05) compared to standard stored samples. Furthermore, a lower proportion of Firmicutes was observed in samples collected using the OMNIgene·GUT collection tubes (p = 0.0025) when compared to the standard frozen condition”.

Precious Orakwe (20:11:56): > <@UBNSEMS3S>@Svetlana Ugarcina Perovic@Aleru Divine@Kate RasheedGood day and a happy new week. > > Please I want to know if Supplementary Fig 1b is curatable in this study.https://bugsigdb.org/37065158Thank you. - Attachment (BugSigDB): Reducing bias in microbiome research: Comparing methods from sample collection to sequencing - BugSigDB > BACKGROUND: Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results.

Mildred Anashie (20:12:12) (in thread): > I specifically said Figure 3B, I’m going to highlight my statement below > > “Well done@Precious OrakweI see some significant results at the Phylum level in Figure 3b that you haven’t curated yet. You can use the P values to curate, See this”We further investigated the microbial composition at the phylum level (Figure 3B, Supplementary Figure 1B )“. > > The text from the article highlighted S1 alongside 3B but that isn’t curatable

Mildred Anashie (20:15:00) (in thread): > I also highlighted the experiments you can curate from therehere - Attachment: Attachment > I see three experiments there, done with Wilcoxon; -80-ZYCON vs RT-ZYCON, -80-ZYCON vs RT-ZYBUF and -80-OMCON vs RT-OMBUF. Also, Fig 8 has a few as well that you haven’t recorded yet you can find the alpha diversity in Supp Fig 4

Adeshile Oluwatosin (20:55:06) (in thread): > Hi@Mildred Anashiedo you mean > Curating the second as “lactobacillus” instead of “gut metagenome” > The fourth as “clostridium leptum” instead of “unclassified clostridium leptum”

Precious Orakwe (21:08:59) (in thread): > If you knew it wasn’t curatable, why did you say it was from your initial statement?

Anne-Marie Sharp (21:39:11) (in thread): > Hello@Precious OrakweSupplementary Fig 1b is not curatable, because the relative abundances are presented without statistical testing & there is no way to know the significance of each signature.

2025-04-07

Adeshile Oluwatosin (00:35:48) (in thread): > Supplementary Figure 1b is not curatable > The caption says “bacteria composition at phylum level, stacked bar chart”. It does not detect differential abundance and you cannot tellwhich is significant or not

chiamaka Uche (00:47:39) (in thread): > Thank you@Anne-Marie Sharp

Dorcas Odetayo (00:58:50) (in thread): > Hi everyone, I would appreciate your reviews on this study.https://bugsigdb.org/39873191Thank you. - Attachment (BugSigDB): Gut microbiota modulation via fecal microbiota transplantation mitigates hyperoxaluria and calcium oxalate crystal depositions induced by high oxalate diet - BugSigDB > Hyperoxaluria, including primary and secondary hyperoxaluria, is a disorder characterized by increased urinary oxalate excretion and could lead to recurrent calcium oxalate kidney stones, nephrocalcinosis and eventually end stage renal disease.

Adeshile Oluwatosin (01:52:16) (in thread): > Alright, well done

Montana-D (02:03:28): > Helloeveryone, Good day. > I just finished curating this very nice study. I’d greatly appreciate your reviews and corrections if any. Thank you so much for your time and knowledge.Link to the curationLink to the articleLink tosupplementary files - Attachment (BugSigDB): Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects - BugSigDB > BACKGROUND: Although there have been significant advancements in reducing the burden of cardiovascular disease (CVD) by modifying traditional CVD risk factors, substantial risks persist, particularly among male subjects who exhibit heightened susceptibility to atherosclerosis. - Attachment (Nature): Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects > Communications Medicine - Akhi et al. study the link between the oral microbiome and atherosclerosis. Microbiome diversity is influenced by atherosclerosis risk factors and in a sub-cohort of males… - Attachment (Nature): Oral microbiome diversity associates with carotid intima media thickness in middle-aged male subjects > Communications Medicine - Akhi et al. study the link between the oral microbiome and atherosclerosis. Microbiome diversity is influenced by atherosclerosis risk factors and in a sub-cohort of males…

Adeshile Oluwatosin (02:11:17) (in thread): > Well done@Montana-D

Precious Chijioke (02:39:07): > Good Morning Everyone And Happy New Week@Kate Rasheedplease I sent a message on GitHub issue

Adeshile Oluwatosin (03:29:23) (in thread): > @Montana-DExperiment 3: sequencing platform should still be illumina > MHT: no > Data Transformation: relative abundance > > Figure 3b is notto becurated though > Figure 3c has three different experiment > (Low vs high of total lgA, total lgA to PCklh, LGM to MAALDL)

Anne-Marie Sharp (04:01:01) (in thread): > @Mildred Anashiein this case where the figures & TableS1 differonlyin the taxonomic level they provide, but TableS1 has fold change values unlike the figures, would it still be curated in same experiment with the figures?

Mildred Anashie (04:07:08) (in thread): > You clearly misunderstood me@Precious Orakweand from my statement I clearly said Fig 3b not Fig S1b > I never said Supplementary Fig 1b was curatable

Mildred Anashie (04:07:55) (in thread): > You’d have to confirm if they use the same statistical test@Anne-Marie Sharp

Bola (04:16:02): > @Montana-DThis is Abimbola

Precious Orakwe (04:23:51) (in thread): > Ok thanks

Mildred Anashie (05:04:29) (in thread): > Clostriduim leptum is actually a species, and I’m wondering why the specie was identified and not the genus. > What I’m saying is for the Unclassified bacterium noted as species, not for taxas identified up to species@Adeshile Oluwatosin

Ameenat Oloko (05:18:04): > Good morning, everyone. Happy new week. > Please, howcan I fix this issue? It was shown in the autocomplete section when I typed it out, and I tried to search for it on NCBI, it brought out “unclassified Oscillospiraceae”. - File (JPEG): IMG_7007

Joy (05:21:49) (in thread): > Well done@Ameenat Olokoon your curation. Use this ID: 473772 (unclassified Oscillospiraceae). That is the current name forUnclassified Ruminococcaceae

Juliana Kentomahun Mautin (05:21:58): > Hello everyone, Happy New Week:blush:. I welcome y’all to the fourth week of our Outreachy contribution phase. I hope you are feeling energized, motivated, and ready to make meaningful progress! Let’s keep up the great work and continue supporting one another.

Ameenat Oloko (05:23:34) (in thread): > @Joy, thanks. I already saw it in the “pages with missing NCBI ID” article.

Juliana Kentomahun Mautin (05:31:47): > I’m currently working on Curating this study, Is anyone available to collaborate with me on curating this study?. Please if you are interested, kindly signify . Thank you:blush:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01721/full. - Attachment (Frontiers): Frontiers | Adhesive Bifidobacterium Induced Changes in Cecal Microbiome Alleviated Constipation in Mice > Constipation, which seriously affects living quality of people, is a common gastrointestinal disease. The engagement of the intestinal flora in the developme…

Anne-Marie Sharp (05:41:47) (in thread): > @Mildred Anashiethey use same statistical test, this is all the info on the statistical tests used ‘The statistical analysis of the data was carried out using the Prism 8 program (GraphPad, San Diego, United States). The values were tested for normal distribution and homogeneity of variance before t-testing or ANOVA testing. The t-test was used to compare two groups. If there was no variance homogeneity, the t-test was corrected according to Welch. When two factors were to be tested, a 2-way analysis of variance (ANOVA) was used. Differences were considered statistically significant if the calculatedp-value was less than 5%. In figures, means±SDs are depicted.’

Anne-Marie Sharp (05:42:21) (in thread): > The only difference is the taxa level and that fold change

Adeshile Oluwatosin (05:43:56) (in thread): > You can create it in same experiment > Do they have same comparison too?@Anne-Marie Sharp

Anne-Marie Sharp (05:45:08) (in thread): > @Adeshile Oluwatosinyes they have same comparison. only difference is the taxa level and the fold change included in the table

Adeshile Oluwatosin (05:45:38) (in thread): > Create all taxa level in same experiment then

Anne-Marie Sharp (05:49:44) (in thread): > okay, thank you

Adeshile Oluwatosin (05:56:04) (in thread): > I get what you mean@Mildred AnashieSo the paper reports species and genus levels > The genus levels have already been curated previously

Joy (06:33:02) (in thread): > Hi@Juliana Kentomahun Mautin, I’ ll collaborate with you on this.

Svetlana Ugarcina Perovic (06:49:52): > IMPORTANT1. Fill out an initial application athttps://www.outreachy.org/eligibility/2. Record a contribution to your project on the Outreachy site. > 3. Complete a final application for your project.The deadline for final applications is April 15, 2025 at 4pm UTC. Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline. > > Applicants who submit a final application will be able to continue recording and editing their contributions to your project.They can record contributions until the intern announcement on May 8, 2025 at 4pm UTC. Applicants who have not submitted a final application will not be able to record or edit their contributions.IN SHORT: complete your final Outreachy application and feel free to continue curating in BugSigDB

Adeshile Oluwatosin (06:50:43) (in thread): > Thank you so much for this reminder > Good morning

Joy (06:52:26) (in thread): > Duly noted@Svetlana Ugarcina Perovic. Thanks

Victoria (Burah) Poromon (07:08:05) (in thread): > Thank you so much for the reminder!

Mildred Anashie (07:19:01) (in thread): > Thank you for the information@Svetlana Ugarcina Perovic

Precious Chijioke (07:19:43) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic

Juliana Kentomahun Mautin (07:23:04) (in thread): > Thank you for very much for the reminder:blush:@Svetlana Ugarcina Perovic

Anne-Marie Sharp (07:50:12) (in thread): > Nice curation@Montana-DI agree with@Adeshile Oluwatosin, although Figure 3c should be (Low vs high of total lgA, lgA to PCklh, Low vs high of total IgM ). I cant see what signifies increase/decrease of signatures in table S1, did you confirm if its curatable?

Anne-Marie Sharp (07:51:27) (in thread): > Noted, thank you for the reminder@Svetlana Ugarcina Perovic

Precious Orakwe (07:52:46) (in thread): > Thanks@Svetlana Ugarcina Perovicnoted

Mildred Anashie (07:55:50) (in thread): > Hi@Montana-DI doubt how curatable Table S1 and S2 are > > I also agree that 3b shouldn’t have been curated

Precious Orakwe (08:01:39): > @Svetlana Ugarcina PerovicGood day, can I be assigned to complete this study.https://bugsigdb.org/40050917 - Attachment (BugSigDB): Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn’s disease: a prospective trial - BugSigDB > BACKGROUND: Clinical data on oral fecal microbiota transplantation (FMT), a promising therapy for Crohn’s disease (CD), are limited.Herein, we determined the short-term safety and feasibility of FMT for pediatric patients with active CD.

Montana-D (08:03:45) (in thread): > Thank you all for noticing, I meant to put in 3C, I’ll correct at once, thank you@Adeshile Oluwatosin@Anne-Marie Sharp@Mildred Anashie

Adeshile Oluwatosin (08:04:49) (in thread): > She mentioned notifying on GitHub instead

Svetlana Ugarcina Perovic (08:05:55) (in thread): > It’s already assigned - Attachment: #640 [Study]: Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn’s disease: a prospective trial > ### Study Title > > Fecal microbiota transplantation restores gut microbiota diversity in children with active Crohn’s disease: a prospective trial > > ### Pubmed ID > > 40050917 > > ### The Digital Object Identifier (DOI) > > https://doi.org/10.1186/s12967-024-05832-1 > > ### First Author > > Zou B. > > ### Journal > > Journal of Translational Medicine > > ### Year > > 2025 > > ### Study Source > > https://pubmed.ncbi.nlm.nih.gov/40050917/ > > ### Code of Conduct Agreement > > • I agree to follow this project’s Code of Conduct

Precious Orakwe (08:06:00) (in thread): > ok, Thank you for letting me know.

Montana-D (08:08:22) (in thread): > Supplementary Tables S1 doesn’t show any criteria for increase nor decrease, but the study shows there’s remarkably significant bacteria and table 1 seems to be a subset to the supplementary table so I thought I could consider same criteria (maybe an ommition by the authors, as the supplementary material looks unfinished) > > What do you all think?

Precious Orakwe (08:09:28) (in thread): > @Svetlana Ugarcina Perovicwhen i find an incomplete study, how do i locate it in GitHub, so that it can be assigned to me

Svetlana Ugarcina Perovic (08:11:05) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issuessearch by Title

Precious Orakwe (08:11:43) (in thread): > Thank@Svetlana Ugarcina Perovic

Oriade Adeola (08:48:29) (in thread): > Superb.

Montana-D (09:22:45) (in thread): > Hi@BolaI shall get to your DM at once > I have been waiting

Montana-D (09:26:48) (in thread): > Noted with thanks:pray:

Adeshile Oluwatosin (10:29:23): > Hello everyone > Kindly reviewhttps://bugsigdb.org/36532754https://pmc.ncbi.nlm.nih.gov/articles/PMC9755208/Gracias! - Attachment (PubMed Central (PMC)): Cannabis sativa L. alleviates loperamide-induced constipation by modulating the composition of gut microbiota in mice > MaZiRenWan (MZRW) is the most frequently used Traditional Chinese Medicine formula to treat chronic constipation, Cannabis sativa L. is regarded as a monarch drug in MZRW. However, the targets of Cannabis sativa L. that enhance colonic motility and …

Victoria (Burah) Poromon (10:43:05) (in thread): > Will do! Well done@Adeshile Oluwatosin

Montana-D (11:19:35) (in thread): > Well done on your curation@Adeshile Oluwatosin, I’ll check it out

Victoria (Burah) Poromon (11:24:58) (in thread): > Do you think that signature is Tyzzerella and not Tuzzerella?In experiment 1/ signature 1? > > I thinkit’sa typographical error from the paper.:thinking_face:

Adeshile Oluwatosin (11:26:03) (in thread): > Apparently I thought about that > I recently even just completed another article with same taxa > > And I realized that tuzzerella and tyzzerella are different > AlthoughI couldn’tget anything tangible on tuzzerella itself

Victoria (Burah) Poromon (11:27:25) (in thread): > Right, Tyzzerella is also a genus in the Lachnospiraceae family. And it corresponds with what is in the paper.

Montana-D (11:32:57) (in thread): > I agree with@Victoria (Burah) Poromon, I couldn’t find tuzzeralla, but Tyzzerella is found

Montana-D (11:33:08) (in thread): > Please, why did you choose mus muscullus and not rattus rattus?

Montana-D (11:34:40) (in thread): > If you saw it in 2 different articles, then there’s a possibility it does exist then

Adeshile Oluwatosin (11:39:58) (in thread): > Mice is different from rats

Adeshile Oluwatosin (11:40:35) (in thread): > Yeah, I had to go the extra mile to search for already reviewed article > Seems like I found something on tuzerrella but i still doubt ifit’s abacteria

Adeshile Oluwatosin (11:43:38) (in thread): > Botanical name of mice is mus musculus > Rats is rattus rattus or rattus norvegicus

Montana-D (11:44:56) (in thread): > Thank you for this clarification. makes perfect sense:100:

Adeshile Oluwatosin (11:49:15) (in thread): > Idon’tsee anything useful in figure 7C > Do you agree as well@Victoria (Burah) Poromon

Ameenat Oloko (12:30:27) (in thread): > Well done on your curation@Adeshile Oluwatosin. Are you asking if figure 7C is curatable?

Adeshile Oluwatosin (12:35:27) (in thread): > Idon’t thinkit’scuratable > But yes I am

Ameenat Oloko (12:37:51): > Hello, everyone. I just finished curating this paper and would appreciate a review.Study:ArticleSupplementary data - Attachment (BugSigDB): Comparison of DNA extraction methods for human gut microbial community profiling - BugSigDB > The human gut harbors a vast range of microbes that have significant impact on health and disease.Therefore, gut microbiome profiling holds promise for use in early diagnosis and precision medicine development.

Ameenat Oloko (12:39:45) (in thread): > Okay. Let me check.

Precious Chijioke (12:43:41) (in thread): > @Adeshile Oluwatosinwell done on your curation. I didn’t see anything tangible in figure 7C. I’ll wait for someone else to confirm as well.

Victoria (Burah) Poromon (13:00:17) (in thread): > I see signatures but I don’t think it’s curatable. The description says “correlation analysis” not “differential analysis”.@Adeshile Oluwatosin

Adeshile Oluwatosin (13:00:56) (in thread): > Exactly,I didn’tcurate it > Thank you

Victoria (Burah) Poromon (13:01:30) (in thread): > Well done!@Ameenat OlokoI will take a look.

Adeshile Oluwatosin (13:02:19) (in thread): > Well done@Ameenat Oloko

Precious Chijioke (13:02:43) (in thread): > Well done@Ameenat Oloko

Ameenat Oloko (13:04:26) (in thread): > @Adeshile Oluwatosin, I think Figure 7C is curatable. Based on research, correlation analysis is also curatable, particularly when using methods like Pearson’s or Spearman’s correlation.

Ameenat Oloko (13:11:55) (in thread): > I think you’re going to curate it based on the colour codes (red- positively associated organisms, blue- negatively associated organisms) and stars(****).

Ameenat Oloko (13:16:40) (in thread): > Also@Adeshile Oluwatosin,since figure 7 states that“the p-value was corrected using the Benjamini-Hochberg test (FDR<0.001, FDR<0.01 and FDR<0.1). Don’t you think MHR correction should beyes? (***In reference to the curation policy - the use of MHT correction is usually denoted by the name of the correction in the methods or results {e.g “Bonferroni”, “False Discovery rate”,”FDR”, “Benjamini-Hochberg”}

Anne-Marie Sharp (13:16:57) (in thread): > You’re welcome@Montana-DTable1 I am viewing isClinical characteristics of the study cohort. I still think TableS1&2 should not be curated, since there is no info like fold change to indicate increase/decrease.

Precious Chijioke (13:18:05) (in thread): > @Ameenat Olokohow will it be recorded on BugSigDB, is Correlation analysis an option under data transformation? > > Asking because I haven’t taken note of it.

Victoria (Burah) Poromon (13:23:57) (in thread): > I found this “Spearman’s correlation analysis of bacterial abundances and constipation-related biomarkers was analyzed. As shown inFigure 7C,Parasutterella, andTuzzerellawere positively correlated with intestinal inflammation but negatively related to clinical presentations or mucosal barrier.” I know we curate Spearman’s correlation, but for this study, it was done to analyze biomarkers associated with constipation. - Attachment (PubMed Central (PMC)): Cannabis sativa L. alleviates loperamide-induced constipation by modulating the composition of gut microbiota in mice > MaZiRenWan (MZRW) is the most frequently used Traditional Chinese Medicine formula to treat chronic constipation, Cannabis sativa L. is regarded as a monarch drug in MZRW. However, the targets of Cannabis sativa L. that enhance colonic motility and …

Adeshile Oluwatosin (13:26:18) (in thread): > @Ameenat Olokonot all spearman correlation analysis are curatable. Hence, why we read further within text. > Victoria already explained deeply why this is not curatable > Thank you all so much for taking time to go through the study

Mildred Anashie (13:43:50) (in thread): > Well done@Ameenat OlokoI’ll look through

Anne-Marie Sharp (13:50:31) (in thread): > Neat curation@Ameenat Olokowell done. I think you should have separate experiments for the different kits ie. TS kit in Exp1 & QS kit in Exp2. And adjust the source accordingly(S7a & S7b)

Mildred Anashie (13:53:03) (in thread): > Hi@Ameenat OlokoI see only 1 experiment in your curation but from the supplementals it should be 2 experiments from S7. > Experiment from S7a is bead-beating TS kit vs no bead-beating TS kit > Experiment from SS7b is bead-beating QS kit vs no bead-beating QS kit > Your statistical test would be just lefse

Adeshile Oluwatosin (13:56:56) (in thread): > I agree with them

Ameenat Oloko (14:02:08) (in thread): > Thank you@Mildred Anashie,@Anne-Marie Sharpand@Adeshile Oluwatosin. > > I have a few questions. 1) it doesn’t matter if 2 out of 3 kits are analysed using LefSe, right? {in this case, TS and QS kits only}. > > 2) The organisms classified in the bead-beating group aresomewhatthe same in both the TS and QS kits. I’m supposed to add signatures based on group 1 (bead-beating group), how am I supposed to report this?

Juliana Kentomahun Mautin (14:03:49): > Hello everyone, I’m currently curating this study, andit was stated that In this study, constipated mice induced by loperamide were used to investige the alleviation of constipation by Bifidobacteria. Bifidobacteria was sorted out according to their adhesive properties into two groups. One group combined multiple strains of Bifidobacterium with adhesion property (CMB1), the other combined multiple strains of Bifidobacterium without adhesion property (CMB2).My questions are: > > 1) I’m not sure what the case group and control group in this study is. > > 2)For the statistical testIt was stated thatThe differences between the samples were analyzed by one-way ANOVA with Duncan’s multiple range test. I can’t find Duncan’s Multiple range test among the options for statistical test on BugsigDB. > > Please kindly help out.https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01721/full. - Attachment (Frontiers): Frontiers | Adhesive Bifidobacterium Induced Changes in Cecal Microbiome Alleviated Constipation in Mice > Constipation, which seriously affects living quality of people, is a common gastrointestinal disease. The engagement of the intestinal flora in the developme…

Mildred Anashie (14:12:07) (in thread): > They are not entirely the same and Yes it’s okay to curate as different experiments with the same statistical test@Ameenat Oloko

Anne-Marie Sharp (14:13:51) (in thread): > @Ameenat Oloko1)this is tricky, perhaps you could leave a note in the discussions page that there was no curatable figure/table for QP kit.

Anne-Marie Sharp (14:15:48) (in thread): > 2)For experiment 1, bead-beating TS kit vs no bead-beating TS kit will be the contrast, hence no-bead-beating in group 0 and bead-beating in group1. So the signatures you will add should be those that are increased in Group1.

Ameenat Oloko (14:15:59) (in thread): > Please,how do I add notes in the discussion page?@Anne-Marie Sharp

Victoria (Burah) Poromon (14:16:44) (in thread): > Hi@Ameenat OlokoI agree witheveryone’sreview. > > And yes, the organisms identified with the different kits are similar, but QS has more.

Victoria (Burah) Poromon (14:17:25) (in thread): > To add notes, just click on the 3 dots (…) beside the search box.You’ll see a drop down, then click on “discussion”. It will open another page, then click “start discussion”That’show you add notes

Anne-Marie Sharp (14:19:41) (in thread): > @Ameenat Olokolike@Victoria (Burah) Poromonsaid, click the 3dots at the top of the page beside the search box. Click on start a discussion. And clearly explain the situation.

Mildred Anashie (14:21:11) (in thread): > Hi@Juliana Kentomahun MautinFor the second question, Duncan Multiple range test is one of the post hoc test that can be done when ANOVA shows there’s a difference, but you want to pinpointwherethat difference lies among multiple groups. > So in this case I believe recording ANOVA as the statistical test is okay since Duncan isn’t available. > > I’ll go through the study for your first question, Well done

Juliana Kentomahun Mautin (14:30:51) (in thread): > Hi@Mildred Anashie, Thank you very much for the clarification.

Mildred Anashie (14:50:40) (in thread): > In my opinion,**** ****adhesion is an important factor and**** CMB2is thecontrolgroupfor adhesioneffects,CMB1is thetest group**evaluating how adhesion contributes to the treatment outcome. > > So CMB2 would be Group 0 and CMB1 would be Group 1@Juliana Kentomahun Mautin

Victoria (Burah) Poromon (15:04:37) (in thread): > Hi@Juliana Kentomahun MautinFor question 1; there are 4 groups (from the > Normal (healthy mice) > Control (constipation mice) > CMB1 (constipation mice treated with CMB with adhesion properties) > CMB2 (constipation mice treated with CMB with no adhesion properties) > > From the text, comparisons were made between the CMB groups and control and then in CMB2 and CMB1. > That is CMB1 vs. Control > CMB2 vs. Control > CMB2 vs. CMB1.

Victoria (Burah) Poromon (15:06:52) (in thread): > See an excerpt here: “Oscillibacter and Ruminococcus decreased significantly in CMB groups compared to control group. Meanwhile, the relative abundance of Clostridium and Sporobacter were higher in CMB2 treatment group than that in CMB1 group.”

Svetlana Ugarcina Perovic (15:12:56): > Anitaand I chatted about open source tools, databases and community around the microbiome science in the new ep of #OpenSourceDiaries - Attachment (YouTube): How microbiologists use open source to decode microbial life

Adeshile Oluwatosin (15:15:54) (in thread): > Heading to youtube:running:Thank you so much for sharing

Montana-D (15:28:50) (in thread): > Okay noted@Anne-Marie SharpThank you for this clarification:pray:

Joy (15:36:54) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing. This absolutely helpful!

Precious Chijioke (15:38:18) (in thread): > Thank you@Svetlana Ugarcina Perovicfor sharing. This will really be helpful. Heading to YouTube right away.

Mildred Anashie (15:44:37) (in thread): > As a Microbiologist, I’m sure there’ll be a lot to learn from this > Thank you for sharing@Svetlana Ugarcina Perovic:pray:

Precious Chijioke (15:52:24) (in thread): > Hello@Ameenat OlokoI agree with everyone’s review

Aiysha shahid (16:11:17) (in thread): > Thank you for sharing@Svetlana Ugarcina Perovic:tulip:

Juliana Kentomahun Mautin (17:01:03) (in thread): > Thank you so much@Svetlana Ugarcina Perovicfor sharing. > One thing that stood out for me is when you talked about how the role of open data can advance the role of Microbiome research and how it allows scientist to access and analyze diverse dataset just like the BugsigDB database which is very important when looking for a robust findings.

Mildred Anashie (18:10:53) (in thread): > Hi@Precious OrakweI’ll like to know if you have this all sorted out now

2025-04-08

Precious Chijioke (02:36:49): > Good Morning Everyone > Please I’ll love a peer review on this paper I curated with@chiamaka Uchehttps://bugsigdb.org/39642873Study link:https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(24)00607-4?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2666379124006074%3Fshowall%3Dtrue#fig3 - Attachment (BugSigDB): The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children - BugSigDB > Respiratory syncytial virus (RSV) is the leading cause of infant respiratory infections and hospitalizations.

Mildred Anashie (02:43:26) (in thread): > Good morning@Precious ChijiokeWell done on your curation, I’ll take a look at this

Adeshile Oluwatosin (02:45:39) (in thread): > Well done@Precious ChijiokeCheck out figure 3E and 3F, 4A and 4B. > They seem curatable

Adeshile Oluwatosin (02:55:02) (in thread): > Figure 2E and 2F test seems to be MaAslin2 > > “Differential abundance analyses at genus level (MaAsLin2) largely confirmed our cluster-based analyses, with a higher relative abundance of Haemophilus spp. (adjusted for age, gender, and study site [random effect]; log2FC = 2.45, q value = 0.017) and lower abundance of Corynebacterium and Dolosigranulum spp. during RSV infection (log2FC = −2.43 and −2.18, respectively, both q value ≤ 0.021). Interestingly, Moraxella spp. were more abundant at RSV convalescence when compared to healthy controls (Figures 2E and 2F; log2FC = 1.91, q value 0.023). “

Precious Chijioke (02:59:41) (in thread): > Thank you@Adeshile Oluwatosin

Mildred Anashie (03:52:31) (in thread): > I think all the curatable figures used MaAsLin2 from the figure caption. See this,“Differential abundant ASVs between groups were identified using linear mixed effects models, similar to the implementation in the MaAsLin2-framework (default parameters; log2-normalisation; lmerTest R-package).45* For each comparison ASVs present at >0.1% relative abundance in ≥5% of samples were selected. q-Values of below 0.05 were considered statistically significant.”*Also in the first experiment, Shannon is Unchanged and not decreased@Precious Chijioke

Anne-Marie Sharp (04:17:51) (in thread): > Interesting conversation. Thank you for sharing@Svetlana Ugarcina PerovicIts niceknowing ways one canlearn &grow in this community andinopen sourcecommunityat large.

Precious Chijioke (04:33:21) (in thread): > Thank you@Mildred Anashiefor the review. I checked after@Adeshile Oluwatosinreview and also noted MaAsLin2 was used in all the experiment.

Juliana Kentomahun Mautin (04:40:34) (in thread): > Thank you so much for the clarification:relaxed:

Victoria (Burah) Poromon (05:37:45): > Hi everyone, Good morning.@Mildred Anashieand I are currently curating a study and we have some questions. > > From figure 5c the Dots (•) were said to be confounded but not significant and not included alongside the FDR. > > But from Supplementary figure S4 the dots are said to be confounded but not stated if they are significant or not significant and they are reported alongside the asterisks (•/*) > > Our question is, should be curate the taxa with the dots as well or leave them out? > > Thank you so much!@Svetlana Ugarcina Perovic@Kate Rasheed<@UBNSEMS3S>@Aleru DivineArticle link:https://www.amjtransplant.org/article/S1600-6135(25)00093-0/fulltextSupplement - File (Word Document): mmc1 (1)

Anne-Marie Sharp (06:11:52) (in thread): > Good morning@Precious Chijioke@chiamaka Uchewell done with your curation. I agree with the above comments. From my observation, Figure2 e & f should have 3groups: Differentially abundant taxa in**** healthy controls, in infantsduring RSV infection, andduring RSV convalescence. **When you curate from figures 3 & 4, there will also be more than 2groups. Kindly confirm.

Adeshile Oluwatosin (07:27:53) (in thread): > Well done@Victoria (Burah) PoromonI will have a look

Anne-Marie Sharp (07:37:55): > Good day everyone, please I want to clarify the statistical test in the article I’m curatinghttp://dx.doi.org/10.3389/fphar.2024.1453989One part of the article stated ‘The differences in the abundance of the various phyla, families, and genera were described with the tool ANCOMBC (0.99.4,https://www.bioconductor.org/packages/release/bioc/vignettes/ANCOMBC/inst/doc/ANCOMBC.html) using differential abundance analysis (DAA)’ > > But the figure descriptions in Fig5 ,6, 7 stated ‘absolute abundances; the statistical comparison was made with an unpaired t-test when values were Gaussian distributed (considering Welch correction when variances differed) or by using Mann-Whitney test as a nonparametric test’ > > And Fig. S3B,4B & Table S1 seem to have no statistical test attached - Attachment (Frontiers): Frontiers | Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan > IntroductionTreatment of rodents with the AT1 blocker (ARB) telmisartan (TEL) has an anti-adipose effect. Among other mechanisms, we also have attributed the…

Ndukauba Oluchi (07:47:23): > Hello everyone:wave:.@Halima Momohand I are curating this study and we just want to confirm if figure 3 in this paper is curatable? > link to paper :https://www.mdpi.com/1422-0067/26/3/1236 - Attachment (MDPI): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. To explore how these structural differences impact constipation intervention, a 14-day study was conducted on loperamide-induced constipated mice using five dietary fibers: soluble dietary fiber from steamed sweet potato (SDF-S), oat β-glucan (OB), polydextrose (PD), arabinogalactan (AG), and inulin (IN). The results showed that four fibers, excluding PD, significantly improved gastrointestinal (GI) transit rate (p < 0.05), although PD had the highest fecal moisture, it was significantly different from the lowest IN (p < 0.05). AG and IN resulted in higher 6 h fecal weights compared to other fibers. SDF-S and OB were more effective in modulating serum levels of gastrointestinal hormones. The different monosaccharide compositions and glycosidic bonds of these fibers led to distinct changes in gut microbiota composition and SCFA profiles. Galactose and arabinose in AG were linked to increased abundance of Lachnospiraceae_UCG-006, Bacteroides, and Odoribacter, promoting butyrate fermentation, which is positively correlated with GI transit rate. Glucose in SDF-S, OB, and PD favored acetate fermentation positively correlated with fecal moisture. Fructose in IN encouraged the proliferation of Muribaculaceae_unclassified and Ruminococcus, associated with butyrate fermentation and increased 6 h stool weight, respectively. The β-glycosidic bonds in OB may lead to high butyrate production through the selective proliferation of Lachnospiraceae_unclassified. Minor components like fucose, rhamnose, and ribose were positively correlated with the abundance of Oscillospiraceae_unclassified, Anaerotignum, and Lachnospiraceae_unclassified. In conclusion, the unique monosaccharide compositions and glycosidic bond differences in dietary fibers selectively promote the proliferation of fiber-degrading and butyrate-producing bacteria, resulting in varied effects on constipation relief.

Anne-Marie Sharp (08:04:35) (in thread): > Hello@Ndukauba Oluchi@Halima MomohI can’t see a statistical test used for figure 3, and the article stated that the results from figure 3 was further analyzed with Kruskal-Wallis(Figure 4). I dont think its curatable.

Joy (08:04:53) (in thread): > Well done@Anne-Marie Sharpon your curation. > 1. I want to believe that the Statistical test employed here is ANCOM-BC, since it > is designed for compositional microbiome data and is appropriate for identifying taxa that differ significantly between groups after correcting for biases. > > In addition, the article states that “differences in the abundance of various phyla, families, and genera were described with ANCOM-BC” — this refers to differential abundance analysis (DAA) using relative abundances. > > 2. As for Fig. S3B, 4B & Table S1 that seem to have no statistical test attached, it’s best to reach out to the authors. > > You can check with the mentors.

Precious Chijioke (08:10:46) (in thread): > Thank you@Anne-Marie Sharpfor pointing that out. I noted that too. Figures 2e & 2f, and 3 have the 3 groups you mentioned ieHealthy controls vs RSV Infection + RSV Convalescencewhile Figure 4 the difference abundant taxa is recorded forRSV Infection and RSV Convalescence Microbiota deviations following RSV infection > Additionally, we wondered if we could detect “microbial scars” during RSV convalescence, speculating that residual microbial deviations would be more extreme following more severe disease. Using ASV-level differential abundance analyses (MaAsLin2), we found limited support for this hypothesis, with only several rare Corynebacterium spp. (18, 81, and 131) being associated with previous severe RSV infection (compared to previous mild disease; q value = 0.165; p value ≤ 0.006). After correction for use of antibiotics during infection, these differences were no longer significant. We also tested whether symptoms (blocked nose/cough/wheeze) during convalescence were related to remaining microbiota perturbations. We indeed found that persistence of respiratory symptoms were associated with a high relative abundance of Haemophilus and lack of Dolosigranulum (linear mixed-effects model including the covariates (remaining) respiratory symptoms, age at recovery, time since RSV infection, and gender [fixed effects] and study site [random effect]; log2FC = 1.70, q value = 0.029 and log2FC = −1.47, q value = 0.056, respectively; Figure 4).@Anne-Marie Sharpplease kindly recheck and confirm so that I’ll be sure

Victoria (Burah) Poromon (08:15:00) (in thread): > Hi@Ndukauba OluchiFigure 3 is not curatable.It’sonly showing relative abundance, not the difference.

Adeshile Oluwatosin (08:28:08) (in thread): > Figure 3 is not curatable as it does not reflect differential analysis

Montana-D (08:29:34) (in thread): > I agree with the others . Figure 3 talks about relative abundances and we don’t curate relative abundances

Ndukauba Oluchi (08:30:38) (in thread): > Alright, thank you all:grin:

Adeshile Oluwatosin (08:30:47) (in thread): > My opinion from this below tells me that only taxa with asterisks are significant with MHT as yes. Hence, I believe you should focus on curating these alone excluding the confounded ones. > > “(C) Heatmap comparison of genus-level alterations between prerejection and postrejection samples reveals significant directional changes in microbial populations after a rejection event, contrasting with the stable profiles observed in nonrejection controls. Prerejection comparison is taken from Figure 3F. Asterisks indicate significance levels: false discovery rate (FDR) <0.1∗; FDR <0.01∗∗; FDR <0.001∗∗∗. Confounded signals are shown as circles. Effect size is shown as Cliff’s delta with pink enriched and green depleted.”

USLACKBOT (08:31:01): > This message was deleted.

Adeshile Oluwatosin (08:31:45) (in thread): > @Montana-Dwe actually curate relative abundances between two/more groups but when the differences are clear enough and not represented in such manner

Montana-D (08:32:34) (in thread): > Hi@iniobong simeon, requests for deletion are done in the GitHub issue > Please tag the mentor there with the link to the signature or experiment you want deleted

iniobong simeon (08:33:33) (in thread): > ok thanks

Montana-D (08:34:55) (in thread): > ohhhh, Thank you@Adeshile Oluwatosin. Noted with thanks:pray:

Victoria (Burah) Poromon (08:35:54) (in thread): > Thank you so much!@Adeshile Oluwatosin

Mildred Anashie (08:38:04) (in thread): > Hi@Adeshile OluwatosinThat seems to be describing 5C but S4 description is a bit different, hence the confusion. > > See here, ’Supplementary Figure S4. Impact of rejection state on gut microbiome composition.Analysis of fecal samples from patients experiencing kidney rejection at any time compared to patients never experiencing graft rejection. Heatmap showing associations of bacterial genera with kidney transplant rejection. Meta-variables with significant association are shown. Stars indicate de-confounded significant associations; grey dots indicate confounded associations. °/FDR< 0.1, °°/FDR< 0.01, °°°/**FDR< 0.001’.

Adeshile Oluwatosin (08:38:11) (in thread): > Let me explain further > So you would see results stated,seperated in one colour each represented per group and not colours stacked together. > Stated as relative abundance between group A and B or groups

Adeshile Oluwatosin (08:42:06) (in thread): > Hi@Mildred AnashieEven Figure S4 stated that stars in this case are the de-confounded taxa and also significant. > Dots which I believe is circle in this case still was not stated to be significant, there was only mention of it being confounded. > Stars = asterisks(deconfounded), significant > Dots = circles (confounded), not significantIt aligns with what I can see from 5C

Mildred Anashie (08:43:54) (in thread): > See this also, °/FDR< 0.1, °°/FDR< 0.01, °°°/**FDR< 0.001’ > It’s part of S4 and different from 5C:thinking_face:

Adeshile Oluwatosin (08:44:36) (in thread): > The only difference is that in S4 there was adjustments done for the confounded taxa but they still didn’t state significance for them

Mildred Anashie (08:46:54) (in thread): > This point makes sense@Adeshile OluwatosinThank you, we have actually curated some using just the asterisk but we needed to be sure before proceeding

Adeshile Oluwatosin (08:48:17) (in thread): > You are welcome

Victoria (Burah) Poromon (08:49:35) (in thread): > Uhmm, it’s true they didn’t mention that the confounded associations were significant. > Our major concern was that they included the confounded associations while adjusting. > > So I agree we shouldn’t curate those, since they didn’t state their significance.@Mildred AnashieYou think so too?

Victoria (Burah) Poromon (08:55:30) (in thread): > Okay, Thank you again!@Adeshile Oluwatosin

Adeshile Oluwatosin (08:55:46) (in thread): > Welcome

Adeshile Oluwatosin (08:57:50) (in thread): > @Anne-Marie SharpChloe explained something like this in the last office hour. > > Fig 5, 6 and 7 statistical test are both t-test and Mann Whitney test as stated in the caption. > > The representation of the figures already states thatit’s forabsolute abundance

Ifunanya Benita Obiaku (09:17:51): > Hello everyone > > While curating, I was unable to find Oscillibacter sp. NSJ62. What do I do?

Ameenat Oloko (09:22:19) (in thread): > Have you checked NCBI andUniProt?@Ifunanya Benita Obiaku

Adeshile Oluwatosin (09:24:08) (in thread): > Fig S3B, 4B, Table s1 use ANCOMBC

Ameenat Oloko (09:26:28) (in thread): > I just checked both databases and no results were found. In this case, you leave it as it is.https://community-bioc.slack.com/archives/C04RATV9VCY/p1710169786476189 - Attachment: Attachment > We noticed that a lot of people are still confused about mapping NCBI IDs to taxa. I wrote this to provide some clarity. > The goal of using the NCBI taxonomy is to classify reported taxa as precisely as possible, or to communicate something about the lineage in cases where you don’t find the precise taxa. The benefit of linking taxa on bugSigDB to NCBI is that if NCBI updates that taxa, the changes will be reflected in BugSigDB. > When curating species, if you do not find the exact match or a synonym on NCBI or UNIPROT, please leave it as it is. This is because species are very specific. For example, you can’t replace Escherichia coli with Escherichia. They are not the same, the first is a species while the latter is a genus. I’ve seen questions on Lachnoclostridium lactaris, Let’s try to solve that together: > > I searched for Lachnoclostridium lactaris on NCBI and Uniprot, got no results. I checked the discussion page and saw that it has not been entered. Then I did a google search, there was no definite result. I then went back on uniport and searched for Lachnoclostridium. While scrolling through the search results, I found Uncultured lachnoclostridium sp. This is a good replacement because it has the correct rank of species. It shows a relationship to the lineage “lachnoclostridium”, and it is not representing an entirely different taxon. I went to study 373/experiment 1/signature 2 and replaced it. I also added a note to state what was originally reported (that is why you can see that orange bubble beside the taxon. However, you do not have this permission yet. You can include the note in the talk page instead.). I then went to add it to the discussion page under “unresolved nomenclature existing in BugSigDB”. If I had not found Uncultured lachnoclostridium sp, another fix would have been to use something that shows the lineage but has no rank such as in the case of Uncultured Oscillospiraceae bacterium for Ruminococcaceae_UCG (check the discussion page, under “some useful nomenclature”). > > If you have not watched the 2-hour video of @U1LCB8WEA solving issues like these, I strongly suggest that you do. It’ll provide you with a lot of insight. > Do not forget to always ask BEFORE you make edits. You might not get a reply immediately but please note your change somewhere and wait for us to reply before you change anything. > Thank you for your work so far:bouquet::rose:

Svetlana Ugarcina Perovic (09:58:22) (in thread): > @iniobong simeondo not delete your question. All questions and answers are valuable, we all learn from them, thanks!

Ameenat Oloko (10:20:33) (in thread): > I agree with@Adeshile Oluwatosin. The statistical tests employed in figures 5,6&7 are t-test and Mann-Whitney test,@Anne-Marie Sharp.a) relative abundance describes the proportion of one species compared to other species in the same area while b) Absolute abundance refers to the total number of individuals of a species in a given area.

Ameenat Oloko (10:31:45) (in thread): > According to this“The differences in the abundance of the various phyla, families, and genera were described with the tool ANCOMBC (0.99.4, https://www.bioconductor.org/packages/release/bioc/ vignettes/ANCOMBC/inst/doc/ANCOMBC.html) using differential abundance analysis (DAA).”, Therefore,Table S1 and Fig S3B were determined by ANCOM-BC. @Anne-Marie SharpBased on research,ANCOM-BC is used to statistically compare the microbiome composition between groups, and to identifysignificantly differentmicrobesat various taxonomic levels(phylum, family, and genus levels). - Attachment (bioconductor.org): Bioconductor - 3.20 Software Packages > The Bioconductor project aims to develop and share open source software for precise and repeatable analysis of biological data. We foster an inclusive and collaborative community of developers and data scientists.

Ameenat Oloko (10:32:50) (in thread): > I’m not sure what statistical test was used for figure 4B

Svetlana Ugarcina Perovic (10:47:31): > :question:Please fill in this survey on your experience with BugSigDB during your Outreachy contribution. > If you already did it before, during previous rounds, please do it again:slightly_smiling_face:hopefully your experience with us has been improved…Your feedback will help us to improve the experience for future contributors, thank you!https://docs.google.com/forms/d/e/1FAIpQLScYzrN2imOTcv5fjLr27uuCgKer0sIN4AMwgDMlnsAfRFWNRw/viewform?fbzx=8337124519102598305

Ameenat Oloko (10:54:31) (in thread): > Thank you,@Svetlana Ugarcina Perovic. I just filled out the survey form.

Anne-Marie Sharp (11:19:46) (in thread): > Hello@Ifunanya Benita Obiakuyou should curate it as it appears in the article since its not on NCBI/UNIPROT

Anne-Marie Sharp (11:20:25) (in thread): > Okay. will do that.

Anne-Marie Sharp (11:29:25) (in thread): > @Joy@Adeshile Oluwatosin@Ameenat OlokoThank you all so much. From your suggestions:point_right:Supplementary data: ANCOM-BC, Main article data: T-test & Mann-Whitney test

Anne-Marie Sharp (11:31:07) (in thread): > @Adeshile Oluwatosinyou mentioned the representation of the figures already states that it’s for absolute abundance, but its still curatable right? since its showing differences between the different groups.

Anne-Marie Sharp (11:36:53) (in thread): > Okay@Precious Chijiokesorry, I don’t understand what I’m to recheck, please can you explain

Adeshile Oluwatosin (12:01:04) (in thread): > Alright, will do

Adeshile Oluwatosin (12:01:29) (in thread): > Yes it is curatable

Anne-Marie Sharp (12:13:53): > Hello everyone, please what is the data transformation for ANCOM-BC? and does it automatically do MHT correction?

Ameenat Oloko (12:15:03) (in thread): > I think it is log-ratio transformation,@Anne-Marie Sharp. You can check this threadhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1734625441914479 - Attachment: Attachment > @Svetlana Ugarcina Perovic @UBNSEMS3S please what is the data Transformation for ANCOM-BC?

Anne-Marie Sharp (12:19:36) (in thread): > thank you@Ameenat OlokoI had already checked but I wish there was a curation link attached there for me to confirm what she finally used

Ameenat Oloko (12:20:50) (in thread): > I think she left it blank, and added some notes from the paper(https://www.nature.com/articles/s41467-020-17041-7)@Anne-Marie Sharp. The mentors confirmed that towards the end of the thread. - Attachment (Nature): Analysis of compositions of microbiomes with bias correction > Nature Communications - Differential abundance analysis of microbiome data continues to be challenging due to data complexity. The authors propose a method which estimates the unknown sampling…

Anne-Marie Sharp (12:42:13) (in thread): > @Ameenat Olokothank you! the article also confirms that it does MHT correction:partying_face:

Anne-Marie Sharp (12:48:39) (in thread): > Okay

Joy (13:34:07) (in thread): > Thank you@Svetlana Ugarcina Perovicwill surely do.

Precious Chijioke (13:58:06) (in thread): > @Anne-Marie Sharpplease recheck Figure 4 if it’s 3 groups. I think it’s 2 groups. The difference abundant taxa is recorded forRSV Infection and RSV Convalescence

Mildred Anashie (14:05:03) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (14:19:19) (in thread): > Hi@Anne-Marie SharpAncom BC uses log transformation as shared, also I think you should leave it as No if the paper doesn’t say they applied correction.

Juliana Kentomahun Mautin (14:26:58) (in thread): > Thank you@Svetlana Ugarcina Perovic. I would fill it now

Anne-Marie Sharp (14:33:20) (in thread): > @Precious Chijiokefigure 4 is confusing because both A&B have : no symptoms compared to blocked/runny nose, cough wheeze, any symptoms but the legend beside states that B should be no symptoms compared to blocked/runny nose, any symptoms

Anne-Marie Sharp (14:35:45) (in thread): > I would suggest Group1 be blocked/runny nose, cough wheeze, any symptoms in Figure 4A and Group1 be blocked/runny nose, any symptoms in Figure 4B. Perhaps others can also take a look into it.

Precious Chijioke (14:37:51) (in thread): > @Anne-Marie Sharpthank you for the suggestion.

Precious Chijioke (14:40:07) (in thread): > @Anne-Marie SharpI agree with what@Ameenat Olokoand@Mildred Anashiesaid

Anne-Marie Sharp (14:45:05) (in thread): > thank you@Precious Chijioke@Mildred AnashieOkay. from what I understood in the ANCOM-BC article, ANCOM-BC incorporates MHT correction: ‘Note that ANCOM-BC is the first method in the literature that can not only identify differentially abundant taxa while controlling the FDR for multiple testing, it also provides 95% simultaneous confidence intervals for the mean DA of each taxon in the two experimental groups’ and in the chat it waslinear regression framework but analagous to log-ratio transformation.

Anne-Marie Sharp (14:48:52) (in thread): > Please also help me check to confirm

Ameenat Oloko (15:06:33) (in thread): > @Anne-Marie Sharp, I think you’re supposed to check the evidence of MHT correction from the article you’re curating (based on the curation policy) and not the ANCOM-BC article. I think the ANCOM-BC article should just give an idea on MHC corrections but not the final conclusion.

Ameenat Oloko (15:08:16) (in thread): > You could share the article link so we can verify it.

Anne-Marie Sharp (15:37:57) (in thread): > @Ameenat OlokoOkay, here is the article linkhttp://dx.doi.org/10.3389/fphar.2024.1453989 - Attachment (Frontiers): Frontiers | Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan > IntroductionTreatment of rodents with the AT1 blocker (ARB) telmisartan (TEL) has an anti-adipose effect. Among other mechanisms, we also have attributed the…

Mildred Anashie (15:51:01) (in thread): > Hi@Anne-Marie SharpThe MHT should be recorded based on what was done in the article you are curating. Let me state an example, from information we know that MHT for LefSe should be NO but some authors state that MHT was done with LefSe and<@UBNSEMS3S>and@Svetlana Ugarcina Perovicalways advice to record what is reported in the article. Which would mean MHT=Yes, despite the test being LEfSe. > I’ve gone through your article and I do not see anything that implies MHT correction was done, so I think it should be No even though the statistical test is ANCOM BC

Ameenat Oloko (15:57:40) (in thread): > @Anne-Marie Sharp, I just went through the article, and there was no evidence of MHT correction (Bonferroni, the Holm-, the Hochberg-corrections, FDR, or q-value calculations). So you should record it as “No”.

Anne-Marie Sharp (16:01:53) (in thread): > @Mildred Anashie@Ameenat Olokookay noted, thank you both for clarifying, I appreciate

Ameenat Oloko (16:03:45) (in thread): > You’re welcome,@Anne-Marie Sharp. Well done:clap:

Mildred Anashie (16:12:15) (in thread): > You are welcome@Anne-Marie Sharp

Montana-D (19:15:35) (in thread): > Right Away

2025-04-09

Precious Orakwe (00:19:14) (in thread): > I don’t think figure 3b is curatble

Precious Orakwe (01:05:31): > good morning everyone, please do we curate relative abundance?

Adeshile Oluwatosin (01:18:19) (in thread): > Good morning > Yes > Relative abundance between two groups

Adeshile Oluwatosin (01:19:36) (in thread): > Check this conversation:https://community-bioc.slack.com/archives/C04RATV9VCY/p1731017565837069?thread_ts=1731017055.253719&channel=C04RATV9VCY&message_ts=1731017565.837069 - Attachment: Attachment > Relative abundance is how much of a bacterial taxon is present in a sample/site/environment relative to other taxa. Let’s say I own a zoo and I have 10 tigers and 2 lions. The relative abundance of tigers is 5 relative to the lions (which would be 1). > Differential abundance is when I compare relative abundances between groups to see if there was a statistically significant difference. So my friend’s zoo has 20 tigers and 2 lions. His relative abundance of tigers is 10 which I would use a statistical test to compare to my 5. > Note that for our purposes that differential abundance can include lots of different measures of abundance (the different data transformations). The important thing to look for is: did they identify specific microbial taxa that were different between groups using some sort of statistical test? Then that’s curatable.

Precious Orakwe (01:22:50) (in thread): > Thank you@Adeshile Oluwatosin

Dorcas Odetayo (02:07:09) (in thread): > Hi everyone, Could someone please guide me on how to curate Figures S2a–d and S1 from the supplementary materials? I’m a bit unsure which parts to curate and how to approach them. Thanks! - File (Word Document): Supplementary Figure (1).doc - File (Word Document): Supplementary Figure Legend (1).doc - File (Word Document): Supplementary Table (2).doc

Precious Orakwe (02:14:24): > I and @nith are working on this study, please i want to know if we are on the right track. Thank youhttps://bugsigdb.org/40013832 - Attachment (BugSigDB): Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer - BugSigDB > UNLABELLED: The incidence of colorectal cancer (CRC) has been increasing in recent decades.

Mildred Anashie (03:36:46) (in thread): > Hi@Dorcas OdetayoWell done, I’m unsure 2b and d can be curated but for 2a and c, you have 2 experiments from each and from the legend 2a used LEfse and 2c used MaAslin. > You’d curate the statistical tests as those and for the grouping and signatures. You would curate the taxas beside the green bars as Decreased and those beside the red bars as increased then look closely at each of the plots and you would see something like this (see attached image), that is what is telling you the comparison that was done.And Table S1 is beta diversity, wedon’tcurate beta diversity in BugSigdb. - File (JPEG): IMG_6472

Svetlana Ugarcina Perovic (04:18:58): > Good morning:teapot::coffee:I’m drinking:coffee:and thinking how YOU ARE ALL AMAZING:I am privileged and happy to work with you.So far, we curated56 studies :clap:**** ****for 23 days since Outreachy contributions started.

Adeshile Oluwatosin (04:20:02) (in thread): > Good morning:coffee:Yayy:relaxed:

Dorcas Odetayo (04:30:17) (in thread): > Thanks so much@Mildred Anashie:raised_hands:

Precious Orakwe (04:35:58) (in thread): > Good morning@Svetlana Ugarcina Perovic, > Wow, that’s amazing

Mildred Anashie (04:40:33) (in thread): > That’samazing:grinning_face_with_star_eyes:Good morning:coffee:@Svetlana Ugarcina Perovic

Anne-Marie Sharp (04:41:15) (in thread): > Well done with your curation. Your description for figure6 can be as stated in the article > ‘Correlation heatmap analysis of blood biochemical indicators and differential genera. Red represents positive correlation, and blue represents negative correlation’ for both Signatures in Experiment2

Anne-Marie Sharp (04:43:54) (in thread): > Good morning@Svetlana Ugarcina Perovicthat’sgreat! the feeling is mutual

Dorcas Odetayo (04:49:20) (in thread): > Hi@Kate Rasheedyou mentioned that Fig. S1 is also curatable in your feedback, could you please explain how I should go about curating it? Would really appreciate your guidance!:blush:

Mildred Anashie (04:49:36) (in thread): > Hi@Precious Orakwe@nithyaWell done:raised_hands:I’ll keep looking though but I just scanned the article and curation and I see you curated Figure 3bbut itisn’treally showing the differential abundance but the text is, soI’dsay you include text as a source in the curation

Mildred Anashie (04:52:10) (in thread): > I just noticed you asked about figure S1 and not table s1:woman-facepalming:@Dorcas OdetayoLet me look through that

Precious Orakwe (04:52:59) (in thread): > @Mildred AnashieI was thinking 3b is not curatable

Precious Orakwe (04:54:18) (in thread): > @Mildred AnashieI should include fig 3a and 3b as the source?

Mildred Anashie (04:55:39) (in thread): > I think including text as a source would be better, becausethat’sactually where you curated from even though it was referencing 3b@Precious Orakwe

Precious Orakwe (04:56:03) (in thread): > Please guys can you take a look at fig 4, that is my experiment 4, I want to know if we are on the right track

Mildred Anashie (04:56:43) (in thread): > Also in my opinion 3b on its owncan’tbe easily curatable but the text helped soit’sbest to include “Results text” as your source@Precious Orakwe

Precious Orakwe (04:58:25) (in thread): > Ok, thank you@Mildred Anashie

Dorcas Odetayo (04:59:08) (in thread): > Good Morning@Svetlana Ugarcina PerovicNice to hear that:partying_face:

Anne-Marie Sharp (05:05:22) (in thread): > @Precious Orakwe@Mildred AnashieFigure 3B actually goes with Figure 3A, so both can be put as the source

Precious Orakwe (05:07:06) (in thread): > Understood@Anne-Marie Sharp, can you take a look at experiment 4

Mildred Anashie (05:09:51) (in thread): > So Fig S1 is curatable as already stated@Dorcas OdetayoThe visualization used is boxplot, the color code inside each box (Something that looks like the imageI’mattaching), tells us what each box plot represents and the lines above each tells us what comparisons was done. > > The asterisk:keycap_star:tells us which of the comparisons is significant. > > When curating the line inside each plot tells us which group is increased compared to the other and that’s how you’d curate it. > Let me know if this is clear enough

Mildred Anashie (05:10:16) (in thread): > See image here please - File (JPEG): IMG_6473

Juliana Kentomahun Mautin (05:20:56) (in thread): > Good morning@Svetlana Ugarcina PerovicThis is great news. I’m currently having hot tea here because the weather is so cold here.

Mildred Anashie (05:26:32) (in thread): > Hi@Precious OrakweFrom my end, I don’t see Experiment 4 in the curation > > Can you see it?@Anne-Marie Sharp

Precious Chijioke (05:32:45) (in thread): > Good Morning@Svetlana Ugarcina PerovicWao! That’s great

Anne-Marie Sharp (05:35:55) (in thread): > @Mildred AnashieExperiment4 was curated but its not yet reflecting, you’ll have to search manually. And you tagged the wrong person:face_with_peeking_eye:@Precious Orakwetry saving it as complete then incomplete and back to complete so that the signatures in experiment4 will show. I will look through it.

Mildred Anashie (05:36:34) (in thread): > Thank you@Anne-Marie Sharp:grinning:

Montana-D (05:39:38) (in thread): > Good morning@Svetlana Ugarcina PerovicThat’s great news:tada::raised_hands:

Anne-Marie Sharp (05:49:31) (in thread): > @Precious OrakweI think Experiment4 should be the entire figure4 not just figure4 a&b. You can also make the source description clearer.

Dorcas Odetayo (06:09:49) (in thread): > @Mildred AnashieThanks so much for the explanation:heart:Just to confirm - will I be curating each comparison as a separate experiment? For example, wouldNormal - 0 day vs Normal - 15 daybe one experiment, andNormal - 0 day vs Normal - 15 dayanother? Thank You:raised_hands:

Precious Chijioke (06:11:20) (in thread): > @Adeshile Oluwatosin@Mildred Anashieplease I will like you to take a look over what@Anne-Marie Sharpsuggested. Thank you

chiamaka Uche (06:22:53): > Hello Everyone. > > I curated this paper with@Precious Chijiokeand will love a peer review before submitting for mentor’s review. Here’s the link:https://bugsigdb.org/39642873Thank you. - Attachment (BugSigDB): The respiratory microbiome is linked to the severity of RSV infections and the persistence of symptoms in children - BugSigDB > Respiratory syncytial virus (RSV) is the leading cause of infant respiratory infections and hospitalizations.

D-coder111 (06:26:40) (in thread): > Good morning@Svetlana Ugarcina Perovic, that’s amazing news:tada::raised_hands:

Joy (06:28:12) (in thread): > Well done@chiamaka Ucheand@Precious Chijiokeon your curation. We will have a look

Mildred Anashie (06:29:53) (in thread): > Yes it would be > > But also confirm the statistical test used and if youhaven’tcreated an experiment with that comparison and same statistical test yet. If youhavethen you include the taxas in those experiments but if not, you can create new experiments for each

Dorcas Odetayo (06:40:50) (in thread): > Okay Thanks For the clarification

Mildred Anashie (06:48:06) (in thread): > Hi@Precious Chijioke@chiamaka UcheWell done:raised_hands:Well take a look

Mildred Anashie (06:48:38) (in thread): > I’lltake a look soon@Precious Chijioke

Adeshile Oluwatosin (06:49:32) (in thread): > Well done@Precious ChijiokeI’lltake a look

Ameenat Oloko (06:55:44) (in thread): > Wow!That’sgreat!!:star-struck:Good morning,@Svetlana Ugarcina Perovic.

iniobong simeon (06:58:11) (in thread): > okay

Anne-Marie Sharp (06:59:18) (in thread): > Well done@Precious Chijioke@chiamaka Uchewe’ll review

Adeshile Oluwatosin (07:22:44) (in thread): > Well done:+1:

Aiysha shahid (07:34:13) (in thread): > Well done, I would also go through it:raised_hands:

Ifunanya Benita Obiaku (08:11:40): > Good afternoon everyone,@Victoria (Burah) Poromonand I curated this paper and we’d appreciate a peer review.https://bugsigdb.org/39976263 - Attachment (BugSigDB): Roseburia hominis improves host metabolism in diet-induced obesity - BugSigDB > Next-generation live biotherapeutics are promising to aid the treatment of obesity and metabolic diseases.

Ifunanya Benita Obiaku (08:12:39) (in thread): > Thank you so much@Anne-Marie Sharp.

Joy (08:21:46) (in thread): > That’s good to know@Svetlana Ugarcina Perovic!:sunny::teapot::coffee:That’s such a lovely message to start the day — thank you!:blush:Huge kudos to everyone —56 studies in just 23 days is seriously impressive! :clap::fire:Feeling super grateful to be part of such an inspiring and hardworking team. Let’s keep the momentum going!:rocket::muscle:****(And yes, coffee + awesome people = best combo!****:coffee::heart:)

Oriade Adeola (08:31:42): > Hello everyone please i need a peer review on this.https://bugsigdb.org/36875281 - Attachment (BugSigDB): Characteristics of fecal microbiota in different constipation subtypes and association with colon physiology, lifestyle factors, and psychological status - BugSigDB > BACKGROUND: Patients with chronic constipation (CC) show altered gut microbial composition.OBJECTIVES: To compare the fecal microbiota with different constipation subtypes and to identify potential influencing factors.DESIGN: This is a prospective cohort study.

Mildred Anashie (08:48:39) (in thread): > Well done:raised_hands:@Ifunanya Benita Obiakuand@Victoria (Burah) PoromonWe’ll have a look

Mildred Anashie (08:49:33) (in thread): > Well done:raised_hands:@Oriade AdeolaI’llhave a look

Mildred Anashie (09:02:31) (in thread): > From your curation, I see youhaven’tmarked the signatures as complete yet

Aiysha shahid (09:28:48) (in thread): > Hi@Oriade Adeola,the paper is actually referring to thefamilylevel, but the taxonomy used was at thegenuslevel for******Christensenellaceae******, which was incorrect. I’ve updated it to the correctfamilyrank as per NCBI taxonomy.Please double-check the rest of the taxa you’ve curated to ensure their ranks are accurate too.Also, just a reminder—when we’re asking for apeer revieworofficial review, we should make sure totag our collaborator, like others have been doing, so they’re properly looped in. > One more thing—can you let me know where****“unclassified Actinomycetota”****was sourced from? It’s not clear where that came in. > Thanks!

Aiysha shahid (09:34:41) (in thread): > Hi, well done! I’ll go through it. > Meanwhile, kindly mark all the signatures ascomplete {If it’s been complete from your end}Also, please note the following curation updates for Signature-2: > * Berryella intestinalis→ID-1531429 > * Berryella→ID-2815775 > * Olsenella sp. LZLJ 2should be curated asThermophilibacter immobilis→ID-2779519 > Thanks!

Precious Chijioke (09:35:00): > Good Day Everyone > Please I’m curating a paper and I am a bit confused on the identification of the signatures (increased and decreased) in Fig 5. I’ll appreciate your reviewhttps://www.frontiersin.org/files/Articles/956438/fmicb-13-956438-HTML/image_m/fmicb-13-956438-g005.jpgDo we curate Correction coefficient: Figure 6:https://www.frontiersin.org/files/Articles/956438/fmicb-13-956438-HTML/image_m/fmicb-13-956438-g006.jpgStudy link:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.956438/full - Attachment: Attachment - Attachment: Attachment - Attachment (Frontiers): Frontiers | Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation > Treatments targeted for gut microbial regulation are newly developed strategies in constipation management. In this study, the alleviating effects of gut mic…

Precious Chijioke (09:35:52) (in thread): > Well done@Oriade AdeolaI’ll have a look

nithya (09:44:28) (in thread): > @Precious OrakweFigure 4 is the first experiment

nithya (09:59:56) (in thread): > @Precious OrakweExperiment 4 i see you have merged healthy and polyps as group 0 and cancer as group 1. If you see figure 4 the healthy and polyps signature genera had difference in their abundance.

Ameenat Oloko (10:07:37) (in thread): > Well done on your curation,@Oriade Adeola. > > For the study design, although it was stated in the article that it’s a prospective cohort study. But according to the curation policy,the cross-sectional observation, not case control study was the best description. > > I think you’re supposed to have7 Experiments: > HC vs CC (Fig.2b and 2d); > STC vs NTC; > STC vs HC; > CC(DD and non-DD)vs HC[within texts]DD vs non-DD ; > non-DD vs HC; and > DD vs HC > > For experiment 2, Singnature 1, Christensenellaceae is on NCBI. The Taxonomy ID is 990719.

Ifunanya Benita Obiaku (10:11:15) (in thread): > Thank you so much@Aiysha shahid

Ifunanya Benita Obiaku (10:14:06) (in thread): > @Mildred Anashieyes please, that will be adjusted. Thanks for the review

Aiysha shahid (10:27:45) (in thread): > Hi@Ameenat Oloko, kindly into this text from the paper-Remarkably,Bacteroidaceaeshowed a significantly lower relative abundance in the STC group than in theNTC and HC groups(adjustedp< 0.01;p= 0.05) but comparable relative abundance between theNTC and HC groups(adjustedp= 0.95), indicating that the relative abundance ofBacteroidaceaemay be highly influenced by colonic transit (Figure 3(b)). It’s mentioned relative abundance between NTC AND HC, Also from the fig 3, we can see relative adundance in both the groups. Hence, we have curated it as an exp.

Juliana Kentomahun Mautin (10:28:16): > Hi everyone, Just a reminder that our office hour is at 9 AM EDT on Thursday, Looking forward to seeing you there. > > Please use this application to find the time in your local time zone so you don’t miss it:https://www.timeanddate.com/worldclock/converter.html?iso=20250320T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Aiysha shahid (10:29:55) (in thread): > Thanks for the reminder@Juliana Kentomahun Mautin:raised_hands:

Mildred Anashie (10:32:31) (in thread): > Hi@Juliana Kentomahun MautinOffice hours are Thursdays fromhere

Juliana Kentomahun Mautin (10:34:25) (in thread): > Hi@Mildred AnashieThank you for the correction, that’s a typo from my end, I’ve corrected it.

Aiysha shahid (10:37:17): > Hi, > I would like to request a peer review of this study:https://bugsigdb.org/39854172Paper link:https://academic.oup.com/jid/advance-article/doi/10.1093/infdis/jiaf043/7978852#502884056Note- I haven’t done the NCBI taxonomy for Experiment-2 yet, as I believe that Figures S3 and S4 may not be curatable. However, I’d appreciate it if someone from the team could double-check and confirm. If they are curatable, I’ll go ahead and curate them; otherwise, I’ll request their deletion. Thanks! - Attachment (BugSigDB): Associations between the gut microbiome, inflammation and cardiovascular profiles in people with HIV - BugSigDB > BACKGROUND: Inflammation and innate immune activation are associated with chronic HIV infection, despite effective treatment.Although gut microbiota alterations are linked to systemic inflammation, the relationships between the gut microbiome, inflammation and HIV remain unclear.

Svetlana Ugarcina Perovic (11:41:15) (in thread): > Please correct the link with this one:https://www.timeanddate.com/worldclock/converter.html?iso=20250410T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Svetlana Ugarcina Perovic (11:41:53) (in thread): > The one you shared is outdated showing the wrong time.

Precious Orakwe (12:12:15) (in thread): > Hi guys, good evening, > Can you please go through this write-up? Is it supposed to be one experiment here or two? Please guide me. > > Overall,******Peptostreptococcus**********, **********Parvimonas**********, **********Shewanella**********, **********Oscillibacter**********, **********Catonella**********, **********Eggerthella,********** and **********Gemella********** were significantly enriched in patients with CRC compared to healthy cohorts(Fig. 3B).****Fenollaria**********, **********Staphylococcus**********, **********Ezakiella**********, **********Finegoldia**********, **********Corynebacterium**********, **********Varibaculum**********, **********Neisseria,********** and **********Peptoniphilu*********s were significantly enriched in healthy individuals and patients with polyps***(Fig. 3B). It was important to note that the diagnostic accuracy was not compromised by low sample size (Fig. 3C). > > The first taxa were enriched in patients with CRC compared to the healthy cohort, and the second taxa were enriched in healthy individuals and patients with polyps. - Attachment (PubMed Central (PMC)): Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer > The incidence of colorectal cancer (CRC) has been increasing in recent decades. Current methods for CRC screening have their own drawbacks, thus there is an urgent need to identify the key microbes that drive the development of CRC for wider …

Juliana Kentomahun Mautin (12:19:55) (in thread): > I’ve updated it. Thank you@Svetlana Ugarcina Perovicfor the correction:blush:

Precious Orakwe (12:20:15): > Hi guys, good evening, > Can you please go through this write-up? Is it supposed to be one experiment here or two? Please guide me. > > Overall,******Peptostreptococcus**********, **********Parvimonas**********, **********Shewanella**********, **********Oscillibacter**********, **********Catonella**********, **********Eggerthella,********** and **********Gemella********** were significantly enriched in patients with CRC compared to healthy cohorts(Fig. 3B).****Fenollaria**********, **********Staphylococcus**********, **********Ezakiella**********, **********Finegoldia**********, **********Corynebacterium**********, **********Varibaculum**********, **********Neisseria,********** and **********Peptoniphilu*********s were significantly enriched in healthy individuals and patients with polyps***(Fig. 3B). It was important to note that the diagnostic accuracy was not compromised by low sample size (Fig. 3C). > > The first taxa were enriched in patients with CRC compared to the healthy cohort, and the second taxa were enriched in healthy individuals and patients with polyps.

Anne-Marie Sharp (12:21:17) (in thread): > Thanks for the reminder@Juliana Kentomahun Mautin

Victoria (Burah) Poromon (12:26:36) (in thread): > Hi@Precious ChijiokeFrom the image alone, it might be difficult to tell what is increasing or decreasing in figure 5. But the text above the figure explains it. > > Akkermansia is increased in the model group compared to the controls. So if your comparison is Model vs. MP group, Akkermansia will be recorded as decreased. Depending on what your group 0 and 1 is. > > The red color denotes increase, while the blue color denotesdecrease. > For figure 5, I’d curate what is stated as increased or decreased from the text, it explains the figure.

Ameenat Oloko (12:48:40) (in thread): > No, we do not curate correlate coefficients.Figure 6 isn’t curatable,@Precious Chijioke.

Ameenat Oloko (13:05:01) (in thread): > @Victoria (Burah) PoromonI guess you mean the blue colour denotes decrease. I agree with what Victoria said.I guess we can say the deeper the red, the more abundant that taxon is in the sample while the deeper the blue colour is, the less abundant it is.

Victoria (Burah) Poromon (13:06:56) (in thread): > Yes yes, thank you so much@Ameenat Olokothat was a typo

Ameenat Oloko (13:33:41) (in thread): > Hi,@Aiysha shahid. Well done:clap:.I think FigS3 is curatable based on this excerpt from the articleIn people with HIV, an increased abundance of the bacterium Bifidobacterium pseudocatenulatum, a potentially probiotic microbe that is associated with SCFA production and bile acid metabolism, correlated with a lower Agatston score and overall CAP burden. Similarly, an increased abundance of Megamonas hypermegale and Selenomonas ruminantium, both SCFA-producing bacteria involved in carbohydrate fermentation, was linked to a lower CAP burden in people with HIV.Fig S4, on the other hand, may not be curatable based onNo significant associations at the genus level were associated with Agatston score or CAP burden. > > > I believe you’re on the right track on Experiment 2, Signatures 1&2. You just need to remove FigS4 from the source.

Ameenat Oloko (14:10:26) (in thread): > Yea, you’re right,@Aiysha shahid. You’re to add an experiment comparing NTC and HC groups.

Aiysha shahid (14:15:55) (in thread): > Ohk rest seem’s good to you?@Ameenat Oloko

Ameenat Oloko (14:16:32) (in thread): > Please, what do you mean by “therest”?@Aiysha shahid

Aiysha shahid (14:18:48) (in thread): > I mean, Apart from Experiment-2, is the rest of the study good to go?

Ameenat Oloko (14:21:14) (in thread): > Oh, I am yet to go through the study thoroughly.I only focused on the supplementary figures you mentioned,@Aiysha shahid.

Ameenat Oloko (14:31:30) (in thread): > There are two experiments here,@Precious Orakwe:CRC vs healthy cohorts andhealthy individuals vs patients with polyps.

Precious Chijioke (14:46:34) (in thread): > @Victoria (Burah) Poromonthank you. What you said is exactly my thoughts. While writing out the comparisons and signatures in my note I used the text because it explains it well and using the image alone is a bit difficult in as much as I understood the color indication box. > > I wanted to confirm my thoughts before curating it in BugSigDB. Thank you for confirming my thoughts.

Mildred Anashie (14:47:32) (in thread): > Hi@Aiysha shahidand@Oriade AdeolaWell done on this:raised_hands: > * From Fig 2b and d I see only 3 decreased taxas but you have up to 7 (Streptococcaceae, Prevotellaceae and Bacteroidetes). Rikenellaceae is recorded as decreased when it should have been recorded as Increased. Kindly go through the taxas for all the experiments again > * The statistical test for experiments in Fig 2 and 3 is Mann whitney, please remove the other 3 > * I do not see where the study mentioned confounders being controlled for, I believe it should be left blank. > * The alpha diversity was reported for only CC vs HC, please remove it across other comparison that isn’t this. > * Lastly, Table 2 and Table 3 appears curatable and the test is Spearman correlation. You should curate based on the asterisk (*).

Precious Chijioke (14:48:54) (in thread): > Thank you@Ameenat Olokofor helping me to be sure of my thoughts on the curation of correlate coefficients.

Precious Chijioke (14:52:07) (in thread): > Thank you@Joy@Mildred Anashie@Anne-Marie Sharp@Adeshile Oluwatosin@Aiysha shahidlooking forward to your reviews

Mildred Anashie (14:58:02) (in thread): > Hi@Ifunanya Benita Obiaku@Victoria (Burah) PoromonWell done again. > I believe Fig 4e is curatable, see the caption ’Correlation between basic characteristics and differential species in mice between HFD-PBS and HFD-RH groups.’ :thinking_face:

Svetlana Ugarcina Perovic (15:00:01) (in thread): > @Juliana Kentomahun Mautinit’s still the old link with wrong date and timing

Juliana Kentomahun Mautin (15:04:26) (in thread): > @Svetlana Ugarcina Perovicis this the correct Link?https://www.timeanddate.com/worldclock/converter.html?iso=20250403T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Svetlana Ugarcina Perovic (15:05:14) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1744213275231129?thread_ts=1744208896.111679&cid=C04RATV9VCY - Attachment: Attachment > Please correct the link with this one: https://www.timeanddate.com/worldclock/converter.html?iso=20250410T130000&p1=179&p2=37&p3=176&p4=3395&p5=125

Juliana Kentomahun Mautin (15:06:13) (in thread): > Thank you:blush:

Precious Chijioke (15:07:26) (in thread): > @Oriade AdeolaI agree with what@Ameenat Olokoand@Mildred Anashiesaid. > > When curating a paper you can always use Ctrl+F or Come+F to search for words like the case of confounders, you can search for it in the paper alongside other words you want to confirm or easily trace. > > Also for taxa confirmation you can read through the study over and over and check the image in figure noting the signature direction show as either as a color direct box or notation, * or #.

Anne-Marie Sharp (15:08:42) (in thread): > @Precious Chijioke@chiamaka Uche1)There was no matched on for gender, the match for age was between only control group & RSV. Only the experiment between control & RSV should have matched on for age. > 2)There are two study designs: prospective cohort and case-control > 3)I mentioned earlier to confirm the grouping, there may be more experiments, eg Exp1 will be healthy controls vs RSV infection & Exp2 will be healthy controls vs RSV(convalescent) and so on.

Precious Chijioke (15:12:32) (in thread): > Thank you@Anne-Marie Sharp@Adeshile Oluwatosin@Mildred Anashieplease while reviewing our curation can you help us confirm the grouping/comparisons

Precious Chijioke (15:20:08) (in thread): > @Ifunanya Benita Obiaku@Victoria (Burah) Poromonwell done on your curation. > I agree with what@Aiysha shahidand@Mildred Anashiesaid.

Precious Chijioke (15:21:23) (in thread): > @Aiysha shahidwell done on your curation. I’ll look through it

Precious Chijioke (15:23:06) (in thread): > @Precious Orakwefrom the write-up it’s 2 experiments as already stated by@Ameenat Oloko

Mildred Anashie (15:42:28) (in thread): > Hi@Aiysha shahidWell done > > I think you should curate Fig S1 alongside, Fig 2 and S2. Also, I think we need to confirm if you should go ahead with curating the heatmaps in this study during the office hours tomorrow because it truly is alot (They all look like something that can be curated though)

Aiysha shahid (15:54:15) (in thread): > Hi@Mildred Anashie, In Exp-1, I didn’t use S1 in the signature as it was highly contradictory to the text and Fig-2. Specifically, the text and Fig-2 show that**** **********Odoribacter splanchnicus******is decreased in HIV+ people, but S1 indicates an increase. It’s same for another taxa as well. As earlier told that for heatmap we need to curate single experiment, but For Fig-4, S3 and S4, there couldn’t be any particular condition. So, I think it’s not curatable. Also S3 and S4 have similar result as Fig-2,only difference is that fig-2 is in bar plot and fig- s3 and s4 are in form of heatmaps. - File (Word Document): Supplementary_Data.docx

Mildred Anashie (15:55:30) (in thread): > Okay, You can just confirm again during office hours@Aiysha shahid

Anne-Marie Sharp (16:01:26) (in thread): > @Ifunanya Benita Obiaku@Victoria (Burah) PoromonWell done on a neat curation, I agree with the above suggestions. Also, the group names can be made clearer e.g Group 0 name: HFD-PBS(High Fat Diet - Phosphate Buffered Saline), Group 1 name: HFD-RH(High Fat Diet - > Roseburia Hominis).@Mildred AnashieHFD-PBS and HFD-RH groups are not represented in Fig 4e so I doubt it is curatable.

Adeshile Oluwatosin (16:04:23) (in thread): > Well done@Ifunanya Benita ObiakuFigure 4E seems curatable > Write the group names in full as stated above > > E.g Group 0: low BMI > Group 1: high BMIOn a straight line, taxa represented in blue are decreased signatures, those in red are increased

Anne-Marie Sharp (16:13:15) (in thread): > @Adeshile Oluwatosinokay! this was what we discussed earlier. but in this case of Figure 4E, the asterisks * should signify significance, right?

Adeshile Oluwatosin (16:14:21) (in thread): > Yes, curate only taxa with asterisks

Anne-Marie Sharp (16:23:45): > Hello everyone, I would appreciate a peer review of this curation:https://bugsigdb.org/39624839Thank you! - Attachment (BugSigDB): Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan - BugSigDB > INTRODUCTION: Treatment of rodents with the AT1 blocker (ARB) telmisartan (TEL) has an anti-adipose effect.Among other mechanisms, we also have attributed the anti-adipose action to diet-independent alterations in gut microbiota.

Adeshile Oluwatosin (16:28:24) (in thread): > Hi@Precious Chijioke > * I think you should change the group 1 name for Experiment 1 as “Respiratory Syncytial virus infection (RSV) /Respiratory Syncytial virus infection (RSV) convalescence group. > > * Figure 2E and F confounders are: age, gender and study site. See”E and F) Log2 fold change (FC) of features (genera [E]/ASVs [F]) based on MaAsLin2 (linear mixed-effects model) with health status (healthy controls, RSV infection, and convalescence) as variable of interest, adjusted for age, gender (fixed effects), and study site (random effect) “ > > * Only age is a matched on factor “As a control group, nasopharyngeal samples were collected from age-matched healthy term born infants with no RSV infection.” > > * use the same idea to rename the group names for experiment 2. > * I think the best approach to curating Figure 3E and 3F is pairwise comparison between Healthy and mild RSV, Healthy and moderate RSV, Healthy and severe RSV. Use the colors to depict which signature would be curated in these experiments. MHT is yes > Same idea for 4A and 4B, MHT is yes. > * For the study design,use prospective cohort for now. You can confirm during the office hour

Adeshile Oluwatosin (16:29:35) (in thread): > Check the supplementary material for any important details

Ndukauba Oluchi (16:30:55): > Hello everyone, I would love a peer review on this paper > Link:https://bugsigdb.org/39950489 - Attachment (BugSigDB): Probiotic supplementation mitigates sex-dependent nociceptive changes and gut dysbiosis induced by prenatal opioid exposure - BugSigDB > The gut microbiome has emerged as a promising target for modulating adverse effects of opioid exposure due to its significant role in health and disease.

Adeshile Oluwatosin (16:31:21) (in thread): > Well done@Anne-Marie Sharp

Adeshile Oluwatosin (16:31:31) (in thread): > Well done

Mildred Anashie (16:32:12) (in thread): > Well done on your curation@Anne-Marie SharpWill take a look

Ndukauba Oluchi (16:32:14) (in thread): > Great work!@Anne-Marie Sharpwill look at this

Montana-D (16:32:48) (in thread): > Great work on your curation@Anne-Marie Sharp

Mildred Anashie (16:33:20) (in thread): > Okay@Ndukauba OluchiI’lltake a look at it,well done

Adeshile Oluwatosin (16:35:06) (in thread): > I don’t think the condition is correct > Curate Patescibacteria group as “candidatusaltimarinota”

Adeshile Oluwatosin (16:37:33) (in thread): > Write a note on the curation of the statistical test

Anne-Marie Sharp (16:38:16) (in thread): > @Adeshile Oluwatosinthank you.Yes I was deliberating on weight loss, body weight, obesity,body weight regulation.There is a discussion for the curation already for the statistical test and the data transformation

Adeshile Oluwatosin (16:38:23) (in thread): > “Alistipes_A”, curate as Alistipes

Montana-D (16:39:20) (in thread): > Great work on your curation

Ndukauba Oluchi (16:42:30) (in thread): > Well, I think the condition should be Response to treatment

Adeshile Oluwatosin (16:46:31) (in thread): > * Curate clostridium sensu stricto 1 as clostridium > * Lachnospiraceae UGC 001: always ensure the taxa starts with a capital letter > * data transformation wasnotspecified in experiment 2 > * when inputting V4 in the variable region, do that in the first column, leave the second empty

Anne-Marie Sharp (16:50:50) (in thread): > @Ndukauba Oluchithank you

Mildred Anashie (17:04:02) (in thread): > * You haven’t recorded the data transformation for the first experiment(Log transformation). > * Also I think CAG:495 can be curated as thishttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi > * For the condition, the mice underwent Faecal Microbiota transfer (FMT) and were treated as well during the duration of the study, so I agree with@Ndukauba Oluchifor the condition to be Response to treatment or Transplant outcome measurement.:thinking_face: - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Precious Chijioke (17:17:39) (in thread): > Alright > Thank you@Adeshile Oluwatosin

Mildred Anashie (17:21:37) (in thread): > * Also curate lachnospirsceae_NK4A136 as this 877420 > * Shannon is decreased in the MSAL_F group in Exp 1 > * I think you switched your signature curation or mixed up the group names for the first experiment, this because from the figure blue is for MSAL_F and red is for CSAL_F but that isn’t what was curated, please cross check the curation again@Ndukauba Oluchi

Ndukauba Oluchi (17:22:34) (in thread): > @Mildred AnashieResponse to treatment would be the best fit.

Ndukauba Oluchi (17:23:44) (in thread): > @Mildred Anashiethe mixup is just for experiment 1 ?

Mildred Anashie (17:24:55) (in thread): > I’m still looking through, thought to point that out first > I just confirmed it isn’t the group names, it’s the signatures

Mildred Anashie (17:27:58) (in thread): > @Ndukauba OluchiIts same as Experiment 2 but 3 is okay

Anne-Marie Sharp (17:37:41) (in thread): > @Ndukauba OluchiI agree with@Mildred Anashiethe signatures were swapped in Experiments 1&2

Anne-Marie Sharp (17:46:06) (in thread): > Thank you@Mildred Anashieplease the link you shared doesn’t open to a search result

Mildred Anashie (17:50:58) (in thread): > I apologise, this is the ID-1262987 and the taxa-Proteobacteria bacterium CAG:495

Anne-Marie Sharp (18:17:14) (in thread): > Okay@Mildred Anashiethank you

Precious Orakwe (19:00:09) (in thread): > Thanks@Ameenat Olokoand@Precious Chijioke

Eseoghene Cynthia Princewill-Ukot (21:07:19): > Hi fellow curators, > I’ve started curating this article:https://pubmed.ncbi.nlm.nih.gov/39791884/I’ve completed an initial draft, but I’d love to collaborate with one of you to finalize the curation and ensure we capture all the relevant details accurately. > If you’re interested in collaborating, please let me know, and we can divide up the tasks or work together on specific sections. > Thanks. - Attachment (PubMed): Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice - PubMed > Foods contain thousands of unique and biologically important compounds beyond the macro- and micro-nutrients listed on nutrition facts labels. In mammals, many of these compounds are metabolized or co-metabolized by the community of microbes in the colon. These microbes may impact the thousands of b …

nithya (22:45:56): > 40013832. Dear members, Figure 6 is a correlation heatmap. We curate relative abundance. Correlation is not curated. Correct? - Attachment (PubMed): Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer - PubMed > Identifying the key microbes that drive the development of colorectal cancer (CRC) has been important in this field. We delved into the research on the association between CRC and fecal microbiota in this study, providing a detailed analysis of the characteristics of fecal microbiota during the tran …

2025-04-10

Ameenat Oloko (00:39:20) (in thread): > Hi,@nithya. Figure 6 isnotcuratablesincewe only curate differential abundance results. Based on the texts, itexplores the relationship between blood biochemical indicators and key differential genera. > > Differential abundance comparesbacterial abundance across different groups (in this case, patients with CRC vs. healthy individuals) to identify taxa that are more or less in one group over the other group. > https://community-bioc.slack.com/archives/C04RATV9VCY/p1710765400695549?thread_ts=1710764138.716929&channel=C04RATV9VCY&message_ts=1710765400.695549 - Attachment: Attachment > differential abundance testing == comparing the (relative) taxon abundance between two groups

Adeshile Oluwatosin (00:53:33) (in thread): > Good morning > Figure 6 is not curatable

Adeshile Oluwatosin (00:54:07) (in thread): > Sometimeswe curate correlation analaysis, it depends on how useful the details are in the figure

Ameenat Oloko (00:54:53) (in thread): > Good morning ,@Eseoghene Cynthia Princewill-Ukot. I’d like to collaborate with you on this article.

Eseoghene Cynthia Princewill-Ukot (01:14:37) (in thread): > Awesome!@Ameenat OlokoI’m in your DM!:joy::joy:

Precious Orakwe (02:48:39) (in thread): > Hi guys, good morning > Can you please go through this write-up? Is it supposed to be one experiment here or two? Please guide me. > > Overall, Peptostreptococcus, Parvimonas, Shewanella, Oscillibacter, Catonella, Eggerthella, and Gemella were significantly enriched in patients with CRC compared to healthy cohorts (Fig. 3B). Fenollaria, Staphylococcus, Ezakiella, Finegoldia, Corynebacterium, Varibaculum, Neisseria, and Peptoniphilus were significantly enriched in healthy individuals and patients with polyps (Fig. 3B). It was important to note that the diagnostic accuracy was not compromised by low sample size (Fig. 3C). > > The first taxa were enriched in patients with CRC compared to the healthy cohort, and the second taxa were enriched in healthy individuals and patients with polyps.

Precious Orakwe (02:49:32) (in thread): > @Adeshile Oluwatosincan you check this out

Adeshile Oluwatosin (03:00:59) (in thread): > Good morning@Precious OrakweI thinkit’sbest to ask this question outside this thread > I will go through it and respond when you post it outside this thread

Victoria (Burah) Poromon (03:22:48) (in thread): > Hi everyone, thank you all so much for your suggestions!@Ifunanya Benita Obiakuplease curate Figure 4e as well. The statistical test used is Spearman’s correlation. > You’ll create 9 experiments. Please follow@Adeshile Oluwatosin’s suggestion for the group names. Also, please remember to write the group names in full. (If you scroll down on the page, you will see the expanded group names in Figure 4e). The blue colors with asterisks indicate a decrease, while the red colors with asterisks indicate an increase. Well done!

chiamaka Uche (03:27:48) (in thread): > Thank you@Adeshile Oluwatosin

Ifunanya Benita Obiaku (03:44:00) (in thread): > Thank you so much for your contributions@Adeshile Oluwatosin@Mildred Anashie@Precious Chijioke@Anne-Marie Sharp@Victoria (Burah) PoromonI’ll curate it. 8 experiments as Body weight has no associated specie.

Victoria (Burah) Poromon (03:45:36) (in thread): > Yes, I already removed body weight and got 9.

Svetlana Ugarcina Perovic (04:02:25): > Reminder for our weekly team meeting:today at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your SPECIFIC questions!We do not discuss if some Figure/Table is curatable or not.cc<@UBNSEMS3S>NOTE: You can check your time here:https://www.timeanddate.com/worldclock/converter.html?iso=20250410T130000&p1=179&p2=37&p3=176&p4=3395&p5=125

Ameenat Oloko (04:03:35) (in thread): > Good morning,@Svetlana Ugarcina Perovic. Thank you for the reminder.

Adeshile Oluwatosin (04:04:47) (in thread): > Good morning@Svetlana Ugarcina PerovicThank you

Mildred Anashie (04:04:50) (in thread): > Duly noted@Svetlana Ugarcina PerovicThank you for the reminder

Ndukauba Oluchi (04:06:17) (in thread): > Hi@Anne-Marie Sharp@Mildred AnashieI am quite confused on how i switched signatures in experiments 1 and 2.

Ndukauba Oluchi (04:07:48) (in thread): > The blue colour is MSAL_F which is group 1 > the Red colour is CSAL_F which is group 0 . CSAL_F is increased while MSAL_F is decreased

Aiysha shahid (04:16:18) (in thread): > Hi@Mildred Anashie, thanks! Please have a look at the image—Fig. 2. In it, the black plots represent CC and the grey ones represent HC. On zooming in, I noticed thatStreptococcaceae,Prevotellaceae,Bacteroidetes, andRikenellaceaeare increased in HC (the grey plots). I would appreciate it if you could cross-check this once. Link to the image-https://journals.sagepub.com/doi/10.1177/17562848231154101These additional experiments were added based on the review provided by the co-mentor. She didn’t mention Table 2 and 3 as curatable, so I believe they are not.@Oriade Adeola, if u want to add anything to this text you can do it!

Anne-Marie Sharp (04:27:15) (in thread): > Thank you for the reminder@Svetlana Ugarcina Perovic

Aiysha shahid (04:27:48) (in thread): > Kindly don’t revert the changes made for “********Christensenellaceae”, the taxa you are curating it’s not available on the NCBI, I have again corrected it. @Oriade Adeola*** *****

Victoria (Burah) Poromon (04:28:34): > Hi@Svetlana Ugarcina Perovic, Good morning.I’mcurrently writing my final application and I would like to ask if there are any tasks that we should prioritise while drafting the project timeline. > > Thank you so much.

Ndukauba Oluchi (04:28:57): > Morning everyone. > Please I have a question. For this paper:https://www.mdpi.com/1422-0067/26/3/1236Please is Figure 4 and 6 curatable. - Attachment (MDPI): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. To explore how these structural differences impact constipation intervention, a 14-day study was conducted on loperamide-induced constipated mice using five dietary fibers: soluble dietary fiber from steamed sweet potato (SDF-S), oat β-glucan (OB), polydextrose (PD), arabinogalactan (AG), and inulin (IN). The results showed that four fibers, excluding PD, significantly improved gastrointestinal (GI) transit rate (p < 0.05), although PD had the highest fecal moisture, it was significantly different from the lowest IN (p < 0.05). AG and IN resulted in higher 6 h fecal weights compared to other fibers. SDF-S and OB were more effective in modulating serum levels of gastrointestinal hormones. The different monosaccharide compositions and glycosidic bonds of these fibers led to distinct changes in gut microbiota composition and SCFA profiles. Galactose and arabinose in AG were linked to increased abundance of Lachnospiraceae_UCG-006, Bacteroides, and Odoribacter, promoting butyrate fermentation, which is positively correlated with GI transit rate. Glucose in SDF-S, OB, and PD favored acetate fermentation positively correlated with fecal moisture. Fructose in IN encouraged the proliferation of Muribaculaceae_unclassified and Ruminococcus, associated with butyrate fermentation and increased 6 h stool weight, respectively. The β-glycosidic bonds in OB may lead to high butyrate production through the selective proliferation of Lachnospiraceae_unclassified. Minor components like fucose, rhamnose, and ribose were positively correlated with the abundance of Oscillospiraceae_unclassified, Anaerotignum, and Lachnospiraceae_unclassified. In conclusion, the unique monosaccharide compositions and glycosidic bond differences in dietary fibers selectively promote the proliferation of fiber-degrading and butyrate-producing bacteria, resulting in varied effects on constipation relief.

Adeshile Oluwatosin (04:29:30) (in thread): > I was about to ask this. We would appreciate a response@Svetlana Ugarcina PerovicThank you so much

Anne-Marie Sharp (04:32:52) (in thread): > Good morning@Ndukauba OluchiI believe they are both curatable

Adeshile Oluwatosin (04:48:24) (in thread): > Figure 4 is curatable, Figure 6 is not

Svetlana Ugarcina Perovic (04:48:56): > IMPORTANTFinal applicationThere are no community-specific questions.As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page:https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Svetlana Ugarcina Perovic (04:49:19) (in thread): > I answered it herehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539 - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Adeshile Oluwatosin (04:49:42) (in thread): > Thank you so much

Victoria (Burah) Poromon (04:50:36) (in thread): > Oh thank you so much!@Svetlana Ugarcina Perovic

Mildred Anashie (04:54:05) (in thread): > Good morning@Ndukauba OluchiFigure 4 is curatable but I am unsure about Fig 6

Mildred Anashie (04:55:00) (in thread): > Thank you@Svetlana Ugarcina Perovic:pray:

Aiysha shahid (04:58:25) (in thread): > Thanks a lot@Svetlana Ugarcina Perovic:blush::tulip:

Ameenat Oloko (05:03:40) (in thread): > Good morning,@Ndukauba Oluchi. Figure 4 is curatable, but Figure 6 is not curatable.

Anne-Marie Sharp (05:06:00) (in thread): > Thank you@Svetlana Ugarcina Perovic

Mildred Anashie (05:07:33) (in thread): > Okay@Aiysha shahidIf the mentors already reviewed it thenthat’sokay > > ButI’vetaken a second look and Rikkenellaceaeisn’teven significant andshouldn’tbe curated > > See the image below - File (JPEG): IMG_6497

Aiysha shahid (05:21:08) (in thread): > Ohk, Rikkenellaceae is been removed. Thanks@Mildred Anashie:raised_hands:

Precious Chijioke (05:24:26) (in thread): > Thank you@Svetlana Ugarcina Perovic

Joy (05:46:35) (in thread): > This is truly appreciated@Svetlana Ugarcina Perovic:pray:

Aiysha shahid (06:15:01) (in thread): > @Oriade Adeola, all the peer review changes have been made, if you have cross-checked the NCBI taxonomy of the taxa’s, we are good to go. Let me know, once you’re done.

Daberechi Okorie (06:58:26): > Good morning everyone, > > PleaseI’dlovea peer review on this article curationhttps://bugsigdb.org/38125567https://pmc.ncbi.nlm.nih.gov/articles/PMC10731029/

Oriade Adeola (07:06:57) (in thread): > @Aiysha shahidI’m soo sorry for not tagging you earlier, i was in a hurry to drop the review i didn’t remember. i’m going through it now. I’m soo sory once againg. Thank you everyone for the peer review

Mildred Anashie (07:09:17) (in thread): > Hi@Daberechi OkorieWell done, I’ll take a look

Daberechi Okorie (07:09:52) (in thread): > Alright, thank you Mildred

Oriade Adeola (07:11:43) (in thread): > I’m soo sorry for not tagging you earlier:pray:My bad

Oriade Adeola (07:13:47) (in thread): > Thank you for implementing all the changes from the peer review. I have gone through them. I guess we are good to go.

Amaka (08:14:22): > Good afternoon mentors@Svetlana Ugarcina Perovic@Aleru Divine@Scholastica Urua@Kate RasheedCan you please help me confirm curating these signatures > Should “Absconditabacteria_(SR1)(G-1); s_bacterium_HMT_874” be curated exactly as this or curated as “bacterium_HMT_874. > > This is another instance, Bacteroidetes_(G-5); s_bacterium_HMT_507 > > for Prevotella; s_sp.HMT_292, should this be curated exactly as stated or as sp.HMT_292

Ndukauba Oluchi (08:20:17) (in thread): > Great work!@AmakaI would advise you curate those signatures as it is.

Amaka (08:20:45) (in thread): > Ok, thank you

Juliana Kentomahun Mautin (08:24:27) (in thread): > Thank you so much for the insight@Svetlana Ugarcina Perovic

Mildred Anashie (08:31:41) (in thread): > Hi@AmakaFrom what you shared, It looks like s_bacterium_HMT_874 is the species but I’ll advice you share a link to get an idea on how it was reported in the article. But if it is exactly how you have shared then I believe curating the species might be best (based on the curation policy).

Ndukauba Oluchi (08:31:53) (in thread): > Great job@Daberechi Okoriejust a few corrections. > The Statistical test is Lefse > MHT is YES > LDA IS 3

Svetlana Ugarcina Perovic (08:33:40) (in thread): > In 30 min starts our meeting.Please note we do not discuss if some Figure/Table is curatable or not. That can be discussed here between curators. > > Specific questions and doubts are appropriate topic for our weekly meetings.

Adeshile Oluwatosin (08:35:41) (in thread): > https://bugsigdb.org/39848958

Adeshile Oluwatosin (08:35:52) (in thread): > https://pmc.ncbi.nlm.nih.gov/articles/PMC11757712/ - Attachment (PubMed Central (PMC)): Microbiome analysis in individuals with human papillomavirus oral infection > Microbiome gained attention as a cofactor in cancers originating from epithelial tissues. High-risk (hr)HPV infection causes oropharyngeal squamous cell carcinoma but only in a fraction of hrHPV+ individuals, suggesting that other factors play a …

Adeshile Oluwatosin (08:36:26) (in thread): > @Mildred Anashiethe wholeTaxalisted out is actually the species

Adeshile Oluwatosin (08:36:31) (in thread): > I would send the link

Ndukauba Oluchi (08:36:57) (in thread): > Thank you@Svetlana Ugarcina Perovic, but can we ask how a particular figure could be curated?

Mildred Anashie (08:37:04) (in thread): > Okay thenIt’sbest to curate it as it is then@Adeshile Oluwatosin

Adeshile Oluwatosin (08:46:14) (in thread): > That’s what we did for now

Ndukauba Oluchi (08:49:40) (in thread): > Finally, i also think that the Condition of this study should be “Response to treatment” or “Treatment Outcome Measurement” See this: However, frequent usage of laxatives can result in drug dependence and a cathartic colon; therefore, a laxative is not a satisfactory therapy for FC patients (Yao et al.,2022).Therefore, there is a perceived need to perform further research into the mechanism of FC, with the aim of enhancing the efficacy of treatment strategies.

UBNSEMS3S (08:54:51) (in thread): > Thanks Svetlana. I wrote a reminder last night but realized I forgot to send it.:face_exhaling:@Ndukauba OluchiI would ask that questions like “Is this figure curatable?” and “How do I curate this table?” be asked here on Slack. I only have a few minutes to look at the table or figure during the meeting and that’s just not enough time to figure it out with confidence. I’ve gotten it wrong more than a few times in the past few months. > > I would prefer we reserve the meeting for more conceptual questions or difficult problems that have arisen in curation (e.g. “I have trouble determining study design–can we review those?”). In previous years, team meetings were a chance to have more of an educational component–I would often give impromptu lectures on various subjects–but I haven’t been able to do that because I am spot reviewing so many tables and figures. > > Thank you for the good question.

Mildred Anashie (08:58:15) (in thread): > Okay@Adeshile OluwatosinI’llgive this a look

Ndukauba Oluchi (08:58:42) (in thread): > Oh! Thanks for the clarification!<@UBNSEMS3S>That makes a lot of sense, and I appreciate you taking the time to explain it. I’ll be sure to post those kinds of questions here on Slack moving forward so you have the time and context to review them properly.

Svetlana Ugarcina Perovic (09:30:47): > Today’s Lesson: CLDs show statistical significance between groups using letters. The key rule: groups sharing the same letter are NOT significantly different, while groups with different letters ARE significantly different.@Joyhas been curating this studyhttps://github.com/waldronlab/BugSigDBcuration/issues/675and shared today with us this figurehttps://www.frontiersin.org/files/Articles/463461/fmicb-10-01721-HTML/image_m/fmicb-10-01721-g003.jpg(attached too)with a compact letter display (CLD):https://en.wikipedia.org/wiki/Compact_letter_displayThanks<@UBNSEMS3S>! - File (PNG): Screenshot 2025-04-10 at 15.21.12.png

Precious Chijioke (09:54:50): > Thank you<@UBNSEMS3S>and@Svetlana Ugarcina Perovicfor today’s office hour.

Adeshile Oluwatosin (09:56:04) (in thread): > @Ndukauba OluchiThank you > * LEFse is specific to Figure 2A and 2B and it was curated as such. > * The conditions are specific to each experiments and I believe they are correct as well. The study has about nine experiments. We used a reviewed study as a case study. > * Experiment 2 is also curated appropriately.FC is the case(group 1). Hence all taxa represented in red is increased abundance.

Mildred Anashie (10:02:27) (in thread): > Hi@Ndukauba OluchiI agree with@Adeshile OluwatosinThe curation looks good to me, but conclusivelyI’lltake a second look

Joy (10:02:48): > Thank you@Svetlana Ugarcina Perovicand<@UBNSEMS3S>for today’s office hour! Thanks for the great summary and lesson oncompact letter display(CLDs)!:raised_hands:It was really helpful to see how the letters indicate statistical significance across groups—super useful for interpreting the figure. Looking forward to curating more of these studies.@Juliana Kentomahun Mautin

Victoria (Burah) Poromon (10:03:42) (in thread): > I remember looking at this figure when it was first shared on the channel and Icouldn’ttell what was significant, this is a very interesting way to represent it. > > Thank you!<@UBNSEMS3S>And@Joyfor sharing this figure.

Anne-Marie Sharp (10:20:45) (in thread): > Thank you@Mildred Anashie@Ndukauba Oluchi

Daberechi Okorie (10:22:54) (in thread): > Thank you guys:heart:I’d go through the taxa one more time just to be sure.

Precious Orakwe (10:53:03): > Good day teammates, please i would love a peer review of this study, Thank you.https://bugsigdb.org/40180909 - Attachment (BugSigDB): A prebiotic dietary pilot intervention restores faecal metabolites and may be neuroprotective in Parkinson’s Disease - BugSigDB > Current treatment of Parkinson’s Disease (PD) remains symptomatic, and disease-modifying approaches are urgently required.A promising approach is to modify intestinal microbiota and key metabolites of bacterial fermentation: short-chain fatty acids (SCFA), which are decreased in PD.

Anne-Marie Sharp (11:07:29) (in thread): > Well done@Precious Orakwewe’ll review

Dorcas Odetayo (11:08:39) (in thread): > Hello@Mildred Anashie, I noticed that the experimentNormal-0day vs Normal-15dayshows the same taxa and direction of change as the comparisons below: > * Normal-0day vs Normal-30day > * Normal-0day vs Normal-45day > Should I still curate each as a separate experiment, or just note that the same results apply across these comparisons? - File (PNG): s1.png

Mildred Anashie (11:09:00) (in thread): > Since the comparisons are different, I’d saycurate separately

Adeshile Oluwatosin (11:10:39) (in thread): > Hi@Dorcas Odetayocurate seperately in this case regardless

Dorcas Odetayo (11:12:03) (in thread): > Alright@Mildred Anashie@Adeshile Oluwatosin, I’ll go ahead and curate them as separate experiments then.

Mildred Anashie (11:12:44) (in thread): > Hi@Precious OrakweWell done, I’ll take a look at this

Adeshile Oluwatosin (11:27:21) (in thread): > Well done@Precious Orakwe

Joy (11:39:53) (in thread): > Well done@Precious Orakweon your curation. We will have a look.

Joy (11:53:56) (in thread): > @Precious OrakweThe antibiotics exclusion criteria are detailed in the****“Methods” section.: Specifically, exclusion criterion (4) states:”the use of laxatives, antibiotics, or immunosuppressive agents in the past three months (note that n=1 PD took 1 day of antibiotics 4 weeks before study).”**You should include that.

Mildred Anashie (12:09:41) (in thread): > That’s correct@Ndukauba OluchiThe blue signatures should be curated as Signature 1 (since this is your increased signatures (Increased in Group 1) and the Red should be curated as Signature 2, Decreased (Increased in Group 0). > > But I see what you did now, you curated decrease before increase

Mildred Anashie (12:10:24) (in thread): > Typically, you should curate it the other way round. But I can’t say if it needs to be changed or left that way

Anne-Marie Sharp (12:19:09) (in thread): > @Ndukauba OluchiI would advise you to change it, for signature1 to be increased abundance & signature2 to be decreased abundance. I have seen a review recently where similar was corrected.

Mildred Anashie (12:24:19) (in thread): > Hi@Adeshile OluwatosinI’ve looked through as well and I could resolve a few based on the genus > * Change S_Oralis to thishttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=28134&lvl=3&keep=1&srchmode=1&unlock > * Change S_parvum to thishttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=1501329&lvl=3&keep=1&srchmode=1&unlock > * Change S_auratiaca to thishttps://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Tree&id=596085&lvl=3&keep=1&srchmode=1&unlock - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Adeshile Oluwatosin (12:25:18) (in thread): > I’m not done with correcting. > Thank you for checking it out > I would still ask amaka to post for peer review later on > Thank you once again@Mildred Anashie

Mildred Anashie (12:26:53) (in thread): > Okay then:+1:

Adeshile Oluwatosin (12:35:10) (in thread): > I would use this study as a case study:https://bugsigdb.org/34248903/Experiment_2 - Attachment (BugSigDB): 34248903/Experiment 2 > .

Mildred Anashie (13:03:22) (in thread): > Hi@Precious OrakweI think you should have 2 experiments from Supplementary figure 3. > 1. CO before and CO after > 2. PD before and PD after > Also, the participants underwent diet intervention so I think the condition should be “Response to Diet”. You can scan through methods, you would see a better definition for the groups. > > Well done again:+1:

Precious Orakwe (13:04:47) (in thread): > I thought as much but was not sure, Thanks@Mildred Anashie

nithya (14:01:23): > https://pubmed.ncbi.nlm.nih.gov/40013832/Dearmembers in our morning meeting we had a discussion with a multiple group paper. - Attachment (PubMed): Fecal bacterial biomarkers and blood biochemical indicators as potential key factors in the development of colorectal cancer - PubMed > Identifying the key microbes that drive the development of colorectal cancer (CRC) has been important in this field. We delved into the research on the association between CRC and fecal microbiota in this study, providing a detailed analysis of the characteristics of fecal microbiota during the tran …

Anne-Marie Sharp (14:14:02) (in thread): > Hello@nithyawe will look at it. please leave all your comments/questions regarding this paper in this specific thread, so it will be easier to follow the discussion

nithya (14:15:08) (in thread): > In Figure 4 we have 6 different groups 4 stages of cancer and one healthy and one polyps patient

nithya (14:15:23) (in thread): > while curating should i create a seperate experiment for each groups like: expt1 : c1 vs healthy, expt 2: c2 vs healthy, expt 3: c3 vs healthy and expt 4: c4 vs healthy. should i repeat the same for cancer groups whereae polyps too.

nithya (14:16:40) (in thread): > if you look at fig 4D (Oscillibacter) C1(denoted by letter a ) has statistical difference with healthy groups (denoted by b) whereas other cancer groups (C2,C3,C4 => ab,b,ab) are not statistical significant with healthy groups (b). So, to get all the signature genera do i need to curate each cancer groups seperate experiment?

Anne-Marie Sharp (14:34:02) (in thread): > @Precious Orakwe1)for the antibiotics exclusion, maybe you put it as three months and add a note explaining thatn= 1 PD took 1 day of antibiotics 4 weeks before study. 2)In supplementary figure 3c, you have 2 comparisons as@Mildred Anashiementioned. You also have the same comparisons in Figure3

Montana-D (15:34:11) (in thread): > To me I think you are on the right track

Montana-D (15:36:03): > Please@Svetlana Ugarcina Peroviccan we have the last office hour please. There’s some lessons I missed and would like to go back on them:palms_up_together:

Anne-Marie Sharp (15:43:13) (in thread): > @nithyathat’s a good way to capture the different genera in each group accurately. let’s still hear from others

Adeshile Oluwatosin (16:12:13) (in thread): > Ididn’tgo through the study but from your explanation yes you are to curate the experiments seperately if there are significant taxa to curate as The comparison is different in this case.@nithya

UBNSEMS3S (18:11:16): > Office hour recording. Thanks everyone who attended. - File (MPEG 4 Video): bsdb_2025_04_10.mp4

Anne-Marie Sharp (18:24:12) (in thread): > Thank you fortoday’soffice hour:pray:and thank you for sharing

Montana-D (18:45:57) (in thread): > Thank you so much for sharing:pray:

Joy (19:26:57) (in thread): > Thanks for sharing!

Oriade Adeola (20:16:03) (in thread): > @Aiysha shahidHello Aiysha. My apologies once again for not tagging you earlier. please should we proceed to submitting our curation for review on git up now, or are there other changes you would like to make?

Vanisha Garg (23:49:16): > @Svetlana Ugarcina Perovic, to all my colleagues and mentors , I sincerely apologize for not being able to keep up with messages and for falling behind on curating the articles. I was not keeping well health-wise, which affected my ability to respond and stay on track. > I’m truly sorry for any inconvenience or disruption this may have caused you. I deeply value your time and support, and I appreciate your patience during this time. > I’m feeling much better now and will be continuing the curation process with full focus and commitment. > Thank you for your understanding.

2025-04-11

Joy (01:00:44) (in thread): > Thank you for your heartfelt message,@Vanisha Garg. Sorry to hear you weren’t feeling well and hope you’re now fully on the mend. —we truly appreciate your dedication and are glad to have you back.

Ifunanya Benita Obiaku (01:12:30) (in thread): > @Vanisha GargWelcome back, I’m glad you’re feeling better. We’re all here to support and assist you make the process easier and a success. Glad to have you back.

Adeshile Oluwatosin (01:38:27) (in thread): > @Vanisha GargI am happy you feel way better now. We are all here to support you. Kindly let us know if you need any form of assistance or help. Also, please take your time. > Welcome

Anne-Marie Sharp (02:28:13) (in thread): > Welcome back@Vanisha Garggladyou’refeeling better now.We’realways here to assist you in your curation process

Precious Chijioke (02:55:23) (in thread): > @nithyagoing through the paper and your explanation I agree with what@Anne-Marie Sharpand@Adeshile Oluwatosinsaid. Curate the experiments differently.

Precious Chijioke (02:57:13) (in thread): > Welcome back@Vanisha GargI’m happy you’re feeling much better now. We’ll always assist you when you need help.

Svetlana Ugarcina Perovic (03:01:30) (in thread): > No worries at all! Take your time and continue curating at your pace!

Svetlana Ugarcina Perovic (03:02:13) (in thread): > @Joyplease select with@Vanisha Garganother paper and curate it togetheras a team!

Svetlana Ugarcina Perovic (03:05:01): > :question:In your opinion and now experience (this week focus was a teamwork),what are the key components of good teamwork? Happy Friday:teapot::coffee:

Joy (03:06:29) (in thread): > Duly noted@Svetlana Ugarcina Perovic! Thank you, I’ll connect with@Vanisha Gargand we’ll work together on selecting and curating another paper. I appreciate the guidance and opportunity to collaborate!.

Montana-D (03:09:18) (in thread): > Welcome back@Vanisha Garg. I’m glad to hear you feel better. Don’t hesitate to ask for assistance whenever needed

Joy (03:10:19) (in thread): > Happy Friday!:coffee::teapot:Reflecting on this week’s focus on teamwork, I’ve come to appreciate several key components that contribute to effective collaboration: > > 1. Open Communication:
> > > 2. Trust and Respect:
> > > 3. Shared Goals and Accountability:
> > > 4. Defined Roles and Responsibilities:
> > > 5. Adaptability:
> I am glad to be part of the BugSigDB community:sparkles:Wishing everyone a productive and enjoyable weekend!

Precious Chijioke (03:11:02) (in thread): > Refecting on the week’s goal, I’ll say that the key components of a good teamwork are: > 1. Open and effective effective communication is very important for sharing information, exchanging ideas, and providing feedback. It prevents misunderstandings and promotes better decision-making. > 2. Collaboration: working towards a common goal improves team efficiency and produces better results. > 3. Commitment to the team’s goals ensures that everyone is working towards the same vision. It promotes productivity and success. > 4. Accountability makes team members responsible for their actions and contributions. > 5. Setting defined goals provides direction and focus for the team. > 6. Trust and respect fosters better collaboration and communication. > Have a beautiful weekend

Aiysha shahid (03:15:07) (in thread): > Hi@Oriade Adeola, yes if you have gone through this-https://community-bioc.slack.com/archives/C04RATV9VCY/p1744205328511739?thread_ts=1743509477.225039&cid=C04RATV9VCY, then we should go ahead and submit it. - Attachment: Attachment > Hi @Oriade Adeola,the paper is actually referring to the family level, but the taxonomy used was at the genus level for Christensenellaceae, which was incorrect. I’ve updated it to the correct family rank as per NCBI taxonomy. > Please double-check the rest of the taxa you’ve curated to ensure their ranks are accurate too. > Also, just a reminder—when we’re asking for a peer review or official review, we should make sure to tag our collaborator, like others have been doing, so they’re properly looped in. > One more thing—can you let me know where “unclassified Actinomycetota” was sourced from? It’s not clear where that came in. > Thanks!

Anne-Marie Sharp (03:19:42) (in thread): > Happy Friday @svetlana_up1) clear communication has been the most important > 2) respect for others opinions > 3)being committed to achieve set goals
> 4)positive mindset and good vibes > 5)being open to learn from peers

Daberechi Okorie (03:28:26) (in thread): > Hey@Svetlana Ugarcina Perovic, happy Friday! > > This week really showed me how powerful teamwork can be. > So for me, the key components of good teamwork are: > * Support– having someone’s there when you’re stuck makes such a difference. > * Patience – especially when learning something new. > * Willingness to share know ledge– everyone brought something valuable to the table. > * Respect – no one made anyone feel less for asking questions. > It’s been a great reminder that we grow faster and better together.

Victoria (Burah) Poromon (03:29:25) (in thread): > Happy Friday@Svetlana Ugarcina PerovicIn my opinionI’llsay the key components are; > * Communication: Being able to clearly and effectively communicate your ideas and opinions. And also the tone of communication matters a lot. > * Respect: Respect each other’s opinions > * Understanding: understanding thatit’sokay to have conflicting opinions, and > * Being open to accepting feedback from others.

Montana-D (03:44:53) (in thread): > Happy Friday@Svetlana Ugarcina Perovicand everyone:coffee:Based on my experience on this week’s collaboration, I’d say to ensure a good teamwork, both parties have to > 1. Communicate clearly and most especially respectfully Pay attention to and understanding what the others are saying even if you feel you know better > 2. Always give constructive feedbacks in a way that is helpful to the others and the team as a whole. > 3. Work together in identifying and solving any challenges and recognizing that the success of the team depends on everyone’s contribution > 4. Understand that you all must not always agree on a particular point, but you should trust your teammates decision and not impose your decisions or conclusions on them. Be willing to learn from each other:- always view conflicts as an opportunity to grow and find mutually acceptable solutions > 5. Lastly, but not least, appreciate and congratulate each and everyone’s efforts, it goes a long way to boost their confidence and make them feel valued. > These are all what has made my teamworks a success in the past weeks.

Mildred Anashie (03:56:19) (in thread): > Happy Friday:coffee:It’s great to see clearand effectivecommunication topping almost everyone’s list because it’s same for me:blush:From my experience and in my opinion, > * Clearly communicating what you want to say so others do not misunderstand you. > * Also, good teamwork is about two-way communication. I talk, and also listen. > * Being responsive is key. > * I’ve also learned to be patient. Everyone works differently. > * And most importantly, to respect people’s time and opinions. That makes teamwork smoother. > Thank you for encouraging teamwork@Svetlana Ugarcina Perovic:raised_hands:

Ameenat Oloko (04:03:30) (in thread): > We’reglad to have you back,@Vanisha Garg. I hope you feel much better. Please, take your time and take things a step at a time. We are all here to support and encourage you. Please,feel free to communicate if you need any assistance.

Svetlana Ugarcina Perovic (04:10:17): > CONFERENCE > > Today I have a special invitation for you:join us next week at MVIF (Microbiome Virtual International Forum), a virtual, free and inclusive alternative to a traditional multi-day microbiome conference.https://www.microbiome-vif.org/en-USWe’ve been organizing this event monthly since 2021, you can see recordings here:https://www.youtube.com/@MicrobiomeVIF/playlists - Attachment (YouTube): Microbiome Virtual International Forum > Microbiome Virtual International Conference (MVIF) is a recurring bite-sized alternative to multi-day microbiome conference: > Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference! > > Every month there is an event, with a great speaker from the microbiome field and 3 selected talks and many research highlights! > Follow the event live… > But if you miss it… in this channel you will find the videos of the events!

Ameenat Oloko (04:14:07) (in thread): > Good morning,@Svetlana Ugarcina Perovic. Happy Friday!:partying_face: > 1. Teamwork encourages seeing things in other people’s perspectives. It also allows you to take into account any important details one might have missed. > 2. Teamwork improves (open) communication. It allows one to brainstorm on ideas before reaching a final decision/solution. > 3. Teamwork increases productivity. > 4. It fosters patience between people.

Joy (04:16:41) (in thread): > Thank you@Svetlana Ugarcina Perovicfor this invition. We will definitely attend!:pray:

Ameenat Oloko (04:16:42) (in thread): > Thank you for the invite.I’ll make sure to tune in. Do we need to fill any form to attend,@Svetlana Ugarcina Perovic?

Svetlana Ugarcina Perovic (04:17:43) (in thread): > Please do free registration, the link is available on the website.

Anne-Marie Sharp (04:23:20) (in thread): > Thank you for the invite@Svetlana Ugarcina Perovic, will attend:white_heart:

Montana-D (04:34:55) (in thread): > Thank you for the invite. > I look forward to attending

Aiysha shahid (04:40:52) (in thread): > Thanks for the invite, will surely attend!:tulip:

Victoria (Burah) Poromon (05:35:21): > Hi everyone, Good morning.@Mildred Anashieand I just finished curating a study and we’re putting it up for peer review. > > Study link:https://bugsigdb.org/39978595Article/paper link:https://www.amjtransplant.org/article/S1600-6135(25)00093-0/fulltextThank you so much for your feedback/suggestions in advance.

Joy (05:40:57) (in thread): > Well done@Victoria (Burah) Poromonand@Mildred Anashieon your curation, we will have a look.

Anne-Marie Sharp (05:41:14) (in thread): > Good morning and well done@Victoria (Burah) Poromon@Mildred Anashiewe’ll review

Mildred Anashie (05:41:22) (in thread): > Hi@Vanisha GargWelcome back > It’s great to hear you are better, We are all here to support you and you continue curation:blush:

Mildred Anashie (05:56:45): > Happy Friday Everyone:blush:Hi@Svetlana Ugarcina Perovic@Kate Rasheed@Aleru Divine@Scholastica Urua<@UBNSEMS3S>@Daberechi Okorieand I are working on curating this article and would appreciate your inputs. > > We have gone through the study and identified the curatable figures but our concern is Figure 2C and D and Supplementary Table 13. > * In Fig 2c and d we are unclear on what the comparisons are and if it should be curated separately as HLCD increasing vs HLCD Decreasing (just using only HLCD as an example) or curated together with Supplementary Figure 2 which shows Baseline and Endpoint comparisons. This is what the article says though “Microbiome taxonomic profiles were significantly altered during this caloric-restricted feeding trial, and the patterns of alteration between groups differed. Cladograms with taxonomic labels for lineage having a significant change are provided inFigure S2. Linear discriminant analysis identified 9, 8, 11, and 6 species-level alterations during a 12-week feeding trial among participants randomized to HLCD, non-HLCD, TRE, and non-TRE groups, respectively (Figures 2C and 2D).” > * For Table S13 the comparisons are clear but the FDR isn’t significant. The authors however, made bold the significant P-values even though the adjusted P-values weren’t significant, so we are unsure if we should curate the comparisons there using the P values or leave the table out since the adjusted p-values wasn’t significant. > Thank you in advance for your feedback and suggestions > Link to study:https://pubmed.ncbi.nlm.nih.gov/39454570/ - Attachment (PubMed): Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT - PubMed > The effect of a healthy low-carbohydrate diet (HLCD) and time-restricted eating (TRE), alone or in combination, on body weight and gut microbiome beyond caloric restriction remains unclear. In this 12-week two-by-two factorial randomized trial with a 28-week follow-up among 96 participants with over …

Adeshile Oluwatosin (06:13:35) (in thread): > Well done@Mildred AnashieI will go through it

Adeshile Oluwatosin (06:13:50) (in thread): > Well done,I’llgo through it

Adeshile Oluwatosin (06:15:36) (in thread): > Happy Friday:coffee:@Svetlana Ugarcina PerovicHere are the key components of good teamwork, based on my opinion and this week’s experience: > * Clear and open communication – Just having honest conversations about how to approach things, letting everyone share their thoughts, and being kind but clear when something needs correcting. It really helps everyone stay on the same page. > > * Listening and moving at a shared pace – I learned that it’s important to make sure no one’s left behind. Encouraging people to ask questions and following proper steps together made things smoother for everyone. > > * Respecting people’s time and opinions – Whether it’s showing up on time for meetings or being open to different ideas, respect goes a long way. And if someone can’t make it, just communicating that helps keep the team in sync. > > * Splitting tasks smartly – After discussions, it helped to divide tasks in a way that gave everyone a chance to grow. Sometimes picking something you’re not familiar with is the best way to learn. > > * Being open to feedback – Feedback can be tough sometimes, but I’ve seen how helpful it is when we’re open to it. It’s all part of growing and working better together.

Vanisha Garg (06:18:51) (in thread): > Thankyou everyone for believing in me and trusting me that yes I could again give it a start. > Yes@JoyI will be curating the article with you , Thankyou@Svetlana Ugarcina Perovicfor helping me throughout this phase

Aiysha shahid (06:20:36) (in thread): > Well Done, I would also go through this@Mildred Anashie

Joy (06:21:24) (in thread): > I am just curious, for Figure 6C, the metabolites: Butyrate and Propionate produced some genera stated thus:******C) Abundance of bacterial taxa involved in butyrate and propionate production between HC and CKD patients, reflecting a decrease in these beneficial taxa in CKD. ****Why didn’t you curate those? > > Well done once again!@Victoria (Burah) Poromonand@Mildred Anashie

Mildred Anashie (06:25:40) (in thread): > Hi@JoyFigure 6C doesn’t show differential abundance in my opinion > > There could be something we missed though:thinking_face:

Adeshile Oluwatosin (06:30:12) (in thread): > Figure 6C is not curatable,there’sno reflection of differential abundance even from the caption.

Joy (06:46:37) (in thread): > Ok, thanks@Mildred Anashieand@Adeshile Oluwatosin

iniobong simeon (07:20:26) (in thread): > Task Assistance: stepping in to help colleagues who are struggling with their curation . This involves offering expertise, or even taking on some of their responsibilities temporarily by reviewing their curation and going through their articles. > > Emotional Support: encouragement, empathy, and understanding during stressful periods or when one is facing personal challenges. This emotional backing helps maintain morale and reduces burnout risk. > > Knowledge Sharing: some members actively share their skills, experiences, and insight.

Adeshile Oluwatosin (07:32:21) (in thread): > From the excerpt, Figure 2C and 2D seems to be seperate experiments itself with group names > * non-HLCD (group 0), HLCD (group 1). > * non- TRE (group 0), TRE (group 1). > * Although there was description of the cladogram, supplementary figure 2 seems to have a more specific and defined group name so should be curated seperately > You can say something like 1. Baseline (HLCD) vs Endpoint (HLCD). 2. Baseline (Non-HLCD) vs Endpoint (Non-HLCD), do the same for TRE and non-TRE. > > As I cannot see any further details from the article. So no assumptions to curate with the initial experiment. > * Table S13:I had a similar curation of recent and Chloe mentioned to curate the unadjusted p values as they may be useful, I think you should curate the significant p values in this case since they were highlighted, stating MHT as no and writing a note on the table curation. If youdon’tget a direct response from a mentor. You can use the study I curated as a case study during review.

Adeshile Oluwatosin (07:34:06) (in thread): > I would need to take my time with this review, if youdon’tmind. Well done

Mildred Anashie (07:35:57) (in thread): > Thank you@Adeshile OluwatosinFrom 2c and d we can see the direction of increase and decrease for each group and HLCD & NON-HLCD were reported separately, same as TRE & NON- TRE:thinking_face:

Adeshile Oluwatosin (07:37:12) (in thread): > Although in normal cases, we are to curate just significant adjusted q values. You can curate the significant p values here . > Alright, let me check this

Eseoghene Cynthia Princewill-Ukot (07:37:35) (in thread): > Thanks for the invite@Svetlana Ugarcina Perovic. I will definitely attend.

Adeshile Oluwatosin (07:44:26) (in thread): > @Mildred AnashieI just saw the caption of supplementary figure 2 “Cladogram of significantly changed gut microbiome during the 12-week feeding trial, related to figure 2. > > You are to curate Figure 2C, 2D and Figure S2 as a source for an experiment as they are related. So we have 4 different experiments from the stated figures. I listed out how they should be grouped. Baseline (red) and Endpoint (Green)

Adeshile Oluwatosin (07:46:18) (in thread): > Baseline (HLCD) vs Endpoint (HLCD). > Baseline (Non-HLCD) vs Endpoint (Non-HLCD), > Baseline (TRE) vs Endpoint (TRE) > Baseline (non-TRE) vs Endpoint (non-TRE)

Mildred Anashie (07:48:13) (in thread): > Thank you so much@Adeshile OluwatosinWe get the grouping for S2 and have already started curating but we were unsure about including Figure 2 into S2 curation or curating separately. > > Thank you again

Adeshile Oluwatosin (07:48:37) (in thread): > No, its related > Sodon’t curateseperately

Eseoghene Cynthia Princewill-Ukot (07:53:14) (in thread): > Happy Friday@Svetlana Ugarcina Perovic, everyone! In my opinion and experience this week, the key components of good teamwork will be: > 1. Open Communication: Honest and transparent communication reduces misunderstandings and fosters trust. > 2. Concrete Goals: Tangible objectives broken down into milestones help teams stay focused and measure progress. > 3. Empowerment and Autonomy: Allowing team members to make decisions independently boosts morale and creativity. > 4. Trust: Trust among team members is essential for collaboration and commitment to shared goals. > 5. Flexibility: Teams must adapt to changing conditions, workflows, or goals without losing cohesion

Svetlana Ugarcina Perovic (08:01:28) (in thread): > If I had to name only one point:PATIENCE –**** ****the capacity to accept or tolerate delays or misunderstandings without becoming annoyed or anxious. > > If there is no patience then all the rest on your lists:slightly_smiling_face:can not be achieved.

Victoria (Burah) Poromon (08:10:27) (in thread): > Thank you@JoyAnd@Adeshile OluwatosinPlease take your time:blush:

Eseoghene Cynthia Princewill-Ukot (08:27:12): > Hello curators! I have been curating this article and I would like a peer review. Thanks.https://pubmed.ncbi.nlm.nih.gov/29133803/,https://bugsigdb.org/29133803 - Attachment (PubMed): Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women - PubMed > We measured the microbial community structure of genital ulcers in women. Swabs from clinically detected ulcers were tested for HSV-2 and Treponema pallidum by polymerase chain reaction (PCR). HSV-2 and T. pallidum were detected by serum antibody testing. Microbial community structure was characteri … - Attachment (BugSigDB): Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women - BugSigDB > We measured the microbial community structure of genital ulcers in women.Swabs from clinically detected ulcers were tested for HSV-2 and Treponema pallidum by polymerase chain reaction (PCR).HSV-2 and T.pallidum were detected by serum antibody testing.

Precious Chijioke (08:31:58): > Good Day Everyone > I curated this study and would love a peer review > Thank youhttps://bugsigdb.org/36016793 - Attachment (BugSigDB): Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation - BugSigDB > Treatments targeted for gut microbial regulation are newly developed strategies in constipation management.In this study, the alleviating effects of gut micro-ecologically regulatory treatments on constipation in mice were investigated.

Mildred Anashie (08:59:47) (in thread): > Hi@Eseoghene Cynthia Princewill-UkotWell done:raised_hands:I’lltake a look

Mildred Anashie (09:00:24) (in thread): > Hi@Precious ChijiokeI’ll take a look > Well done

Daberechi Okorie (09:06:05): > Hello everyone, Good afternoon > > Could you kindly confirm the curation of UCG-005, UCG-002 and UCG-003 in this article. > It was only stated to be Oscillospiraceae UCG-002 in experiment 1 (Figure 1E). We don’t want to assume the three taxa to be Oscillospiraceae UCG-005/003/002. > > Thank you so muchhttps://pmc.ncbi.nlm.nih.gov/articles/PMC10731029/#Curation link:https://bugsigdb.org/38125567 - Attachment (PubMed Central (PMC)): The gut microbiome and metabolites are altered and interrelated in patients with functional constipation > Gut microbiota and metabolites have been identified to contribute to the pathogenesis of functional constipation (FC); however, the underlying mechanism(s) have not been elucidated, and the relationship between the gut microbiota and metabolites in …

Adeshile Oluwatosin (09:06:30) (in thread): > Hi@Precious Orakwewell done

Adeshile Oluwatosin (09:08:40) (in thread): > Well done@Eseoghene Cynthia Princewill-Ukot

Antonia Beatriz Soler Riera (09:55:37): > Hello I am Antonia, from Argentina. I just joined and will try to contribute to this project. I am a Biomedical Engineer but for the last 20 years I have not worked in the field. Now that my kids have grown up I am trying to go back to my career, and for the last 3 years I have been studying and applying to remote jobs in the field of software development, machine learning, AI, both in the biomedical field and other areas, but haven’t succeeded so far. I applied for this internship opportunity, and 2 days ago I was accepted, and I chose this project. I don’t know if this is the right project or if I have enough time to make a contribution. I also have programming skills in Python, Javascript, SQL. In case I am not a good fit to this project, let me know. Thank you.

Svetlana Ugarcina Perovic (10:01:09) (in thread): > Welcome to the team! Please go throughhttps://community-bioc.slack.com/docs/T35G93A5T/F05URJ0P021And feel free to ask your questions here! The community is open to clarify your specific doubts.

Svetlana Ugarcina Perovic (10:02:26) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1744022992210139 - Attachment: Attachment > IMPORTANT > > 1. Fill out an initial application at https://www.outreachy.org/eligibility/ > 2. Record a contribution to your project on the Outreachy site. > 3. Complete a final application for your project. > > The deadline for final applications is April 15, 2025 at 4pm UTC. Applicants will not be able to create a final application after the deadline. Applicants can edit their final application until the deadline. > > Applicants who submit a final application will be able to continue recording and editing their contributions to your project. They can record contributions until the intern announcement on May 8, 2025 at 4pm UTC. Applicants who have not submitted a final application will not be able to record or edit their contributions. > > IN SHORT: complete your final Outreachy application and feel free to continue curating in BugSigDB

Anne-Marie Sharp (10:12:35) (in thread): > You’rewelcome@Antonia Beatriz Soler Riera

Precious Chijioke (10:13:20) (in thread): > @Daberechi Okoriewell done on your curation > Curate UCG-005, UCG-002, UCG-003 taxa as seen in Figure 1E image. I curated a study with same taxa and I was told by a mentor to curate as seen.

Precious Chijioke (10:15:08) (in thread): > You’re welcome@Antonia Beatriz Soler Riera

Mildred Anashie (10:28:24) (in thread): > Noted > > Thank you:blush:

Joy (10:29:18) (in thread): > Welcome to the community@Antonia Beatriz Soler Riera!

Mildred Anashie (10:29:20) (in thread): > Welcome to the community@Antonia Beatriz Soler Riera

Gonza Gertrude (10:30:05): > @Gonza Gertrude has left the channel

Aiysha shahid (10:30:17) (in thread): > Welcome to the community@Antonia Beatriz Soler Riera:tulip:

Aiysha shahid (10:33:22) (in thread): > Hi@Precious Chijioke, Welll done, we would go through this. Meanwhile, Exp-1, Signature-2. Firmicutes can be curated as ID-1239

Aiysha shahid (10:38:36) (in thread): > Well Done on this Curation, I would go through this. Just an overview till then- The DOI link mentioned in your study is broken. Correct link-https://www.nature.com/articles/s41598-017-15554-8. Also In Exp 2 and 3, Signature-1, there’s a typo error it’sSneathia ID-168808 - Attachment (Nature): Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women > Scientific Reports - Microbial Diversity of Genital Ulcers of HSV-2 Seropositive Women

Anne-Marie Sharp (10:42:11): > Hello everyone, please I need some help in understanding a figure, Figure S5B in the document/link. > d0 is group0 & d49 is Group1, how do I know which signatures are increased or decreased in Group1? > Do I use the colours, the effect size points, or both? > Thank you. > This is the link for the main article:https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1453989/fullThis is the link for the supplementary material if you can’t access the document:https://www.frontiersin.org/journals/pharmacology/articles/10.3389/fphar.2024.1453989/full#supplementary-material - Attachment (Frontiers): Frontiers | Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan > IntroductionTreatment of rodents with the AT1 blocker (ARB) telmisartan (TEL) has an anti-adipose effect. Among other mechanisms, we also have attributed the… - Attachment (Frontiers): Frontiers | Increase in body weight is lowered when mice received fecal microbiota transfer from donor mice treated with the AT1 receptor antagonist telmisartan > IntroductionTreatment of rodents with the AT1 blocker (ARB) telmisartan (TEL) has an anti-adipose effect. Among other mechanisms, we also have attributed the… - File (Word Document): Data Sheet 1

Anne-Marie Sharp (10:51:06) (in thread): > @Victoria (Burah) Poromon@Mildred AnashieWell done again on a very extensive curation:raised_hands:, it seems good to go

nithya (10:52:34) (in thread): > Thank you all for your replies:pray:

Mildred Anashie (10:53:53) (in thread): > Well done again@Eseoghene Cynthia Princewill-Ukot, I have a few observations, > * Your statistical test is only Kruskal Wallis, please remove the others > * I see some comparisons in Table 5 using linear regression with significant p values and I think it should be curated, read to text to guide you. > * In table 4 I see a lot of non significant adjusted p values andI’mwondering if they should have been curated in the first place > @Adeshile Oluwatosin@Victoria (Burah) Poromonwhat do you think?:thinking_face:

Precious Chijioke (10:55:44): > Good Evening Everyone > Please should I curate taxa with numbers e.g Moraxella (2) as seen in the image in Figure 3F or curate them without the numbers? This concern is also seen in Figure 2F and Figure 4. I want to confirm how to correct the taxa and implement it while curating all signatures with numbers.https://www.cell.com/cms/10.1016/j.xcrm.2024.101836/asset/46499d60-3108-4340-9199-6a0d5f3e6f0d/main.assets/gr3_lrg.jpgStudy link:https://www.cell.com/cell-reports-medicine/fulltext/S2666-3791(24)00607-4?_returnUR[…]vier.com%2Fretrieve%2Fpii%2FS2666379124006074%3Fshowall%3Dtrue

Mildred Anashie (10:55:48) (in thread): > Hi@Daberechi OkorieI’llsay you curate as seen for each experiment

Daberechi Okorie (10:57:57) (in thread): > Oh okay, thank you@Precious Chijioke@Mildred Anashie

Adeshile Oluwatosin (10:59:46) (in thread): > Hello@Precious Chijiokecurate without the numbers > I guess the numbering states how many times it was mentioned as there are several experiments embedded in a single figure

Precious Chijioke (11:00:38) (in thread): > Alright > Thank you@Adeshile Oluwatosin

Victoria (Burah) Poromon (11:18:47) (in thread): > Welcome to the team!@Antonia Beatriz Soler Riera

Anne-Marie Sharp (11:41:33) (in thread): > Thanks for the link@Aiysha shahidwell done with your curation@Eseoghene Cynthia Princewill-UkotI agree with the above suggestions. Also, in Experiment3, the Group1 description can be clearer e.g. Women with circumcised male partners, as self-reported by the women

Anne-Marie Sharp (11:54:38) (in thread): > Well done with your curation@Precious ChijiokeI doubt figure 3 is curatable. You can make your group1 descriptions clearer e.g Mice in P (postbiotics) group were treated every day with loperamide (10 mg/kg body weight), and with corresponding products (Postbiotics)1 h after loperamide administration.

Aiysha shahid (12:17:11) (in thread): > * Hi@Oriade Adeola, I have made the these three review changes-RemoveVeillonellaceaefrom experiment 1 signature 2, it wasn’t significant. > * In experiment 2 is having taxa that shouldn’t be there. Curate only taxa with # (see figure caption) > * Please add antibiotics exclusion in experiment 3 downwards

Aiysha shahid (12:18:21) (in thread): > Kindly make the other review changes told by co-mentor, and let’s finalize this curation by tomorrow. If you stuck somewhere let me know@Oriade Adeola

Anne-Marie Sharp (12:32:16) (in thread): > Good evening@Precious Chijiokethe numbers normally represent ASVs hence Corynebacterium(3) is associated with severe RSV but Corynebacterium(131) with mild. They’re different & for clarity, should be curated as it appears if possible:thinking_face:But let’s also hear from others.

Mildred Anashie (12:36:07) (in thread): > Hi@Anne-Marie SharpI think you should use the effect size and also curate alongside Table S1 > > See this from within text, “Sorted by decreasing effect size, at the genus level, the abundances of Duncaniella, Turicimonas, and Paramuribaculum in particular were considerably lower at d0 than at d49 (Cohens d < -2), but, conversely, those of Lawsonibacter, Alistipes, Oscillospiraceae uncl., Ruminococcaceae uncl., Oscillibacter Ligilactobacillus Anaerotignum Acetatifactor, Desulfovibrionia uncl., Kineothrix Bacteroidales, Parabacteroides, and Faecalibaculum (Cohens d > 2) were noticeably higher at d49 than at d0 (Supplementary Figure S5; Supplementary Table S1).”

Anne-Marie Sharp (12:43:28) (in thread): > Thank you@Mildred AnashieI have curated table s1 & I now want to add this figure to it. how about those points that fall in between the line like Schaedlerella, Lachnospiraceae, do I curate them as decreased or omit them?

Victoria (Burah) Poromon (12:45:57) (in thread): > @Mildred Anashie, I agree with table 4, only the first 2 taxa says <0.01, the rest of them are above the threshold.

Juliana Kentomahun Mautin (13:44:54) (in thread): > Welcome@Antonia Beatriz Soler Riera

Juliana Kentomahun Mautin (13:52:59) (in thread): > Thank you so much for the office hour<@UBNSEMS3S>

Adeshile Oluwatosin (13:53:28) (in thread): > In Table 5,the text within article seems to report significance for some taxa. You can use that in curating.In Table 4, only Porphyromonas and Prevotella is curatable.

Eseoghene Cynthia Princewill-Ukot (13:54:07) (in thread): > Thanks alot for your review,….well noted!@Mildred Anashie@Anne-Marie Sharp@Victoria (Burah) Poromon

Eseoghene Cynthia Princewill-Ukot (13:57:41) (in thread): > @Adeshile Oluwatosin:pray:

Precious Chijioke (15:19:24) (in thread): > Thank you@Anne-Marie Sharp

Precious Chijioke (15:20:48) (in thread): > Thank you@Aiysha shahidand@Anne-Marie Sharp

Precious Chijioke (19:02:40) (in thread): > @Anne-Marie Sharpwell done on your curation. I think you should use both the colors and the effect size points so as to curate accurately. I’ll go through the study again with my PC and make any other suggestion.

Juliana Kentomahun Mautin (19:42:12) (in thread): > Happy Friday@Svetlana Ugarcina Perovic:smiling_face_with_3_hearts::smiling_face_with_3_hearts:From my experience this week in BugSigDB, key components of good teamwork include: > > Clear communication > Defined roles and responsibilities > Mutual respect and support > Active collaboration > Timely feedback and accountability > > These elements helped us stay aligned, productive, and efficient.

2025-04-12

Anne-Marie Sharp (03:09:49) (in thread): > Thank you:pray:@Precious Chijioke

Aiysha shahid (05:20:05): > Hi everyone, Hope you all doing great!. I would love to have per review over this study-https://bugsigdb.org/37329328, Full study pdf is been attached below. Thanks. - Attachment (BugSigDB): Ischaemic stroke patients present sex differences in gut microbiota - BugSigDB > BACKGROUND: Gut microbiota plays a role in the pathophysiology of ischaemic stroke (IS) through the bidirectional gut-brain axis.Nevertheless, little is known about sex-specific microbiota signatures in IS occurrence.METHODS: A total of 89 IS patients and 12 healthy controls were enrolled. - File (PDF): Euro.J.of.Neurology.-.2023.-.Lledos.-.Ischaemic.stroke.patients.present.sex.differences.in.gut.microbiota.pdf

Adeshile Oluwatosin (05:21:52) (in thread): > Well done@Aiysha shahid

Adeshile Oluwatosin (05:47:35) (in thread): > Seems like you did good, just check the supplementary materials for any further details

Aiysha shahid (05:52:01) (in thread): > Thanks@Adeshile Oluwatosin, I have checked couldn’t find any such information, Attaching that as well. - File (Word Document): supp.docx

Adeshile Oluwatosin (06:11:34) (in thread): > Yeah,there’snothing useful here

Anne-Marie Sharp (06:22:12) (in thread): > Well done with your curation@Aiysha shahidNice one. I noticed a typo error in group1 definition, should be: female patients who have been diagnosed…not who have diagnosed

Ameenat Oloko (06:33:41) (in thread): > Well done,@Aiysha shahid. I agree with@Anne-Marie Sharpon the typo in group 1 definition.

Ameenat Oloko (06:39:18) (in thread): > Also, Ididn’tsee anything like “Fusobacteriota” in Fig.2b and Table 2. Instead,it’s“Fusobacteria”.

Aiysha shahid (07:00:58) (in thread): > Hi@Ameenat Oloko, > According to the NCBI Taxonomy, another name forFusobacteriaat the phylum rank isFusobacteriota. You can check it here:https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=32066&lvl=3&p=has_linkout&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlockThanks! - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Aiysha shahid (07:01:33) (in thread): > Thanks@Anne-Marie Sharp, it has been fixed now!:raised_hands:

Ameenat Oloko (07:01:40) (in thread): > Oh, okay. Noted! > > Well done, once again@Aiysha shahid.

Amaka (07:25:13): > Good afternoon everyone > I would appreciate a peer review on this studyhttps://bugsigdb.org/39848958https://pmc.ncbi.nlm.nih.gov/articles/PMC11757712/#Tab1 - Attachment (BugSigDB): Microbiome analysis in individuals with human papillomavirus oral infection - BugSigDB > This study looked at how the oral microbiome (the bacteria in the mouth) is affected by human papillomavirus (HPV) infection, especially in people with and without HIV. - Attachment (PubMed Central (PMC)): Microbiome analysis in individuals with human papillomavirus oral infection > Microbiome gained attention as a cofactor in cancers originating from epithelial tissues. High-risk (hr)HPV infection causes oropharyngeal squamous cell carcinoma but only in a fraction of hrHPV+ individuals, suggesting that other factors play a …

Anne-Marie Sharp (07:29:28) (in thread): > You’re welcome@Aiysha shahid

Adeshile Oluwatosin (08:41:32): > Good afternoon everyone > I am currently curating this study and was told to collaborate on the study. > Kindly reach out if interestedso we can discusshttps://pmc.ncbi.nlm.nih.gov/articles/PMC11855768/#app1-ijms-26-01676Thank you

Mildred Anashie (08:43:55) (in thread): > Hi@AmakaI’lltake a look > Well done

Adeshile Oluwatosin (08:49:56) (in thread): > Just one person is fine > Thank you so much

Mildred Anashie (08:52:51) (in thread): > Hi@Adeshile OluwatosinI don’tmind collaborating with you on this

Adeshile Oluwatosin (08:55:58) (in thread): > Great

Adeshile Oluwatosin (08:56:33) (in thread): > Please comment here, thank you so muchhttps://github.com/waldronlab/BugSigDBcuration/issues/642#event-17159479401

Mildred Anashie (09:25:59) (in thread): > Anyone else interested before I comment?

Ameenat Oloko (09:27:47) (in thread): > Well done,@Amaka. This study seems good. Although, I was a bit confused by the sample sizes:smiley:

Ameenat Oloko (09:29:36) (in thread): > You can go ahead,@Mildred Anashie.Afterall,you said it first.

Mildred Anashie (09:40:26) (in thread): > Okay@Ameenat OlokoThanks

Amaka (09:48:22) (in thread): > Thank you@Ameenat Oloko, it was confusing initially.

Ameenat Oloko (12:47:15): > Good evening, everyone. Happy weekend!@Eseoghene Cynthia Princewill-Ukotand I collaborated on this curation and would appreciate a review. Thank you.StudyArticle - Attachment (BugSigDB): Appearance of green tea compounds in plasma following acute green tea consumption is modulated by the gut microbiome in mice - BugSigDB > UNLABELLED: Studies have suggested that phytochemicals in green tea have systemic anti-inflammatory and neuroprotective effects.

Montana-D (12:48:33) (in thread): > Great job on your curation@Amaka

Anne-Marie Sharp (12:53:19) (in thread): > Nice work@Amakawell done on your curation

Montana-D (12:55:51) (in thread): > Well done on your curation@Ameenat Oloko@Eseoghene Cynthia Princewill-UkotI will take a look through

Mildred Anashie (13:32:15) (in thread): > Well done@Eseoghene Cynthia Princewill-Ukot@Ameenat OlokoI’ll look through

Anne-Marie Sharp (13:37:41) (in thread): > Happy weekend and well done with your curation@Ameenat Oloko@Eseoghene Cynthia Princewill-Ukot.

Anne-Marie Sharp (13:37:43) (in thread): > 1)I doubt figure 2 should be curated. 2)For Figure 8b description, ‘Heatmap of Green Tea Compound Metabolites Associated with Specific Genera in HU Mice’, seems well enough

Mildred Anashie (13:49:27) (in thread): > Everything looks good to me@Adeshile Oluwatosin@Amaka

Mildred Anashie (14:07:09) (in thread): > I agree with@Anne-Marie SharpFigure 2b doesn’t look curatable. I’m also wondering how you were able to curate Fig 8b. > > I’ll look through the paper again, but for now I haven’t sighted a figure or table showing differential abundance. I probably need to read in between lines

Amaka (14:33:10) (in thread): > Thank you all

Vanisha Garg (14:34:34): > @JoyShould I start curating the left article?? > Will it be okayy?

Ameenat Oloko (14:38:58) (in thread): > I curatedFig 2from this excerpt,@Anne-Marie Sharp,@Mildred Anashie.LCM and HU mouse microbiomes differed in community composition (pseudo-F = 5.9, P = 0.005). LCM mice were colonized almost entirely by Firmicutes, with six of the nine mice having high levels of unassigned ASVs in the family Peptostreptococcaceae (Fig. 2, P = 0.005). Additionally, LCM mice had higher relative abundances of Epulopiscium (ANCOM-BC; P = 0.015) and Turicibacter (ANCOM-BC; P = 0.002) in their microbiomes compared with HU mice (Fig. 2).Microbiome composition was very similar within HU mouse replicates (UniFrac distance within pairs mean [95% CI] = 0.25 [0.21–0.30]), and variable between mice colonized with different human donors (UniFrac distances between centroids mean [95% CI] =0.50 [0.49–0.52]) (Fig. 2). This is supported by a PERMANOVA, demonstrating larger variance in phylogenetic composition between pairs than within pairs (R2 = 0.87, psuedo-F = 7.6, P < 0.001). The microbiome of all but two pairs of HU mice had Akkermansia present at high relative abundances (≥20%). All HU pairs had representation of Bacteroidetes, primarily including Bacteroides, Parabacteroides, and Alistipes. Proteobacteria were present in the microbiome of all HU but not LCM mice, and this phylum predominantly consisted of ASVs belonging to Bilophila and Sutterella. Some HU pairs also had low relative abundances (<5%) of Fusobacteria in their fecal microbiome.**

Ameenat Oloko (14:40:34) (in thread): > **** > *******For fig 8b**,the GT compound wilforlide was positively associated with an ASV in the genus Anaerorhabdus (β = 15.1, P < 0.001). Spiramycin was positively associated with taxa in the genera Gemmiger (β = 13.7, P < 0.001) and Lactobacillus (β = 12.9, P < 0.001, *Fig. 8B). Although multiple unannotated compounds had multiple significantly associated microbes, spiramycin was the annotated compound with more than one significant relationship with individual taxa (after FDR correction).

Vanisha Garg (14:51:06) (in thread): > @JoyI have curated this article , left with signatures , Please review it once and if any changes please inform me

Adeshile Oluwatosin (15:18:53) (in thread): > Thank you guys:heart:

Vanisha Garg (15:20:00): > Hello everyone ! > I hope you all are doing good and wanted to update that yes I am also good , recovering fast!:heart:I have few doubts regarding the “matched on” column as there are factors which got matched but aren’t there in the drop down option.Matched on:Transit time; Body mass index; Age; Stool consistency; Diet ; In vivo donor microbiota adaptation > Confounders controlled for: > Age; Diet; Health status; Antibiotic history (excluded); Donor variability (controlled via SHIME design and donor pre-screening); Faecal sample consistency (via Bristol Stool Scale) > > Please help me in this@Mildred Anashieis helping me out in this curation

Vanisha Garg (15:26:46): > Link to my article ishttps://bugsigdb.org/Special:FormEdit/Experiment/37926855/Experiment_1?reload=1&returnto=37926855 - Attachment (BugSigDB): Special:FormEdit/Experiment/37926855/Experiment 1

Adeshile Oluwatosin (15:29:16) (in thread): > Well done@Vanisha Garg

Adeshile Oluwatosin (15:29:54) (in thread): > For matched on factors not in the drop down, please write it as stated in the paper

Adeshile Oluwatosin (15:31:09) (in thread): > This is the correct study link:https://bugsigdb.org/37926855 - Attachment (BugSigDB): Gut microbiota response to in vitro transit time variation is mediated by microbial growth rates, nutrient use efficiency and adaptation to in vivo transit time - BugSigDB > BACKGROUND: Transit time is an important modulator of the human gut microbiome.The inability to modify transit time as the sole variable hampers mechanistic in vivo microbiome research.

Joy (15:34:03) (in thread): > Duly noted@Vanisha Garg. Thanks

Vanisha Garg (15:34:22) (in thread): > Okay@Adeshile Oluwatosin

Mildred Anashie (15:34:36) (in thread): > Hi@Vanisha GargI’m glad you are feeling good and recovering fast > > I sent a DM regarding this curation > > For the matched on you can curate that way, it would be flagged butthat’sokay

Vanisha Garg (15:35:28) (in thread): > @Adeshile OluwatosinIf possible could you please share with me the the final application process , how do we have to fill in that form ? > I tried finding that message in the chat but was unable to locate one. > Thank you so much:heart:

Vanisha Garg (15:36:12) (in thread): > Thankyou@Mildred Anashiefor your kind words:heart:and yes I will have a look at them too!

Adeshile Oluwatosin (15:36:43) (in thread): > @Vanisha Garghttps://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539 - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Mildred Anashie (15:39:18) (in thread): > Hi@Vanisha GargYou could check this out in addition to what@Adeshile Oluwatosinsharedhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539This office hour also has some information about final applicationhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1744323076990479 - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project. - Attachment: Attachment > Office hour recording. Thanks everyone who attended.

Vanisha Garg (15:40:08) (in thread): > If we are working on more than 1 projevct then how are we supposed to make the final application? > Like since I guess there is only 1 final submission right? > Also since we are getting it reviewd by our mentors , how it will get related to what date it got merged?

Vanisha Garg (15:40:52) (in thread): > @Mildred Anashie@Adeshile OluwatosinPlease help me in this too. > Thankyou@Mildred Anashiefor sharing that link too!

Adeshile Oluwatosin (15:41:28) (in thread): > Prioritize completing your final application as deadline for that is on Tuesday > > You can record contributions for curations still ongoing. > Leave date merged blank till you submit for review. > For articles under review by mentors, you still can record your contributions regardless as we can keep doing this till May 8th

Vanisha Garg (15:48:36) (in thread): > Okay

Vanisha Garg (15:49:02) (in thread): > also if i am working on 2 projects then how to sumbit final application of both of the project

Anne-Marie Sharp (15:49:57) (in thread): > Hello@Vanisha Garggood to know you’re recovering fast. Do you mean working on bugsigdb and another outreachy project?

Mildred Anashie (15:58:15) (in thread): > Hi@Vanisha GargPlease check your mail, a reminder was sent a few days ago regarding this, go through it carefully as everything you need to know is contained there with links too > > If you didn’t get one, here’s what it contained; > Recording Contributions > — > You will need to record your contributions for each project you’re applying for. > Please record your contributions even if the contribution is not merged or accepted yet. > You can record your contributions following these steps: > 1. Log into the Outreachy website: > https://www.outreachy.org/login/2.Find your project listed on the project selection page:https://www.outreachy.org/apply/project-selection/.3.Click the project’s title to be taken to the project details page.4.Click the ‘record your contributions and create a final application’ link.5.Repeat steps 2-4 to record your contributions for each project you are applying for.Once you have recorded a contribution to a project, a link to record more contributions or create a final application for that project will be available on your dashboard: After the final application deadline, you are encouraged (but not required) to continue working on contributions with your project mentor. You will be able to record or edit contributions until May 8, 2025 at 4pm UTC. > > Final Applications > > You can create a final application by following these steps: > 1. Log into the Outreachy website: > 2. Find your project listed on the project selection page:https://www.outreachy.org/apply/project-selection/. > 3. Click the project’s title to be taken to the project details page. > 4. Follow the ‘create a final application’ link. > 5. Repeat steps 2-4 to create a final application for each project. - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website! - Attachment (outreachy.org): Outreachy | Internships Supporting Diversity in Tech > An internship program that supports diversity in free and open source software. Learn more by visiting our website!

Joy (21:56:35) (in thread): > Hi@Vanisha GargCan you check your Slack DM, I have left some messages there. > > Hi@Vanisha Garg, based on our study, we will be curating Figures: 2A & D, Fig. 3B, Fig. 4A and Fig. 6D > > Kindly check your DM. Thanks.https://bmcwomenshealth.biomedcentral.com/articles/10.1186/s12905-025-03689-0#Fig2 - Attachment (BioMed Central): Gut microbiome in patients with early-stage and late-stage endometriosis - BMC Women’s Health > Background Endometriosis is a chronic inflammatory gynecological disease. Previous studies have explored relationships between endometriosis and the microbiota, but none have focused on differences in gut microbiota between early-stage and late-stage endometriosis patients or their connections to dysmenorrhea symptoms. This study compared gut microbiota compositions between early-stage and late-stage endometriosis patients using amplicon sequencing and further analyzed their dysmenorrhea symptoms. Methods To minimize seasonal and dietary impacts, we recruited Guangdong residents hospitalized for surgery at Zhujiang Hospital. Participants underwent preoperative screening based on enrollment criteria and fecal samples were collected. Endometriosis was classified according to the American Society for Reproductive Medicine (ASRM) staging system based on surgincal and pathological findings. Stage I-II cases were designated as early-stage endometriosis, and Stage III-IV as late-stage endometriosis. Results A total of 112 patient fecal samples were collected, with 75 (median age, 32 years [range, 18–49 years]) meeting the enrollment criteria, including 39 early-stage (32 Stage I and 7 Stage II) and 36 late-stage (16 Stage III and 20 Stage IV) patients. The gut microbiota structure and functions in early-stage patients significantly differed from those in late-stage cases. Dysmenorrhea was associated with specific microbial traits. Late-stage patients with dysmenorrhea displayed distinctly different gut profiles compared to other endometriosis groups. Bartonella, Snodgrassella, and other taxa were enriched in late-stage cases, while Bacteroides, and Prevotella were decreased. Conclusion The gut microbial community structure in early-stage endometriosis patients significantly differs from that in late-stage cases, with late-stage patients experiencing dysmenorrhea displaying particularly distinct gut profiles. Predicted functional analysis indicated suppressed steroid biosynthesis pathways in the gut of late-stage endometriosis patients. In conclusion, it is plausible that the multiple effects of steroids on the lower gastrointestinal tract may involve microbiota alterations, suggesting the need for further investigations.

2025-04-13

Vanisha Garg (00:12:40) (in thread): > Thank you so much@Mildred Anashiefor guiding me on this.

Aiysha shahid (06:28:01): > Hi everyone, happy weekend!:sunny:If anyone has some time, I’d really appreciate a peer review of this study:https://bugsigdb.org/36905309. > I’ve also attached the PDF of the study and its supplementary document for reference. > Thanks in advance! - File (Word Document): ene15776-sup-0001-supinfo.docx - File (PDF): Euro.J.of.Neurology.-.2023.-.Yang.-.Association.of.aberrant.brain.network.dynamics.with.gut.microbial.composition.uncovers.pdf

Mildred Anashie (06:47:53) (in thread): > You are welcome@Vanisha Garg

Anne-Marie Sharp (07:35:08) (in thread): > Happy weekend@Aiysha shahidwe’ll review

Montana-D (08:03:25) (in thread): > Great job on your curation and Happy weekend to you too

Anne-Marie Sharp (08:17:28) (in thread): > Well done with your curation@Aiysha shahidnice work. I believe the data transformation for DeSeq2 should be raw counts

Montana-D (08:36:42) (in thread): > I agree with@Anne-Marie Sharpon that@Aiysha shahid

Aiysha shahid (08:37:20) (in thread): > Thanks@Anne-Marie Sharp@Montana-D, I have edited that earlier,but it wasn’t refelecting. I have re-edited it. Can you kindly re-check

Anne-Marie Sharp (08:39:58) (in thread): > You’rewelcome. Okay.It’sshowing now:+1:

Aiysha shahid (08:40:22) (in thread): > Thanks a lot!:blush:

Montana-D (09:23:24): > Hello everyone. Good Day > I am currently curating a study and i would like your suggestions on whether supplementary table 1 of the study is curatable, Below is the link to the article and the supplementary material - File (Excel Spreadsheet): 394_2025_3668_MOESM1_ESM.xlsx - File (PDF): s00394-025-03668-z.pdf

Mildred Anashie (09:45:09) (in thread): > Hi@Aiysha shahidWell done and happy weekend > I’ll take a look

Precious Orakwe (12:49:38) (in thread): > Good day@Montana-DSupplementary table 1 is curatable if it was mentioned in the main study and if it has the p-values

Joy (12:51:44) (in thread): > Hi@Montana-Dwell done on your curation. I don’t seep valuesin it. Hence it is not curatable.

Anne-Marie Sharp (13:12:25) (in thread): > Hello@Montana-DTable 2 seems to be derived from Supplementary Table 1, so it should be curatable. That’s a whole lot of taxa!:flushed:I’ll be glad to assist if you need help

Anne-Marie Sharp (13:14:27) (in thread): > Hello@JoyI think there are actually p values:thinking_face:but its denoted by just p, even q values and log fold change, they’re abbreviated

Precious Orakwe (13:16:54) (in thread): > can it be that the p-values are in page 9 of the supplementary material

Joy (13:17:32) (in thread): > Ok@Anne-Marie Sharp, I only checked the supplementary Table 1, I didn’t check Table 2. You are right. Well done.:ok_hand:

Ndukauba Oluchi (13:27:22): > Happy Sunday everyone, and Happy new week:hugging_face:Regarding our final application, there’s a space for this question**** “Some communities or projects may want you to answer additional questions. Please check with your mentor and community coordinator to see if you need to provide any additional information after you save your final application.”****So i was wondering if there are any addition questions our mentors will like us to answer in that field. > CC:@Svetlana Ugarcina Perovic

Svetlana Ugarcina Perovic (13:29:38) (in thread): > 3rd line here:https://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539 - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Montana-D (14:25:03) (in thread): > Thank you all@Anne-Marie Sharp@Joy@Precious Orakwefor your suggestion, I figured so and I currently recording taxa 150 and counting:sweat_smile:

Precious Orakwe (14:27:00) (in thread): > @Montana-DI am@Precious OrakweOrakwe not@Precious Chijioke, you are welcome

Mildred Anashie (14:53:04) (in thread): > Hi@Montana-DI see p values and adjusted p values, there’s also a direction of increase and decrease (Log fold change) > > But what I do not see is the groups (comparisons):thinking_face:

Mildred Anashie (15:04:58) (in thread): > Okay@Ameenat OlokoThat works then. > > Please include ‘Results text’ to your source

Anne-Marie Sharp (16:44:49) (in thread): > @Mildred Anashiethat’s good to know, just learning we can add text as a source.@Ameenat OlokoOkay, I’m still unsure but will follow up with your curation to learn, thank you for sharing this.

Mildred Anashie (17:27:04) (in thread): > Yea@Anne-Marie SharpThey are a couple of studies like that > See here,https://bugsigdb.org/33565055,https://bugsigdb.org/36869345 - Attachment (BugSigDB): Inferences in microbial structural signatures of acne microbiome and mycobiome - BugSigDB > Acne vulgaris, commonly known as acne, is the most common skin disorder and a multifactorial disease of the sebaceous gland.Although the pathophysiology of acne is still unclear, bacterial and fungal factors are known to be involved in. - Attachment (BugSigDB): Assessment of microbiota in the gut and upper respiratory tract associated with SARS-CoV-2 infection - BugSigDB > BACKGROUND: The human microbiome plays an important role in modulating the host metabolism and immune system.

Anne-Marie Sharp (17:37:10) (in thread): > Wow:smile:@Mildred Anashiethis is really interesting, we always talk about figure/table for curations, one would never guess you could curate entirely from text too. thank you for sharing:hugging_face:

Adeshile Oluwatosin (17:51:12) (in thread): > @Montana-DSupplementary Table 1 and Table 2 should be just one experiment and is definitely curatable as it’s explained to reflect differential abundance within the article. > > The statistical test is ANCOMBC with MHT as yes. > Confounders : baseline age, sex, diet quality, smoking status, medication use, BMI. > The group names are not clear but I’m thinking > Group 0; low risk alcohol consumers > Group 1: high risk alcohol consumers

Bola (21:29:52): > Hallo everyone, Happy Monday! I will really appreciate a peer review of this study:https://bugsigdb.org/33505487 - Attachment (BugSigDB): Acupoint Massage Therapy Alters the Composition of Gut Microbiome in Functional Constipation Patients - BugSigDB > RESULTS: Results showed the overall structure of gut microbiome has no significant difference between experimental and control groups.

2025-04-14

Adeshile Oluwatosin (01:17:25) (in thread): > Well done@Bola

Adeshile Oluwatosin (01:47:05) (in thread): > Good morning, We communicate strictly in BugsigDB and not outreachy channel. I guess the channel is just for introduction.

Precious Orakwe (01:56:22) (in thread): > Yes the group names are not cleared and also the group sizes.

Adeshile Oluwatosin (01:58:41) (in thread): > Specific to the study: I noticed these > * Figure 4B is a lefse result, hence it’s curatable and you would have another experiment > * Remove LDA score from experiment 1( We curate LDA scores only for lefse analysis) > * red is control, green is experimental group > * curate Mann-U Whitney result seperately > * From this “The Chao1 and Shannon diversity index suggested no significant difference in species richness and evenness between experimental and control group (Figure S1). Other estimators of alpha diversity such as PD whole tree, Simpson, and observed species also displayed no significant difference between two groups (Figure S1).” > only CHAO1, Shannon, richness, Simpson, pielou are unchanged, henceleave faith blank and curate unchanged for pielou (evenness).

Precious Orakwe (02:26:02) (in thread): > Good morning@Bolawell done. > > As@Adeshile Oluwatosinsaid there are two experiments in the study, the Frist experiment was control Vs experiment, the second experiment will be the Experiment group vs the control group. > > In total, the LEfSe analysis revealed 6 discriminative features (linear discriminant analysis (LDA) >3, P < 0.05, Figure 4(b)) in the genus levels. Members of the Ruminiclostridium, Pseudobutyrivibrio, Prevotell_9, and Prevotellaceae were enriched in the experiment samples, whereas members of the Fusicatenibacter and Anaerostipes were enriched in the control samples.

Anne-Marie Sharp (02:36:48) (in thread): > Happy Monday@Bolawell done with your curation. I agree with@Adeshile Oluwatosin. Do well to let us all review again when you make the corrections.

Anne-Marie Sharp (02:39:20): > Hello everyone, happy new week:hugging_face:Please, I would appreciate a peer review of this study:https://bugsigdb.org/33185912Thank you so much. - Attachment (BugSigDB): Gut microbiota and metabolome distinctive features in Parkinson disease: Focus on levodopa and levodopa-carbidopa intrajejunal gel - BugSigDB > BACKGROUND AND PURPOSE: Recent data suggest that imbalances in the composition of the gut microbiota (GM) could exacerbate the progression of Parkinson disease (PD).

Anne-Marie Sharp (02:41:44) (in thread): > This is the pdf of the article: - File (PDF): 10.1111@ene.14644.pdf

Mildred Anashie (03:18:29) (in thread): > Hi@Aiysha shahidWell done, I think everything is on point but I see Ruminococcaceae missing from Figure 5c. It’s increased in HC

Mildred Anashie (03:26:24) (in thread): > I agree with@Adeshile OluwatosinI noticed 4a was curated alongside 4b, so they’ll have to create a different experiment for it and curate separately. > Well done@Bola

Mildred Anashie (03:27:49) (in thread): > Hi@Anne-Marie SharpI’ll take a look well done

Aiysha shahid (03:30:14) (in thread): > Hi@Mildred Anashie, thanks! According to the NCBI taxonomy, Ruminococcaceae is curated as Oscillospiraceae, you check it here-https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=216572&lvl=3&p=ha[…]&p=blast_url&p=genome_blast&lin=f&keep=1&srchmode=1&unlock. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (03:31:12) (in thread): > Okay Okay then > Everything good to go in my opinion

Anne-Marie Sharp (03:43:58) (in thread): > Thank you@Mildred Anashie

Svetlana Ugarcina Perovic (03:45:38) (in thread): > This Wednesday:arrow_up:

Svetlana Ugarcina Perovic (03:46:13) (in thread): > Reminder:arrow_up:

Svetlana Ugarcina Perovic (03:46:51) (in thread): > Thanks for your feedback. Happy Monday!

Eseoghene Cynthia Princewill-Ukot (03:47:58) (in thread): > Noted

Eseoghene Cynthia Princewill-Ukot (03:48:20) (in thread): > Happy New Week, everyone!

Juliana Kentomahun Mautin (03:50:17) (in thread): > Thank you:blush:

Mildred Anashie (04:18:46): > Good morning everyone > Happy Monday:tulip:I’m working on curating thisarticlewith@Daberechi Okorieand we curated the experiments from Table S13 (link to table attached). But after curating we realized Increase and decrease isn’t really clear and would appreciate some help in identifying the abundance direction from the table. > Or should this be left out? > > Thank you in anticipation for your responseshttps://www.cell.com/cms/10.1016/j.xcrm.2024.101801/attachment/eaf8ea74-d23c-46d0-bb40-42329bee222e/mmc2.xlsx

Adeshile Oluwatosin (04:19:30) (in thread): > Well done, I will check this out:clap:

Mildred Anashie (04:22:49) (in thread): > Thank you@Adeshile Oluwatosin

Anne-Marie Sharp (04:40:30) (in thread): > Good morning@Mildred Anashie@Daberechi Okoriewell done with your curation. I suspect that along side the p-value, the mean base/mean end can tell us the direction of change. We can confirm from the article (just noticed its included) I will check it out

Mildred Anashie (04:46:17) (in thread): > Thank you@Anne-Marie SharpThe article doesn’t really say and some taxa have exact values for Mean base and Mean end but were said to be significant

Anne-Marie Sharp (05:01:48) (in thread): > @Mildred AnashieIn Table S13, I observed only 6significant taxa in HLCD VS non-HLCD & they all have varying mean base/mean end. > The article states: ‘Specifically, HLCD significantly decreased the abundance of Ruminococcus callidus, which was an obesity associated genus in Western populations’ > And in Table S13 the mean end value for Ruminococcus callidus is decreased.

Mildred Anashie (05:03:39) (in thread): > Scroll down a bit for the other comparison to see what I mean

Anne-Marie Sharp (05:06:18) (in thread): > Yes I observed but at the end of the table it states that ‘Bold font indicated that p < 0.05’ and only 6taxa have that bold font(significance), so I dont think you should bother about the others that are not significant as they wont be curated

Mildred Anashie (05:07:55) (in thread): > The point you raised is exactly why I curated because I was going to curate using that but I noticed the taxas with the same Mean base and Mean end values@Anne-Marie Sharpthere are two comparisons in the table, look closely you’ll see the bold taxas for the second comparison (TRE vs Non-TRE)

Adeshile Oluwatosin (05:16:48) (in thread): > @Mildred Anashieyou would use the Mean Base/ Mean End to signify the abundance > For Taxa stated to be significant but have same mean base/mean end. “Clostridiaceae bacterium 0M08 6BH” between TRE vs Non-TRE, I advice not to curate…write a note on it

Mildred Anashie (05:18:00) (in thread): > Okay then@Adeshile OluwatosinWe have about 3-4 taxas that way > Thank you@Adeshile Oluwatosin@Anne-Marie Sharp:pray:

Adeshile Oluwatosin (05:18:52) (in thread): > In that case,I’mthinking once again if we should just ignore the table curation then > Because even the significant unadjusted taxa stillwon’tbe curated. It does not seem valuable enough

Adeshile Oluwatosin (05:20:37) (in thread): > The experiment is not worthy to be curated > Focus on the significant adjusted taxa in the article then

Anne-Marie Sharp (05:26:41) (in thread): > @Mildred Anashiethis table is tricky because some significant taxa like Bacteroides intestinalis were significant between TRE vs non-TRE but the article goes ahead to say : ‘ TRE intervention increased probiotic species Parabacteroides distasonis, Bacteroides intestinalis, Parabacteroides goldsteinii, and Escherichia coli, compared to the non-TRE group (all p < 0.05 before false discovery rate [FDR] correction).However, these differences were not significant after FDR correction. This lack of significance may be due to limited statistical power..’ Like@Adeshile Oluwatosinsaid, it may be best to ignore the table curation. But let’s also hear from others.

Mildred Anashie (05:27:30) (in thread): > Hi@Kate Rasheed@Aleru Divine@Svetlana Ugarcina Perovic<@UBNSEMS3S>a little help here please:pray:@Daberechi Okorieand I are a bit unsure of what to do regarding this Table, we have 2 experiments there, the adjusted p valuesdoesn’tshow significance but the p values do. We curated with the intention of using the p values to curate the signatures but noticed the mean base and mean end for some of the taxas are exactly the same in the second comparison and we are wondering if this should still be curated or be left out of the curation. > > Thank you

Svetlana Ugarcina Perovic (05:28:41) (in thread): > If it’s not crystal clear skip it.

Mildred Anashie (05:29:42) (in thread): > Duly noted@Svetlana Ugarcina PerovicThank you:pray:

Mildred Anashie (05:30:08) (in thread): > Thank you@Adeshile Oluwatosin@Anne-Marie Sharp:pray:

Anne-Marie Sharp (05:33:25) (in thread): > Thanks for clarifying@Svetlana Ugarcina Perovic.@Mildred Anashieyou’re welcome

Victoria (Burah) Poromon (06:06:15): > Hi, everyone. Good morning, I’m looking for someone to collaborate with me on this curation. Preferably a first-time applicant. Thank you so much. > > Please leave a comment on the GitHub issuehttps://github.com/waldronlab/BugSigDBcuration/issues/733

Anne-Marie Sharp (06:07:09) (in thread): > Hello@Victoria (Burah) Poromongood morning. I would love to collaborate with you on this

Victoria (Burah) Poromon (06:07:45) (in thread): > Great! > Please leave a comment on the GitHub issue and we can get started

Anne-Marie Sharp (06:08:04) (in thread): > Okay, done that. thank you

Oriade Adeola (06:32:29) (in thread): > @Aiysha shahidi’m done with the review change please check to confirm. if you’re ok with that then we can proceed

Daberechi Okorie (06:44:40): > Hi everyone, > > I’m working on curating thisarticlewith@Mildred Anashie. > Here’s thecuration link. > Quick question: regarding the condition for Non-Time Restricted Eating at baseline (Non-TRE) since TRE is fasting, what do you think Non-TRE’s condition should be? > > Would it be accurate to curate the condition for Non-TRE as eating behavior? - Attachment (BugSigDB): Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT - BugSigDB > The effect of a healthy low-carbohydrate diet (HLCD) and time-restricted eating (TRE), alone or in combination, on body weight and gut microbiome beyond caloric restriction remains unclear.

Aiysha shahid (07:00:12) (in thread): > Hi@Oriade Adeola, let me check. Will get back to you soon

Adeshile Oluwatosin (07:05:53) (in thread): > I can see that Binge eating is curatable, it seems closer to Non-TRE to eating behaviour@Daberechi Okorie

Aiysha shahid (07:06:28) (in thread): > @Oriade Adeola, I can still see the taxa that was need to be removed.

Daberechi Okorie (07:10:55) (in thread): > I see. Thank you@Adeshile OluwatosinBut the Non-Time Restricted Eating (TRE) alone group were not instructed to follow the 10-h TRE.

Daberechi Okorie (07:11:23) (in thread): > Does that also constitute as binge eating?

Adeshile Oluwatosin (07:12:10) (in thread): > In the studyI don’tthink they aimed to check out eating behaviour. > > Binge eating does not also really substitute for nonTRE butit’sthe closest curatable condition I can see for now.

Mildred Anashie (07:12:45) (in thread): > So from searching Binge eating seems to mean uncontrollable eating and some sort of eating disorder (Over eating) > I’m thinking it doesn’t fit as the study was checking the groups based on assigning them to fast 10hourly thereby resting their eating:thinking_face:

Mildred Anashie (07:16:20) (in thread): > But in the sense where the TRE had their eating controlled just maybe we could say the non TRE were eating uncontrollably implying overeating:blush:@Adeshile Oluwatosindo you think just “Control” might work here? (Check EFO)

Adeshile Oluwatosin (07:34:17) (in thread): > It’sseeming as if the 10 hours restriction was for TRE only > See “The average eating window, defined as the duration from the start to the end of eating each day, was 10.47 (0.38) h for the TRE group, meeting the requirements for a 10-h TRE27; meanwhile, the non-TRE group had an average eating window of 11.76 (0.45) h. “

Mildred Anashie (07:36:14) (in thread): > Yea@Adeshile OluwatosinThe restriction was for the TRE while the non TRE had no restrictions

Adeshile Oluwatosin (07:42:23) (in thread): > So no time restriction eating, does that not mean they can feed as they could though. > > More overthis is what I saw as the definition of control in bugsigdb “A control role is borne by a material in a process in which results obtained from an experimental sample and a control sample are compared.”

Mildred Anashie (07:43:58) (in thread): > Yea that’s the definition > Wanted to be sure it’s okay to rule that out

Mildred Anashie (07:44:20) (in thread): > @Daberechi OkorieI think we can go with binge eating for now

Adeshile Oluwatosin (07:46:11) (in thread): > I don’t think we can use control > There are no experiment with“control” as a condition.It’stoo generic

Mildred Anashie (07:47:19) (in thread): > Thanks@Adeshile Oluwatosin

Daberechi Okorie (08:25:13) (in thread): > Alright, thank you@Adeshile Oluwatosin

Precious Chijioke (08:26:04) (in thread): > Thank you@Svetlana Ugarcina Perovicfor the invite

Daberechi Okorie (08:31:02): > Good afternoon everyone@Mildred Anashieand I collaborated on thiscurationand would appreciate a review. Thank you. - Attachment (BugSigDB): Effects of healthy low-carbohydrate diet and time-restricted eating on weight and gut microbiome in adults with overweight or obesity: Feeding RCT - BugSigDB > The effect of a healthy low-carbohydrate diet (HLCD) and time-restricted eating (TRE), alone or in combination, on body weight and gut microbiome beyond caloric restriction remains unclear.

Mildred Anashie (08:31:19): > Hello Everyone > I am working on curating this article with@Adeshile Oluwatosinhttps://www.mdpi.com/1422-0067/26/4/1676We are done with curating other figures but we left Figure 8 out and we have doubts if we should have curated it, so we’d like to confirm if Figure 8 is curatable > Thank you:blush: - Attachment (MDPI): Correlations Between Amelioration of Rotenone-Induced Parkinson’s Symptoms by Amomum tsaoko Flavonoids and Gut Microbiota in Mice > Parkinson’s disease (PD) is the second most common neurodegenerative disease, but the existing therapeutic drugs for PD have limitations; thus, there is an urgent need to discover new methods of prevention and treatment. Amomum tsaoko Crevost et Lemarie (AT) is a classic traditional Chinese medicine and food. Its main pharmacological effect is the regulation of the gastrointestinal tract. To date, no studies on the use of AT or its extracts to treat PD have been reported. In this study, a rotenone-induced PD mouse model was utilized to evaluate the protective effect of Amomum tsaoko flavonoids (ATFs) and to elucidate the role of the gut microbiota in this effect. The results demonstrated that ATFs not only ameliorated the motor and constipation symptoms but also reduced the loss of nigrostriatal dopaminergic neurons. Furthermore, ATFs reduced the expression of inflammation-related genes (TNF-α, IL-1β, IL-6, COX-2, and MCP-1) and increased the expression of gut barrier-related genes (Muc-2, ZO-1, Occludin, Claudin3, and Claudin4) in the colon. Notably, ATFs were able to reverse rotenone-induced gut dysbiosis, including a significant decrease in the abundance of conditionally pathogenic bacteria (Desulfovibrio, Provotellaceae UCG-001, the Lachnospiraceae_NK4A136_group, norank_f_Erysipelotrichacea, and the Eubacterium nodatum group) and an increase in the abundance of probiotics (Bifidobacterium and Faecalibaculum). Interestingly, these genera were found to be significantly associated with PD motor symptoms and constipation indicators. This suggests that ATFs have the potential to alleviate PD symptoms through the modulation of gut microbes. These findings provide a solid foundation for further investigations into the anti-PD mechanism of ATFs and their potential in the prevention and treatment of PD.

Montana-D (08:36:45) (in thread): > Hi@Mildred Anashie@Adeshile OluwatosinGreat job on your curation. > > As per my opinion, they look very much curatable if the comparisons are feasible > If they are, then it sure looks curatable

Montana-D (08:38:19) (in thread): > Hi@Daberechi Okorie@Mildred Anashie. > This is detailed work done. Good job on your curation:raised_hands:. I’ll go through again

Daberechi Okorie (08:39:23) (in thread): > Thank you@Montana-DDestiny

Adeshile Oluwatosin (08:51:42) (in thread): > Gracias! Figure 8A does not really seem useful butI’msure of figure 8B

Montana-D (08:59:40) (in thread): > Please could you clarify why Fig8A is seemingly useless? > Cuz I think they both move together > It is either they both are or are not > Their comparisons seem similar though > Unless motility phenotype parameters are not of importance to the curation

Mildred Anashie (09:00:17) (in thread): > Thank you@Montana-D:blush:

Oriade Adeola (09:02:40) (in thread): > Pseudomonadota as been removed

Adeshile Oluwatosin (09:03:01) (in thread): > I believe in 8B the correlation between differential genera and defecation parameters shows differential analysis related to the study explaining constipation. > > 8A on the other hand is showing correlation between generaandmobility parameters like grip strength value, climbing pole time, hence I’m wondering how related it’s to the study

Montana-D (09:06:54) (in thread): > Ohhh > That makes sense, then it shouldn’t be curated then > 8b would be nice to curate if others and@Mildred Anashieagree to it. > Otherwise you both have done a really good and thorough job with your curation:raised_hands:

Adeshile Oluwatosin (09:09:41) (in thread): > Link to the study:https://bugsigdb.org/40004140 - Attachment (BugSigDB): Correlations Between Amelioration of Rotenone-Induced Parkinson’s Symptoms by Amomum tsaoko Flavonoids and Gut Microbiota in Mice - BugSigDB > Parkinson’s disease (PD) is the second most common neurodegenerative disease, but the existing therapeutic drugs for PD have limitations; thus, there is an urgent need to discover new methods of prevention and treatment.

Aiysha shahid (09:13:32) (in thread): > * @Oriade Adeola, I am talking about these, curate only taxa with > When * are above a box, it means that group is compared with Healthy controls and you curate only those taxa > * When # are above a box, it means that group is compared with Normal transit constipation (NTC)/non-DD and you curate only those taxa > PS. In experiment 2-7, we are having taxa that shouldn’t be there.

Mildred Anashie (09:16:14) (in thread): > Thank you@Montana-DI agree with that

Montana-D (09:18:42) (in thread): > Does experiment 3 have any signatures? > Because it doesn’t reflect on my end

Adeshile Oluwatosin (09:21:18) (in thread): > https://bugsigdb.org/40004140/Experiment_3/Signature_1 - Attachment (BugSigDB): 40004140/Experiment 3/Signature 1 > Source: Figure 7D, S1A and S1B Description: Linear discriminant analysis (LDA) of three groups NCD (normal chow diet), ROT (rotenone gavage), and ATF (Amomum tsaoko…

Oriade Adeola (09:25:05) (in thread): > @Aiysha shahidhonestly speaking, from the very beginning i didn’t understand this all curation thing, from the videos i watched online i was able to understand it a little, that was why i got stucked in the first place. I’m trying to do the best i can, going back to watch more videos and to understand better and i’m still stuggling, confused and fustrated. I have spent too much time trying to figure this out, and the deadline for the final submission is tommorow. if i continue to go back and forth on that article and the curation paper i might end up making mistakes and and deleting things i’m not supposed to delete, so please i beg of you, if you know what to do, please kindly help me so we don’t waste anymore time on this and end up not submiting this before the final deadline. Most of the time i reply late cause i’m working on other projects that i also have to submit. i’m done with those ones now as i understand them properly and it’s only this one i’m struggling with. Please so i don’t hold us back, if you know the right thing to do please help me. Thank you.

Montana-D (09:25:42) (in thread): > Well done on your curation@Anne-Marie Sharp, you did awesome to me.

Aiysha shahid (09:31:33) (in thread): > @Oriade AdeolaOh, no issue’s then I will fix it up!:raised_hands:

Aiysha shahid (09:43:16): > Hi Everyone! :tulip:I noticed that the study mentions using theMann–Whitney testfor statistical analysis, and the results are provided inTable S1(attached below). However, fromFigure 1A and 1C, it’s quite evident that the data is alsocuratable. > In this case, should I mentionboth statistical tests—Mann–WhitneyandLEfSe—under the “Statistical test” field? And for the source, can I cite it as:Source: Figure 1A, 1C; Table S1? Link of the paper-https://onlinelibrary.wiley.com/doi/10.1111/ene.15679, Or should I curate different experiments? - File (Word Document): ene15679-sup-0001-tables1.docx

Antonia Beatriz Soler Riera (09:55:20): > Hello everyone, I tried to do my first contribution during the weekend, I would like to know if it is ok and what are next steps.

Montana-D (09:56:41) (in thread): > I would suggest you use the old trick so it appears on the home curation aswell

Svetlana Ugarcina Perovic (09:57:40) (in thread): > Have you done the 1st taskhttps://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRw? - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy First Task > BugSigDB Outreachy First Task

Montana-D (09:57:44) (in thread): > Hi@Antonia Beatriz Soler RieraGood job on finishing your first contribution.

Oriade Adeola (09:57:54) (in thread): > Thank you.

Svetlana Ugarcina Perovic (09:58:22) (in thread): > It seems that the first task expired.<@UBNSEMS3S>will prolong it asap.

Antonia Beatriz Soler Riera (09:58:47) (in thread): > I tried to do it but it says Sorry, this survey has already expired.

Svetlana Ugarcina Perovic (09:59:25) (in thread): > Anyway, do not worry, share your 2nd contribution here for a peer review and then request an official review.

Svetlana Ugarcina Perovic (10:01:36): > URGENT: a peer review forhttps://bugsigdb.org/32021942by@Antonia Beatriz Soler RieraAnd, 1st task activation please<@UBNSEMS3S> - Attachment (BugSigDB): Gut microbiome structure and adrenocortical activity in dogs with aggressive and phobic behavioral disorders - BugSigDB > Accompanying human beings since the Paleolithic period, dogs has been recently regarded as a reliable model for the study of the gut microbiome connections with health and disease.

Adeshile Oluwatosin (10:03:20) (in thread): > Alright, noted > Well done@Antonia Beatriz Soler Riera:clap::clap::clap:

Adeshile Oluwatosin (10:03:38) (in thread): > Yeah, we did it

Ameenat Oloko (10:04:18) (in thread): > Well done,@Antonia Beatriz Soler Riera. > I’ll takea look into it.

Antonia Beatriz Soler Riera (10:05:00) (in thread): > thank you all

Montana-D (10:05:47) (in thread): > It still doesn’t reflect > Please try repeating the incomplete/complete and refresh only for exp. 3, to save you posting plenty links

Mildred Anashie (10:06:28) (in thread): > Well done@Antonia Beatriz Soler RieraI’llalso take a look

Montana-D (10:08:12) (in thread): > Good job@Antonia Beatriz Soler RieraBased on my observations, > 1. Figure 1B is rather curatable and not 1A > 2. Figure 3 is also curatable

Adeshile Oluwatosin (10:09:49) (in thread): > * The statistical test is random forest analysis only > * Figure 1A and 1Bis not curatable as the differences is not clear enough for curation, > * Hence, curate only Figure 3 with just 2 significant taxa > * You can curate as normal vs aggressive and phobic vs aggressiveas this was stated; > ”Specifically, our analysis revealed two ‘aggressive-discriminatory’ bacterial genera: Catenibacterium and Megamonas.”@Antonia Beatriz Soler Riera

Mildred Anashie (10:10:15) (in thread): > I think it should be curated differently since the statistical tests are not the same@Aiysha shahid

Ameenat Oloko (10:26:56) (in thread): > I agree with@Montana-DthatFig. 1Bis curatable (from the results texts). You’re to curate experiments onnormalvs.aggressive,normalvs.phobic andphobicvsaggressive groups****. ****Figure 3 is curatable, as previously stated.

Adeshile Oluwatosin (10:28:36) (in thread): > Figure 1B is not curatable > Chloe has confirmed that

Adeshile Oluwatosin (10:29:48) (in thread): > If the differences are not clear enough, we ignore the figures/tables. Figure 1B does not tell us clearly which taxa is significant in the comparisons

Ameenat Oloko (10:29:57) (in thread): > Oh! I thought it was, from the texts@Adeshile Oluwatosin.

Montana-D (10:31:07) (in thread): > Okay noted. > Please for better clarification; when the difference is not totally clear in the figure, the text should be negleted aswell ?@Adeshile Oluwatosin

Adeshile Oluwatosin (10:31:54) (in thread): > I didn’t see any clear stated significancebetween the comparisonsin the text as well

Ameenat Oloko (10:32:14) (in thread): > See this,@Adeshile Oluwatosin. “At family level, Lachnospiraceae, Erysipelotrichaceae and Clostridiaceae constitute the major components of the normal behavior group (relative abundance >10%). A depletion in the relative abundance of Bacteriodaceae, Alcaligenaceae and [Paraprevotellaceae], as well as an increase in Erysipelotrichaceae (P-value < 0.05) was observed in the aggressive group compared to the normal behavior group. The phobic group was instead characterized by an increase in the relative abundance of the family Rikenellaceae (P-value ¼ 0.04) when compared to the normal behavior group. Aggressive and phobic groups were found to be distinguishable due to different proportions in the relative abundance of the bacterial families [Mogibacteriaceae] and Veillonellaceae, respectively depleted and enriched in the aggressive group (P-value < 0.04

Adeshile Oluwatosin (10:33:21) (in thread): > They didn’t state which taxa is significant > They only mentioned abundance which could be increased or decreased and still over the significant threshold. > In cases like this we look at the figure > Andthat’salso not clear

iniobong simeon (10:38:07): > Hi Everyone, > I am done with this curation and need review please. > Thanks.https://bugsigdb.org/34690948 - Attachment (BugSigDB): Fecal Microbiota Transplantation Modulates the Gut Flora Favoring Patients With Functional Constipation - BugSigDB > Intestinal dysmotility is common in many diseases and is correlated with gut microbiota dysbiosis and systemic inflammation.Functional constipation (FC) is the most typical manifestation of intestinal hypomotility and reduces patients’ quality of life.

Montana-D (10:43:04) (in thread): > Well done on your curation@iniobong simeonI’ll have a look through

Joy (10:44:05) (in thread): > Well done@Antonia Beatriz Soler Rieraon your curation. I think the study is best described as across-sectional observational studyand nota Case control.Because the > * Objective:To investigate the relationship between gut microbiome composition and behavioral phenotypes (aggressive, phobic, and normal behavior) in dogs, and to examine associated adrenocortical activity (via fecal cortisol and testosterone). and > * Behavior Classification:Conducted by a behaviorist veterinarian using a validated behavioral grid.

Mildred Anashie (11:00:38) (in thread): > Hi@Antonia Beatriz Soler RieraI agree with@Adeshile OluwatosinFig 1a is not curatable and 1b doesn’t show clearly what the contrasts are. > For the condition I’m thinking instead of having two condition then “behavior or behavioral disorder measurement” might fit better (you’d find it this way on Bugsigdb).

Ameenat Oloko (11:01:49) (in thread): > Yes, mention the two statistical tests that were used,@Aiysha shahid.

Ifunanya Benita Obiaku (11:05:28): > Good evening everyone,@Victoria (Burah) Poromonand I curated this paper and we’d appreciate a peer review.https://bugsigdb.org/39976263

Ifunanya Benita Obiaku (11:06:08): > @Svetlana Ugarcina Perovicplease delete experiment 10https://bugsigdb.org/39976263

Ameenat Oloko (11:07:09) (in thread): > Hi,@Ifunanya Benita Obiaku. This should be done in the GitHub comment.

Victoria (Burah) Poromon (11:08:15) (in thread): > Hi@Aiysha shahidYou curate separate experiments like@Mildred Anashiesaid. > For Figure 1a and c, the statistical test is LEfSe

Ameenat Oloko (11:12:53) (in thread): > Well done,@Ifunanya Benita Obiakuand@Victoria (Burah) Poromon. I’ll take a look into it.

Precious Chijioke (11:14:02) (in thread): > Well done on your curation@Antonia Beatriz Soler RieraI agree with@Adeshile Oluwatosin

Precious Chijioke (11:15:30) (in thread): > Well done@Ifunanya Benita Obiakuand@Victoria (Burah) Poromon. I’ll take a look into it.

Victoria (Burah) Poromon (11:19:43) (in thread): > @Ifunanya Benita ObiakuPlease remove all the matched-on factors in the experiments > > Please include Group1 definition from experiment 2 to the end > > Please remove the LDA score in any of the other experiments except experiment 1

Victoria (Burah) Poromon (11:23:07) (in thread): > Also specify the sequencing platform for every experiment. > > The NCBI ID for Butyrivibrio fibrisolvens is 831 > ID for Clostridium innocuum is 1522

Precious Chijioke (11:26:39) (in thread): > @Ifunanya Benita Obiakugroup 1 definition from experiment 2 down is not captured. The 16S variable region is not indicated from experiment.

Antonia Beatriz Soler Riera (11:40:23) (in thread): > Ok, thanks a lot. Now I should edit my curation and modify it according to your comments?

Ameenat Oloko (11:41:24) (in thread): > Yes, you should@Antonia Beatriz Soler Riera. Well done:clap:

Svetlana Ugarcina Perovic (11:42:47) (in thread): > https://github.com/waldronlab/BugSigDBcuration/issues/658

Precious Chijioke (11:43:55) (in thread): > @Ifunanya Benita Obiakuyou’re to make this request in GitHub.

iniobong simeon (12:11:17) (in thread): > Okay thanks

Mildred Anashie (12:14:40) (in thread): > Okay@iniobong simeonWell done

Aiysha shahid (12:50:07) (in thread): > Thank you all!:tulip:

Aiysha shahid (12:55:07) (in thread): > Hi@iniobong simeon, well done! For signature’sDescription, you add this “LEfSe analysis revealed significant changes in the fecal microbiota compositions before and after FMT.”

Mildred Anashie (13:14:25) (in thread): > Hi@Anne-Marie SharpI think you missed an experiment in Table 2(Tab 2) which is LD vs LCIG done with GLM and that’s where all the confounders belong. I think you should remove it from the first three experiments. > See an excerpt, “However, after correction for confounders, the LCIG-Group showed a significant higher abundance of the Enterobacteriaceae family, Escherichia and Serratia genera compared to the LD-Group (Tab.2)”. > Also, the alpha diversity for the first 3 experiments was just Chao1, Richness (ACE) and Fisher they said Shannon and simpson was excluded from this while for the LCIG vs LD you can now curate all the indices mentioned but to be unchanged. > See an excerpt,“No significant differences were found between the LD and LCIG groups in alpha diversity, as estimated throughout different indices ACE, Chao, Fisher, Shannon and Simpson (p > 0.05) (data not shown). On the contrary, the microbial beta-diversity analysis significantly differed between the two treatment groups (R2 = 0.037, p <0.001) (Fig. 1A ).The alpha-diversity differences were instead observed in the comparison between the LD and LCIG groups vs Naïve-Group with ACE, Chao and Fisher indexes (p-values ≤ 0.0001) (Fig. 2 A-C), except for Shannon and Simpson measuraments (pvalues ≥ 0.05) (data not shown).”

Oriade Adeola (13:28:11) (in thread): > @Aiysha shahidhello aiysha how is it going?

iniobong simeon (13:30:51) (in thread): > Ok:+1:

Mildred Anashie (13:39:12) (in thread): > Well done again@iniobong simeonYou should write FMT in full > Condition should be transplant outcome measurement. Asides that I think you are on track because figure 4 doesn’t show significance and I’m uncertain how figure 5 can be curated or if it should be curated

Antonia Beatriz Soler Riera (13:49:01) (in thread): > I made these modifications according to the comments: 1) used information in fig 3 for the experiments. 2) In experiment 1 I modified the groups to compare aggresive to normal, and changed Signature 2 to account for a decrease in Bacteroidaceae according to Fig 1b. Maybe that signature should be deleted if Fig 1b is not curable. 3) added 2 more experiments comparing phobic to normal and aggressive to phobic. 4) Left only random forest as statistical analysis. 5) in the signatures considerated only Catenibacterium, Megamonas (and Bacteroidaceae) and deleted all the rest. 6) changed the study design from case-study to cross-sectional observational. 7) Changed the experimental condition to “behavior or behavioral disorder measurement”

Oriade Adeola (14:45:32) (in thread): > Can we submit to final review?

UBNSEMS3S (15:19:50) (in thread): > It has been fixed. Apologies.

Svetlana Ugarcina Perovic (15:22:12) (in thread): > @Antonia Beatriz Soler Rierahttps://cunysph.az1.qualtrics.com/jfe/form/SV_cHdZEAkVk4tTqRwis now open, please do it asap - Attachment (cunysph.az1.qualtrics.com): BugSigDB Outreachy First Task > BugSigDB Outreachy First Task

Svetlana Ugarcina Perovic (15:23:28) (in thread): > KUDOS to everyone in this thread:clap:

Antonia Beatriz Soler Riera (16:37:19) (in thread): > When trying to complete the initial task, this linkhttp://https//bugsigdb.org/34436669causes an error.

UBNSEMS3S (16:44:09) (in thread): > Looks like it should be:https://bugsigdb.org/34436669 - Attachment (BugSigDB): Compositional profile of mucosal bacteriome of smokers and smokeless tobacco users - BugSigDB > INTRODUCTION: Smoked, and especially smokeless, tobacco are major causes of oral cancer globally.Here, we examine the oral bacteriome of smokers and of smokeless tobacco users, in comparison to healthy controls, using 16S rRNA gene sequencing.

Antonia Beatriz Soler Riera (16:58:51) (in thread): > Thank you, I could complete now the two pages of the task. Had to start over.

Antonia Beatriz Soler Riera (17:03:22) (in thread): > How do I request the official review of my 2nd contribution?

Montana-D (17:09:41) (in thread): > Please go to the GitHub issue to which you requested the article from and paste the link to the curation, notifying it is ready for reviewing, then you shall be assigned a reviewer

Antonia Beatriz Soler Riera (18:05:50) (in thread): > @Svetlana Ugarcina Perovicalready did. Thank you Svetlana. Thank you all for your help and kindness, you are amazing.

Anne-Marie Sharp (18:45:06) (in thread): > Thank you@Montana-DI appreciate

Anne-Marie Sharp (18:58:00) (in thread): > Thank you for pointing out Table 2@Mildred AnashieI will remove the confounders from the others. Let me confirm, 1) Enterobacteriaceae, Escherichia & Serratia are already listed in Fig3C, so can I just add Table2 as the second source in Experiment3(LD vs LCIG)? or do I need to create a 4th experiment of LD vs LCIG done with GLM then include justEnterobacteriaceae, Escherichia and Serratia?

Anne-Marie Sharp (19:45:02) (in thread): > For the alpha diversity, as per the curation policy:****‘If there is an alpha diversity test without statistically significant results between the two groups, put “unchanged” for that test’****The article mentions: ‘Alpha-diversity indices (ACE, Chao, Fisher, Shannon and Simpson) and beta-diversity analysis were performed on the Microbiome Analyst tool’ & > “The alpha-diversity differences were instead observed in the comparison between the LD and LCIG groups vs Naïve-Group with ACE, Chao and Fisher indexes (p-values ≤ 0.0001) (Fig. 2 A-C), except for Shannon and Simpson measurements (pvalues ≥ 0.05) (data not shown).” > > So I think all the alpha diversity tests were done (Shannon&Simpson were also done/measured), just that Shannon & Simpson had no statistically significant results (pvalues were > 0.05), that’s why I put unchanged for Shannon & Simpson in LCIG vs Naïve & LD vs Naïve. What do you think?

Mildred Anashie (20:08:11) (in thread): > Yes the statistical test is different and they controlled for confounders in the GLM model > > I get your point on the alpha diversity

Anne-Marie Sharp (20:10:49) (in thread): > Hello@Mildred Anashie@Daberechi Okorie@Adeshile OluwatosinI also think that > “Eating behaviour: Behaviors associated with the ingesting of food; includes rhythmic patterns of eating (time intervals - onset and duration), frequency and satiety as well as the types of food chosen”is a better match than”binge eating” because Eating behaviour broadly covers patterns like eating timing and frequency, which aligns with the contrast in Non-TRE, but “binge eating” refers to a specific disordered eating pattern not relevant to this context.

Anne-Marie Sharp (20:13:30) (in thread): > Okay, I would have completely missed that out. Thank you very much

Mildred Anashie (20:33:55) (in thread): > The Non TRE group in the study weren’t grouped based on pattern of eating or restricted eating, that’s for the TRE group@Anne-Marie Sharp:thinking_face:

Anne-Marie Sharp (20:57:54) (in thread): > TRE was restricted eating hence you used fasting as the condition. but Non-TRE is non-restricted eating, more like just normal/free eating. > You’d also notice that thedifference in the timingwasn’tmuch: ‘The average eating window, defined as the duration from the start to the end of eating each day, was 10.47 (0.38) h for the TRE group, meeting the requirements for a 10-h TRE; meanwhile, the non-TRE group had an average eating window of 11.76 (0.45) h’

Anne-Marie Sharp (20:59:04) (in thread): > Honestly, eating behavior isn’t a perfect match but it is better than binge eating which is uncontrolled eatingin a short time

Anne-Marie Sharp (21:07:19) (in thread): > Well done on your curation@Daberechi Okorie@Mildred Anashie1)In Experiment7 Group1 definition: the abbreviation in bracket should be (Non-TRE) not (TRE) > 2)The Group1 definitions in your curation are defining both Group0&1, they are incomplete as they do not include the explanation of ‘endpoint’ which is Group1.

Mildred Anashie (21:15:33) (in thread): > Thanks@Anne-Marie SharpNumber 1 would be corrected, but reading through based on what the study said. The 12 week feeding trail was the end of that intervention arm which is included in the definition (“during the 12 week feeding trial”).

Anne-Marie Sharp (21:36:11) (in thread): > You’re welcome@Mildred AnashieCheck these out: > ‘For adaptations of the gut microbiome during the intervention, a significant difference between baseline and endpoint (week 12) in beta diversity was found in the HLCD and TRE groups’ & > ‘Similarly, week 12 results reflected the adjusted change between week 12 follow-up outcomes and baseline’ > -I feel it’ll be more appropriate to indicate in Group1 definition that endpoint was at week12/end of week12.‘during the 12 week feeding trial’ doesn’t indicate when the endpoint actually was, it just indicates a duration.

Anne-Marie Sharp (21:44:02) (in thread): > Well done@iniobong simeonI believe with the above corrections, your curation is good to go:raised_hands:

Anne-Marie Sharp (22:15:40) (in thread): > Well done@Ifunanya Benita Obiaku@Victoria (Burah) PoromonI agree with your suggestions above. > 1)All abbreviations should also be written in full eg BMI - Body Mass Index > 2)In Experiment1 your group names should be HFD-RH & HFD-PBS. Then also write them in full in brackets as (High Fat Diet - Roseburia hominis) & (High Fat Diet - Phosphate-buffered saline) > 3)In Experiment5, group0 should be Absence of insulin receptor & group1 should be Presence… > 4)In Experiment8, Group0 should be Low in aspartate aminotransferase and Group1 should be High…. > 5)In Experiment11, Group0 should be Low Hepatic triglycerides and Group1 should be High…

2025-04-15

Ameenat Oloko (01:27:04) (in thread): > Hello,@Antonia Beatriz Soler Riera. Good morning. > Have you now completed your first contribution?In case youdon’tknow how to go about recording it on the Outreachy website, these are the steps below:https://community-bioc.slack.com/archives/C04RATV9VCY/p1727849386260229 - Attachment: Attachment > Recording your first contribution: > > It is very important to record your contribution upon submission, as projects may close once they have enough applicants participating. This ensures you don’t miss out on the opportunity to be considered for that project. > > So, here are the steps to record your first contribution: > > 1. Visit the Outreachy website. > 2. Select the ‘Microbiome Study Curation’ project. > 3. Click on ‘Record Contributions and Apply to This Project’. > 4. Proceed to record your contribution. > Please note: For your first contribution, the “merged date” refers to the date you submit your contribution. > > Here’s the link to the curation form that will serve as your Contribution URL: > https://cunysph.az1.qualtrics.com/jfe/form/SV_1RfUgk72TYmcBHE > > I’ve added images for better visual guidance. > > Good Morning and Happy Wednesday everyone :sparkles::sunny:

Ameenat Oloko (01:40:52): > Good morning, everyone. This is to remind you that the final application deadline is today at 4 p.m. UTC. Good luck!Final Steps for Applying————————- > > In order to be eligible to be selected as an Outreachy intern, you must: > 1. Verify your time commitments are correct in your initial application. > 2. Record at least one in-progress contribution you’ve made to an Outreachy internship project. The contribution must be recorded through the Outreachy website. > 3. Create a final application for that project. The final application must be submitted through the Outreachy website. > You must create a final application for each project. If you don’t create a final application for a project, you aren’t eligible to be selected as an intern for that project.Verify Your Time Commitments—————————- > > Your approval to participate in Outreachy is based on the time commitments you listed in your initial application. You can check your listed time commitments by following these steps: > * Log into the Outreachy website: > https://www.outreachy.org/login/ > * Check the time commitments listed on your initial application: > https://www.outreachy.org/eligibility-results/If your time commitments are incorrect or have changed since you filled out an initial application, please contact us immediately:https://www.outreachy.org/contact/applicant-help/Please check to see if your initial application is missing information your current or future job, a new job offer, your school time commitments, your online classes, or your coding school information. Please check that the hours of your time commitments are correct. Get in touch with us immediately to correct any missing or incorrect time commitments. > > If you are selected as an intern, you will be required to sign a legal internship agreement which asserts that the details in your initial application are correct. It’s very important that your time commitments stated in the initial application are correct. > > The final application will have a field for you to note any time commitment changes. If your final application shows incorrect time commitments, please note any time commitment changes in your final application.Recording Contributions———————– > > You will need to record your contributions for each project you’re applying for. > > Please record your contributions even if the contribution is not merged or accepted yet. > > You can record your contributions following these steps: > 1. Log into the Outreachy website: > https://www.outreachy.org/login/2. Find your project listed on the project selection page:https://www.outreachy.org/apply/project-selection/3. Click the project’s title to be taken to the project details page. > > 4. Click the ‘record your contributions and create a final application’ link. > > 5. Repeat steps 2-4 to record your contributions for each project you are applying for. > > Once you have recorded a contribution to a project, a link to record more contributions or create a final application for that project will be available on your dashboard:https://www.outreachy.org/dashboard/After the final application deadline, you are encouraged (but not required) to continue working on contributions with your project mentor. You will be able to record or edit contributions until May 8, 2025 at 4pm UTC. > *****Final Applications*—————— > > You will need to create a final application for each project you’re applying for. Only applicants that complete a final application for that project will be eligible to be selected as an intern for that project. > > You can create a final application by following these steps: > 1. Log into the Outreachy website: > https://www.outreachy.org/login/2. Find your project listed on the project selection page:https://www.outreachy.org/apply/project-selection/3. Click the project’s title to be taken to the project details page. > > 4. Follow the ‘create a final application’ link. > > 5. Repeat steps 2-4 to create a final application for each project you are applying for. > > You can edit your final application(s) until April 15, 2025 at 4pm UTC. Once you create a final application, a link to edit it will appear on your dashboard:https://www.outreachy.org/dashboard/The final application will ask you to fill out a timeline for the internship project. For guidance on how to prepare your project timeline, please refer to our documentation.https://www.outreachy.org/docs/applicant/#final-applicationYour project timeline doesn’t need to be perfect, but it should be flexible enough to accommodate any changes in plans and time commitments, or unexpected blockers. Please submit your final application even if your project timeline isn’t complete — if you’re selected as an intern, you will have the chance to review it alongside your mentors.https://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539 - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority**): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Svetlana Ugarcina Perovic (02:37:50): > Good luck with your FINAL APPLICATION:arrow_up:We, mentors, have been amazed by your dedication and high-quality curation! THANK YOU for building with us this great community and important microbiome resource. > > Please be aware that**** you are more than welcome to continue curating ****:potted_plant:<@U1LCB8WEA>**** ****<@UBNSEMS3S>**** ****@Svetlana Ugarcina Perovic**** ****@Kate Rasheed**** ****@Aleru Divine**** ****@Scholastica Urua**** ****@Chioma Onyido**** ****@Peace Sandy**** ****@Esther Afuape**** ****

Adeshile Oluwatosin (02:38:58) (in thread): > Thank you so much for impacting in us knowledge as well. I am honored to be part of this community.

Aiysha shahid (03:04:08) (in thread): > I am on it, we can submit it by today eod.

Aiysha shahid (03:05:09) (in thread): > Thanks a lot!:tulip:

Mildred Anashie (03:15:00): > Good morning everyone > It’s officially the last day of contribution and it has been an amazing journey so far:hugging_face:Thank you to our mentors and my fellow contributors:heart:I have a question and would appreciate your feedbacks on it, I am working on curating this study and it has experiments done on humans and mice models and I am unsure what the actual study design is (went with Laboratory experiment though). Also, is Fig 3g curatable? > > Link to curation:https://bugsigdb.org/38477534 - Attachment (BugSigDB): Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism - BugSigDB > Disrupted gastrointestinal (GI) motility is highly prevalent in patients with inflammatory bowel disease (IBD), but its potential causative role remains unknown.Herein, the role and the mechanism of impaired GI motility in colitis pathogenesis are investigated.

Anne-Marie Sharp (03:16:23) (in thread): > Thank you so much to all our mentors

Adeshile Oluwatosin (03:20:36) (in thread): > Good morning@Mildred AnashieThe study design should be randomized controlled trial > Figure 3G is not curatable

Adeshile Oluwatosin (03:21:18) (in thread): > See the description “In addition, we used fluorescent in situ hybridization to examine the spatial distribution of Lactobacillus and A. muciniphila along the gut tracts of WT and Kitwsh/wsh mice. The abundance of the two bacterial groups in the colon showed the greatest difference between the WT and Kitwsh/wsh mice (Figure 3F,G).”

Mildred Anashie (04:21:39) (in thread): > Okay@Adeshile OluwatosinThank you:pray:

Mildred Anashie (04:26:26) (in thread): > Thank you to all our mentors:heart:

Anne-Marie Sharp (04:31:51) (in thread): > Good morning:hugging_face:@Mildred AnashieThe study design should be randomized controlled trial. I think Figure 3g is curatable, it shows differentially abundant taxa between groups, there’s also statistical test used.

Joy (04:36:32) (in thread): > Thanks a million to our amazing mentors. We truly appreciate all you do for us!:sparkles:

Ameenat Oloko (04:51:39) (in thread): > Thank you for making this community a safe space for us.

Montana-D (05:16:08) (in thread): > Thank you to all my mentors and co- contributors. I have had plenty of fun and growing in this past 3 weeks being in this amazing community:heart::pray::man-bowing:

Montana-D (05:22:32) (in thread): > Good morning@Mildred AnashieI do agree with the others about the study design, as for fig. 3g, I do not think it is curatable

Ndukauba Oluchi (05:23:57) (in thread): > Thank you to everyone:heavy_heart_exclamation_mark_ornament::heavy_heart_exclamation_mark_ornament:

Ameenat Oloko (05:25:11) (in thread): > Good morning,@Mildred Anashie. Well done:clap:. > I think the study design is a laboratory experiment, as you stated, based on the following points: > * ******Mice******* with GI dysmotility *******induced *****by genetic mutation or chemical insult *******exhibit increased susceptibility to colitis*******, dependent on the gut microbiota. > ******mice******* *******receiving fecal microbiota from CC patients******* displayed an increased susceptibility to colitis. * > Fig 3g is not curatable.

Mildred Anashie (05:33:13) (in thread): > Okay@Anne-Marie SharpI actually felt it was curatable because of the statistical test and the way abundance was reported but I took another look at the caption and what the results text says and got a little confusedHere, “ G) Quantification of Lactobacillus and A. muciniphila positive probes per field of F.” > > Itdoesn’tseem to be differential abundance analysis:thinking_face:

Mildred Anashie (05:34:44) (in thread): > On a second thought, I’m curious as to why it is a randomized controlled trial@Adeshile Oluwatosin@Anne-Marie SharpIs there something I missed? Please point me to it:pray:

Adeshile Oluwatosin (05:35:26) (in thread): > I have worked on a similar article and Chloe confirmed it to be so. > I also saw that this present article mentions randomized controlled trial

Mildred Anashie (05:40:58) (in thread): > I see:eyes:I’lltake a second look > > Thank you again > > Also, could you help review this@Anne-Marie Sharp@Adeshile Oluwatosin@Ameenat OlokoIcan’tfigure out the condition for the experiments marked as incomplete and would appreciate some help, thank you:pray:

Anne-Marie Sharp (05:47:15) (in thread): > @Mildred AnashieQuantification of positive probes per field refers to counting the no. of bacteria in a microscopic field. It measures abundance of those taxa in a tissue sample(tissue samples were used in Fig. 3F & 3G) and its comparing these counts between the 2mice groups. Also, the figure description stated that t-test was used. That’s why I think it could be curatable.

Precious Chijioke (05:52:18) (in thread): > Thank you to our amazing mentors.

Adeshile Oluwatosin (05:53:26) (in thread): > There was a similar figure where Svetlana mentioned that we do not curate counts in the office hour chat box. > This article I guess,@Precious Orakweworked on ithttps://bugsigdb.org/37065158

Anne-Marie Sharp (06:13:51) (in thread): > @Adeshile OluwatosinYes, I thought as much, I still have that article. But those counts in that article were ASV counts. Probe counts unlike raw ASV counts directly measure specific bacterial taxa and show statistical differences between groups. It could still be omitted if its much of a hassle, but I feel it can be curated.

Mildred Anashie (06:41:46) (in thread): > @Anne-Marie SharpI know probe counts can be used to detect the presence/absence or quantity of specific genes or organisms and the study doesn’t mention that the tissue samples were used for differential abundance > > Yes they performed statistical comparison and they checked significant between group comparisons but it doesn’t seem to be derived from a typical sequencing technique:thinking_face:This is a bit tricky though

Joy (06:50:23): > Hi everyone,@Vanisha Gargand I would appreciate a peer review of this study we curated. Thanks.https://bugsigdb.org/40189515https://bmcwomenshealth.biomedcentral.com/articles/10.1186/s12905-025-03689-0#Fig6 - Attachment (BugSigDB): Gut microbiome in patients with early-stage and late-stage endometriosis - BugSigDB > BACKGROUND: Endometriosis is a chronic inflammatory gynecological disease. - Attachment (BioMed Central): Gut microbiome in patients with early-stage and late-stage endometriosis - BMC Women’s Health > Background Endometriosis is a chronic inflammatory gynecological disease. Previous studies have explored relationships between endometriosis and the microbiota, but none have focused on differences in gut microbiota between early-stage and late-stage endometriosis patients or their connections to dysmenorrhea symptoms. This study compared gut microbiota compositions between early-stage and late-stage endometriosis patients using amplicon sequencing and further analyzed their dysmenorrhea symptoms. Methods To minimize seasonal and dietary impacts, we recruited Guangdong residents hospitalized for surgery at Zhujiang Hospital. Participants underwent preoperative screening based on enrollment criteria and fecal samples were collected. Endometriosis was classified according to the American Society for Reproductive Medicine (ASRM) staging system based on surgincal and pathological findings. Stage I-II cases were designated as early-stage endometriosis, and Stage III-IV as late-stage endometriosis. Results A total of 112 patient fecal samples were collected, with 75 (median age, 32 years [range, 18–49 years]) meeting the enrollment criteria, including 39 early-stage (32 Stage I and 7 Stage II) and 36 late-stage (16 Stage III and 20 Stage IV) patients. The gut microbiota structure and functions in early-stage patients significantly differed from those in late-stage cases. Dysmenorrhea was associated with specific microbial traits. Late-stage patients with dysmenorrhea displayed distinctly different gut profiles compared to other endometriosis groups. Bartonella, Snodgrassella, and other taxa were enriched in late-stage cases, while Bacteroides, and Prevotella were decreased. Conclusion The gut microbial community structure in early-stage endometriosis patients significantly differs from that in late-stage cases, with late-stage patients experiencing dysmenorrhea displaying particularly distinct gut profiles. Predicted functional analysis indicated suppressed steroid biosynthesis pathways in the gut of late-stage endometriosis patients. In conclusion, it is plausible that the multiple effects of steroids on the lower gastrointestinal tract may involve microbiota alterations, suggesting the need for further investigations.

Anne-Marie Sharp (07:07:40) (in thread): > @Mildred AnashieIt really is tricky I agree:weary:. Yes sequencing was used for only fecal samples, no sequencing was used for tissue samples. They mentioned the tissue samples in between the lines. They first used fecal samples then In addition used tissue samples(gut tract: duodenum, ileum and colon). Check it out: > 1)‘In addition, we used fluorescent in situ hybridization to examine the spatial distribution ofLactobacillusandA. muciniphilaalong the gut tracts of WT and Kitwsh/wsh mice. The abundance of the two bacterial groups in the colon showed the greatest difference between the WT and Kitwsh/wsh mice (Figure 3F, G)’ > > 2) ’….F) Representative fluorescent in situ hybridization images ofLactobacillusandA. muciniphilain duodenum, ileum and colon tissues of WT and Kitwsh/wsh mice. Scale bar, 25 µm. G) Quantification ofLactobacillusandA. muciniphilapositive probes per field of F. In A, D, E and G, data represent mean ± SEM; P < 0.05, P < 0.01, ****P < 0.001 by two-sided Studentttest.

Antonia Beatriz Soler Riera (07:16:06) (in thread): > Hello, do my contributions need to be Accepted or merged to be able to fill the application?

Antonia Beatriz Soler Riera (07:18:00) (in thread): > I didnt complete the field that says “Date contribution was accepted or merged”

Mildred Anashie (07:23:27) (in thread): > Hi@Antonia Beatriz Soler RieraYou can leave that blank and update whenit’sreviewed, I believewe’llbe able to edit and record our contributions till the intern announcement is made

Precious Orakwe (07:30:37) (in thread): > Well done@Joy

Precious Chijioke (07:31:00) (in thread): > Hi@Antonia Beatriz Soler Rierago ahead and fill the application. You don’t need to wait till your contributions are merged. you can always edit the date, leave the merged date blank at the moment.

Juliana Kentomahun Mautin (07:45:32) (in thread): > Thank you so much@Svetlana Ugarcina Perovicand to the amazing Mentors, thank you so much for your continuous support. I really do appreciate, I feel so excited to be part of this amazing community.

Mildred Anashie (07:48:55) (in thread): > Well done@Vanisha Gargand@JoyI’lltake a look

Adeshile Oluwatosin (07:49:02) (in thread): > Hello@Antonia Beatriz Soler RieraDate contributed was accepted or merged is the date the needs review tag was placed on your issue. > Since, you are currently still working on your curation > Leave it blank as stated > Then edit later on, we can continue to do this till May 8th

Antonia Beatriz Soler Riera (07:50:52) (in thread): > Ok I did so. In the timeline I should estimate what i could do to improve in the curation tasks during the internship?

Precious Chijioke (07:55:11) (in thread): > @Antonia Beatriz Soler Rierafor the timeline, it should cover what you’ll be doing during the 12-13 weeks of the internship. Check this template and create your timeline.https://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539?thread_ts=1744274936.668539&cid=C04RATV9VCY - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Ameenat Oloko (07:55:27) (in thread): > Hello,@Antonia Beatriz Soler Riera. The timeline should describe what you intend to do after you have been accepted as an intern. It should serve as a guide.https://community-bioc.slack.com/archives/C04RATV9VCY/p1744274936668539 - Attachment: Attachment > IMPORTANT > > Final application > There are no community-specific questions. > As for the timeline, the internship begins June 2, 2025 and runs until August 29, 2025 and you are expected to work 30 hours a week. During that time, a BugSigDB intern can provide a variety of contributions including (in the order of priority): > > 1. Review of existing curations. A large portion of the curations in BugSigDB have not been reviewed. The review process involves spot checking the curation for issues using the original paper. > 2. Fixing curation issues when possible. As presented on this page: https://bugsigdb.org/Help:Contents#TODO_for_reviewers > 3. The curation of published microbiome research that has not been previously curated in BugSigDB. This would include locating published research using online databases, reading the research reports, and curating the research accordingly > 4. Analysis of BugSigDB data and drafting an article for publication. Based on a condition or disease of interest, you can conduct a review of published microbiome studies, curate any that are not already in BugSigDB, then use the BugSigDB data to analyze the signatures. > 5. The development of a BugSigDB dashboard and other resources to help promote BugSigDB to researchers. > Our hope is that our intern can spend a lot of their time working on reviewing curations (bullet point number one) so I would recommend emphasizing that in your timeline. Also please review the description of the project as detailed on Outreachy as you develop your timeline. > When we review your application, we will consider the thoughtfulness and achievability of your timeline as well as how it aligns with the goals of the project.

Ameenat Oloko (07:57:50) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1698252093823959?thread_ts=1698178098.103179&channel=C04RATV9VCY&message_ts=1698252093.823959 - Attachment: Attachment > @Chiagoziem David Our expectation is not that if selected as an intern you will make progress but we don’t expect you to complete any of the bulleted items as they will be ongoing for as long as the project exists. > > I will say what we look for in the timeline is that you have an understanding of how BugSigDB works and how as an intern you can contribute to the project. Realistic goals are preferred.

Ameenat Oloko (08:17:30): > Good day, everyone.Please, how do we add a study to BugSigDB if the PMID is not available?

Svetlana Ugarcina Perovic (08:19:08) (in thread): > Yes. If the PMID isn’t available, the you can just fill the DOI and the URL

Oriade Adeola (08:44:10) (in thread): > ok. Thank you.

Ameenat Oloko (08:46:58) (in thread): > Please, do we delete PMID on BugSigDB?@Svetlana Ugarcina PerovicI filled in the DOI in place of PMID so I could add the study.Then, Imanually entered the remaining details, but the PMID is incorrect.https://bugsigdb.org/Https://doi.org/10.3389/fevo.2022.742369 - Attachment (BugSigDB): Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese - BugSigDB > Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology.For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness.

Aiysha shahid (08:50:44) (in thread): > Well Done! I’ll would also go through it

Svetlana Ugarcina Perovic (08:52:01) (in thread): > Please do it again by skipping PMID. I deleted the study previously created.

Ameenat Oloko (08:53:14) (in thread): > Okay, I’ll redo it. Thank you.

Aiysha shahid (08:58:42) (in thread): > I am curious that have you guys,curated S1A. As I can’t see it in source section? But in the paper it’s mentioned. See this-“We next determined differential genus and species abundance between groups (Fig.2D; Supplement Fig.1A). In total, genusGilliamella,Bartonella,Snodgrassellaand 10 other genera were more abundant in the Late-stage Group, while genusSaccharofermentansand 10 other genera were enriched in the Early-stage Group.” - Attachment (BioMed Central): Gut microbiome in patients with early-stage and late-stage endometriosis - BMC Women’s Health > Background Endometriosis is a chronic inflammatory gynecological disease. Previous studies have explored relationships between endometriosis and the microbiota, but none have focused on differences in gut microbiota between early-stage and late-stage endometriosis patients or their connections to dysmenorrhea symptoms. This study compared gut microbiota compositions between early-stage and late-stage endometriosis patients using amplicon sequencing and further analyzed their dysmenorrhea symptoms. Methods To minimize seasonal and dietary impacts, we recruited Guangdong residents hospitalized for surgery at Zhujiang Hospital. Participants underwent preoperative screening based on enrollment criteria and fecal samples were collected. Endometriosis was classified according to the American Society for Reproductive Medicine (ASRM) staging system based on surgincal and pathological findings. Stage I-II cases were designated as early-stage endometriosis, and Stage III-IV as late-stage endometriosis. Results A total of 112 patient fecal samples were collected, with 75 (median age, 32 years [range, 18–49 years]) meeting the enrollment criteria, including 39 early-stage (32 Stage I and 7 Stage II) and 36 late-stage (16 Stage III and 20 Stage IV) patients. The gut microbiota structure and functions in early-stage patients significantly differed from those in late-stage cases. Dysmenorrhea was associated with specific microbial traits. Late-stage patients with dysmenorrhea displayed distinctly different gut profiles compared to other endometriosis groups. Bartonella, Snodgrassella, and other taxa were enriched in late-stage cases, while Bacteroides, and Prevotella were decreased. Conclusion The gut microbial community structure in early-stage endometriosis patients significantly differs from that in late-stage cases, with late-stage patients experiencing dysmenorrhea displaying particularly distinct gut profiles. Predicted functional analysis indicated suppressed steroid biosynthesis pathways in the gut of late-stage endometriosis patients. In conclusion, it is plausible that the multiple effects of steroids on the lower gastrointestinal tract may involve microbiota alterations, suggesting the need for further investigations. - Attachment (BioMed Central): Gut microbiome in patients with early-stage and late-stage endometriosis - BMC Women’s Health > Background Endometriosis is a chronic inflammatory gynecological disease. Previous studies have explored relationships between endometriosis and the microbiota, but none have focused on differences in gut microbiota between early-stage and late-stage endometriosis patients or their connections to dysmenorrhea symptoms. This study compared gut microbiota compositions between early-stage and late-stage endometriosis patients using amplicon sequencing and further analyzed their dysmenorrhea symptoms. Methods To minimize seasonal and dietary impacts, we recruited Guangdong residents hospitalized for surgery at Zhujiang Hospital. Participants underwent preoperative screening based on enrollment criteria and fecal samples were collected. Endometriosis was classified according to the American Society for Reproductive Medicine (ASRM) staging system based on surgincal and pathological findings. Stage I-II cases were designated as early-stage endometriosis, and Stage III-IV as late-stage endometriosis. Results A total of 112 patient fecal samples were collected, with 75 (median age, 32 years [range, 18–49 years]) meeting the enrollment criteria, including 39 early-stage (32 Stage I and 7 Stage II) and 36 late-stage (16 Stage III and 20 Stage IV) patients. The gut microbiota structure and functions in early-stage patients significantly differed from those in late-stage cases. Dysmenorrhea was associated with specific microbial traits. Late-stage patients with dysmenorrhea displayed distinctly different gut profiles compared to other endometriosis groups. Bartonella, Snodgrassella, and other taxa were enriched in late-stage cases, while Bacteroides, and Prevotella were decreased. Conclusion The gut microbial community structure in early-stage endometriosis patients significantly differs from that in late-stage cases, with late-stage patients experiencing dysmenorrhea displaying particularly distinct gut profiles. Predicted functional analysis indicated suppressed steroid biosynthesis pathways in the gut of late-stage endometriosis patients. In conclusion, it is plausible that the multiple effects of steroids on the lower gastrointestinal tract may involve microbiota alterations, suggesting the need for further investigations.

Ameenat Oloko (08:59:43) (in thread): > Please,thisis what is showing,@Svetlana Ugarcina Perovic. Should I type the title of the research paper? - File (JPEG): IMG_7035

Svetlana Ugarcina Perovic (09:05:45) (in thread): > Work on this onehttps://bugsigdb.org/10.3389/fevo.2022.742369 - Attachment (BugSigDB): - BugSigDB > .

Svetlana Ugarcina Perovic (09:06:14) (in thread): > cc<@UBNSEMS3S>we need to fix this bug, when study does not have PMID how to create a study

Svetlana Ugarcina Perovic (09:11:06): > After submitting your FINAL APPLICATION > please fill in (if you did not already during this round) a short survey on your experience with BugSigDB during your Outreachy contribution. > If you already did it before, during previous rounds, please do it again:slightly_smiling_face:hopefully your experience with us has been improved…Your feedback will help us to improve the experience for future contributors, thank you!https://docs.google.com/forms/d/e/1FAIpQLScYzrN2imOTcv5fjLr27uuCgKer0sIN4AMwgDMlnsAfRFWNRw/viewform?fbzx=8337124519102598305

Ameenat Oloko (09:11:15) (in thread): > Okay, thank you so much@Svetlana Ugarcina Perovic:heart:

Svetlana Ugarcina Perovic (09:11:36) (in thread): > Only half of the current applicants did it :(

Antonia Beatriz Soler Riera (09:13:17) (in thread): > I think I already commited my Final Application. Will I get a confirmation by email or something?

Ameenat Oloko (09:14:54) (in thread): > I filled it in the middle of the contribution phase when you posted it; should I fill it in again?

Svetlana Ugarcina Perovic (09:16:19) (in thread): > No, Thanks!

Adeshile Oluwatosin (09:16:28) (in thread): > No youwouldn’tThat’sfine that way

Ameenat Oloko (09:16:28) (in thread): > No, Idon’tthink so.

Joy (09:24:35) (in thread): > Thank you@Aiysha shahid, we did in Fig 2D, it Captured all the taxa.

Precious Chijioke (09:29:43): > Hello everyone, please in place of Bacteroidetes can I useBacteroidia. In NCBI, The heterotypic synonym ofBacteroidiais Bacteroidetes while the NCBI BLAST name isCFB group bacteria, rank is class.**** ****Also, the equivalent name ofBacteroidotais Bacteroidetes with NCBI BLAST name asCFB group bacteria, rank is phylum. Which one is the correct one to use for “Bacteroidetes” or should I enter the taxa Bacteroidetes as it appears. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms. - Attachment (ncbi.nlm.nih.gov): Attachment > THE NCBI Taxonomy database allows browsing of the taxonomy tree, which contains a classification of organisms.

Mildred Anashie (09:32:42) (in thread): > Hi@Precious ChijiokeI think it depends on what the paper reported, if the paper reported it as class then you enter Bacteroidia but if it was reported as phylum then you enter Bacteroidota

Precious Chijioke (09:34:49) (in thread): > @Mildred Anashieit’s not reported as either class or phylum in the paper. It is recorded as only Bacteroidetes.

Anne-Marie Sharp (09:35:42) (in thread): > Hello@Precious Chijiokeyou can share the article and let us know the table/figure you are trying to curate the Bacteroidetes from, let us confirm with you

Anne-Marie Sharp (09:36:36) (in thread): > Well done@Joy@Vanisha Gargwe’ll review

Precious Chijioke (09:39:20) (in thread): > This is the article:https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2022.956438/fullCheck under “The synbiotics changed gut microbial composition in mice section”. Please ignore the figure and look at: MP administration upregulated Actinobacteria, Patescibacteria, and Firmicutes in constipated mice, and down-regulated Bacteroidetes. The proportion of Verrucomicrobia and Bacteroidetes increased in the P group compared with the model group, while Firmicutes decreased. A significant increase in Actinobacteria was observed in S and MPP groups. - Attachment (Frontiers): Frontiers | Alleviating effects of gut micro-ecologically regulatory treatments on mice with constipation > Treatments targeted for gut microbial regulation are newly developed strategies in constipation management. In this study, the alleviating effects of gut mic…

Anne-Marie Sharp (09:49:48) (in thread): > Okay, the other taxa mentioned with Bacteroidetes are all phylum, so it should be phylum too - Bacteroidota

Precious Chijioke (09:50:32) (in thread): > Alright, thank you@Anne-Marie Sharp

Anne-Marie Sharp (09:52:11) (in thread): > You’re welcome@Precious Chijiokethis should confirm it: ‘Alterations in the fecal microbiome were detected in constipated control mice, including the decreased Actinobacteria and Patescibacteria as well as the raised Bacteroidetes at the phylum level, suggesting gut microbial alterations due to loperamide treatment’

Mildred Anashie (09:52:19) (in thread): > Are you curating from Fig 3?

Mildred Anashie (09:54:07) (in thread): > If that is it, then it should be Phylum > > AlthoughI don’timmediately see how figure 3 can be curated but the text you shared seems to be leading to something that can be curated@Precious Chijioke

Precious Chijioke (09:56:38) (in thread): > @Mildred Anashieno I am not curating Fig 3 but Fig. 5 is not giving a full picture of the significant increase/decrease as seen in the text. So the signature source should be traced Within-text result of “The synbiotics changed gut microbial composition in mice” section”.

Antonia Beatriz Soler Riera (10:01:32) (in thread): > Hello@Svetlana Ugarcina PerovicI just filled the survey. Thank you for all the support.

Mildred Anashie (10:09:00) (in thread): > Okay then@Precious ChijiokeWell done

Adeshile Oluwatosin (10:35:02) (in thread): > Hi@Precious ChijiokeFigure 5 itself is not curatable > Ican’tsee any significant taxa stated in the figure

Precious Chijioke (10:40:47) (in thread): > @Adeshile OluwatosinFigure 5 is the only figure that is curatable in the study. While it’s a bit difficult to denote the increase and decrease taxa from the image. Read through the text, you’ll see the increase and decrease taxa. Figure 6 is not curatable because we don’t curate correlation analysis.

Aiysha shahid (11:03:41): > Hi Everyone!:tulip:I would appreciate a peer review on this-https://bugsigdb.org/36651357, Paper link-https://onlinelibrary.wiley.com/doi/10.1111/ene.15679, Supplementary doc is attached below. - Attachment (BugSigDB): The gut microbiome in intravenous immunoglobulin-treated chronic inflammatory demyelinating polyneuropathy - BugSigDB > BACKGROUND AND PURPOSE: The gut microbiome is involved in autoimmunity.Data on its composition in chronic inflammatory demyelinating polyneuropathy (CIDP), the most common chronic autoimmune disorder of peripheral nerves, are currently lacking. - File (Word Document): ene15679-sup-0001-tables1.docx

Adeshile Oluwatosin (11:28:40) (in thread): > Alright, well done

Mildred Anashie (11:31:33) (in thread): > Okay@Aiysha shahidWell done

Adeshile Oluwatosin (11:32:29) (in thread): > I explained in a previous discussion why a similar figure is notcuratable. In cases like this, there should be asterisk stating which taxa is significant across the comparison where the colours would dictate which is increased/decreasedI can’t see anything significant in figure 5

Adeshile Oluwatosin (11:35:09) (in thread): > Even the text is not vividly telling me which taxa is significant. It could be increased/decreased and over the threshold > How do we know ifit’sover or below the significant threshold if there are no clear p/q values or stated significant taxa within text

Mildred Anashie (11:36:10) (in thread): > I agree with@Adeshile OluwatosinI do not see statistical significance in Fig 5, same as the text

Precious Chijioke (11:42:06) (in thread): > @Adeshile Oluwatosindoes it mean that no figure is curatable in the study?

Adeshile Oluwatosin (11:59:23) (in thread): > Yes,there’sno curatable figure in the study

Anne-Marie Sharp (13:13:24) (in thread): > Hello@Aiysha shahidwell done with your curation. We’ll review

Precious Orakwe (13:22:57) (in thread): > Well done@Aiysha shahid

Precious Chijioke (13:46:01) (in thread): > Alright@Adeshile OluwatosinThank you > I’ll wait for a mentor’s review on the study and know what should be done if a study is not curatable.

Anne-Marie Sharp (13:48:39) (in thread): > @Precious ChijiokeI agree with@Adeshile Oluwatosin@Mildred Anashieand since the study is not curatable you can mention it in the GitHub issue and whenit’sconfirmed, you can request for another.

Precious Chijioke (13:49:43) (in thread): > Noted@Anne-Marie Sharp

Adeshile Oluwatosin (13:50:11) (in thread): > If you have not submitted for review. > Tag Svetlana and mention that you cannot find any curatable figure/table in the article

Adeshile Oluwatosin (13:50:35) (in thread): > If you have submitted, you’d need to await response from a mentor

Anne-Marie Sharp (14:39:07) (in thread): > 1)Figure 2A, 3B are not curatable > 2)If Experiment6 is Late-Stage-F vs Late-Stage-T then I think Signature2 should have just Lactobacillales > 3)Please help explain how you curated the matchstick plots (eg Fig 4A), I observed that you didn’t curate all the enriched taxa as increased. > 4) I’m suggesting you confirm the curation of ‘uncultured’ during office hour

Aiysha shahid (15:16:09) (in thread): > It’s done@Oriade Adeola, I have submitted. Tagged you as well on github.

UBNSEMS3S (15:34:02) (in thread): > @Svetlana Ugarcina PerovicAgreed. I asked the developers to not make any major updates during the Outreachy application period but I will put in an issue asking them to figure out a solution.

Joy (15:35:48) (in thread): > Thank you@Anne-Marie Sharpfor your feedback, I’ll effect the changes.

Ameenat Oloko (15:37:28) (in thread): > Thank you,<@UBNSEMS3S>. I already started working on the link@Svetlana Ugarcina Perovicshared, though.https://bugsigdb.org/10.3389/fevo.2022.742369 - Attachment (BugSigDB): Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese - BugSigDB > Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology.For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness.

Anne-Marie Sharp (15:51:10) (in thread): > @Aiysha shahid1)Use Taxonomy ID: 39488 for Eubacterium hallii group and Taxonomy ID: 33039 for Ruminococcus torques group > 2)Both Peptostreptococcales and Tissierellales are separated as 2 different orders on NCBI so you may have to curate them as separate orders.

Adeshile Oluwatosin (15:52:55) (in thread): > No,it’snot meant to be seperatedIt’sto be curated as seen

Anne-Marie Sharp (15:56:24) (in thread): > @Adeshile Oluwatosinnoted:ok_hand:

Montana-D (16:02:04) (in thread): > Well done on your curation@Aiysha shahid

Montana-D (16:06:32): > Hi everyone,@Precious Orakweand I just finished curatingthis studyand would appreciate a peer review - Attachment (BugSigDB): Associations of alcohol with the human gut microbiome and prospective health outcomes in the FINRISK 2002 cohort - BugSigDB > BACKGROUND AND AIMS: Alcohol remains a global risk factor for non-communicable diseases with the gut microbiome emerging as a novel elucidator. - File (PDF): s00394-025-03668-z.pdf - File (Excel Spreadsheet): 394_2025_3668_MOESM1_ESM.xlsx

Anne-Marie Sharp (16:09:44) (in thread): > Nice work with so many taxa:raised_hands:well done@Montana-D@Precious Orakwewe’ll review

UBNSEMS3S (16:11:51) (in thread): > @Ameenat OlokoThat’s good. Any fix that the developer implements won’t be ready for a few weeks most likely.

Eseoghene Cynthia Princewill-Ukot (16:14:13) (in thread): > I filled this earlier@Svetlana Ugarcina Perovic

Mildred Anashie (16:26:42) (in thread): > Hi@Joy@Vanisha Garg > * Figure 2a and 3b is not curatable as mentioned > * Figure 2D should be curated alongside Supp fig 1A. See this “We next determined differential genus and species abundance between groups (Fig. 2D; Supplement Fig. 1A).” > * You should have only increased taxas from Early stage T vs Early stage F in figure 4a while the late stage T vs Late stage F should have only 1 decreased taxa (as stated by@Anne-Marie Sharp) > * The statistical test for figure 6D is spearman correlation, for the late stage group (late stage T vs Late stage F) you should have only 4 increased taxas as stated in the article which are “Genus Bartonella, Snodgrassella, Bombella, and Commensalibacter were enriched in the late-stage group” while for the early stage group* (Early stage T vs Early stage F) you would have 6 increased taxa”Genus Bacteroidales, F082.5, Succiniclasticum, Rikenellaceae, and taxa Prevotella ruminicola and Bacteroides caecimuris were increased in early-stage endometriosis” > In total I see only 5 experiments and the statistical test for the match ratio plots is still very unclear to me but I’d read through again

Ameenat Oloko (16:36:16) (in thread): > Oh, thanks for clarifying that! Initially, I had plans to return to this thread after I’ve completed the curations to ask if I could submit for review on GitHub. Once again, thank you,@Svetlana Ugarcina Perovicand<@UBNSEMS3S>, for your assistance.

Mildred Anashie (16:55:55) (in thread): > Everything seems to be in order once you use the NCBI Id for last two taxa in the second experiment > Well done@Aiysha shahid

Mildred Anashie (17:20:50) (in thread): > Hi@Montana-D@Precious OrakweWell done, this looks like a lot of work > I noticed you still have a lot of unresolved taxas that can be resolved on NCBI > > I’m a bit confused, I see 2 experiments curated from Supp Table 1 whereas only one experiment is reported there. Also I believe this paper has only one experiment as Table 2 and Supp Table 1 should have been curated together. See an excerpt“The top 10 species by the absolute value of their estimate in model 2 are displayed in Table 2. For a comprehensive listing of all significant species-level results in the fully adjusted model please see Supplemental Table 1.”

Montana-D (17:56:18) (in thread): > Thank you@Mildred AnashieSo to mean, we experiment 1 is supposed to be a combination and not separated? > > Also my co-contributor and I got into a disagreement about whether or not all significant taxa In supplementary table 1 are to be curated or not > Her basis of all not being curatable was on the excerpt “Differential abundance analysis found significant associa- tions for 344 species that displayed a consistent association regardless of model configuration (q<0.05). Of these, 248 associations were positive and 96 negative. Notable taxa among the species that were negatively associated were multiple putatively beneficial species from the Lactobacillus (n=6) and Bifidobacterium (n=6) genera, and the spe- cies Akkermansia muciniphila. The positively associated group of bacterial taxa was dominated by members of the Gram-negative genera Bacteroides (n=19) and Prevotella (n=16). The top 10 species by the absolute value of their estimate in model 2 are displayed in Table 2. For a comprehensive listing of all significant species-level results in the fully adjusted model please see Supplemental Table 1.” > What’s your take on that please > Cuz I thought all significant bacteria have to be curated

Montana-D (17:57:16) (in thread): > Please how do we go about resolving those taxa, we couldn’t find on NCBI

Mildred Anashie (18:19:23) (in thread): > I also think the taxas that appear this way with the “Nanogingivalis sp010014525” you should curate as “Nanogingivalis sp.” because the number seems to be accession number or something like that. > > I don’t really see what is pointing to not curating all significant taxas, the only thing I noticed is repetition of some taxas in table S1 so you’d curate only once and leave out the others@Montana-D

Anne-Marie Sharp (18:28:07) (in thread): > @Montana-DI also believe all significantly differential taxa should be curated.Those 6 were notable but they are all significant

Juliana Kentomahun Mautin (18:28:53): > Hello everyone, is anyone experiencing this on BugsigDB site at the moment? - File (PNG): image.png

Montana-D (18:29:40) (in thread): > It does so from time to time > Just be patient, it’ll be restored

Anne-Marie Sharp (18:29:45) (in thread): > Hello@Juliana Kentomahun Mautinyes, same here.Let’sgive it a while

Juliana Kentomahun Mautin (18:33:21) (in thread): > Ok… Thank you@Anne-Marie Sharpand@Montana-D

Anne-Marie Sharp (18:35:14) (in thread): > You’rewelcome

Precious Chijioke (18:42:07) (in thread): > @Svetlana Ugarcina PerovicI filled it when you shared the form in the middle of the contribution.

Mildred Anashie (18:45:09) (in thread): > Yea@Juliana Kentomahun MautinI’veexperienced this a couple of times but after a while it gets restored, just be patient as advised already:blush:

Adeshile Oluwatosin (19:02:31) (in thread): > The site goes down a few times > Check back in few minutes > You just need patience

Juliana Kentomahun Mautin (19:22:08) (in thread): > Okay > Thank y’all, I would just be patient till it comes up.

nithya (21:00:26) (in thread): > Hi does supplementary table gives information about increases or decreases wrt disease conditions

nithya (21:02:54) (in thread): > I see association positive and negative. We curate increase or decrease in relative abundance this looks like correlation so we do not curate correlation outputs

2025-04-16

Svetlana Ugarcina Perovic (02:20:57) (in thread): > Reminder: Today we discuss microbiome and citizen science > > There is still time to register for #MVIF 38, visithttps://cassyni.com/s/mvif-38See you soon! - Attachment (Cassyni): MVIF 38 - Special event on Microbiome and Citizen Science - Schedule of sessions · Cassyni > Microbiome Virtual International Forum (MVIF) is a recurring bite-sized alternative to multi-day microbiome conferences: Regular short-format (~3 hours) conferences that provide all the key elements of a traditional conference. > > Forum n. 38 is a Special Pacific-first event, with live panel talks starting 15th April 2025, 10 am Tokyo time (see what time it is where you are here and add to your calendar here). > > For Atlantic time zones, recorded panel talks with live hosting and discussion will start on 16th April at 9 am New York time (see what time and date it is where you are here and add to your calendar here). > > MVIF is a non-profit association registered in Italy > If you’d like to support MVIF, you can donate to our crowdfunding campaign . > > Thanks to our co-organizing non-commercial partners the Seerave Foundation and CUNY Graduate School of Public Health & Health Policy for their support.

Eseoghene Cynthia Princewill-Ukot (02:34:03): > Good morning@Svetlana Ugarcina Perovic! What should I fill in for Affiliation/Organization? - File (JPEG): Screenshot_20250416-073153.jpg

Svetlana Ugarcina Perovic (02:35:33) (in thread): > You can put Outreachy.

Eseoghene Cynthia Princewill-Ukot (02:39:35): > @Svetlana Ugarcina PerovicThere are lists of organizations when you click on it and Outreachy is not an option. > But there’s ‘I can’t find my Organization’. Can I go with that?

Mildred Anashie (02:40:25) (in thread): > Hi@nithyaIt does show increase and decrease, the Log fold change column (lfc)

Aiysha shahid (03:27:46) (in thread): > Hi, thanks!@Anne-Marie SharpI had seen it earlier, but I thought thatRuminococcus torquesandAnaerobutyricum halliiare ranked as species, while the ones mentioned in the paper are at the genus level. So I was wondering—would that create any difference?

Precious Chijioke (04:00:17) (in thread): > Type Outreachy and continue your registration it’ll go through. > In the organization session there’s Other in bracket so Outreachy falls under (Other).

Eseoghene Cynthia Princewill-Ukot (04:06:08) (in thread): > Yes, I have registered already. Thanks.

Anne-Marie Sharp (04:22:18) (in thread): > You’rewelcome@Aiysha shahidIt’sbest to curate as it is in the article but the guidance I was given by a mentor about this type of situation is that there are similar instances for example: where a particular species in NCBI is assigned the genus rank in an article. Escherichia/Shigella sp. as an example; we curate the way it’s stated in NCBI not minding if some article assigns it to the genus rank

Anne-Marie Sharp (04:23:51) (in thread): > You could also try searching for that taxa on Bugsigdb main page, to see how it has been curated from past curations/articles.

Montana-D (04:26:25) (in thread): > Good morning everyone > > Please@Mildred Anashie, those other species with additional numerical figures indicate different species types which maybe have not been assigned names yet, so you mean I forget about and sum all to a single species name? For example we could have “Prevotella sp000758925 and Prevotella sp004792655” > I should curate justPrevotella sp ?

Mildred Anashie (04:26:57) (in thread): > Also@Aiysha shahidwhen curating you can use the discussion page to search taxas that have already been resolvedHere’sthe linkhttps://bugsigdb.org/Category_talk:Pages_with_missing_NCBI_ID - Attachment (BugSigDB): Category talk:Pages with missing NCBI ID > Use this space to make notes about pages where you tried but were unable to resolve missing NCBI IDs from Category:Pages_with_missing_NCBI_ID. If you succeed in…

Aiysha shahid (04:28:17) (in thread): > Thanks a lot@Mildred Anashieand@Anne-Marie Sharp:hugging_face:

Adeshile Oluwatosin (04:51:51) (in thread): > Good morning to add to the discussion, you cannot make changes to a reviewed article with a taxa with probably a new name or updated details (asin itlonger has a missing NCBI ID) unless approved by a mentor.

Ameenat Oloko (08:39:21) (in thread): > The conference has begun, everyone. Please, join in.

Joy (08:45:09) (in thread): > Joined

Oriade Adeola (09:55:24) (in thread): > Thank you so much@Aiysha shahidGod bless you. i really do appreciate you. Thank you. I wish you Goodluck in your application

nithya (09:59:04) (in thread): > @Mildred AnashieOk. I downloaded it in excel where i see 3 supplement tables. I replied seeing supplement 3. Now again checked supplement one. thank you.

Mildred Anashie (10:27:56) (in thread): > It’stotally fine@nithyaIt was table 1 we were talking about

nithya (10:40:08) (in thread): > Yes I understood now. Thank you@Mildred Anashie

Ameenat Oloko (13:00:48) (in thread): > Good day,@Svetlana Ugarcina Perovicand<@UBNSEMS3S>. Please, what can I do in this case where the “abundance in group 1” is incomplete? I mean it’s only showing “Increased abundance in” without including the group 1 name.Link - Attachment (BugSigDB): Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese - BugSigDB > Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology.For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness. - File (PNG): Screenshot 2025-04-16 175859.png

Juliana Kentomahun Mautin (13:05:02): > Hello everyone, now that the contribution phase has ended, will there still be an office hour tomorrow?

Ameenat Oloko (13:06:49) (in thread): > Good evening,@Juliana Kentomahun Mautin. They’ll likely communicate that to us.

Adeshile Oluwatosin (13:07:12) (in thread): > Yes, the office hour will hold > Same zoom link@Juliana Kentomahun Mautin

Adeshile Oluwatosin (13:07:50): > Good evening everyone > Please leave a peer reviewhttps://bugsigdb.org/40004140https://pmc.ncbi.nlm.nih.gov/articles/PMC11855768/ - Attachment (BugSigDB): Correlations Between Amelioration of Rotenone-Induced Parkinson’s Symptoms by Amomum tsaoko Flavonoids and Gut Microbiota in Mice - BugSigDB > Parkinson’s disease (PD) is the second most common neurodegenerative disease, but the existing therapeutic drugs for PD have limitations; thus, there is an urgent need to discover new methods of prevention and treatment. - Attachment (PubMed Central (PMC)): Correlations Between Amelioration of Rotenone-Induced Parkinson’s Symptoms by Amomum tsaoko Flavonoids and Gut Microbiota in Mice > Parkinson’s disease (PD) is the second most common neurodegenerative disease, but the existing therapeutic drugs for PD have limitations; thus, there is an urgent need to discover new methods of prevention and treatment. Amomum tsaoko Crevost et …

Svetlana Ugarcina Perovic (13:08:44) (in thread): > We always have weekly team meetings on Thursdays and you are always welcome to join.

Juliana Kentomahun Mautin (13:44:52) (in thread): > Thank you@Svetlana Ugarcina Perovic@Adeshile Oluwatosinand@Ameenat Oloko

Juliana Kentomahun Mautin (13:46:52) (in thread): > Welldone@Adeshile Oluwatosin, let me go through it.

Montana-D (14:18:16) (in thread): > Thank you all so much for your assistance and clarifications

Ameenat Oloko (15:28:37): > Good evening, everyone. I’d appreciate a peer review of this study. Thank you.ArticleStudy - Attachment (Frontiers): Frontiers | Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese > Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology. For example, habitat use can affect microbiome dive… - Attachment (BugSigDB): Relationships Between Migration and Microbiome Composition and Diversity in Urban Canada Geese - BugSigDB > Microbiome analysis presents an opportunity to understand how urban environments affect avian physiology.For example, habitat use can affect microbiome diversity and composition, and hosts with more diverse gut microbiota are thought to be more resistant to pathogens and have increased fitness.

Anne-Marie Sharp (15:45:14) (in thread): > Well done@Adeshile Oluwatosinwe’ll review

Ameenat Oloko (16:06:47) (in thread): > Well done@Adeshile Oluwatosinand@Mildred Anashie. > * I realise that you didn’t add the data transformation for experiment 4 (ANOVA) and experiment 6 (Spearman correlation) > * For experiment 10, what if you rewrite the group names “Decreased gastrointestinal transit rate” and “Increased gastrointestinal transit rate”? > * Same for experiment 7: Decreased Fecal Number(FN) and Increased Fecal Number (FN) > * Experiment 6 too: Increased Fecal Weight (FW) and Decreased Fecal Weight (FW)

Mildred Anashie (16:53:06) (in thread): > Hi@Ameenat OlokoThank you > > So for the data transformationit’sactually recorded but not reflecting becauseit’svisible in the previous experiments > > What do you think the names should be re written to?

Ameenat Oloko (16:54:00) (in thread): > Oh, I thought as much,@Mildred Anashie. I wrote the names in the bullet points.

Mildred Anashie (16:56:58) (in thread): > Okay okay > > I see it now, butI’mthinkingit’sbetter that way:thinking_face:

Ameenat Oloko (16:58:44) (in thread): > You mean how it is written in the curated study, right?

Mildred Anashie (16:59:32) (in thread): > Yes

Ameenat Oloko (17:00:47) (in thread): > Err…maybe. At least we understand the ‘message’.That’sthe most important!

Adeshile Oluwatosin (17:03:02): > Hello everyone > Kindly give a review to this study curationhttps://bugsigdb.org/34225483https://pmc.ncbi.nlm.nih.gov/articles/PMC8406289/

Adeshile Oluwatosin (17:04:57) (in thread): > ANOVA was stated to be used for comparison among three groups. No other test was stated to be used for differential analysisasides Lefse clearly for experiment 4 and 5So I’m thinking shouldANOVA be recorded as the test used for comparison among two groups in this case.

Adeshile Oluwatosin (17:06:57) (in thread): > Have a look at the sample sizes, thank you

Mildred Anashie (17:09:46) (in thread): > I think the test is okay > > The comparison in 4 and 5 is among three groups but between two groups if what I typed makessense:smile:@Adeshile Oluwatosin

Anne-Marie Sharp (18:06:02) (in thread): > Nice curation@Adeshile Oluwatosin@Mildred Anashie1 )I also think the statistical test is okay > 2)There is a typo error in some experiments, Amomum is written as Amonum > 3)Sample sizes for the major groups should be 12 not 4 : ‘A total of 48….mice (20–22 g) were purchased, the mice were randomly divided intofour groups (******n********** = 12)****, namely the normal chow diet (NCD)group, the rotenone gavage (ROT) group, the positive control Madopar (MDR) group, and theAmomum tsaokoflavonoid (ATF)group, with four mice in each cage’ > #Each group has 12mice, that is..1group of mice eg. ATF was put in (3)cages of 4mice each, but each group still has a total of 12mice.

Anne-Marie Sharp (18:37:14) (in thread): > Well done with your curation@Ameenat Oloko1)Firmicutes should also be curated as a phylum from Table 4 > 2)**** ****I noticed in Signature1 the abundance description isn’t complete,**** Abundance in Group 1:****increased abundance in …..

Anne-Marie Sharp (20:01:16): > Hello everyone. Please, I would appreciate a peer review of this study:https://bugsigdb.org/33185912Thank you so much. The article pdf is attached below. - File (PDF): 10.1111@ene.14644.pdf

Anne-Marie Sharp (20:14:31) (in thread): > Hello@Precious Orakwe@Montana-Dplease can we still give a peer review on this?

Ameenat Oloko (21:56:59) (in thread): > Thank you@Anne-Marie Sharp. I thought to add Firmicutes too, but I didn’t based on this comment:https://community-bioc.slack.com/archives/C04RATV9VCY/p1698177815616049?thread_ts=1698080347.724249&channel=C04RATV9VCY&message_ts=1698177815.616049Forthe second point, I think it’s a glitch ’cause I tried to refresh and edit it several times, it still didn’t change:pensive:. I’ve also informed Chloe and Svetlana but they’re yet to reply. - Attachment: Attachment > Please only curate the lowest taxonomic rank. That is to say in this case for the first row do not curate Bacteroidetes, bacteroidia, or bacteroidales–instead curate S24-7 which is a family better known as muribaculaceae (https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=2005473&lvl=3&lin=f&keep=1&srchmode=1&unlock)

Montana-D (23:42:42) (in thread): > Sure you can

2025-04-17

Montana-D (00:05:39) (in thread): > Hi@Ameenat OlokoWell done on your curation > 1. I noticed you the curation in experiment 1 was gotten from text and not the table, you could as well add the text as source, what do you think? > 2. Also, table 4 shows much more significant taxa that the 4 you recorded, I guess it was stated that the significance threshold was q<0.05, and all fall into that category, do you agree with this?

Montana-D (00:07:27) (in thread): > Good morning@Adeshile Oluwatosin@Mildred AnashieWell done on your
> I agree to@Anne-Marie Sharp’s observation, it should be 12 per group

Adeshile Oluwatosin (00:49:33) (in thread): > Thank you everyone, yeah you are right > 12 per group.

Montana-D (01:05:55) (in thread): > Good job in your curation@Adeshile Oluwatosin. > > From the figures description, I noticed, it was stated 3 or 5 mice in each group, so your group 0 and 1 should have same number, either 3 or 5

Montana-D (01:51:29) (in thread): > Well done on your curation > You did great, I thought you missed out one of the taxa in fig. 1A, after making a count of 41 in the article and found only 40 in your article. I only discovered later that there’s an updated taxa, thereby making a repetition > > Well done@Anne-Marie SharpEverything looks for to me

Ameenat Oloko (01:56:14) (in thread): > Hi,@Montana-D. Thank you. > 1. The source can also be the table as it’s curatable and straightforward. > 2. Yea. Thanks.

Ameenat Oloko (01:59:35) (in thread): > If you look closely,you’ll see that they are the same organisms as those under Phylum Firmicutes at the top of the table, except for Clostridium.

Ameenat Oloko (02:04:40): > Good morning,everyone.Please, does anyone know what I can do about the incomplete “abundance in group 1”, as shown in the image below. I’ve refreshed and edited the signatures multiple times,butit’sstill the same. Thank you. > > Cc:@Svetlana Ugarcina Perovicand<@UBNSEMS3S> - File (PNG): IMG_7049

Adeshile Oluwatosin (02:23:41) (in thread): > From materials and methods: > “After acclimation for 1 week, mice were divided into four groups (n = 6): two groups were fed the control diet (CE-2; CLEA Japan Inc., Tokyo, Japan), and two groups were fed HFD (HFD32; CLEA Japan, Inc.) for 12 weeks (34).”, then IBATIi and HFD + iBATi” > > This tells me control diet : 2, HFD : 2, IBATi: 1 and HFD + IBATi : 1

Precious Orakwe (02:27:10) (in thread): > Well done@Adeshile Oluwatosin

Precious Orakwe (02:29:52): > Good morning everyone, trust we all are doing great. please I would love a pair review on my study, every correction is appreciated.https://bugsigdb.org/38057705thank you. - Attachment (BugSigDB): Multi-omics analysis of fecal microbiota transplantation’s impact on functional constipation and comorbid depression and anxiety - BugSigDB > BACKGROUND: Depression and anxiety are common comorbid diseases of constipation.Fecal microbiota transplantation (FMT) significantly relieves gastrointestinal-related symptoms, but its impact on psychiatric symptoms remains uncharted.

Precious Orakwe (02:32:55) (in thread): > Try clicking on the edit button change it to incomplete and change it back again to complete and save, than if it still don’t come up, wait for a while, it is probably network problem.

Precious Orakwe (02:35:43) (in thread): > Great job@Anne-Marie Sharp

Adeshile Oluwatosin (02:49:04) (in thread): > But from figure S1B I can see 3 rats represented in eachgroups

Ameenat Oloko (02:55:36) (in thread): > Thank you,@Precious Chijioke. I’ve done that countless times:pensive:

Anne-Marie Sharp (02:57:30) (in thread): > You’re welcome@Ameenat OlokoI understand your concerns with the Firmicutes, that should be when it is listed with other lower taxa level as they did in ‘Genera level’ . But in this case, it was also listed as a phylum on its own under ‘Phylum level’ before they went on tolist ‘Genera level’ and reading through the article you’ll notice Firmicutes itself as a phylum is mentioned severally as being significant.

Adeshile Oluwatosin (02:58:40) (in thread): > I will use the pictorial diagram to re curate the sample sizes

Anne-Marie Sharp (03:09:19) (in thread): > I think we should use the 3rats represented in each groups in the diagrams:thumbsup:

Adeshile Oluwatosin (03:10:23) (in thread): > Definitely, just saw > That’s the best approach

Anne-Marie Sharp (03:12:20) (in thread): > Good morning@Ameenat Olokolike you said earlier,it appears to be a glitch:thinking_face:apart from editing the signatures, did you try editing the experiment itself?

Anne-Marie Sharp (03:16:09) (in thread): > Thank you@Montana-Dyes the famous Ruminococcaceae/Oscillospiraceae:smile::ok_hand:

Anne-Marie Sharp (03:16:38) (in thread): > Thank you@Precious Orakwe

Precious Chijioke (03:22:00) (in thread): > Good Morning@Ameenat Oloko, like@Anne-Marie Sharpsaid, try editing the experiment to incomplete and change it back to complete. Refresh the page when you’re done it’ll reflect. The problem is usually caused by a bug.

Precious Chijioke (03:25:54) (in thread): > Well done on your curation@Anne-Marie SharpI agree with@Montana-D

Ameenat Oloko (03:27:27) (in thread): > Yea. Thank you so much,@Anne-Marie Sharp.

Ameenat Oloko (03:28:32) (in thread): > Thank you,@Precious Chijiokeand@Anne-Marie Sharp. Yes, I edited the experiment and changed it from ‘complete to incomplete’ several times (till I got tired), but nothing changed.

Adeshile Oluwatosin (03:41:17): > Good morning everyone > > Kindly leave a reviewhttps://bugsigdb.org/40008452https://pmc.ncbi.nlm.nih.gov/articles/PMC11866968/#f0010

Aiysha shahid (03:47:09) (in thread): > Well Done! will go through it.

Adeshile Oluwatosin (03:51:48) (in thread): > Well done@Precious Orakwe

Ameenat Oloko (03:53:09) (in thread): > Well done@Anne-Marie Sharp. > Just one thing to correct. The data transformation for Linear regression isrelative abundance. It’s in the curation policy.https://community-bioc.slack.com/archives/C04RATV9VCY/p1699808143495129?thread_ts=1699704087.950319&channel=C04RATV9VCY&message_ts=1699808143.495129 - Attachment: Attachment > Oh wow > Could you correct this list please? @Levi Waldron > > ANCOM: centered log ratio > > Deseq2 -raw counts > > Kruskall Wallis: relative abundances > > LeFSe: relative abundances > > Linear models: raw counts, relative abundances, arcsine square root (rarely). > > Linear regression: relative abundances > > MaAsLin2: arscine square root > > Mann Whitney U: relative abundance > > Negative binomial: raw counts > > Poisson: raw counts > > T-test: relative abundance

Mildred Anashie (03:54:00) (in thread): > Hi@Adeshile OluwatosinWell done, following the discussion here I agree with using 3 for the sample size > If it was stated in the figure then that’s what you should follow

Ndukauba Oluchi (03:54:26): > Hello, Goodmorning everyone. > Please I do have a question. > I’m currently curating a study and figure 6 in this paper is curatable, But I don’t know how to curate it. How do i curate it? > Cc:<@UBNSEMS3S>Link:https://www.mdpi.com/1422-0067/26/3/1236 - Attachment (MDPI): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. To explore how these structural differences impact constipation intervention, a 14-day study was conducted on loperamide-induced constipated mice using five dietary fibers: soluble dietary fiber from steamed sweet potato (SDF-S), oat β-glucan (OB), polydextrose (PD), arabinogalactan (AG), and inulin (IN). The results showed that four fibers, excluding PD, significantly improved gastrointestinal (GI) transit rate (p < 0.05), although PD had the highest fecal moisture, it was significantly different from the lowest IN (p < 0.05). AG and IN resulted in higher 6 h fecal weights compared to other fibers. SDF-S and OB were more effective in modulating serum levels of gastrointestinal hormones. The different monosaccharide compositions and glycosidic bonds of these fibers led to distinct changes in gut microbiota composition and SCFA profiles. Galactose and arabinose in AG were linked to increased abundance of Lachnospiraceae_UCG-006, Bacteroides, and Odoribacter, promoting butyrate fermentation, which is positively correlated with GI transit rate. Glucose in SDF-S, OB, and PD favored acetate fermentation positively correlated with fecal moisture. Fructose in IN encouraged the proliferation of Muribaculaceae_unclassified and Ruminococcus, associated with butyrate fermentation and increased 6 h stool weight, respectively. The β-glycosidic bonds in OB may lead to high butyrate production through the selective proliferation of Lachnospiraceae_unclassified. Minor components like fucose, rhamnose, and ribose were positively correlated with the abundance of Oscillospiraceae_unclassified, Anaerotignum, and Lachnospiraceae_unclassified. In conclusion, the unique monosaccharide compositions and glycosidic bond differences in dietary fibers selectively promote the proliferation of fiber-degrading and butyrate-producing bacteria, resulting in varied effects on constipation relief.

Adeshile Oluwatosin (03:54:47) (in thread): > Thank you, I changed it intially to 3

Montana-D (04:03:05) (in thread): > Good job on your curation:raised_hands:

Precious Chijioke (04:07:12): > Good Morning Everyone, I am curating this paper and would like to confirm the experimental condition and the number of experiments in the study:https://www.cell.com/cell-reports/fulltext/S2211-1247(24)00281-X?_returnURL=https%3[…]vier.com%2Fretrieve%2Fpii%2FS221112472400281X%3Fshowall%3Dtrue

Ameenat Oloko (04:07:45) (in thread): > Also, it was only 12 confounders that were explicitly stated in the article.I can see that you have more than 12 confounders in your curation.

Mildred Anashie (04:08:47) (in thread): > Hi@Ndukauba OluchiSo I have gone through the article and figure 6 does show significance but because of some of the parameters tested, I’m thinking you might have to leave it out but lets wait for other responses (Just incase there’s something I missed). But fig4 looks curatable with up to 7 comparisons all against the MC group > Well done:clap:

Adeshile Oluwatosin (04:16:27) (in thread): > Hello@Ndukauba OluchiWell done:thumbsup:Figure 6 should not be curated, it contains some unrelated defeceationparameters not useful. Hence, leave it out. > > Focus on figure 4 as initially stated. You can read through the text within to clearly understand the comparison. > The supplementary material contains no vital details we need.

Adeshile Oluwatosin (04:17:41) (in thread): > Well done@Precious Chijioke

Precious Chijioke (04:25:55) (in thread): > Hello@Ndukauba OluchiI have gone through the study and I agree with what@Mildred Anashieand@Adeshile Oluwatosinsaid. You can also ask further questions during the office hours.

Mildred Anashie (04:27:45) (in thread): > Hi@Adeshile OluwatosinWell done,I’lllook through

Mildred Anashie (04:28:06) (in thread): > Okay@Precious OrakweWell done

Mildred Anashie (04:29:35) (in thread): > Hi@Anne-Marie SharpI’llgo through, well done

Ameenat Oloko (04:33:36) (in thread): > Well done,@Precious Orakwe. > * I think the statistical tests should be 2 (t-test and Wilcoxon) for experiment 1 based on this “Differences were determined using Student’s t-test if the data conformed to a normal distribution, otherwise, Wilcoxon rank-sum test was used..” > * The antibiotics exclusion was mentioned only once in the article andthat’s6 months.

Precious Chijioke (04:35:51) (in thread): > Thank you@Adeshile OluwatosinI know that Experiment 1 is in Figure 2K and 2M and the increased and decreased taxa. I want to confirm if it’s only one experiment ie Control vs ChAT+ or there are other experiments in the paper.

Anne-Marie Sharp (04:40:19) (in thread): > Thank you@Precious Chijioke@Mildred Anashie

Adeshile Oluwatosin (04:41:09) (in thread): > Fecal samples. > * Figure 2K (CHAT+); control CHAT+ vs Activated CHAT+ > * Figure 2M (TH+);controlTH+vs ActivatedTH+ > Cecal samples > * Figure S6 (chat+);control CHAT+ vs Activated CHAT+ > * FigureS7 (TH+);control TH+ vs Activated TH+ > So we have four seperate experiments between control and activated

Anne-Marie Sharp (04:41:15) (in thread): > Thank you@Ameenat OlokoI will correct the data transformation, it was actually Linear model used, not linear regression itself, but I’ve seen that it should relative abundance. All the confounders were listed in Table 2

Precious Chijioke (04:44:03) (in thread): > Alright, thank you@Adeshile OluwatosinFor Figure S6 and S7, the Supplemental information is not opening, I have downloaded it over and over and it keep saying file we can’t open this file. > Any idea on the experimental condition, I need confirmation to it.

Adeshile Oluwatosin (04:54:57) (in thread): > Can you ask Svetlana to kindly send the pdf on githubIalready closed the pdf:pleading_face:I’llneed to properly go through the study to figure out a condition. If youdon’tget a response on time from me > You can ask during today’s office hour > Well done

Precious Chijioke (04:56:32) (in thread): > Thank you@Adeshile Oluwatosin

Ameenat Oloko (04:57:00) (in thread): > Oh! Ifyou’rechanging it to linear model, you can leave it as raw counts,@Anne-Marie Sharp.https://community-bioc.slack.com/archives/C04RATV9VCY/p1697145085673689?thread_ts=1697141457.022309&channel=C04RATV9VCY&message_ts=1697145085.673689 - Attachment: Attachment > Data transformations are often dependent on the statistical test. This can be difficult to figure out so I recommend asking questions if you’re not sure but generally speaking: > > Raw counts -> poisson, negative binomial, linear models, DeSeq2 > > Relative abundances -> This is most common. Mann Whitney U, Kruskall Wallis, LeFSe, many others > > Centered log ratio -> Rare. ANCOM > > Arcsine square-root -> Rare. MaAsLin2 sometimes. Some linear models rarely.

Anne-Marie Sharp (04:57:07) (in thread): > Hello@Ndukauba Oluchiwell done with your curation. I also don’t think you should curate Fig. 6 because of the other parameters included.

Adeshile Oluwatosin (04:57:22) (in thread): > Figure S6 and S7 details are vital. Ensure you curate

Anne-Marie Sharp (05:00:53) (in thread): > Okay, sorry about that. You could bring it up during office hours then.

Ameenat Oloko (05:01:46) (in thread): > I already saw the remaining confounders. Thank you for directing me there:smile:.

Ndukauba Oluchi (05:09:17) (in thread): > wow! Thank you all for you inputs

Precious Orakwe (05:19:36) (in thread): > @Ameenat Olokosee this;Exclusion criteria were as follows: organic or neurological constipation; diagnosed with other mental diseases; pregnant or lactating women; diagnosed with IBD, malignant tumors, or gastrointestinal surgery; abnormal thyroid function; use of antidepressants, probiotics, prebiotics, and antibiotics within two weeks before the study

Anne-Marie Sharp (05:21:04) (in thread): > Good morning@Precious Chijiokewell done with your curation. I agree with the above. But also, Figures 2J & L should be curated along side Figures 2K & M. Curate J + K, & L + M.

Anne-Marie Sharp (05:24:01) (in thread): > Okay@Ameenat OlokoI rechecked & didn’t see any mention of raw counts, that’s why I put it as the relative abundances you suggested, which is also used as a data transformation for linear models. Please help me check again. thank you

Anne-Marie Sharp (05:25:45) (in thread): > And in Table 2 where I curated the linear model from, relative abundance was stated

Ameenat Oloko (05:26:50) (in thread): > From the first link I shared, written by Esther, it was stated that the types of data transformation that could be used for linear models are raw counts, relative abundances and arscine square roots. > Meanwhile Chloe, from the second link, said we could use raw counts.That’swhy I said you can leave it as raw counts.

Ameenat Oloko (05:28:19) (in thread): > Yea, I saw that in the table 2 description too. Let’s just leave it asrelative abundances.

Anne-Marie Sharp (05:30:17) (in thread): > Okay, thank you:raised_hands:

Ameenat Oloko (05:30:47) (in thread): > Oh! I didn’t see that while reading the article. Thank you for pointing me to that part,@Precious Orakwe. Please, add “e” to experiment 1, group 0 name. You wrote “befor” . You also omitted an “s” in experiment 3 for 6 months.

Precious Orakwe (05:49:50) (in thread): > Thank you

Precious Orakwe (06:17:47): > Good day@Svetlana Ugarcina Perovici was trying to do some NCBI Cleaning I found this study. In this “******Reduced incidence of Prevotella and other fermenters in intestinal microflora of autistic children******.” > I noticed some issues in the curation ofIncertae_Sedis_XII.Fusibacterfrom the study > 1. Incorrect source: In experiment 1 signature 2, the current source is listed asFigure S7, but the taxon appears inTable S7. > 2. Miscurated taxon: InExperiment 2, Signature 2,Incertae_Sedis_XII.Fusibacterwas: > > * Curated asIncertae_Sedis_XIIin one instance > * Curated asIncertae_Sedis_XIin another (likely in error) > * Repeatedtwicein the same signature > > 1. Taxonomic update: According to NCBI,Fusibacteris a valid genus (NCBI:218485) underFusibacteraceae. The prefix “Incertae Sedis XII” is outdated. > With your permission, I’d like to: > * Update the source toTable S7 > * Replace both instances withFusibacter (NCBI: 218485) > * Remove the duplicate entry in Signature 2 > Please let me know if I can go ahead with these corrections. Thank you.

Svetlana Ugarcina Perovic (06:24:19): > Reminder for our weekly team meeting:today at 9 AM EST athttps://us02web.zoom.us/j/2737200499Bring your SPECIFIC questions!We do not discuss if some Figure/Table is curatable or not.cc<@UBNSEMS3S>NOTE: You can check your time here:https://www.timeanddate.com/worldclock/converter.html?iso=20250417T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Mildred Anashie (06:27:40) (in thread): > Hi@Precious ChijiokeI agree with everything said, even though J and Ldoesn’tlook easily curatable I think it should not be left out > Well done again

Precious Chijioke (06:33:12) (in thread): > Tank you@Mildred Anashie

Anne-Marie Sharp (06:35:32) (in thread): > Well done with your curation:raised_hands:@Precious Orakwe1)Fig.2D & Table S1 should not be curated, I cant see any significance there > 2)In Exp.4 Group 1 definition should be Patients with Functional constipation and comorbid depression/anxiety after undergoing fecal microbiota transplantation (FMT).

Mildred Anashie (06:37:13) (in thread): > I realized I’velooked through this before and I think everything is good > Well done@Anne-Marie Sharp

Anne-Marie Sharp (06:37:56) (in thread): > :hugging_face:Yes thank you@Mildred AnashieI took time to effect the corrections you made earlier

Anne-Marie Sharp (07:02:13) (in thread): > 3)I also observed all the taxa were not curated from Table S2

Precious Orakwe (07:08:09) (in thread): > @Anne-Marie SharpPlease take a look at this; At the species level, the top 35 relative abundances were displayed in Fig. 2b and Table S1, showing***** that the microbial composition differed in the Fa and Fb groups. *****I curated Fig. 2d from the colour pattern, and Table S1 has no p-values, so I was confused, and I curated only Figure 2d

Precious Orakwe (07:30:11): > Good afternoon, please, I would appreciate a peer review on this study; every correction is highly welcome.https://bugsigdb.org/29017394 - Attachment (BugSigDB): A preliminary study of gut dysbiosis in children with food allergy - BugSigDB > Gut microbiota of food allergic children was analyzed by high throughput 16S rRNA gene sequencing.Signs of gut dysbiosis, which is likely associated with gut inflammation, was observed in children with food allergies.

Montana-D (07:33:36) (in thread): > Well done on your curation > Will have a look

Montana-D (07:39:33) (in thread): > Could you please provide us with the article?

Precious Orakwe (08:07:26): - File (PDF): inoue2017.pdf

Mildred Anashie (08:11:16) (in thread): > Hi@Precious OrakweI totally agree, I don’t think Fig 2B and Table S1 should have been curated as it doesn’t appear curatable. What you should curate in Figure 2 is C-F > And I can also see missing taxa’s from Table S2, I’m still looking through to know if you should have curated Table S2 separate from Table 3

Precious Orakwe (08:11:38) (in thread): > https://community-bioc.slack.com/archives/C04RATV9VCY/p1744891646840799That’s the link to the article - Attachment: Attachment

Precious Orakwe (08:16:52) (in thread): > Thanks@Mildred Anashie

Victoria (Burah) Poromon (08:20:36) (in thread): > Hi@Precious OrakweI’ll take a look. > > Idon’tknow ifit’sjust on my end, bugsigdb is not opening.

Precious Orakwe (08:21:22) (in thread): > Maybe it’s network

Montana-D (08:25:47) (in thread): > BugSigDB is currently unavailable for like 25mins now just be patient for a bit@Victoria (Burah) Poromon

Anne-Marie Sharp (08:32:08) (in thread): > Yes@Precious OrakweYour experiment source had Fig.2D & TableS1. In figure 2d Ican’tsee anything signifying significance

Mildred Anashie (08:36:16) (in thread): > Fig 2d is actually showingsomething but I think itshouldn’tbe curated because it appears to be same as 2C.Please@Precious Orakwewhen I say curate 2C-f I meant 2C and 2E (the test is Kruskal wallis)

Precious Orakwe (08:41:07) (in thread): > Ok guys, thank you so much for your time, I will do the corrections

Mildred Anashie (08:43:21) (in thread): > I think its due to connection@Victoria (Burah) PoromonIt’s working but slowly and I require a lot of patience:sweat_smile:

Victoria (Burah) Poromon (08:46:41) (in thread): > Oh, okay.It’snot opening on my end at all.

Mildred Anashie (08:51:17) (in thread): > I forgot to add, the condition should be either “Response to transplant” or “Transplant outcome Measurement”. And check your definition and group names it seems to be mixed up somehow

Montana-D (08:51:37) (in thread): > It is now active guys

Mildred Anashie (09:00:32) (in thread): > It’s time guys:dancer:

Juliana Kentomahun Mautin (09:01:55) (in thread): > Thank you:blush:

Montana-D (09:02:08): > Meeting has begun

Montana-D (09:20:22) (in thread): > @Precious Orakwe, I think statistical test should be t-test and not Wilcoxon > See the excerpt “The relative abundance of bacterial abundance of bacterial genus between groups was analyzed by White’s non-parametric t-test, which is a method developed to compare bacterial abundance.”

Adeshile Oluwatosin (09:41:21) (in thread): > I saw this article. Yes the statistical test is t-test

U01MW62UDQR (09:47:34): > FYI,bugsigdb.orgappears to be a little slow, possibly having issues with its cache. I’ve submitted a ticket to wikiworks.

Adeshile Oluwatosin (09:48:36) (in thread): > Thank you for notifying

Precious Orakwe (09:50:11) (in thread): > Okay, thank you

Precious Orakwe (09:51:25) (in thread): > Thank you for the update, noted

Anne-Marie Sharp (09:58:05) (in thread): > Thank you for the update

Joy (10:09:56) (in thread): > Duly noted<@U01MW62UDQR>!

Anne-Marie Sharp (10:10:16) (in thread): > Well done@Adeshile Oluwatosinwe’ll review

Anne-Marie Sharp (10:12:24) (in thread): > Well done@Precious Orakwewe’ll review

Precious Chijioke (10:19:26): > Please, who else is experiencing backend bug on BugSigDB. It’s been hours now, and it’s loading with technical errors and backend failed.

Anne-Marie Sharp (10:20:06) (in thread): > Hello@Precious Chijiokewe all arehttps://community-bioc.slack.com/archives/C04RATV9VCY/p1744897654615039 - Attachment: Attachment > FYI, bugsigdb.org appears to be a little slow, possibly having issues with its cache. I’ve submitted a ticket to wikiworks.

Anne-Marie Sharp (10:20:50) (in thread): > Let’sgive it a while

Adeshile Oluwatosin (10:32:28) (in thread): > The site is currently down, check back later

Juliana Kentomahun Mautin (11:03:11) (in thread): > I’m also experiencing the same, it’s been very slow since morning. Let’s be patience, it would be resolved

Anne-Marie Sharp (13:03:10): > Hello, good evening everyone. My co-curator@Victoria (Burah) Poromonand I will appreciate a peer review on our curation:https://bugsigdb.org/33879267Article link:https://jasbsci.biomedcentral.com/articles/10.1186/s40104-021-00573-3Thank you very much. - Attachment (BugSigDB): Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation - BugSigDB > BACKGROUND: Sows are frequently subjected to various stresses during late gestation and lactation, which trigger inflammatory response and metabolic disorders. - Attachment (BioMed Central): Impact of sugar beet pulp and wheat bran on serum biochemical profile, inflammatory responses and gut microbiota in sows during late gestation and lactation - Journal of Animal Science and Biotechnology

Adeshile Oluwatosin (13:03:53) (in thread): > Well done guys

Montana-D (13:08:36) (in thread): > Well done on your curation:raised_hands:

Precious Orakwe (13:56:12) (in thread): > Well done

Anne-Marie Sharp (14:08:52) (in thread): > In Exp3 & 4, Source should be only 7b for signature1 and 7c for signature2, similar to Exp2 & 5

UBNSEMS3S (14:26:27): > Office Hours recording. Thank you everyone who attended. - File (MPEG 4 Video): bsdb_2025_04_17.mp4

Mildred Anashie (14:28:15) (in thread): > Thank you:blush:<@UBNSEMS3S>

Anne-Marie Sharp (14:45:20) (in thread): > Thank you for today’s office hour:pray:

U01MW62UDQR (15:17:49): > Hi everyone, thanks for your patience. I thinkbugsigdb.orgis back to normal.

Precious Orakwe (15:29:08) (in thread): > Thank you<@U01MW62UDQR>

Anne-Marie Sharp (16:34:47) (in thread): > Hello@Precious ChijiokeIn your article Neuron activation is the condition between ChAT+ and TH+ . But the closest match I could find on EFO isCell activation: A multicellular organismal process by which exposure to an activating factor such as a cellular or soluble ligand results in a change in the morphology or behavior of a cell. > Although it is a general term, neurons are also cells, andCell activationdescribes how exposure to activating factors (such as chemogenetic modulators: DREADD) triggers changes in cellular activity and responses, which is consistent with the observed impact of stimulating ChAT+ and TH+ neurons in the enteric nervous system, leading to alterations in the gut microbiota. > So, I would use ‘Cell activation’ as the condition

Mildred Anashie (16:58:28) (in thread): > That makes a lot of sense@Anne-Marie Sharp

Adeshile Oluwatosin (17:00:25) (in thread): > Iagree as well

Precious Chijioke (17:15:01) (in thread): > Thank you<@U01MW62UDQR>

Precious Chijioke (17:18:34) (in thread): > Well done on your curation@Anne-Marie Sharp@Victoria (Burah) PoromonExperiment 5&6 is showing incomplete. Kindly edit it to complete so that the signatures will become visible.

Anne-Marie Sharp (17:31:25) (in thread): > Thank you everyone:raised_hands:

Anne-Marie Sharp (17:31:26) (in thread): > Thank you@Precious Chijiokethey’re showing complete from my end, some experiments in the curation have just 1 signature

Precious Chijioke (17:32:01) (in thread): > The tax id for Clostridium is 1485 > > Every other thing looks good for me. I’ll wait for others to review.

Precious Chijioke (17:33:27) (in thread): > @Anne-Marie Sharpall the signatures are showing now and the experiment complete.

Adeshile Oluwatosin (17:52:33) (in thread): > Thank you:pleading_face:

Anne-Marie Sharp (18:10:52) (in thread): > Hello@Precious OrakweYou can rephrase your source definition to be: ’Composition of gut microbiota of healthy and food allergic children. Significant differences (p < 0.05) in mean relative abundance between groups are indicated with an asterisk (*)’ > Or simply ‘Composition of gut microbiota of healthy and food allergic children’

Anne-Marie Sharp (18:13:49) (in thread): > Okay@Precious Chijiokethank you > The Clostridium stated in the article is not exactly same as 1485, so we curated as seen

Mildred Anashie (18:29:46) (in thread): > Hi<@UBNSEMS3S>I was totally logged off earlier and hoped to watch the office hours, I realized my second question wasn’t answered. > > Can you kindly have a look, here’s a link to the articlehttps://doi.org/10.1007/s00284-023-03361-6The question was if Figure 5 should be curated as two experiments with only increased signatures or a single experimentThank you:pray::skin-tone-5: - Attachment (SpringerLink): Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing > Current Microbiology - Metabolic diseases like obesity, diabetes, and hypertension are considered major risk factors associated with endometrial cancer. Considering that an imbalance in the gut…

Precious Orakwe (20:21:24) (in thread): > Thank you for today’s office hour<@UBNSEMS3S>@Svetlana Ugarcina Perovic:heart::hugging_face::pray:

Montana-D (20:58:52) (in thread): > Thank you<@U01MW62UDQR>

2025-04-18

Adeshile Oluwatosin (01:22:18) (in thread): > * Clostridium senso stricto 1 is clostridium > * It’s better to be specific with your group names > Add lactation and gestation to both groups across all experiments, as a reader it was harder differentiating

Adeshile Oluwatosin (01:23:31) (in thread): > E.g: CON (control) gestationSBP gestation etc

Adeshile Oluwatosin (01:26:04) (in thread): > @Precious Chijiokeif you experience any issuewhilecurating this article let me know

Precious Chijioke (02:25:28): > Good Morning Everyone > I’m curating this paper with@Mildred Anashiewe’ll like to confirm if we should curate Fig. 5B as 1 experiment or different experiments. The relative abundance is identified in Histogram and Cladogram respectively. > > Paper link:https://link.springer.com/article/10.1007/s00284-023-03361-6 - Attachment (SpringerLink): Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing > Current Microbiology - Metabolic diseases like obesity, diabetes, and hypertension are considered major risk factors associated with endometrial cancer. Considering that an imbalance in the gut…

Svetlana Ugarcina Perovic (03:02:43): > Our mentoring team is taking a break for the holidays. We’ll resume on Tuesday, April 22.:cherry_blossom:Happy Friday! Happy holidays!:cherry_blossom:

Adeshile Oluwatosin (03:04:02) (in thread): > Duly noted, thank you for all

Mildred Anashie (03:04:36) (in thread): > Duly noted@Svetlana Ugarcina PerovicHappy Holidays:cherry_blossom::tulip:

Anne-Marie Sharp (03:10:29) (in thread): > Noted, thank you all & happy holidays:cherry_blossom:

Eseoghene Cynthia Princewill-Ukot (03:22:01) (in thread): > @Svetlana Ugarcina PerovicThank you for your guidance and patience. Happy holidays:tulip:

Aiysha shahid (03:25:12) (in thread): > Dully noted! Thank you and Happy Holiday!:tulip:

Anne-Marie Sharp (03:25:29) (in thread): > Good morning@Precious Chijioke@Mildred AnashieI think you should curate Fig 5A & 5B as 1experiment. Both are outputs of a LEfSe analysis, just different visual representations of the same result.

Mildred Anashie (03:26:46) (in thread): > Hi@Anne-Marie SharpGood morning > Thank you:pray:The question is more of if 5B should be two experiments with only increased abundance or one experiment

Anne-Marie Sharp (03:41:42) (in thread): > You’re welcome. If your contrast is N vs EC then it should be 1experiment with increase & decrease. Similar figure to 5B in your article was curated in Exp1 here:https://bugsigdb.org/38344423 - Attachment (BugSigDB): Characteristics of Oral-Gut Microbiota in Model Rats with CUMS-Induced Depression - BugSigDB > PURPOSE: The diversity and composition of the oral and gut microbiota of depressed rats were analyzed to explore the microbiological etiology of major depressive disorder (MDD).METHODS: The depressed rat model was established by inducing chronic unpredictable mild stress (CUMS).

Mildred Anashie (03:43:23) (in thread): > Okay okay > > Thank you:pray:

Precious Chijioke (04:17:43) (in thread): > Duly noted@Svetlana Ugarcina PerovicHappy holiday

Montana-D (04:18:49) (in thread): > Thank you and happy Holidays:white_flower:

Victoria (Burah) Poromon (04:27:17) (in thread): > Thank you@Svetlana Ugarcina PerovicHappy holidays.

Precious Chijioke (04:36:45) (in thread): > Thank you@Anne-Marie Sharp

Precious Orakwe (05:00:03) (in thread): > Thank you for the update, have a wonderful holiday and rest.@Svetlana Ugarcina Perovic<@UBNSEMS3S>@Kate Rasheed@Aleru Divine:hugging_face::hugging_face::hugging_face::hugging_face:

Precious Orakwe (05:14:12) (in thread): > I agree with@Anne-Marie Sharp:white_check_mark::white_check_mark:

Anne-Marie Sharp (05:18:51): > Happy weekend & holidays everyone:hugging_face:. I’ll like to collaborate with someone on finalizing this curation:https://bugsigdb.org/28870194If you’re interested please let me know. Thank you - Attachment (BugSigDB): A yeast fermentate improves gastrointestinal discomfort and constipation by modulation of the gut microbiome: results from a randomized double-blind placebo-controlled pilot trial - BugSigDB > BACKGROUND: Constipation and symptoms of gastrointestinal discomfort such as bloating are common among otherwise healthy individuals, but with significant impact on quality of life.

Adeshile Oluwatosin (05:19:20) (in thread): > We can work on it together > Well done@Anne-Marie Sharp

Anne-Marie Sharp (05:21:42) (in thread): > Okay@Adeshile OluwatosinI’min your DM:dancer:

Utibe Ita (05:42:48) (in thread): > We can work on it together@Anne-Marie SharpYou have done agoodjob

Anne-Marie Sharp (05:52:56) (in thread): > Thanks@Utibe Itawe’reonly making corrections to finalize it, & someone has indicated interest. ButI’lllove to collaborate with you soon.

Anne-Marie Sharp (07:06:17) (in thread): > @Precious Chijioke@Adeshile Oluwatosinthank you for the corrections, we’ll effect them.

Ndukauba Oluchi (13:47:46): > Hello everyone:wave:has anyone ever been in a situation when while curating your signatures, you discover that 2 different signatures have the same taxonomy ID? > for exampleunclassified Oscillospiraceaeandunclassified Ruminococcaceae both share Taxonomy ID: 473772 > > so how do I curate this? > Cc:@Svetlana Ugarcina Perovic

Adeshile Oluwatosin (13:50:43) (in thread): > Curate it as “473772” > Oscillospiraceae is also RuminococcaceaeHence unclassified oscillospiraceae is also unclassified ruminococcaceaeYou can learn morehere - Attachment: Oscillospiraceae > Oscillospiraceae, also commonly called Ruminococcaceae, is a family of bacteria in the class Clostridia. All Oscillospiraceae are obligate anaerobes. However, members of the family have diverse shapes, with some rod-shaped and others cocci. > Within the family, Faecalibacterium prausnitzii is notable as an abundant commensal bacteria of the human gut microbiota. In addition, several members of Ruminococcus are found in the human gut. The Oscillospira genus and its impact on human health has led to numerous theories on its development and its involvement in human health.

Anne-Marie Sharp (13:56:28) (in thread): > Yes@Ndukauba OluchiLike@Adeshile Oluwatosinsaid, curate it as 473772, they are the same thing

Ndukauba Oluchi (13:57:16) (in thread): > yeah when i do that, since i already have “473772” asunclassified Oscillospiraceaeit doesn’t reflect

Anne-Marie Sharp (13:58:41) (in thread): > Most articles list both unclassified oscillospiraceae and unclassified ruminococcaceae.It’sokay if you curate it just once as 473772

Ndukauba Oluchi (15:36:23): > Hello everyone, Please i just want to clarify something in this study:https://www.mdpi.com/1422-0067/26/3/1236inFigure 4:it says “****#” indicates significant differences between the MC and other groups (**********p********** < 0.05).*******link : ***https://www.mdpi.com/ijms/ijms-26-01236/article_deploy/html/images/ijms-26-01236-g004.pngDoes that mean i am going to curate for MC versus all other groups? or just the groups with the “#” symbol above it? i am a bit confused here. - Attachment (MDPI): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. To explore how these structural differences impact constipation intervention, a 14-day study was conducted on loperamide-induced constipated mice using five dietary fibers: soluble dietary fiber from steamed sweet potato (SDF-S), oat β-glucan (OB), polydextrose (PD), arabinogalactan (AG), and inulin (IN). The results showed that four fibers, excluding PD, significantly improved gastrointestinal (GI) transit rate (p < 0.05), although PD had the highest fecal moisture, it was significantly different from the lowest IN (p < 0.05). AG and IN resulted in higher 6 h fecal weights compared to other fibers. SDF-S and OB were more effective in modulating serum levels of gastrointestinal hormones. The different monosaccharide compositions and glycosidic bonds of these fibers led to distinct changes in gut microbiota composition and SCFA profiles. Galactose and arabinose in AG were linked to increased abundance of Lachnospiraceae_UCG-006, Bacteroides, and Odoribacter, promoting butyrate fermentation, which is positively correlated with GI transit rate. Glucose in SDF-S, OB, and PD favored acetate fermentation positively correlated with fecal moisture. Fructose in IN encouraged the proliferation of Muribaculaceae_unclassified and Ruminococcus, associated with butyrate fermentation and increased 6 h stool weight, respectively. The β-glycosidic bonds in OB may lead to high butyrate production through the selective proliferation of Lachnospiraceae_unclassified. Minor components like fucose, rhamnose, and ribose were positively correlated with the abundance of Oscillospiraceae_unclassified, Anaerotignum, and Lachnospiraceae_unclassified. In conclusion, the unique monosaccharide compositions and glycosidic bond differences in dietary fibers selectively promote the proliferation of fiber-degrading and butyrate-producing bacteria, resulting in varied effects on constipation relief. - Attachment: Attachment

Anne-Marie Sharp (15:51:18) (in thread): > > Hello@Ndukauba Oluchi, I think you should curate this as pairwise comparisons between the MC group and each fiber group that shows a**** “#”****, rather than as a single “MC vs all others” contrast. For example:MC vs PT,MC vs SDF-S,MC vs OB, etc., one at a time.

Ndukauba Oluchi (15:52:37) (in thread): > Oh cool, I thought so too. > Thank you@Anne-Marie Sharp

Anne-Marie Sharp (15:58:53) (in thread): > Okay, you’re welcome

Juliana Kentomahun Mautin (16:21:46) (in thread): > Duly noted@Svetlana Ugarcina Perovic. Happy holidays:fireworks::fireworks:

Juliana Kentomahun Mautin (16:23:07) (in thread): > Thank you@Andres Wokaty

Juliana Kentomahun Mautin (16:23:29) (in thread): > Thank you<@UBNSEMS3S>

Precious Orakwe (17:40:17) (in thread): > Yes, I have been in this situation before@Ndukauba OluchiI curated one with the NCBI number and curated the other one the way it appeared, so the mentors suggested another taxa to use and replace one of them. So you can talk to the mentors about it.

Ndukauba Oluchi (18:08:38): > Hello everyone > Please kindly leave a review on this study :https://bugsigdb.org/39941005 - Attachment (BugSigDB): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features - BugSigDB > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects.

2025-04-19

Anne-Marie Sharp (02:17:22) (in thread): > Well done@Ndukauba Oluchiwe’ll review

Adeshile Oluwatosin (02:20:13) (in thread): > Well done

Adeshile Oluwatosin (02:33:46) (in thread): > There was no mention of age and body weight as matched onfactors.

Joy (03:02:27) (in thread): > Well done@Ndukauba Oluchion your curation, we will review.

Precious Chijioke (03:27:37) (in thread): > Well done@Ndukauba Oluchion your curation

Precious Chijioke (03:33:29) (in thread): > @Ndukauba OluchiI’ve been in same situation before and I curated with the ID. Just like@Adeshile Oluwatosinsaid Oscillospiraceae is same as Ruminococcaceae so curate with the Taxanomy ID.

Mildred Anashie (03:50:49) (in thread): > Well done on your curation@Ndukauba OluchiI’llhave a look

Anne-Marie Sharp (03:54:48) (in thread): > @Ndukauba Oluchi1)I agree there was no matched on factor > 2)The alpha diversities should be curated as unchanged, it was stated that the differences were not statistically significant. > - You should curate only those taxa that have significant differences with MC (with # on top). Apply this to the other experiments also. > 3)In Exp1 there should be no increased abundance in MC, only decreased > 4) In Exp1, signature 2, taxa with no significant difference (p < 0.05) with MC example : Desulfovibrionaceae_unclassified,Firmicutes_unclassified etc should not be curated

Joy (04:10:27) (in thread): > The Body Site: Several were mentioned, like:GI Tract, Colon, Feces, and Serum (Blood). Would it be safe to curateFeces? What do you guys think?@Anne-Marie Sharp@Anne-Marie Sharp@Mildred Anashie@Ndukauba Oluchi

Anne-Marie Sharp (04:25:31) (in thread): > @JoyI dont think it should be feces, feces is different from cecum content. It should be Cecum: ‘The cecum contents were collected, sealed, and placed on dry ice immediately for gut microbiota analysis.’

Anne-Marie Sharp (04:26:05) (in thread): > The other samples were used for other analysis, not for microbiota analysis

Ndukauba Oluchi (04:31:03) (in thread): > @Anne-Marie SharpIn number 2, do you mean that I’m not supposed to have 14 experiments?

Precious Orakwe (04:32:07) (in thread): > If she curate it with the ID for the both of them she will have incomplete taxa, because one of them will disappear. > > She should curate one with the taxonomy ID and the other with the full name, that’s what I did and the mentors now gave me an alternative to replace it.

Mildred Anashie (04:37:17) (in thread): > * Anaerotignum was increased in only SDF-S but I see it in almost all the experiments, please curate only the taxa showing significance in each group with (#) > > * I’m thinking you have to be consistent, with MC as group 0 because it’s group 1 in Experiment 1. > > * Experiment 1 and 8 seems to be exactly the same only difference is Experiment 8 is correct compared to 1. > * I agree with the matched on not being mentioned in the study and the alpha diversity being unchanged, see this“The differences in the average values of these two indices among groups suggested that fiber intervention had the potential to promote community richness and diversity, though the differences were not statistically significant due to the relatively short intervention duration.” > * Also@JoyI think Caecum works for the body site because that is what 16s rRNA sequencing was done and the sequencing was used for gut microbiome analysis. See this “The microbiota diversity of the mice gut was evaluated by 16S rDNA gene sequencing. Community richness was characterized by the Chao1 index (Figure 2A), and community diversity was characterized by the Shannon index (Figure 2B).”

Anne-Marie Sharp (04:37:58) (in thread): > @Ndukauba OluchiThe experiments are not yet showing complete, if you can edit as incomplete/complete for Exp9 to the last so they will reflect. You may not have same experiments. Not all the taxa in that figure are significant between each comparison. Curate only those with #

Anne-Marie Sharp (04:48:27) (in thread): > The comparisons werefiber group vs MC, not fiber group vs fiber group.****# indicates significant differences between the MC and other groups (p < 0.05)****So when you see a # over a fiber group (e.g., SDF-S), it means: that fiber group(SDF -S)differs significantly from the MC group. > It does not mean it’s different from another fiber group (e.g. SDF-S vs PD). > Hence, Eg. Exp2 should be MC vs PT, Exp3 should be MC vs (SDF-S)….and so on

Aiysha shahid (04:49:01): > Hi everyone, happy holidays!:hugging_face:Hope you’re all doing well. > > I’d like to collaborate with someone on finalizing this curation:https://bugsigdb.org/28494241Thanks in advance!:tulip: - Attachment (BugSigDB): Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases - BugSigDB > The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation.

Utibe Ita (04:49:48) (in thread): > You have done a nice jobI’lllove to collaborate with you

Mildred Anashie (04:50:03) (in thread): > Hi@Aiysha shahidI’lllove to collaborate with you

Mildred Anashie (04:52:47) (in thread): > Oops I see@Utibe Itacommented firstI can still join the party ifthat’sokay

Anne-Marie Sharp (05:09:00) (in thread): > Hello@Precious Orakweplease can you share the link for that curation where you curated like that.

Aiysha shahid (05:10:19) (in thread): > Thanks for showing interest@Mildred Anashieand@Utibe Ita, I am just looking for one collaborataor, so as Utibe commented first, I would like to go ahead with her. But I would really love to collaborate with you in any other study@Mildred Anashie:hugging_face:

Adeshile Oluwatosin (05:10:21) (in thread): > @Precious Orakweshe does not need to curate unclassified oscillospiraceae and unclassified ruminoccocaceae seperately > > They should be reported as one taxa > Hence, if she was to curate 15 taxa, she would have a total of 14 taxa when she saves.

Mildred Anashie (05:11:08) (in thread): > That’s absolutely fine > Looking forward to it

Adeshile Oluwatosin (05:25:42) (in thread): > I agree with all notes stated by@Mildred Anashie

Precious Orakwe (05:31:25) (in thread): > @Anne-Marie Sharphere is the link:https://bugsigdb.org/37065158experiment 4 signature 2 - Attachment (BugSigDB): Reducing bias in microbiome research: Comparing methods from sample collection to sequencing - BugSigDB > BACKGROUND: Microbiota profiles are strongly influenced by many technical aspects that impact the ability of researchers to compare results.

Anne-Marie Sharp (05:34:43) (in thread): > @Precious OrakweThank you for sharing, let’s sort this out, please do you remember the taxa that the mentors asked you to curate with the NCBI number and to curate the other one the way it appeared? Let us know, so we crosscheck

Precious Orakwe (05:37:25) (in thread): > Actinomycetota and Actinobacteriota has the same taxonomy ID, so i curated Actinobacteriota without the taxonomy ID and the mentor said i should replace Actinobacteriota with ****[Acidimicrobiia]

Adeshile Oluwatosin (06:13:15) (in thread): > Did you check out the rank, acidimicorbiia has rank “class”

Anne-Marie Sharp (06:31:09) (in thread): > @Precious OrakweInFig. S2d, where you curated from, bothActinobacteriaandActinobacteriotaare listed, they’re both labeled asphylum in NCBI Taxonomy. > Normally, you should curate the correct phylum-level name, which isActinobacteriota (NCBI:201174)— as you originally curated. > ButFig. S2d includes mixed taxonomic levels(genus, class, phylum, etc.), andAcidimicrobiia, which is a class, is sometimes calledActinobacteriain older naming systems. > That may be why you were asked to curateone as a phylum and the other as a class— even though the names sound overlapping

Anne-Marie Sharp (06:32:49) (in thread): > But in this very case of unclassified Oscillospiraceae and Ruminococcaceae, they are both same rank in the article and on NCBI, & that’s how we have observed it being curated on BugsigDB, we curate it as one.

Montana-D (15:37:11): > Hello everyone. Hopefully you are all doing well and a good festive period > > I’d like your clarifications on a study we are currently curating for which we are unsure of exactly how it should be done. > > so from the article provided below, we have the following questions:palms_up_together: > 1. From figure 8A, we observed a certain taxon named Biophilia, but after searching the NCBI and BugSigDB databases, we rather found Bilophila (Taxonomy ID: 35832), should we curate what is in the figure? or assume it was a typo and curate the latter. > 2. Looking at Figure 4 of same article, we would love to clarify if the significant taxa appearing on the zero or midline should be curated or just those with significant number values > 3. Lastly, we would like for you to check out the supplementary figure 5 in the PowerPoint provided below, This pie charts in it represents the percentages of the study population for different groups, our question is this, since we do know the total population, in the various experiments to which this chart is involved and the sample sizes not provided, should we go ahead to use these percentages to calculate the group sizes, or we allow it blank since it wasn’t stated anywhere in the text. > Thank you for your time to look through it and most especially your response. we are sorry to interrupt your restful holidays - File (PDF): s00535-018-1488-5 (1).pdf - File (PowerPoint Presentation): 535_2018_1488_MOESM2_ESM (1).pptx

Adeshile Oluwatosin (17:11:38) (in thread): > Well done@Montana-D > 1. I could not find a related or convincing article online, so curate as “bilophila”. Then write a note in the discussion page. > 2. Yes, as long as they were reported to be significant > You can use this to guide on how to curate: > 3. Are the groups in supplementary figure 5 the groups you are currently curating for comparison? - File (JPEG): IMG_4304

Mildred Anashie (17:48:13) (in thread): > Hi@Montana-D > 1. I think you should curate as Bilophila and drop a note as@Adeshile Oluwatosinsuggests. > 2. From this text I believe you should curate all, because the article says they were increased in either male or female and were significant. See this, “As shown in Fig. 4, the comparison of the microbial changes between male and female subjects showed a significant increase in the abundance of 14 genera in male subjects and a significant increase in 11 genera in female subjects”. > 3. The pie chart is showing the percentages per group based on stool consistency, see this “Pie charts indicating stool consistency using the Bristol stool score (BSS) for all subjects, male subjects, and female subjects in each age group”. For the sample sizes I believe it’s indicated in each group, you’d see something like (N=47), (N=130) and (N=100). And when you look at Table 1 in the article (Distribution of the enrolled subjects) you’d get your exact sample sizes from there. The ages were grouped into 3 (20-39, 40-59 and 60 and above) the total number of samples from Table 1 for each group (based on the 3 categories) aligns with what is stated as the (N) in the supplementals. So looking at the Table you would know the sample size by adding them. Let’s take an example for the first age group (20-39 which is 47, I.e 18 + 29) Males are 5 + 14 =19and Females 13 + 15 =28. > I hope this is clear

Precious Orakwe (23:30:37): > Good morning, everyone. > Please, I would appreciate a peer review on this study.https://bugsigdb.org/39588509 - Attachment (BugSigDB): Intestinal microbiome changes and mechanisms of maintenance hemodialysis patients with constipation - BugSigDB > BACKGROUND: Constipation is a common symptom in maintenance hemodialysis patients and greatly affects the quality of survival of hemodialysis patients.

2025-04-20

Montana-D (01:16:59) (in thread): > Thank you so much both for taking out time to help out > > Happy Easter:tada:

Anne-Marie Sharp (02:16:44) (in thread): > Good morning@Precious Orakwewell done > 1)From Figure5 you should have 2contrast groups: HCG vs MHDCG & HCG vs MHDNCG. > Replace MHD with MHDCG in Experiment1 and curate another experiment for the second contrast > 2)In Experiment5 include the lda score > 3)In Experiment5 Signature1, curate all the taxa for MHDCG(red bars) > In Signature2, curate all the taxa for MHDNCG(green bars) > 4)Also curate the alpha diversity for each experiment > 5)The condition should be gut microbiome measurement or similar > 6)All sample sizes should be 157)In the experimentsyoucurated from Figure6, I’ll suggest you also curate from the text that describes Figure6, in order to capture all taxa.Eg. in Exp2 Sig1, Enterococcus & Akkermansia are missing

Adeshile Oluwatosin (02:26:28) (in thread): > Well done@Precious Orakwe

Precious Orakwe (04:03:24) (in thread): > There was no LDA score mentioned in the study, should i put it as 4?

Anne-Marie Sharp (04:05:53) (in thread): > @Precious Orakweif itwasn’tmentioned,use a default score of 2, not 4.

Precious Orakwe (04:06:37) (in thread): > Ok, thank you

Juliana Kentomahun Mautin (04:24:07): > Hello everyone. In the spirit of teamwork and collaboration. I and@Joycollaborated on this study. Please kindly help us review it. Thank you.https://bugsigdb.org/31456752.https://www.frontiersin.orghttps//www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2019.01721/full

Anne-Marie Sharp (04:26:49) (in thread): > Well done@Joy@Juliana Kentomahun Mautinwe’ll review

Aiysha shahid (04:27:17) (in thread): > Well done, we would go through it!:raised_hands:

Juliana Kentomahun Mautin (04:32:57) (in thread): > Well done@Precious Orakwe

Juliana Kentomahun Mautin (04:33:24) (in thread): > Thank you@Anne-Marie Sharpand@Aiysha shahid

Anne-Marie Sharp (06:09:03) (in thread): > @Juliana Kentomahun Mautin@Joywell done again > -I think you should curate Figures 3,4,5 (fecal microbial taxa) together > -Then curate Figures 6,7,8 (cecal microbial taxa) together > -Curate Figures 9,10,11 (cecal & fecal microbial taxa) together > -There are 4groups for Figures 3,4,5 & 6,7,8: 1)Normal 2)Control 3)CMB1 4)CMB2 > -There are 8groups for Figures 9,10,11 > -There should be pairwise comparisons between these groups not one against all comparisons.

Adeshile Oluwatosin (06:35:39) (in thread): > Well done@Juliana Kentomahun MautinThere were repeated comparisons in your study curation. > * As long as the comparisons are same with same statistical test curate the different figures together as a source. > * As Chloe said comparison between same letters are not significant > We want it to be very clear on which taxa increased/decreasedbetween a specific comparison, while ensuring that we do not curate irrelevant experiments. Hence curate as pairwise comparisons, those with same letter stated leave them out as our major aim is to curate significant differential abundance in Bugsigdb. > * According to the body sites stated above; we have three experiments like that with the stated figures as the source. > * Within each figure: use the letters for comparison. > * Instead of curating seperate experiments per figure, curate seperate experiments per group comparison.

Anne-Marie Sharp (06:45:32) (in thread): > @Juliana Kentomahun Mautin@Joyalso take note of the body sites when making corrections. Experiments from Fig3,4,5: Feces > Experiments from Fig6,7,8: Cecum > Experiments from Fig9,10,11 that will have both fecal & cecal groups in them(eg CMB1 vs C-CMB1): Feces, Cecum

Adeshile Oluwatosin (06:53:27) (in thread): > 1. Sample size for both control group and Maintenance Hemodialysis group is 15 each. > ”15 in the maintenance hemodialysis non-constipation group and 15 in the healthy control group. “ > “From these 100 patients, 15 was randomly selected as the maintenance hemodialysis constipation group (MHDCG). And the same number of people were set up in the maintenance hemodialysis non-constipated group (MHDNCG) and the healthy control group (HCG) respectively. “ > > 2. Figure5has two contrast: > HCG (Grp 0) and MHDCG (Grp 1) > HCG (Grp 0) and MHDNCG (Grp 1) > > 3. Lefse default LDA Score is 2 for experiment 5 > 4. Use figure 2 to curate the alpha diversity across the experiments. > 5. The condition cannot be gut microbiome measurement

Precious Orakwe (06:56:36) (in thread): > Thank you

Joy (07:12:18) (in thread): > Thank you guys for these peer review. We will definitely update the curated study.@Anne-Marie Sharp@Adeshile Oluwatosin@Aiysha shahid

Precious Chijioke (10:43:12): > Happy Easter Everyone > Hope you’re enjoying your holidays? > Please I would love a review on this studyhttps://bugsigdb.org/38517896 - Attachment (BugSigDB): Peripheral neuronal activation shapes the microbiome and alters gut physiology - BugSigDB > The gastrointestinal (GI) tract is innervated by intrinsic neurons of the enteric nervous system (ENS) and extrinsic neurons of the central nervous system and peripheral ganglia.

Aiysha shahid (11:10:32) (in thread): > Well Done! will go through it@Precious Chijioke

Aiysha shahid (11:15:26) (in thread): > Kindly put these ID’s to for the following taxa’s: > 1.Marinilabiliaceae, ID-558415 2.Ruminococcaceae, ID-216572 3.Varicellovirus, ID-10319 > 4.Fluvicola,ID-196029

Anne-Marie Sharp (11:19:26) (in thread): > Well done@Precious Chijioke1)Use a default score of 2 for the LDA, not 10 > 2)Study design should be laboratory experiment > 3)In Experiment3, body site should be cecum not cecal tonsil > 4)Curate Figure 2J&K together, 2L&M together : ‘(J–M) Linear discriminant analysis effect size (LEfSe) of the cecal microbiome. Cladograms show differential phylogenetic clusters and family-level differences in activated and control (J and K) ChAT+ and (L and M) TH+ mice.’ Use the colours as a guide. 5)Experiments curated from Figure2(LefSe) should have the body site ‘Cecum’ not feces. : ‘Linear discriminant analysis effect size (LEfSe) of thececal microbiome’ > 6):thinking_face:Fig 2N looks curatable, eg Control vs Activated of CHAT+group at Day 10 and in Cecum, Akkermansia … should be increased in Activated, please confirm this.

Mildred Anashie (11:21:24) (in thread): > Hi@Precious ChijiokeWell doneI’lltake a look

Anne-Marie Sharp (12:29:11): > Happy holidays everyone:tulip:My co-curator@Montana-Dand I want to clarify, In supplementary figure 4A & B should we: > 1) curate both Prevotella & [Prevotella] as one – Prevotella? > 2) curate Pseudoramibacter_Eubacterium as it appears, or as two separate genus? > 3) curate only Enterococcus or curate both Coriobacteriaceae & Enterococcus separately? (becauseEnterococcusbelongs to the familyEnterococcaceae not* Coriobacteriaceae*) > 4)curate Clostridium3 as clostridium in Figure 4? Thank you:pray: - File (PowerPoint Presentation): 535_2018_1488_MOESM2_ESM (1).pptx - File (PDF): s00535-018-1488-5 (1).pdf

Adeshile Oluwatosin (12:34:38) (in thread): > 1. Curate both seperately > 2. Curate as seenas they are closely related. > 3. Curate Enterococcus, it’s the lowest rank > 4. I didn’t see “clostridium3” but if stated as this…curate as seen

Mildred Anashie (12:59:53) (in thread): > Hi@Anne-Marie Sharp@Montana-DI agree with all of@Adeshile Oluwatosinpoints

Anne-Marie Sharp (13:19:21) (in thread): > Thank you@Adeshile Oluwatosin@Mildred Anashie > 1. When Prevotella is typed/curated, we can’t enter another Prevotella, & putting it in brackets[] raises an error. So how do we curate both? > 3. We understand that we should curate the lowest rank when the different taxa levels are listed but in this case, Coriobacteriaceae is not the family for Enterococcus,that’sthe confusion.

Adeshile Oluwatosin (13:30:10) (in thread): > @Anne-Marie Sharpuse round brackets instead : (Prevotella) > See:https://community-bioc.slack.com/archives/C04RATV9VCY/p17373008516182293. Curate what was reported to be genus regardless - Attachment: Attachment > Hello everyone, when I enter signatures in a format including [ ], e.g. Bifidobacterium sp. [C catenulatum/kashiwanohense], this seems to break the page a little. Picture attached of how it shows, when I click the link I get the message “The requested page title contains invalid characters:”[“.” . This is for this experiment https://bugsigdb.org/Study_1174#Experiment_6 . Wondering if I should remove the brackets or if this is a bug.

Precious Chijioke (13:57:22) (in thread): > Thank you@Aiysha shahidRuminococcaceae and Oscillospiraceae    > is same and have same ID so I curated Oscillospiraceae. Some taxa ID’s is not displaced when you’re curating rather you’ll see unclassified and the rest that’s why I curated as seen in the study. I’ll still recheck and have a work around it.

Anne-Marie Sharp (14:00:27) (in thread): > Noted. Thank you:pray:@Adeshile Oluwatosin

Precious Chijioke (14:20:51) (in thread): > Thank you@Anne-Marie SharpI used the colors for the identification of the signatures. The experiments curated from Figure 2 is not Cecum. There’s no ceal microbiome in LEfSe. > > I’m not sure if Figure 2N is curatable. I’ll wait for another confirmation.

Juliana Kentomahun Mautin (15:33:38) (in thread): > Thank you so much@Adeshile Oluwatosin@Anne-Marie Sharpfor the feedback. Me and@Joywould make the corrections.

Precious Chijioke (15:40:44): > Good Evening Everyone > I curated this study with@Mildred Anashieand we would love a peer reviewhttps://bugsigdb.org/37294364 - Attachment (BugSigDB): Gut Microbiome Dysbiosis in Patients with Endometrial Cancer vs. Healthy Controls Based on 16S rRNA Gene Sequencing - BugSigDB > Metabolic diseases like obesity, diabetes, and hypertension are considered major risk factors associated with endometrial cancer.

Anne-Marie Sharp (16:27:11) (in thread): > Well done:raised_hands:@Precious Chijioke@Mildred Anashie

Anne-Marie Sharp (16:27:17) (in thread): > I noticedGemmiger formicilis wasn’t curated in Exp.1 Signature 2

Precious Orakwe (16:39:23) (in thread): > Well done@Precious Chijioke@Mildred Anashie

Montana-D (17:01:39) (in thread): > Well done@Precious Chijioke@Mildred Anashie:raised_hands:

Mildred Anashie (17:03:27) (in thread): > That’sright@Anne-Marie SharpThank you:blush:

Montana-D (17:54:09): > Hello everyone.@Anne-Marie Sharpand I would greatly appreciate your reviews on our studyBugSigDB link - Attachment (BugSigDB): Differences in gut microbiota associated with age, sex, and stool consistency in healthy Japanese subjects - BugSigDB > BACKGROUND: Human gut microbiota is involved in host health and disease development.Investigations of age-related and sex-related alterations in gut microbiota are limited, and the association between stool consistency and gut microbiota has not been fully investigated. - File (PDF): s00535-018-1488-5 (1).pdf - File (PowerPoint Presentation): 535_2018_1488_MOESM2_ESM (1).pptx

Precious Chijioke (18:08:12) (in thread): > Thank you@Anne-Marie Sharp,@Precious Orakweand@Aiysha shahid

Precious Chijioke (18:10:44) (in thread): > Well done on your curation@Montana-Dand@Anne-Marie Sharpwe’ll take a look

2025-04-21

Precious Orakwe (01:08:10) (in thread): > Its all the alpha diversity for the study decrease.

Adeshile Oluwatosin (02:45:10) (in thread): > Well done@Montana-D@Anne-Marie SharpWedon’tcurate “gut microbiome measurement” as a condition. You can check out the welcome material

Joy (04:04:23) (in thread): > Well done@Montana-Dand@Anne-Marie Sharp, we will have a look.

Precious Orakwe (08:25:18): > good afternoon, everyone, happy new week. > > Please, how can I determine the increase and decrease of taxa using the mean relative abundance? > here is the link to the table. - File (Google Sheets): 12866_2023_3123_MOESM4_ESM

Adeshile Oluwatosin (09:33:24) (in thread): > I need access to view the file

Precious Orakwe (11:31:07) (in thread): > Thank you Tosin, I’ve figured it out.

Anne-Marie Sharp (12:32:12) (in thread): > @Adeshile Oluwatosinthank you for pointing that out, been using the other curation policy. What’s your suggestion on these conditions? 1)Experiment1: Biological sex > 2)Experiment 2 to 7: Abnormal stool composition > 3)Experiment 8 to 10: Biological sex & Age at assessment

2025-04-22

Svetlana Ugarcina Perovic (06:23:45): > :question:Quiz time!https://worldmicrobiomeday.com/human-microbiome/ - Attachment (World Microbiome Day): Human Microbiome - World Microbiome Day > The Human Microbiome – Quiz The human microbiome is the collection of microorganisms that include bacteria, protozoa, fungi, viruses and other one-celled organisms in and on the body. Human-microbe interactions…

Adeshile Oluwatosin (06:29:47) (in thread): > Failed one, now I knowfirst microbiome research was in 1700s:hugging_face: - File (JPEG): IMG_4387

Montana-D (06:31:36) (in thread): > Amazing questions > Failed just one:grin:

Montana-D (06:32:12) (in thread): > Same here@Adeshile Oluwatosin, how did you get your score, I didn’t see where to submit

Anne-Marie Sharp (06:34:08) (in thread): > Interesting questions. Didn’t know the large intestine has themost microbes

Anne-Marie Sharp (06:34:34) (in thread): > @Montana-Dthe score shows just after the last question

Montana-D (06:36:09) (in thread): > @Anne-Marie SharpI just noticed it shows only in desktop mode as I used my phone when answering > Thank you

Adeshile Oluwatosin (06:46:48) (in thread): > It showed on my phone@Montana-D

Juliana Kentomahun Mautin (06:54:54) (in thread): > Very Interesting quiz:slightly_smiling_face:, I scored 78%

Mildred Anashie (07:04:25) (in thread): > I enjoyed taking this quiz@Svetlana Ugarcina PerovicThis quizzes keep me thinking, Thank you for making learning engaging and interesting:blush:

Eseoghene Cynthia Princewill-Ukot (07:12:50) (in thread): > Interesting@Svetlana Ugarcina Perovic! I scored 78%

Precious Orakwe (07:45:20) (in thread): > This is so interesting and enjoyable. I passed.:dancer::man_dancing:

Utibe Ita (07:47:55) (in thread): > I enjoyed taking the quiz@Svetlana Ugarcina PerovicGlad that I got everything correct

Precious Orakwe (07:52:54): > Hello everyone, good afternoon, happy new week, i hope we all had a wonderful weekend. > > please, I would appreciate a peer review of this study, and I have a few questions. 16S variable region, I can see a lot of V’s (******Six hypervariable regions (Primer set V2, V4, V8 and Primer set V3, V6-7, V9) of 16S rRNA gene were amplified in two reactions/sample),******how can i go about this, which one should i use. I also want to know the data transformation I used, relative abundance, and the statistical test of the study, which I used, Mann-Whitney (Wilcoxon). > please, I want to know if I am on the right track.https://bugsigdb.org/33596997Thank you. - Attachment (BugSigDB): Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors - BugSigDB > BACKGROUND: Gastric adenocarcinoma is associated with H.pylori infection and inflammation that can result in the dysbiosis of gastric microbiota.

Joy (08:06:28) (in thread): > Such a fun and informative way to test my knowledge!:brain::petri_dish:I really enjoyed learning more about how our bodies interact with the trillions of microbes we carry around. Thanks,@svetlana_up, for putting this! #MicrobiomeMatters

Anne-Marie Sharp (08:42:01) (in thread): > Well done@Precious Orakwe, you can only curate a continuous region on bugsigdb, so maybe you curate one region and leave a note on the others:thinking_face:

Anne-Marie Sharp (09:16:51) (in thread): > The article states ‘We usedALDEx2to identify taxonomic groups that showed significant (p < = 0.05) differences in paired group comparisons. The ALDEx2 R implementation takes advantage of theclr transformationfor relative abundances to remove compositionality bias, and provides empirical p-values with Benjamini–Hochberg FDR correction’ > PS: Following this thread to learn how to curate ALDEx2 as a statistical test:upside_down_face:

Precious Orakwe (09:18:24) (in thread): > which thread please?@Anne-Marie Sharp

Anne-Marie Sharp (09:20:14) (in thread): > @Precious OrakweI mean this comment section, I mean I want to read other reviews other people will give here, to learn.

Precious Orakwe (09:20:42) (in thread): > I saw all that, but I am confused because I can’t find anything like ALDEx2 and clr transformation, could the clr be log transformation? of them in BugSigDB when curating.

Mildred Anashie (10:19:27) (in thread): > Hi@Precious OrakweCLR is CenteredLog-Ratioon BugSigdbI’lllook through the article for your other question

Precious Orakwe (10:57:35) (in thread): > Yes,@Mildred Anashie, that is it, thank you, I wanted to be sure and for the ALDEx2, I am thinking of using DEseq or ANCOM-BC, what do everyone think?

Mildred Anashie (11:01:59) (in thread): > Still going through to understand the data transformation but for the statistical test I think recording Mann-whitney (Wilcoxon) works. I got that from this article and out of all the test listed, this fits {Mann-whitney (Wilcoxon)} based on your articlehttps://www.bioconductor.org/packages/release/bioc/html/ALDEx2.htmlFor the variable region I believe choosing V2 for lower and V9 for upper would work as that covers all the mentioned regions and then you drop a note on it. - Attachment (Bioconductor): ALDEx2 > A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcoxon Rank Sum test and Welch’s t-test (via aldex.ttest), a Kruskal-Wallis test (via aldex.kw), a generalized linear model (via aldex.glm), or a correlation test (via aldex.corr). All tests report predicted p-values and posterior Benjamini-Hochberg corrected p-values. ALDEx2 also calculates expected standardized effect sizes for paired or unpaired study designs. ALDEx2 can now be used to estimate the effect of scale on the results and report on the scale-dependent robustness of results.

Adeshile Oluwatosin (12:01:52) (in thread): > Well done@Precious Orakwe > * Table 2, Figure 4 and Table 3 statistical test is ALDEx2, they specified in the article that it was used for pairwise comparison which reflects in the stated table/figures. > > * Since it’s not currently curatable. There was mention of mann-U Whitney to test significance of group comparisons, so you can use this. MHT is yes. > * Data transformation should becentered log ratio in this case > * Record the region to be V2-V9 I believe (it covers all)

Precious Chijioke (14:52:56) (in thread): > Well done on your curation@Precious OrakweHaving gone through the article, I agree with what@Adeshile Oluwatosinand@Mildred Anashiesaid.

Precious Chijioke (15:02:42) (in thread): > Amazing quiz. I had fun answering the questions and learning more on how our bodies interact with microbes to function effectively. I failed only one. Thank you@Svetlana Ugarcina Perovicfor sharing the quiz for us to participate.

Antonia Beatriz Soler Riera (16:17:15): > Hello I hope you are all fine, I am very happy that@Anne-Marie Sharpand I worked together in this curationhttps://bugsigdb.org/39748236. We would like a peer-review please. - Attachment (BugSigDB): A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population - BugSigDB > BACKGROUND: The complex relationship among sleep, exercise, and the gut microbiome presents a unique opportunity to improve health and wellness.

Mildred Anashie (19:36:10) (in thread): > Well done@Antonia Beatriz Soler Rieraand@Anne-Marie SharpI’lltake a look

2025-04-23

Adeshile Oluwatosin (02:20:11) (in thread): > Well done@Anne-Marie Sharp@Antonia Beatriz Soler RieraGood morning > * Figure 4B, Table 2comparison was strictly between Placebo and Probiotics. Hence, placebo (group 0) and probiotics (group 1). > * Curate figure 4D seperately [Baseline (group 0) vs probiotics (group 1) ] see here: “The abundance of the Lactobacillaceae family increases with probiotic use but not placebo” if you read further it was stated to be significant. > * I can’t find the mention of linear model as a test. Statistical test seems to be t-test. See “A two-tailed t-test was performed to determine whether there were significant differences between the groups.” > * Shannon is unchanged for the experiments as

Anne-Marie Sharp (03:17:19) (in thread): > Good morning, thank you@Adeshile Oluwatosin1)Figure4b seems to be plotted from Table2. Figure 4b caption: A longitudinal analysis.….change over timewith placebo ******and / or with******* probiotic.** That is: 1)With both placeboandprobiotic 2)With placeboor*3)with probiotic > 2)That’s why we curated fig 4d with baseline vs probiotic in Exp2. Our concern is, figure 4d uses log transformation so should it still be curated separately from Exp2? > 3)The two-tailed t-test was for testosterone analysis > 4)The statistical test used was: ‘Qiime2 longitudinal module, specifically volatility analysis, was used to calculate net average abundance changes of taxa over the course of the study.’ > And this Qiime2 volatility analysis is stated to be a supervised regression model in the Qiime2 documentation. Please what do you suggest in this case?

Anne-Marie Sharp (03:20:38) (in thread): > 5)The comparison of either probiotic/placebo is from baseline: ’However, a longitudinal analysis of the data using net average change in abundance calculated as a part of Qiime2’s longitudinal module volatility analysis identified 11 taxa that significantly increased or decreased in relative abundancefrom baseline(Fig. 4b, Table 2)

Adeshile Oluwatosin (03:33:41) (in thread): > I understand your interpretation. It seems to be more appropriate curating as analyzed. > > I will need togo overthe article one more time

Svetlana Ugarcina Perovic (04:09:06) (in thread): > Recording V2-V9 is misleading. Please leave also a note: Primer set V2, V4, V8 and Primer set V3, V6-7, V9 was used in sequencing.

Adeshile Oluwatosin (04:10:06) (in thread): > Thank you for clarifying:pray:@Precious Orakwesee this

Svetlana Ugarcina Perovic (04:19:41): > :coffee::teapot::tulip:Good morning, I’m back! (Yesterday, BugSigDB did not work for me, imagine that?! Now, everything is ok.) I will reply to you all asap. > > Just wanted to share with you some microbiome/bioinformatics learning/fun resources that might be of your interest. Some time ago, I started compiling several lists (& still regularly updating them!):Microbiome eventshttps://github.com/SvetlanaUP/Microbiome-conferences-cMicrobiome podcastshttps://github.com/SvetlanaUP/Microbiome-etc-PodcastsBioinformatics learning resourceshttps://github.com/SvetlanaUP/A-microbiologist-wants-to-compute

Adeshile Oluwatosin (04:20:54) (in thread): > Another day to say thank you for all you do:pleading_face:

Adeshile Oluwatosin (04:22:34) (in thread): > R and python:muscle:

Mildred Anashie (04:23:23) (in thread): > Glad to have you back@Svetlana Ugarcina PerovicThank you for the resources:blush:

Montana-D (04:25:05) (in thread): > Thank you for these resources:raised_hands::fire:

Adeshile Oluwatosin (04:26:12) (in thread): > I think it should be pinned:pleading_face:@Svetlana Ugarcina PerovicGreat resources

Aiysha shahid (04:27:23) (in thread): > Thanks a lot of these resources!:tulip:

Ameenat Oloko (04:35:36) (in thread): > Thank you for sharing these resources,@Svetlana Ugarcina Perovic. Glad to have you back:heart:

Ameenat Oloko (04:49:18) (in thread): > This was an interesting quiz! I got all the answers:partying_face:I liked how they explained the concept of each answer, as it provided more insights. Thank you for putting this out,@Svetlana Ugarcina Perovic.You’re highly appreciated:face_holding_back_tears:

Joy (04:51:20) (in thread): > It’s wonderful to have you back@Svetlana Ugarcina Perovic. Glad to hear BugSigDB is working now! Thanks for the resources:sparkles:

Eseoghene Cynthia Princewill-Ukot (04:52:02) (in thread): > Glad to have you back@Svetlana Ugarcina Perovic. Thanks for sharing these resources and thanks for all you do:tulip::kissing_heart:

Anne-Marie Sharp (04:52:17) (in thread): > Welcome back@Svetlana Ugarcina Perovicthank you for sharing these,it’slike an entire roadmap:heart:

Precious Orakwe (04:52:43) (in thread): > Thank so much@Svetlana Ugarcina Perovic

Precious Orakwe (04:54:33) (in thread): > Thank you@Svetlana Ugarcina Perovicand welcome back

Precious Chijioke (05:03:50) (in thread): > Thank you for the clarity@Svetlana Ugarcina Perovic

Precious Chijioke (05:06:52) (in thread): > Welcome back@Svetlana Ugarcina PerovicThank you for sharing these resources > Glad to hear that BugSigDB is working now

Svetlana Ugarcina Perovic (05:27:39) (in thread): > I also like the explanation part!

Juliana Kentomahun Mautin (08:45:54) (in thread): > Awesome:sunglasses::sunglasses::sunglasses:…Thank you for this treasure trove of resources, I’m genuinely impressed by how thoughtfully curated and regularly updated these lists are. It’s clear you’ve poured a lot of time, care, and curiosity into them. Thank you so much once again@Svetlana Ugarcina Perovicfor all you do for us here. I’m glad to hear BugSigDB is back up and running.

Juliana Kentomahun Mautin (08:50:19): > Hello everyone:blush:, Just a quick reminder about our weekly team meeting: Thursday at 9 AM EST athttps://us02web.zoom.us/j/2737200499cc<@UBNSEMS3S>NOTE: You can check your time here:https://www.timeanddate.com/worldclock/converter.html?iso=20250417T130000&p1=179&p2=37&p3=176&p4=3395&p5=125 - Attachment (timeanddate.com): Time Zone Converter – Time Difference Calculator > Find the exact time difference with the Time Zone Converter – Time Difference Calculator which converts the time difference between places and time zones all over the world.

Precious Chijioke (11:05:57): > Good Day Everyone, I would love a peer review on this studyhttps://bugsigdb.org/40059170 - Attachment (BugSigDB): Smoking-related gut microbiota alteration is associated with obesity and obesity-related diseases: results from two cohorts with sibling comparison analyses - BugSigDB > BACKGROUND: Individuals who smoke tend to have a lower body mass index (BMI) but face an increased risk of obesity-related diseases.This study investigates this paradox from the perspective of gut microbiota.

Precious Chijioke (11:15:45) (in thread): > Well done@Antonia Beatriz Soler Rieraand@Anne-Marie Sharpon your curation

Anne-Marie Sharp (11:44:19) (in thread): > Well done@Precious Chijiokewe’ll review

Mildred Anashie (11:48:54) (in thread): > Well done@Precious ChijiokeWe’ll take a look

Mildred Anashie (11:51:01): > Hi Everyone > I just finished curating this study and I am putting it up for peer review. Thank you in anticipation for your feedback (I would appreciate a second pair of eyes on the conditions just to be sure)https://bugsigdb.org/35985814 - Attachment (BugSigDB): Inflammation in Children with CKD Linked to Gut Dysbiosis and Metabolite Imbalance - BugSigDB > BACKGROUND: CKD is characterized by a sustained proinflammatory response of the immune system, promoting hypertension and cardiovascular disease.The underlying mechanisms are incompletely understood but may be linked to gut dysbiosis.

Precious Chijioke (12:01:20) (in thread): > @Anne-Marie Sharp@Antonia Beatriz Soler Rieracurate Figure 4d differently. The abundance of the Lactobacillaceae family increases with probiotic use but not placebo. Group 0 as Placebo and Group 1 as Probiotic.

Precious Chijioke (12:02:19) (in thread): > Well done@Mildred AnashieWe’ll take a look

Mildred Anashie (12:18:14) (in thread): > I thibk 4d should be curated separately@Anne-Marie SharpFor the test, what I saw was that it is “A supervised learning regressor is used to identify important features and assess their ability to predict sample states.” > > So I am unsure if Linear model really works here

Precious Orakwe (12:48:28) (in thread): > Well done@Mildred Anashiethe condition is ok

Precious Orakwe (13:00:56) (in thread): > Well done@Precious Chijioke

Anne-Marie Sharp (14:29:47) (in thread): > We’ll confirm which statistical test to use during office hour@Mildred Anashiethank you, to curate 4d separately from Exp2 with the data transformation as log transformation, right?:thinking_face:

Montana-D (15:40:43) (in thread): > well done on your curation@Precious Chijioke

Anne-Marie Sharp (15:55:15) (in thread): > Well done again@Precious ChijiokeI have some observations

Anne-Marie Sharp (15:55:22) (in thread): > 1)Confounders controlled for should be: ‘unmeasured confounders shared within families’ or ‘unmeasured familial factors’ as stated in the article, which include genetic factors, environmental factors etc. ‘Sibling’ doesn’t seem appropriate. > 2)Include the statistical test in Exp 2 > 3)Body site is feces > 4)Curate the Sequencing details(Illumina, V3 -V4 etc) & all the alpha diversities from the supplementary material

Anne-Marie Sharp (15:56:52) (in thread): > Well done@Mildred Anashiewe’ll review

Precious Chijioke (16:01:55) (in thread): > Thank you@Anne-Marie Sharp

Montana-D (16:04:19) (in thread): > Great job on your curation:raised_hands:

Mildred Anashie (16:42:53) (in thread): > Well done again@Precious Chijioke > * I agree with siblings not being the confounder@Anne-Marie Sharp, the caption for figure 1 and Table S2 states the actual confounders and it looks like it’s only for the Well-china cohort. See this excerpt, and read the caption to understand better “comparing different smoking status, adjusted for age, marital status, education, annual income, alcohol consumption, physical activity, diet energy intakes, nutritional supplements, district of residence, antibiotics use (except for Lanxi cohort due to the lack of corresponding information)”. > * I do not see Group 0 sample size for the experiments, check the supplementary material for that information also Table S2 is curatable > * C2 and D2 should be curated differently from C1 and D1. This is an excerpt from the article, “These genera demonstrated a positive association with various obesity metrics, including BMI, body fat percentage, and central fat distribution parameters such as waist circumference, WHR, android fat percentage, and AOI, while exhibited a negative association with gynoid fat percentage (Fig. 1* C2 & D2).” > You have more alpha diversity indices in Fig S2 all are Unchanged though, but curate them all. > * I don’t see Matched on being mentioned, you could probably point me to it I might have missed it.

2025-04-24

Joy (03:22:21): > Hi everyone,@Montana-Dand I have completed the curation of our studyhttps://bugsigdb.org/39843443and would really appreciate your peer review and feedback. > Please note that some unrelated experiments are still pending deletion, so feel free to focus on the main curated content. Thanks in advance for your time and input!

Mildred Anashie (03:51:51) (in thread): > Well done@Montana-D@Joy

Mildred Anashie (03:52:48) (in thread): > This is a little confusing > Is it just experiment 1 and the other experiments would be deleted?

Anne-Marie Sharp (03:55:29) (in thread): > Nice work@Mildred AnashieI think the conditions are okay > 1)For the sample sizes of each group, from Fig. S1 you should use the stool sample sizes(the actual number of samples that were analyzed), not the general group sample size. > 2)Exp3 should also have matched on

Anne-Marie Sharp (04:03:16) (in thread): > Well done@Montana-D@Joykindly confirm if the entire curation is just Exp1 .

Mildred Anashie (04:08:13) (in thread): > Thank you@Anne-Marie SharpFor the sample sizes, I am not entirely convinced if I should record the stool sample sizes because the groups are patients (Humans) and I believe it should be the humans recruited for the study:thinking_face:

Anne-Marie Sharp (04:11:45) (in thread): > You’re welcome@Mildred AnashieYou can confirm it, but I think it should be the samples analyzed

Svetlana Ugarcina Perovic (04:13:07) (in thread): > Update: 39843443/Experiment 2-39 deleted

Mildred Anashie (04:14:10) (in thread): > Okay > Thank you for the update@Svetlana Ugarcina Perovic

Joy (04:14:59) (in thread): > Yes@Mildred Anashie. Yes@Anne-Marie Sharp

Joy (04:15:23) (in thread): > Thank you@Svetlana Ugarcina Perovic

Anne-Marie Sharp (04:16:18) (in thread): > @Mildred AnashieCheck out Fig 2d caption: ‘Analysis of gut microbiota from 16S ribosomal RNA sequencing in children (n=32)’ It states 32, and its the stool sample sizes for each group that add up to 32. If you use the general group sizes you will have 48

Adeshile Oluwatosin (04:20:24) (in thread): > Well done@JoyI will look through

Precious Chijioke (04:23:57) (in thread): > Thank you,@Mildred Anashie, the actual sample size for the experiments is in the supplementary material.

Precious Chijioke (04:25:26) (in thread): > Well done@Joyand@Montana-DI’ll look through

Mildred Anashie (04:28:24) (in thread): > Yes@Precious ChijiokeThat’s what I pointed out, but it’s not recorded in the experiments you curated

Precious Chijioke (04:31:52) (in thread): > @Mildred AnashieYes, I curated the group size in the study and needed to confirm the Group 0 size. Thank you for referring to the supplementary material earlier. I found the actual size for each group in the supplementary information.

Precious Chijioke (04:38:24) (in thread): > Hello@Mildred Anashie, the condition is okay. > I agree with what@Anne-Marie Sharpsaid. However, you can also confirm the sample sizes to be used during the office hours.

Mildred Anashie (04:49:56) (in thread): > Hi@Joy@Montana-D > * The condition should be ‘Diet measurement’ because they were checking effect of the diet in the intervention group and the volunteers were undergoing measurement checks > * Can someone confirm Figure S4 isn’t curatable > * I think only BMI was used as a covariate, I didn’t see mention of Sex and Age maybe you could point me to it. See the excerpt, “The randomization by minimization technique was applied in assigning volunteers to the treatment arms with a 1:1 allocation criteria. ******The BMI measured during the screening visit was used as the covariate ******to ensure the two intervention arms are balanced.”**

Mildred Anashie (04:51:32) (in thread): > Okay > > Thank you@Precious ChijiokeThanks again@Anne-Marie Sharp

Anne-Marie Sharp (05:06:05) (in thread): > 1)I didn’t see antibiotics exclusion > 2) I think the confounders controlled for should be only ‘Sex’. Sex was controlled for because participants were stratified by sex during randomization, while BMI was only used to balance the groups not analyzed or adjusted for statistically. > 3)I also think Figure S4 should be curated

Mildred Anashie (05:11:25) (in thread): > Hi@Anne-Marie SharpI have looked through again and I see where they mentioned stratifying for sex, so the confounders should be sex and BMI (BMI was definitely a confounder controlled for as it was used as a covariate)

Joy (05:15:55) (in thread): > Thank you@Mildred Anashieand@Anne-Marie Sharpfor your feedbacks. The antibiotics exclusion was mentioned in the supplementary material. This one.:point_down: - File (Word Document): 41467_2025_56084_MOESM6_ESM.docx

Joy (05:16:24) (in thread): > We will effect the changes. Thank you all.@Mildred AnashieFig S4a & b was curated alongside Fig. 3F

Precious Chijioke (05:22:52) (in thread): > @JoyI agree with what@Mildred Anashie@Anne-Marie Sharpsaid. Figure S4 is curatable. I have seen the antibiotics exclusion in the supplementary material you shared. If you curated Fig. 4a & b alongside Fig. 3F you should mention it in the signature source.

Anne-Marie Sharp (05:23:53) (in thread): > Thank you for pointing that out@Joyyou should include it in your source then.@Mildred AnashieYou’re right that BMI was used as a covariate during randomization,:thinking_face:but I’m thinking as per curation rules, that is considered design balancing, not statistical control. To count as a confounder controlled for, BMI would need to have been included in aregression modelor used tostratify results, neither of which is mentioned for BMI itself.

Joy (05:28:01) (in thread): > Sure. Thanks

Mildred Anashie (05:45:17) (in thread): > I think it should have been curated separately, even though it was cited together in text, we can see that the results in S4 is based on different weeks@Anne-Marie SharpMy opinion is thatBMIwasused as a covariateduring therandomization by minimizationprocess. > This means the researchers wanted to ensure that BMI wasevenly distributedbetween the intervention and control groups avoiding a situation where one group has significantly more overweight or underweight participants going by this I believe BMI should be recorded because it was reported by the researchers and I don’t see why it should be left out

Montana-D (06:00:21) (in thread): > @Mildred Anashie@Anne-Marie Sharp@Precious Chijioke, thank you all for your reviews an inputs, we greatly appreciate:raised_hands:

Montana-D (08:58:02): > It is Office Hour O’clock Ladies:bioc:https://community-bioc.slack.com/archives/C04RATV9VCY/p1745412619869849 - Attachment: Attachment > Hello everyone :blush:, Just a quick reminder about our weekly team meeting: Thursday at 9 AM EST at https://us02web.zoom.us/j/2737200499 > > cc @UBNSEMS3S > > NOTE: You can check your time here: https://www.timeanddate.com/worldclock/converter.html?iso=20250417T130000&p1=179&p2=37&p3=176&p4=3395&p5=125

Juliana Kentomahun Mautin (09:02:51) (in thread): > Thank you

Svetlana Ugarcina Perovic (09:05:57): > FYIhttps://waldronlab.io/BugSigDBStats/articles/BugSigDBStats.html

Joy (09:28:08) (in thread): > Thank you@Svetlana Ugarcina Perovic

Precious Chijioke (09:28:55) (in thread): > Thank you@Svetlana Ugarcina Perovic

Precious Chijioke (09:29:26): > Thank you for today’s office hour@Svetlana Ugarcina Perovic<@UBNSEMS3S>

Ameenat Oloko (10:01:39): > Good day, everyone. Kindly give a peer review of this study. Thank you.StudyArticle - Attachment (BugSigDB): Stunted microbiota and opportunistic pathogen colonization in caesarean-section birth - BugSigDB > Immediately after birth, newborn babies experience rapid colonization by microorganisms from their mothers and the surrounding environment1.Diseases in childhood and later in life are potentially mediated by the perturbation of the colonization of the infant gut microbiota2. - Attachment (PubMed Central (PMC)): Stunted microbiota and opportunistic pathogen colonisation in caesarean section birth > Immediately after birth, newborn babies experience rapid colonisation by microorganisms from their mothers and the surrounding environment1. Diseases in childhood and later in life are potentially mediated through perturbation of the infant gut …

Montana-D (10:04:05) (in thread): > Great job on your curation. Will have a look

Ameenat Oloko (10:06:43) (in thread): > I added some notes regarding the condition of the experiment, too.https://bugsigdb.org/w/index.php?title=Talk%3A31534227#Condition_of_the_Experiment - Attachment (BugSigDB): Talk:31534227 > .

Antonia Beatriz Soler Riera (10:11:54): > Hello everyone,@Anne-Marie Sharpand I are still curating this articlehttps://bugsigdb.org/39748236and we have 2 doubts after peer review. > We weren’t able to ask the questions during office hour due to connection problems. > We need help with the statistical test. 1)In page 5 section “metagenomics data processing and analysis” the last sentence says “we opted to use Wilcoxon tests to compare treatments, unless otherwise stated.” Is that enough to assume Wilcoxon in the curation of figure 4b & Table 2? > 2)Figure 4d depicts relative abundance of a different taxa than 4b in log scale, should this be curated in a different experiment with data transformation as log transformation? > Please@Svetlana Ugarcina Perovicand<@UBNSEMS3S>give us your opinion when you have time. Thank you. - Attachment (BugSigDB): A Lactobacillus consortium provides insights into the sleep-exercise-microbiome nexus in proof of concept studies of elite athletes and in the general population - BugSigDB > BACKGROUND: The complex relationship among sleep, exercise, and the gut microbiome presents a unique opportunity to improve health and wellness.

Anne-Marie Sharp (10:20:23) (in thread): > Well done@Ameenat Olokowe’ll review

UBNSEMS3S (10:25:41) (in thread): > QIIME2’s longitudinal module uses mixed effects regression so that’s the answer for Figure 4B/Table 2.

UBNSEMS3S (10:27:23) (in thread): > 4D does appear to be Kruskal-Wallis and therefore a different test and experiment.

Antonia Beatriz Soler Riera (10:28:38) (in thread): > Thank you

Anne-Marie Sharp (10:29:25) (in thread): > Thank you:pray:

UBNSEMS3S (10:29:51): > Office hours recording. Thank you all who attended. As a reminder, we are not meeting next week. We will reconvene on May 8th. - File (MPEG 4 Video): bsdb 2025_04_24.mp4

Montana-D (10:33:50) (in thread): > Thank you so much

Anne-Marie Sharp (10:40:31) (in thread): > Noted. Thank you:pray:

Mildred Anashie (10:47:42) (in thread): > Thank you for the office hours<@UBNSEMS3S>

Mildred Anashie (10:49:45) (in thread): > Hi@Ameenat OlokoI’lltake a look

Montana-D (10:55:42) (in thread): > @Ameenat Oloko > 1. I don’t think Fig. 3a, Extended Data Fig. 4, Supplementary Table 4 should be curated together. > 2. I don’t thinkStreptococcus vestibularis should be curated as i don’t see any differences in their migrations

Joy (10:58:40) (in thread): > Thanks<@UBNSEMS3S>

Precious Orakwe (11:43:01) (in thread): > Noted, thank you.

Precious Orakwe (11:47:35): > Good day everyone. I would love a peer review for this study. Also see the condition if it’s ok, and the body sites , there was no sequencing platform and type in the study, i don’t know if i’m wrong. > Every corrections and suggestions are highly welcome.https://bugsigdb.org/34264976Thank you. - Attachment (BugSigDB): Effect of the HXBM408 bacteria on rat intestinal bacterial diversity and the metabolism of soybean isoflavones - BugSigDB > The purpose of this study was to investigate the effect of the HXBM408 bacteria on the diversity of rat intestinal bacteria and the metabolism of soybean isoflavones.The control group was administered sterilized water and daidzein by gavage for 7 days.

Juliana Kentomahun Mautin (11:53:52) (in thread): > Thank you<@UBNSEMS3S>

Mildred Anashie (11:59:53) (in thread): > Hi@Precious OrakweWell doneI’lltake a look at this

Ndukauba Oluchi (12:10:01): > Hello everyone, please i would love a peer review on this studyhttps://bugsigdb.org/39941005Link to paper:https://www.mdpi.com/1422-0067/26/3/1236 - Attachment (BugSigDB): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features - BugSigDB > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. - Attachment (MDPI): Different Efficacy of Five Soluble Dietary Fibers on Alleviating Loperamide-Induced Constipation in Mice: Influences of Different Structural Features > Different dietary fibers have distinct structures, leading to significant variations in their laxative effects. To explore how these structural differences impact constipation intervention, a 14-day study was conducted on loperamide-induced constipated mice using five dietary fibers: soluble dietary fiber from steamed sweet potato (SDF-S), oat β-glucan (OB), polydextrose (PD), arabinogalactan (AG), and inulin (IN). The results showed that four fibers, excluding PD, significantly improved gastrointestinal (GI) transit rate (p < 0.05), although PD had the highest fecal moisture, it was significantly different from the lowest IN (p < 0.05). AG and IN resulted in higher 6 h fecal weights compared to other fibers. SDF-S and OB were more effective in modulating serum levels of gastrointestinal hormones. The different monosaccharide compositions and glycosidic bonds of these fibers led to distinct changes in gut microbiota composition and SCFA profiles. Galactose and arabinose in AG were linked to increased abundance of Lachnospiraceae_UCG-006, Bacteroides, and Odoribacter, promoting butyrate fermentation, which is positively correlated with GI transit rate. Glucose in SDF-S, OB, and PD favored acetate fermentation positively correlated with fecal moisture. Fructose in IN encouraged the proliferation of Muribaculaceae_unclassified and Ruminococcus, associated with butyrate fermentation and increased 6 h stool weight, respectively. The β-glycosidic bonds in OB may lead to high butyrate production through the selective proliferation of Lachnospiraceae_unclassified. Minor components like fucose, rhamnose, and ribose were positively correlated with the abundance of Oscillospiraceae_unclassified, Anaerotignum, and Lachnospiraceae_unclassified. In conclusion, the unique monosaccharide compositions and glycosidic bond differences in dietary fibers selectively promote the proliferation of fiber-degrading and butyrate-producing bacteria, resulting in varied effects on constipation relief.

Ndukauba Oluchi (12:13:11) (in thread): > Great job@Precious Orakweplease drop the link to the paper as well

Precious Orakwe (12:17:11) (in thread): > The link to the paper is in the study, click on the PMID number or the doi link.

Montana-D (12:17:49) (in thread): > Well done, I’ll have a look

Precious Chijioke (12:17:57) (in thread): > Noted, thank you<@UBNSEMS3S>

Precious Chijioke (12:20:31) (in thread): > Well done on your curation@Ameenat Oloko

Precious Orakwe (12:32:10): > Well done@Ndukauba Oluchi

Montana-D (12:39:51) (in thread): > Well done on your curation

Montana-D (12:41:40) (in thread): > Does experiment 7 have any signatures?

Mildred Anashie (12:41:43) (in thread): > I agree with@Montana-DFigure 3a should not be curated with Extended data Fig 4. > * You have two experiments from figure 3a Vaginal vs Caesarean Early transmission (Neonatal period) and Vaginal vs Caesarean Late transmission (Infancy period), while Extended data figure 4 is still this Vaginal vs Caesarean Early transmission (Neonatal period) but different sample sizes and the statistical tests for this three experiments would be Welch’s t test as stated in the article > * Supplementary table 5 has about 12 covariates adjusted for in a model using MaAsLin and it’s showing increase and decreased taxas, I think you should focus on the significant q values (adjusted p values) to streamline the work. The only thing I’m unclear of is why some taxas were highlighted in green and red. Someone should please help crosscheck that. > Well done again:clap:

Ndukauba Oluchi (12:49:31) (in thread): > Okay@Precious Orakwe > 1. So i think the Condition of the study should be ” Treatment Outcome measurement” seeTherefore, in this study, the soybean isoflavone transformant HXBM408 (Pediococcus acidilactici) isolated from the fresh feces of pregnant horses was cultured in vitro, and the cultured fresh broth was orally administered to SD rats to investigate the transformation of soybean isoflavones. > 2. The body site is “Feces and Intestine secretion(that is the closest to intestinal content)” because those where the samples used for the Lefse analysis. > 3. Statistical tests should be “Lefse”

Ndukauba Oluchi (12:50:46) (in thread): > yes@Montana-Dhttps://bugsigdb.org/39941005/Experiment_7/Signature_1 - Attachment (BugSigDB): 39941005/Experiment 7/Signature 1 > Source: 4D,F,G,K,L Description: Relative Abundance of genera in the gut microbiota of mice Abundance in Group 1: increased abundance in Inulin group (IN) Revision…

Montana-D (12:54:39) (in thread): > I’m unable to find the reason for the color differences aswell

Montana-D (12:56:22) (in thread): > There’s this little trick to make it appear, > * edit the experiment 7 and change it to incomplete and save > * edit the same experiment again. This time, edit as complete and save > * This should solve it and make it appear

Ameenat Oloko (13:19:44) (in thread): > Thank you so much@Mildred Anashieand@Montana-D. I’ll make these corrections.

Amaan (13:41:10): > :wave:Hello, team! Myself Amaan

Montana-D (14:17:14) (in thread): > Hello@AmaanWelcome

Ameenat Oloko (14:56:55) (in thread): > @Mildred Anashie,@Montana-DFigure 3a (early and late transmission) has the same organisms. The decrease in microbial signatures was calculated by short/missing blue bars (caesarean section),that’swhyI curated them together. > > Also, extended data in Figure 4 has organisms similar to those in Figure 3, so I contemplated curating it separately to avoid duplication.Do you think curating them separately (even with the same microbial signatures)would be appropriate?

Ameenat Oloko (14:59:04) (in thread): > For the statistical tests, are you saying I should remove Fischer’s exact test and write Welch’s test instead?

Ameenat Oloko (15:01:58) (in thread): > See this@Mildred Anashie,to assess if the neonatal microbiota variation could be attributed to differential transmission of maternal microbiota, we profiled the bacterial strain transmission across 178 mother-baby dyads. We show that the majority of maternal strain transmissions during the neonatal period occurred in vaginally delivered babies (74.39%), at much higher frequency in comparison with those delivered by C-section (12.56%, Fisher’s exact test, P<0.0001, Fig 3a, Extended Data Fig. 4, Supplementary Table 4).

Mildred Anashie (15:03:18) (in thread): > Not entirely the same@Ameenat OlokoI can see up to 4 taxas increased in C section for Late but all taxas for early are increased in Vaginal which means for Late you’d have both increase and decrease signatures > > Fig 4a doesn’t appear curatable to me and Extended fig 4 has same groups but the contrast is a bit different with different sample size, that means a different experiment > > Yes, you’d replace Fishers with Welch

Aiysha shahid (15:05:19) (in thread): > Hi@Amaan, Welcome to the community!:raised_hands:

Mildred Anashie (15:06:01) (in thread): > I missed this:woman-facepalming:@Ameenat Olokoto assess if the neonatal microbiota variation could be attributed to differential transmission of maternal microbiota, we profiled the bacterial strain transmission across 178 mother-baby dyads. We show that the majority of maternal strain transmissions during the neonatal period occurred in vaginally delivered babies (74.39%), at much higher frequency in comparison with those delivered by C-section (12.56%, Fisher’s exact test, P<0.0001, Fig 3a, Extended Data Fig. 4, Supplementary Table 4).Thank you for pointing it out, please retain the test - Attachment (PubMed Central (PMC)): Stunted microbiota and opportunistic pathogen colonisation in caesarean section birth > Immediately after birth, newborn babies experience rapid colonisation by microorganisms from their mothers and the surrounding environment1. Diseases in childhood and later in life are potentially mediated through perturbation of the infant gut … - Attachment (PubMed Central (PMC)): Stunted microbiota and opportunistic pathogen colonisation in caesarean section birth > Immediately after birth, newborn babies experience rapid colonisation by microorganisms from their mothers and the surrounding environment1. Diseases in childhood and later in life are potentially mediated through perturbation of the infant gut … - Attachment (PubMed Central (PMC)): Stunted microbiota and opportunistic pathogen colonisation in caesarean section birth > Immediately after birth, newborn babies experience rapid colonisation by microorganisms from their mothers and the surrounding environment1. Diseases in childhood and later in life are potentially mediated through perturbation of the infant gut …

Ameenat Oloko (15:08:17) (in thread): > Okay, thank you@Mildred Anashie. > To be clear on the curations, I should curate both the early and late transmissions for figure 3 (as they’re not entirely duplicates). Am I right?

Ameenat Oloko (15:10:23) (in thread): > Hello,@Amaan. Welcome!

Ameenat Oloko (15:11:49) (in thread): > I curated figure 4a because they stated in the article that it was significant.*The significance (P values indicated to the right of the bars) of the difference in mean **relative abundance and combined pathogen-carriage frequency between babies delivered vaginally or via caesarean section was determined by two-sided Wilcoxon signed-rank test and Fisher’s exact tests, respectively. *

Anne-Marie Sharp (15:14:30) (in thread): > Hello@Ameenat OlokoI also think you should curate the early & late transmissions for Fig 3 separately in 2 experiments. Figure 4a is curatable as you said

Mildred Anashie (15:14:36) (in thread): > Yes > > For 3a

Ameenat Oloko (15:16:12) (in thread): > Gotcha! Thank you,@Mildred Anashieand@Anne-Marie Sharp.

Precious Chijioke (15:19:05) (in thread): > @Ameenat OlokoI agree with what@Montana-D,@Mildred Anashieand@Anne-Marie Sharpsaid.

Precious Chijioke (15:20:40) (in thread): > Well done on your curation@Ndukauba OluchiWe’ll take a look

Precious Chijioke (15:21:32) (in thread): > Hello@AmaanWelcome to the community

Anne-Marie Sharp (15:29:40) (in thread): > Hello@Amaanyou are welcome

Ameenat Oloko (15:32:20) (in thread): > Well done,@Precious Orakwe. > * Yea, you’re right about the missing sequencing platform and type in the study.

Ndukauba Oluchi (15:39:29) (in thread): > @Ameenat Olokothat’s because Non was stated in the study.

Ameenat Oloko (15:40:46) (in thread): > Yea, I know that,@Ndukauba Oluchi.That’swhat I meant by that statement.

Ndukauba Oluchi (15:41:14) (in thread): > Oops!:joy::ok_hand:

Anne-Marie Sharp (15:50:33) (in thread): > Well done@Precious Orakweyou’re right on the sequencing details. I agree with@Ndukauba Oluchion the condition and body site. blood plasma should be removed from Exp1

Ameenat Oloko (15:53:41) (in thread): > @Ndukauba Oluchi, I didn’t see “intestine secretion” in the EFO database. Is it on the BugSigDB website?

Ndukauba Oluchi (16:01:16) (in thread): > On the EFO database@Ameenat Oloko

Ndukauba Oluchi (16:02:20) (in thread): > When you are adding an experiment, under the body cite, Click on “find a term” then you input the term you want to find.

Anne-Marie Sharp (16:08:19) (in thread): > @Precious Orakwe1) there’s a typo error in Exp1, Sig 1& 2, change ‘i testinal’ to ‘intestinal’ 2)Maintain Group0 as Control group & Group1 as Trial Group through your curation and if there is only decrease in the Trial group like in Exp6, then curate just one signature as decreased

Anne-Marie Sharp (16:08:36) (in thread): > @Ameenat Olokointestine secretion is actually on bugsigdb

Ameenat Oloko (16:19:44) (in thread): > Well done@Ndukauba Oluchi. I’m surprised, as I have only experiment 1 showing over here:confused:. I don’t know how Montana could see up to 7 experiments.

Anne-Marie Sharp (16:26:40) (in thread): > Well done with your curation@Ndukauba OluchiYour source should be exactly were you curated from, example, Exp1 should be Figure 4A,D,E,G,H,I,J,K,L

Anne-Marie Sharp (16:27:19) (in thread): > @Ameenat Olokotry refreshing the page, I can see up to Exp7 but you will have to manually search for Exp7 signature

Precious Orakwe (16:32:54) (in thread): > Hello@Amaan, welcome

Precious Orakwe (16:36:39) (in thread): > Yea i know@Anne-Marie SharpSig 2 in experiment 6 is a mistake,@Svetlana Ugarcina Perovicwill delete it, I’ve reported it already.

Precious Orakwe (16:38:41) (in thread): > Ok, thanks everyone for that, I thought my eye was paining me, because I have been searching the study since yesterday. This is what too much cassava flakes can cause.

Precious Orakwe (16:39:57) (in thread): > Its every other thing okay?

Anne-Marie Sharp (16:41:01) (in thread): > @Precious Orakweokay, still swap the groups in that Exp6 as I mentioned. Trial should be Group1, then you record the taxa as decreased. Everything else seems fine for me

Mildred Anashie (16:47:11) (in thread): > Hi@Precious Orakwe > * There’s a signature 3 in Experiment 2 you should request to delete it > * In Table 5 just Proteobacteria is significant and that is one experiment (35d intestinal - Control vs Trial). The body site for this experiment would be intestinal. Read the text for table 5 to get and the caption explains how to interpret the table (notice the letters attached to the values for proteobacteria). See an excerpt from the text,In rat feces, there was no significant difference between the experimental group and the control group at the portal level (P > 0.05), and the intestinal proteobacteria in the rat intestine group was significantly higher than that in the control group (P < 0.05). The difference at the other phylum levels was not significant (P > 0.05). > * This observation is same for Table 6 so you’d have to edit the experiments from this tables and use the letters denoted as superscripts to interpret significance. > * Each experiment should have just one body site, either feces or intestinal and the article denoted this beside each reported result. Like the Lefse A,B and C the body site is feces while D the body site is intestine secretion. Follow this for the tables too.

Anne-Marie Sharp (16:47:19) (in thread): > @Ndukauba OluchiCorrect the Group1 definitions in Exp 5 to 7, it should be soluble fibre doses of 400mg/kg bw/d not 70mg/kg bw/d and not phenolphthalein. Use the format in Exp1

Precious Orakwe (20:03:40) (in thread): > The experiment 6 and 7 is emphasising on the control group.

Precious Orakwe (20:06:18) (in thread): > @Mildred Anashiethank you

2025-04-25

Svetlana Ugarcina Perovic (02:08:30) (in thread): > Hello@Amaanwelcome to the community! Feel free to introduce yourself and ask questions: just to let you know:slightly_smiling_face:here are super cool people-happy and ready- to help you.

Amaan (02:16:14) (in thread): > Hello everyone!:blush:Thank you so much for the warm welcome — I truly appreciate it! > I’m Amaan Arif from India, currently in my final year of BTech Biotechnology. I’m passionate aboutbioinformatics, data analysis, and the microbiome-gut-brain axis. I’ve been working on personal and academic projects involving Python, R, and various bioinformatics tools.

Amaan (02:16:44) (in thread): > I joined this community tolearn, collaborate, and growwith like-minded people. I’m always open to guidance, mentorship

Svetlana Ugarcina Perovic (02:22:39) (in thread): > Anyone free to team up with@Amaanand do a very first his curation in a pair? I just approved his bugsigdb account.

Anne-Marie Sharp (02:25:33) (in thread): > Hello@Svetlana Ugarcina PerovicI can team up with@Amaan

Svetlana Ugarcina Perovic (02:26:57) (in thread): > Excellent.@Amaan@Anne-Marie Sharpenjoy your teamwork!

Anne-Marie Sharp (02:31:30) (in thread): > Thank you@Svetlana Ugarcina Perovic,@AmaanI have sent you a direct message in your inbox here on Slack

Svetlana Ugarcina Perovic (02:32:45) (in thread): > Since@Amaanis particularly interested in themicrobiome-gut-brain axisI opened this issue for you**** ****https://github.com/waldronlab/BugSigDBcuration/issues/780please make a comment there so I can assigned to you both.

Amaan (02:52:19) (in thread): > Hi@Svetlana Ugarcina Perovic, > Thank you so much for assigning this issue to us. I’m truly excited to begin my very first curation with@Anne-Marie Sharpand contribute to BugSigDB.

Amaan (02:52:27) (in thread): > Looking forward to working together!:raised_hands:

Adeshile Oluwatosin (03:45:56) (in thread): > Welcome@Amaan:clap:

Mildred Anashie (04:00:39) (in thread): > Welcome to the community@Amaan:raised_hands:

Mildred Anashie (04:01:48) (in thread): > I remember this@Ndukauba OluchiWell done, I’ll take a look

Precious Chijioke (04:02:34) (in thread): > Good Morning@Mildred Anashie, in Table S2, using the color differentiation, I discovered that most of the taxa recorded as increased is also found in decrease. e.g Clostridia, Clostridiales, Firmicutes, Ruminococcaceae, Gammaproteobacteria, etc are recorded as both increased and decreased taxa. How can it be curated? I haven’t seen where same taxa is recorded as both increased and decreased. I think Table S2 is not curatable. Please kindly help me confirm the recording of the signatures if it is curatable. Thank you

Ndukauba Oluchi (04:10:01) (in thread): > welcome@Amaan:tada:

Mildred Anashie (04:19:41) (in thread): > Good morning@Precious ChijiokeI was looking for this threads so you can go through, I don’t think that table should be left outhttps://community-bioc.slack.com/archives/C04RATV9VCY/p1710516856042729https://community-bioc.slack.com/archives/C04RATV9VCY/p1702466454771639 - Attachment: Attachment > Hi everyone > Is it possible for one taxa to be differentially abundant in two contrasting groups? - Attachment: Attachment > During today’s talk by Liao Herui (PhD Student of City University of Hong Kong) about his work on strain identification analysis (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10433603/), I remembered our discussion on why some signatures have the same species in decrease and increase reported? > > One of Liao’s slides had a nice illustration and helpful comment that I would like to share with you: > Different bacterial strains may have different biological properties due to the different genes: > for example, E. coli CFT073 and E. coli Nissle 1917, which are pathogenic and probiotic respectively, have a sequence similarity of 99.98% [https://pubmed.ncbi.nlm.nih.gov/30837975/]

Precious Chijioke (04:21:59) (in thread): > Thank you@Mildred Anashie, for sharing the thread. It’s very helpful.

Anne-Marie Sharp (04:23:05) (in thread): > Thank you for sharing this@Mildred Anashieit’s worthy to note:raised_hands:

Joy (04:38:06) (in thread): > Hi@Amaan, welcome to the community!

Amaan (04:45:59) (in thread): > Thank you all so much for the warm welcome — it truly means a lot to me!

Montana-D (04:48:21) (in thread): > Feel free to ask the dumpiest of questions and expect a constructive response from someone here > Anything which helps you understand better or remove blockers in your path

Mildred Anashie (04:48:54) (in thread): > You are welcome@Precious Chijioke@Anne-Marie SharpI just went through the table@Precious Chijiokeand thats not exactly the case here because i see both increase and decrease for Well China and for Lanxi and I believe that implies two separate experiments. > > See where it’s explained in the article and what the groupings are, ’’In the WELL-China cohort (the discovery cohort), 50 microbial genera displayed an association with current smoking compared to never smoking (Additional file 1: Table S2). Similarly, in the Lanxi cohort (the replication cohort), 19 microbial genera showed an association with current smoking. Nine smoking-related gut microbial genera in the WELL-China cohort were successfully replicated in the Lanxi cohort (FDR < 0.25).’’It also appears to be the same comparison and statistical test with the experiments you have curated in C1 and D1, I’m thinking it should be curated together > > And C2:D2 looks like associations based on obesity metrics such as BMI, body fat percentage, and central fat distribution parameters such as waist circumference, WHR, android fat percentage, and AOI. > This was stated above and I believe it should be curated based on each metric but I’ll like some other opinions on this.@Adeshile Oluwatosin@Anne-Marie Sharp@Victoria (Burah) Poromon@Montana-Da little help here please.

Precious Chijioke (05:03:56) (in thread): > @Mildred Anashieyes, there are 2 experiments in Table S2, and same comparison and statistical test with the experiments I curated C1 and D1. The increase and decrease taxa for Well China and for Lanxi is recorded differently and some taxa are same for both increased and decreased which you have already addressed earlier. > Check this: > Bacteria.Firmicutes.Clostridia.Clostridiales.Lachnospiraceae.Tyzzerella_4 (Increased) > Bacteria.Firmicutes.Clostridia.Clostridiales.Ruminococcaceae.Ruminococcaceae_UCG.013 > > Bacteria.Firmicutes.Clostridia.Clostridiales.Lachnospiraceae.Hungatella (Decreased) > Bacteria.Firmicutes.Clostridia.Clostridiales.Ruminococcaceae.Ruminococcaceae_UCG.004 > > I curated C2 and D2 differently because it’s association is based on obesity metrics.

Montana-D (05:14:31): > Good day everyone@Mildred Anashieand I just completed the curation of this study (BugSigDB Link) > We will greatly appreciate a review of it, every response will be greatly appreciated > Thank you all - Attachment (BugSigDB): Gut microbiome in endometriosis: a cohort study on 1000 individuals - BugSigDB > BACKGROUND: Endometriosis, defined as the presence of endometrial-like tissue outside of the uterus, is one of the most prevalent gynecological disorders.Although different theories have been proposed, its pathogenesis is not clear.

Anne-Marie Sharp (05:31:16) (in thread): > 1)For C2:D2 I’m not entirely sure if these associations should be curated as correlations; like we usually curate spearman/pearson correlations of taxa with clinical parameters. > If the associations can be curated as correlations then there will be 7experiments for C2 & 7 for D2. > 2)If Table S2 has overlapping taxa & same info with C1,D1 then it should be curated alongside C1 & D1 and then include TableS2 in the Source. > 3)In the curation, the Source description for D2 should explain just D2(not both C2 & D2), same with C2

Anne-Marie Sharp (05:37:13) (in thread): > Well done@Montana-D@Mildred Anashiewe’ll review:+1:

Joy (05:59:36) (in thread): > Well done@Montana-Dand@Mildred Anashie, we’ll have a look!

Adeshile Oluwatosin (06:20:13) (in thread): > Good morning@Mildred Anashie@Precious ChijiokeI would take a look at this > Apologies for the late response

Precious Orakwe (08:00:06): > Hello everyone, good afternoon, i would love a peer review for this study.https://bugsigdb.org/38678197 - Attachment (BugSigDB): Connection of pre-competition anxiety with gut microbiota and metabolites in wrestlers with varying sports performances based on brain-gut axis theory - BugSigDB > OBJECTIVE: The purpose of this study is to investigate the connection of pre-competition anxiety with gut microbiota and metabolites in wrestlers with different sports performances.METHODS: One week prior to a national competition, 12 wrestlers completed anxiety questionnaires.

Ndukauba Oluchi (08:06:21) (in thread): > Welldone@Anne-Marie Sharpand@Montana-Dyou both did a great job. > here are my observations > 1. I think MHT should be YES see“Statistical significance was set to 0.05 for all analyses (i.e., p-value or q-value < 0.05 for analyses using Benjamini–Hochberg false discovery rate (FDR) for multiple correction)”

Anne-Marie Sharp (08:13:43) (in thread): > @Ndukauba OluchiThank you:smiling_face_with_smiling_eyes_and_hand_covering_mouth:but you should tag@Mildred Anashieinstead

Mildred Anashie (08:14:50) (in thread): > Hi@Ndukauba OluchiYes MHT was done but we curated p values and not adjusted p valuessince the adjusted pvalues didn’tshow significancethat’swhy MHT is No

Anne-Marie Sharp (08:25:17) (in thread): > @Mildred Anashie@Montana-Dwell done again on this neat curation > 1)Exp1 Group1 definition, I think it will be more appropriate to use > ‘…participants/patients diagnosed with endometriosis’ > instead of ‘..considered having..’. According to the article: ‘the endometriosis group comprised of 136 patients diagnosed with this disease’. > 2)In Exp1 signatures, change Tables S2 to Table S2

Anne-Marie Sharp (08:26:40) (in thread): > Good afternoon@Precious Orakwewell done, we’ll review

Mildred Anashie (08:37:50) (in thread): > Thank you@Anne-Marie SharpThat makes sense to me as well

Mildred Anashie (08:38:24) (in thread): > Hi@Precious OrakweWe’ll have a look

Anne-Marie Sharp (08:40:34) (in thread): > @Precious OrakweInclude Figure 3B1 in your source, its also LefSe and has same taxa with Figure 3B2

Mildred Anashie (08:41:00) (in thread): > Just to mention I see you have two increased signatures andthat’smaking you have signature 3 > > You should request to delete signature 2 or edit signature 2 and request to delete signature 3

Ndukauba Oluchi (09:23:24) (in thread): > @Anne-Marie Sharp:joy:

Juliana Kentomahun Mautin (09:25:04) (in thread): > Hello@Amaanyou are welcome:relaxed:

Montana-D (13:22:24) (in thread): > Thank you all so much for your suggestions and corrections > We shall effect changes > > You are awesome:pray:

Svetlana Ugarcina Perovic (14:20:28): > This made my day - Attachment: Attachment > Feel free to ask the dumpiest of questions and expect a constructive response from someone here > Anything which helps you understand better or remove blockers in your path

Svetlana Ugarcina Perovic (14:20:59): > Thank you for your awesome teamwork!

Antonia Beatriz Soler Riera (15:32:53) (in thread): > Hello@Amaanwelcome and good luck with your first curation.@Anne-Marie Sharpis a wonderful coworker!!

Anne-Marie Sharp (15:46:26) (in thread): > :face_holding_back_tears:Thank you:pray:@Antonia Beatriz Soler Rieraand you too, collaborating with you was such a smooth and fun experience:raised_hands:

Amaan (16:57:53) (in thread): > Thank you all so much for the kind words and support!:face_holding_back_tears::dizzy:I truly feel welcomed and encouraged already. I’m really excited to begin this journey, and I know I’m in great company here!

Amaan (16:59:14) (in thread): > Huge thanks again to@Svetlana Ugarcina Perovicma’am for the opportunity, and to@Anne-Marie Sharpfor being such a supportive teammate. I’m already learning a lot just from the way this community supports one another — looking forward to contributing and growing with you all!

Precious Orakwe (17:00:25) (in thread): > Done, thank you, please can you take a look at the condition, thank you.

Precious Orakwe (17:03:39) (in thread): > Such an amazing community filled with wonderful people, kind and always willing to assist. Thank you everyone and to our mentors:muscle::muscle::muscle::hugging_face::hugging_face::hugging_face:

Mildred Anashie (19:37:33) (in thread): > I think the condition is a good fit@Precious Orakwe

2025-04-26

Precious Orakwe (01:48:26) (in thread): > Thank you so much.

Mildred Anashie (04:00:01): > Hi Everyone > Happy weekend > > I really need other pair of eyes to look at Figure 4L in this study please:pray:Should it be curated and how can it be curated? The text in the article says something about taxa’s increasing and decreasing in the control group but doesn’t explicitly say which increased in the other groups (although the PCOS group is a little clear but not Omega -3). > Taking a look at the color box with the taxa I see it correlates with what the text says about control. > > So I’m wondering if just control should be curated, the statistical test is not stated either and it leaves me thinking if 4L should be omitted. > Thank you in anticipation for your feedbacks. > > Link to study:https://ovarianresearch.biomedcentral.com/articles/10.1186/s13048-023-01227-w - Attachment (BioMed Central): Effects of gut microbiota on omega-3-mediated ovary and metabolic benefits in polycystic ovary syndrome mice - Journal of Ovarian Research > Background Polycystic ovary syndrome (PCOS) is a common reproductive endocrine disorder that frequently exhibits low-grade inflammation, pro-oxidant activity, and gut dysbiosis. PCOS has become one of the leading causes of female infertility worldwide. Recently, omega-3 polyunsaturated fatty acids (PUFAs) have been proven to benefit metabolic disorders in PCOS patients. However, its roles in the regulation of metabolic and endocrinal balances in PCOS pathophysiology are not clear. In the present study, we aimed to explore how omega-3 PUFAs alleviate ovarian dysfunction and insulin resistance in mice with dehydroepiandrosterone (DHEA)-induced PCOS by modulating the gut microbiota. Methods We induced PCOS in female mice by injecting them with DHEA and then treated them with omega-3 PUFAs. 16S ribosomal DNA (rDNA) amplicon sequencing, fecal microbiota transplantation (FMT) and antibiotic treatment were used to evaluate the role of microbiota in the regulation of ovarian functions and insulin resistance (IR) by omega-3 PUFAs. To further investigate the mechanism of gut microbiota on omega-3-mediated ovarian and metabolic protective effects, inflammatory and oxidative stress markers in ovaries and thermogenic markers in subcutaneous and brown adipose tissues were investigated. Results We found that oral supplementation with omega-3 PUFAs ameliorates the PCOS phenotype. 16S rDNA analysis revealed that omega-3 PUFA treatment increased the abundance of beneficial bacteria in the gut, thereby alleviating DHEA-induced gut dysbiosis. Antibiotic treatment and FMT experiments further demonstrated that the mechanisms underlying omega-3 benefits likely involve direct effects on the ovary to inhibit inflammatory cytokines such as IL-1β, TNF-α and IL-18. In addition, the gut microbiota played a key role in the improvement of adipose tissue morphology and function by decreasing multilocular cells and thermogenic markers such as Ucp1, Pgc1a, Cited and Cox8b within the subcutaneous adipose tissues. Conclusion These findings indicate that omega-3 PUFAs ameliorate androgen-induced gut microbiota dysbiosis. The gut microbiota plays a key role in the regulation of omega-3-mediated IR protective effects in polycystic ovary syndrome mice. Moreover, omega-3 PUFA-regulated improvements in the ovarian dysfunction associated with PCOS likely involve direct effects on the ovary to inhibit inflammation. Our findings suggest that omega-3 supplementation may be a promising therapeutic approach for the treatment of PCOS by modulating gut microbiota and alleviating ovarian dysfunction and insulin resistance.

Montana-D (04:21:40) (in thread): > Happy weekend to you too Mildred. > > I too don’t know if it should be curated or not. But if at all it can be, this is how I suggest it should be curated. > > From the text, it indicates that blue is decreased in the control group, meaning increase in the case groups > > As per the comparisons, I’m not sure if it is pairwise or 1 vs all. This is because comparing PCOS and Omega, although the heat map shows significant differences, the genus (Since I think you should be curating genuses) attributed isn’t clear enough, > > In all, I think it should be omitted

Adeshile Oluwatosin (04:34:40) (in thread): > Good morning@Mildred AnashieI don’t see figure 4L curatable > Although this was mentioned “In control mice, treatment with DHEA significantly increased 6 operational taxonomic units (OTUs) and decreased 15 OTUs (Fig. 4L).” > > The figure itself does not seem clear enough to curateamong the groupsHence leave it out

Mildred Anashie (04:37:07) (in thread): > Okay then > > Thank you@Montana-D@Adeshile OluwatosinAnd Good Morning

Mildred Anashie (04:41:43) (in thread): > Also, is it okay if I record ANOVA for the test for the significant taxas in 4B-K?Surprisingly only Fig 4 doesn’t say what statistical test was used, but following other figures I see ANOVA was used for multiple group comparisons and I went with that:thinking_face:

Mildred Anashie (04:43:12) (in thread): > Link to curation:https://bugsigdb.org/37443082 - Attachment (BugSigDB): Effects of gut microbiota on omega-3-mediated ovary and metabolic benefits in polycystic ovary syndrome mice - BugSigDB > BACKGROUND: Polycystic ovary syndrome (PCOS) is a common reproductive endocrine disorder that frequently exhibits low-grade inflammation, pro-oxidant activity, and gut dysbiosis.PCOS has become one of the leading causes of female infertility worldwide.

Anne-Marie Sharp (04:44:02) (in thread): > Hello@Mildred AnashieIt seems curatable since significance was mentioned, if it is then you would have to curate Control vs PCOS by mapping each named taxon from the heatmap, record whether it is increased or decreased in PCOS, ignore OTU numbers, and only curate Control vs omega-3 if the taxon is still different after treatment.

Mildred Anashie (04:45:29) (in thread): > How do you tell significance in Omega-3it’spretty unclear, plus all three groups are showing both increase and decrease (based on the color code)@Anne-Marie Sharp

Adeshile Oluwatosin (04:47:54) (in thread): > See this:https://community-bioc.slack.com/archives/C04RATV9VCY/p1742333820987559?thread_ts=1742326919.941969&channel=C04RATV9VCY&message_ts=1742333820.987559@Mildred Anashie - Attachment: Attachment > @Adeshile Oluwatosin how do you know here in Fig2I what’s significant and even differential abundance result?

Adeshile Oluwatosin (04:52:34) (in thread): > Thank you:pray:

Anne-Marie Sharp (04:54:12) (in thread): > @Mildred Anashieyeah its unclear thats why I said if. Just that in your own article significance was mentioned in the heatmap, while in this link no significance was mentioned. But I believe the link above shared by@Adeshile Oluwatosinclears this up:raised_hands:

Adeshile Oluwatosin (04:59:34) (in thread): > For the statistical test: I saw this “Student’s t test, the Mann–Whitney test, and one-way analysis of variance (ANOVA) followed by Tukey’s post hoc test were used.” > > There was also no explicit state in the caption or text. We are also unsure if it’s ANOVA as well, because Figure 4B-J seems like a pairwise comparison.

Adeshile Oluwatosin (05:01:07) (in thread): > Regardless, I would say use anova and write a note for now

Anne-Marie Sharp (05:06:40) (in thread): > I believe it’s ANOVA as referenced in the Statistical Analysis section, and Figures 4B to 4K appear to compare three groups using one-way ANOVA followed by Tukey’s post hoc test, since the study tested for normality, involved three groups, and used star notation to indicate significant p-values in pairwise comparisons

Mildred Anashie (05:08:23) (in thread): > I’llleave a note@Adeshile OluwatosinYes it’s Pairwise and Anova can be used for multiple comparisons andfollowedby post hoc for pairwise andthat’swhat they said they did. Although not explicitly for that figure > > Thank you@Anne-Marie Sharp

Precious Chijioke (05:09:32): > Good Morning and Happy Weekend Everyone > I and@Joycurated this study and we would appreciate a peer review. Thank youhttps://bugsigdb.org/40259408 - Attachment (BugSigDB): Initial gut microbiota composition is a determining factor in the promotion of colorectal cancer by oral iron supplementation: evidence from a murine model - BugSigDB > BACKGROUND: Colorectal cancer (CRC) development is influenced by both iron and gut microbiota composition.While iron supplementation is routinely used to manage anemia in CRC patients, it may also impact gut microbiota and promote tumorigenesis.

Adeshile Oluwatosin (05:21:22) (in thread): > Well done@Joy@Precious Chijioke > * Figure 2D: MHT is yes for the Lefse result > ” (LEfSe, LDA > 3.0 and P < 0.05, FDR corrected)” > * Figure 2C seems to be a comparison between FMT-HC and FMT-CRC > see: “Differences in response to iron supplementation between FMT-HC and FMT-CRC emerged at the family level (48 families detected, Fig. 2C)” use the caption to curate accurately > * Figure 2B comparisons are FMT-HC 50 vs FMT-HC 500, FMT-CRC 50 vs FMT-CRC 500. > > * Data transformation for deseq2 is raw count; check the welcome material

Aiysha shahid (05:37:11) (in thread): > Well Done!:hugging_face:

Precious Chijioke (05:47:11) (in thread): > Thank you@Adeshile OluwatosinFig. 2D LDA and MHT is recorded in experiment 2. > There’s 2 experiments in Fig. 2B with the comparisons you pointed

Anne-Marie Sharp (06:57:41) (in thread): > Happy weekend and well done@Joy@Precious Chijiokewe’ll review

Anne-Marie Sharp (09:15:23) (in thread): > 1)As mentioned above, the data transformation for Deseq2 is raw counts then for LefSe it will still be relative abundances > 2) Figure 2B comparisons are 1)FMT-HC 50 vs FMT-HC 500, 2)FMT-CRC 50 vs FMT-CRC 500 : These 2comparisons will give 2 separate experiments > 3)For Figure 2C the contrast is FMT-HC vs FMT-CRC > 4) From my observation Table S4 provides only significance levels but not the direction (increase or decrease) I don’t see how it can be curated.

Precious Chijioke (13:07:06) (in thread): > Thank you@Anne-Marie Sharpfor your suggestions. We’ll implement all corrections given so far. Curating Fig 2C as FMT-HC vs FMT-CRC, are we curating FMT-HC (n= 24 (50 ppm) vs FMT-CRC (n= 27 (500 ppm) or FMT-HC (n= 24 (50 ppm);n= 26 (500 ppm)) and FMT-CRC (n= 25 (50 ppm);n= 27 (500 ppm)@Anne-Marie Sharp@Adeshile Oluwatosinplease help.

Anne-Marie Sharp (14:42:12) (in thread): > You’re welcome@Precious ChijiokeBased on the explanations in the article, you should add the sample sizes for 50ppm & 500ppm in each contrast group. That is, FMT-HC: 24 + 26 = 50…and so on.

Precious Chijioke (14:43:51) (in thread): > Thank you@Anne-Marie Sharp, that’s my thought and needed to sure about it.

Adeshile Oluwatosin (14:48:45) (in thread): > Hi@Precious ChijiokeFigure 2C > FMT-HC : 24 + 26 = 50 > FMT-CRC: 25 + 27 = 52

Precious Orakwe (20:01:03): > Hello everyone, happy weekend, I trust we are all doing great. > Please, I would love a peer review for this study;https://bugsigdb.org/37936084Thank you so much, every correction is highly appreciated. > > Thank you. - Attachment (BugSigDB): Cingulate white matter mediates the effects of fecal Ruminococcus on neuropsychiatric symptoms in patients with amyloid-positive amnestic mild cognitive impairment - BugSigDB > BACKGROUND: Microbiota-gut-brain axis interacts with one another to regulate brain functions.

2025-04-27

Aiysha shahid (03:50:55) (in thread): > Well done,will go through it!

Anne-Marie Sharp (03:52:38) (in thread): > Hello@Precious Orakwewell done with your curation > 1)In Experiment 2, Group0 should be HC and Group1 should be aMCI+ > 2)Exp2 signature 1 will be decreased abundance in aMCI+ and you will curate those 2 taxa there. > 3)MHT correction should be No : Multiple hypothesis testing correction (Benjamini-Hochberg FDR) was explicitly applied to Spearman’s rank correlation results, but not to differential abundance results from Mann–Whitney U tests > 4)Study design should be case-control > 5)In Exp1 Group1 definition, change amnesic to amnestic

Montana-D (04:54:30) (in thread): > Hi@Precious Orakwe, > Well done on your curation > > I do agree with@Anne-Marie Sharp. You should take a look again

Precious Orakwe (04:55:46) (in thread): > Thank you

Adeshile Oluwatosin (04:58:32) (in thread): > Well done@Precious Orakwe

Adeshile Oluwatosin (05:00:27) (in thread): > All corrections have been stated

Precious Orakwe (05:02:43) (in thread): > Thank you@Anne-Marie SharpI will effect the changes.

Anne-Marie Sharp (15:31:36): > Hello everyone, trust we’re all good. I am curating this articlehttps://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0260-z#Sec2with@Utibe Itaand we have a question, we will appreciate every input, thank you.****- Figure 4C - Fshows differences between groups, but the text/explanation beneath Figure 4 states there are no significant differences between many of the groups.- Distasonis(OTU) is shown inFigure 4B, but the article doesn’t mention if there’s a significant difference between the groups. > 1)Table S5is a comparison across all 3groups unlike Figure 4 that is pairwise comparisons, so Table S5 doesn’t match the results inFigure 4/Figure 4 explanation. In this case should we focus only on curating figure 4C – F? or how best can we go about it? - Attachment (BioMed Central): Differences in gut microbial composition correlate with regional brain volumes in irritable bowel syndrome - Microbiome > Background Preclinical and clinical evidence supports the concept of bidirectional brain-gut microbiome interactions. We aimed to determine if subgroups of irritable bowel syndrome (IBS) subjects can be identified based on differences in gut microbial composition, and if there are correlations between gut microbial measures and structural brain signatures in IBS. Methods Behavioral measures, stool samples, and structural brain images were collected from 29 adult IBS and 23 healthy control subjects (HCs). 16S ribosomal RNA (rRNA) gene sequencing was used to profile stool microbial communities, and various multivariate analysis approaches were used to quantitate microbial composition, abundance, and diversity. The metagenomic content of samples was inferred from 16S rRNA gene sequence data using Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt). T1-weighted brain images were acquired on a Siemens Allegra 3T scanner, and morphological measures were computed for 165 brain regions. Results Using unweighted Unifrac distances with hierarchical clustering on microbial data, samples were clustered into two IBS subgroups within the IBS population (IBS1 (n = 13) and HC-like IBS (n = 16)) and HCs (n = 23) (AUROC = 0.96, sensitivity 0.95, specificity 0.67). A Random Forest classifier provided further support for the differentiation of IBS1 and HC groups. Microbes belonging to the genera Faecalibacterium, Blautia, and Bacteroides contributed to this subclassification. Clinical features distinguishing the groups included a history of early life trauma and duration of symptoms (greater in IBS1), but not self-reported bowel habits, anxiety, depression, or medication use. Gut microbial composition correlated with structural measures of brain regions including sensory- and salience-related regions, and with a history of early life trauma. Conclusions The results confirm previous reports of gut microbiome-based IBS subgroups and identify for the first time brain structural alterations associated with these subgroups. They provide preliminary evidence for the involvement of specific microbes and their predicted metabolites in these correlations. - File (Word Document): Table S5.docx

Adeshile Oluwatosin (15:42:49) (in thread): > Well done > For figure 4C-4F; curate from the text specifically for the groups stated to have significance. > > Relative abundance between groups was specific within Figure 4C -4F hence leave out 4B (leave a note on this) as we can’t tell if it’s significant or not. > > Table S5 is also a pairwise comparison, so curate along side Figure 4C-4F as a source. Within text it was referenced along side Figure 4

Mildred Anashie (15:49:02) (in thread): > Hi@Anne-Marie SharpIn my opinion, Fig 4 isn’t showing clear significance and looks like relative abundance but I’m thinking curating from text would be better than leaving it out. > > Table S5 on the other hand can and should be curated as pairwise and I think it would be IBS vs HC and IBS vs HC- like IBS

Anne-Marie Sharp (16:00:31) (in thread): > Thank you@Adeshile Oluwatosin@Mildred AnashieI mentioned that the results in Table S5 do not match with the results the article explained for Figure 4C to F and there are different q-values for same taxa. > Example: > 1)In Table S5, between IBS1 AND HC-like IBS, Clostridia is significantly increased in IBS1, but in the main article there is no significant difference

Adeshile Oluwatosin (16:01:21) (in thread): > In this case follow Table S5 with vivid stated q values@Anne-Marie Sharp

Mildred Anashie (16:07:46) (in thread): > In my opinion, You either follow table S5 as stated by@Adeshile Oluwatosinor curate separately since the results are not entirely the same@Anne-Marie Sharp

Juliana Kentomahun Mautin (16:20:02): > Hello everyone, Happy Weekend to y’all:blush::blush::blush:. I hope y’all are having a restful weekend.

Juliana Kentomahun Mautin (16:21:34): > I just finished curating this article and I would appreciate a peer review on this.https://bugsigdb.org/37210496https://bmcmicrobiol.biomedcentral.com/articles/10.1186/s12866-023-02880-3 - Attachment (BugSigDB): Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic - BugSigDB > BACKGROUND: Functional constipation (FC) in children affects their growth, development and quality of life.L-pipecolic acid (L-PA) was decreased in FC children based on gut microbiome and serum metabolomic. - Attachment (BioMed Central): Protective effect of L-pipecolic acid on constipation in C57BL/6 mice based on gut microbiome and serum metabolomic - BMC Microbiology > Background Functional constipation (FC) in children affects their growth, development and quality of life. L-pipecolic acid (L-PA) was decreased in FC children based on gut microbiome and serum metabolomic. In this study, loperamide-induced constipation in mice was used to evaluate the effects of L-PA on constipated mice. Method 26 FC and 28 healthy children were recruited. Stool samples and serum samples were subjected to 16S rDNA sequencing and ultra-performance liquid chromatography/quadrupole time of flight (UPLC-Q/TOF-MS) approach, respectively. A loperamide-induced mouse constipation model was developed, and all mice were randomly divided into control (Con), loperamide (Lop) and L-PA (Lop + L-PA) treatment groups (6 mice per group). The mice in the Lop + L-PA group were given L-PA (250 mg/kg, once a day) and loperamide; the Lop group was given loperamide for 1 week, and the Con group was given saline. The fecal parameters and intestinal motility of mice in each group were detected. serum 5-HT levels and colon 5-HT expression were detected by ELISA and immunohistochemistry, respectively; qRT-PCR was used to detect the expression of AQP3 and 5-HT4R mRNA in each group. Results 45 differential metabolites and 18 significantly different microbiota were found in FC children. The α and β diversity of gut microbiota in FC children was significantly reduced. Importantly, serum L-PA was significantly reduced in FC children. The KEGG pathway enrichment were mainly enriched in fatty acid biosynthesis, lysine degradation, and choline metabolism. L-PA was negatively associated with Ochrobactrum, and N6, N6, N6-trimethyl-l-lysine was positively associated with Phascolarcrobacterium. In addition, L-PA improved the fecal water content, intestinal transit rate, and increased the serum 5-HT levels in constipated mice. Moreover, L-PA increased the expression of 5-HT4R, reduced AQP3, and regulated constipation-associated genes. Conclusions Gut microbiota and serum metabolites were significantly altered in children with FC. The abundance of Phascolarctobacterium and Ochrobactrum and serum L-PA content were decreased in FC children. L-PA was found to alleviate the fecal water content, increase intestinal transit rate and the first black stool defecation time. L-PA improved constipation by increasing 5-HT and 5-HT4R expression while down-regulating AQP3 expression.

Anne-Marie Sharp (16:32:30) (in thread): > Okay, thank you@Adeshile Oluwatosin@Mildred Anashiethough we are still unsure, we might curate separately. Because the article explanation for figure 4C - F also has vivid stated q-values as well as Table S5. Just that the results for both are not matching.

Anne-Marie Sharp (16:39:05) (in thread): > Hello@Juliana Kentomahun Mautinwell done with this, we’ll review

Montana-D (16:40:06) (in thread): > Well done on your curation. I’ll have a look

Montana-D (16:44:17) (in thread): > 1. Your group 1 definition is too long, get summary of it. What truly defines functional constipation in the study > 2. You don’t need to state the source of your alpha diversity when curating so, I guess your experiment 1 source should be 1F > 3. Experiment 2 signatures aren’t visible, please use the trick of complete and incomplete changes to make it appear so we can have look

Mildred Anashie (16:46:24) (in thread): > Well done on your curation@Juliana Kentomahun MautinI’lltake a look

Anne-Marie Sharp (16:47:47) (in thread): > 1)Make Exp1 Group1 description clearer e.g. children/patients with functional constipation, with infrequent bowel movements and who fulfilled the Roman IV diagnostic criteria > 2)Figure 1B is not curatable, it shows taxa but doesn’t show statistically significant increase/decrease > 3)Body site is feces only > 4)Group 0 name should be Control > 5)The study design shouldn’t be laboratory experiment > 6)In alpha diversity, also Curate ACE as richness

Juliana Kentomahun Mautin (17:38:32) (in thread): > @Montana-Dthere’s no signature for experiment 2

Anne-Marie Sharp (17:42:27) (in thread): > @Juliana Kentomahun MautinAsthere’sno signature for Exp2, leave a comment on the GitHub issue with the link for that Experiment2 and tag Svetlana to help you delete it

Juliana Kentomahun Mautin (17:52:34) (in thread): > Yes…sure, I would do that@Anne-Marie Sharp

Montana-D (17:53:16) (in thread): > So I noticed@Juliana Kentomahun Mautin, so I’ll advise that subsequently you shouldn’t create experiments unless you have valid signatures to curate, if you follow the steps stated by@Anne-Marie Sharp, you would have it deleted in no time

Juliana Kentomahun Mautin (17:54:16) (in thread): > @Anne-Marie Sharpwhat do you suggest for the Study design? > > From my understanding of what we have in the curation policy, study that use animal models should be tagged as a laboratory experiment.

Juliana Kentomahun Mautin (17:55:33) (in thread): > You can as well go through the study to see if you would find any signature for experiment 2?

Juliana Kentomahun Mautin (17:57:26) (in thread): > For No 4 it was stated in the study that Healthy children and FC children were recruited. Meaning Group 0 is the healthy Children which is also the control group. Please kindly explain why you suggest I change it to control@Anne-Marie Sharp

Anne-Marie Sharp (17:58:57) (in thread): > -I’ll have to study the article more. But yes:thinking_face:they used animal models, but specific to your curation, it was a contrast between humans. Let’s get opinions from others also. > -If Figure 1F is the only curatable figure in the article, then you would have just 1 experiment. The number of your experiments depends on the curatable figures/tables-You are curating from the figure, in the figure, the contrast groups were stated as Control and FC

Juliana Kentomahun Mautin (18:24:09) (in thread): > Oh…I just saw the part where it says healthy controls versus Children with FC . I would just change it to healthy control. Thank you:blush:

Mildred Anashie (18:39:52) (in thread): > Hi@Juliana Kentomahun MautinI’m not sure where the second experiment was curated from, and I do not see any signatures for it (I checked manually and didn’t find any). > > Also I see one experiment and I believe with that, the study design should be Case-control (because it’s between healthy controls and cases -functional constipation) but I seeFig 4 andI’mthinkingitcan be curated and that is the figure that has the mice as host species.If Fig 4 is curatable thenyou’dhave a case of two study designs but if not you can stick with just one experiment and case-control as the study design.I’lllook through again for fig 4

2025-04-28

Precious Chijioke (03:29:45) (in thread): > Well done on your curation@Precious Orakwe, O agree with@Anne-Marie Sharp

Precious Chijioke (03:43:47) (in thread): > Well done on your curation@Juliana Kentomahun MautinI agree with all suggestions said

Precious Chijioke (03:45:31) (in thread): > Well done@Anne-Marie Sharpand@Utibe ItaI agree with what@Adeshile Oluwatosinand@Mildred Anashiesaid

Precious Chijioke (03:47:34): > Good Morning and Happy New Week Everyone@Svetlana Ugarcina Perovicplease I sent a message to you on GitHub

Eseoghene Cynthia Princewill-Ukot (05:14:18): > Good morning everyone! > Happy New Week:tulip:

Utibe Ita (06:10:55): > Hello everyone, trust we’re all good. I am curating this articlehttps://www.cell.com/cell-host-microbe/fulltext/S1931-3128(17)30156-7?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1931312817301567%3Fshowall%3Dtruewith@Aiysha shahidand we will love a peer review > This is the bugsigDB link-https://bugsigdb.org/28494241We have already asked@Svetlana Ugarcina Perovicto help us delete experiment 3 signature 2 > > We will appreciate all the inputs we can get > Thank you - Attachment (BugSigDB): Gut Microbiome Function Predicts Response to Anti-integrin Biologic Therapy in Inflammatory Bowel Diseases - BugSigDB > The gut microbiome plays a central role in inflammatory bowel diseases (IBDs) pathogenesis and propagation.

Mildred Anashie (06:21:17) (in thread): > Well done@Utibe Ita@Aiysha shahidI’lltake a look

Juliana Kentomahun Mautin (06:21:30) (in thread): > Hello@Mildred AnashieI checked fig 4 closely and discovered it can’t be curatable because The heatmap shows Spearman correlations between gut microbes and metabolites, not direct comparisons between two biological groups.

Adeshile Oluwatosin (06:28:09) (in thread): > Well done@Utibe Ita

Svetlana Ugarcina Perovic (07:03:27): > Hi all, next Monday afternoon (14:30 - 17:00 CET) there will be**** an MVIF focusing on the Nagoya protocol**, with very practical guidelines shared by world experts in the field. > > We’ll discuss also DSI (Digital Sequence Information, aka genetic sequences) to which Nagoya has not historically applied but is soon going to apply as well. > > Practically speaking, benefit-sharing mechanisms will apply also to sequencing data. This may be particularly relevant for those re-analysing data from countries parties of the Nagoya protocol, listed herehttps://www.cbd.int/abs/nagoya-protocol/signatoriesIf you want to know more about the topic and ask your questions, join the panel on Monday afternoon. > > Registration here:cassyni.com/s/mvif-39

Montana-D (07:06:59) (in thread): > Well done@Utibe Ita@Aiysha shahid

Mildred Anashie (07:11:52) (in thread): > Figure 1e and 1f appears curatablebut not easily though as Ihaven’tfigured out how it can be curated > > For the study design,I’mleaning more towards Longitudinal than prospective cohort (It should be just one study design)

Utibe Ita (07:22:24) (in thread): > Thank you@Mildred AnashieI’ll let you know if I have other questions

Adeshile Oluwatosin (07:22:33) (in thread): > * Experiment 2: Data transformation is relative abundance > * Fisher’s alpha diversity is species richness > * Figure 1e and 1f are curatable (2 seperate experiments from here) > non- remitters CD vs remitters CD: exp 1 > non- remitters UC vs remitters UC: exp 1 > Take a look at the relative abundance, the farther the colour indicates an increase. Green (remitters) and red (non-remitters)

Anne-Marie Sharp (07:30:34) (in thread): > Well done@Utibe Ita@Aiysha shahid1)In Exp1, Group0 & 1names + the source description should be specific to CD & include Crohn’s Disease, as the study was about IBS: either CD/UC . > e.g Remitters at Baseline(Crohn’s disease) > 2)Rephrase Exp1 Group1 definition like: Crohn’s Disease patients whose baseline samples were collected before treatment and who later achieved clinical remission at week 14. > 3)In figure3c the contrast groups should be non-remission(CD) vs remission(CD) and non-remission(UC) vs remission(UC)

Montana-D (07:46:34) (in thread): > I think it is a prospective cohort study only. You should consider changing your study design

Svetlana Ugarcina Perovic (07:46:38): > All messages answered. Thank you for your patience andwishing you a good week :tulip:

Montana-D (07:47:35) (in thread): > Thank you and do have a great one yourself:raised_hands:

Anne-Marie Sharp (07:48:10) (in thread): > Thank you, have a good week too

Eseoghene Cynthia Princewill-Ukot (08:09:07): > Hello curators, i have been curating this study and I’m putting it up for peer review.https://bugsigdb.org/36593694 - Attachment (BugSigDB): Gut microbiota dysbiosis in Parkinson disease: A systematic review and pooled analysis - BugSigDB > BACKGROUND AND PURPOSE: The role of the gut microbiome in the pathogenesis of Parkinson disease (PD) is under intense investigation, and the results presented are still very heterogeneous.

Eseoghene Cynthia Princewill-Ukot (08:44:34) (in thread): > Firstly it was stated that this study covered six different countries but from Table 1, I can only see five. Secondly, while curating Signatures i found both the Phylum and Family present, do I curate both?

Adeshile Oluwatosin (08:47:41) (in thread): > Well done@Eseoghene Cynthia Princewill-Ukot

Juliana Kentomahun Mautin (08:49:34) (in thread): > Thank you@Svetlana Ugarcina Perovic. Have an amazing Week too:relaxed:

Juliana Kentomahun Mautin (08:49:59) (in thread): > Welldone@Eseoghene Cynthia Princewill-Ukot

Precious Chijioke (08:56:42) (in thread): > Thank you@Svetlana Ugarcina Perovic, have an amazing new week.

Precious Chijioke (08:57:52) (in thread): > Well done on your curation@Eseoghene Cynthia Princewill-UkotWe’ll take a look

Eseoghene Cynthia Princewill-Ukot (09:04:23) (in thread): > :hugging_face:

Aiysha shahid (09:47:29) (in thread): > Thank you all for the review, we would surely make the changes!:tulip:

Aiysha shahid (09:54:41) (in thread): > I think so it’s a -prospective cohort > > Check out this text-“To determine whether the gut microbiome may predict responses to IBD therapy,we conducted a prospective studywith Crohn’s disease (CD) or ulcerative colitis (UC) patients initiating anti-integrin therapy (vedolizumab)”@Mildred AnashieThanks@Montana-D

Aiysha shahid (10:01:20) (in thread): > Well Done@Eseoghene Cynthia Princewill-Ukot

Precious Chijioke (10:59:14) (in thread): > Hello@Eseoghene Cynthia Princewill-Ukot, curate both phylum and family as seen in the study. I did not see the sixth country in the paper. However, I’ll wait for suggestions from others about the sixth country. > Figure 4 is curatable.

Montana-D (11:59:40) (in thread): > Well done@Eseoghene Cynthia Princewill-UkotMy opinion > 1. Record the provided countries > 2. Record every taxonomic level provided, we only choose between levels when they are provided for same bacteria > 3. Figure 4, figure 5 and supplementary table E.1 are all curatable > I suggest you check them out

Eseoghene Cynthia Princewill-Ukot (12:44:43) (in thread): > Thanks for your peer review@Montana-D. I will check it out

Eseoghene Cynthia Princewill-Ukot (12:47:20) (in thread): > @Montana-DIf taxonomic levels are provided for the same bacteria, how do I go about that?

Ameenat Oloko (13:59:27) (in thread): > Well done@Eseoghene Cynthia Princewill-Ukot. > * As previously stated, you should only write the 5 countries provided in the research paper (Table 1). > * Alpha diversity was not done using inverse Simpson. It’s just these 3:richness, Shannon, and Simpson (within texts, Figure 2).**** ****So you should leave the inverse Simpson blank, and curate that forrichness. > * The data transformation for ANCOM-BC islog transformation. > * Antibiotic exclusion was not stated in the article, so you should leave that blank. > * Group 1 name should beParkinson disease (PD) patients (from the article)

Ameenat Oloko (14:17:53) (in thread): > I don’t think Table 2 is curatable, as it doesn’t show any significance. > > Rather, curate figures 4 and 5

Montana-D (14:32:31) (in thread): > Happy to help@Eseoghene Cynthia Princewill-UkotWhen that becomes the case, according to our curation policy, we go with the Lowest level present according to the taxonomic hierarchy

Eseoghene Cynthia Princewill-Ukot (15:04:01) (in thread): > Thanks@Montana-Dfor your help. In a situation where the lowest rank is not found in NCBI but the phylum is found ,what should I do?

Anne-Marie Sharp (15:51:24) (in thread): > Well done@Eseoghene Cynthia Princewill-Ukot1) Since Table 2 used a 99% credible range (CR) to assess significance, I’m thinking, should the significance threshold still be 0.05? I don’t think p-value was used in this case. > 2) I also agree that Figure 4, figure 5 and supplementary table E.1 are all curatable > 3) For curating taxa, if the lowest rank mentioned in the article is not on NCBI then you should curate it as stated in the article.

Eseoghene Cynthia Princewill-Ukot (15:55:23) (in thread): > Thanks everyone for your peer review.

Eseoghene Cynthia Princewill-Ukot (15:55:35) (in thread): > Well noted.

Precious Orakwe (17:08:54): > Good evening, everyone. I trust we are all doing great. please, I would love a peer review for this study. > > I am having a hard time identifying the accurate group sizes, the group’s appropriate names, and the condition of the study. Please help me.https://bugsigdb.org/38384431Thank you so much. - Attachment (BugSigDB): Short-term pectin-enriched smoothie consumption has beneficial effects on the gut microbiota of low-fiber consumers - BugSigDB > Adequate consumption of fiber has a positive effect on health.The crossover study examined the effect of a pectin-enriched smoothie on gut microbiota and health parameters.During 3 weeks, 31 adults consumed two smoothies (11.6 or 4.

Montana-D (19:31:37) (in thread): > Well done on your curation:raised_hands:

Anne-Marie Sharp (19:58:46) (in thread): > Well done with your curation @Precious > 1)For the group name, use what’s in the figure, eg in Figure 2: Base, HPect, WO-HPect, LPect, WO-LPect., there are comparisons between these groups. > 2)Figure 2 has 8contrasts > -Group1: Base vs HPect > -Group1: HPect vs WO-HPect > -Group1: WO-HPect vs LPect > -Group1: LPect vs WO-LPect > & > -Group2: Base vs LPect > -Group2:LPect vs WO-LPect > -Group2: WO-LPect vs HPect > -Group2: HPect vs WO-HPect > -Curate only the contrasts that are significant(* on top). Curate each significant contrast in 1 experiment each. > 3)Any contrast from Group1 above, the sample size for both group0&1 is 17 > 4)Any contrast from Group2 above, the sample size for both group0&1 is 14 > 3)Body site is feces only > 4)In Exp1 to Exp3 change Signature 1 to be increased abundance and Signature2 should be decreased > 5)Curate Figure 3B in one experiment on its own. For LF sample size is 22, for HF sample size is 9 > 6)Figure 4A,B,C,6A(LF)should be curated together and have 2comparisons: > -base vs LPect > -base vs HPect > 7) Figure 5A,B,C,6B(HF)should be curated together and have 2comparisons: > -base vs LPect > -base vs HPect

2025-04-29

Joy (03:56:06) (in thread): > Well done@Precious Orakweon your curation, I’ll also have a look.

Precious Chijioke (06:47:26) (in thread): > Well done@Precious Orakweon your curation

Precious Chijioke (08:31:29) (in thread): > Hello@Precious OrakweI agree with@Anne-Marie SharpI’m trying to figure out the condition of the study

Mildred Anashie (11:29:24): > Hello Everyone > How’s the new week coming along? > I curated thisstudyand I’m putting up for peer review. > I have a few concerns, the statistical test for Experiment 2 wasn’t explicitly stated but somewhere within the article it said Wilcoxon was used to test significance for boxplots, that’s why I went with Wilcoxon (Do you all agree or should it have been curated with 2B)? > Also, this taxa was reported in Figure 2b (Streptococcus_mitis_oralis_pneumoniae) I curated this way, was that rightly done? > > Thank you in anticipation for your feedback and responses. - Attachment (BugSigDB): Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations - BugSigDB > Psoriasis is a chronic, inflammatory skin disease that affects 2‒3% of the global population.Besides skin manifestations, patients with psoriasis have increased susceptibility to a number of comorbidities, including psoriatic arthritis, cardiovascular disease, and inflammatory bowel disease.

Adeshile Oluwatosin (11:29:51) (in thread): > Well done@Mildred AnashieI will look through

Mildred Anashie (11:32:05) (in thread): > Thank you@Adeshile Oluwatosin

Adeshile Oluwatosin (13:16:28) (in thread): > * Experiment 1/sig 2: you can curate “Peptostreptococcaceae_noname_unclassified” as unclassified peptostreptococcaceae”:1411023 > * can you specify where Wilcoxon was mentioned to test for significance > * Yes, curate exactly as seen@Mildred Anashie

Mildred Anashie (13:17:51) (in thread): > Within the figure captions for a few figures that have boxplots@Adeshile Oluwatosin

Anne-Marie Sharp (13:23:40) (in thread): > Well done with your curation@Mildred Anashie1)You should use Deseq2 since it is mentioned explicitly for the analysis of microbial species > 2)Yes, the way you curated that taxa was rightly done

Mildred Anashie (13:24:18) (in thread): > This was mentioned in Figure 4 caption “The statistical significance in boxplots was determined by Wilcox test on pairwise comparison of each group of interest.” > > And all boxplots within the article were plotted same way@Adeshile Oluwatosin

Mildred Anashie (13:25:02) (in thread): > If I use Deseq2 that would mean curating it alongside 2B and S1?@Anne-Marie Sharp

Anne-Marie Sharp (13:28:11) (in thread): > Yes, curating it alongside with the others. I saw that boxplots/wilcox, but that was specifically for immune cell response in that Figure4

Adeshile Oluwatosin (13:29:15) (in thread): > * I’m also thinking curate with Deseq2 as Wilcoxon was also used to test for alpha diversity. > * Let’s follow these statement: “To identify the microbial features that are differentially abundant between gut microbiome from patients with psoriasis and healthy individuals, we performed differentially abundance analysis using DEseq2 (Love et al., 2014),” > * Figure 4 was explaining this “Boxplots showing circulating host immune responses measured by flow cytometry.” > * @Mildred AnashieCurate alongside the previousexperiment

Mildred Anashie (13:39:31) (in thread): > Okay then > > Thank you@Anne-Marie Sharp@Adeshile OluwatosinIt feels good to know thatyou’llalways have people to put you on the right track:hugging_face:Is every other thing okay?

Adeshile Oluwatosin (13:41:46) (in thread): > * Simpson and Shannon are increased, chao1 unchanged in Experiment 1 > * Experiment 3-5 has no alpha diversity

Anne-Marie Sharp (13:42:35) (in thread): > You’re welcome@Mildred Anashie:hugging_face:1)Patients were matched on age and sex > 2)Between healthy and PSO, Shannon and Simpson should be increased, and chao1 unchanged. Will keep looking through

Mildred Anashie (13:44:13) (in thread): > For which?@Adeshile OluwatosinLook closely they did alpha diversity for microbial species, pathway and meta something…. > > But the alpha diversity for microbial species for Healthy and PSO are in supplementary figure 1 and not figure 2:blush:

Mildred Anashie (13:54:52) (in thread): > @Anne-Marie Sharpit says within results text that they controlled for confounding factors including Experimental batch. See this, “To identify the microbial features that are differentially abundant between gut microbiome from patients with psoriasis and healthy individuals, we performed differentially abundance analysis using DEseq2 (Love et al., 2014), which is designed for RNA-seq analysis but is widely adapted for microbiome data (McMurdie and Holmes, 2014). We estimated differential abundant features using a negative binomial model after controlling for known confounding factors for gut microbiome such as sex, age, and experimental batch.”

Adeshile Oluwatosin (13:56:15) (in thread): > They are also matched on factorsfor experiment 1. See”This multiomic cohort consists of 26 subjects with psoriasis and 14 age- and sex-matched healthy subjects (Table 2)”@Mildred Anashie

Mildred Anashie (14:00:03) (in thread): > Yea yea > > Thank you@Anne-Marie Sharp@Adeshile Oluwatosinfor pointing that out

Adeshile Oluwatosin (14:02:44) (in thread): > This, I mean “We recruited a cohort of 33 subjects with psoriasis not on systemic therapy and 15 age- and sex-matched healthy individuals (Table 1)”

Anne-Marie Sharp (15:45:17) (in thread): > @Mildred AnashieI observed in Exp3 – 5, only Table S5 shows statistical significance, figure 3c and the results text do not, perhaps you should curate from only Table S5

Mildred Anashie (15:59:11) (in thread): > Hi@Anne-Marie SharpThe results text does show significance and the increase and decrease as mentioned correlates with table S5 and I added 3c since it was referenced within text > > See here, “Both PSO2 and PSO3 are dominated by subjects with psoriasis, suggesting that these are two distinct psoriasis-specific subgroups. We identified several common microbial features shared by these psoriasis subgroups as well as some microbial features that are distinct to each subgroup (Figure 3c and Supplementary Tables S5‒7). Although psoriasis samples have a lower abundance in P. succinatutens than healthy controls (Figure 2c), the reduced abundance of P. succinatutens is specific to PSO2 and PSO3 but not to PSO1 (Figure 3c). In addition, samples in PSO2 and PSO3 are less abundant with Turicibacter sanguinis and unclassified Turicibacter species (Figure 3c). Samples in PSO2 are more abundant with Bacteroides xylanisolvens and less abundant with Prevotella copri, Streptococcus thermophilus, and Coprococcus sp ART55 1 (Figure 3c). On the contrary, samples in PSO3 have a lower abundance in Ruminococcaceae bacterium D16 and Lachnospiraceae bacterium 1 1 57FAA (Figure 3c).”

Anne-Marie Sharp (16:04:13) (in thread): > From my understanding, the text is talking about abundance but not significance. But everything(abundance, significance, increase/decrease, p-values) is included in Table S5. Let me clarify, if the source we are curating from is ‘Results text’ do we still need to include the figure that the Results text referenced?

Mildred Anashie (16:10:25) (in thread): > In my opinion the abundance in this case denotes significancebecauseit’s not a coincidence that it correlates with S5(could be choice of words by the authors).With regards to including the source, I thinkit’sappropriate to do so

2025-04-30

Svetlana Ugarcina Perovic (03:03:44): > Reminder: tomorrow there is NO TEAM MEETING, see you next week as usual!

Adeshile Oluwatosin (03:04:14) (in thread): > Duly noted > Good morning

Precious Chijioke (03:06:27) (in thread): > Good Morning@Svetlana Ugarcina PerovicThank you for the reminder

Joy (03:10:51) (in thread): > Good morning@Svetlana Ugarcina Perovic. Thank you for the reminder.

Mildred Anashie (03:11:49) (in thread): > Thank you for the reminder@Svetlana Ugarcina PerovicGood morning

Anne-Marie Sharp (03:25:07) (in thread): > Thank you for the reminder, see you next week

Juliana Kentomahun Mautin (03:35:04) (in thread): > Thank you@Svetlana Ugarcina Perovic, see you next week

Eseoghene Cynthia Princewill-Ukot (05:20:03) (in thread): > Well noted@Svetlana Ugarcina PerovicGood morning:tulip:

Precious Orakwe (07:45:46) (in thread): > Good day@Svetlana Ugarcina Perovic, thanks for the update.

Precious Orakwe (07:49:55): > Good afternoon, everyone. How have we all been? Trust, we are all doing great. > I would appreciate a review of this study.https://bugsigdb.org/38710815please, I used buccal epithelium for the buccal swab sample; I don’t know if it corresponds. Thank you.

Joy (08:05:36) (in thread): > Well done@Precious Orakweon your curation. We will have a look. > > Hi@Precious OrakweI think your paper uses across-sectional observational designwith mediation analysis because the > * Participants: 20 patients with amyloid-positive amnestic mild cognitive impairment (aMCI+) and 20 healthy controls (HCs), mostly spouses of patients. > Therefore, the design allows the researchers to investigate associations and potential mediation pathways but does not establish causality due to its cross-sectional nature.

Precious Orakwe (08:09:51) (in thread): > Well done@Mildred Anashie

Adeshile Oluwatosin (08:14:32) (in thread): > Well done@Precious Orakwe

Precious Orakwe (08:18:42) (in thread): > Hi@Joy, this is a different study, please check the link

Joy (08:21:40) (in thread): > Oh. Ok. My bad. Thanks@Precious Orakwe. Well done once again on your curation.

Anne-Marie Sharp (09:22:17) (in thread): > Well done with your curation@Precious Orakwewe’llreview

Joy (10:03:23): > Good afternoon, great curators, I would appreciate a peer review of this study I just curated. Thankshttps://bugsigdb.org/40164980This is the:Paper - Attachment (BugSigDB): Genomic and functional co-diversification imprint African Hominidae microbiomes to signal dietary and lifestyle adaptations - BugSigDB > In the diverse landscape of African hominids, the obligate relationship between the host and its microbiome narrates signals of adaptation and co-evolution.

Anne-Marie Sharp (10:06:52) (in thread): > Well done@Joywe’ll review

Eseoghene Cynthia Princewill-Ukot (10:08:55) (in thread): > Well done@Joy

Eseoghene Cynthia Princewill-Ukot (10:10:02) (in thread): > Well done@Precious Orakwe

Mildred Anashie (10:33:44) (in thread): > Well done on your curation@Joy

Adeshile Oluwatosin (10:36:35) (in thread): > Well done@Joy > * Experiment 1 alpha diversity should be blank as I cannot see the comparisons in Figure 2. > * Exp 1/sig 1: Add UBA11524 (is there a reason for omitting) > * Exp /sig 2: Add UBA7160, UBA636, UBA6398, > * Experiment 2; source should be Figure 3E & S3 instead > * Exp 2 description can be “Statistically significant genera between Hadza humans (indigenous hunter-gatherers) and Non-indigenous humans (urban/rural Tanzanian adults and children). > * No specific alpha diversity for Exp 2. > * figure 7E does not seem curatable

Precious Orakwe (11:00:45) (in thread): > Well done@Joy

Anne-Marie Sharp (11:02:08) (in thread): > 1)Matched on factors: enter sex in place of gender, enter Age in small letters ‘age’. > 2)In figure 4 there are 3 pairwise comparisons: cg vs st, vg vs nu, st vs nu for saliva & buccal swab separately, these should give 6experiments > 3)Study design should be prospective cohort > 4)Figure S8 doesn’t show statistical significance, I don’t think it should be curated > 5)Figure S9 should be curated separately from figure 4, it has different comparisons: buccal vs saliva in cg, in st and in nu. These should give 3experiments > 6)In Exp6 it will be better to put Smokeless tobacco user (ST) as Group1 like you did in Exp7, you can delete exp6 and curate Figure 5B properly in Exp7 > 7)Curate figure 6a in one experiment of its own, curate figure 6b in one experiment of its own

Anne-Marie Sharp (11:17:59) (in thread): > Hello@Joyplease can you share the supplementary material? I can’t access it

Precious Chijioke (11:20:59) (in thread): > Well done on your curation@Joy

Precious Chijioke (11:23:17) (in thread): > Well done on your curation@Precious Orakwe

Precious Orakwe (11:27:05) (in thread): > Thank you,@Anne-Marie Sharp, this is already done

Mildred Anashie (11:28:01) (in thread): > * The source for Experiment 2 should be Figure 3E and not 3D > * @Adeshile OluwatosinThe article says they used CLR for Welch’s t test and I’m wondering if it should be maintained or if relative abundance should be recorded. Also, I see the groups for experiment 2 in Figure 2 > * Here@Anne-Marie SharpTableshttps://drive.google.com/drive/folders/1ds-0_xvmeCbO_AmZJnAhK_UHRX9xIGTz?usp=sharingFigureshttps://drive.google.com/drive/folders/1Xe6CRgq_NRrE_WgQnNvBKqzEvaA_wBIs?usp=sharing

Adeshile Oluwatosin (11:30:05) (in thread): > In this case, she should record as CLR as stated by the article@Mildred AnashieYes, what I mean is comparison is specific to Chimpanzees and humans (not sub-groups) which ican’tsee in figure 2. Do you get

Anne-Marie Sharp (13:32:10) (in thread): > 1)I also agree that Figure 7e doesn’t look curatable and Exp2 source should be Figure 3E & S3 instead, also adjust exp2 source description. > 2)For the alpha diversities, > For Exp1 the article states: ‘Chimpanzee microbiomes, especially the Mahale population, harbored significantly richer and more diverse bacterial species than human guts when reads were mapped directly to the bacterial database (Figure 2a,b; Table S2; Wilcoxon test,p< 0.05)’ so they should be decreased > & for exp2 the alpha diversity is really unclear.

Joy (14:29:48) (in thread): > Thank you@Adeshile Oluwatosin > 1. The alpha diversity is stated in the discussion part of the paper. > 2. UBA7160is curated asLachnospiraceae bacterium UBA7160 and it islisted in the NCBI Taxonomy Browser under the nameLachnospiraceae bacterium UBA7160. It is classified within the familyLachnospiraceae, which belongs to the orderLachnospiralesin the phylumFirmicutes, UBA6398 is curated as Prevotellaceae bacterium UBA6398 and UBA636 is curated as Solobacterium sp. UBA636. Thanks for this UBA11524, I’ll add it to the appropriate signature.

Joy (14:30:56) (in thread): > @Anne-Marie Sharp, I have granted you access to the supplementary material. Thank you all for your feedbacks.

Adeshile Oluwatosin (14:34:51) (in thread): > I think Chloe has once mentioned to focus majorly on the paper itself instead of the discussion aspect of articles. From the results, Icouldn’treally see the exact group comparisons curated (since they were combinations)

Precious Chijioke (15:06:25) (in thread): > @JoyI agree with what@Anne-Marie Sharp,@Adeshile Oluwatosinand@Mildred Anashiesaid.

2025-05-01

Svetlana Ugarcina Perovic (01:13:59): > Our mentoring team is taking a break for the holidays. We’ll resume on Monday, May 5.:cherry_blossom:Happy holidays!:cherry_blossom:

Adeshile Oluwatosin (01:14:39) (in thread): > Good morning,Happy holidays:relaxed:

Joy (01:48:08) (in thread): > Duly noted@Svetlana Ugarcina Perovic. Happy holidays:sparkles:

Anne-Marie Sharp (02:03:24) (in thread): > Noted. Happy holidays to you all:cherry_blossom:

Precious Chijioke (03:22:19) (in thread): > Good Morning@Svetlana Ugarcina PerovicHappy holidays to you all

Precious Chijioke (03:23:07): > Good Morning Everyone. I would love a peer review on this study.https://bugsigdb.org/37277785 - Attachment (BugSigDB): Integrated fecal microbiota and metabolomics analysis of the orlistat intervention effect on polycystic ovary syndrome rats induced by letrozole combined with a high-fat diet - BugSigDB > BACKGROUND: This study aimed to compare the characteristics of the gut microbiota and their metabolite profiles between polycystic ovary syndrome (PCOS) and orlistat-treated PCOS rats (ORL-PCOS), which could help to better understand the underlying mechanism of the effect of orlistat on PCOS.

Aiysha shahid (03:29:44) (in thread): > Dully Noted!, Happy Holidays to you all.:tulip:

Anne-Marie Sharp (04:53:16) (in thread): > Good morning@Precious ChijiokeWell done with your curation > 1)Since figure 4a and b are both LeFse, same statistical test and comparison, I think they should be curated together > 2)Condition should be treatment > 3)I really doubt Figure 8 is curatable. If it is then it will be each fecal metabolite vs gut microbiota not PCOS vs ORL-PCOS > 4)I couldn’t spot antibiotics exclusion also

Precious Orakwe (05:02:49) (in thread): > Good morning@Svetlana Ugarcina Perovic, Noted, a happy and amazing holidays to you all.:heart::heart::hugging_face::muscle:

Adeshile Oluwatosin (05:18:32) (in thread): > Well done@Precious Chijioke > * Condition in this case is Treatment outcome measurement > * Fig 4A and 4B are both Lefse results. Curate as one experiment > * Figure 8 is not to be curated. > * This study should have just one experiment

Precious Orakwe (05:23:25) (in thread): > Well done@Precious Chijiokeon your curation, I agree that figure 8 is not curatable, and this study should be one experiment. Thank you.

Mildred Anashie (05:48:10) (in thread): > Happy holidays to you all:heart:

Mildred Anashie (06:02:03) (in thread): > Well done@Precious ChijiokeI do agree, 4a and b should be curated together

Anne-Marie Sharp (06:27:37): > Good morning and happy holidays everyone. Please I need guidance, in this article I am curating, humans were first analyzed for gut microbiota, then mice were also analyzed. In this case, should I curate both studies/analyses in one curation and as different experiments? or should this be two separate curations?https://www.pnas.org/doi/10.1073/pnas.2419689122Thank you

Mildred Anashie (06:29:18) (in thread): > Well done@Anne-Marie SharpI’lltake a look at what was done but ifthere’sa case of human and then animals,it’sbest to curate separately as the host species are different

Adeshile Oluwatosin (06:33:50) (in thread): > Please curate seperately, we can only have one host species in an experiment

Precious Chijioke (07:14:00) (in thread): > Thank you everyone for your suggestions

Precious Chijioke (07:18:00) (in thread): > @Anne-Marie SharpI agree that you curate them separately.

Anne-Marie Sharp (07:20:42) (in thread): > @Mildred Anashie@Adeshile Oluwatosin@Precious Chijiokeplease do you mean 1) To curate the article with 2study designs, and with humans & mice in separate experiments or 2)To curate the article in 2separate curations if possible?

Adeshile Oluwatosin (07:22:16) (in thread): > No the article has just one study design: last time Mildred curated a similar article: Chloe mentioned cross sectional. > > Curate seperate experiments in the study , each with Homo sapiens as body site for exp 1 and mus musculus as exp 2@Anne-Marie Sharp

Mildred Anashie (07:22:46) (in thread): > @Anne-Marie SharpI recently curated an article with similar content (humans and animals) and was advised by@Svetlana Ugarcina Perovicand<@UBNSEMS3S>to record two study designs for now

Mildred Anashie (07:23:46) (in thread): > @Adeshile OluwatosinI was asked to record bothand in my caselaboratory experiment and cross sectional

Anne-Marie Sharp (07:23:54) (in thread): > :face_with_peeking_eye::grimacing:that’smy confusion right here

Anne-Marie Sharp (07:24:08) (in thread): > @Mildred Anashieplease help me share the curation link here thank you

Mildred Anashie (07:26:08) (in thread): > https://bugsigdb.org/38477534 - Attachment (BugSigDB): Gastrointestinal Dysmotility Predisposes to Colitis through Regulation of Gut Microbial Composition and Linoleic Acid Metabolism - BugSigDB > Disrupted gastrointestinal (GI) motility is highly prevalent in patients with inflammatory bowel disease (IBD), but its potential causative role remains unknown.Herein, the role and the mechanism of impaired GI motility in colitis pathogenesis are investigated.

Adeshile Oluwatosin (07:27:59) (in thread): > Yes, I followed the conversation@Mildred AnashieIn the office hour, I thought Chloe mentioned to leave it as cross sectional.That’sfine then

Anne-Marie Sharp (07:29:06) (in thread): > Thank you all for helping out:pray:I’ll use the curation as a guide. I appreciate

Precious Chijioke (07:30:21) (in thread): > @Anne-Marie SharpI wanted to say you curate as separate experiments in the study, but since@Mildred Anashierecently curated an article with similar content, I believe you should go with the guidance given to her by@Svetlana Ugarcina Perovicand<@UBNSEMS3S>. I’ll also go through the curation@Mildred Anashiedid to learn as well.

Precious Chijioke (07:36:20) (in thread): > @Anne-Marie SharpFor antibiotics exclusion, see: > The remaining thirty rats were randomly allocated into three groups, which were then supplemented with different doses of orlistat (low-20 mg/kg/d; medium-40 mg/kg/d; high-80 mg/kg/d; Lunan Pharmaceutical Group Corporation; Shandong, Linyi, China.) over the next 12 weeks.

Mildred Anashie (07:38:14) (in thread): > Hi@Precious ChijiokeFrom this text the rats were given antibiotics so it shouldn’t be an exclusion

Precious Chijioke (07:39:33) (in thread): > Thank you@Mildred Anashie

Juliana Kentomahun Mautin (10:32:29) (in thread): > Hello@Svetlana Ugarcina Perovic. Happy holidays:blush::blush::blush:

Juliana Kentomahun Mautin (10:36:28): > Hello everyone, please I need clarification on this. This study look like it has two study design which are prospective cohort and Case control. Should I input the two study design on BugsigDB? Please take a look at the method and results sections.https://onlinelibrary.wiley.com/doi/10.1002/jcsm.12804

Joy (11:29:24) (in thread): > Well done@Juliana Kentomahun Mautinon your curation. Yes, tagging both study designs is accurate and reflective of the methodology used.

Anne-Marie Sharp (11:35:43) (in thread): > Hello@Juliana Kentomahun Mautinthe article states that the study design is a cross-sectional case–control study. I’ll suggest you use Cross-sectional, as your curation will involve not just case vs control contrasts but cross-sectional contrasts also.

Mildred Anashie (11:35:50) (in thread): > In cases like this its advisable to use the primary study design@Juliana Kentomahun MautinI’ll go through to confirm

Joy (11:43:05) (in thread): > Oh my bad!@Juliana Kentomahun Mautin, I just checked. The study is aCross-sectional case–control study with prospective data collection.This is how it should be curated in BugSigDB. Thank you@Anne-Marie SharpKindly disregard my earlier statement.

Mildred Anashie (11:46:13) (in thread): > @Juliana Kentomahun MautinIt’s a cross sectional study as@Anne-Marie Sharphas pointed out. The contrasts involves cases and controls but i also see contrasts between other groups so I believe it’s appropriate to record Cross sectional. > A study has only one study design except in very rare cases.

Juliana Kentomahun Mautin (11:52:39) (in thread): > Ok… Thank you so much for the clarification@Mildred Anashie@Anne-Marie Sharp@Joy

Juliana Kentomahun Mautin (11:55:31) (in thread): > The study design would have to be cross- sectional observational , not case control because Cross sectional study only is not in the option.

Mildred Anashie (11:56:03) (in thread): > Yes@Juliana Kentomahun MautinThat works

Juliana Kentomahun Mautin (11:56:19) (in thread): > Thank you:blush: